From e692cb6035d29bd44b950d20c03200c4677ff1a2 Mon Sep 17 00:00:00 2001 From: zimoun Date: Mon, 5 Dec 2022 16:38:51 +0100 Subject: [PATCH 001/790] gnu: julia-documenter: Fix test suite regression. MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * gnu/packages/julia-xyz.scm (julia-documenter)[arguments]<#:phases>: Substitute a work around to fix the change of 'git submodule' default behaviour introduced by Git v2.38.1. Signed-off-by: Ludovic Courtès --- gnu/packages/julia-xyz.scm | 9 +++++++++ 1 file changed, 9 insertions(+) diff --git a/gnu/packages/julia-xyz.scm b/gnu/packages/julia-xyz.scm index 28c759a5c0..ac6584825b 100644 --- a/gnu/packages/julia-xyz.scm +++ b/gnu/packages/julia-xyz.scm @@ -1472,6 +1472,15 @@ valuable enough at this time.") (("pip install") (string-append (search-input-file inputs "bin/pip") " install"))))) + (add-after 'link-depot 'fix-test-git-submodule + ;; Git v2.38.1 fixes security issues and changes the default + ;; behaviour of `git submodule`. This substitution is a backport + ;; of the upstream patch, not yet released, fixing the test suite. + ;; https://github.com/JuliaDocs/Documenter.jl/commit/b5a5c65d02d136743e7c18ffebf8baba900484fc + (lambda* (#:key inputs #:allow-other-keys) + (substitute* "test/utilities.jl" + (("submodule add") + "-c protocol.file.allow=always submodule add")))) (add-after 'link-depot 'remove-javascript-downloads (lambda _ (substitute* "src/Writers/HTMLWriter.jl" From 43e18fd6c66b311e7f8266e80d8d8e49fe4a11f0 Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Mon, 28 Nov 2022 14:10:14 -0500 Subject: [PATCH 002/790] system: Add e2fsprogs to %base-packages-utils. Rationale: Even when not using an ext file system, the utilities provided by e2fsprogs are useful, for example to set the copy-on-write attribute of a Btrfs file system. * gnu/system.scm (%base-packages-utils): Add e2fsprogs. --- gnu/system.scm | 2 ++ 1 file changed, 2 insertions(+) diff --git a/gnu/system.scm b/gnu/system.scm index 3478afcec4..3891d5a467 100644 --- a/gnu/system.scm +++ b/gnu/system.scm @@ -858,6 +858,8 @@ of PROVENANCE-SERVICE-TYPE to its services." (cons* procps psmisc which (@ (gnu packages admin) shadow-with-man-pages) ;for 'passwd' + e2fsprogs ;for lsattr, chattr, etc. + guile-3.0-latest ;; The packages below are also in %FINAL-INPUTS, so take them from From aeecd06ab9f748b0b40573e5520ea6c642060e12 Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Mon, 28 Nov 2022 13:57:58 -0500 Subject: [PATCH 003/790] system: Rename and move %base-packages-disk-utilities. Rationale: It is only used in INSTALLATION-OS and doesn't make sense to be used in another context, given that file systems now automatically pull their dependencies since commit 45eac6cdf5c8d9d7b0c564b105c790d2d2007799 (services: Add file system utilities to profile). * gnu/system.scm (%base-packages-disk-utilities): Deprecate and rename to... * gnu/system/install.scm (%installer-disk-utilities): ... this. (installation-os) [packages]: Adjust accordingly. --- gnu/system.scm | 19 ++----------------- gnu/system/install.scm | 19 ++++++++++++++++++- 2 files changed, 20 insertions(+), 18 deletions(-) diff --git a/gnu/system.scm b/gnu/system.scm index 3891d5a467..62c8e0c2b6 100644 --- a/gnu/system.scm +++ b/gnu/system.scm @@ -38,6 +38,7 @@ #:use-module (guix gexp) #:use-module (guix records) #:use-module (guix packages) + #:use-module (guix deprecation) #:use-module (guix derivations) #:use-module (guix profiles) #:use-module ((guix utils) #:select (substitute-keyword-arguments)) @@ -49,9 +50,6 @@ #:use-module (gnu packages bash) #:use-module (gnu packages compression) #:use-module (gnu packages cross-base) - #:use-module (gnu packages cryptsetup) - #:use-module (gnu packages disk) - #:use-module (gnu packages file-systems) #:use-module (gnu packages firmware) #:use-module (gnu packages gawk) #:use-module (gnu packages guile) @@ -898,20 +896,7 @@ of PROVENANCE-SERVICE-TYPE to its services." ;; many people are familiar with, so keep it around. iw wireless-tools)) -(define %base-packages-disk-utilities - ;; A well-rounded set of packages for interacting with disks, - ;; partitions and filesystems, included with the Guix installation - ;; image. - (list parted gptfdisk ddrescue - ;; We used to provide fdisk from GNU fdisk, but as of version 2.0.0a - ;; it pulls Guile 1.8, which takes unreasonable space; furthermore - ;; util-linux's fdisk is already available, in %base-packages-linux. - cryptsetup mdadm - dosfstools - btrfs-progs - f2fs-tools - jfsutils - xfsprogs)) +(define-deprecated %base-packages-disk-utilities #f '()) (define %base-packages ;; Default set of packages globally visible. It should include anything diff --git a/gnu/system/install.scm b/gnu/system/install.scm index 003c49a3e7..d34d974338 100644 --- a/gnu/system/install.scm +++ b/gnu/system/install.scm @@ -48,6 +48,9 @@ #:use-module (gnu packages bootloaders) #:use-module (gnu packages certs) #:use-module (gnu packages compression) + #:use-module (gnu packages cryptsetup) + #:use-module (gnu packages disk) + #:use-module (gnu packages file-systems) #:use-module (gnu packages fonts) #:use-module (gnu packages fontutils) #:use-module (gnu packages guile) @@ -458,6 +461,20 @@ Access documentation at any time by pressing Alt-F2.\x1b[0m \x1b[1;33mUse Alt-F2 for documentation.\x1b[0m ") +(define %installer-disk-utilities + ;; A well-rounded set of packages for interacting with disks, partitions and + ;; file systems, included with the Guix installation image. + (list parted gptfdisk ddrescue + ;; We used to provide fdisk from GNU fdisk, but as of version 2.0.0a + ;; it pulls Guile 1.8, which takes unreasonable space; furthermore + ;; util-linux's fdisk is already available, in %base-packages-linux. + cryptsetup mdadm + dosfstools + btrfs-progs + f2fs-tools + jfsutils + xfsprogs)) + (define installation-os ;; The operating system used on installation images for USB sticks etc. (operating-system @@ -530,7 +547,7 @@ Access documentation at any time by pressing Alt-F2.\x1b[0m font-dejavu font-gnu-unifont grub ; mostly so xrefs to its manual work nss-certs) ; To access HTTPS, use git, etc. - %base-packages-disk-utilities + %installer-disk-utilities %base-packages)))) (define* (os-with-u-boot os board #:key (bootloader-target "/dev/mmcblk0") From ba4aed0f1feff98559e5712bf11190be78e2aadc Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Mon, 28 Nov 2022 14:03:58 -0500 Subject: [PATCH 004/790] install: Add missing e2fsprogs utility. * gnu/system/install.scm (%installer-disk-utilities): Add e2fsprogs. Reported-by: Adam Kandur --- gnu/system/install.scm | 1 + 1 file changed, 1 insertion(+) diff --git a/gnu/system/install.scm b/gnu/system/install.scm index d34d974338..f6f1923121 100644 --- a/gnu/system/install.scm +++ b/gnu/system/install.scm @@ -471,6 +471,7 @@ Access documentation at any time by pressing Alt-F2.\x1b[0m cryptsetup mdadm dosfstools btrfs-progs + e2fsprogs f2fs-tools jfsutils xfsprogs)) From 2493de0d1a481f079580a354430b26977afbdbd1 Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Mon, 5 Dec 2022 10:51:25 -0500 Subject: [PATCH 005/790] Revert "tests: install: Fix iso-image-installer test." MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit This reverts commit 0f66ef9aa99d2043abccbc80d858bdeca57534ac. e2fsprogs is now included in the installation operating system since 34f69bc6e6ea555929ecca83ee7592f5261ff5f2, making this workaround obsolete. Suggested-by: Ludovic Courtès --- gnu/tests/install.scm | 2 -- 1 file changed, 2 deletions(-) diff --git a/gnu/tests/install.scm b/gnu/tests/install.scm index 30a9026d5f..4e0e274e66 100644 --- a/gnu/tests/install.scm +++ b/gnu/tests/install.scm @@ -471,8 +471,6 @@ reboot\n") (mlet* %store-monad ((images (run-install %minimal-os-on-vda %minimal-os-on-vda-source - #:packages - (list e2fsprogs) #:script %simple-installation-script-for-/dev/vda #:installation-image-type From f59aa79ca342ef311a20dafc782adea6eed29b1a Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ludovic=20Court=C3=A8s?= Date: Tue, 6 Dec 2022 15:06:35 +0100 Subject: [PATCH 006/790] system: vm: Non-volatile 'run-vm.sh' creates a CoW image. Previously, copying the image would consume a lot of space and was I/O-intensive, to the point that the marionette connection timeout of 20s could be reached when running tests like "docker-system". * gnu/system/vm.scm (common-qemu-options): Pass 'format=' for each '-drive' option. (system-qemu-image/shared-store-script)[copy-image]: New variable. [builder]: Use it when VOLATILE? is false. --- gnu/system/vm.scm | 27 ++++++++++++++++++--------- 1 file changed, 18 insertions(+), 9 deletions(-) diff --git a/gnu/system/vm.scm b/gnu/system/vm.scm index c2f7efa966..b7bccd72a4 100644 --- a/gnu/system/vm.scm +++ b/gnu/system/vm.scm @@ -1,5 +1,5 @@ ;;; GNU Guix --- Functional package management for GNU -;;; Copyright © 2013, 2014, 2015, 2016, 2017, 2018, 2019, 2020, 2021 Ludovic Courtès +;;; Copyright © 2013-2022 Ludovic Courtès ;;; Copyright © 2016 Christine Lemmer-Webber ;;; Copyright © 2016, 2017 Leo Famulari ;;; Copyright © 2017 Mathieu Othacehe @@ -234,8 +234,8 @@ with '-virtfs' options for the host file systems listed in SHARED-FS." #$@(map virtfs-option shared-fs) #$@(if rw-image? - #~((format #f "-drive file=~a,if=virtio" #$image)) - #~((format #f "-drive file=~a,if=virtio,cache=writeback,werror=report,readonly=on" + #~((format #f "-drive file=~a,format=qcow2,if=virtio" #$image)) + #~((format #f "-drive file=~a,format=raw,if=virtio,cache=writeback,werror=report,readonly=on" #$image))))) (define* (system-qemu-image/shared-store-script os @@ -303,17 +303,26 @@ useful when FULL-BOOT? is true." "-m " (number->string #$memory-size) #$@options)) + (define copy-image + ;; Script that "copies" BASE-IMAGE to /tmp. Make a copy-on-write image, + ;; which is much cheaper than actually copying it. + (program-file "copy-image" + (with-imported-modules '((guix build utils)) + #~(begin + (use-modules (guix build utils)) + (unless (file-exists? #$rw-image) + (invoke #+(file-append qemu "/bin/qemu-img") + "create" "-b" #$base-image + "-F" "raw" "-f" "qcow2" #$rw-image)))))) + (define builder #~(call-with-output-file #$output (lambda (port) (format port "#!~a~%" #+(file-append bash "/bin/sh")) - (when (not #$volatile?) - (format port "~a~%" - #$(program-file "copy-image" - #~(unless (file-exists? #$rw-image) - (copy-file #$base-image #$rw-image) - (chmod #$rw-image #o640))))) + #$@(if volatile? + #~() + #~((format port "~a~%" #+copy-image))) (format port "exec ~a \"$@\"~%" (string-join #$qemu-exec " ")) (chmod port #o555)))) From 6232959311b5717c19552e1116f6e4fea9797282 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ludovic=20Court=C3=A8s?= Date: Tue, 6 Dec 2022 15:10:24 +0100 Subject: [PATCH 007/790] tests: docker-system: Increase image size. * gnu/tests/docker.scm (run-docker-system-test)[vm]: Increase 'disk-image-size'. --- gnu/tests/docker.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/tests/docker.scm b/gnu/tests/docker.scm index 3e780d8a60..4267ff89a8 100644 --- a/gnu/tests/docker.scm +++ b/gnu/tests/docker.scm @@ -1,6 +1,6 @@ ;;; GNU Guix --- Functional package management for GNU ;;; Copyright © 2019 Danny Milosavljevic -;;; Copyright © 2019, 2020, 2021 Ludovic Courtès +;;; Copyright © 2019-2022 Ludovic Courtès ;;; ;;; This file is part of GNU Guix. ;;; @@ -209,7 +209,7 @@ inside %DOCKER-OS." (virtual-machine (operating-system os) (volatile? #f) - (disk-image-size (* 5000 (expt 2 20))) + (disk-image-size (* 5500 (expt 2 20))) (memory-size 2048) (port-forwardings '()))) From 9ad14196ce48d5161fcaa7fc5fd26259e517cb30 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ludovic=20Court=C3=A8s?= Date: Tue, 6 Dec 2022 15:11:44 +0100 Subject: [PATCH 008/790] image: Clarify comment. * gnu/system/image.scm: Adjust comment. --- gnu/system/image.scm | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/gnu/system/image.scm b/gnu/system/image.scm index f07a4a5217..d518a05a51 100644 --- a/gnu/system/image.scm +++ b/gnu/system/image.scm @@ -972,9 +972,9 @@ image, depending on IMAGE format." (G_ "~a: unsupported image format") image-format))))))) -;; -;; Image detection. -;; +;;; +;;; Image type discovery. +;;; (define (image-modules) "Return the list of image modules." From fe563a87ad7c171448c56ed6b628c8e32a52c94a Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ludovic=20Court=C3=A8s?= Date: Tue, 6 Dec 2022 15:21:21 +0100 Subject: [PATCH 009/790] gnu: texinfo, info-reader: Do not run tests when cross-compiling. Fixes a regression introduced in a3264f31df9774ea514e18ed8e7b6bcb44061edc. Reported by Mathieu Othacehe . * gnu/packages/texinfo.scm (texinfo)[arguments]: Change #:tests? to not run tests when cross-compiling. --- gnu/packages/texinfo.scm | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/gnu/packages/texinfo.scm b/gnu/packages/texinfo.scm index 25498ae36e..7108d1e067 100644 --- a/gnu/packages/texinfo.scm +++ b/gnu/packages/texinfo.scm @@ -75,7 +75,8 @@ %standard-phases) ;; XXX: Work around . - #:tests? ,(not (hurd-target?)))) + #:tests? ,(and (not (hurd-target?)) + (not (%current-target-system))))) (inputs (list ncurses perl)) ;; When cross-compiling, texinfo will build some of its own binaries with ;; the native compiler. This means ncurses is needed both in both inputs From e45c83c3979c2554119fafdee7bb204d27e138b5 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ludovic=20Court=C3=A8s?= Date: Tue, 6 Dec 2022 17:05:34 +0100 Subject: [PATCH 010/790] services: fail2ban: 'stop' returns #f when the dameon is stopped. * gnu/services/security.scm (fail2ban-shepherd-service): Change FAIL2BAN-ACTION to return an 'invoke' gexp. Adjust the shepherd 'start' and 'stop' fields accordingly. Have 'stop' return #f on success. --- gnu/services/security.scm | 20 +++++++++++--------- 1 file changed, 11 insertions(+), 9 deletions(-) diff --git a/gnu/services/security.scm b/gnu/services/security.scm index 15fae7a628..2d048ab47b 100644 --- a/gnu/services/security.scm +++ b/gnu/services/security.scm @@ -356,13 +356,12 @@ provided as a list of file-like objects.")) (config-dir (file-append (config->fail2ban-etc-directory config) "/etc/fail2ban")) (fail2ban-action (lambda args - #~(lambda _ - (invoke #$fail2ban-server - "-c" #$config-dir - "-p" #$pid-file - "-s" #$socket-file - "-b" - #$@args))))) + #~(invoke #$fail2ban-server + "-c" #$config-dir + "-p" #$pid-file + "-s" #$socket-file + "-b" + #$@args)))) ;; TODO: Add 'reload' action. (list (shepherd-service @@ -371,8 +370,11 @@ provided as a list of file-like objects.")) (requirement '(user-processes)) (modules `((ice-9 match) ,@%default-modules)) - (start (fail2ban-action "start")) - (stop (fail2ban-action "stop"))))))) + (start #~(lambda () + #$(fail2ban-action "start"))) + (stop #~(lambda (_) + #$(fail2ban-action "stop") + #f))))))) ;successfully stopped (define fail2ban-service-type (service-type (name 'fail2ban) From a508b5c7785bcd040c5a9e890be71ccd97f198fb Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ludovic=20Court=C3=A8s?= Date: Tue, 6 Dec 2022 17:07:46 +0100 Subject: [PATCH 011/790] services: fail2ban: Remove unnecessary Shepherd 'modules' field. * gnu/services/security.scm (fail2ban-shepherd-service): Remove unnecessary 'modules' field. --- gnu/services/security.scm | 2 -- 1 file changed, 2 deletions(-) diff --git a/gnu/services/security.scm b/gnu/services/security.scm index 2d048ab47b..2010f9143a 100644 --- a/gnu/services/security.scm +++ b/gnu/services/security.scm @@ -368,8 +368,6 @@ provided as a list of file-like objects.")) (provision '(fail2ban)) (documentation "Run the fail2ban daemon.") (requirement '(user-processes)) - (modules `((ice-9 match) - ,@%default-modules)) (start #~(lambda () #$(fail2ban-action "start"))) (stop #~(lambda (_) From a420b4f34e7449319f6ec73301ffb932845b66d6 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ludovic=20Court=C3=A8s?= Date: Tue, 6 Dec 2022 17:46:45 +0100 Subject: [PATCH 012/790] services: fail2ban: Start server in the foreground. Previously, we were passing '-b', thereby starting the server in the background. Consequently the 'start' method could complete before the server was ready to accept connections on its socket, leading to non-deterministic test failures. Reported by Mathieu Othacehe . * gnu/services/security.scm (fail2ban-shepherd-service): Change FAIL2BAN-ACTION to invoke 'fail2ban-client'. Change 'start' method to use 'make-forkexec-constructor'; start the server in the foreground with '-f' and pass '-x' to force execution of the server, as done upstream in 'fail2ban.service.in'. --- gnu/services/security.scm | 18 +++++++++--------- 1 file changed, 9 insertions(+), 9 deletions(-) diff --git a/gnu/services/security.scm b/gnu/services/security.scm index 2010f9143a..50111455fb 100644 --- a/gnu/services/security.scm +++ b/gnu/services/security.scm @@ -1,5 +1,6 @@ ;;; GNU Guix --- Functional package management for GNU ;;; Copyright © 2022 muradm +;;; Copyright © 2022 Ludovic Courtès ;;; ;;; This file is part of GNU Guix. ;;; @@ -351,25 +352,24 @@ provided as a list of file-like objects.")) (match-record config (fail2ban run-directory) (let* ((fail2ban-server (file-append fail2ban "/bin/fail2ban-server")) + (fail2ban-client (file-append fail2ban "/bin/fail2ban-client")) (pid-file (in-vicinity run-directory "fail2ban.pid")) (socket-file (in-vicinity run-directory "fail2ban.sock")) (config-dir (file-append (config->fail2ban-etc-directory config) "/etc/fail2ban")) (fail2ban-action (lambda args - #~(invoke #$fail2ban-server - "-c" #$config-dir - "-p" #$pid-file - "-s" #$socket-file - "-b" - #$@args)))) + #~(invoke #$fail2ban-client #$@args)))) - ;; TODO: Add 'reload' action. + ;; TODO: Add 'reload' action (see 'fail2ban.service.in' in the source). (list (shepherd-service (provision '(fail2ban)) (documentation "Run the fail2ban daemon.") (requirement '(user-processes)) - (start #~(lambda () - #$(fail2ban-action "start"))) + (start #~(make-forkexec-constructor + (list #$fail2ban-server + "-c" #$config-dir "-s" #$socket-file + "-p" #$pid-file "-xf" "start") + #:pid-file #$pid-file)) (stop #~(lambda (_) #$(fail2ban-action "stop") #f))))))) ;successfully stopped From 754a7660a1716998b557aedeb805ee9040afdcdf Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ludovic=20Court=C3=A8s?= Date: Sat, 19 Nov 2022 17:23:04 +0100 Subject: [PATCH 013/790] records: 'match-record' checks fields at macro-expansion time. This allows 'match-record' to be more efficient (field offsets are computed at compilation time) and to report unknown fields at macro-expansion time. * guix/records.scm (map-fields): New macro. (define-record-type*)[rtd-identifier]: New procedure. Define TYPE as a macro and use a separate identifier for the RTD. (lookup-field, match-record-inner): New macros. (match-record): Rewrite in terms of 'match-error-inner'. * tests/records.scm ("match-record, simple") ("match-record, unknown field"): New tests. * gnu/services/cuirass.scm (cuirass-shepherd-service): Rename 'log-file' local variable to 'main-log-file'. * gnu/services/getmail.scm (serialize-getmail-configuration-file): Move after definition. --- gnu/services/cuirass.scm | 4 +- gnu/services/getmail.scm | 22 +++++----- guix/records.scm | 87 +++++++++++++++++++++++++++++++++++----- tests/records.scm | 33 +++++++++++++++ 4 files changed, 122 insertions(+), 24 deletions(-) diff --git a/gnu/services/cuirass.scm b/gnu/services/cuirass.scm index 52de5ca7c0..d7c6ab9877 100644 --- a/gnu/services/cuirass.scm +++ b/gnu/services/cuirass.scm @@ -125,7 +125,7 @@ (let ((cuirass (cuirass-configuration-cuirass config)) (cache-directory (cuirass-configuration-cache-directory config)) (web-log-file (cuirass-configuration-web-log-file config)) - (log-file (cuirass-configuration-log-file config)) + (main-log-file (cuirass-configuration-log-file config)) (user (cuirass-configuration-user config)) (group (cuirass-configuration-group config)) (interval (cuirass-configuration-interval config)) @@ -169,7 +169,7 @@ #:user #$user #:group #$group - #:log-file #$log-file)) + #:log-file #$main-log-file)) (stop #~(make-kill-destructor))) ,(shepherd-service (documentation "Run Cuirass web interface.") diff --git a/gnu/services/getmail.scm b/gnu/services/getmail.scm index fb82d054ca..19faea782f 100644 --- a/gnu/services/getmail.scm +++ b/gnu/services/getmail.scm @@ -215,17 +215,6 @@ lines.") (parameter-alist '()) "Extra options to include.")) -(define (serialize-getmail-configuration-file field-name val) - (match-record val - (retriever destination options) - #~(string-append - "[retriever]\n" - #$(serialize-getmail-retriever-configuration #f retriever) - "\n[destination]\n" - #$(serialize-getmail-destination-configuration #f destination) - "\n[options]\n" - #$(serialize-getmail-options-configuration #f options)))) - (define-configuration getmail-configuration-file (retriever (getmail-retriever-configuration (getmail-retriever-configuration)) @@ -237,6 +226,17 @@ lines.") (getmail-options-configuration (getmail-options-configuration)) "Configure getmail.")) +(define (serialize-getmail-configuration-file field-name val) + (match-record val + (retriever destination options) + #~(string-append + "[retriever]\n" + #$(serialize-getmail-retriever-configuration #f retriever) + "\n[destination]\n" + #$(serialize-getmail-destination-configuration #f destination) + "\n[options]\n" + #$(serialize-getmail-options-configuration #f options)))) + (define (serialize-symbol field-name val) "") (define (serialize-getmail-configuration field-name val) "") diff --git a/guix/records.scm b/guix/records.scm index ed94c83dac..13463647c8 100644 --- a/guix/records.scm +++ b/guix/records.scm @@ -1,5 +1,5 @@ ;;; GNU Guix --- Functional package management for GNU -;;; Copyright © 2012, 2013, 2014, 2015, 2016, 2017, 2018, 2019, 2020, 2021 Ludovic Courtès +;;; Copyright © 2012-2022 Ludovic Courtès ;;; Copyright © 2018 Mark H Weaver ;;; ;;; This file is part of GNU Guix. @@ -104,6 +104,10 @@ error-reporting purposes." (() #t))))))) +(define-syntax map-fields + (lambda (x) + (syntax-violation 'map-fields "bad use of syntactic keyword" x x))) + (define-syntax-parameter this-record (lambda (s) "Return the record being defined. This macro may only be used in the @@ -325,6 +329,15 @@ This expression returns a new object equal to 'x' except for its 'name' field and its 'loc' field---the latter is marked as \"innate\", so it is not inherited." + (define (rtd-identifier type) + ;; Return an identifier derived from TYPE to name its record type + ;; descriptor (RTD). + (let ((type-name (syntax->datum type))) + (datum->syntax + type + (string->symbol + (string-append "% " (symbol->string type-name) " rtd"))))) + (define (field-default-value s) (syntax-case s (default) ((field (default val) _ ...) @@ -428,10 +441,31 @@ inherited." field))) field-spec))) #`(begin - (define-record-type type + (define-record-type #,(rtd-identifier #'type) (ctor field ...) pred field-spec* ...) + + ;; Rectify the vtable type name... + (set-struct-vtable-name! #,(rtd-identifier #'type) 'type) + (cond-expand + (guile-3 + ;; ... and the record type name. + (struct-set! #,(rtd-identifier #'type) vtable-offset-user + 'type)) + (else #f)) + + (define-syntax type + (lambda (s) + "This macro lets us query record type info at +macro-expansion time." + (syntax-case s (map-fields) + ((_ map-fields macro) + #'(macro (field ...))) + (id + (identifier? #'id) + #'#,(rtd-identifier #'type))))) + (define #,(current-abi-identifier #'type) #,cookie) @@ -535,19 +569,50 @@ pairs. Stop upon an empty line (after consuming it) or EOF." (else (error "unmatched line" line)))))))) + +;;; +;;; Pattern matching. +;;; + +(define-syntax lookup-field + (lambda (s) + "Look up FIELD in the given list and return an expression that represents +its offset in the record. Raise a syntax violation when the field is not +found." + (syntax-case s () + ((_ field offset ()) + (syntax-violation 'lookup-field "unknown record type field" + s #'field)) + ((_ field offset (head tail ...)) + (free-identifier=? #'field #'head) + #'offset) + ((_ field offset (_ tail ...)) + #'(lookup-field field (+ 1 offset) (tail ...)))))) + +(define-syntax match-record-inner + (lambda (s) + (syntax-case s () + ((_ record type (field rest ...) body ...) + #`(let-syntax ((field-offset (syntax-rules () + ((_ f) + (lookup-field field 0 f))))) + (let* ((offset (type map-fields field-offset)) + (field (struct-ref record offset))) + (match-record-inner record type (rest ...) body ...)))) + ((_ record type () body ...) + #'(begin body ...))))) + (define-syntax match-record (syntax-rules () "Bind each FIELD of a RECORD of the given TYPE to it's FIELD name. +The order in which fields appear does not matter. A syntax error is raised if +an unknown field is queried. + The current implementation does not support thunked and delayed fields." - ((_ record type (field fields ...) body ...) + ;; TODO support thunked and delayed fields + ((_ record type (fields ...) body ...) (if (eq? (struct-vtable record) type) - ;; TODO compute indices and report wrong-field-name errors at - ;; expansion time - ;; TODO support thunked and delayed fields - (let ((field ((record-accessor type 'field) record))) - (match-record record type (fields ...) body ...)) - (throw 'wrong-type-arg record))) - ((_ record type () body ...) - (begin body ...)))) + (match-record-inner record type (fields ...) body ...) + (throw 'wrong-type-arg record))))) ;;; records.scm ends here diff --git a/tests/records.scm b/tests/records.scm index 00c58b0736..8504c8d5a5 100644 --- a/tests/records.scm +++ b/tests/records.scm @@ -528,4 +528,37 @@ Description: 1st line, '("a" "b" "c") '("a"))) +(test-equal "match-record, simple" + '((1 2) (a b)) + (let () + (define-record-type* foo make-foo + foo? + (first foo-first (default 1)) + (second foo-second)) + + (list (match-record (foo (second 2)) + (first second) + (list first second)) + (match-record (foo (first 'a) (second 'b)) + (second first) + (list first second))))) + +(test-equal "match-record, unknown field" + 'syntax-error + (catch 'syntax-error + (lambda () + (eval '(begin + (use-modules (guix records)) + + (define-record-type* foo make-foo + foo? + (first foo-first (default 1)) + (second foo-second)) + + (match-record (foo (second 2)) + (one two) + #f)) + (make-fresh-user-module))) + (lambda (key . args) key))) + (test-end) From 883aa80b45c10628322c52f9912188d3a85b5639 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ludovic=20Court=C3=A8s?= Date: Sat, 19 Nov 2022 22:40:35 +0100 Subject: [PATCH 014/790] doc: Recommend 'match-record'. * doc/contributing.texi (Data Types and Pattern Matching): Recommend 'match-record'. --- doc/contributing.texi | 7 ++++++- 1 file changed, 6 insertions(+), 1 deletion(-) diff --git a/doc/contributing.texi b/doc/contributing.texi index 40ae33ecac..6a8ffd6524 100644 --- a/doc/contributing.texi +++ b/doc/contributing.texi @@ -1089,11 +1089,16 @@ and then to browse them ``by hand'' using @code{car}, @code{cdr}, notably the fact that it is hard to read, error-prone, and a hindrance to proper type error reports. +@findex define-record-type* +@findex match-record +@cindex pattern matching Guix code should define appropriate data types (for instance, using @code{define-record-type*}) rather than abuse lists. In addition, it should use pattern matching, via Guile’s @code{(ice-9 match)} module, especially when matching lists (@pxref{Pattern Matching,,, guile, GNU -Guile Reference Manual}). +Guile Reference Manual}); pattern matching for records is better done +using @code{match-record} from @code{(guix records)}, which, unlike +@code{match}, verifies field names at macro-expansion time. @node Formatting Code @subsection Formatting Code From 93d37985da59fbd5a42c0d868dc3616b0f8d05cc Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ludovic=20Court=C3=A8s?= Date: Sat, 19 Nov 2022 17:37:24 +0100 Subject: [PATCH 015/790] home: services: Use 'match-record' instead of 'match'. * gnu/home/services/mcron.scm (home-mcron-shepherd-services): Use 'match-record' instead of 'match'. * gnu/home/services/shells.scm (home-bash-extensions): Likewise. * gnu/home/services/xdg.scm (serialize-xdg-desktop-entry): Likewise. --- gnu/home/services/mcron.scm | 58 ++++++++++++++++++------------------ gnu/home/services/shells.scm | 50 +++++++++++++++---------------- gnu/home/services/xdg.scm | 36 +++++++++++----------- 3 files changed, 72 insertions(+), 72 deletions(-) diff --git a/gnu/home/services/mcron.scm b/gnu/home/services/mcron.scm index 1d294a997c..5f35bfe054 100644 --- a/gnu/home/services/mcron.scm +++ b/gnu/home/services/mcron.scm @@ -77,35 +77,35 @@ Each message is also prefixed by a timestamp by GNU Shepherd.")) (define shepherd-schedule-action (@@ (gnu services mcron) shepherd-schedule-action)) -(define home-mcron-shepherd-services - (match-lambda - (($ mcron '()) ; no jobs to run - '()) - (($ mcron jobs log? log-format) - (let ((files (job-files mcron jobs))) - (list (shepherd-service - (documentation "User cron jobs.") - (provision '(mcron)) - (modules `((srfi srfi-1) - (srfi srfi-26) - (ice-9 popen) ; for the 'schedule' action - (ice-9 rdelim) - (ice-9 match) - ,@%default-modules)) - (start #~(make-forkexec-constructor - (list (string-append #$mcron "/bin/mcron") - #$@(if log? - #~("--log" "--log-format" #$log-format) - #~()) - #$@files) - #:log-file (string-append - (or (getenv "XDG_LOG_HOME") - (format #f "~a/.local/var/log" - (getenv "HOME"))) - "/mcron.log"))) - (stop #~(make-kill-destructor)) - (actions - (list (shepherd-schedule-action mcron files))))))))) +(define (home-mcron-shepherd-services config) + (match-record config + (mcron jobs log? log-format) + (if (null? jobs) + '() ;no jobs to run + (let ((files (job-files mcron jobs))) + (list (shepherd-service + (documentation "User cron jobs.") + (provision '(mcron)) + (modules `((srfi srfi-1) + (srfi srfi-26) + (ice-9 popen) ;for the 'schedule' action + (ice-9 rdelim) + (ice-9 match) + ,@%default-modules)) + (start #~(make-forkexec-constructor + (list (string-append #$mcron "/bin/mcron") + #$@(if log? + #~("--log" "--log-format" #$log-format) + #~()) + #$@files) + #:log-file (string-append + (or (getenv "XDG_LOG_HOME") + (format #f "~a/.local/var/log" + (getenv "HOME"))) + "/mcron.log"))) + (stop #~(make-kill-destructor)) + (actions + (list (shepherd-schedule-action mcron files))))))))) (define home-mcron-profile (compose list home-mcron-configuration-mcron)) diff --git a/gnu/home/services/shells.scm b/gnu/home/services/shells.scm index 3e346c3813..b529c8e798 100644 --- a/gnu/home/services/shells.scm +++ b/gnu/home/services/shells.scm @@ -25,6 +25,7 @@ #:use-module (gnu packages bash) #:use-module (guix gexp) #:use-module (guix packages) + #:use-module (guix records) #:use-module (srfi srfi-1) #:use-module (srfi srfi-26) #:use-module (ice-9 match) @@ -479,31 +480,30 @@ with text blocks from other extensions and the base service.") with text blocks from other extensions and the base service.")) (define (home-bash-extensions original-config extension-configs) - (match original-config - (($ _ _ environment-variables aliases - bash-profile bashrc bash-logout) - (home-bash-configuration - (inherit original-config) - (environment-variables - (append environment-variables - (append-map - home-bash-extension-environment-variables extension-configs))) - (aliases - (append aliases - (append-map - home-bash-extension-aliases extension-configs))) - (bash-profile - (append bash-profile - (append-map - home-bash-extension-bash-profile extension-configs))) - (bashrc - (append bashrc - (append-map - home-bash-extension-bashrc extension-configs))) - (bash-logout - (append bash-logout - (append-map - home-bash-extension-bash-logout extension-configs))))))) + (match-record original-config + (environment-variables aliases bash-profile bashrc bash-logout) + (home-bash-configuration + (inherit original-config) + (environment-variables + (append environment-variables + (append-map + home-bash-extension-environment-variables extension-configs))) + (aliases + (append aliases + (append-map + home-bash-extension-aliases extension-configs))) + (bash-profile + (append bash-profile + (append-map + home-bash-extension-bash-profile extension-configs))) + (bashrc + (append bashrc + (append-map + home-bash-extension-bashrc extension-configs))) + (bash-logout + (append bash-logout + (append-map + home-bash-extension-bash-logout extension-configs)))))) (define home-bash-service-type (service-type (name 'home-bash) diff --git a/gnu/home/services/xdg.scm b/gnu/home/services/xdg.scm index 63c6041cd4..3c6cb773ad 100644 --- a/gnu/home/services/xdg.scm +++ b/gnu/home/services/xdg.scm @@ -383,25 +383,25 @@ configuration." (define (serialize-alist config) (generic-serialize-alist append format-config config)) - (define (serialize-xdg-desktop-action action) - (match action - (($ action name config) - `(,(format #f "[Desktop Action ~a]\n" - (string-capitalize (maybe-object->string action))) - ,(format #f "Name=~a\n" name) - ,@(serialize-alist config))))) + (define (serialize-xdg-desktop-action desktop-action) + (match-record desktop-action + (action name config) + `(,(format #f "[Desktop Action ~a]\n" + (string-capitalize (maybe-object->string action))) + ,(format #f "Name=~a\n" name) + ,@(serialize-alist config)))) - (match entry - (($ file name type config actions) - (list (if (string-suffix? file ".desktop") - file - (string-append file ".desktop")) - `("[Desktop Entry]\n" - ,(format #f "Name=~a\n" name) - ,(format #f "Type=~a\n" - (string-capitalize (symbol->string type))) - ,@(serialize-alist config) - ,@(append-map serialize-xdg-desktop-action actions)))))) + (match-record entry + (file name type config actions) + (list (if (string-suffix? file ".desktop") + file + (string-append file ".desktop")) + `("[Desktop Entry]\n" + ,(format #f "Name=~a\n" name) + ,(format #f "Type=~a\n" + (string-capitalize (symbol->string type))) + ,@(serialize-alist config) + ,@(append-map serialize-xdg-desktop-action actions))))) (define-configuration home-xdg-mime-applications-configuration (added From 156a8810019dd5b8d19f2026be80f199f8e40015 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ludovic=20Court=C3=A8s?= Date: Sat, 19 Nov 2022 17:54:26 +0100 Subject: [PATCH 016/790] services: base: Use 'match-record' instead of 'match'. * gnu/services/base.scm (agetty-shepherd-service) (mingetty-shepherd-service) (nscd.conf-file) (udev-shepherd-service) (udev-etc) (gpm-shepherd-service) (network-set-up/linux) (network-tear-down/linux) (static-networking-shepherd-service) (greetd-agreety-tty-session-command) (greetd-agreety-tty-xdg-session-command): Use 'match-record' instead of 'match'. (guix-accounts): Use accessors. (udev-service-type): Use accessors. --- gnu/services/base.scm | 882 +++++++++++++++++++++--------------------- 1 file changed, 440 insertions(+), 442 deletions(-) diff --git a/gnu/services/base.scm b/gnu/services/base.scm index d99548573d..370696a55e 100644 --- a/gnu/services/base.scm +++ b/gnu/services/base.scm @@ -977,148 +977,148 @@ to use as the tty. This is primarily useful for headless systems." ((device-name _ ...) device-name)))))))) -(define agetty-shepherd-service - (match-lambda - (($ agetty tty term baud-rate auto-login - login-program login-pause? eight-bits? no-reset? remote? flow-control? - host no-issue? init-string no-clear? local-line extract-baud? - skip-login? no-newline? login-options chroot hangup? keep-baud? timeout - detect-case? wait-cr? no-hints? no-hostname? long-hostname? - erase-characters kill-characters chdir delay nice extra-options - shepherd-requirement) - (list - (shepherd-service - (documentation "Run agetty on a tty.") - (provision (list (symbol-append 'term- (string->symbol (or tty "console"))))) +(define (agetty-shepherd-service config) + (match-record config + (agetty tty term baud-rate auto-login + login-program login-pause? eight-bits? no-reset? remote? flow-control? + host no-issue? init-string no-clear? local-line extract-baud? + skip-login? no-newline? login-options chroot hangup? keep-baud? timeout + detect-case? wait-cr? no-hints? no-hostname? long-hostname? + erase-characters kill-characters chdir delay nice extra-options + shepherd-requirement) + (list + (shepherd-service + (documentation "Run agetty on a tty.") + (provision (list (symbol-append 'term- (string->symbol (or tty "console"))))) - ;; Since the login prompt shows the host name, wait for the 'host-name' - ;; service to be done. Also wait for udev essentially so that the tty - ;; text is not lost in the middle of kernel messages (see also - ;; mingetty-shepherd-service). - (requirement (cons* 'user-processes 'host-name 'udev - shepherd-requirement)) + ;; Since the login prompt shows the host name, wait for the 'host-name' + ;; service to be done. Also wait for udev essentially so that the tty + ;; text is not lost in the middle of kernel messages (see also + ;; mingetty-shepherd-service). + (requirement (cons* 'user-processes 'host-name 'udev + shepherd-requirement)) - (modules '((ice-9 match) (gnu build linux-boot))) - (start - (with-imported-modules (source-module-closure - '((gnu build linux-boot))) - #~(lambda args - (let ((defaulted-tty #$(or tty (default-serial-port)))) - (apply - (if defaulted-tty - (make-forkexec-constructor - (list #$(file-append util-linux "/sbin/agetty") - #$@extra-options - #$@(if eight-bits? - #~("--8bits") - #~()) - #$@(if no-reset? - #~("--noreset") - #~()) - #$@(if remote? - #~("--remote") - #~()) - #$@(if flow-control? - #~("--flow-control") - #~()) - #$@(if host - #~("--host" #$host) - #~()) - #$@(if no-issue? - #~("--noissue") - #~()) - #$@(if init-string - #~("--init-string" #$init-string) - #~()) - #$@(if no-clear? - #~("--noclear") - #~()) + (modules '((ice-9 match) (gnu build linux-boot))) + (start + (with-imported-modules (source-module-closure + '((gnu build linux-boot))) + #~(lambda args + (let ((defaulted-tty #$(or tty (default-serial-port)))) + (apply + (if defaulted-tty + (make-forkexec-constructor + (list #$(file-append util-linux "/sbin/agetty") + #$@extra-options + #$@(if eight-bits? + #~("--8bits") + #~()) + #$@(if no-reset? + #~("--noreset") + #~()) + #$@(if remote? + #~("--remote") + #~()) + #$@(if flow-control? + #~("--flow-control") + #~()) + #$@(if host + #~("--host" #$host) + #~()) + #$@(if no-issue? + #~("--noissue") + #~()) + #$@(if init-string + #~("--init-string" #$init-string) + #~()) + #$@(if no-clear? + #~("--noclear") + #~()) ;;; FIXME This doesn't work as expected. According to agetty(8), if this option ;;; is not passed, then the default is 'auto'. However, in my tests, when that ;;; option is selected, agetty never presents the login prompt, and the ;;; term-ttyS0 service respawns every few seconds. - #$@(if local-line - #~(#$(match local-line - ('auto "--local-line=auto") - ('always "--local-line=always") - ('never "-local-line=never"))) - #~()) - #$@(if tty - #~() - #~("--keep-baud")) - #$@(if extract-baud? - #~("--extract-baud") - #~()) - #$@(if skip-login? - #~("--skip-login") - #~()) - #$@(if no-newline? - #~("--nonewline") - #~()) - #$@(if login-options - #~("--login-options" #$login-options) - #~()) - #$@(if chroot - #~("--chroot" #$chroot) - #~()) - #$@(if hangup? - #~("--hangup") - #~()) - #$@(if keep-baud? - #~("--keep-baud") - #~()) - #$@(if timeout - #~("--timeout" #$(number->string timeout)) - #~()) - #$@(if detect-case? - #~("--detect-case") - #~()) - #$@(if wait-cr? - #~("--wait-cr") - #~()) - #$@(if no-hints? - #~("--nohints?") - #~()) - #$@(if no-hostname? - #~("--nohostname") - #~()) - #$@(if long-hostname? - #~("--long-hostname") - #~()) - #$@(if erase-characters - #~("--erase-chars" #$erase-characters) - #~()) - #$@(if kill-characters - #~("--kill-chars" #$kill-characters) - #~()) - #$@(if chdir - #~("--chdir" #$chdir) - #~()) - #$@(if delay - #~("--delay" #$(number->string delay)) - #~()) - #$@(if nice - #~("--nice" #$(number->string nice)) - #~()) - #$@(if auto-login - (list "--autologin" auto-login) - '()) - #$@(if login-program - #~("--login-program" #$login-program) - #~()) - #$@(if login-pause? - #~("--login-pause") - #~()) - defaulted-tty - #$@(if baud-rate - #~(#$baud-rate) - #~()) - #$@(if term - #~(#$term) - #~()))) - (const #f)) ; never start. - args))))) - (stop #~(make-kill-destructor))))))) + #$@(if local-line + #~(#$(match local-line + ('auto "--local-line=auto") + ('always "--local-line=always") + ('never "-local-line=never"))) + #~()) + #$@(if tty + #~() + #~("--keep-baud")) + #$@(if extract-baud? + #~("--extract-baud") + #~()) + #$@(if skip-login? + #~("--skip-login") + #~()) + #$@(if no-newline? + #~("--nonewline") + #~()) + #$@(if login-options + #~("--login-options" #$login-options) + #~()) + #$@(if chroot + #~("--chroot" #$chroot) + #~()) + #$@(if hangup? + #~("--hangup") + #~()) + #$@(if keep-baud? + #~("--keep-baud") + #~()) + #$@(if timeout + #~("--timeout" #$(number->string timeout)) + #~()) + #$@(if detect-case? + #~("--detect-case") + #~()) + #$@(if wait-cr? + #~("--wait-cr") + #~()) + #$@(if no-hints? + #~("--nohints?") + #~()) + #$@(if no-hostname? + #~("--nohostname") + #~()) + #$@(if long-hostname? + #~("--long-hostname") + #~()) + #$@(if erase-characters + #~("--erase-chars" #$erase-characters) + #~()) + #$@(if kill-characters + #~("--kill-chars" #$kill-characters) + #~()) + #$@(if chdir + #~("--chdir" #$chdir) + #~()) + #$@(if delay + #~("--delay" #$(number->string delay)) + #~()) + #$@(if nice + #~("--nice" #$(number->string nice)) + #~()) + #$@(if auto-login + (list "--autologin" auto-login) + '()) + #$@(if login-program + #~("--login-program" #$login-program) + #~()) + #$@(if login-pause? + #~("--login-pause") + #~()) + defaulted-tty + #$@(if baud-rate + #~(#$baud-rate) + #~()) + #$@(if term + #~(#$term) + #~()))) + (const #f)) ; never start. + args))))) + (stop #~(make-kill-destructor)))))) (define agetty-service-type (service-type (name 'agetty) @@ -1148,42 +1148,42 @@ the tty to run, among other things." (clear-on-logout? mingetty-clear-on-logout? ;Boolean (default #t))) -(define mingetty-shepherd-service - (match-lambda - (($ mingetty tty auto-login login-program - login-pause? clear-on-logout?) - (list - (shepherd-service - (documentation "Run mingetty on an tty.") - (provision (list (symbol-append 'term- (string->symbol tty)))) +(define (mingetty-shepherd-service config) + (match-record config + (mingetty tty auto-login login-program + login-pause? clear-on-logout?) + (list + (shepherd-service + (documentation "Run mingetty on an tty.") + (provision (list (symbol-append 'term- (string->symbol tty)))) - ;; Since the login prompt shows the host name, wait for the 'host-name' - ;; service to be done. Also wait for udev essentially so that the tty - ;; text is not lost in the middle of kernel messages (XXX). - (requirement '(user-processes host-name udev virtual-terminal)) + ;; Since the login prompt shows the host name, wait for the 'host-name' + ;; service to be done. Also wait for udev essentially so that the tty + ;; text is not lost in the middle of kernel messages (XXX). + (requirement '(user-processes host-name udev virtual-terminal)) - (start #~(make-forkexec-constructor - (list #$(file-append mingetty "/sbin/mingetty") + (start #~(make-forkexec-constructor + (list #$(file-append mingetty "/sbin/mingetty") - ;; Avoiding 'vhangup' allows us to avoid 'setfont' - ;; errors down the path where various ioctls get - ;; EIO--see 'hung_up_tty_ioctl' in driver/tty/tty_io.c - ;; in Linux. - "--nohangup" #$tty + ;; Avoiding 'vhangup' allows us to avoid 'setfont' + ;; errors down the path where various ioctls get + ;; EIO--see 'hung_up_tty_ioctl' in driver/tty/tty_io.c + ;; in Linux. + "--nohangup" #$tty - #$@(if clear-on-logout? - #~() - #~("--noclear")) - #$@(if auto-login - #~("--autologin" #$auto-login) - #~()) - #$@(if login-program - #~("--loginprog" #$login-program) - #~()) - #$@(if login-pause? - #~("--loginpause") - #~())))) - (stop #~(make-kill-destructor))))))) + #$@(if clear-on-logout? + #~() + #~("--noclear")) + #$@(if auto-login + #~("--autologin" #$auto-login) + #~()) + #$@(if login-program + #~("--loginprog" #$login-program) + #~()) + #$@(if login-pause? + #~("--loginpause") + #~())))) + (stop #~(make-kill-destructor)))))) (define mingetty-service-type (service-type (name 'mingetty) @@ -1260,46 +1260,47 @@ the tty to run, among other things." (define (nscd.conf-file config) "Return the @file{nscd.conf} configuration file for @var{config}, an @code{} object." - (define cache->config - (match-lambda - (($ (= symbol->string database) - positive-ttl negative-ttl size check-files? - persistent? shared? max-size propagate?) - (string-append "\nenable-cache\t" database "\tyes\n" + (define (cache->config cache) + (match-record cache + (database positive-time-to-live negative-time-to-live + suggested-size check-files? + persistent? shared? max-database-size auto-propagate?) + (let ((database (symbol->string database))) + (string-append "\nenable-cache\t" database "\tyes\n" - "positive-time-to-live\t" database "\t" - (number->string positive-ttl) "\n" - "negative-time-to-live\t" database "\t" - (number->string negative-ttl) "\n" - "suggested-size\t" database "\t" - (number->string size) "\n" - "check-files\t" database "\t" - (if check-files? "yes\n" "no\n") - "persistent\t" database "\t" - (if persistent? "yes\n" "no\n") - "shared\t" database "\t" - (if shared? "yes\n" "no\n") - "max-db-size\t" database "\t" - (number->string max-size) "\n" - "auto-propagate\t" database "\t" - (if propagate? "yes\n" "no\n"))))) + "positive-time-to-live\t" database "\t" + (number->string positive-time-to-live) "\n" + "negative-time-to-live\t" database "\t" + (number->string negative-time-to-live) "\n" + "suggested-size\t" database "\t" + (number->string suggested-size) "\n" + "check-files\t" database "\t" + (if check-files? "yes\n" "no\n") + "persistent\t" database "\t" + (if persistent? "yes\n" "no\n") + "shared\t" database "\t" + (if shared? "yes\n" "no\n") + "max-db-size\t" database "\t" + (number->string max-database-size) "\n" + "auto-propagate\t" database "\t" + (if auto-propagate? "yes\n" "no\n"))))) - (match config - (($ log-file debug-level caches) - (plain-file "nscd.conf" - (string-append "\ + (match-record config + (log-file debug-level caches) + (plain-file "nscd.conf" + (string-append "\ # Configuration of libc's name service cache daemon (nscd).\n\n" - (if log-file - (string-append "logfile\t" log-file) - "") - "\n" - (if debug-level - (string-append "debug-level\t" - (number->string debug-level)) - "") - "\n" - (string-concatenate - (map cache->config caches))))))) + (if log-file + (string-append "logfile\t" log-file) + "") + "\n" + (if debug-level + (string-append "debug-level\t" + (number->string debug-level)) + "") + "\n" + (string-concatenate + (map cache->config caches)))))) (define (nscd-action-procedure nscd config option) ;; XXX: This is duplicated from mcron; factorize. @@ -1797,17 +1798,15 @@ proxy of 'guix-daemon'...~%") (define (guix-accounts config) "Return the user accounts and user groups for CONFIG." - (match config - (($ _ build-group build-accounts) - (cons (user-group - (name build-group) - (system? #t) + (cons (user-group + (name (guix-configuration-build-group config)) + (system? #t) - ;; Use a fixed GID so that we can create the store with the right - ;; owner. - (id 30000)) - (guix-build-accounts build-accounts - #:group build-group))))) + ;; Use a fixed GID so that we can create the store with the right + ;; owner. + (id 30000)) + (guix-build-accounts (guix-configuration-build-accounts config) + #:group (guix-configuration-build-group config)))) (define (guix-activation config) "Return the activation gexp for CONFIG." @@ -2130,95 +2129,94 @@ item of @var{packages}." (udev-rule "90-kvm.rules" "KERNEL==\"kvm\", GROUP=\"kvm\", MODE=\"0660\"\n")) -(define udev-shepherd-service +(define (udev-shepherd-service config) ;; Return a for UDEV with RULES. - (match-lambda - (($ udev) - (list - (shepherd-service - (provision '(udev)) + (let ((udev (udev-configuration-udev config))) + (list + (shepherd-service + (provision '(udev)) - ;; Udev needs /dev to be a 'devtmpfs' mount so that new device nodes can - ;; be added: see - ;; . - (requirement '(root-file-system)) + ;; Udev needs /dev to be a 'devtmpfs' mount so that new device nodes can + ;; be added: see + ;; . + (requirement '(root-file-system)) - (documentation "Populate the /dev directory, dynamically.") - (start - (with-imported-modules (source-module-closure - '((gnu build linux-boot))) - #~(lambda () - (define udevd - ;; 'udevd' from eudev. - #$(file-append udev "/sbin/udevd")) + (documentation "Populate the /dev directory, dynamically.") + (start + (with-imported-modules (source-module-closure + '((gnu build linux-boot))) + #~(lambda () + (define udevd + ;; 'udevd' from eudev. + #$(file-append udev "/sbin/udevd")) - (define (wait-for-udevd) - ;; Wait until someone's listening on udevd's control - ;; socket. - (let ((sock (socket AF_UNIX SOCK_SEQPACKET 0))) - (let try () - (catch 'system-error - (lambda () - (connect sock PF_UNIX "/run/udev/control") - (close-port sock)) - (lambda args - (format #t "waiting for udevd...~%") - (usleep 500000) - (try)))))) + (define (wait-for-udevd) + ;; Wait until someone's listening on udevd's control + ;; socket. + (let ((sock (socket AF_UNIX SOCK_SEQPACKET 0))) + (let try () + (catch 'system-error + (lambda () + (connect sock PF_UNIX "/run/udev/control") + (close-port sock)) + (lambda args + (format #t "waiting for udevd...~%") + (usleep 500000) + (try)))))) - ;; Allow udev to find the modules. - (setenv "LINUX_MODULE_DIRECTORY" - "/run/booted-system/kernel/lib/modules") + ;; Allow udev to find the modules. + (setenv "LINUX_MODULE_DIRECTORY" + "/run/booted-system/kernel/lib/modules") - (let* ((kernel-release - (utsname:release (uname))) - (linux-module-directory - (getenv "LINUX_MODULE_DIRECTORY")) - (directory - (string-append linux-module-directory "/" - kernel-release)) - (old-umask (umask #o022))) - ;; If we're in a container, DIRECTORY might not exist, - ;; for instance because the host runs a different - ;; kernel. In that case, skip it; we'll just miss a few - ;; nodes like /dev/fuse. - (when (file-exists? directory) - (make-static-device-nodes directory)) - (umask old-umask)) + (let* ((kernel-release + (utsname:release (uname))) + (linux-module-directory + (getenv "LINUX_MODULE_DIRECTORY")) + (directory + (string-append linux-module-directory "/" + kernel-release)) + (old-umask (umask #o022))) + ;; If we're in a container, DIRECTORY might not exist, + ;; for instance because the host runs a different + ;; kernel. In that case, skip it; we'll just miss a few + ;; nodes like /dev/fuse. + (when (file-exists? directory) + (make-static-device-nodes directory)) + (umask old-umask)) - (let ((pid (fork+exec-command - (list udevd) - #:environment-variables - (cons* - ;; The first one is for udev, the second one for - ;; eudev. - "UDEV_CONFIG_FILE=/etc/udev/udev.conf" - "EUDEV_RULES_DIRECTORY=/etc/udev/rules.d" - (string-append "LINUX_MODULE_DIRECTORY=" - (getenv "LINUX_MODULE_DIRECTORY")) - (default-environment-variables))))) - ;; Wait until udevd is up and running. This appears to - ;; be needed so that the events triggered below are - ;; actually handled. - (wait-for-udevd) + (let ((pid (fork+exec-command + (list udevd) + #:environment-variables + (cons* + ;; The first one is for udev, the second one for + ;; eudev. + "UDEV_CONFIG_FILE=/etc/udev/udev.conf" + "EUDEV_RULES_DIRECTORY=/etc/udev/rules.d" + (string-append "LINUX_MODULE_DIRECTORY=" + (getenv "LINUX_MODULE_DIRECTORY")) + (default-environment-variables))))) + ;; Wait until udevd is up and running. This appears to + ;; be needed so that the events triggered below are + ;; actually handled. + (wait-for-udevd) - ;; Trigger device node creation. - (system* #$(file-append udev "/bin/udevadm") - "trigger" "--action=add") + ;; Trigger device node creation. + (system* #$(file-append udev "/bin/udevadm") + "trigger" "--action=add") - ;; Wait for things to settle down. - (system* #$(file-append udev "/bin/udevadm") - "settle") - pid)))) - (stop #~(make-kill-destructor)) + ;; Wait for things to settle down. + (system* #$(file-append udev "/bin/udevadm") + "settle") + pid)))) + (stop #~(make-kill-destructor)) - ;; When halting the system, 'udev' is actually killed by - ;; 'user-processes', i.e., before its own 'stop' method was called. - ;; Thus, make sure it is not respawned. - (respawn? #f) - ;; We need additional modules. - (modules `((gnu build linux-boot) ;'make-static-device-nodes' - ,@%default-modules))))))) + ;; When halting the system, 'udev' is actually killed by + ;; 'user-processes', i.e., before its own 'stop' method was called. + ;; Thus, make sure it is not respawned. + (respawn? #f) + ;; We need additional modules. + (modules `((gnu build linux-boot) ;'make-static-device-nodes' + ,@%default-modules)))))) (define udev.conf (computed-file "udev.conf" @@ -2226,14 +2224,15 @@ item of @var{packages}." (lambda (port) (format port "udev_rules=\"/etc/udev/rules.d\"~%"))))) -(define udev-etc - (match-lambda - (($ udev rules) - `(("udev" - ,(file-union - "udev" `(("udev.conf" ,udev.conf) - ("rules.d" ,(udev-rules-union (cons* udev kvm-udev-rule - rules)))))))))) +(define (udev-etc config) + (match-record config + (udev rules) + `(("udev" + ,(file-union "udev" + `(("udev.conf" ,udev.conf) + ("rules.d" + ,(udev-rules-union (cons* udev kvm-udev-rule + rules))))))))) (define udev-service-type (service-type (name 'udev) @@ -2243,11 +2242,11 @@ item of @var{packages}." (service-extension etc-service-type udev-etc))) (compose concatenate) ;concatenate the list of rules (extend (lambda (config rules) - (match config - (($ udev initial-rules) - (udev-configuration - (udev udev) - (rules (append initial-rules rules))))))) + (let ((initial-rules + (udev-configuration-rules config))) + (udev-configuration + (inherit config) + (rules (append initial-rules rules)))))) (default-value (udev-configuration)) (description "Run @command{udev}, which populates the @file{/dev} @@ -2385,23 +2384,23 @@ instance." (options gpm-configuration-options ;list of strings (default %default-gpm-options))) -(define gpm-shepherd-service - (match-lambda - (($ gpm options) - (list (shepherd-service - (requirement '(udev)) - (provision '(gpm)) - ;; 'gpm' runs in the background and sets a PID file. - ;; Note that it requires running as "root". - (start #~(make-forkexec-constructor - (list #$(file-append gpm "/sbin/gpm") - #$@options) - #:pid-file "/var/run/gpm.pid" - #:pid-file-timeout 3)) - (stop #~(lambda (_) - ;; Return #f if successfully stopped. - (not (zero? (system* #$(file-append gpm "/sbin/gpm") - "-k")))))))))) +(define (gpm-shepherd-service config) + (match-record config + (gpm options) + (list (shepherd-service + (requirement '(udev)) + (provision '(gpm)) + ;; 'gpm' runs in the background and sets a PID file. + ;; Note that it requires running as "root". + (start #~(make-forkexec-constructor + (list #$(file-append gpm "/sbin/gpm") + #$@options) + #:pid-file "/var/run/gpm.pid" + #:pid-file-timeout 3)) + (stop #~(lambda (_) + ;; Return #f if successfully stopped. + (not (zero? (system* #$(file-append gpm "/sbin/gpm") + "-k"))))))))) (define gpm-service-type (service-type (name 'gpm) @@ -2654,32 +2653,64 @@ to CONFIG." "/servers/socket/2") #f)))) -(define network-set-up/linux - (match-lambda - (($ addresses links routes) - (scheme-file "set-up-network" - (with-extensions (list guile-netlink) - #~(begin - (use-modules (ip addr) (ip link) (ip route)) +(define (network-set-up/linux config) + (match-record config + (addresses links routes) + (scheme-file "set-up-network" + (with-extensions (list guile-netlink) + #~(begin + (use-modules (ip addr) (ip link) (ip route)) - #$@(map (lambda (address) - #~(begin - (addr-add #$(network-address-device address) - #$(network-address-value address) - #:ipv6? - #$(network-address-ipv6? address)) - ;; FIXME: loopback? - (link-set #$(network-address-device address) - #:multicast-on #t - #:up #t))) - addresses) - #$@(map (match-lambda - (($ name type arguments) - #~(link-add #$name #$type - #:type-args '#$arguments))) - links) - #$@(map (lambda (route) - #~(route-add #$(network-route-destination route) + #$@(map (lambda (address) + #~(begin + (addr-add #$(network-address-device address) + #$(network-address-value address) + #:ipv6? + #$(network-address-ipv6? address)) + ;; FIXME: loopback? + (link-set #$(network-address-device address) + #:multicast-on #t + #:up #t))) + addresses) + #$@(map (match-lambda + (($ name type arguments) + #~(link-add #$name #$type + #:type-args '#$arguments))) + links) + #$@(map (lambda (route) + #~(route-add #$(network-route-destination route) + #:device + #$(network-route-device route) + #:ipv6? + #$(network-route-ipv6? route) + #:via + #$(network-route-gateway route) + #:src + #$(network-route-source route))) + routes) + #t))))) + +(define (network-tear-down/linux config) + (match-record config + (addresses links routes) + (scheme-file "tear-down-network" + (with-extensions (list guile-netlink) + #~(begin + (use-modules (ip addr) (ip link) (ip route) + (netlink error) + (srfi srfi-34)) + + (define-syntax-rule (false-if-netlink-error exp) + (guard (c ((netlink-error? c) #f)) + exp)) + + ;; Wrap calls in 'false-if-netlink-error' so this + ;; script goes as far as possible undoing the effects + ;; of "set-up-network". + + #$@(map (lambda (route) + #~(false-if-netlink-error + (route-del #$(network-route-destination route) #:device #$(network-route-device route) #:ipv6? @@ -2687,80 +2718,47 @@ to CONFIG." #:via #$(network-route-gateway route) #:src - #$(network-route-source route))) - routes) - #t)))))) - -(define network-tear-down/linux - (match-lambda - (($ addresses links routes) - (scheme-file "tear-down-network" - (with-extensions (list guile-netlink) - #~(begin - (use-modules (ip addr) (ip link) (ip route) - (netlink error) - (srfi srfi-34)) - - (define-syntax-rule (false-if-netlink-error exp) - (guard (c ((netlink-error? c) #f)) - exp)) - - ;; Wrap calls in 'false-if-netlink-error' so this - ;; script goes as far as possible undoing the effects - ;; of "set-up-network". - - #$@(map (lambda (route) + #$(network-route-source route)))) + routes) + #$@(map (match-lambda + (($ name type arguments) #~(false-if-netlink-error - (route-del #$(network-route-destination route) - #:device - #$(network-route-device route) - #:ipv6? - #$(network-route-ipv6? route) - #:via - #$(network-route-gateway route) - #:src - #$(network-route-source route)))) - routes) - #$@(map (match-lambda - (($ name type arguments) - #~(false-if-netlink-error - (link-del #$name)))) - links) - #$@(map (lambda (address) - #~(false-if-netlink-error - (addr-del #$(network-address-device - address) - #$(network-address-value address) - #:ipv6? - #$(network-address-ipv6? address)))) - addresses) - #f)))))) + (link-del #$name)))) + links) + #$@(map (lambda (address) + #~(false-if-netlink-error + (addr-del #$(network-address-device + address) + #$(network-address-value address) + #:ipv6? + #$(network-address-ipv6? address)))) + addresses) + #f))))) (define (static-networking-shepherd-service config) - (match config - (($ addresses links routes - provision requirement name-servers) - (let ((loopback? (and provision (memq 'loopback provision)))) - (shepherd-service + (match-record config + (addresses links routes provision requirement name-servers) + (let ((loopback? (and provision (memq 'loopback provision)))) + (shepherd-service - (documentation - "Bring up the networking interface using a static IP address.") - (requirement requirement) - (provision provision) + (documentation + "Bring up the networking interface using a static IP address.") + (requirement requirement) + (provision provision) - (start #~(lambda _ - ;; Return #t if successfully started. - (load #$(let-system (system target) - (if (string-contains (or target system) "-linux") - (network-set-up/linux config) - (network-set-up/hurd config)))))) - (stop #~(lambda _ - ;; Return #f is successfully stopped. + (start #~(lambda _ + ;; Return #t if successfully started. (load #$(let-system (system target) (if (string-contains (or target system) "-linux") - (network-tear-down/linux config) - (network-tear-down/hurd config)))))) - (respawn? #f)))))) + (network-set-up/linux config) + (network-set-up/hurd config)))))) + (stop #~(lambda _ + ;; Return #f is successfully stopped. + (load #$(let-system (system target) + (if (string-contains (or target system) "-linux") + (network-tear-down/linux config) + (network-tear-down/hurd config)))))) + (respawn? #f))))) (define (static-networking-shepherd-services networks) (map static-networking-shepherd-service networks)) @@ -2873,33 +2871,33 @@ to handle." (extra-env greetd-agreety-extra-env (default '())) (xdg-env? greetd-agreety-xdg-env? (default #t))) -(define greetd-agreety-tty-session-command - (match-lambda - (($ _ command args extra-env) - (program-file - "agreety-tty-session-command" - #~(begin - (use-modules (ice-9 match)) - (for-each (match-lambda ((var . val) (setenv var val))) - (quote (#$@extra-env))) - (apply execl #$command #$command (list #$@args))))))) +(define (greetd-agreety-tty-session-command config) + (match-record config + (command command-args extra-env) + (program-file + "agreety-tty-session-command" + #~(begin + (use-modules (ice-9 match)) + (for-each (match-lambda ((var . val) (setenv var val))) + (quote (#$@extra-env))) + (apply execl #$command #$command (list #$@command-args)))))) -(define greetd-agreety-tty-xdg-session-command - (match-lambda - (($ _ command args extra-env) - (program-file - "agreety-tty-xdg-session-command" - #~(begin - (use-modules (ice-9 match)) - (let* - ((username (getenv "USER")) - (useruid (passwd:uid (getpwuid username))) - (useruid (number->string useruid))) - (setenv "XDG_SESSION_TYPE" "tty") - (setenv "XDG_RUNTIME_DIR" (string-append "/run/user/" useruid))) - (for-each (match-lambda ((var . val) (setenv var val))) - (quote (#$@extra-env))) - (apply execl #$command #$command (list #$@args))))))) +(define (greetd-agreety-tty-xdg-session-command config) + (match-record config + (command command-args extra-env) + (program-file + "agreety-tty-xdg-session-command" + #~(begin + (use-modules (ice-9 match)) + (let* + ((username (getenv "USER")) + (useruid (passwd:uid (getpwuid username))) + (useruid (number->string useruid))) + (setenv "XDG_SESSION_TYPE" "tty") + (setenv "XDG_RUNTIME_DIR" (string-append "/run/user/" useruid))) + (for-each (match-lambda ((var . val) (setenv var val))) + (quote (#$@extra-env))) + (apply execl #$command #$command (list #$@command-args)))))) (define-gexp-compiler (greetd-agreety-session-compiler (session ) From 416a691cff8b75d0fcba50412c6e347212ab5973 Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Wed, 29 Sep 2021 17:43:10 +0200 Subject: [PATCH 017/790] guix-install.sh: Authorize all project build farms at once. MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * etc/guix-install.sh (sys_authorize_build_farms): Iterate over all hosts. Co-authored-by: Ludovic Courtès --- etc/guix-install.sh | 22 +++++++++++++++------- 1 file changed, 15 insertions(+), 7 deletions(-) diff --git a/etc/guix-install.sh b/etc/guix-install.sh index 6bef21bb7e..fb9006b3e2 100755 --- a/etc/guix-install.sh +++ b/etc/guix-install.sh @@ -492,14 +492,22 @@ sys_enable_guix_daemon() } sys_authorize_build_farms() -{ # authorize the public key of the build farm +{ # authorize the public key(s) of the build farm(s) + local hosts=( + ci.guix.gnu.org + bordeaux.guix.gnu.org + ) + if prompt_yes_no "Permit downloading pre-built package binaries from the \ -project's build farm?"; then - guix archive --authorize \ - < ~root/.config/guix/current/share/guix/ci.guix.gnu.org.pub \ - && _msg "${PAS}Authorized public key for ci.guix.gnu.org" - else - _msg "${INF}Skipped authorizing build farm public keys" +project's build farms?"; then + for host in "${hosts[@]}"; do + local key=~root/.config/guix/current/share/guix/$host.pub + [ -f "$key" ] \ + && guix archive --authorize < "$key" \ + && _msg "${PAS}Authorized public key for $host" + done + else + _msg "${INF}Skipped authorizing build farm public keys" fi } From 0406df0b9b1bf39caa39eba50f918c897ea204e6 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ludovic=20Court=C3=A8s?= Date: Thu, 8 Dec 2022 16:30:52 +0100 Subject: [PATCH 018/790] environment: '-C' doesn't throw when the NSS is dysfunctional. Previously, if the name service switch was dysfunctional, as can happen on foreign distros lacking nscd, "guix shell -C" would crash with a backtrace on the uncaught 'getpwuid' exception. To address that, catch the exception and deal with it gracefully. Reported by remsd1 on #guix. * guix/scripts/environment.scm (launch-environment/container): Wrap 'getpwuid' call in 'false-if-exception'. --- guix/scripts/environment.scm | 15 +++++++++++---- 1 file changed, 11 insertions(+), 4 deletions(-) diff --git a/guix/scripts/environment.scm b/guix/scripts/environment.scm index 64597f6e9f..ab11b35335 100644 --- a/guix/scripts/environment.scm +++ b/guix/scripts/environment.scm @@ -728,14 +728,21 @@ WHILE-LIST." (home (getenv "HOME")) (uid (if user 1000 (getuid))) (gid (if user 1000 (getgid))) - (passwd (let ((pwd (getpwuid (getuid)))) + + ;; On a foreign distro, the name service switch might be + ;; dysfunctional and 'getpwuid' throws. Don't let that hamper + ;; operations. + (passwd (let ((pwd (false-if-exception (getpwuid (getuid))))) (password-entry - (name (or user (passwd:name pwd))) - (real-name (if user + (name (or user + (and=> pwd passwd:name) + (getenv "USER") + "charlie")) + (real-name (if (or user (not pwd)) "" (passwd:gecos pwd))) (uid uid) (gid gid) (shell bash) - (directory (if user + (directory (if (or user (not pwd)) (string-append "/home/" user) (passwd:dir pwd)))))) (groups (list (group-entry (name "users") (gid gid)) From 755c4b496e24f2df5f1b0f4a3873e9e00bae1fdc Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ludovic=20Court=C3=A8s?= Date: Fri, 9 Dec 2022 16:40:53 +0100 Subject: [PATCH 019/790] system: Remove unused yggdrasil OS template. This file was added in fe1cd098d2b83737e96f19438612291f5a9316e4 but it's not referenced from anywhere, not even gnu/local.mk. Furthermore, we don't normally add full OS examples for the purposes of illustrating the use of a single service. * gnu/system/examples/yggdrasil.tmpl: Remove. --- gnu/system/examples/yggdrasil.tmpl | 60 ------------------------------ 1 file changed, 60 deletions(-) delete mode 100644 gnu/system/examples/yggdrasil.tmpl diff --git a/gnu/system/examples/yggdrasil.tmpl b/gnu/system/examples/yggdrasil.tmpl deleted file mode 100644 index 4d34f49b54..0000000000 --- a/gnu/system/examples/yggdrasil.tmpl +++ /dev/null @@ -1,60 +0,0 @@ -;; This is an operating system configuration template -;; for a "bare bones" setup, with no X11 display server. - -(use-modules (gnu)) -(use-service-modules networking ssh) -(use-package-modules admin curl networking screen) - -(operating-system - (host-name "ruby-guard-5545") - (timezone "Europe/Budapest") - (locale "en_US.utf8") - - ;; Boot in "legacy" BIOS mode, assuming /dev/sdX is the - ;; target hard disk, and "my-root" is the label of the target - ;; root file system. - (bootloader (bootloader-configuration - (bootloader grub-bootloader) - (targets '("/dev/sdX")))) - (file-systems (cons (file-system - (device (file-system-label "my-root")) - (mount-point "/") - (type "ext4")) - %base-file-systems)) - (users (cons (user-account - (name "alice") - (comment "Bob's sister") - (group "users") - ;; adding her to the yggdrasil group means she can use - ;; yggdrasilctl to modify the configuration - (supplementary-groups '("wheel" "yggdrasil"))) - %base-user-accounts)) - - ;; Globally-installed packages. - (packages (cons* screen curl %base-packages)) - - ;; Add services to the baseline: a DHCP client and - ;; an SSH server. - ;; If you add an /etc/yggdrasil-private.conf, you can log in to ssh - ;; using your Yggdrasil IPv6 address from another machine running Yggdrasil. - ;; Alternatively, the client can sit behind a router that has Yggdrasil. - ;; That file is specifically _not_ handled by Guix, because we don't want its - ;; contents to sit in the world-readable /gnu/store. - (services - (append - (list - (service dhcp-client-service-type) - (service yggdrasil-service-type - (yggdrasil-configuration - (log-to 'stdout) - (log-level 'debug) - (autoconf? #f) - (json-config - ;; choose a few from - ;; https://github.com/yggdrasil-network/public-peers - '((peers . #("tcp://1.2.3.4:1337")))) - (config-file #f))) - (service openssh-service-type - (openssh-configuration - (port-number 2222)))) - %base-services))) From 556520a33c8a62fc80ac9ab925f86f08986d138b Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ludovic=20Court=C3=A8s?= Date: Fri, 9 Dec 2022 16:43:25 +0100 Subject: [PATCH 020/790] services: nscd: Use nscd from 'glibc-final' on native builds. This reduces the closure size of systems by removing one glibc copy--namely (@ (gnu packages base) glibc) in addition to (@ (gnu packages commencement) glibc-final). * gnu/services/base.scm ()[glibc]: Change default value to use 'let-system' and 'canonical-package' as appropriate. --- gnu/services/base.scm | 11 +++++++++-- 1 file changed, 9 insertions(+), 2 deletions(-) diff --git a/gnu/services/base.scm b/gnu/services/base.scm index 370696a55e..2b1974d77e 100644 --- a/gnu/services/base.scm +++ b/gnu/services/base.scm @@ -61,7 +61,8 @@ util-linux xfsprogs)) #:use-module (gnu packages bash) #:use-module ((gnu packages base) - #:select (coreutils glibc glibc-utf8-locales tar)) + #:select (coreutils glibc glibc-utf8-locales tar + canonical-package)) #:use-module ((gnu packages compression) #:select (gzip)) #:autoload (gnu packages guile-xyz) (guile-netlink) #:autoload (gnu packages hurd) (hurd) @@ -1211,7 +1212,13 @@ the tty to run, among other things." (name-services nscd-configuration-name-services ;list of file-like (default '())) (glibc nscd-configuration-glibc ;file-like - (default glibc))) + (default (let-system (system target) + ;; Unless we're cross-compiling, arrange to use nscd + ;; from 'glibc-final' instead of pulling in a second + ;; glibc copy. + (if target + glibc + (canonical-package glibc)))))) (define-record-type* nscd-cache make-nscd-cache nscd-cache? From 591af24ade1021d91a3e7c62fcc7a8c90f00d4bb Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ludovic=20Court=C3=A8s?= Date: Fri, 9 Dec 2022 17:47:08 +0100 Subject: [PATCH 021/790] installer: Print progress bars and such as soon as \r is read. Fixes . Previously progress bars and related things would be buffered by 'run-external-command-with-line-hooks' until \n is read. * gnu/installer/utils.scm (run-external-command-with-line-hooks): Use 'read-delimited' rather than 'get-line'. Pass 'concat as the last argument. (%display-line-hook): Remove. (run-command): Use 'display' instead of '%display-line-hook'. (%syslog-line-hook): Add "\n" when LINE doesn't end in \n. (%installer-log-line-hook): Do not add an extra newline. (installer-log-line): Add an extra newline. --- gnu/installer/newt.scm | 2 +- gnu/installer/utils.scm | 26 ++++++++++++++------------ 2 files changed, 15 insertions(+), 13 deletions(-) diff --git a/gnu/installer/newt.scm b/gnu/installer/newt.scm index 798ff53af2..e1c4453168 100644 --- a/gnu/installer/newt.scm +++ b/gnu/installer/newt.scm @@ -116,7 +116,7 @@ report it by email to ~a.") uploaded-name %guix-bug-report-address) (define command-output "") (define (line-accumulator line) (set! command-output - (string-append/shared command-output line "\n"))) + (string-append/shared command-output line))) (define result (run-external-command-with-line-hooks (list line-accumulator) args)) (define exit-val (status:exit-val result)) diff --git a/gnu/installer/utils.scm b/gnu/installer/utils.scm index 061493e6a7..6838410166 100644 --- a/gnu/installer/utils.scm +++ b/gnu/installer/utils.scm @@ -1,6 +1,6 @@ ;;; GNU Guix --- Functional package management for GNU ;;; Copyright © 2018, 2020 Mathieu Othacehe -;;; Copyright © 2019, 2020 Ludovic Courtès +;;; Copyright © 2019, 2020, 2022 Ludovic Courtès ;;; ;;; This file is part of GNU Guix. ;;; @@ -159,7 +159,9 @@ COMMAND will be run in a pseudoterminal. Returns the integer status value of the child process as returned by waitpid." (define (handler input) (and - (and=> (get-line input) + ;; Lines for progress bars etc. end in \r; treat is as a line ending so + ;; those lines are printed right away. + (and=> (read-delimited "\r\n" input 'concat) (lambda (line) (if (eof-object? line) #f @@ -186,7 +188,7 @@ in a pseudoterminal." (installer-log-line "running command ~s" command) (define result (run-external-command-with-line-hooks - (list %display-line-hook) command + (list display) command #:tty? tty?)) (define exit-val (status:exit-val result)) (define term-sig (status:term-sig result)) @@ -264,7 +266,10 @@ values." (or port (%make-void-port "w"))))) (define (%syslog-line-hook line) - (format (syslog-port) "installer[~d]: ~a~%" (getpid) line)) + (let ((line (if (string-suffix? "\r" line) + (string-append (string-drop-right line 1) "\n") + line))) + (format (syslog-port) "installer[~d]: ~a" (getpid) line))) (define-syntax syslog (lambda (s) @@ -293,11 +298,7 @@ values." port))) (define (%installer-log-line-hook line) - (format (installer-log-port) "~a~%" line)) - -(define (%display-line-hook line) - (display line) - (newline)) + (display line (installer-log-port))) (define %default-installer-line-hooks (list %syslog-line-hook @@ -309,9 +310,10 @@ values." (syntax-case s () ((_ fmt args ...) (string? (syntax->datum #'fmt)) - #'(let ((formatted (format #f fmt args ...))) - (for-each (lambda (f) (f formatted)) - %default-installer-line-hooks)))))) + (with-syntax ((fmt (string-append (syntax->datum #'fmt) "\n"))) + #'(let ((formatted (format #f fmt args ...))) + (for-each (lambda (f) (f formatted)) + %default-installer-line-hooks))))))) ;;; From b129026e2e242e9068158ae6e6fcd8d7c5ea092e Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ludovic=20Court=C3=A8s?= Date: Sat, 10 Dec 2022 10:56:48 +0100 Subject: [PATCH 022/790] deduplicate: Use 'sendfile' for small file copies. * guix/store/deduplication.scm (dump-file/deduplicate): Use 'sendfile' instead of 'dump-port'. * tests/store-deduplication.scm ("copy-file/deduplicate, below %deduplication-minimum-size"): New test. --- guix/store/deduplication.scm | 4 ++-- tests/store-deduplication.scm | 17 ++++++++++++++++- 2 files changed, 18 insertions(+), 3 deletions(-) diff --git a/guix/store/deduplication.scm b/guix/store/deduplication.scm index ab982e3b3d..9953675319 100644 --- a/guix/store/deduplication.scm +++ b/guix/store/deduplication.scm @@ -1,6 +1,6 @@ ;;; GNU Guix --- Functional package management for GNU ;;; Copyright © 2017 Caleb Ristvedt -;;; Copyright © 2018-2021 Ludovic Courtès +;;; Copyright © 2018-2022 Ludovic Courtès ;;; ;;; This file is part of GNU Guix. ;;; @@ -262,7 +262,7 @@ down the road." (deduplicate file (dump-and-compute-hash) #:store store) (call-with-output-file file (lambda (output) - (dump-port input output size))))) + (sendfile output input size 0))))) (define* (copy-file/deduplicate source target #:key (store (%store-directory))) diff --git a/tests/store-deduplication.scm b/tests/store-deduplication.scm index 2950fbc1a3..f1845035d8 100644 --- a/tests/store-deduplication.scm +++ b/tests/store-deduplication.scm @@ -1,5 +1,5 @@ ;;; GNU Guix --- Functional package management for GNU -;;; Copyright © 2018, 2020-2021 Ludovic Courtès +;;; Copyright © 2018, 2020-2022 Ludovic Courtès ;;; ;;; This file is part of GNU Guix. ;;; @@ -136,6 +136,21 @@ (cons (apply = (map (compose stat:ino stat) identical)) (map (compose stat:nlink stat) identical)))))) +(test-assert "copy-file/deduplicate, below %deduplication-minimum-size" + (call-with-temporary-directory + (lambda (store) + (let ((source (string-append store "/input"))) + (call-with-output-file source + (lambda (port) + (display "Hello!\n" port))) + (copy-file/deduplicate source + (string-append store "/a") + #:store store) + (and (not (directory-exists? (string-append store "/.links"))) + (file=? source (string-append store "/a")) + (not (= (stat:ino (stat (string-append store "/a"))) + (stat:ino (stat source))))))))) + (test-assert "copy-file/deduplicate" (call-with-temporary-directory (lambda (store) From 1ab48edb1674e0454d4368fdbed16cbbdfd9bf06 Mon Sep 17 00:00:00 2001 From: Mathieu Othacehe Date: Thu, 8 Dec 2022 13:24:02 +0100 Subject: [PATCH 023/790] installer: Detect mapped installation devices. Fixes: * gnu/installer/parted.scm (mapped-device?, mapped-device-parent-partition): New procedures. (eligible-devices): Detect mapped installation devices using the new procedures. --- gnu/installer/parted.scm | 34 +++++++++++++++++++++++++++++++++- 1 file changed, 33 insertions(+), 1 deletion(-) diff --git a/gnu/installer/parted.scm b/gnu/installer/parted.scm index 82375d29e3..51fa7cf9d9 100644 --- a/gnu/installer/parted.scm +++ b/gnu/installer/parted.scm @@ -379,12 +379,44 @@ fail. See rereadpt function in wipefs.c of util-linux for an explanation." (define %min-device-size (* 2 GIBIBYTE-SIZE)) ;2GiB +(define (mapped-device? device) + "Return #true if DEVICE is a mapped device, false otherwise." + (string-prefix? "/dev/dm-" device)) + +;; TODO: Use DM_TABLE_DEPS ioctl instead of dmsetup. +(define (mapped-device-parent-partition device) + "Return the parent partition path of the mapped DEVICE." + (let* ((command `("dmsetup" "deps" ,device "-o" "devname")) + (parent #f) + (handler + (lambda (input) + ;; We are parsing an output that should look like: + ;; 1 dependencies : (sda2) + (let ((result + (string-match "\\(([^\\)]+)\\)" + (get-string-all input)))) + (and result + (set! parent + (format #f "/dev/~a" + (match:substring result 1)))))))) + (run-external-command-with-handler handler command) + parent)) + (define (eligible-devices) "Return all the available devices except the install device and the devices which are smaller than %MIN-DEVICE-SIZE." (define the-installer-root-partition-path - (installer-root-partition-path)) + (let ((root (installer-root-partition-path))) + (cond + ((mapped-device? root) + ;; If the partition is a mapped device (/dev/dm-X), locate the parent + ;; partition. It is the case when Ventoy is used to host the + ;; installation image. + (let ((parent (mapped-device-parent-partition root))) + (installer-log-line "mapped device ~a -> ~a" parent root) + parent)) + (else root)))) (define (small-device? device) (let ((length (device-length device)) From 61b7e9687757aff013b99e4ab15669a950c8b222 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ludovic=20Court=C3=A8s?= Date: Sat, 10 Dec 2022 14:33:51 +0100 Subject: [PATCH 024/790] install: 'umount-cow-store' retries upon EBUSY. Possibly fixes . * gnu/build/install.scm (umount*): New procedure. (unmount-cow-store): Use it instead of 'umount'. --- gnu/build/install.scm | 23 +++++++++++++++++++++-- 1 file changed, 21 insertions(+), 2 deletions(-) diff --git a/gnu/build/install.scm b/gnu/build/install.scm index 33a9616c0d..d4982650c1 100644 --- a/gnu/build/install.scm +++ b/gnu/build/install.scm @@ -1,5 +1,5 @@ ;;; GNU Guix --- Functional package management for GNU -;;; Copyright © 2013, 2014, 2015, 2016, 2017, 2018, 2019, 2020 Ludovic Courtès +;;; Copyright © 2013-2020, 2022 Ludovic Courtès ;;; Copyright © 2016 Chris Marusich ;;; Copyright © 2022 Maxim Cournoyer ;;; @@ -282,12 +282,31 @@ disk." (mount "/.rw-store" (%store-directory) "" MS_MOVE) (rmdir "/.rw-store"))) +(define (umount* directory) + "Unmount DIRECTORY, but retry a few times upon EBUSY." + (let loop ((attempts 5)) + (catch 'system-error + (lambda () + (umount directory)) + (lambda args + (if (and (= EBUSY (system-error-errno args)) + (> attempts 0)) + (begin + (sleep 1) + (loop (- attempts 1))) + (apply throw args)))))) + (define (unmount-cow-store target backing-directory) "Unmount copy-on-write store." (let ((tmp-dir "/remove")) (mkdir-p tmp-dir) (mount (%store-directory) tmp-dir "" MS_MOVE) - (umount tmp-dir) + + ;; We might get EBUSY at this point, possibly because of lingering + ;; processes with open file descriptors. Use 'umount*' to retry upon + ;; EBUSY, leaving a bit of time. See . + (umount* tmp-dir) + (rmdir tmp-dir) (delete-file-recursively (string-append target backing-directory)))) From 7866294e32f1e758d06fce4e1b1035eca3a7d772 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ludovic=20Court=C3=A8s?= Date: Sat, 10 Dec 2022 18:12:59 +0100 Subject: [PATCH 025/790] deduplicate: Use 'sendfile' only with file ports. Fixes a regression introduced in b129026e2e242e9068158ae6e6fcd8d7c5ea092e. * guix/store/deduplication.scm (dump-file/deduplicate): Use 'sendfile' only when INPUT' is a file port. --- guix/store/deduplication.scm | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/guix/store/deduplication.scm b/guix/store/deduplication.scm index 9953675319..acb6ffcc4a 100644 --- a/guix/store/deduplication.scm +++ b/guix/store/deduplication.scm @@ -262,7 +262,10 @@ down the road." (deduplicate file (dump-and-compute-hash) #:store store) (call-with-output-file file (lambda (output) - (sendfile output input size 0))))) + (if (file-port? input) + (sendfile output input size 0) + (dump-port input output size + #:buffer-size %deduplication-minimum-size)))))) (define* (copy-file/deduplicate source target #:key (store (%store-directory))) From 6dbdb5fcf5640c126ac65479b835aba83aea2a6d Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ludovic=20Court=C3=A8s?= Date: Sat, 10 Dec 2022 18:19:22 +0100 Subject: [PATCH 026/790] gnu: guix: Update to 1.4.0rc2. --- gnu/packages/package-management.scm | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/gnu/packages/package-management.scm b/gnu/packages/package-management.scm index b5b6b3875c..5a09b1fcf8 100644 --- a/gnu/packages/package-management.scm +++ b/gnu/packages/package-management.scm @@ -164,8 +164,8 @@ ;; Latest version of Guix, which may or may not correspond to a release. ;; Note: the 'update-guix-package.scm' script expects this definition to ;; start precisely like this. - (let ((version "1.4.0rc1") - (commit "020184fd39c6244e0336db3c608d3946b8d20490") + (let ((version "1.4.0rc2") + (commit "7866294e32f1e758d06fce4e1b1035eca3a7d772") (revision 0)) (package (name "guix") @@ -182,7 +182,7 @@ (commit commit))) (sha256 (base32 - "1489fdxdb86shx6bnfs8kihhvw44xqiv6fkx3b67cyw1dakxh1m4")) + "0np4fw5kq882nrkfgsvvwgcxqwvm6bzn3dbdf8p48nr7mfrm3rz9")) (file-name (string-append "guix-" version "-checkout")))) (build-system gnu-build-system) (arguments From 3677b97030e5954fa26bdb435e0d3379a1a4ec43 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ludovic=20Court=C3=A8s?= Date: Mon, 12 Dec 2022 14:55:32 +0100 Subject: [PATCH 027/790] pki: 'public-keys->acl' deduplicates entries. Reported by Tobias Geerinckx-Rice in . * guix/pki.scm (public-keys->acl): Add call to 'delete-duplicates'. * tests/pki.scm ("public-keys->acl deduplication"): New test. --- guix/pki.scm | 8 +++++--- tests/pki.scm | 6 +++++- 2 files changed, 10 insertions(+), 4 deletions(-) diff --git a/guix/pki.scm b/guix/pki.scm index 6326e065e9..c5b2fb9634 100644 --- a/guix/pki.scm +++ b/guix/pki.scm @@ -1,5 +1,5 @@ ;;; GNU Guix --- Functional package management for GNU -;;; Copyright © 2013, 2014, 2016 Ludovic Courtès +;;; Copyright © 2013, 2014, 2016, 2022 Ludovic Courtès ;;; ;;; This file is part of GNU Guix. ;;; @@ -21,6 +21,7 @@ #:use-module (gcrypt pk-crypto) #:use-module ((guix utils) #:select (with-atomic-file-output)) #:use-module ((guix build utils) #:select (mkdir-p)) + #:autoload (srfi srfi-1) (delete-duplicates) #:use-module (ice-9 match) #:use-module (ice-9 rdelim) #:use-module (ice-9 binary-ports) @@ -61,9 +62,10 @@ element in KEYS must be a canonical sexp with type 'public-key'." ;; want to have name certificates and to use subject names instead of ;; complete keys. `(acl ,@(map (lambda (key) - `(entry ,(canonical-sexp->sexp key) + `(entry ,key (tag (guix import)))) - keys))) + (delete-duplicates + (map canonical-sexp->sexp keys))))) (define %acl-file (string-append %config-directory "/acl")) diff --git a/tests/pki.scm b/tests/pki.scm index d6a6b476c7..86daff8ddf 100644 --- a/tests/pki.scm +++ b/tests/pki.scm @@ -1,5 +1,5 @@ ;;; GNU Guix --- Functional package management for GNU -;;; Copyright © 2013, 2014 Ludovic Courtès +;;; Copyright © 2013, 2014, 2022 Ludovic Courtès ;;; ;;; This file is part of GNU Guix. ;;; @@ -66,6 +66,10 @@ (test-assert "authorized-key? public-key singleton" (authorized-key? %public-key (public-keys->acl (list %public-key)))) +(test-equal "public-keys->acl deduplication" + (public-keys->acl (list %public-key)) + (public-keys->acl (make-list 10 %public-key))) + (test-assert "signature-case valid-signature" (let* ((hash (sha256 #vu8(1 2 3))) (data (bytevector->hash-data hash #:key-type (key-type %public-key))) From b8b4d631370e46a8d1918bc91b524aa0a6876f73 Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Mon, 12 Dec 2022 11:46:10 +0100 Subject: [PATCH 028/790] gnu: OpenLDAP: Update to 2.6.3. * gnu/packages/openldap.scm (openldap-2.6): Update to 2.6.3. --- gnu/packages/openldap.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/openldap.scm b/gnu/packages/openldap.scm index c8a47e45d5..78f96e6190 100644 --- a/gnu/packages/openldap.scm +++ b/gnu/packages/openldap.scm @@ -126,7 +126,7 @@ (define-public openldap-2.6 (package (inherit openldap) - (version "2.6.1") + (version "2.6.3") (source (origin (method url-fetch) ;; See for a list of @@ -142,7 +142,7 @@ "openldap-release/openldap-" version ".tgz"))) (sha256 (base32 - "1wz6f3g3bbqgbbxs20zlappmmhapqbl791c0waibhz9djsk6wmwx")))) + "0ihddk8c6hg9lkjv0wk0w13g8kb75r8dfsn1n6b77mzk3pbs38nj")))) (arguments (substitute-keyword-arguments (package-arguments openldap) ((#:phases phases) From f9fb8460ce9399d40481501c7af8ee1605dca389 Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Mon, 12 Dec 2022 12:06:59 +0100 Subject: [PATCH 029/790] gnu: tracker-miners: Remove obsolete input. * gnu/packages/gnome.scm (tracker-miners)[native-inputs]: Remove INTLTOOL. Add GETTEXT-MINIMAL. --- gnu/packages/gnome.scm | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/gnu/packages/gnome.scm b/gnu/packages/gnome.scm index c2edd7a553..b6ff8d4fe7 100644 --- a/gnu/packages/gnome.scm +++ b/gnu/packages/gnome.scm @@ -9724,7 +9724,7 @@ endpoint and it understands SPARQL.") "--no-suite" "slow"))))))) (native-inputs (list dbus - intltool + gettext-minimal `(,glib "bin") docbook-xsl docbook-xml From 6bfde85d36618818e2432494aa5fb993d6038444 Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Mon, 12 Dec 2022 13:06:04 +0100 Subject: [PATCH 030/790] gnu: wxsvg: Update to 1.5.24. * gnu/packages/wxwidgets.scm (wxsvg): Update to 1.5.24. --- gnu/packages/wxwidgets.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/wxwidgets.scm b/gnu/packages/wxwidgets.scm index 2d34b49d93..0183e07c31 100644 --- a/gnu/packages/wxwidgets.scm +++ b/gnu/packages/wxwidgets.scm @@ -322,14 +322,14 @@ provide a 100% native look and feel for the application.") (define-public wxsvg (package (name "wxsvg") - (version "1.5.23") + (version "1.5.24") (source (origin (method url-fetch) (uri (string-append "mirror://sourceforge/wxsvg/wxsvg/" version "/wxsvg-" version ".tar.bz2")) (sha256 - (base32 "1fdbvihw1w2vm29xj54cqgpdabhlg0ydf3clkb0qrlf7mhgkc1rz")))) + (base32 "10i4bv1bfbfgrrpxvfdjrr5svgn64v471lkcl2pzx9fhz28k4ixf")))) (build-system glib-or-gtk-build-system) (inputs (list wxwidgets cairo ffmpeg)) From 85ea2dfc4cafca62a6543a74f10f6d30e4e1abbd Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Mon, 12 Dec 2022 13:27:03 +0100 Subject: [PATCH 031/790] gnu: vapoursynth: Update to 61. * gnu/packages/video.scm (vapoursynth): Update to 61. --- gnu/packages/video.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/video.scm b/gnu/packages/video.scm index 5a6d6827b9..d35a07d877 100644 --- a/gnu/packages/video.scm +++ b/gnu/packages/video.scm @@ -3039,7 +3039,7 @@ capabilities.") (define-public vapoursynth (package (name "vapoursynth") - (version "53") + (version "61") (source (origin (method git-fetch) (uri (git-reference @@ -3048,7 +3048,7 @@ capabilities.") (file-name (git-file-name name version)) (sha256 (base32 - "0qcsfkpkry0cmvi60khjwvfz4fqhy23nqmn4pb9qrwll26sn9dcr")))) + "0v0dp3hydqzam0dp2d9zbrccrsvhy6n61s4v7ca2qbw69vpsm594")))) (build-system gnu-build-system) (arguments `(#:phases From 3dc667b6f81ef32d041cfd6b6abceb078d1e02c3 Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Mon, 12 Dec 2022 13:27:30 +0100 Subject: [PATCH 032/790] gnu: vapoursynth: Remove input labels. * gnu/packages/video.scm (vapoursynth)[native-inputs]: Remove labels. --- gnu/packages/video.scm | 12 ++++++------ 1 file changed, 6 insertions(+), 6 deletions(-) diff --git a/gnu/packages/video.scm b/gnu/packages/video.scm index d35a07d877..1f9b2dff7a 100644 --- a/gnu/packages/video.scm +++ b/gnu/packages/video.scm @@ -3063,12 +3063,12 @@ capabilities.") (wrap-program (string-append out "/bin/vspipe") `("PYTHONPATH" ":" = (,site))))))))) (native-inputs - `(("autoconf" ,autoconf) - ("automake" ,automake) - ("cython" ,python-cython) - ("libtool" ,libtool) - ("pkg-config" ,pkg-config) - ("yasm" ,yasm))) + (list autoconf + automake + python-cython + libtool + pkg-config + yasm)) (inputs (list ffmpeg libass python tesseract-ocr zimg)) (home-page "http://www.vapoursynth.com/") From dce40ccc47ea43d2243e58d166c512a993ef5181 Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Mon, 12 Dec 2022 13:30:41 +0100 Subject: [PATCH 033/790] gnu: motion: Update to 4.5.0. * gnu/packages/video.scm (motion): Update to 4.5.0. --- gnu/packages/video.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/video.scm b/gnu/packages/video.scm index 1f9b2dff7a..06024cc3e2 100644 --- a/gnu/packages/video.scm +++ b/gnu/packages/video.scm @@ -4548,7 +4548,7 @@ It counts more than 100 plugins.") (define-public motion (package (name "motion") - (version "4.3.2") + (version "4.5.0") (home-page "https://motion-project.github.io/") (source (origin (method git-fetch) @@ -4557,7 +4557,7 @@ It counts more than 100 plugins.") (commit (string-append "release-" version)))) (sha256 (base32 - "09xs815jsivcilpmnrx2jkcxirj4lg5kp99fkr0p2sdxw03myi95")) + "1rqy98g3xjjzjxiw8j3qdka0rbhcgzgczz6qgj157ck9116j18dq")) (file-name (git-file-name name version)))) (build-system gnu-build-system) (native-inputs From 1572071b6820a271d4801dd169685e0309de8628 Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Mon, 12 Dec 2022 13:31:07 +0100 Subject: [PATCH 034/790] gnu: motion: Remove input labels. * gnu/packages/video.scm (motion)[native-inputs, inputs]: Remove labels. --- gnu/packages/video.scm | 10 ++-------- 1 file changed, 2 insertions(+), 8 deletions(-) diff --git a/gnu/packages/video.scm b/gnu/packages/video.scm index 06024cc3e2..a2cbc53f8c 100644 --- a/gnu/packages/video.scm +++ b/gnu/packages/video.scm @@ -4561,15 +4561,9 @@ It counts more than 100 plugins.") (file-name (git-file-name name version)))) (build-system gnu-build-system) (native-inputs - `(("autoconf" ,autoconf) - ("automake" ,automake) - ("gettext" ,gettext-minimal) - ("pkg-config" ,pkg-config))) + (list autoconf automake gettext-minimal pkg-config)) (inputs - `(("libjpeg" ,libjpeg-turbo) - ("ffmpeg" ,ffmpeg) - ("libmicrohttpd" ,libmicrohttpd) - ("sqlite" ,sqlite))) + (list libjpeg-turbo ffmpeg libmicrohttpd sqlite)) (arguments '(#:phases (modify-phases %standard-phases (replace 'bootstrap From 240c823ae132d6d34c6743d388d362f531a08fbd Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Mon, 12 Dec 2022 13:37:19 +0100 Subject: [PATCH 035/790] gnu: pianobar: Update to 2022.04.01. * gnu/packages/music.scm (pianobar): Update to 2022.04.01. --- gnu/packages/music.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/music.scm b/gnu/packages/music.scm index d02d893f02..026bb22770 100644 --- a/gnu/packages/music.scm +++ b/gnu/packages/music.scm @@ -3554,7 +3554,7 @@ tune-in sender list from @url{http://opml.radiotime.com}.") (define-public pianobar (package (name "pianobar") - (version "2020.11.28") + (version "2022.04.01") (source (origin (method git-fetch) (uri (git-reference @@ -3563,7 +3563,7 @@ tune-in sender list from @url{http://opml.radiotime.com}.") (file-name (git-file-name name version)) (sha256 (base32 - "13qx52a1yj2wghf7yd9jf4ar92scbc8zgqdq0kkqf4p9isf1phf3")))) + "14s97fx83dg8szbib2y608hjzfdhz20hch2ify3gqhji58v69wil")))) (build-system gnu-build-system) (arguments `(#:tests? #f ; no tests From bf9d119e3277fe8b641e907af39afae2b0a4bdae Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Mon, 12 Dec 2022 14:25:39 +0100 Subject: [PATCH 036/790] gnu: Sort module imports in (gnu packages scheme). * gnu/packages/scheme.scm: Sort imports. Remove one duplicate. --- gnu/packages/scheme.scm | 39 +++++++++++++++++++-------------------- 1 file changed, 19 insertions(+), 20 deletions(-) diff --git a/gnu/packages/scheme.scm b/gnu/packages/scheme.scm index f0fbbb6331..cbe9d1d948 100644 --- a/gnu/packages/scheme.scm +++ b/gnu/packages/scheme.scm @@ -48,40 +48,39 @@ #:use-module (guix build-system gnu) #:use-module (guix build-system trivial) #:use-module (gnu packages autotools) - #:use-module (gnu packages bdw-gc) + #:use-module (gnu packages avahi) + #:use-module (gnu packages base) #:use-module (gnu packages bash) + #:use-module (gnu packages bdw-gc) #:use-module (gnu packages compression) #:use-module (gnu packages databases) + #:use-module (gnu packages emacs) + #:use-module (gnu packages fontutils) + #:use-module (gnu packages gcc) + #:use-module (gnu packages ghostscript) + #:use-module (gnu packages gl) + #:use-module (gnu packages glib) + #:use-module (gnu packages gtk) + #:use-module (gnu packages image) + #:use-module (gnu packages libedit) #:use-module (gnu packages libevent) + #:use-module (gnu packages libffi) + #:use-module (gnu packages libphidget) #:use-module (gnu packages libunistring) + #:use-module (gnu packages linux) #:use-module (gnu packages lisp-check) #:use-module (gnu packages lisp-xyz) #:use-module (gnu packages m4) #:use-module (gnu packages multiprecision) #:use-module (gnu packages ncurses) - #:use-module (gnu packages pcre) - #:use-module (gnu packages emacs) - #:use-module (gnu packages ghostscript) #:use-module (gnu packages netpbm) - #:use-module (gnu packages texinfo) - #:use-module (gnu packages tex) - #:use-module (gnu packages base) - #:use-module (gnu packages compression) + #:use-module (gnu packages pcre) #:use-module (gnu packages pkg-config) - #:use-module (gnu packages avahi) - #:use-module (gnu packages libphidget) - #:use-module (gnu packages gcc) - #:use-module (gnu packages glib) - #:use-module (gnu packages gtk) - #:use-module (gnu packages libffi) - #:use-module (gnu packages fontutils) - #:use-module (gnu packages image) - #:use-module (gnu packages xorg) #:use-module (gnu packages sqlite) + #:use-module (gnu packages tex) + #:use-module (gnu packages texinfo) #:use-module (gnu packages tls) - #:use-module (gnu packages gl) - #:use-module (gnu packages libedit) - #:use-module (gnu packages linux) + #:use-module (gnu packages xorg) #:use-module (srfi srfi-1) #:use-module (ice-9 match)) From 79564bf9977ebba0b31d8dc291eb039142f51f68 Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Mon, 12 Dec 2022 14:27:05 +0100 Subject: [PATCH 037/790] gnu: ffmpeg: Promote version 5 to the default. * gnu/packages/video.scm (ffmpeg): Alias to FFMPEG-5. (mlt-6)[inpust]: Replace "ffmpeg" with FFMPEG-4. (transcode, libquicktime, ffmpegthumbnailer, mplayer, obs, simplescreenrecorder, handbrake, ffms2, libopenshot, wlstream)[inputs]: Change from FFMPEG to FFMPEG-4. * gnu/packages/arcan.scm (arcan)[inputs]: Likewise. * gnu/packages/astronomy.scm (stackistry, libskry)[inputs]: Likewise. * gnu/packages/audio.scm (aubio, bs1770gain)[inputs]: Likewise. * gnu/packages/education.scm (openboard)[inputs]: Likewise. * gnu/packages/emulators.scm (dolphin-emu, retroarch, pcsxr, ppsspp)[inputs]: Likewise. * gnu/packages/game-development.scm (warsow-qfusion)[inputs]: Likewise. * gnu/packages/games.scm (oshu, hedgewars)[inputs]: Likewise. * gnu/packages/gnunet.scm (libextractor)[inputs]: Likewise. * gnu/packages/graphics.scm (openscenegraph)[inputs]: Likewise. * gnu/packages/image-processing.scm (opencv, paraview-5.9)[inputs]: Likewise. * gnu/packages/julia-jll.scm (julia-ffmpeg-jll)[inputs]: Likewise. * gnu/packages/kde-multimedia.scm (kid3)[inputs]: Likewise. * gnu/packages/kodi.scm (kodi)[inputs]: Likewise. * gnu/packages/linphone.scm (mediastreamer2)[inputs]: Likewise. * gnu/packages/linux.scm (pipewire)[inputs]: Likewise. (pipewire-0.3)[inputs]: Replace "ffmpeg" with FFMPEG. * gnu/packages/mp3.scm (chromaprint)[inputs]: Change from FFMPEG to FFMPEG-4. * gnu/packages/music.scm (musikcube)[inputs]: Likewise. * gnu/packages/rdesktop.scm (freerdp)[inputs]: Likewise. * gnu/packages/qt.scm (qtwebengine-5)[inputs]: Likewise. --- gnu/packages/arcan.scm | 2 +- gnu/packages/astronomy.scm | 4 ++-- gnu/packages/audio.scm | 8 ++++++-- gnu/packages/education.scm | 2 +- gnu/packages/emulators.scm | 8 ++++---- gnu/packages/game-development.scm | 2 +- gnu/packages/games.scm | 4 ++-- gnu/packages/gnunet.scm | 2 +- gnu/packages/graphics.scm | 2 +- gnu/packages/image-processing.scm | 4 ++-- gnu/packages/julia-jll.scm | 2 +- gnu/packages/kde-multimedia.scm | 2 +- gnu/packages/kodi.scm | 2 +- gnu/packages/linphone.scm | 2 +- gnu/packages/linux.scm | 3 ++- gnu/packages/mp3.scm | 2 +- gnu/packages/music.scm | 2 +- gnu/packages/qt.scm | 2 +- gnu/packages/rdesktop.scm | 2 +- gnu/packages/video.scm | 23 ++++++++++++----------- 20 files changed, 43 insertions(+), 37 deletions(-) diff --git a/gnu/packages/arcan.scm b/gnu/packages/arcan.scm index c25d64903c..7483777ff0 100644 --- a/gnu/packages/arcan.scm +++ b/gnu/packages/arcan.scm @@ -123,7 +123,7 @@ (files '("share/arcan/scripts"))))) (inputs `(("apr" ,apr) - ("ffmpeg" ,ffmpeg) + ("ffmpeg" ,ffmpeg-4) ("freetype" ,freetype) ("glib" ,glib) ("glu" ,glu) diff --git a/gnu/packages/astronomy.scm b/gnu/packages/astronomy.scm index c59f4d02a4..f99dbcbf06 100644 --- a/gnu/packages/astronomy.scm +++ b/gnu/packages/astronomy.scm @@ -813,7 +813,7 @@ astronomical fields. SkyMaker is part of the EFIGI (native-inputs (list pkg-config)) (inputs - (list gtkmm-3 libskry ffmpeg)) + (list gtkmm-3 libskry ffmpeg-4)) (home-page "https://github.com/GreatAttractor/stackistry") (synopsis "Astronomical lucky imaging/image stacking tool") (description @@ -1714,7 +1714,7 @@ arrays with NumPy as its only dependency.") (copy-recursively "include" include)) #t))))) (inputs - (list ffmpeg)) + (list ffmpeg-4)) (home-page "https://github.com/GreatAttractor/libskry") (synopsis "Astronimical lucky imaging library") (description diff --git a/gnu/packages/audio.scm b/gnu/packages/audio.scm index e480ce9e58..5e471d34e9 100644 --- a/gnu/packages/audio.scm +++ b/gnu/packages/audio.scm @@ -603,7 +603,11 @@ Filter) modules follow the convention of 1V / Octave.") "--enable-samplerate" "--enable-avcodec"))) (inputs - (list jack-1 libsndfile libsamplerate fftwf ffmpeg)) ; for libavcodec + (list jack-1 + libsndfile + libsamplerate + ffmpeg-4 ;for libavcodec + fftwf)) (native-inputs (list pkg-config)) (home-page "https://aubio.org/") @@ -4442,7 +4446,7 @@ simplified, although really accurate, measuring tools.") ,home-page)) #t)))) (build-system gnu-build-system) - (inputs (list ffmpeg sox)) + (inputs (list ffmpeg-4 sox)) (synopsis "Tool to adjust loudness of media files") (description "BS1770GAIN is a loudness scanner compliant with ITU-R BS.1770 and its diff --git a/gnu/packages/education.scm b/gnu/packages/education.scm index c0f7778c1c..0e3dd08c23 100644 --- a/gnu/packages/education.scm +++ b/gnu/packages/education.scm @@ -547,7 +547,7 @@ specialized device.") (inputs (list alsa-lib coreutils-minimal ;for patched 'env' shebang - ffmpeg + ffmpeg-4 freetype lame libass diff --git a/gnu/packages/emulators.scm b/gnu/packages/emulators.scm index 5054ae3da5..11d1cda46f 100644 --- a/gnu/packages/emulators.scm +++ b/gnu/packages/emulators.scm @@ -323,7 +323,7 @@ console.") bluez curl eudev - ffmpeg + ffmpeg-4 font-wqy-microhei freetype glew @@ -1471,7 +1471,7 @@ as RetroArch.") "--disable-builtinminiupnpc"))))))) (inputs `(("alsa-lib" ,alsa-lib) - ("ffmpeg" ,ffmpeg) + ("ffmpeg" ,ffmpeg-4) ("freetype" ,freetype) ("libxinerama" ,libxinerama) ("libxkbcommon" ,libxkbcommon) @@ -2035,7 +2035,7 @@ assembler, and debugger for the Intel 8085 microprocessor. (list libcdio sdl2 gtk+ - ffmpeg + ffmpeg-4 libxv libarchive pulseaudio)) @@ -2322,7 +2322,7 @@ elseif(FALSE)")) (native-inputs (list pkg-config python)) (inputs (list bash cityhash - ffmpeg + ffmpeg-4 glew glslang libpng diff --git a/gnu/packages/game-development.scm b/gnu/packages/game-development.scm index 4a0435045b..8fec474d0b 100644 --- a/gnu/packages/game-development.scm +++ b/gnu/packages/game-development.scm @@ -2665,7 +2665,7 @@ utilities frequently used in roguelikes.") `(("alsa-lib" ,alsa-lib) ("curl" ,curl) ("freetype" ,freetype) - ("ffmpeg" ,ffmpeg) + ("ffmpeg" ,ffmpeg-4) ("libjpeg" ,libjpeg-turbo) ("libogg" ,libogg) ("libpng" ,libpng) diff --git a/gnu/packages/games.scm b/gnu/packages/games.scm index d8c5a34a41..4c5f28a55c 100644 --- a/gnu/packages/games.scm +++ b/gnu/packages/games.scm @@ -8478,7 +8478,7 @@ to download and install them in @file{$HOME/.stepmania-X.Y/Songs} directory.") (native-inputs (list pkg-config)) (inputs - (list cairo ffmpeg pango sdl2 sdl2-image)) + (list cairo ffmpeg-4 pango sdl2 sdl2-image)) (home-page "https://github.com/fmang/oshu/") (synopsis "Rhythm game in which you click on circles") (description "@i{oshu!} is a minimalist variant of the @i{osu!} rhythm game, @@ -9318,7 +9318,7 @@ play with up to four players simultaneously. It has network support.") (string-append "../hedgewars-src-" #$version) (install-file "misc/hedgewars.png" icons)))))))) (inputs - (list ffmpeg + (list ffmpeg-4 freeglut ghc-entropy ghc-hslogger diff --git a/gnu/packages/gnunet.scm b/gnu/packages/gnunet.scm index b477fee537..c98ceefad7 100644 --- a/gnu/packages/gnunet.scm +++ b/gnu/packages/gnunet.scm @@ -100,7 +100,7 @@ `(("exiv2" ,exiv2) ("bzip2" ,bzip2) ("flac" ,flac) - ("ffmpeg" ,ffmpeg) + ("ffmpeg" ,ffmpeg-4) ("file" ,file) ;libmagic, for the MIME plug-in ("glib" ,glib) ("giflib" ,giflib) diff --git a/gnu/packages/graphics.scm b/gnu/packages/graphics.scm index efe1deede4..4642dfbe36 100644 --- a/gnu/packages/graphics.scm +++ b/gnu/packages/graphics.scm @@ -1308,7 +1308,7 @@ visual effects work for film.") ("jasper" ,jasper) ("librsvg" ,librsvg) ("libxrandr" ,libxrandr) - ("ffmpeg" ,ffmpeg) + ("ffmpeg" ,ffmpeg-4) ("mesa" ,mesa))) (synopsis "High-performance real-time graphics toolkit") (description diff --git a/gnu/packages/image-processing.scm b/gnu/packages/image-processing.scm index fb45e9b141..ab796d7719 100644 --- a/gnu/packages/image-processing.scm +++ b/gnu/packages/image-processing.scm @@ -620,7 +620,7 @@ integrates with various databases on GUI toolkits such as Qt and Tk.") (sha256 (base32 "0ga0l4ranp1834gxgp487ll1amvmssa02l2nk5ja5w0rx4d8hh26")))))) (inputs - (list ffmpeg + (list ffmpeg-4 gtk+ gtkglext hdf5 @@ -925,7 +925,7 @@ recalculates.") double-conversion eigen expat - ffmpeg + ffmpeg-4 freetype gdal gl2ps diff --git a/gnu/packages/julia-jll.scm b/gnu/packages/julia-jll.scm index 594c36b6ce..2b0f644736 100644 --- a/gnu/packages/julia-jll.scm +++ b/gnu/packages/julia-jll.scm @@ -254,7 +254,7 @@ build tree Yggdrasil.") ;; There's a Julia file for each platform, override them all (find-files "src/wrappers/" "\\.jl$"))))))) (inputs - (list ffmpeg)) + (list ffmpeg-4)) (propagated-inputs (list julia-jllwrappers julia-bzip2-jll diff --git a/gnu/packages/kde-multimedia.scm b/gnu/packages/kde-multimedia.scm index 9fb3572909..d635eca26d 100644 --- a/gnu/packages/kde-multimedia.scm +++ b/gnu/packages/kde-multimedia.scm @@ -334,7 +334,7 @@ This package is part of the KDE multimedia module.") (native-inputs (list docbook-xsl extra-cmake-modules - ffmpeg + ffmpeg-4 kdoctools libxslt python-wrapper diff --git a/gnu/packages/kodi.scm b/gnu/packages/kodi.scm index 402ee221c5..18791359f2 100644 --- a/gnu/packages/kodi.scm +++ b/gnu/packages/kodi.scm @@ -399,7 +399,7 @@ alternatives. In compilers, this can reduce the cascade of secondary errors.") ("dcadec" ,dcadec) ("dbus" ,dbus) ("eudev" ,eudev) - ("ffmpeg" ,ffmpeg) + ("ffmpeg" ,ffmpeg-4) ("flac" ,flac) ("flatbuffers" ,flatbuffers) ("fmt" ,fmt-7) diff --git a/gnu/packages/linphone.scm b/gnu/packages/linphone.scm index 7b5efeb588..130097ef40 100644 --- a/gnu/packages/linphone.scm +++ b/gnu/packages/linphone.scm @@ -645,7 +645,7 @@ API. It also comprises a simple HTTP/HTTPS client implementation.") ("bcg729" ,bcg729) ("bcmatroska2" ,bcmatroska2) ("bctoolbox" ,bctoolbox) - ("ffmpeg" ,ffmpeg) + ("ffmpeg" ,ffmpeg-4) ("glew" ,glew) ("glu" ,glu) ("glx" ,mesa-utils) diff --git a/gnu/packages/linux.scm b/gnu/packages/linux.scm index c476940eed..9ea77069ca 100644 --- a/gnu/packages/linux.scm +++ b/gnu/packages/linux.scm @@ -8991,7 +8991,7 @@ types and interfaces and translates so that the X server can use them.") (list alsa-lib dbus eudev - ffmpeg + ffmpeg-4 gstreamer gst-plugins-base libva @@ -9035,6 +9035,7 @@ of Linux application development.") (modify-inputs (package-native-inputs pipewire) (prepend python-docutils))) (inputs (modify-inputs (package-inputs pipewire) + (replace "ffmpeg" ffmpeg) (prepend avahi bluez jack-2 diff --git a/gnu/packages/mp3.scm b/gnu/packages/mp3.scm index e2b112832b..03e4485618 100644 --- a/gnu/packages/mp3.scm +++ b/gnu/packages/mp3.scm @@ -643,7 +643,7 @@ command-line tool.") (inputs ;; requires one of FFmpeg (prefered), FFTW3 or vDSP ;; use the same ffmpeg version as for acoustid-fingerprinter - (list ffmpeg boost)) + (list ffmpeg-4 boost)) (home-page "https://acoustid.org/chromaprint") (synopsis "Audio fingerprinting library") (description "Chromaprint is a library for calculating audio diff --git a/gnu/packages/music.scm b/gnu/packages/music.scm index 026bb22770..e3cb67b413 100644 --- a/gnu/packages/music.scm +++ b/gnu/packages/music.scm @@ -6806,7 +6806,7 @@ choice.") (list alsa-lib boost curl - ffmpeg + ffmpeg-4 lame libev libmicrohttpd diff --git a/gnu/packages/qt.scm b/gnu/packages/qt.scm index 519a7d1548..6406fd5c49 100644 --- a/gnu/packages/qt.scm +++ b/gnu/packages/qt.scm @@ -2546,7 +2546,7 @@ using the Enchant spell-checking library.") cups-minimal curl dbus - ffmpeg + ffmpeg-4 fontconfig harfbuzz icu4c diff --git a/gnu/packages/rdesktop.scm b/gnu/packages/rdesktop.scm index 12a1d3e9eb..84a07e6ba9 100644 --- a/gnu/packages/rdesktop.scm +++ b/gnu/packages/rdesktop.scm @@ -101,7 +101,7 @@ to remotely control a user's Windows desktop.") (inputs `(("alsa-lib" ,alsa-lib) ("cups" ,cups) - ("ffmpeg" ,ffmpeg) + ("ffmpeg" ,ffmpeg-4) ("libjpeg" ,libjpeg-turbo) ("libusb" ,libusb) ("libx11" ,libx11) diff --git a/gnu/packages/video.scm b/gnu/packages/video.scm index a2cbc53f8c..a15c86ee07 100644 --- a/gnu/packages/video.scm +++ b/gnu/packages/video.scm @@ -273,7 +273,7 @@ python-wrapper)) (inputs (list alsa-lib - ffmpeg + ffmpeg-4 freetype imagemagick lame @@ -450,7 +450,7 @@ as a joint effort between the BBC and Fluendo.") (list gettext-minimal doxygen pkg-config)) (inputs (list alsa-lib - ffmpeg + ffmpeg-4 gtk+-2 lame libdv @@ -1876,7 +1876,7 @@ audio/video codec library.") (format #t "setting LD_LIBRARY_PATH to ~s~%" path) (setenv "LD_LIBRARY_PATH" path))))))))) -(define-public ffmpeg ffmpeg-4) +(define-public ffmpeg ffmpeg-5) (define-public ffmpeg-for-stepmania (hidden-package @@ -1923,7 +1923,7 @@ audio/video codec library.") (native-inputs (list pkg-config)) (inputs - (list ffmpeg libjpeg-turbo libpng gvfs)) + (list ffmpeg-4 libjpeg-turbo libpng gvfs)) (arguments `(#:configure-flags (list "-DENABLE_GIO=ON" "-DENABLE_THUMBNAILER=ON"))) (home-page "https://github.com/dirkvdb/ffmpegthumbnailer") @@ -2102,7 +2102,7 @@ streaming protocols.") (inputs `(("alsa-lib" ,alsa-lib) ("cdparanoia" ,cdparanoia) - ("ffmpeg" ,ffmpeg) + ("ffmpeg" ,ffmpeg-4) ("fontconfig" ,fontconfig) ("freetype" ,freetype) ("giflib" ,giflib) @@ -3296,6 +3296,7 @@ tools, XML authoring components, and an extensible plug-in based API.") ,@(package-arguments mlt))) (inputs (modify-inputs (package-inputs mlt) + (replace "ffmpeg" ffmpeg-4) (replace "gtk+" gtk+-2))))) (define-public v4l-utils @@ -3409,7 +3410,7 @@ be used for realtime video capture via Linux-specific APIs.") bash-minimal curl eudev - ffmpeg + ffmpeg-4 fontconfig freetype glib @@ -3679,7 +3680,7 @@ making @dfn{screencasts}.") ;; As a result, they are omitted. Please add them back if problems appear. (inputs (list alsa-lib - ffmpeg + ffmpeg-4 glu jack-1 libxi @@ -3872,7 +3873,7 @@ supported players in addition to this package.") (inputs `(("bzip2" ,bzip2) ("dbus-glib" ,dbus-glib) - ("ffmpeg" ,ffmpeg) + ("ffmpeg" ,ffmpeg-4) ("fontconfig" ,fontconfig) ("freetype" ,freetype) ("glib" ,glib) @@ -4313,7 +4314,7 @@ and ITU-T H.222.0.") (inputs (list zlib)) (propagated-inputs - (list ffmpeg)) + (list ffmpeg-4)) (native-inputs (list pkg-config)) (synopsis "Cross-platform wrapper around ffmpeg/libav") @@ -4743,7 +4744,7 @@ create smoother and stable videos.") (list alsa-lib zlib)) (propagated-inputs ;all referenced in installed headers (list cppzmq - ffmpeg + ffmpeg-4 imagemagick jsoncpp libopenshot-audio @@ -4968,7 +4969,7 @@ speed and correctness.") "01qbcgfl3g9kfwn1jf1z9pdj3bvf5lmg71d1vwkcllc2az24bjqp")))) (build-system meson-build-system) (native-inputs (list libdrm pkg-config)) - (inputs (list ffmpeg pulseaudio wayland wayland-protocols)) + (inputs (list ffmpeg-4 pulseaudio wayland wayland-protocols)) (home-page "https://github.com/atomnuker/wlstream") (synopsis "Screen capture tool for Wayland sessions") (description "Wlstream is a screen capture tool for recording audio and From 16f87d883b79b38da7d4297e8eb30c8f6eb735c1 Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Mon, 12 Dec 2022 14:57:02 +0100 Subject: [PATCH 038/790] services: zabbix-server: Increase Shepherd grace period. * gnu/services/monitoring.scm (zabbix-server-shepherd-service)[stop]: Add #:grace-period. --- gnu/services/monitoring.scm | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/gnu/services/monitoring.scm b/gnu/services/monitoring.scm index 9a88351566..44e2e8886c 100644 --- a/gnu/services/monitoring.scm +++ b/gnu/services/monitoring.scm @@ -404,7 +404,10 @@ configuration file.")) /etc/ssl/certs" "SSL_CERT_FILE=/run/current-system/profile\ /etc/ssl/certs/ca-certificates.crt"))) - (stop #~(make-kill-destructor)))))) + (stop #~(make-kill-destructor + ;; The server needs to finish database work on shutdown + ;; which can take a while for big or busy databases. + #:grace-period 60)))))) (define zabbix-server-service-type (service-type From b5f3a1b84e2bd3e03452c57ef2785a8f98124361 Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Mon, 12 Dec 2022 15:12:08 +0100 Subject: [PATCH 039/790] gnu: Remove unused module import. * gnu/packages/version-control.scm: Don't import (guix build python-build-system). --- gnu/packages/version-control.scm | 1 - 1 file changed, 1 deletion(-) diff --git a/gnu/packages/version-control.scm b/gnu/packages/version-control.scm index e44ae7c966..5da93fa0ce 100644 --- a/gnu/packages/version-control.scm +++ b/gnu/packages/version-control.scm @@ -71,7 +71,6 @@ #:use-module (guix download) #:use-module (guix git-download) #:use-module (guix hg-download) - #:use-module (guix build python-build-system) #:use-module (guix build-system cmake) #:use-module (guix build-system copy) #:use-module (guix build-system gnu) From 8fe6d3e8446944294856950ef192cac83e03e58b Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Sun, 4 Dec 2022 01:00:52 +0100 Subject: [PATCH 040/790] =?UTF-8?q?gnu:=20yajl:=20Drop=20custom=20?= =?UTF-8?q?=E2=80=98lib-=E2=80=99=20prefix.?= MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * gnu/packages/web.scm (yajl): New variable, renamed from… (libyajl): …this one, which is now a DEPRECATED-PACKAGE alias of yajl. Adjust all users. --- gnu/packages/containers.scm | 2 +- gnu/packages/monitoring.scm | 2 +- gnu/packages/mpd.scm | 2 +- gnu/packages/python-xyz.scm | 4 ++-- gnu/packages/virtualization.scm | 6 +++--- gnu/packages/web.scm | 7 +++++-- gnu/packages/wm.scm | 4 ++-- 7 files changed, 15 insertions(+), 12 deletions(-) diff --git a/gnu/packages/containers.scm b/gnu/packages/containers.scm index 59eea423a1..e2d698dcc2 100644 --- a/gnu/packages/containers.scm +++ b/gnu/packages/containers.scm @@ -91,7 +91,7 @@ (inputs (list libcap libseccomp - libyajl)) + yajl)) (native-inputs (list automake autoconf diff --git a/gnu/packages/monitoring.scm b/gnu/packages/monitoring.scm index 37b9335ac8..74ec7b6cdf 100644 --- a/gnu/packages/monitoring.scm +++ b/gnu/packages/monitoring.scm @@ -636,7 +636,7 @@ devices.") ;; Required because of patched sources. (invoke "autoreconf" "-vfi")))))) (inputs - (list rrdtool curl libyajl)) + (list rrdtool curl yajl)) (native-inputs (list autoconf automake libtool pkg-config)) (home-page "https://collectd.org/") diff --git a/gnu/packages/mpd.scm b/gnu/packages/mpd.scm index e0bd7633bc..5439d89f4a 100644 --- a/gnu/packages/mpd.scm +++ b/gnu/packages/mpd.scm @@ -170,7 +170,7 @@ interfacing MPD in the C, C++ & Objective C languages.") zlib)) (native-inputs (list cmake pkg-config python-sphinx)) ;; Missing optional inputs: - ;; libyajl + ;; yajl ;; libcdio_paranoia ;; libmms ;; libadplug diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index 8591423116..9629012a80 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -29784,9 +29784,9 @@ simple mock/record and a complete capture/replay framework.") (when tests? (invoke "pytest" "-vv"))))))) (inputs - ;; libyajl is optional, but compiling with it makes faster + ;; yajl is optional, but compiling with it makes faster ;; backends available to ijson: - (list libyajl)) + (list yajl)) (native-inputs (list python-pytest)) (build-system python-build-system) diff --git a/gnu/packages/virtualization.scm b/gnu/packages/virtualization.scm index c0334f1760..1218112a20 100644 --- a/gnu/packages/virtualization.scm +++ b/gnu/packages/virtualization.scm @@ -1363,7 +1363,7 @@ pretty simple, REST API.") openssl readline cyrus-sasl - libyajl + yajl audit dmidecode dnsmasq @@ -1403,7 +1403,7 @@ to integrate other virtualization mechanisms if needed.") (build-system meson-build-system) (inputs (list openssl cyrus-sasl lvm2 ; for libdevmapper - libyajl)) + yajl)) (native-inputs (list pkg-config intltool `(,glib "bin") vala)) @@ -2269,7 +2269,7 @@ override CC = " (assoc-ref inputs "cross-gcc") "/bin/i686-linux-gnu-gcc")) ("iproute" ,iproute) ; TODO: patch invocations. ("libaio" ,libaio) ("libx11" ,libx11) - ("libyajl" ,libyajl) + ("yajl" ,yajl) ("ncurses" ,ncurses) ("openssl" ,openssl) ("ovmf" ,ovmf) diff --git a/gnu/packages/web.scm b/gnu/packages/web.scm index c1e9e943c0..efb0313f05 100644 --- a/gnu/packages/web.scm +++ b/gnu/packages/web.scm @@ -1395,9 +1395,9 @@ current version of any major web browser.") style API.") (license license:expat))) -(define-public libyajl +(define-public yajl (package - (name "libyajl") + (name "yajl") (version "2.1.0") (source (origin (method git-fetch) @@ -1424,6 +1424,9 @@ style API.") parser written in ANSI C and a small validating JSON generator.") (license license:isc))) +(define-public libyajl + (deprecated-package "libyajl" yajl)) + (define-public libwebsockets (package (name "libwebsockets") diff --git a/gnu/packages/wm.scm b/gnu/packages/wm.scm index d3a7716c23..18fe606c7b 100644 --- a/gnu/packages/wm.scm +++ b/gnu/packages/wm.scm @@ -287,7 +287,7 @@ or musca). (list alsa-lib libconfuse libnl - libyajl + yajl pulseaudio)) (native-inputs (list asciidoc @@ -342,7 +342,7 @@ commands would.") xcb-util-xrm libxkbcommon libev - libyajl + yajl xmlto perl-pod-simple libx11 From 2a779dc9bdb10fbac4d2a43837e35e6558d1a6e9 Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Sun, 4 Dec 2022 01:00:04 +0100 Subject: [PATCH 041/790] gnu: yajl: Remove trailing #t from phases. * gnu/packages/web.scm (yajl)[arguments]: Don't explicitly return #t from phases. --- gnu/packages/web.scm | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/gnu/packages/web.scm b/gnu/packages/web.scm index efb0313f05..f6e07f4247 100644 --- a/gnu/packages/web.scm +++ b/gnu/packages/web.scm @@ -1415,8 +1415,7 @@ style API.") (add-after 'patch-source-shebangs 'patch-tests (lambda _ (substitute* "test/parsing/run_tests.sh" - (("`which echo`") (which "echo"))) - #t))))) + (("`which echo`") (which "echo")))))))) (home-page "https://lloyd.github.io/yajl/") (synopsis "C library for parsing JSON") (description From 776632c0be107efcb0fb83d3d4ac4a7282acea97 Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Sun, 4 Dec 2022 01:00:02 +0100 Subject: [PATCH 042/790] gnu: yajl: Improve description. * gnu/packages/web.scm (yajl)[synopsis, description]: Edit. Mark up. Note generator. --- gnu/packages/web.scm | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/gnu/packages/web.scm b/gnu/packages/web.scm index f6e07f4247..d59a5c0a3c 100644 --- a/gnu/packages/web.scm +++ b/gnu/packages/web.scm @@ -1417,10 +1417,10 @@ style API.") (substitute* "test/parsing/run_tests.sh" (("`which echo`") (which "echo")))))))) (home-page "https://lloyd.github.io/yajl/") - (synopsis "C library for parsing JSON") + (synopsis "C library for parsing and generating JSON") (description - "Yet Another JSON Library (YAJL) is a small event-driven (SAX-style) JSON -parser written in ANSI C and a small validating JSON generator.") + "@acronym{YAJL, Yet Another JSON Library} is a small event-driven +(SAX-style) JSON parser and validating generator written in ANSI C.") (license license:isc))) (define-public libyajl From 6bb9424f22239a0a2f50133f8051c635bf9a409a Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Sun, 4 Dec 2022 01:00:00 +0100 Subject: [PATCH 043/790] .guix-authorizations: Authorise John Kehayias. * .guix-authorizations (podiki): Add OpenPGP key fingerprint. --- .guix-authorizations | 3 +++ 1 file changed, 3 insertions(+) diff --git a/.guix-authorizations b/.guix-authorizations index b42448449c..24db547d98 100644 --- a/.guix-authorizations +++ b/.guix-authorizations @@ -90,6 +90,9 @@ (;; primary: "B68B DF22 73F9 DA0E 63C1 8A32 515B F416 9242 D600" "C699 ED09 E51B CE89 FD1D A078 AAC7 E891 896B 568A" (name "pgarlick")) + (;; primary: "7E9F 5BF6 1680 4367 127B 7A87 F9E6 9FB8 5A75 54F1" + "A420 7B56 C255 109F 2CB3 157E 4990 97AE 5EA8 15D9" + (name "podiki")) ("CD2D 5EAA A98C CB37 DA91 D6B0 5F58 1664 7F8B E551" (name "raghavgururajan")) ("BCA6 89B6 3655 3801 C3C6 2150 197A 5888 235F ACAC" From 97b36ca4d3ab99190962a90da9627d559475dbd9 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?M=C4=83d=C4=83lin=20Ionel=20Patra=C8=99cu?= Date: Mon, 5 Dec 2022 16:21:51 +0100 Subject: [PATCH 044/790] gnu: Add r-makecdfenv. * gnu/packages/bioconductor.scm (r-makecdfenv): New variable. --- gnu/packages/bioconductor.scm | 27 +++++++++++++++++++++++++++ 1 file changed, 27 insertions(+) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index c62c5970b8..1d1aae322c 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -6010,6 +6010,33 @@ reduction (between group analysis) and joint dimension reduction of two datasets (coinertia analysis).") (license license:artistic2.0))) +(define-public r-makecdfenv + (package + (name "r-makecdfenv") + (version "1.74.0") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "makecdfenv" version)) + (sha256 + (base32 + "0bvj5dg6yfjnhga1z8788zmb98d8shyz8pzz0ggnml87c1p2gy25")))) + (properties `((upstream-name . "makecdfenv"))) + (build-system r-build-system) + (inputs (list zlib)) + (propagated-inputs + (list r-affy + r-affyio + r-biobase + r-zlibbioc)) + (home-page "https://bioconductor.org/packages/makecdfenv") + (synopsis "Chip description file environment maker") + (description + "This package implements two functions. One of them reads an Affymetrix +@acronym{CDF, chip description file} and creates a hash table environment +containing the location/probe set membership mapping. The other one creates a +package that automatically loads that environment.") + (license license:gpl2+))) + (define-public r-metaneighbor (package (name "r-metaneighbor") From 85d5ce49015dfd93c1b3d37cafe83d017eedcfd4 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?M=C4=83d=C4=83lin=20Ionel=20Patra=C8=99cu?= Date: Mon, 5 Dec 2022 16:21:52 +0100 Subject: [PATCH 045/790] gnu: Add r-altcdfenvs. * gnu/packages/bioconductor.scm (r-altcdfenvs): New variable. --- gnu/packages/bioconductor.scm | 31 +++++++++++++++++++++++++++++++ 1 file changed, 31 insertions(+) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 1d1aae322c..fbd23d0f6d 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -2492,6 +2492,37 @@ mapped reads). It is currently designed for un-stranded paired-end RNA-seq data.") (license license:gpl2+))) +(define-public r-altcdfenvs + (package + (name "r-altcdfenvs") + (version "2.60.0") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "altcdfenvs" version)) + (sha256 + (base32 + "0fm4l93j6nm1w1w57zzryc1hkzapp8l16pkwjzdzllvwvsnsg8r0")))) + (properties `((upstream-name . "altcdfenvs"))) + (build-system r-build-system) + (propagated-inputs + (list r-affy + r-biobase + r-biocgenerics + r-biostrings + r-hypergraph + r-makecdfenv + r-s4vectors)) + (home-page "https://bioconductor.org/packages/altcdfenvs") + (synopsis + "Convenience data structures and functions to handle CDF environments") + (description + "The package is usable with Affymetrix GeneChip short oligonucleotide +arrays, and it can be adapted or extended to other platforms. It is able to +modify or replace the grouping of probes in the probe sets. Also, the package +contains simple functions to read R connections in the FASTA format and it can +create an alternative mapping from sequences.") + (license license:gpl2+))) + (define-public r-aneufinder (package (name "r-aneufinder") From 8363719476f9bf5e4170435ad89d71f595d85853 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?M=C4=83d=C4=83lin=20Ionel=20Patra=C8=99cu?= Date: Mon, 5 Dec 2022 16:21:53 +0100 Subject: [PATCH 046/790] gnu: Add r-harshlight. * gnu/packages/bioconductor.scm (r-harshlight): New variable. --- gnu/packages/bioconductor.scm | 27 +++++++++++++++++++++++++++ 1 file changed, 27 insertions(+) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index fbd23d0f6d..07f8f658f4 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -5854,6 +5854,33 @@ testing and other simple calculations.") Enrichment Analysis} (GSEA).") (license license:artistic2.0))) +(define-public r-harshlight + (package + (name "r-harshlight") + (version "1.70.0") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "Harshlight" version)) + (sha256 + (base32 + "0asjgcnwawg8x7ql0srhb2011rvb4kr2cpsa1cy28nfmjfvdf0qm")))) + (properties `((upstream-name . "Harshlight"))) + (build-system r-build-system) + (propagated-inputs + (list r-affy + r-altcdfenvs + r-biobase)) + (home-page "http://asterion.rockefeller.edu/Harshlight/") + (synopsis "Corrective make-up program for microarray chips") + (description + "The package detects extended diffuse and compact blemishes on microarray +chips. Harshlight marks the areas in a collection of chips (affybatch +objects). A corrected @code{AffyBatch} object will result. The package +replaces the defected areas with @code{N/A}s or the median of the values of +the same probe. The new version handles the substitute value as a whole +matrix to solve the memory problem.") + (license license:gpl2+))) + (define-public r-hpar (package (name "r-hpar") From ec2388d6b4f4aa8973855987163c90d1f13f62b9 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?M=C4=83d=C4=83lin=20Ionel=20Patra=C8=99cu?= Date: Mon, 5 Dec 2022 18:27:24 +0100 Subject: [PATCH 047/790] gnu: Add r-clustercrit. * gnu/packages/cran.scm (r-clustercrit): New variable. --- gnu/packages/cran.scm | 24 ++++++++++++++++++++++++ 1 file changed, 24 insertions(+) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 5c5258d6e0..bf2bba2412 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -14094,6 +14094,30 @@ problems into least squares ones first.") exact and interval-censored observations.") (license license:gpl2+))) +(define-public r-clustercrit + (package + (name "r-clustercrit") + (version "1.2.8") + (source (origin + (method url-fetch) + (uri (cran-uri "clusterCrit" version)) + (sha256 + (base32 + "10pz1bikdbkm2ky3xnagp0qv60whalavp6j39b4p7d75jj5xcxgk")))) + (properties `((upstream-name . "clusterCrit"))) + (build-system r-build-system) + (native-inputs (list gfortran)) + (home-page "https://www.r-project.org/") + (synopsis "Computing clustering validation indices") + (description + "The @code{clusterCrit} package provides an implementation of the +following indices: Czekanowski-Dice, Folkes-Mallows, Hubert Γ, Jaccard, +McNemar, Kulczynski, Phi, Rand, Rogers-Tanimoto, Russel-Rao or Sokal-Sneath. +ClusterCrit defines several functions which compute internal quality indices +or external comparison indices. The partitions are specified as an integer +vector giving the index of the cluster each observation belongs to.") + (license license:gpl2+))) + (define-public r-clusteval (package (name "r-clusteval") From 84392cd0246ac0b5c6e5e9a6ff85130fc766ef26 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?M=C4=83d=C4=83lin=20Ionel=20Patra=C8=99cu?= Date: Mon, 5 Dec 2022 18:27:25 +0100 Subject: [PATCH 048/790] gnu: Add r-waffle. * gnu/packages/cran.scm (r-waffle): New variable. --- gnu/packages/cran.scm | 29 +++++++++++++++++++++++++++++ 1 file changed, 29 insertions(+) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index bf2bba2412..0cffa61246 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -15146,6 +15146,35 @@ Processing.") "This package provides a framework for text mining applications within R.") (license license:gpl3))) +(define-public r-waffle + (package + (name "r-waffle") + (version "0.7.0") + (source (origin + (method url-fetch) + (uri (cran-uri "waffle" version)) + (sha256 + (base32 + "1qjmai33p96cyavi9lgi6k30h6fj7db5sr569v9jf4kwx92c61df")))) + (properties `((upstream-name . "waffle"))) + (build-system r-build-system) + (propagated-inputs + (list r-extrafont + r-ggplot2 + r-gridextra + r-gtable + r-rcolorbrewer)) + (home-page "https://github.com/hrbrmstr/waffle/tree/cran") + (synopsis "Creating waffle chart visualizations in R") + (description + "This package creates square pie charts also known as waffle charts. +These can be used to communicate parts of a whole for categorical quantities. +To emulate the percentage view of a pie chart, a 10x10 grid should be used. +In this way each square is representing 1% of the total. Waffle provides +tools to create charts as well as stitch them together. Isotype pictograms +can be made by using glyphs.") + (license license:gpl2+))) + (define-public r-waveslim (package (name "r-waveslim") From 5fb5af5658b7575a945579a7cf51c193600b76bb Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?M=C4=83d=C4=83lin=20Ionel=20Patra=C8=99cu?= Date: Mon, 5 Dec 2022 18:27:26 +0100 Subject: [PATCH 049/790] gnu: Add r-amplican. * gnu/packages/bioconductor.scm (r-amplican): New variable. --- gnu/packages/bioconductor.scm | 47 +++++++++++++++++++++++++++++++++++ 1 file changed, 47 insertions(+) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 07f8f658f4..85c07605ca 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -2202,6 +2202,53 @@ conditions or various species. @code{AMOUNTAIN} aims to search active modules in multi-layer WGCN using a continuous optimization approach.") (license license:gpl2+))) +(define-public r-amplican + (package + (name "r-amplican") + (version "1.20.0") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "amplican" version)) + (sha256 + (base32 + "1c990i6gxbarcpbdpkz017x94spwzap95l95synlizbkyif4z8ij")))) + (properties `((upstream-name . "amplican"))) + (build-system r-build-system) + (propagated-inputs + (list r-biocgenerics + r-biocparallel + r-biostrings + r-clustercrit + r-data-table + r-dplyr + r-genomeinfodb + r-genomicranges + r-ggplot2 + r-ggthemes + r-gridextra + r-gtable + r-iranges + r-knitr + r-matrix + r-matrixstats + r-rcpp + r-rmarkdown + r-s4vectors + r-shortread + r-stringr + r-waffle)) + (native-inputs (list r-knitr)) + (home-page "https://github.com/valenlab/amplican") + (synopsis "Automated analysis of CRISPR experiments") + (description + "The package performs alignment of the amplicon reads, normalizes +gathered data, calculates multiple statistics (e.g. cut rates, frameshifts) +and presents the results in the form of aggregated reports. Data and +statistics can be broken down by experiments, barcodes, user defined groups, +guides and amplicons allowing for quick identification of potential +problems.") + (license license:gpl3))) + (define-public r-amaretto (package (name "r-amaretto") From 8d2222fac6d1adf99cef4ead7389f86d4a6b77a8 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?M=C4=83d=C4=83lin=20Ionel=20Patra=C8=99cu?= Date: Wed, 7 Dec 2022 06:18:26 +0100 Subject: [PATCH 050/790] gnu: Add r-statip. * gnu/packages/cran.scm (r-statip): New variable. --- gnu/packages/cran.scm | 31 +++++++++++++++++++++++++++++++ 1 file changed, 31 insertions(+) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 0cffa61246..16329b5871 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -6452,6 +6452,37 @@ color labels, layout, etc.") ;; Any version of the GPL (license license:gpl2+))) +(define-public r-statip + (package + (name "r-statip") + (version "0.2.3") + (source (origin + (method url-fetch) + (uri (cran-uri "statip" version)) + (sha256 + (base32 + "0kymc3ds1nx0h11ffmm3vmqr1w34gd0k788vf72x2v45h8c1ma2n")))) + (properties `((upstream-name . "statip"))) + (build-system r-build-system) + (propagated-inputs + (list r-clue r-rpart)) + (home-page "https://github.com/paulponcet/statip") + (synopsis "Statistical functions for probability distributions and regression") + (description + "This package provides a collection of miscellaneous statistical +functions for: +@itemize +@item probability distributions, +@item probability density estimation, +@item most frequent value estimation, +@item other statistical measures of location, +@item construction of histograms, +@item calculation of the Hellinger distance, +@item use of classical kernels, and +@item univariate piecewise-constant regression. +@end itemize") + (license license:gpl3))) + (define-public r-stringdist (package (name "r-stringdist") From 977a15d8e8e85c1cf074df4a28b9923a8827d959 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?M=C4=83d=C4=83lin=20Ionel=20Patra=C8=99cu?= Date: Wed, 7 Dec 2022 06:18:27 +0100 Subject: [PATCH 051/790] gnu: Add r-rmutil. * gnu/packages/cran.scm (r-rmutil): New variable. --- gnu/packages/cran.scm | 23 +++++++++++++++++++++++ 1 file changed, 23 insertions(+) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 16329b5871..46652a7d13 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -16280,6 +16280,29 @@ functions. To this end, the package interfaces with the @dfn{Multiple Precision Floating-Point Reliable} (MPFR) library.") (license license:gpl2+))) +(define-public r-rmutil + (package + (name "r-rmutil") + (version "1.1.10") + (source (origin + (method url-fetch) + (uri (cran-uri "rmutil" version)) + (sha256 + (base32 + "1yd5gkg4jg3rvqrfl8c5r07lcr37n1p9h1a7b6s45iswd77dg7w1")))) + (properties `((upstream-name . "rmutil"))) + (build-system r-build-system) + (native-inputs (list gfortran)) + (home-page "https://www.commanster.eu/rcode.html") + (synopsis + "Utilities for nonlinear regression and repeated measurements models") + (description + "This package provides a toolkit of functions for nonlinear regression +and repeated measurements. It was designated to be imported by other packages +such as @code{gnlm}, @code{stable}, @code{growth}, @code{repeated}, and +@code{event}.") + (license license:gpl2+))) + (define-public r-assertive-base (package (name "r-assertive-base") From 9c81ab8b3930a45277fdc2aad086120f47350421 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?M=C4=83d=C4=83lin=20Ionel=20Patra=C8=99cu?= Date: Wed, 7 Dec 2022 06:18:28 +0100 Subject: [PATCH 052/790] gnu: Add r-stable. * gnu/packages/cran.scm (r-stable): New variable. --- gnu/packages/cran.scm | 22 ++++++++++++++++++++++ 1 file changed, 22 insertions(+) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 46652a7d13..90dd74e0c2 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -6452,6 +6452,28 @@ color labels, layout, etc.") ;; Any version of the GPL (license license:gpl2+))) +(define-public r-stable + (package + (name "r-stable") + (version "1.1.6") + (source (origin + (method url-fetch) + (uri (cran-uri "stable" version)) + (sha256 + (base32 + "194xsa291v5f0jya1c3aigbclg8cci427ffpb8brxamm6n57hf12")))) + (properties `((upstream-name . "stable"))) + (build-system r-build-system) + (propagated-inputs (list r-rmutil)) + (home-page "https://www.commanster.eu/rcode.html") + (synopsis + "Probability functions and regression models for stable distributions") + (description + "This package provides density, distribution, quantile and hazard +functions of a stable variate, as well as generalized regression models for +the parameters of a stable distribution.") + (license license:gpl2+))) + (define-public r-statip (package (name "r-statip") From 9e03e01aae3ef338af879be229a0a0741ccd5704 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?M=C4=83d=C4=83lin=20Ionel=20Patra=C8=99cu?= Date: Wed, 7 Dec 2022 06:18:29 +0100 Subject: [PATCH 053/790] gnu: Add r-gss. * gnu/packages/cran.scm (r-gss): New variable. --- gnu/packages/cran.scm | 20 ++++++++++++++++++++ 1 file changed, 20 insertions(+) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 90dd74e0c2..04dcf8d5c9 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -7224,6 +7224,26 @@ distributions over time or space. This package enables the creation of such plots in @code{ggplot2}.") (license license:gpl2))) +(define-public r-gss + (package + (name "r-gss") + (version "2.2-3") + (source (origin + (method url-fetch) + (uri (cran-uri "gss" version)) + (sha256 + (base32 + "0jr45lkpcndg5nynjsfnxn1wwkh4gkhsgv4hlvw6jn2frw0n8c14")))) + (properties `((upstream-name . "gss"))) + (build-system r-build-system) + (native-inputs (list gfortran)) + (home-page "https://cran.r-project.org/package=gss") + (synopsis "General smoothing splines") + (description + "This package provides a comprehensive collection for structural +multivariate function estimation using smoothing splines.") + (license license:gpl2+))) + (define-public r-cli (package (name "r-cli") From 3e6e0696cc67e2fb98de30c2b9fb334273e09a85 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?M=C4=83d=C4=83lin=20Ionel=20Patra=C8=99cu?= Date: Wed, 7 Dec 2022 06:18:30 +0100 Subject: [PATCH 054/790] gnu: Add r-timeseries. * gnu/packages/cran.scm (r-timeseries): New variable. --- gnu/packages/cran.scm | 22 ++++++++++++++++++++++ 1 file changed, 22 insertions(+) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 04dcf8d5c9..dbde13d912 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -7353,6 +7353,28 @@ standard output and error of the processes, using non-blocking connections. timeout. It can also poll several processes at once.") (license license:expat))) +(define-public r-timeseries + (package + (name "r-timeseries") + (version "4021.105") + (source (origin + (method url-fetch) + (uri (cran-uri "timeSeries" version)) + (sha256 + (base32 + "1k6vihbs20m7zjrxh13y9mmsvnia3844c7j13p0b7m5i9fb6rqxz")))) + (properties `((upstream-name . "timeSeries"))) + (build-system r-build-system) + (propagated-inputs (list r-timedate)) + (home-page + "https://r-forge.r-project.org/scm/viewvc.php/pkg/timeSeries/?root=rmetrics") + (synopsis "Metrics for financial time series objects") + (description + "This package implements S4 classes and various tools for financial time +series. Basic functions such as scaling and sorting, subsetting, mathematical +operations and statistical functions are provided.") + (license license:gpl2+))) + (define-public r-tsp (package (name "r-tsp") From 7ec230fe12853c2136faafc68690ffcb6eeb4cf7 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?M=C4=83d=C4=83lin=20Ionel=20Patra=C8=99cu?= Date: Wed, 7 Dec 2022 06:18:31 +0100 Subject: [PATCH 055/790] gnu: Add r-fbasics. * gnu/packages/cran.scm (r-fbasics): New variable. --- gnu/packages/cran.scm | 31 +++++++++++++++++++++++++++++++ 1 file changed, 31 insertions(+) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index dbde13d912..112190ee21 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -8360,6 +8360,37 @@ functions and random generation functions for a large number of univariate and multivariate distributions.") (license license:gpl2))) +(define-public r-fbasics + (package + (name "r-fbasics") + (version "4021.93") + (source (origin + (method url-fetch) + (uri (cran-uri "fBasics" version)) + (sha256 + (base32 + "1lmmdwzvqhggy6rr7yc9y5f8hxxgyzsgwm3ry0sz5ljbgfijl7g6")))) + (properties `((upstream-name . "fBasics"))) + (build-system r-build-system) + (propagated-inputs + (list r-gss + r-mass + r-spatial + r-stabledist + r-timedate + r-timeseries)) + (home-page + "https://r-forge.r-project.org/scm/viewvc.php/pkg/fBasics/?root=rmetrics") + (synopsis "Metrics for markets and basic statistics") + (description + "This package provides a collection of functions to explore and to +investigate basic properties of financial returns and related quantities. The +covered fields include techniques of explorative data analysis and the +investigation of distributional properties, including parameter estimation and +hypothesis testing. Even more, there are several utility functions for data +handling and management.") + (license license:gpl2+))) + (define-public r-fractal (package (name "r-fractal") From e99b3c0d257c47b16d27e13e02871d81f1d45ada Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?M=C4=83d=C4=83lin=20Ionel=20Patra=C8=99cu?= Date: Wed, 7 Dec 2022 06:18:32 +0100 Subject: [PATCH 056/790] gnu: Add r-modeest. * gnu/packages/cran.scm (r-modeest): New variable. --- gnu/packages/cran.scm | 25 +++++++++++++++++++++++++ 1 file changed, 25 insertions(+) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 112190ee21..2f545f34f8 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -31100,6 +31100,31 @@ expressive statistical grammar that coheres with the Tidy design framework.") model-related packages.") (license license:expat))) +(define-public r-modeest + (package + (name "r-modeest") + (version "2.4.0") + (source (origin + (method url-fetch) + (uri (cran-uri "modeest" version)) + (sha256 + (base32 + "087dw0013y4m7fcl06mxylh9lnp6acysl80d80r9srv4pw4r950s")))) + (properties `((upstream-name . "modeest"))) + (build-system r-build-system) + (propagated-inputs + (list r-fbasics + r-stable + r-stabledist + r-statip)) + (home-page "https://github.com/paulponcet/modeest") + (synopsis "Mode estimations for univariate data or distributions") + (description + "The package provides estimators of the mode of univariate unimodal (and +sometimes multimodal) data and values of the modes of usual probability +distributions.") + (license license:gpl3))) + (define-public r-conflicted (package (name "r-conflicted") From 48e6e6799078a084d637a336067db9cd5f6b2b05 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?M=C4=83d=C4=83lin=20Ionel=20Patra=C8=99cu?= Date: Wed, 7 Dec 2022 06:18:33 +0100 Subject: [PATCH 057/790] gnu: Add r-dirmult. * gnu/packages/cran.scm (r-dirmult): New variable. --- gnu/packages/cran.scm | 19 +++++++++++++++++++ 1 file changed, 19 insertions(+) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 2f545f34f8..613f569cc0 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -399,6 +399,25 @@ visualization of their differences.") (description "This package implements Dirichlet regression models.") (license license:gpl2+))) +(define-public r-dirmult + (package + (name "r-dirmult") + (version "0.1.3-5") + (source (origin + (method url-fetch) + (uri (cran-uri "dirmult" version)) + (sha256 + (base32 + "05whzhl81nyag7321hw98xa63r440s9bgj1764346yvm9bvzjqi4")))) + (properties `((upstream-name . "dirmult"))) + (build-system r-build-system) + (home-page "https://cran.r-project.org/package=dirmult") + (synopsis "Estimation in Dirichlet-Multinomial distribution") + (description + "This package estimates the parameters in Dirichlet-Multinomial and +computes log-likelihoods.") + (license license:gpl2+))) + (define-public r-dixontest (package (name "r-dixontest") From 5154e76a2e6d492419cdbc8338367138a38c4836 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?M=C4=83d=C4=83lin=20Ionel=20Patra=C8=99cu?= Date: Wed, 7 Dec 2022 06:18:34 +0100 Subject: [PATCH 058/790] gnu: Add r-gunifrac. * gnu/packages/cran.scm (r-gunifrac): New variable. --- gnu/packages/cran.scm | 50 +++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 50 insertions(+) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 613f569cc0..eefdc16b4c 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -667,6 +667,56 @@ from CRAN, but also from Bioconductor or even arbitrary git or mercurial repositories, replacing the need for installation via @code{devtools}.") (license license:gpl3+))) +(define-public r-gunifrac + (package + (name "r-gunifrac") + (version "1.7") + (source (origin + (method url-fetch) + (uri (cran-uri "GUniFrac" version)) + (sha256 + (base32 + "13qb5fw9km6p5x8li9x3liqbh833wf2v73npj8jl3msplzfk82vp")))) + (properties `((upstream-name . "GUniFrac"))) + (build-system r-build-system) + (propagated-inputs + (list r-ape + r-dirmult + r-foreach + r-ggplot2 + r-ggrepel + r-mass + r-matrix + r-matrixstats + r-modeest + r-rcpp + r-rmutil + r-statmod + r-vegan)) + (native-inputs (list r-knitr)) + (home-page "https://cran.r-project.org/package=GUniFrac") + (synopsis + "Generalized UniFrac distances and methods for microbiome data analysis") + (description + "This package provides a suite of methods for powerful and robust +microbiome data analysis, including data normalization, data simulation, +community-level association testing and differential abundance analysis. It +implements generalized UniFrac distances, @dfn{Geometric Mean of Pairwise +Ratios} (GMPR) normalization, semiparametric data simulator, distance-based +statistical methods, and feature- based statistical methods. The +distance-based statistical methods include three extensions of PERMANOVA: + +@itemize +@item PERMANOVA using the Freedman-Lane permutation scheme, +@item PERMANOVA omnibus test using multiple matrices, and +@item analytical approach to approximating PERMANOVA p-value. +@end itemize + +Feature-based statistical methods include linear model-based methods for +differential abundance analysis of zero-inflated high-dimensional +compositional data.") + (license license:gpl3))) + (define-public r-ids (package (name "r-ids") From b6873a836c61aa8f8ff28713ea011906eba4a4f1 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?M=C4=83d=C4=83lin=20Ionel=20Patra=C8=99cu?= Date: Wed, 7 Dec 2022 06:18:35 +0100 Subject: [PATCH 059/790] gnu: Add r-gridsvg. * gnu/packages/cran.scm (r-gridsvg): New variable. --- gnu/packages/cran.scm | 24 ++++++++++++++++++++++++ 1 file changed, 24 insertions(+) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index eefdc16b4c..550d220281 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -16061,6 +16061,30 @@ visualization; flexible image manipulation; metadata and sparse image handling.") (license license:gpl2))) +(define-public r-gridsvg + (package + (name "r-gridsvg") + (version "1.7-4") + (source (origin + (method url-fetch) + (uri (cran-uri "gridSVG" version)) + (sha256 + (base32 + "1jspjn56yrkx98hhs98npzm0k0kwpv8x1hg40kphx5ikhvincxmr")))) + (properties `((upstream-name . "gridSVG"))) + (build-system r-build-system) + (propagated-inputs + (list r-jsonlite r-xml)) + (home-page "https://cran.r-project.org/package=gridSVG") + (synopsis "Export grid gaphics as SVG") + (description + "This package provides functions to export graphics drawn with package +grid to SVG format. Extra functions provide access to SVG features that are +not available in standard R graphics, such as hyperlinks, animation, filters, +masks, clipping paths, and gradient and pattern fills.") + ;; Any version of the GPL. + (license (list license:gpl2 license:gpl3)))) + (define-public r-grimport (package (name "r-grimport") From 8f80c99e2bbb8f3025f938a544ffbc598b9d1408 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?M=C4=83d=C4=83lin=20Ionel=20Patra=C8=99cu?= Date: Wed, 7 Dec 2022 06:18:36 +0100 Subject: [PATCH 060/790] gnu: Add r-plotroc. * gnu/packages/cran.scm (r-plotroc): New variable. Co-authored-by: Ricardo Wurmus --- gnu/packages/cran.scm | 51 +++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 51 insertions(+) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 550d220281..2eaeebb3ca 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -21901,6 +21901,57 @@ perspective plots, slice plots, surface plots, scatter plots, etc. It includes data sets from oceanography.") (license license:gpl3+))) +(define-public r-plotroc + (package + (name "r-plotroc") + (version "2.3.0") + (source (origin + (method url-fetch) + (uri (cran-uri "plotROC" version)) + (sha256 + (base32 + "0kaz9hrimi9gi7cf7flag9kc9yrg5fdyylqa5hn53x4dy8vhj37g")) + (snippet + '(delete-file "inst/d3.v3.min.js")))) + (properties `((upstream-name . "plotROC"))) + (build-system r-build-system) + (arguments + (list + #:phases + '(modify-phases %standard-phases + (add-after 'unpack 'process-javascript + (lambda* (#:key inputs #:allow-other-keys) + (let ((source (assoc-ref inputs "d3.v3.js")) + (target "inst/d3.v3.min.js")) + (invoke "esbuild" source "--minify" + (string-append "--outfile=" target)))))))) + (propagated-inputs + (list r-ggplot2 + r-gridsvg + r-plyr + r-rlang + r-shiny)) + (native-inputs + `(("r-knitr" ,r-knitr) + ("esbuild" ,esbuild) + ("d3.v3.js" + ,(origin + (method url-fetch) + (uri "https://d3js.org/d3.v3.js") + (sha256 + (base32 + "1arr7sr08vy7wh0nvip2mi7dpyjw4576vf3bm45rp4g5lc1k1x41")))))) + (home-page "https://sachsmc.github.io/plotROC/") + (synopsis "Generating useful receiver operating characteristic curve charts") + (description + "This package generates @acronym{ROC, receiver operating characteristic} +plots. Most ROC curve plots obscure the cutoff values and inhibit +interpretation and comparison of multiple curves. This attempts to address +those shortcomings by providing plotting and interactive tools. Functions are +provided to generate an interactive ROC curve plot for web use, and print +versions. A Shiny application implementing the functions is also included.") + (license license:expat))) + (define-public r-ggfortify (package (name "r-ggfortify") From e0746ee4c4dab5b4bff9af4cb8b6256ef7888c42 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?M=C4=83d=C4=83lin=20Ionel=20Patra=C8=99cu?= Date: Wed, 7 Dec 2022 06:18:37 +0100 Subject: [PATCH 061/790] gnu: Add r-animalcules. * gnu/packages/bioconductor.scm (r-animalcules): New variable. --- gnu/packages/bioconductor.scm | 59 +++++++++++++++++++++++++++++++++++ 1 file changed, 59 insertions(+) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 85c07605ca..66fa69fade 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -2384,6 +2384,65 @@ Methodologies included in the @code{ANCOMBC} package were designed to correct these biases and construct statistically consistent estimators.") (license license:artistic2.0))) +(define-public r-animalcules + (package + (name "r-animalcules") + (version "1.14.0") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "animalcules" version)) + (sha256 + (base32 + "1alpsamrglgvzhcibkaf7m3gyiv61wbj1gvsq4lw6vjka100j9qr")))) + (properties `((upstream-name . "animalcules"))) + (build-system r-build-system) + (propagated-inputs + (list r-ape + r-assertthat + r-biomformat + r-caret + r-covr + r-deseq2 + r-dplyr + r-dt + r-forcats + r-ggplot2 + r-glmnet + r-gunifrac + r-lattice + r-limma + r-magrittr + r-matrix + r-multiassayexperiment + r-plotly + r-plotroc + r-rentrez + r-reshape2 + r-s4vectors + r-scales + r-shiny + r-shinyjs + r-summarizedexperiment + r-tibble + r-tsne + r-umap + r-vegan + r-xml)) + (native-inputs (list r-knitr)) + (home-page "https://github.com/compbiomed/animalcules") + (synopsis "Interactive microbiome analysis toolkit") + (description + "Animalcules is an R package for utilizing up-to-date data analytics, +visualization methods, and machine learning models to provide users an +easy-to-use interactive microbiome analysis framework. It can be used as a +standalone software package or users can explore their data with the +accompanying interactive R Shiny application. Traditional microbiome analysis +such as alpha/beta diversity and differential abundance analysis are enhanced, +while new methods like biomarker identification are introduced by animalcules. +Powerful interactive and dynamic figures generated by animalcules enable users +to understand their data better and discover new insights.") + (license license:artistic2.0))) + (define-public r-aldex2 (package (name "r-aldex2") From c2d25c7b5ed1bdff7ba62e6f0981ce6f1eb53988 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?M=C4=83d=C4=83lin=20Ionel=20Patra=C8=99cu?= Date: Thu, 8 Dec 2022 20:22:29 +0100 Subject: [PATCH 062/790] gnu: Add r-rcppde. * gnu/packages/cran.scm (r-rcppde): New variable. --- gnu/packages/cran.scm | 21 +++++++++++++++++++++ 1 file changed, 21 insertions(+) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 2eaeebb3ca..cb857e8232 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -4638,6 +4638,27 @@ and Francois (2011, JSS), and the book by Eddelbuettel (2013, Springer); see @code{citation(\"Rcpp\")} for details on these last two.") (license license:gpl2+))) +(define-public r-rcppde + (package + (name "r-rcppde") + (version "0.1.6") + (source (origin + (method url-fetch) + (uri (cran-uri "RcppDE" version)) + (sha256 + (base32 + "1i9jj595nqpb16y22z2b8fcf0gq1fg0pbiisbd837p1cyw4nff69")))) + (properties `((upstream-name . "RcppDE"))) + (build-system r-build-system) + (propagated-inputs + (list r-rcpp r-rcpparmadillo)) + (home-page "https://cran.r-project.org/package=RcppDE") + (synopsis "Global optimization by differential evolution in C++") + (description + "This package provides an iteration of the @code{DEoptim} function. It +performs global optimization by differential evolution.") + (license license:gpl2+))) + (define-public r-rcppml (package (name "r-rcppml") From 1e5c9bb0d212dc4befb63d05e19c17d7de7e95ad Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?M=C4=83d=C4=83lin=20Ionel=20Patra=C8=99cu?= Date: Thu, 8 Dec 2022 20:22:30 +0100 Subject: [PATCH 063/790] gnu: Add r-ptw. * gnu/packages/cran.scm (r-ptw): New variable. --- gnu/packages/cran.scm | 27 +++++++++++++++++++++++++++ 1 file changed, 27 insertions(+) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index cb857e8232..2fdc626ad5 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -4922,6 +4922,33 @@ approach is used to estimate the lower cut-off for the scaling region.") ;; Any of these GPL versions. (license (list license:gpl2 license:gpl3)))) +(define-public r-ptw + (package + (name "r-ptw") + (version "1.9-16") + (source (origin + (method url-fetch) + (uri (cran-uri "ptw" version)) + (sha256 + (base32 + "0rma3h9ksc5qigdvk5vappb4ipd4rpk64wckzcxvxspakr5w71vy")))) + (properties `((upstream-name . "ptw"))) + (build-system r-build-system) + (propagated-inputs (list r-rcppde)) + (home-page "https://github.com/rwehrens/ptw") + (synopsis "Parametric time warping") + (description + "Parametric time warping aligns patterns. It aims to put corresponding +features at the same locations. The algorithm searches for an optimal +polynomial describing the warping. It is possible to align one sample to a +reference, several samples to the same reference, or several samples to +several references. One can choose between calculating individual warpings, +or one global warping for a set of samples and one reference. Two +optimization criteria are implemented: @acronym{RMS, Root Mean Square} error +and @acronym{WCC, Weighted Cross Correlation}. Both warping of peak profiles +and of peak lists are supported.") + (license license:gpl2+))) + (define-public r-compare (package (name "r-compare") From 061ce5500abcaaf67c9e0cf09f8a881525a4fdef Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?M=C4=83d=C4=83lin=20Ionel=20Patra=C8=99cu?= Date: Thu, 8 Dec 2022 20:22:31 +0100 Subject: [PATCH 064/790] gnu: Add r-pepsnmr. * gnu/packages/bioconductor.scm (r-pepsnmr): New variable. --- gnu/packages/bioconductor.scm | 29 +++++++++++++++++++++++++++++ 1 file changed, 29 insertions(+) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 66fa69fade..1ceee9d77d 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -8514,6 +8514,35 @@ classification and ranking tasks. @dfn{Area under curve} (AUC), precision at a given recall, F-score for single and multiple classes are available.") (license license:gpl2+))) +(define-public r-pepsnmr + (package + (name "r-pepsnmr") + (version "1.16.0") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "PepsNMR" version)) + (sha256 + (base32 + "02i29jinawssqlb33wvj0h9w6cfcvamlyfxdynd38jmwx23l15l5")))) + (properties `((upstream-name . "PepsNMR"))) + (build-system r-build-system) + (propagated-inputs + (list r-ggplot2 + r-gridextra + r-matrix + r-matrixstats + r-ptw + r-reshape2)) + (native-inputs (list r-knitr)) + (home-page "https://github.com/ManonMartin/PepsNMR") + (synopsis "Pre-process 1H-NMR FID signals") + (description + "This package provides R functions for common pre-processing steps that +are applied on @acronym{1H-NMR, proton nuclear magnetic resonance} data. It +also provides a function to read the @acronym{FID, free induction decay} +signals directly in the Bruker format.") + (license license:gpl2))) + ;; This is a CRAN package, but it depends on a Bioconductor package. (define-public r-codedepends (package From b9014985beb92d040b7da195353b405c7c768378 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?M=C4=83d=C4=83lin=20Ionel=20Patra=C8=99cu?= Date: Thu, 8 Dec 2022 20:22:32 +0100 Subject: [PATCH 065/790] gnu: Add r-asics. * gnu/packages/bioconductor.scm (r-asics): New variable. --- gnu/packages/bioconductor.scm | 34 ++++++++++++++++++++++++++++++++++ 1 file changed, 34 insertions(+) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 1ceee9d77d..ec1bbb99d1 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -2857,6 +2857,40 @@ biological knowledge. Genes, and clinical pathways are incorporated in the model as latent variables.") (license license:gpl3))) +(define-public r-asics + (package + (name "r-asics") + (version "2.14.0") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "ASICS" version)) + (sha256 + (base32 + "0c2b3gdza58vqhharhw8967p2w2knnrm5s2svvnnjbf67qbg45b7")))) + (properties `((upstream-name . "ASICS"))) + (build-system r-build-system) + (propagated-inputs + (list r-biocparallel + r-ggplot2 + r-glmnet + r-gridextra + r-matrix + r-mvtnorm + r-pepsnmr + r-plyr + r-quadprog + r-ropls + r-summarizedexperiment + r-zoo)) + (native-inputs (list r-knitr)) + (home-page "https://bioconductor.org/packages/ASICS") + (synopsis "Automatic statistical identification in complex spectra") + (description + "ASICS quantifies concentration of metabolites in a complex spectrum. +The identification of metabolites is performed by fitting a mixture model to +the spectra of the library with a sparse penalty.") + (license license:gpl2+))) + (define-public r-aspli (package (name "r-aspli") From ca7141234d0268a55ee1e06d00cb7ed952451745 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?M=C4=83d=C4=83lin=20Ionel=20Patra=C8=99cu?= Date: Thu, 8 Dec 2022 22:13:16 +0100 Subject: [PATCH 066/790] gnu: Add r-logging. * gnu/packages/cran.scm (r-logging): New variable. --- gnu/packages/cran.scm | 20 ++++++++++++++++++++ 1 file changed, 20 insertions(+) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 2fdc626ad5..7d069dcf49 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -17157,6 +17157,26 @@ Lumley & Pepe (Biometrics, Vol 56 No 2, 2000, PP 337-344)") discovery rates.") (license license:gpl2))) +(define-public r-logging + (package + (name "r-logging") + (version "0.10-108") + (source (origin + (method url-fetch) + (uri (cran-uri "logging" version)) + (sha256 + (base32 + "13gd40ygx586vs6xcp6clg69a92aj8zxlk1rn3xzkx8klfjimjc5")))) + (properties `((upstream-name . "logging"))) + (build-system r-build-system) + (home-page "https://github.com/WLOGSolutions/r-logging") + (synopsis "R logging implementation of log4j") + (description + "This package implements the R version of the @code{log4j} package. It offers +hierarchic loggers, multiple handlers per logger, level based filtering, space +handling in messages and custom formatting.") + (license license:gpl3))) + (define-public r-longitudinal (package (name "r-longitudinal") From 61124bc7b0b03dd9c1208446109e91fbc147bc03 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?M=C4=83d=C4=83lin=20Ionel=20Patra=C8=99cu?= Date: Thu, 8 Dec 2022 22:13:17 +0100 Subject: [PATCH 067/790] gnu: Add r-shinycustomloader. * gnu/packages/cran.scm (r-shinycustomloader): New variable. --- gnu/packages/cran.scm | 23 +++++++++++++++++++++++ 1 file changed, 23 insertions(+) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 7d069dcf49..d904e5d00e 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -17808,6 +17808,29 @@ intersecting sets using a novel matrix design, along with visualizations of several common set, element and attribute related tasks.") (license license:expat))) +(define-public r-shinycustomloader + (package + (name "r-shinycustomloader") + (version "0.9.0") + (source (origin + (method url-fetch) + (uri (cran-uri "shinycustomloader" version)) + (sha256 + (base32 + "1klx71vr26g0gjf6hbiia1qidqii5d467i1sdjvlrg1hxdcggqff")))) + (properties `((upstream-name . "shinycustomloader"))) + (build-system r-build-system) + (propagated-inputs + (list r-glue + r-shiny)) + (home-page "https://cran.r-project.org/package=shinycustomloader") + (synopsis "Custom loader for Shiny outputs") + (description + "This package provides a custom @code{CSS/HTML} or @code{GIF/image} file +for the loading screen in R @code{Shiny}. It also can use the marquee to have +a custom text loading screen.") + (license license:gpl3))) + ;; This package includes a JavaScript file, which is not minified. When ;; upgrading please check that there are no new minified JavaScript files. (define-public r-shinybs From 75a9ee5b8e59ac02b6ab8051bd30fbb7454e509c Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?M=C4=83d=C4=83lin=20Ionel=20Patra=C8=99cu?= Date: Thu, 8 Dec 2022 22:13:18 +0100 Subject: [PATCH 068/790] gnu: Add r-anytime. * gnu/packages/cran.scm (r-anytime): New variable. --- gnu/packages/cran.scm | 24 ++++++++++++++++++++++++ 1 file changed, 24 insertions(+) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index d904e5d00e..6623636e2c 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -25878,6 +25878,30 @@ They are based on clustering, the statistical concept of data depth, statistical shape analysis and archetypal analysis.") (license license:gpl2+))) +(define-public r-anytime + (package + (name "r-anytime") + (version "0.3.9") + (source (origin + (method url-fetch) + (uri (cran-uri "anytime" version)) + (sha256 + (base32 + "0jjpqynai5nd7mfy1smb44356f3d5bmpxhs1i9x9jw5c959c35hh")))) + (properties `((upstream-name . "anytime"))) + (build-system r-build-system) + (propagated-inputs + (list r-bh + r-rcpp)) + (home-page "http://dirk.eddelbuettel.com/code/anytime.html") + (synopsis "Converter of input to POSIXct or Date") + (description + "The package converts the input in any one of character, integer, numeric, +factor, or an ordered type into @code{POSIXct} (or @code{Date}) objects, using +one of a number of predefined formats, and relying on Boost facilities for date +and time parsing.") + (license license:gpl2+))) + (define-public r-anndata (package (name "r-anndata") From 79ecb5f35f1ec7d5885fd159a13a206fce23c225 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?M=C4=83d=C4=83lin=20Ionel=20Patra=C8=99cu?= Date: Thu, 8 Dec 2022 22:13:20 +0100 Subject: [PATCH 069/790] gnu: Add r-attempt. * gnu/packages/cran.scm (r-attempt): New variable. --- gnu/packages/cran.scm | 25 +++++++++++++++++++++++++ 1 file changed, 25 insertions(+) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 6623636e2c..2588bd9238 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -7425,6 +7425,31 @@ information} (NMI), @dfn{adjusted mutual information} (AMI), @dfn{normalized variation information} (NVI) and entropy.") (license license:gpl3+))) +(define-public r-attempt + (package + (name "r-attempt") + (version "0.3.1") + (source (origin + (method url-fetch) + (uri (cran-uri "attempt" version)) + (sha256 + (base32 + "1ylgg7jcp8wqmxgf1mydnvh26k0mr8jyjla4hw06730r40yrs58m")))) + (properties `((upstream-name . "attempt"))) + (build-system r-build-system) + (propagated-inputs (list r-rlang)) + (native-inputs (list r-knitr)) + (home-page "https://github.com/ColinFay/attempt") + (synopsis "Tools for defensive programming") + (description + "This package provides tools for defensive programming. It is inspired +by @code{purrr} mappers and based on @code{rlang}. Attempt extends and +facilitates defensive programming by providing a consistent grammar, and a set +of functions for common tests and conditions. Attempt only depends on +@code{rlang}, and focuses on speed, so it can be integrated with other +functions and used in the data analysis.") + (license license:expat))) + (define-public r-debugme (package (name "r-debugme") From 3640310d6965598e37a6a32363d23b2755a95e8a Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?M=C4=83d=C4=83lin=20Ionel=20Patra=C8=99cu?= Date: Thu, 8 Dec 2022 22:13:21 +0100 Subject: [PATCH 070/790] gnu: Add r-golem. * gnu/packages/cran.scm (r-golem): New variable. --- gnu/packages/cran.scm | 37 +++++++++++++++++++++++++++++++++++++ 1 file changed, 37 insertions(+) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 2588bd9238..340a63cab1 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -11369,6 +11369,43 @@ noncentral hypergeometric distribution (also called extended hypergeometric distribution).") (license license:gpl3))) +(define-public r-golem + (package + (name "r-golem") + (version "0.3.5") + (source (origin + (method url-fetch) + (uri (cran-uri "golem" version)) + (sha256 + (base32 + "0rjkl1r83h0hcn30zssx64qm07sdx3g4v5rdxn56gbzfghw7ddcl")))) + (properties `((upstream-name . "golem"))) + (build-system r-build-system) + (propagated-inputs + (list r-attempt + r-cli + r-config + r-crayon + r-desc + r-fs + r-here + r-htmltools + r-pkgload + r-roxygen2 + r-rstudioapi + r-shiny + r-usethis + r-yaml)) + (native-inputs (list r-knitr)) + (home-page "https://github.com/ThinkR-open/golem") + (synopsis "Framework for robust Shiny applications") + (description + "This package implements an opinionated framework for building a +production- ready Shiny application. Golem contains a series of tools like +dependency management, version management, easy installation and deployment or +documentation management.") + (license license:expat))) + (define-public r-goplot (package (name "r-goplot") From 999783b92d549dfd53a305ad744fcc0048fa2479 Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Mon, 12 Dec 2022 16:41:57 +0100 Subject: [PATCH 071/790] gnu: ungoogled-chromium: Build with ffmpeg@4. This is a follow-up to commit 79564bf9977ebba0b31d8dc291eb039142f51f68. * gnu/packages/chromium.scm (ungoogled-chromium)[inputs]: Change from FFMPEG to FFFMPEG-4. --- gnu/packages/chromium.scm | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/gnu/packages/chromium.scm b/gnu/packages/chromium.scm index 983a754215..299a4edcbe 100644 --- a/gnu/packages/chromium.scm +++ b/gnu/packages/chromium.scm @@ -899,7 +899,7 @@ dbus expat flac - ffmpeg + ffmpeg-4 fontconfig fp16 freetype From 58e33da5f5261bbc3f76fd10b4807ff493ad587c Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Mon, 12 Dec 2022 16:54:29 +0100 Subject: [PATCH 072/790] gnu: f2fs-tools: Reverse inheritance relationship. * gnu/packages/linux.scm (f2fs-tools): Update to 1.14.0. [arguments]: Remove obsolete #:configure-flags and trailing #t in phase. [inputs]: Remove labels. (f2fs-tools-1.7): Inherit from above; add #:configure-flags. [inputs]: Remove labels. --- gnu/packages/linux.scm | 84 +++++++++++++++++++++--------------------- 1 file changed, 42 insertions(+), 42 deletions(-) diff --git a/gnu/packages/linux.scm b/gnu/packages/linux.scm index 9ea77069ca..ad892a332d 100644 --- a/gnu/packages/linux.scm +++ b/gnu/packages/linux.scm @@ -5932,49 +5932,8 @@ uncompressed size will not match the number given by @command{tar} or obviously it can be shared with files outside our set).") (license license:gpl2+))) -(define-public f2fs-tools-1.7 - (package - (name "f2fs-tools") - (version "1.7.0") - (source (origin - (method url-fetch) - (uri (string-append - "https://git.kernel.org/cgit/linux/kernel/git/jaegeuk" - "/f2fs-tools.git/snapshot/f2fs-tools-" version ".tar.gz")) - (sha256 - (base32 - "1m6bn1ibq0p53m0n97il91xqgjgn2pzlz74lb5bfzassx7159m1k")))) - - (build-system gnu-build-system) - (arguments - `(#:configure-flags '("CFLAGS=-fcommon") - #:phases - (modify-phases %standard-phases - (add-after 'install 'install-headers - (lambda* (#:key outputs #:allow-other-keys) - (let* ((out (assoc-ref outputs "out")) - (out-include (string-append out "/include"))) - (install-file "include/f2fs_fs.h" out-include) - (install-file "mkfs/f2fs_format_utils.h" out-include) - #t)))))) - (native-inputs - (list autoconf automake libtool pkg-config)) - (inputs - `(("libuuid" ,util-linux "lib") - ("libselinux" ,libselinux))) - (home-page "https://f2fs.wiki.kernel.org/") - (synopsis "Userland tools for f2fs") - (description - "F2FS, the Flash-Friendly File System, is a modern file system -designed to be fast and durable on flash devices such as solid-state -disks and SD cards. This package provides the userland utilities.") - ;; The formatting utility, libf2fs and include/f2fs_fs.h is dual - ;; GPL2/LGPL2.1, everything else is GPL2 only. See 'COPYING'. - (license (list license:gpl2 license:lgpl2.1)))) - (define-public f2fs-tools (package - (inherit f2fs-tools-1.7) (name "f2fs-tools") (version "1.14.0") (source (origin @@ -5985,8 +5944,49 @@ disks and SD cards. This package provides the userland utilities.") (sha256 (base32 "1lab1446c78xsjwhpki7s85z4171m8p9279c8yhm4882wba674k1")))) + (build-system gnu-build-system) + (arguments + '(#:phases + (modify-phases %standard-phases + (add-after 'install 'install-headers + (lambda* (#:key outputs #:allow-other-keys) + (let* ((out (assoc-ref outputs "out")) + (out-include (string-append out "/include"))) + (install-file "include/f2fs_fs.h" out-include) + (install-file "mkfs/f2fs_format_utils.h" out-include))))))) + (native-inputs + (list autoconf automake libtool pkg-config)) (inputs - `(("libuuid" ,util-linux "lib"))))) + (list `(,util-linux "lib"))) ;for libuuid + (home-page "https://f2fs.wiki.kernel.org/") + (synopsis "Userland tools for f2fs") + (description + "F2FS, the Flash-Friendly File System, is a modern file system +designed to be fast and durable on flash devices such as solid-state +disks and SD cards. This package provides the userland utilities.") + ;; The formatting utility, libf2fs and include/f2fs_fs.h is dual + ;; GPL2/LGPL2.1, everything else is GPL2 only. See 'COPYING'. + (license (list license:gpl2 license:lgpl2.1)))) + +(define-public f2fs-tools-1.7 + (package + (inherit f2fs-tools) + (name "f2fs-tools") + (version "1.7.0") + (source (origin + (method url-fetch) + (uri (string-append + "https://git.kernel.org/cgit/linux/kernel/git/jaegeuk" + "/f2fs-tools.git/snapshot/f2fs-tools-" version ".tar.gz")) + (sha256 + (base32 + "1m6bn1ibq0p53m0n97il91xqgjgn2pzlz74lb5bfzassx7159m1k")))) + (inputs + (list `(,util-linux "lib") libselinux)) + (arguments + (substitute-keyword-arguments (package-arguments f2fs-tools) + ((#:configure-flags _ #~'()) + #~'("CFLAGS=-fcommon")))))) (define-public f2fs-tools/static (static-package From 61f67290b95adb537eebde13251d5c1c2dfc1687 Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Mon, 12 Dec 2022 17:00:11 +0100 Subject: [PATCH 073/790] gnu: f2fs-tools: Don't fetch autogenerated git snapshot. * gnu/packages/linux.scm (f2fs-tools)[source]: Switch to GIT-FETCH. --- gnu/packages/linux.scm | 12 +++++++----- 1 file changed, 7 insertions(+), 5 deletions(-) diff --git a/gnu/packages/linux.scm b/gnu/packages/linux.scm index ad892a332d..485bc6d0f5 100644 --- a/gnu/packages/linux.scm +++ b/gnu/packages/linux.scm @@ -5937,13 +5937,15 @@ obviously it can be shared with files outside our set).") (name "f2fs-tools") (version "1.14.0") (source (origin - (method url-fetch) - (uri (string-append - "https://git.kernel.org/cgit/linux/kernel/git/jaegeuk" - "/f2fs-tools.git/snapshot/f2fs-tools-" version ".tar.gz")) + (method git-fetch) + (uri (git-reference + (url "https://git.kernel.org/pub/scm/linux/kernel\ +/git/jaegeuk/f2fs-tools.git") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) (sha256 (base32 - "1lab1446c78xsjwhpki7s85z4171m8p9279c8yhm4882wba674k1")))) + "06ss05n87i1c3149qb3n7j1qp2scv3g2adx0v6ljkl59ab9b5saj")))) (build-system gnu-build-system) (arguments '(#:phases From e1fc45b3eaaa2d09e3e202aff023b8aea6debbc9 Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Mon, 12 Dec 2022 17:00:33 +0100 Subject: [PATCH 074/790] gnu: f2fs-tools@1.7: Don't fetch autogenerated git snapshot. * gnu/packages/linux.scm (f2fs-tools-1.7)[source]: Switch to GIT-FETCH. --- gnu/packages/linux.scm | 12 +++++++----- 1 file changed, 7 insertions(+), 5 deletions(-) diff --git a/gnu/packages/linux.scm b/gnu/packages/linux.scm index 485bc6d0f5..d483970dbb 100644 --- a/gnu/packages/linux.scm +++ b/gnu/packages/linux.scm @@ -5976,13 +5976,15 @@ disks and SD cards. This package provides the userland utilities.") (name "f2fs-tools") (version "1.7.0") (source (origin - (method url-fetch) - (uri (string-append - "https://git.kernel.org/cgit/linux/kernel/git/jaegeuk" - "/f2fs-tools.git/snapshot/f2fs-tools-" version ".tar.gz")) + (method git-fetch) + (uri (git-reference + (url (git-reference-url + (origin-uri (package-source f2fs-tools)))) + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) (sha256 (base32 - "1m6bn1ibq0p53m0n97il91xqgjgn2pzlz74lb5bfzassx7159m1k")))) + "0wpzklw8smnngng0dm25jdmi7v5zfhpz02dksyxpz0a7kzzvnqqm")))) (inputs (list `(,util-linux "lib") libselinux)) (arguments From a2c6cc43548bd88871772cbc17bae55da9138cb2 Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Mon, 12 Dec 2022 17:03:05 +0100 Subject: [PATCH 075/790] gnu: f2fs-tools: Update to 1.15.0. * gnu/packages/linux.scm (f2fs-tools): Update to 1.15.0. (f2fs-tools/static)[arguments]: Add #:make-flags. Remove make-static phase. --- gnu/packages/linux.scm | 15 +++------------ 1 file changed, 3 insertions(+), 12 deletions(-) diff --git a/gnu/packages/linux.scm b/gnu/packages/linux.scm index d483970dbb..4113e8e981 100644 --- a/gnu/packages/linux.scm +++ b/gnu/packages/linux.scm @@ -5935,7 +5935,7 @@ obviously it can be shared with files outside our set).") (define-public f2fs-tools (package (name "f2fs-tools") - (version "1.14.0") + (version "1.15.0") (source (origin (method git-fetch) (uri (git-reference @@ -5945,7 +5945,7 @@ obviously it can be shared with files outside our set).") (file-name (git-file-name name version)) (sha256 (base32 - "06ss05n87i1c3149qb3n7j1qp2scv3g2adx0v6ljkl59ab9b5saj")))) + "1ffws8pbpzp9730v0wy5xjas698lnbd2p7wpr2gl4mx45rsay9a5")))) (build-system gnu-build-system) (arguments '(#:phases @@ -6008,18 +6008,9 @@ disks and SD cards. This package provides the userland utilities.") "-I" libuuid "/include/blkid") (string-append "libblkid_LIBS=-L" libuuid-static "/lib -lblkid"))) #:disallowed-references (,util-linux) + #:make-flags '("LDFLAGS=-all-static") #:phases (modify-phases %standard-phases ; TODO: f2fs phases. - (add-after 'unpack 'make-static - (lambda _ - (define (append-to-file name body) - (let ((file (open-file name "a"))) - (display body file) - (close-port file))) - (append-to-file "mkfs/Makefile.am" "\nmkfs_f2fs_LDFLAGS = -all-static\n") - (append-to-file "fsck/Makefile.am" "\nfsck_f2fs_LDFLAGS = -all-static\n") - (append-to-file "tools/Makefile.am" "\nf2fscrypt_LDFLAGS = -all-static -luuid\n") - #t)) (add-after 'install 'remove-store-references (lambda* (#:key outputs #:allow-other-keys) ;; Work around bug in our util-linux. From 9fc171b62a4992415803aec76fdb9c3bf9133f75 Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Mon, 12 Dec 2022 17:36:02 +0100 Subject: [PATCH 076/790] gnu: f2fs-tools: Remove obsolete phase. * gnu/packages/linux.scm (f2fs-tools)[arguments]: Remove. (f2fs-tools-1.7)[arguments]: Add #:phases. --- gnu/packages/linux.scm | 21 +++++++++------------ 1 file changed, 9 insertions(+), 12 deletions(-) diff --git a/gnu/packages/linux.scm b/gnu/packages/linux.scm index 4113e8e981..08e6d855eb 100644 --- a/gnu/packages/linux.scm +++ b/gnu/packages/linux.scm @@ -5947,15 +5947,6 @@ obviously it can be shared with files outside our set).") (base32 "1ffws8pbpzp9730v0wy5xjas698lnbd2p7wpr2gl4mx45rsay9a5")))) (build-system gnu-build-system) - (arguments - '(#:phases - (modify-phases %standard-phases - (add-after 'install 'install-headers - (lambda* (#:key outputs #:allow-other-keys) - (let* ((out (assoc-ref outputs "out")) - (out-include (string-append out "/include"))) - (install-file "include/f2fs_fs.h" out-include) - (install-file "mkfs/f2fs_format_utils.h" out-include))))))) (native-inputs (list autoconf automake libtool pkg-config)) (inputs @@ -5988,9 +5979,15 @@ disks and SD cards. This package provides the userland utilities.") (inputs (list `(,util-linux "lib") libselinux)) (arguments - (substitute-keyword-arguments (package-arguments f2fs-tools) - ((#:configure-flags _ #~'()) - #~'("CFLAGS=-fcommon")))))) + '(#:configure-flags '("CFLAGS=-fcommon") + #:phases + (modify-phases %standard-phases + (add-after 'install 'install-headers + (lambda* (#:key outputs #:allow-other-keys) + (let* ((out (assoc-ref outputs "out")) + (out-include (string-append out "/include"))) + (install-file "include/f2fs_fs.h" out-include) + (install-file "mkfs/f2fs_format_utils.h" out-include))))))))) (define-public f2fs-tools/static (static-package From 2c1b488d19831702288b8bdee4cecf661da91b60 Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Mon, 7 Feb 2022 23:14:04 +0100 Subject: [PATCH 077/790] tests: Add system tests for each supported kernel version. * gnu/tests/base.scm (%test-basic-os): Rename to ... (test-basic-os): ... this, and turn into procedure that takes optional KERNEL argument. (%test-basic-os): Use that procedure. (%test-linux-libre-5.15, %test-linux-libre-5.10, %test-linux-libre-5.4, %test-linux-libre-4.19, %test-linux-libre-4.14, %test-linux-libre-4.9): New tests. --- gnu/tests/base.scm | 46 +++++++++++++++++++++++++++++++++++++++++----- 1 file changed, 41 insertions(+), 5 deletions(-) diff --git a/gnu/tests/base.scm b/gnu/tests/base.scm index fe7ca35f60..844039f5f8 100644 --- a/gnu/tests/base.scm +++ b/gnu/tests/base.scm @@ -2,6 +2,7 @@ ;;; Copyright © 2016, 2017, 2018, 2019, 2020, 2022 Ludovic Courtès ;;; Copyright © 2018 Clément Lassieur ;;; Copyright © 2022 Maxim Cournoyer +;;; Copyright © 2022 Marius Bakke ;;; ;;; This file is part of GNU Guix. ;;; @@ -46,10 +47,17 @@ #:use-module (guix monads) #:use-module (guix modules) #:use-module (guix packages) + #:use-module (guix utils) #:use-module ((srfi srfi-1) #:hide (partition)) #:use-module (ice-9 match) #:export (run-basic-test %test-basic-os + %test-linux-libre-5.15 + %test-linux-libre-5.10 + %test-linux-libre-5.4 + %test-linux-libre-4.19 + %test-linux-libre-4.14 + %test-linux-libre-4.9 %test-halt %test-root-unmount %test-cleanup @@ -533,15 +541,20 @@ info --version") (gexp->derivation name test)) -(define %test-basic-os +(define* (test-basic-os #:optional (kernel linux-libre)) (system-test - (name "basic") + (name (if (eq? kernel linux-libre) + "basic" + (string-append (package-name kernel) "-" + (version-major+minor (package-version kernel))))) (description "Instrument %SIMPLE-OS, run it in a VM, and run a series of basic -functionality tests.") +functionality tests, using the given KERNEL.") (value (let* ((os (marionette-operating-system - %simple-os + (operating-system + (inherit %simple-os) + (kernel kernel)) #:imported-modules '((gnu services herd) (guix combinators)))) (vm (virtual-machine os))) @@ -549,7 +562,30 @@ functionality tests.") ;; set of services as the OS produced by ;; 'system-qemu-image/shared-store-script'. (run-basic-test (virtualized-operating-system os '()) - #~(list #$vm)))))) + #~(list #$vm) + name))))) + +(define %test-basic-os + (test-basic-os)) + +;; Ensure the LTS kernels are up to snuff, too. +(define %test-linux-libre-5.15 + (test-basic-os linux-libre-5.15)) + +(define %test-linux-libre-5.10 + (test-basic-os linux-libre-5.10)) + +(define %test-linux-libre-5.4 + (test-basic-os linux-libre-5.4)) + +(define %test-linux-libre-4.19 + (test-basic-os linux-libre-4.19)) + +(define %test-linux-libre-4.14 + (test-basic-os linux-libre-4.14)) + +(define %test-linux-libre-4.9 + (test-basic-os linux-libre-4.9)) ;;; From c1695bcaddf4ae3aaf2992efd64891dce1922c39 Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Mon, 12 Dec 2022 19:03:48 +0100 Subject: [PATCH 078/790] gnu: re2: Update to 2022-12-01. * gnu/packages/regex.scm (re2): Update to 2022-12-01. --- gnu/packages/regex.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/regex.scm b/gnu/packages/regex.scm index 616c56cc6e..7cdee5afd4 100644 --- a/gnu/packages/regex.scm +++ b/gnu/packages/regex.scm @@ -32,7 +32,7 @@ (define-public re2 (package (name "re2") - (version "2022-02-01") + (version "2022-12-01") (home-page "https://github.com/google/re2") (source (origin (method git-fetch) @@ -40,7 +40,7 @@ (file-name (git-file-name name version)) (sha256 (base32 - "1gzdqy5a0ln9rwd8kmwbgis6qin63hapicwb35xkbnj3y84jj6yx")))) + "0g627a5ppyarhf2ph4gyzj89pwbkwfjfajgljzkmjafjmdyxfqs6")))) (build-system gnu-build-system) (arguments (list #:test-target "test" From d5ad3dd59aeeffd15a6b4c6fac1b12396d4342ff Mon Sep 17 00:00:00 2001 From: Christopher Baines Date: Mon, 12 Dec 2022 19:58:25 +0000 Subject: [PATCH 079/790] services: guix-build-coordinator: Fix service startup. Previously the service would keep starting more and more processes. * gnu/services/guix.scm (guix-build-coordinator-shepherd-services): Fix how make-forkexec-constructor is called. --- gnu/services/guix.scm | 48 +++++++++++++++++++++---------------------- 1 file changed, 24 insertions(+), 24 deletions(-) diff --git a/gnu/services/guix.scm b/gnu/services/guix.scm index 486d9f49d7..65bf0b5a7f 100644 --- a/gnu/services/guix.scm +++ b/gnu/services/guix.scm @@ -336,30 +336,30 @@ (start #~(lambda args (parameterize ((%current-logfile-date-format "")) (apply - make-forkexec-constructor - (list #$(make-guix-build-coordinator-start-script - database-uri-string - allocation-strategy - "/var/run/guix-build-coordinator/pid" - package - #:agent-communication-uri-string - agent-communication-uri-string - #:client-communication-uri-string - client-communication-uri-string - #:hooks hooks - #:parallel-hooks parallel-hooks - #:guile guile)) - #:user #$user - #:group #$group - #:pid-file "/var/run/guix-build-coordinator/pid" - ;; Allow time for migrations to run - #:pid-file-timeout 60 - #:environment-variables - `(,(string-append - "GUIX_LOCPATH=" #$glibc-utf8-locales "/lib/locale") - "LC_ALL=en_US.utf8" - "PATH=/run/current-system/profile/bin") ; for hooks - #:log-file "/var/log/guix-build-coordinator/coordinator.log" + (make-forkexec-constructor + (list #$(make-guix-build-coordinator-start-script + database-uri-string + allocation-strategy + "/var/run/guix-build-coordinator/pid" + package + #:agent-communication-uri-string + agent-communication-uri-string + #:client-communication-uri-string + client-communication-uri-string + #:hooks hooks + #:parallel-hooks parallel-hooks + #:guile guile)) + #:user #$user + #:group #$group + #:pid-file "/var/run/guix-build-coordinator/pid" + ;; Allow time for migrations to run + #:pid-file-timeout 60 + #:environment-variables + `(,(string-append + "GUIX_LOCPATH=" #$glibc-utf8-locales "/lib/locale") + "LC_ALL=en_US.utf8" + "PATH=/run/current-system/profile/bin") ; for hooks + #:log-file "/var/log/guix-build-coordinator/coordinator.log") args)))) (stop #~(make-kill-destructor)) (modules From e4fd04fb92e2da769ca521eba877bbcd936f290e Mon Sep 17 00:00:00 2001 From: jgart Date: Tue, 11 Oct 2022 17:19:21 -0500 Subject: [PATCH 080/790] gnu: Add erlang-jsx. * gnu/packages/erlang.scm (erlang-jsx): New variable. Signed-off-by: Christopher Baines --- gnu/packages/erlang.scm | 18 ++++++++++++++++++ 1 file changed, 18 insertions(+) diff --git a/gnu/packages/erlang.scm b/gnu/packages/erlang.scm index ede46f3a1c..90f290468b 100644 --- a/gnu/packages/erlang.scm +++ b/gnu/packages/erlang.scm @@ -7,6 +7,7 @@ ;;; Copyright © 2020-2022 Hartmut Goebel ;;; Copyright © 2021 Oskar Köök ;;; Copyright © 2021 Cees de Groot +;;; Copyright © 2022 jgart ;;; ;;; This file is part of GNU Guix. ;;; @@ -499,6 +500,23 @@ Erlang's type language, and can also be used for the model-based random testing of stateful systems.") (license license:gpl3+))) +(define-public erlang-jsx + (package + (name "erlang-jsx") + (version "3.1.0") + (source (origin + (method url-fetch) + (uri (hexpm-uri "jsx" version)) + (sha256 + (base32 + "1wr7jkxm6nlgvd52xhniav64xr9rml2ngb35rwjwqlqvq7ywhp0c")))) + (build-system rebar-build-system) + (synopsis "Streaming, evented JSON parsing toolkit") + (description + "An Erlang application for consuming, producing and manipulating json.") + (home-page "https://github.com/talentdeficit/jsx") + (license license:expat))) + (define-public erlang-providers (package (name "erlang-providers") From 1d160f41f5e973ea2bbbf8bc80d216b5d9b0974c Mon Sep 17 00:00:00 2001 From: jgart Date: Tue, 11 Oct 2022 20:07:22 -0500 Subject: [PATCH 081/790] gnu: Add erlang-yamerl. * gnu/packages/erlang.scm (erlang-yamerl): New variable. Signed-off-by: Christopher Baines --- gnu/packages/erlang.scm | 22 ++++++++++++++++++++++ 1 file changed, 22 insertions(+) diff --git a/gnu/packages/erlang.scm b/gnu/packages/erlang.scm index 90f290468b..cfada5a619 100644 --- a/gnu/packages/erlang.scm +++ b/gnu/packages/erlang.scm @@ -281,6 +281,28 @@ Mozilla's canonical set.") printing extending the io:format syntax to add colours.") (license license:expat))) +(define-public erlang-yamerl + (package + (name "erlang-yamerl") + (version "0.10.0") + (source + (origin + (method git-fetch) + (uri (git-reference + ;; There are no tests included on Hex. + (url "https://github.com/yakaz/yamerl") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 "0if8abgmispcfk7zhd0a5dndzwzbsmqrbyrm5shk375r2dbbwak6")))) + (build-system rebar-build-system) + (synopsis "YAML and JSON parser in pure Erlang") + (description + "Erlang application to parse YAML 1.1 and YAML 1.2 documents, as well as +JSON documents.") + (home-page "https://hexdocs.pm/yamerl/") + (license license:bsd-2))) + (define-public erlang-covertool (package (name "erlang-covertool") From c4bcb5db49b210097c5452b678e57a0774014814 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Mon, 12 Dec 2022 21:40:53 +0100 Subject: [PATCH 082/790] gnu: python-typer: Simplify by using pyproject-build-system. * gnu/packages/python-xyz.scm (python-typer)[build-system]: Use pyproject-build-system. [arguments]: Remove extra quoting; remove custom 'build phase; remove custom 'install phase; remove custom 'check phase; add 'pre-check phase. [synopsis]: Pull onto the same line. [description]: Reformat. --- gnu/packages/python-xyz.scm | 74 ++++++++++++++----------------------- 1 file changed, 28 insertions(+), 46 deletions(-) diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index 9629012a80..bb25c35caf 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -22311,60 +22311,42 @@ based on the CPython 2.7 and 3.7 parsers.") (file-name (git-file-name name version)) (sha256 (base32 "1knv353qhkl2imav3jfp6bgq47m8wkkqhq1dzmqg2sv8rsy7zgl7")))) - (build-system python-build-system) + (build-system pyproject-build-system) (arguments - `(#:phases - ,#~(modify-phases %standard-phases - ;; Unfortunately, this doesn't seem to be enough to fix these two - ;; tests, but we'll patch this anyway. - (add-after 'unpack 'patch-shell-reference - (lambda _ - (substitute* "tests/test_completion/test_completion.py" - (("\"bash\"") (string-append "\"" (which "bash") "\"")) - (("\"/bin/bash\"") - (string-append "\"" (which "bash") "\""))))) - (replace 'build - (lambda _ - (invoke "flit" "build"))) - (replace 'install - (lambda* (#:key inputs outputs #:allow-other-keys) - (add-installed-pythonpath inputs outputs) - (for-each - (lambda (wheel) - (format #true wheel) - (invoke "python" "-m" "pip" "install" - wheel (string-append "--prefix=" #$output))) - (find-files "dist" "\\.whl$")))) - (replace 'check - (lambda* (#:key tests? #:allow-other-keys) - (when tests? - (setenv "HOME" "/tmp") ; some tests need it - - ;; This is for completion tests - (with-output-to-file "/tmp/.bashrc" - (lambda _ (display "# dummy"))) - - (setenv "GUIX_PYTHONPATH" - (string-append (getcwd) ":" - (getenv "GUIX_PYTHONPATH"))) - (let ((disabled-tests (list "test_show_completion" - "test_install_completion"))) - (invoke "python" "-m" "pytest" "tests/" - "-k" - (string-append "not " - (string-join disabled-tests - " and not ")))))))))) + (list + #:test-flags + '(let ((disabled-tests (list "test_show_completion" + "test_install_completion"))) + (list "-k" (string-append "not " + (string-join disabled-tests + " and not ")))) + #:phases + #~(modify-phases %standard-phases + ;; Unfortunately, this doesn't seem to be enough to fix these two + ;; tests, but we'll patch this anyway. + (add-after 'unpack 'patch-shell-reference + (lambda _ + (substitute* "tests/test_completion/test_completion.py" + (("\"bash\"") (string-append "\"" (which "bash") "\"")) + (("\"/bin/bash\"") + (string-append "\"" (which "bash") "\""))))) + (add-before 'check 'pre-check + (lambda* (#:key tests? #:allow-other-keys) + (when tests? + (setenv "HOME" "/tmp") ; some tests need it + ;; This is for completion tests + (with-output-to-file "/tmp/.bashrc" + (lambda _ (display "# dummy"))))))))) (propagated-inputs (list python-click)) (native-inputs (list python-coverage python-flit python-pytest python-rich python-shellingham)) (home-page "https://github.com/tiangolo/typer") - (synopsis - "Typer builds CLI based on Python type hints") + (synopsis "Typer builds CLI based on Python type hints") (description - "Typer is a library for building CLI applications. It's based on -Python 3.6+ type hints.") + "Typer is a library for building CLI applications. It's based on Python +3.6+ type hints.") ;; MIT license (license license:expat))) From 8b9c9051ba798572577cef474085cc88adb73ae4 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Mon, 12 Dec 2022 23:45:52 +0100 Subject: [PATCH 083/790] gnu: python-numcodecs: Update to 0.10.2. * gnu/packages/python-xyz.scm (python-numcodecs): Update to 0.10.2. [build-system]: Use pyproject-build-system. [arguments]: Enable tests; add phase 'build-extensions; remove custom 'check phase. [propagated-inputs]: Add python-entrypoints and python-typing-extensions-next. --- gnu/packages/python-xyz.scm | 26 ++++++++++++++------------ 1 file changed, 14 insertions(+), 12 deletions(-) diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index bb25c35caf..ef3043f09c 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -23473,14 +23473,14 @@ tool).") (define-public python-numcodecs (package (name "python-numcodecs") - (version "0.6.4") + (version "0.10.2") (source (origin (method url-fetch) (uri (pypi-uri "numcodecs" version)) (sha256 (base32 - "0kbfr8pl3x9glsypbq8hzim003f16ml1b1cvgrh4w1sdvgal6j7g")) + "1i2rvm1f23dapcf6w3mj4877jzq5f24bhfa0fafbv1nr7xmqr0r2")) (modules '((guix build utils))) (snippet '(begin @@ -23490,11 +23490,11 @@ tool).") "numcodecs/lz4.c" "numcodecs/vlen.c" "numcodecs/zstd.c")))))) - (build-system python-build-system) + (build-system pyproject-build-system) (arguments - `(#:tests? #false ; TODO: unclear why numcodecs.* are not found - #:phases - (modify-phases %standard-phases + (list + #:phases + '(modify-phases %standard-phases (add-after 'unpack 'disable-avx2 (lambda _ (setenv "DISABLE_NUMCODECS_AVX2" "1"))) @@ -23511,16 +23511,18 @@ tool).") "'numcodecs.lz4', libraries=['lz4'], ") (("'numcodecs.blosc',") "'numcodecs.blosc', libraries=['blosc'], ")))) - (replace 'check - (lambda* (#:key tests? inputs outputs #:allow-other-keys) - (when tests? - (add-installed-pythonpath inputs outputs) - (invoke "pytest" "-vv"))))))) + (add-before 'check 'build-extensions + (lambda _ + ;; Cython extensions have to be built before running the tests. + (invoke "python" "setup.py" "build_ext" "--inplace")))))) (inputs (list c-blosc lz4 zlib `(,zstd "lib"))) (propagated-inputs - (list python-numpy python-msgpack)) + (list python-entrypoints + python-numpy + python-msgpack + python-typing-extensions-next)) (native-inputs (list python-cython python-pytest python-setuptools-scm)) (home-page "https://github.com/zarr-developers/numcodecs") From 2c65106cf5bc591ecf8d2303fdfd48d578f47b62 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Mon, 12 Dec 2022 23:47:19 +0100 Subject: [PATCH 084/790] gnu: python-zarr: Update to 2.13.3. * gnu/packages/python-xyz.scm (python-zarr): Update to 2.13.3. --- gnu/packages/python-xyz.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index ef3043f09c..579105e263 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -23552,14 +23552,14 @@ codecs for use in data storage and communication applications.") (define-public python-zarr (package (name "python-zarr") - (version "2.4.0") + (version "2.13.3") (source (origin (method url-fetch) (uri (pypi-uri "zarr" version)) (sha256 (base32 - "026n3sjzjv2gmwx6y72b8ij0hk42bc8zdbvfj5gdqzd4i6wj3ajk")))) + "135ls2q7zc98pk61a5cnh88j4hnnavcwasrswdjqyqvcc68b096v")))) (build-system python-build-system) (arguments `(#:phases From 75331dc6e690e790cccfa7ec0b936ff60e7f517d Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Mon, 12 Dec 2022 23:47:27 +0100 Subject: [PATCH 085/790] gnu: python-anndata: Use pyproject-build-system. * gnu/packages/python-xyz.scm (python-anndata)[build-system]: Use pyproject-build-system. [arguments]: Replace custom 'build phase with 'set-version phase; remove custom 'install phase; disable doctest via build phase 'disable-doctests and the #:test-flags property. [propagated-inputs]: Add python-scikit-learn. [native-inputs]: Add python-boltons. --- gnu/packages/python-xyz.scm | 49 ++++++++++++++++++++----------------- 1 file changed, 26 insertions(+), 23 deletions(-) diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index 579105e263..f5c4e3e9f7 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -201,6 +201,7 @@ #:use-module (gnu packages libusb) #:use-module (gnu packages linux) #:use-module (gnu packages llvm) + #:use-module (gnu packages machine-learning) #:use-module (gnu packages man) #:use-module (gnu packages markup) #:use-module (gnu packages maths) @@ -23601,29 +23602,26 @@ N-dimensional arrays for Python.") (sha256 (base32 "0v7npqrg1rdm8jzw22a45c0mqrmsv05r3k88i3lhzi0pzzxca1i1")))) - (build-system python-build-system) + (build-system pyproject-build-system) (arguments - `(#:phases - (modify-phases %standard-phases - (delete 'check) - (replace 'build - (lambda _ - (setenv "SETUPTOOLS_SCM_PRETEND_VERSION" ,version) - (substitute* "anndata/_metadata.py" - (("__version__ =.*") - (string-append "__version__ = \"" ,version "\"\n"))) - ;; ZIP does not support timestamps before 1980. - (setenv "SOURCE_DATE_EPOCH" "315532800") - (invoke "flit" "build"))) - (replace 'install - (lambda* (#:key inputs outputs #:allow-other-keys) - (add-installed-pythonpath inputs outputs) - (let ((out (assoc-ref outputs "out"))) - (for-each (lambda (wheel) - (format #true wheel) - (invoke "python" "-m" "pip" "install" - wheel (string-append "--prefix=" out))) - (find-files "dist" "\\.whl$")))))))) + (list + #:test-flags + '(list "-k" "not concatenation.rst") + #:phases + #~(modify-phases %standard-phases + ;; Doctests require scanpy from (gnu packages bioinformatics) + (add-after 'unpack 'disable-doctests + (lambda _ + (substitute* "pyproject.toml" + (("--doctest-modules") "")))) + (add-before 'build 'set-version + (lambda _ + (setenv "SETUPTOOLS_SCM_PRETEND_VERSION" #$version) + (substitute* "anndata/_metadata.py" + (("__version__ =.*") + (string-append "__version__ = \"" #$version "\"\n"))) + ;; ZIP does not support timestamps before 1980. + (setenv "SOURCE_DATE_EPOCH" "315532800")))))) (propagated-inputs (list python-h5py python-importlib-metadata @@ -23632,9 +23630,14 @@ N-dimensional arrays for Python.") python-packaging python-pandas python-scipy + python-scikit-learn python-zarr)) (native-inputs - (list python-joblib python-pytest python-toml python-flit + (list python-boltons + python-joblib + python-pytest + python-toml + python-flit python-setuptools-scm)) (home-page "https://github.com/theislab/anndata") (synopsis "Annotated data for data analysis pipelines") From 3d388fe3d0475f2e991ae061cc1364529a97af42 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 7 Dec 2022 10:58:08 +0100 Subject: [PATCH 086/790] gnu: python-graphviz: Update to 0.20.1. * gnu/packages/graphviz.scm (python-graphviz): Update to 0.20.1. [build-system]: Use pyproject-build-system. [arguments]: Remove custom "check" phase; add "prepare-check" phase. [native-inputs]: Remove python-mock. --- gnu/packages/graphviz.scm | 23 +++++++++++------------ 1 file changed, 11 insertions(+), 12 deletions(-) diff --git a/gnu/packages/graphviz.scm b/gnu/packages/graphviz.scm index 51c1de3932..7c2cb1eae0 100644 --- a/gnu/packages/graphviz.scm +++ b/gnu/packages/graphviz.scm @@ -2,7 +2,7 @@ ;;; Copyright © 2013, 2015, 2021 Ludovic Courtès ;;; Copyright © 2015, 2020 Efraim Flashner ;;; Copyright © 2016 Theodoros Foradis -;;; Copyright © 2017, 2018, 2019 Ricardo Wurmus +;;; Copyright © 2017, 2018, 2019, 2022 Ricardo Wurmus ;;; Copyright © 2017, 2018 Tobias Geerinckx-Rice ;;; Copyright © 2017 Gábor Boskovits ;;; Copyright © 2018 Mathieu Lirzin @@ -32,6 +32,7 @@ (define-module (gnu packages graphviz) #:use-module (guix packages) #:use-module (guix build-system gnu) + #:use-module (guix build-system pyproject) #:use-module (guix build-system python) #:use-module (guix download) #:use-module (guix git-download) @@ -180,27 +181,25 @@ interfaces for other technical domains.") (define-public python-graphviz (package (name "python-graphviz") - (version "0.13.2") + (version "0.20.1") (source (origin (method url-fetch) (uri (pypi-uri "graphviz" version ".zip")) (sha256 (base32 - "009alrilzx0v7kl41khbq7k6k8b8pxyvbsi1b1ai933f6kpbxb30")))) - (build-system python-build-system) + "1y1b956r01kg7qarkkrivhn71q64k0gbq6bcybd4gfd3v95g2n4c")))) + (build-system pyproject-build-system) (arguments - '(#:phases (modify-phases %standard-phases - (replace 'check - (lambda* (#:key tests #:allow-other-keys) - (if tests - (invoke "pytest" "-vv") - (format #t "test suite not run~%")) - #t))))) + (list + #:phases + '(modify-phases %standard-phases + (add-before 'check 'prepare-chec + ;; Needed for fontconfig cache directories + (lambda _ (setenv "HOME" (getcwd))))))) (native-inputs (list unzip ;; For tests. graphviz - python-mock python-pytest python-pytest-cov python-pytest-mock)) From de70f957b25ef6774a2cca5697bc8b55a3a20c95 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 8 Dec 2022 15:14:10 +0100 Subject: [PATCH 087/790] gnu: python-hyperopt: Update to 0.2.7. * gnu/packages/machine-learning.scm (python-hyperopt): Update to 0.2.7. [arguments]: Adjust check phase; disable test_distribution_rvs test. [build-system]: Use pyproject-build-system. [propagated-inputs]: Add python-py4j. [native-inputs]: Remove python-ipython and python-ipyparallel. --- gnu/packages/machine-learning.scm | 36 ++++++++++++++++--------------- 1 file changed, 19 insertions(+), 17 deletions(-) diff --git a/gnu/packages/machine-learning.scm b/gnu/packages/machine-learning.scm index fc8de01066..3dbe54a24a 100644 --- a/gnu/packages/machine-learning.scm +++ b/gnu/packages/machine-learning.scm @@ -1552,35 +1552,39 @@ interactive learning.") (define-public python-hyperopt (package (name "python-hyperopt") - (version "0.2.5") + (version "0.2.7") (source (origin (method url-fetch) (uri (pypi-uri "hyperopt" version)) (sha256 - (base32 "1k4ma8ci0bxghw7g4ms944zak1pi83yv2d6bxd7fcslm1zalfq5w")))) - (build-system python-build-system) + (base32 "0jd1ghmm423kbhjvd6pxq92y5vkz25390687fcnd7fshh3jrmy0v")))) + (build-system pyproject-build-system) (arguments - `(#:phases - (modify-phases %standard-phases + (list + #:phases + '(modify-phases %standard-phases (replace 'check - (lambda* (#:key inputs outputs tests? #:allow-other-keys) + (lambda* (#:key tests? #:allow-other-keys) (when tests? - (add-installed-pythonpath inputs outputs) - (invoke "python" "-m" "pytest" "--ignore" + (invoke "python" "-m" "pytest" ;; Needs python-pyspark. - "hyperopt/tests/test_spark.py" + "--ignore" "hyperopt/tests/integration/test_spark.py" ;; Needs both python-scikit-learn and python-lightgbm. - "--ignore" "hyperopt/tests/test_atpe_basic.py" + "--ignore" "hyperopt/tests/unit/test_atpe_basic.py" ;; The tests below need python-lightgbm. - "-k" (string-append "not test_branin" - " and not test_distractor" - " and not test_q1lognormal" - " and not test_quadratic1" - " and not test_twoarms")))))))) + "-k" + (string-append "not test_branin" + " and not test_distractor" + " and not test_q1lognormal" + " and not test_quadratic1" + " and not test_twoarms" + ;; XXX Type error with this version of scipy + " and not test_distribution_rvs")))))))) (propagated-inputs (list python-cloudpickle python-future + python-py4j python-networkx python-numpy python-scipy @@ -1588,8 +1592,6 @@ interactive learning.") python-tqdm)) (native-inputs (list python-black - python-ipython - python-ipyparallel python-nose python-pymongo python-pytest)) From 5167881a6087d3e7fb14380a6700263e954caf54 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 8 Dec 2022 23:14:15 +0100 Subject: [PATCH 088/790] gnu: python-biopython: Update to 1.80. * gnu/packages/bioinformatics.scm (python-biopython): Update to 1.80. [build-system]: Use pyproject-build-system. [arguments]: Remove trailing #T from build phase. --- gnu/packages/bioinformatics.scm | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 207f3c3d28..52abe152ee 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -1237,21 +1237,21 @@ sequencing.") (define-public python-biopython (package (name "python-biopython") - (version "1.76") + (version "1.80") (source (origin (method url-fetch) ;; use PyPi rather than biopython.org to ease updating (uri (pypi-uri "biopython" version)) (sha256 (base32 - "0wlch9xpa0fpgjzyxi6jsfca6iakaq9a05927xg8vqnmvaccnwrq")))) - (build-system python-build-system) + "0hqf3jsxn2sphcx81fx7x3i69sarpjsi70fzw98f8rw7z2d5x02j")))) + (build-system pyproject-build-system) (arguments - `(#:phases + '(#:phases (modify-phases %standard-phases (add-before 'check 'set-home ;; Some tests require a home directory to be set. - (lambda _ (setenv "HOME" "/tmp") #t))))) + (lambda _ (setenv "HOME" "/tmp")))))) (propagated-inputs (list python-numpy)) (home-page "https://biopython.org/") From 6e9518e201396602e92f89712f15c90d274260fa Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Fri, 9 Dec 2022 16:54:34 +0100 Subject: [PATCH 089/790] gnu: python-hicmatrix: Update to 16. * gnu/packages/bioinformatics.scm (python-hicmatrix): Update to 16. [build-system]: Use pyproject-build-system. [arguments]: Shuffle the quote. --- gnu/packages/bioinformatics.scm | 11 ++++++----- 1 file changed, 6 insertions(+), 5 deletions(-) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 52abe152ee..82801e7eeb 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -13373,7 +13373,7 @@ includes operations like compartment, insulation or peak calling.") (define-public python-hicmatrix (package (name "python-hicmatrix") - (version "15") + (version "16") (source (origin ;;Pypi sources do not contain any test @@ -13384,11 +13384,12 @@ includes operations like compartment, insulation or peak calling.") (file-name (git-file-name name version)) (sha256 (base32 - "1dshjxgb16sdfg9k1bhw2yhyngac04k4ca7aqy8g3i3pprr068r5")))) - (build-system python-build-system) + "00b9l62j4knrsdp7l3pawi9cqcsl09diycbhmmnar850bzssmq4f")))) + (build-system pyproject-build-system) (arguments - `(#:phases - (modify-phases %standard-phases + (list + #:phases + '(modify-phases %standard-phases (replace 'check (lambda* (#:key tests? #:allow-other-keys) (when tests? From c3e330cf36dcfe308bcd6d88e60934a5d349b509 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Fri, 9 Dec 2022 17:37:25 +0100 Subject: [PATCH 090/790] gnu: python-pygenometracks: Update to 3.5. * gnu/packages/bioinformatics.scm (python-pygenometracks): Update to 3.5. [build-system]: Use pyproject-build-system. [arguments]: Quote phases instead of full list of arguments; remove trailing #T from build phase. --- gnu/packages/bioinformatics.scm | 16 ++++++++-------- 1 file changed, 8 insertions(+), 8 deletions(-) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 82801e7eeb..e6a8789ea6 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -13466,25 +13466,25 @@ genomic scores), long range contacts and the visualization of viewpoints.") (define-public python-pygenometracks (package (name "python-pygenometracks") - (version "3.3") + (version "3.5") (source (origin (method url-fetch) (uri (pypi-uri "pyGenomeTracks" version)) (sha256 (base32 - "16laa0wnf4qn9fb9ych4w1vqhqwjss70v0y0f6wp4gwqfrlgac0f")))) - (build-system python-build-system) + "1l7smg2gc1vm2181lzmdnywb11gp6s6z6j444dbsigv65car8z8p")))) + (build-system pyproject-build-system) (arguments - `(#:tests? #f ; there are none - #:phases - (modify-phases %standard-phases + (list + #:tests? #f ;there are none + #:phases + '(modify-phases %standard-phases (add-after 'unpack 'relax-requirements (lambda _ (substitute* "setup.py" (("matplotlib ==3.1.1") - "matplotlib >=3.1.1")) - #t))))) + "matplotlib >=3.1.1"))))))) (propagated-inputs (list python-future python-gffutils From b66b6bdf70351881e4e35419bf4b35aeaf4029ff Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Fri, 9 Dec 2022 22:58:23 +0100 Subject: [PATCH 091/790] gnu: python-hicexplorer: Update to 3.7.2. * gnu/packages/bioinformatics.scm (python-hicexplorer): Update to 3.7.2. [build-system]: Use pyproject-build-system. [arguments]: Use gexp; remove phase "loosen-up-requirements"; add test-flags to skip some tests; add phase "remove-dependency-on-krbalancing" to remove a dependency on an unlicensed package; add phase "fix-references"; add phase "run-only-low-mem-tests". [propagated-inputs]: Remove python-configparser and python-six; add python-biopython, python-cleanlab-1, python-fit-nbinom, python-graphviz, python-hic2cool, python-hicmatrix, python-hyperopt, python-imbalanced-learn, python-ipykernel, python-psutil, python-pybedtools, python-pygenometracks, python-scikit-learn, and python-tqdm. [native-inputs]: Add graphviz. --- gnu/packages/bioinformatics.scm | 106 ++++++++++++++++++++++++++++---- 1 file changed, 94 insertions(+), 12 deletions(-) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index e6a8789ea6..ea33311a2c 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -13413,7 +13413,7 @@ the HiCExplorer and pyGenomeTracks packages.") (define-public python-hicexplorer (package (name "python-hicexplorer") - (version "2.1.4") + (version "3.7.2") (source (origin ;; The latest version is not available on Pypi. @@ -13424,32 +13424,114 @@ the HiCExplorer and pyGenomeTracks packages.") (file-name (git-file-name name version)) (sha256 (base32 - "0q5gpbzmrkvygqgw524q36b4nrivcmyi5v194vsx0qw7b3gcmq08")))) - (build-system python-build-system) + "1yavgxry38g326z10bclvdf8glmma05fxj5m73h15m1r2l9xmw3v")))) + (build-system pyproject-build-system) (arguments - `(#:phases - (modify-phases %standard-phases - (add-after 'unpack 'loosen-up-requirements - (lambda _ - (substitute* "setup.py" - (("==") ">=")) - #t))))) + (list + #:test-flags + '(list "hicexplorer/test/general/" + "--ignore" "hicexplorer/test/general/test_hicTADClassifier.py" + "--ignore" "hicexplorer/test/general/test_hicTrainTADClassifier.py" + "-k" + (string-append + ;; Unknown chromosome: ChrX + "not test_build_matrix_restrictionCutFile_two" + ;; fixture 'keepSelfLigation' not found + " and not test_build_matrix_restrictionCutFile_six" + ;; ValueError: object dtype is not supported by sparse matrices + " and not test_hic_transfer_obs_exp_perChromosome" + + ;; No KR balancing available + " and not test_correct_matrix_KR_partial_cool" + " and not test_correct_matrix_KR_cool" + " and not test_correct_matrix_KR_H5")) + #:phases + #~(modify-phases %standard-phases + ;; See https://github.com/deeptools/Knight-Ruiz-Matrix-balancing-algorithm/issues/23 + (add-after 'unpack 'remove-dependency-on-krbalancing + (lambda _ + (substitute* "hicexplorer/hicCorrectMatrix.py" + (("from krbalancing import.*") "") + (("( *)assert\\(args.correctionMethod == 'KR'\\)" m indent) + (string-append m "\n" + indent "log.error('krbalancing not available')\n" + indent "exit(1)"))) + (substitute* "setup.py" + (("\"krbalancing >= 0.0.5\",") "")) + (substitute* "requirements.txt" + (("krbalancing >= 0.0.5") "")))) + (add-after 'unpack 'fix-references + (lambda _ + (let ((site (string-append #$output "/lib/python" + #$(version-major+minor + (package-version python)) + "/site-packages"))) + (substitute* "hicexplorer/lib/tadClassifier.py" + (("model_location = site.getsitepackages\\(\\)\\[0\\]") + (string-append "model_location = \"" site "\"")))) + (substitute* "hicexplorer/hicFindRestSite.py" + (("subprocess.check_output\\(\\[\"cat\"") + (string-append "subprocess.check_output([\"" + (which "cat") "\"")) + (("cmd = 'sort -k1") + (string-append "cmd = '" (which "sort") " -k1"))))) + ;; The tests aim to detect available memory and run more tests when + ;; there is more available memory. Let's run them deterministically + ;; instead and don't run any tests that require more than 1GB of + ;; RAM. + (add-after 'unpack 'run-only-low-mem-tests + (lambda _ + (with-directory-excursion "hicexplorer/test" + (substitute* '("trivial_runs/test_hicBuildMatrix_trivial_runs_2.py" + "trivial_runs/test_hicAggregateContacts_trivial_runs_five.py" + "trivial_runs/test_hicAggregateContacts_trivial_runs_four.py" + "trivial_runs/test_hicAggregateContacts_trivial_runs.py" + "trivial_runs/test_hicAggregateContacts_trivial_runs_two_1.py" + "trivial_runs/test_hicBuildMatrix_trivial_runs.py" + "trivial_runs/test_hicAggregateContacts_trivial_runs_two_3.py" + "trivial_runs/test_hicAggregateContacts_trivial_runs_three.py" + "trivial_runs/test_hicAggregateContacts_trivial_runs_two.py" + "trivial_runs/test_hicAggregateContacts_trivial_runs_two_2.py" + "trivial_runs/test_hicAggregateContacts_trivial_runs_six.py" + "general/test_hicDifferentialTAD.py" + "general/test_hicDetectLoops.py" + "general/test_hicPlotMatrix.py" + "general/test_hicHyperoptDetectLoops.py" + "general/test_hicCreateThresholdFile.py" + "general/test_hicMergeDomains.py" + "general/test_hicHyperoptDetectLoopsHiCCUPS.py" + "general/test_hicAggregateContacts.py" + "general/test_hicInterIntraTAD.py") + (("^memory =.*") "memory = 1\n")))))))) (propagated-inputs (list python-biopython - python-configparser + python-cleanlab-1 python-cooler + python-fit-nbinom python-future + python-graphviz + python-hic2cool + python-hicmatrix + python-hyperopt + python-imbalanced-learn python-intervaltree + python-ipykernel python-jinja2 python-matplotlib python-numpy python-pandas + python-psutil + python-pybedtools python-pybigwig + python-pygenometracks python-pysam + python-scikit-learn python-scipy - python-six python-tables + python-tqdm python-unidecode)) + (native-inputs + (list graphviz)) ;for hicexplorer/test/test_compute_function.py (home-page "https://hicexplorer.readthedocs.io") (synopsis "Process, analyze and visualize Hi-C data") (description From b72df3bbb3625261d6b344c232da3c0589a0f3b7 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 10 Dec 2022 14:39:57 +0100 Subject: [PATCH 092/790] gnu: python-dna-features-viewer: Update to 3.1.1. * gnu/packages/bioinformatics.scm (python-dna-features-viewer): Update to 3.1.1. [build-system]: Use pyproject-build-system. [arguments]: Add build phase to fix a compatibility problem with biopython. [propagated-inputs]: Add python-packaging. --- gnu/packages/bioinformatics.scm | 23 ++++++++++++++++++----- 1 file changed, 18 insertions(+), 5 deletions(-) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index ea33311a2c..371bf1077a 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -16597,18 +16597,31 @@ feature is fast retrieval of range queries into numpy arrays.") (define-public python-dna-features-viewer (package (name "python-dna-features-viewer") - (version "3.0.3") + (version "3.1.1") (source (origin (method url-fetch) (uri (pypi-uri "dna_features_viewer" version)) (sha256 (base32 - "0vci6kg2id6r6rh3cifq7ccnh7j0mb8iqg3hji6rva0ayrdqzafc")))) - (build-system python-build-system) - (arguments '(#:tests? #false)) ; there are none + "10a5pmh73spdgfml88zjqg1rn2j2zdxn06ir8a5q3arspyqvyqcb")))) + (build-system pyproject-build-system) + (arguments + (list + #:tests? #false ;there are none + #:phases + '(modify-phases %standard-phases + ;; See https://github.com/Edinburgh-Genome-Foundry/DnaFeaturesViewer/issues/73 + ;; and https://github.com/Edinburgh-Genome-Foundry/DnaFeaturesViewer/pull/74 + (add-after 'unpack 'fix-biopython-compatibility + (lambda _ + (substitute* "dna_features_viewer/biotools.py" + (("zip\\(aa1 \\+ \"\\*\", aa3 \\+ \\[\"\\*\"\\]\\)") + "zip(aa1 + ('*',), aa3 + ('*',))"))))))) (propagated-inputs - (list python-biopython python-matplotlib)) + (list python-biopython + python-matplotlib + python-packaging)) (home-page "https://github.com/Edinburgh-Genome-Foundry/DnaFeaturesViewer") (synopsis "Plot features from DNA sequences") From 08b9e29d4672d2209026f4b7fa592abb958cbd34 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 10 Dec 2022 22:03:45 +0100 Subject: [PATCH 093/790] gnu: python-bokeh: Skip failing PIL test. The test compares base64-encoded gifs; the gifs look identical but the base64-encoded data differs. Since the result seems fine, disabling this PIL test is probably okay. * gnu/packages/python-xyz.scm (python-bokeh)[arguments]: Ignore failing test_transform_PIL test. --- gnu/packages/python-xyz.scm | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index f5c4e3e9f7..2acba1fa39 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -15466,7 +15466,10 @@ enhancements to optimization and data fitting problems.") (delete-file "tests/unit/bokeh/models/test_sources.py") (delete-file "tests/unit/bokeh/embed/test_bundle.py") - (invoke "pytest" "-v"))))))) + ;; XXX: This one test transforms a gif of a red box. It + ;; transforms it all right but the base64 doesn't look as + ;; expected, probably because of a change in pillow. + (invoke "pytest" "-v" "-k" "not test_transform_PIL"))))))) (propagated-inputs (list node-lts python-jinja2 From 2f1d8fb129511469c553caab5a2f4fd370d09fa5 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 10 Dec 2022 22:04:41 +0100 Subject: [PATCH 094/790] gnu: python-apsw: Update to 3.40.0.0. * gnu/packages/databases.scm (python-apsw): Update to 3.40.0.0. [source]: Remove obsolete patch. [build-system]: Use pyproject-build-system. [native-inputs]: Add python-cython. [arguments]: Move build-extensions phase before build phase. * gnu/local.mk (dist_patch_DATA): Remove patch. * gnu/packages/patches/python-apsw-3.39.2.1-test-fix.patch: Remove file. --- gnu/local.mk | 1 - gnu/packages/databases.scm | 36 +++++++++---------- .../python-apsw-3.39.2.1-test-fix.patch | 27 -------------- 3 files changed, 18 insertions(+), 46 deletions(-) delete mode 100644 gnu/packages/patches/python-apsw-3.39.2.1-test-fix.patch diff --git a/gnu/local.mk b/gnu/local.mk index 6e12f9cdb1..295be3c67c 100644 --- a/gnu/local.mk +++ b/gnu/local.mk @@ -1719,7 +1719,6 @@ dist_patch_DATA = \ %D%/packages/patches/python-3-fix-tests.patch \ %D%/packages/patches/python-3-hurd-configure.patch \ %D%/packages/patches/python-3-no-static-lib.patch \ - %D%/packages/patches/python-apsw-3.39.2.1-test-fix.patch \ %D%/packages/patches/python-aionotify-0.2.0-py3.8.patch \ %D%/packages/patches/python-argcomplete-1.11.1-fish31.patch \ %D%/packages/patches/python-cross-compile.patch \ diff --git a/gnu/packages/databases.scm b/gnu/packages/databases.scm index b74762789a..9d1eec5ea0 100644 --- a/gnu/packages/databases.scm +++ b/gnu/packages/databases.scm @@ -173,6 +173,7 @@ #:use-module (guix build-system go) #:use-module (guix build-system meson) #:use-module (guix build-system perl) + #:use-module (guix build-system pyproject) #:use-module (guix build-system python) #:use-module (guix build-system qt) #:use-module (guix build-system ruby) @@ -3590,7 +3591,7 @@ PickleShare.") (define-public python-apsw (package (name "python-apsw") - (version "3.39.2.1") + (version "3.40.0.0") ;; The compressed release has fetching functionality disabled. (source (origin @@ -3600,24 +3601,23 @@ PickleShare.") version "/apsw-" version ".zip")) (sha256 (base32 - "06x3qgg71xz8l3kz8gz04wkfp5f6zfrg476a4mm1c5hikqyw6ykj")) - ;; Cherry-picked from upstream, remove when bumping to 3.39.3. - (patches - (search-patches "python-apsw-3.39.2.1-test-fix.patch")))) - (build-system python-build-system) - (native-inputs (list unzip)) - (inputs (list sqlite-next)) ;SQLite 3.39 required. + "02sgja00azvd08wi2wm105apmhp2644s7aw9b1zdg3dkcwjnsiad")))) + (build-system pyproject-build-system) + (native-inputs + (list python-cython unzip)) + (inputs (list sqlite-next)) ;SQLite 3.40 required. (arguments - (list #:phases - #~(modify-phases %standard-phases - (replace 'build - (lambda _ - (invoke "python" "setup.py" "build" "--enable-all-extensions" - "--enable=load_extension"))) - (add-after 'build 'build-test-helper - (lambda _ - (invoke "gcc" "-fPIC" "-shared" "-o" "./testextension.sqlext" - "-I." "-Isqlite3" "src/testextension.c")))))) + (list + #:phases + #~(modify-phases %standard-phases + (add-before 'build 'build-extensions + (lambda _ + (invoke "python" "setup.py" "build" "--enable-all-extensions" + "--enable=load_extension"))) + (add-after 'build 'build-test-helper + (lambda _ + (invoke "gcc" "-fPIC" "-shared" "-o" "./testextension.sqlext" + "-I." "-Isqlite3" "src/testextension.c")))))) (home-page "https://github.com/rogerbinns/apsw/") (synopsis "Another Python SQLite Wrapper") (description diff --git a/gnu/packages/patches/python-apsw-3.39.2.1-test-fix.patch b/gnu/packages/patches/python-apsw-3.39.2.1-test-fix.patch deleted file mode 100644 index cc233e3ccd..0000000000 --- a/gnu/packages/patches/python-apsw-3.39.2.1-test-fix.patch +++ /dev/null @@ -1,27 +0,0 @@ -From 1111f902075169bd0d96cdd10607ef8499f0fed5 Mon Sep 17 00:00:00 2001 -From: Roger Binns -Date: Mon, 5 Sep 2022 07:12:25 -0700 -Subject: [PATCH] Deal with mismatched SQLITE_ENABLE_COLUMN_METADATA - -Address #363 ---- - apsw/tests.py | 2 +- - 1 files changed, 1 insertions(+), 1 deletion(-) - -diff --git a/apsw/tests.py b/apsw/tests.py -index b4a94d3..256ead0 100644 ---- a/apsw/tests.py -+++ b/apsw/tests.py -@@ -772,8 +772,8 @@ class APSW(unittest.TestCase): - c.execute("drop table foo; create table foo (%s)" % (", ".join(["[%s] %s" % (n, t) for n, t in cols]), )) - c.execute("insert into foo([x a space]) values(1)") - c.execute("create temp table two(fred banana); insert into two values(7); create temp view three as select fred as [a space] from two") -- has_full=any(o=="ENABLE_COLUMN_METADATA" or o.startswith("ENABLE_COLUMN_METADATA=") for o in apsw.compile_options) -+ has_full=any(o=="ENABLE_COLUMN_METADATA" or o.startswith("ENABLE_COLUMN_METADATA=") for o in apsw.compile_options) if apsw.using_amalgamation else hasattr(c, "description_full") - for row in c.execute("select * from foo"): - self.assertEqual(cols, c.getdescription()) - self.assertEqual(has_full, hasattr(c, "description_full")) - -base-commit: f628374c5857d940067ef26c9ea4e85a08a94f76 --- -2.37.2 From 461dff26518c05c22e946cc1afc89b094159a5d1 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sun, 11 Dec 2022 01:13:52 +0100 Subject: [PATCH 095/790] gnu: python-cgatcore: Update to 0.6.14. * gnu/packages/bioinformatics.scm (python-cgatcore): Update to 0.6.14. [build-system]: Use pyproject-build-system. [arguments]: Disable broken tests with #:test-flags; do not replace 'check phase; add phase 'sqlite-compatibility. [native-inputs]: Drop input labels. --- gnu/packages/bioinformatics.scm | 50 ++++++++++++++++++++------------- 1 file changed, 31 insertions(+), 19 deletions(-) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 371bf1077a..4044ff625e 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -16081,7 +16081,7 @@ coordinates between different assemblies.") (define-public python-cgatcore (package (name "python-cgatcore") - (version "0.6.7") + (version "0.6.14") ;; The version of pypi does not include test data. (source (origin (method git-fetch) @@ -16091,11 +16091,22 @@ coordinates between different assemblies.") (file-name (git-file-name name version)) (sha256 (base32 - "17vk88v1bx7x02ibzkc9i7ir4b5p1hcjr38jpsfzyzxr68352d5k")))) - (build-system python-build-system) + "0fjjaski39j8b7v21wldmbwwsfhicngajah7n4skafi56kdck33p")))) + (build-system pyproject-build-system) (arguments - `(#:phases - (modify-phases %standard-phases + (list + #:test-flags + '(list "-k" + (string-append + ;; This test actually does what it should, but the check fails with + ;; TypeError: cannot unpack non-iterable Namespace object + "not test_start_and_stop_are_logged_with_argparse" + ;; These all attempt to connect to localhost with SSH + " and not test_job_should_use_TMPDIR_and_clean_up" + " and not test_job_should_use_TMPDIR_and_clean_up_after_fail" + " and not test_job_should_write_to_explicit_temp_and_not_clean_up")) + #:phases + '(modify-phases %standard-phases (add-after 'unpack 'fix-references (lambda _ (substitute* "cgatcore/pipeline/execution.py" @@ -16103,21 +16114,22 @@ coordinates between different assemblies.") (("executable=\"/bin/bash\"") (string-append "executable=\"" (which "bash") "\"")) (("\\\\time") (which "time"))))) - (delete 'check) - (add-after 'install 'check - (lambda* (#:key tests? inputs outputs #:allow-other-keys) - (when tests? - (add-installed-pythonpath inputs outputs) - ;; Requires network access - (delete-file "tests/test_pipeline_execution.py") - (invoke "python" "-m" "pytest" "-v"))))))) + (add-after 'unpack 'sqlite-compatibility + (lambda _ + ;; Load apsw (and thus newer sqlite3) before importing Python's + ;; older sqlite3 library. + (substitute* "cgatcore/pipeline/__init__.py" + (("import os") + (string-append "import os\nimport apsw"))) + (substitute* "tests/template_pipeline.py" + (("import sys" m) + (string-append "import apsw\n" m)))))))) (native-inputs - `(("python-pytest" ,python-pytest) - ("lsof" ,lsof) - ("hostname" ,inetutils) - ("openssl" ,openssl))) - (inputs - (list time)) + (list python-pytest + lsof + inetutils + openssl)) + (inputs (list time)) (propagated-inputs (list python-apsw python-gevent From 71dc990f2271dadb8aaa22b87885491466835697 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sun, 11 Dec 2022 13:26:04 +0100 Subject: [PATCH 096/790] gnu: python-flask-restful: Update to 0.3.9. * gnu/packages/python-web.scm (python-flask-restful): Update to 0.3.9. [source]: Remove patch. [build-system]: Use pyproject-build-system. [arguments]: Disable "test_redirect" test; remove 'fix-imports phase. [native-inputs]: Replace python-nose with python-pytest. * gnu/local.mk (dist_patch_DATA): Remove patch. * gnu/packages/patches/python-flask-restful-werkzeug-compat.patch: Remove file. --- gnu/local.mk | 1 - ...python-flask-restful-werkzeug-compat.patch | 36 ------------------- gnu/packages/python-web.scm | 31 +++++++--------- 3 files changed, 12 insertions(+), 56 deletions(-) delete mode 100644 gnu/packages/patches/python-flask-restful-werkzeug-compat.patch diff --git a/gnu/local.mk b/gnu/local.mk index 295be3c67c..60a422fd7e 100644 --- a/gnu/local.mk +++ b/gnu/local.mk @@ -1728,7 +1728,6 @@ dist_patch_DATA = \ %D%/packages/patches/python-docopt-pytest6-compat.patch \ %D%/packages/patches/python-execnet-read-only-fix.patch \ %D%/packages/patches/python-fixtures-remove-monkeypatch-test.patch \ - %D%/packages/patches/python-flask-restful-werkzeug-compat.patch \ %D%/packages/patches/python-ipython-documentation-chars.patch \ %D%/packages/patches/python-ipython-documentation-repro.patch \ %D%/packages/patches/python-keras-integration-test.patch \ diff --git a/gnu/packages/patches/python-flask-restful-werkzeug-compat.patch b/gnu/packages/patches/python-flask-restful-werkzeug-compat.patch deleted file mode 100644 index 0e928ef455..0000000000 --- a/gnu/packages/patches/python-flask-restful-werkzeug-compat.patch +++ /dev/null @@ -1,36 +0,0 @@ -We need one patch on top of 0.3.8 for compatibility with Werkzeug 1.0. - -Taken from upstream: -https://github.com/flask-restful/flask-restful/commit/73376a488907af3042b52678ac4c23f8a8911e5b - -diff --git a/tests/test_api.py b/tests/test_api.py -index f7f8e661..6795d362 100644 ---- a/tests/test_api.py -+++ b/tests/test_api.py -@@ -445,7 +445,9 @@ def test_handle_non_api_error(self): - - resp = app.get("/foo") - self.assertEquals(resp.status_code, 404) -- self.assertEquals('text/html', resp.headers['Content-Type']) -+ # in newer versions of werkzeug this is `text/html; charset=utf8` -+ content_type, _, _ = resp.headers['Content-Type'].partition(';') -+ self.assertEquals('text/html', content_type) - - def test_non_api_error_404_catchall(self): - app = Flask(__name__) -diff --git a/tests/test_reqparse.py b/tests/test_reqparse.py -index 2f1fbedf..9776f17c 100644 ---- a/tests/test_reqparse.py -+++ b/tests/test_reqparse.py -@@ -2,9 +2,9 @@ - import unittest - from mock import Mock, patch - from flask import Flask --from werkzeug import exceptions, MultiDict -+from werkzeug import exceptions - from werkzeug.wrappers import Request --from werkzeug.datastructures import FileStorage -+from werkzeug.datastructures import FileStorage, MultiDict - from flask_restful.reqparse import Argument, RequestParser, Namespace - import six - import decimal diff --git a/gnu/packages/python-web.scm b/gnu/packages/python-web.scm index 7543e05f47..18c0b47b67 100644 --- a/gnu/packages/python-web.scm +++ b/gnu/packages/python-web.scm @@ -3924,35 +3924,28 @@ apps.") (define-public python-flask-restful (package (name "python-flask-restful") - (version "0.3.8") + (version "0.3.9") (source (origin (method url-fetch) (uri (pypi-uri "Flask-RESTful" version)) - (patches (search-patches "python-flask-restful-werkzeug-compat.patch")) (sha256 (base32 - "05b9lzx5yc3wgml2bcq50lq35h66m8zpj6dc9advcb5z3acsbaay")))) - (build-system python-build-system) + "0gm5dz088v3d2k1dkcp9b3nnqpkk0fp2jly870hijj2xhc5nbv6c")))) + (build-system pyproject-build-system) (arguments - `(#:phases - (modify-phases %standard-phases - (add-after 'unpack 'fix-imports - (lambda _ - (substitute* "flask_restful/__init__.py" - (("flask\\.helpers") "flask.scaffold"))))))) + ;; This test fails because '/' is not 'http://localhost/'. + (list #:test-flags '(list "-k" "not test_redirect"))) (propagated-inputs - (list python-aniso8601 python-flask python-pytz)) + (list python-aniso8601 python-flask python-pytz)) (native-inputs - (list ;; Optional dependency of Flask. Tests need it. - python-blinker python-mock ; For tests - python-nose)) ;for tests - (home-page - "https://www.github.com/flask-restful/flask-restful/") - (synopsis - "Flask module for creating REST APIs") + (list python-blinker + python-mock + python-pytest)) + (home-page "https://www.github.com/flask-restful/flask-restful/") + (synopsis "Flask module for creating REST APIs") (description - "This package contains a Flask module for creating REST APIs.") + "This package contains a Flask module for creating REST APIs.") (license license:bsd-3))) (define-public python-flask-basicauth From 0fcba8b01c23af756dba5f863db8712d6f840f36 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sun, 11 Dec 2022 13:44:29 +0100 Subject: [PATCH 097/790] gnu: python-marshmallow: Update to 3.19.0. * gnu/packages/python-xyz.scm (python-marshmallow): Update to 3.19.0. [build-system]: Use pyproject-build-system. [propagated-inputs]: Remove python-dateutil and python-simplejson; add python-packaging. [native-inputs]: Add python-flake8, python-flake8-bugbear, python-mypy, python-pre-commit, and python-simplejson. --- gnu/packages/python-xyz.scm | 31 ++++++++++++++++++------------- 1 file changed, 18 insertions(+), 13 deletions(-) diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index 2acba1fa39..2d013054ec 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -20954,24 +20954,29 @@ while only declaring the test-specific fields.") (define-public python-marshmallow (package (name "python-marshmallow") - (version "3.9.1") + (version "3.19.0") (source (origin - (method url-fetch) - (uri (pypi-uri "marshmallow" version)) - (sha256 - (base32 - "0kizhh3mnhpa08wfnsv1gagy22bpxzxszgbiylkhpz1d8qvwrykk")))) - (build-system python-build-system) + (method url-fetch) + (uri (pypi-uri "marshmallow" version)) + (sha256 + (base32 + "0y6vpq2p5841kcw2qil68la0rx9z1vmxzj3dxjv99kjhsq7jq0wh")))) + (build-system pyproject-build-system) (propagated-inputs - (list python-dateutil python-simplejson)) + (list python-packaging)) (native-inputs - (list python-pytest python-pytz)) + (list python-flake8 + python-flake8-bugbear + python-mypy + python-pre-commit + python-pytest + python-pytz + python-simplejson)) (home-page "https://github.com/marshmallow-code/marshmallow") - (synopsis "Convert complex datatypes to and from native - Python datatypes") - (description "@code{marshmallow} provides a library for converting - complex datatypes to and from native Python datatypes.") + (synopsis "Convert complex datatypes to and from native Python datatypes") + (description "@code{marshmallow} provides a library for converting complex +datatypes to and from native Python datatypes.") (license license:expat))) (define-public python-marshmallow-jsonapi From 99a29b4933144599c29bd54a0eb654b20cbe6500 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sun, 11 Dec 2022 13:45:51 +0100 Subject: [PATCH 098/790] gnu: python-apispec: Update to 6.0.2. * gnu/packages/python-xyz.scm (python-apispec): Update to 6.0.2. [build-system]: Use pyproject-build-system. [arguments]: Disable test through test-flags, not by replacing the 'check phase. [propagated-inputs]: Remove python-pyyaml; add python-packaging. [native-inputs]: Add python-flake8, python-flake8-bugbear, python-mypy, python-pre-commit, and python-pyyaml. --- gnu/packages/python-xyz.scm | 39 ++++++++++++++++++++----------------- 1 file changed, 21 insertions(+), 18 deletions(-) diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index 2d013054ec..0ddb91cf79 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -21012,33 +21012,36 @@ datatypes to and from native Python datatypes.") (define-public python-apispec (package (name "python-apispec") - (version "4.0.0") + (version "6.0.2") (source (origin - (method url-fetch) - (uri (pypi-uri "apispec" version)) - (sha256 + (method url-fetch) + (uri (pypi-uri "apispec" version)) + (sha256 (base32 - "12n4w5zkn4drcn8izq68vmixmqvz6abviqkdn4ip0kaax3jjh3in")))) - (build-system python-build-system) + "11vqxwdxmm7qmyhdbxk4gnx37nbzmn266ah92gi4pvzd76vq0vg7")))) + (build-system pyproject-build-system) (arguments - '(#:phases (modify-phases %standard-phases - (replace 'check - (lambda _ - (invoke "pytest" "-vv" - ;; Disable validation tests since they require - ;; the optional 'prance' library which is not - ;; yet in Guix. - "-k" "not openapi_tools_validate")))))) + (list + ;; Disable validation tests since they require + ;; the optional 'prance' library which is not + ;; yet in Guix. + #:test-flags '(list "-k" "not openapi_tools_validate"))) (propagated-inputs - (list python-pyyaml)) + (list python-packaging)) (native-inputs - (list python-pytest python-marshmallow)) + (list python-flake8 + python-flake8-bugbear + python-marshmallow + python-mypy + python-pre-commit + python-pytest + python-pyyaml)) (home-page "https://github.com/marshmallow-code/apispec") (synopsis "Swagger/OpenAPI specification generator") (description "@code{python-apispec} is a pluggable API specification - generator. It currently supports the OpenAPI specification, formerly known - as Swagger.") +generator. It currently supports the OpenAPI specification, formerly known as +Swagger.") (license license:expat))) (define-public python-apispec-webframeworks From 8c197f990b7ab60e4524567d628d78ea62973c11 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sun, 11 Dec 2022 15:01:42 +0100 Subject: [PATCH 099/790] gnu: python-pyjwt: Update to 2.6.0. * gnu/packages/python-xyz.scm (python-pyjwt): Update to 2.6.0. [build-system]: Use pyproject-build-system. [arguments]: Remove. [native-inputs]: Add pytohn-coverage, python-pre-commit, python-sphinx, and python-sphinx-rtd-theme. --- gnu/packages/python-xyz.scm | 19 +++++++++---------- 1 file changed, 9 insertions(+), 10 deletions(-) diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index 0ddb91cf79..0f7903bdfb 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -4088,23 +4088,22 @@ memory usage and transliteration quality.") (define-public python-pyjwt (package (name "python-pyjwt") - (version "2.4.0") + (version "2.6.0") (source (origin (method url-fetch) (uri (pypi-uri "PyJWT" version)) (sha256 (base32 - "1fmbcwfw1463wjzwbcgg3s16rad6kfb1mc5y7jbkp6v9ihh0hafl")))) - (build-system python-build-system) - (arguments - '(#:phases (modify-phases %standard-phases - (replace 'check - (lambda* (#:key tests? #:allow-other-keys) - (when tests? - (invoke "pytest" "-vv"))))))) + "1z85kwr945rbzrn5wabrsmck5x8disa9wc7b3y5gci7w65z5qa39")))) + (build-system pyproject-build-system) (native-inputs - (list python-cryptography python-pytest)) + (list python-coverage + python-cryptography + python-pre-commit + python-pytest + python-sphinx + python-sphinx-rtd-theme)) (home-page "https://github.com/progrium/pyjwt") (synopsis "JSON Web Token implementation in Python") (description From 9bf2101049eb79430a6b15f0017a6027ad37a1f2 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sun, 11 Dec 2022 15:37:40 +0100 Subject: [PATCH 100/790] gnu: python-flasgger: Update to 0.9.5. * gnu/packages/python-xyz.scm (python-flasgger): Update to 0.9.5. [build-system]: Use pyproject-build-system. [arguments]: Remove custom 'check phase; add 'prepare-check phase; disable "test_swag" test via #:test-flags. [native-inputs]: Add python-apispec-webframeworks and python-flask-jwt. --- gnu/packages/python-xyz.scm | 36 +++++++++++++++++++++--------------- 1 file changed, 21 insertions(+), 15 deletions(-) diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index 0f7903bdfb..2279503d63 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -21074,7 +21074,7 @@ web frameworks.") (define-public python-flasgger (package (name "python-flasgger") - (version "0.6.3") + (version "0.9.5") (source (origin (method git-fetch) @@ -21083,29 +21083,35 @@ web frameworks.") (commit version))) (file-name (git-file-name name version)) (sha256 - (base32 "0yydxsyjnc0clbrjqb1n7587l6cdqvwdagwxk5hkx01qwdfbkvpn")))) - (build-system python-build-system) + (base32 "0a2djgfq905a4in16068qz0ikg88dm4nbckaamhaz2v9khllr0bi")))) + (build-system pyproject-build-system) (arguments - `(#:phases - (modify-phases %standard-phases - (replace 'check - (lambda* (#:key inputs outputs #:allow-other-keys) - (substitute* "Makefile" - (("flake8 flasgger --ignore=F403") - "flake8 flasgger --ignore=E731,F403")) - (invoke "py.test")))))) + (list + ;; This test fails due to missing fixtures + #:test-flags '(list "-k" "not test_swag") + #:phases + '(modify-phases %standard-phases + (add-after 'unpack 'prepare-check + (lambda _ + ;; This requires a dummy package "flasgger_package" to be installed. + (delete-file "examples/package_example.py") + ;; These fail with an internal server error + (for-each delete-file '("examples/marshmallow_apispec.py" + "examples/validation.py"))))))) (propagated-inputs (list python-flask python-pyyaml python-jsonschema python-mistune python-six)) (native-inputs - (list python-decorator + (list python-apispec + python-apispec-webframeworks + python-decorator python-flake8 + python-flask-jwt python-flask-restful python-flex - python-pytest - python-pytest-cov python-marshmallow - python-apispec)) + python-pytest + python-pytest-cov)) (home-page "https://github.com/rochacbruno/flasgger/") (synopsis "Extract Swagger specs from your Flask project") (description "@code{python-flasgger} allows extracting Swagger specs From 1369b53d49769250cad24683ffc033302f9c5045 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sun, 11 Dec 2022 15:47:30 +0100 Subject: [PATCH 101/790] gnu: seqmagick: Update to 0.8.4. * gnu/packages/bioinformatics.scm (seqmagick): Update to 0.8.4. [build-system]: Use pyproject-build-system. [inputs]: Add python-pygtrie. [native-inputs]: Replace python-nose with python-pytest. --- gnu/packages/bioinformatics.scm | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 4044ff625e..e8a8ddc361 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -6945,19 +6945,19 @@ bioinformatics file formats, sequence alignment, and more.") (define-public seqmagick (package (name "seqmagick") - (version "0.8.0") + (version "0.8.4") (source (origin (method url-fetch) (uri (pypi-uri "seqmagick" version)) (sha256 (base32 - "0pf98da7i59q47gwrbx0wjk6xlvbybiwphw80w7h4ydjj0579a2b")))) - (build-system python-build-system) + "0c6skyig8fyylnbj4597pjj9h0dn36rkxrhwd34yrsc6k6f7r8a0")))) + (build-system pyproject-build-system) (inputs - (list python-biopython)) + (list python-biopython python-pygtrie)) (native-inputs - (list python-nose)) + (list python-pytest)) (home-page "https://github.com/fhcrc/seqmagick") (synopsis "Tools for converting and modifying sequence files") (description From e84042fdd4ac2f903224e1b5f366537a22b4d593 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Mon, 12 Dec 2022 11:16:17 +0100 Subject: [PATCH 102/790] gnu: cnvkit: Update to 0.9.9. * gnu/packages/bioinformatics.scm (cnvkit): Update to 0.9.9. [build-system]: Use pyproject-build-system. [arguments]: Relax restriction on python-joblib. [propagated-inputs]: Add python-pomegranate and python-scikit-learn. --- gnu/packages/bioinformatics.scm | 21 ++++++++++++++++----- 1 file changed, 16 insertions(+), 5 deletions(-) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index e8a8ddc361..5e2e0796a0 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -14225,7 +14225,7 @@ polymorphisms) and indels with respect to a reference genome and more.") (define-public cnvkit (package (name "cnvkit") - (version "0.9.5") + (version "0.9.9") (source (origin (method git-fetch) @@ -14234,17 +14234,28 @@ polymorphisms) and indels with respect to a reference genome and more.") (commit (string-append "v" version)))) (file-name (git-file-name name version)) (sha256 - (base32 "0g2f78k68yglmj4fsfmgs8idqv3di9aj53fg0ld0hqljg8chhh82")))) - (build-system python-build-system) + (base32 "1q4l7jhr1k135an3n9aa9wsid5lk6fwxb0hcldrr6v6y76zi4gj1")))) + (build-system pyproject-build-system) + (arguments + (list + #:phases + '(modify-phases %standard-phases + ;; See upstream commit eee0f6eaec57d5c6e58142d661979f3aacc5f76a + (add-after 'unpack 'compatibility + (lambda _ + (substitute* "setup.py" + (("'joblib.*") ""))))))) (propagated-inputs (list python-biopython python-future python-matplotlib python-numpy - python-reportlab python-pandas - python-pysam + python-pomegranate python-pyfaidx + python-pysam + python-reportlab + python-scikit-learn python-scipy ;; R packages r-dnacopy)) From 648b1605dd252bdbe875d88e454078fb9a2966f4 Mon Sep 17 00:00:00 2001 From: Robby Zambito Date: Sat, 10 Dec 2022 17:27:53 -0500 Subject: [PATCH 103/790] gnu: gauche: Update to 0.9.12 MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * gnu/packages/scheme.scm (gauche): Update to 0.9.12. [source]: Project migrated to GitHub. libatomic-ops is no longer in the Gauche source tree. [arguments]: Renamed network test file. Signed-off-by: 宋文武 --- gnu/packages/scheme.scm | 19 ++++++++----------- 1 file changed, 8 insertions(+), 11 deletions(-) diff --git a/gnu/packages/scheme.scm b/gnu/packages/scheme.scm index cbe9d1d948..c13de9d65b 100644 --- a/gnu/packages/scheme.scm +++ b/gnu/packages/scheme.scm @@ -19,6 +19,7 @@ ;;; Copyright © 2021 Foo Chuan Wei ;;; Copyright © 2022 Morgan Smith ;;; Copyright © 2022 jgart +;;; Copyright © 2022 Robby Zambito ;;; ;;; This file is part of GNU Guix. ;;; @@ -887,21 +888,17 @@ The core is 12 builtin special forms and 33 builtin functions.") (define-public gauche (package (name "gauche") - (version "0.9.10") + (version "0.9.12") (home-page "https://practical-scheme.net/gauche/index.html") (source (origin (method url-fetch) (uri (string-append - "mirror://sourceforge/gauche/Gauche/Gauche-" - version ".tgz")) + "https://github.com/shirok/Gauche/releases/download/release" + (string-replace-substring version "." "_") + "/Gauche-" version ".tgz")) (sha256 - (base32 "0ci57ak5cp3lkmfy3nh50hifh8nbg58hh6r18asq0rn5mqfxyf8g")) - (modules '((guix build utils))) - (snippet '(begin - ;; Remove libatomic-ops. - (delete-file-recursively "gc/libatomic_ops") - #t)))) + (base32 "05xnym1phg8i14bacip5d0d3v0gc1nn5mgayd5hnda873f969bml")))) (build-system gnu-build-system) (inputs (list libatomic-ops slib zlib)) @@ -932,8 +929,8 @@ The core is 12 builtin special forms and 33 builtin functions.") (add-before 'check 'patch-network-tests ;; Remove net checks. (lambda _ - (delete-file "ext/net/test.scm") - (invoke "touch" "ext/net/test.scm") + (delete-file "test/net.scm") + (invoke "touch" "test/net.scm") #t)) (add-after 'install 'install-docs (lambda _ From ca735decfb8c1986041fe09e32acaf998e98245f Mon Sep 17 00:00:00 2001 From: Bruno Victal Date: Sat, 10 Dec 2022 13:40:35 +0000 Subject: [PATCH 104/790] gnu: mympd: Update to 10.1.6. MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * gnu/packages/mpd.scm (mympd): Update to 10.1.6. Signed-off-by: 宋文武 --- gnu/packages/mpd.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/mpd.scm b/gnu/packages/mpd.scm index 5439d89f4a..b9b6924451 100644 --- a/gnu/packages/mpd.scm +++ b/gnu/packages/mpd.scm @@ -581,7 +581,7 @@ mpdevil loads all tags and covers on demand.") (define-public mympd (package (name "mympd") - (version "10.1.3") + (version "10.1.6") (source (origin (method git-fetch) (uri (git-reference @@ -590,7 +590,7 @@ mpdevil loads all tags and covers on demand.") (file-name (git-file-name name version)) (sha256 (base32 - "16cvjwbyb1m88kmgylp95p82a4xdjikmrw9arl6kvmgcbyw317yp")))) + "06i8v8dh2x4lrph9lm56h5yy698y95ic5xrgmyisafvxd239sn0x")))) (build-system cmake-build-system) (arguments (list #:tests? #f)) ; no test target From 206b97c10252712ce23bae2cbf45a66d850b2d87 Mon Sep 17 00:00:00 2001 From: Pierre Neidhardt Date: Mon, 12 Dec 2022 12:52:11 +0100 Subject: [PATCH 105/790] gnu: Add cl-colored. * gnu/packages/lisp-xyz.scm (cl-colored, ecl-colored, sbcl-colored): New variables. --- gnu/packages/lisp-xyz.scm | 33 +++++++++++++++++++++++++++++++++ 1 file changed, 33 insertions(+) diff --git a/gnu/packages/lisp-xyz.scm b/gnu/packages/lisp-xyz.scm index 467acc8316..7892f28005 100644 --- a/gnu/packages/lisp-xyz.scm +++ b/gnu/packages/lisp-xyz.scm @@ -10428,6 +10428,39 @@ the library does not depend on X11). (define-public ecl-cl-colors2 (sbcl-package->ecl-package sbcl-cl-colors2)) +(define-public sbcl-colored + (let ((commit "bee87efb0b047da0f071f5cf1457997ab5f93feb") + (revision "1")) + (package + (name "sbcl-colored") + (version (git-version "1.0.0" revision commit)) + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/Shinmera/colored/") + (commit commit))) + (file-name (git-file-name name version)) + (sha256 + (base32 "0mpg91r6yfb9xqccd4r8z3hl2qzjhdj6daswb1cinrm8ffxrvy5k")))) + (build-system asdf-build-system/sbcl) + (native-inputs + (list sbcl-parachute)) + (inputs + (list sbcl-documentation-utils)) + (synopsis "Colour representation, conversion, and operation for Common Lisp") + (description + "This is a library for representing and mapping colours between their +various spaces.") + (home-page "https://shinmera.github.io/colored/") + (license license:zlib)))) + +(define-public cl-colored + (sbcl-package->cl-source-package sbcl-colored)) + +(define-public ecl-colored + (sbcl-package->ecl-package sbcl-colored)) + (define-public sbcl-cl-jpeg (let ((commit "ec557038128df6895fbfb743bfe8faf8ec2534af") (revision "1")) From 752b65935d90a54645460033989969790a07862c Mon Sep 17 00:00:00 2001 From: Pierre Neidhardt Date: Mon, 12 Dec 2022 13:50:45 +0100 Subject: [PATCH 106/790] gnu: Add cl-font-discovery. * gnu/packages/lisp-xyz.scm (cl-font-discovery, ecl-font-discovery, sbcl-font-discovery): New variables. --- gnu/packages/lisp-xyz.scm | 32 ++++++++++++++++++++++++++++++++ 1 file changed, 32 insertions(+) diff --git a/gnu/packages/lisp-xyz.scm b/gnu/packages/lisp-xyz.scm index 7892f28005..6cc0ffd9cb 100644 --- a/gnu/packages/lisp-xyz.scm +++ b/gnu/packages/lisp-xyz.scm @@ -20012,6 +20012,38 @@ developing library for Common Lisp.") (define-public cl-liballegro (sbcl-package->cl-source-package sbcl-cl-liballegro)) +(define-public sbcl-font-discovery + (let ((commit "5101ca79151055f3ec9839aae73b8af42b884528") + (revision "1")) + (package + (name "sbcl-font-discovery") + (version (git-version "1.0.0" revision commit)) + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/Shinmera/font-discovery") + (commit commit))) + (file-name (git-file-name "font-discovery" version)) + (sha256 + (base32 "1p9wkwc23rnif8vcjaj5ih1fmr5g57sidqjlz08qw6k0z4f6bia1")))) + (build-system asdf-build-system/sbcl) + (inputs + (list sbcl-cffi sbcl-documentation-utils sbcl-trivial-indent)) + (home-page "https://shinmera.github.io/font-discovery/") + (synopsis "Find system font files matching a font spec") + (description + "This is a library to find system font files. It works on systems with +FontConfig on Linux, BSD. It does not have any foreign dependencies that +aren't already directly available on the system.") + (license license:zlib)))) + +(define-public ecl-font-discovery + (sbcl-package->ecl-package sbcl-font-discovery)) + +(define-public cl-font-discovery + (sbcl-package->cl-source-package sbcl-font-discovery)) + (define-public sbcl-alloy (let ((commit "e86e22c2887836ec31cd97e039f0bca5248d8f1c") (revision "1")) From 63b508e4fb16e605132ad759e5b6ce2cd5aafbdd Mon Sep 17 00:00:00 2001 From: Pierre Neidhardt Date: Mon, 12 Dec 2022 15:28:14 +0100 Subject: [PATCH 107/790] gnu: Add cl-uax-14. * gnu/packages/lisp-xyz.scm (cl-uax-14, ecl-uax-14, sbcl-uax-14): New variables. --- gnu/packages/lisp-xyz.scm | 47 +++++++++++++++++++++++++++++++++++++++ 1 file changed, 47 insertions(+) diff --git a/gnu/packages/lisp-xyz.scm b/gnu/packages/lisp-xyz.scm index 6cc0ffd9cb..fcf09580b7 100644 --- a/gnu/packages/lisp-xyz.scm +++ b/gnu/packages/lisp-xyz.scm @@ -1425,6 +1425,53 @@ within.") (define-public cl-ubiquitous (sbcl-package->cl-source-package sbcl-ubiquitous)) +(define-public sbcl-uax-14 + (let ((commit "0432162525119c401d3d705bb9bcc9580a03914f") + (revision "1")) + (package + (name "sbcl-uax-14") + (version (git-version "1.0.0" revision commit)) + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/Shinmera/uax-14") + (commit commit))) + (file-name (git-file-name "uax-14" version)) + (sha256 + (base32 "1sb2s58k01yjaggaq8i7kbyfsh6mzyqbiz1vm59smxn9qqwd8apm")))) + (build-system asdf-build-system/sbcl) + (native-inputs + (list sbcl-parachute sbcl-cl-ppcre)) + (inputs + (list sbcl-documentation-utils)) + (arguments + `(#:asd-systems '("uax-14"))) + (home-page "https://shinmera.github.io/uax-14/") + (synopsis "Unicode Standard Annex #14 for standardised line breaking") + (description + "This is an implementation of the Unicode Standards Annex +#14 (@url{http://www.unicode.org/reports/tr14/}) line breaking algorithm. It +provides a fast and convenient way to determine line breaking opportunities in +text. + +Note that this algorithm does not support break opportunities that require +morphological analysis. In order to handle such cases, please consult a system +that provides this kind of capability, such as a hyphenation algorithm. + +Also note that this system is completely unaware of layouting decisions. Any +kind of layouting decisions, such as which breaks to pick, how to space +between words, how to handle bidirectionality, and what to do in emergency +situations when there are no breaks on an overfull line are left up to the +user.") + (license license:zlib)))) + +(define-public ecl-uax-14 + (sbcl-package->ecl-package sbcl-uax-14)) + +(define-public cl-uax-14 + (sbcl-package->cl-source-package sbcl-uax-14)) + (define-public sbcl-uax-15 (package (name "sbcl-uax-15") From 4f64d30b5d67921a68ed6e7637a227f20afea451 Mon Sep 17 00:00:00 2001 From: Pierre Neidhardt Date: Mon, 12 Dec 2022 15:51:16 +0100 Subject: [PATCH 108/790] gnu: Add cl-binpack. * gnu/packages/lisp-xyz.scm (cl-binpack, ecl-binpack, sbcl-binpack): New variables. --- gnu/packages/lisp-xyz.scm | 32 ++++++++++++++++++++++++++++++++ 1 file changed, 32 insertions(+) diff --git a/gnu/packages/lisp-xyz.scm b/gnu/packages/lisp-xyz.scm index fcf09580b7..3d4b833a60 100644 --- a/gnu/packages/lisp-xyz.scm +++ b/gnu/packages/lisp-xyz.scm @@ -17536,6 +17536,38 @@ compiled foreign library collection.") (define-public cl-conspack (sbcl-package->cl-source-package sbcl-cl-conspack)) +(define-public sbcl-binpack + (let ((commit "e67f56bb697bdeac81e28e1cca4a5d117a9cf125") + (revision "1")) + (package + (name "sbcl-binpack") + (version (git-version "0.0.1" revision commit)) + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/lispgames/binpack") + (commit commit))) + (file-name (git-file-name "binpack" version)) + (sha256 + (base32 "1pcnsg60pqywd3k72m5pwimq01sm3jyvc1c3rbkij740r7grdxi1")))) + (build-system asdf-build-system/sbcl) + (native-inputs + (list sbcl-parachute)) + (inputs + (list sbcl-alexandria)) + (home-page "https://github.com/lispgames/binpack") + (synopsis "Common Lisp rectangle packer for sprite/texture atlases") + (description + "This library features a rectangle packer for sprite and texture atlases.") + (license license:expat)))) + +(define-public ecl-binpack + (sbcl-package->ecl-package sbcl-binpack)) + +(define-public cl-binpack + (sbcl-package->cl-source-package sbcl-binpack)) + (define-public sbcl-cl-opengl (let ((commit "e2d83e0977b7e7ac3f3d348d8ccc7ccd04e74d59") (revision "1")) From f0ebbe1598838a26b9cadb6c0de57b69df8984c7 Mon Sep 17 00:00:00 2001 From: Pierre Neidhardt Date: Mon, 12 Dec 2022 15:53:19 +0100 Subject: [PATCH 109/790] gnu: sbcl-cl-vectors: Build all subsystems. * gnu/packages/lisp-xyz.scm (sbcl-cl-vectors)[arguments]: Build cl-paths, cl-aa and cl-aa-misc as well. --- gnu/packages/lisp-xyz.scm | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/gnu/packages/lisp-xyz.scm b/gnu/packages/lisp-xyz.scm index 3d4b833a60..2ce352fb24 100644 --- a/gnu/packages/lisp-xyz.scm +++ b/gnu/packages/lisp-xyz.scm @@ -1639,7 +1639,10 @@ reading and writing.") `(("zpb-ttf" ,sbcl-zpb-ttf))) (arguments '(#:asd-systems '("cl-vectors" - "cl-paths-ttf"))) + "cl-paths" + "cl-paths-ttf" + "cl-aa" + "cl-aa-misc"))) (home-page "http://projects.tuxee.net/cl-vectors/") (synopsis "Create, transform and render anti-aliased vectorial paths") (description From e7eefbf85cfd723e508d559d4bd5f1cbe4a2d630 Mon Sep 17 00:00:00 2001 From: Pierre Neidhardt Date: Mon, 12 Dec 2022 15:54:48 +0100 Subject: [PATCH 110/790] gnu: Add cl-sdf. * gnu/packages/lisp-xyz.scm (cl-sdf, ecl-sdf, sbcl-sdf): New variables. --- gnu/packages/lisp-xyz.scm | 57 +++++++++++++++++++++++++++++++++++++++ 1 file changed, 57 insertions(+) diff --git a/gnu/packages/lisp-xyz.scm b/gnu/packages/lisp-xyz.scm index 2ce352fb24..17d6016d9e 100644 --- a/gnu/packages/lisp-xyz.scm +++ b/gnu/packages/lisp-xyz.scm @@ -10802,6 +10802,63 @@ read/write Bit Map Font (BMF) into text, JSON and XML.") (define-public cl-3b-bmfont (sbcl-package->cl-source-package sbcl-3b-bmfont)) +(define sbcl-3b-bmfont/shinmera + (let ((commit "58e529d24b7799d56b4b3f9c8a953b585d42c7d2") + (revision "1")) + (package (inherit sbcl-3b-bmfont) + (version (git-version "0.0.1" revision commit)) + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/Shinmera/3b-bmfont/") + (commit commit))) + (file-name (git-file-name "3b-bmfont2" version)) + (sha256 + (base32 "17zby669b64rhxhk2szamzdgvispimh6ici05xa6x2vz4rvk71jq"))))))) + +(define-public sbcl-sdf + ;; Shinmera's fork required for Alloy. + (let ((commit "e1ab3ac4ea52c0e0119b832f428c71f580b4d83b") + (revision "1")) + (package + (name "sbcl-sdf") + (version (git-version "0.0.1" revision commit)) + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/Shinmera/sdf") + (commit commit))) + (file-name (git-file-name "sdf" version)) + (sha256 + (base32 "1cyq4hkgiw9mnb87ah6xw19cybfs9hfbjvg1ch2mf4cr0ism0nvn")))) + (build-system asdf-build-system/sbcl) + (inputs + (list sbcl-zpb-ttf + sbcl-cl-vectors + sbcl-opticl + sbcl-binpack + sbcl-3b-bmfont/shinmera + sbcl-pathname-utils)) + (arguments + `(#:asd-systems '("sdf" "sdf/bmfont"))) + (home-page "https://github.com/Shinmera/sdf") + (synopsis "Signed distance font atlas generator") + (description + "This library generates +sdf (@url{https://steamcdn-a.akamaihd.net/apps/valve/2007/SIGGRAPH2007_AlphaTestedMagnification.pdf}), +psdf and +msdf (@url{https://github.com/Chlumsky/msdfgen/files/3050967/thesis.pdf}) +atlases.") + (license license:expat)))) + +(define-public ecl-sdf + (sbcl-package->ecl-package sbcl-sdf)) + +(define-public cl-sdf + (sbcl-package->cl-source-package sbcl-sdf)) + (define-public sbcl-zpng (package (name "sbcl-zpng") From 706dead6796e83653da6c40674e151aae1111aa8 Mon Sep 17 00:00:00 2001 From: Pierre Neidhardt Date: Mon, 12 Dec 2022 16:02:02 +0100 Subject: [PATCH 111/790] gnu: sbcl-3b-bmfont: Update to 20220327. * gnu/packages/lisp-xyz.scm (sbcl-3b-bmfont): Update to 20220327. --- gnu/packages/lisp-xyz.scm | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/gnu/packages/lisp-xyz.scm b/gnu/packages/lisp-xyz.scm index 17d6016d9e..ca238a8642 100644 --- a/gnu/packages/lisp-xyz.scm +++ b/gnu/packages/lisp-xyz.scm @@ -10761,8 +10761,8 @@ performance and correctness.") (sbcl-package->ecl-package sbcl-png-read)) (define-public sbcl-3b-bmfont - (let ((commit "d1b5bec0de580c2d08ec947a93c56b1400f2a37a") - (revision "1")) + (let ((commit "48a38f52d282064829851c484d9e7dee0ffe9e72") + (revision "2")) (package (name "sbcl-3b-bmfont") (version (git-version "0.0.1" revision commit)) @@ -10774,7 +10774,7 @@ performance and correctness.") (commit commit))) (file-name (git-file-name "3b-bmfont" version)) (sha256 - (base32 "12sgf7m0h6fqzhvkas7vmci6mprj3j3fnz778jlbqbsydln6v2yc")))) + (base32 "0v4lcrlpx60ayg0g5b10q2hjh1iaanln4ck0hm1rvjxm39gl2d86")))) (build-system asdf-build-system/sbcl) (arguments `(#:asd-systems From 417604ec25d78f71a287d312d5a7b9b9b358bb53 Mon Sep 17 00:00:00 2001 From: Pierre Neidhardt Date: Mon, 12 Dec 2022 16:12:07 +0100 Subject: [PATCH 112/790] gnu: sbcl-alloy: Update to 20221126. * gnu/packages/lisp-xyz.scm (sbcl-alloy): Update to 20221126. --- gnu/packages/lisp-xyz.scm | 21 +++++++++++++++++---- 1 file changed, 17 insertions(+), 4 deletions(-) diff --git a/gnu/packages/lisp-xyz.scm b/gnu/packages/lisp-xyz.scm index ca238a8642..364be8c7a5 100644 --- a/gnu/packages/lisp-xyz.scm +++ b/gnu/packages/lisp-xyz.scm @@ -20184,8 +20184,8 @@ aren't already directly available on the system.") (sbcl-package->cl-source-package sbcl-font-discovery)) (define-public sbcl-alloy - (let ((commit "e86e22c2887836ec31cd97e039f0bca5248d8f1c") - (revision "1")) + (let ((commit "ea02e4576fd92917201b3c9b63dd3cdc72045dbf") + (revision "2")) (package (name "sbcl-alloy") (version (git-version "0.0.0" revision commit)) @@ -20197,12 +20197,25 @@ aren't already directly available on the system.") (commit commit))) (file-name (git-file-name "alloy" version)) (sha256 - (base32 "1jsqjr6sf86hcdvnjp4gd10qv0r7kfkr9hmda85irb5lha4q9n7w")))) + (base32 "1g8ibvlajhlbdrmny7ck55ilv1shjdpj38q380wri4mavfymjw5f")))) (build-system asdf-build-system/sbcl) (native-inputs (list sbcl-alexandria sbcl-parachute)) (inputs - (list sbcl-array-utils sbcl-closer-mop sbcl-documentation-utils)) + (list sbcl-array-utils sbcl-closer-mop sbcl-documentation-utils + sbcl-float-features sbcl-colored sbcl-stealth-mixin + sbcl-cl-opengl sbcl-font-discovery sbcl-uax-14 sbcl-sdf)) + (arguments + ;; Dismiss alloy-svg, since it is not completed: + ;; https://github.com/Shirakumo/alloy/issues/24 + '(#:asd-systems '("alloy" + "alloy-windowing" + "alloy-animation" + "alloy-simple" + "alloy-simple-presentations" + "alloy-opengl" + "alloy-opengl-msdf" + "alloy-opengl-png"))) (home-page "https://shirakumo.github.io/alloy/") (synopsis "Common Lisp user interface protocol and toolkit implementation") From 01f4617b99ba2d4b971fb0a2762823b4d52ab33d Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Tue, 13 Dec 2022 13:28:25 +0100 Subject: [PATCH 113/790] gnu: gst-kaldi-nnet2-online: Update to 0-3.7888ae5. * gnu/packages/machine-learning.scm (gst-kaldi-nnet2-online): Update to 0-3.7888ae5. [arguments]: Do to quote list; remove trailing #T from build phases; augment CPLUS_INCLUDE_PATH instead of replacing it. [inputs]: Replace openfst with openfst-1.7.3. --- gnu/packages/machine-learning.scm | 64 +++++++++++++++---------------- 1 file changed, 32 insertions(+), 32 deletions(-) diff --git a/gnu/packages/machine-learning.scm b/gnu/packages/machine-learning.scm index 3dbe54a24a..ef7847004b 100644 --- a/gnu/packages/machine-learning.scm +++ b/gnu/packages/machine-learning.scm @@ -1816,8 +1816,8 @@ written in C++.") (find-files "." "\\.h"))))))))))) (define-public gst-kaldi-nnet2-online - (let ((commit "cb227ef43b66a9835c14eb0ad39e08ee03c210ad") - (revision "2")) + (let ((commit "7888ae562a65bd7e406783ce2c33535bc66a30ef") + (revision "3")) (package (name "gst-kaldi-nnet2-online") (version (git-version "0" revision commit)) @@ -1829,12 +1829,13 @@ written in C++.") (file-name (git-file-name name version)) (sha256 (base32 - "1i6ffwiavxx07ri0lxix6s8q0r31x7i4xxvhys5jxkixf5q34w8g")))) + "0xp59a6lmx1y24i8bkmxcm27lhm5x5m6y41670yjzhamcbnx8jcr")))) (build-system gnu-build-system) (arguments - `(#:tests? #f ; there are none - #:make-flags - (list (string-append "SHELL=" + (list + #:tests? #f ; there are none + #:make-flags + '(list (string-append "SHELL=" (assoc-ref %build-inputs "bash") "/bin/bash") (string-append "KALDI_ROOT=" (assoc-ref %build-inputs "kaldi-src")) @@ -1842,33 +1843,32 @@ written in C++.") (assoc-ref %build-inputs "kaldi") "/lib") "KALDI_FLAVOR=dynamic") #:phases - (modify-phases %standard-phases - (add-after 'unpack 'chdir - (lambda _ (chdir "src") #t)) - (replace 'configure - (lambda* (#:key inputs #:allow-other-keys) - (let ((glib (assoc-ref inputs "glib"))) - (setenv "CXXFLAGS" "-fPIC") - (setenv "CPLUS_INCLUDE_PATH" - (string-append glib "/include/glib-2.0:" - glib "/lib/glib-2.0/include:" - (assoc-ref inputs "gstreamer") - "/include/gstreamer-1.0"))) - (substitute* "Makefile" - (("include \\$\\(KALDI_ROOT\\)/src/kaldi.mk") "") - (("\\$\\(error Cannot find") "#")) - #t)) - (add-before 'build 'build-depend - (lambda* (#:key make-flags #:allow-other-keys) - (apply invoke "make" "depend" make-flags))) - (replace 'install - (lambda* (#:key outputs #:allow-other-keys) - (let* ((out (assoc-ref outputs "out")) - (lib (string-append out "/lib/gstreamer-1.0"))) - (install-file "libgstkaldinnet2onlinedecoder.so" lib) - #t)))))) + '(modify-phases %standard-phases + (add-after 'unpack 'chdir + (lambda _ (chdir "src"))) + (replace 'configure + (lambda* (#:key inputs #:allow-other-keys) + (let ((glib (assoc-ref inputs "glib"))) + (setenv "CXXFLAGS" "-fPIC") + (setenv "CPLUS_INCLUDE_PATH" + (string-append glib "/include/glib-2.0:" + glib "/lib/glib-2.0/include:" + (assoc-ref inputs "gstreamer") + "/include/gstreamer-1.0:" + (getenv "CPLUS_INCLUDE_PATH")))) + (substitute* "Makefile" + (("include \\$\\(KALDI_ROOT\\)/src/kaldi.mk") "") + (("\\$\\(error Cannot find") "#")))) + (add-before 'build 'build-depend + (lambda* (#:key make-flags #:allow-other-keys) + (apply invoke "make" "depend" make-flags))) + (replace 'install + (lambda* (#:key outputs #:allow-other-keys) + (let* ((out (assoc-ref outputs "out")) + (lib (string-append out "/lib/gstreamer-1.0"))) + (install-file "libgstkaldinnet2onlinedecoder.so" lib))))))) (inputs - (list glib gstreamer jansson openfst kaldi)) + (list glib gstreamer jansson openfst-1.7.3 kaldi)) (native-inputs `(("bash" ,bash) ("glib:bin" ,glib "bin") ; glib-genmarshal From 79cf84c7ab5fd5a13ad4037e61dc22d73be375e1 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Tue, 13 Dec 2022 13:36:52 +0100 Subject: [PATCH 114/790] gnu: kaldi-gstreamer-server: Remove trailing #T from build phases. * gnu/packages/machine-learning.scm (kaldi-gstreamer-server)[arguments]: Remove trailing #T from build phases. --- gnu/packages/machine-learning.scm | 6 ++---- 1 file changed, 2 insertions(+), 4 deletions(-) diff --git a/gnu/packages/machine-learning.scm b/gnu/packages/machine-learning.scm index ef7847004b..2a70119680 100644 --- a/gnu/packages/machine-learning.scm +++ b/gnu/packages/machine-learning.scm @@ -1927,8 +1927,7 @@ automatically.") "-m" "compileall" "-f" ; force rebuild ,file))) - (find-files "." "\\.py$"))) - #t)) + (find-files "." "\\.py$"))))) (replace 'install (lambda* (#:key inputs outputs #:allow-other-keys) (let* ((out (assoc-ref outputs "out")) @@ -1967,8 +1966,7 @@ exec ~a ~a/~a \"$@\"~%" (list server client worker) (list "master_server.py" "client.py" - "worker.py"))) - #t)))))) + "worker.py"))))))))) (inputs `(("gst-kaldi-nnet2-online" ,gst-kaldi-nnet2-online) ("python" ,python-wrapper) From 8466aceb13655b2129e18ed49c7c55bb418b3ad6 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Tue, 13 Dec 2022 13:37:21 +0100 Subject: [PATCH 115/790] gnu: kaldi-gstreamer-server: Drop input labels. * gnu/packages/machine-learning.scm (kaldi-gstreamer-server)[inputs]: Drop package labels. --- gnu/packages/machine-learning.scm | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) diff --git a/gnu/packages/machine-learning.scm b/gnu/packages/machine-learning.scm index 2a70119680..2d12068c05 100644 --- a/gnu/packages/machine-learning.scm +++ b/gnu/packages/machine-learning.scm @@ -1968,11 +1968,11 @@ exec ~a ~a/~a \"$@\"~%" "client.py" "worker.py"))))))))) (inputs - `(("gst-kaldi-nnet2-online" ,gst-kaldi-nnet2-online) - ("python" ,python-wrapper) - ("python-pygobject" ,python-pygobject) - ("python-pyyaml" ,python-pyyaml) - ("python-tornado" ,python-tornado-6))) + (list gst-kaldi-nnet2-online + python-wrapper + python-pygobject + python-pyyaml + python-tornado-6)) (home-page "https://github.com/alumae/kaldi-gstreamer-server") (synopsis "Real-time full-duplex speech recognition server") (description "This is a real-time full-duplex speech recognition server, From c978ae3c6b8cc1c719f7caa59beee75863f4bda3 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Tue, 13 Dec 2022 13:37:48 +0100 Subject: [PATCH 116/790] gnu: kaldi-gstreamer-server: Update to 0-3.f79e204. * gnu/packages/machine-learning.scm (kaldi-gstreamer-server): Update to 0-3.f79e204. --- gnu/packages/machine-learning.scm | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/gnu/packages/machine-learning.scm b/gnu/packages/machine-learning.scm index 2d12068c05..72458c3f66 100644 --- a/gnu/packages/machine-learning.scm +++ b/gnu/packages/machine-learning.scm @@ -1884,8 +1884,8 @@ automatically.") (define-public kaldi-gstreamer-server ;; This is the tip of the py3 branch - (let ((commit "f68cab490be7eb0da2af1475fbc16655f50a60cb") - (revision "2")) + (let ((commit "f79e204d751a5964918001822e4520fa2acfd246") + (revision "3")) (package (name "kaldi-gstreamer-server") (version (git-version "0" revision commit)) @@ -1897,7 +1897,7 @@ automatically.") (file-name (git-file-name name version)) (sha256 (base32 - "17lh1368vkg8ngrcbn2phvigzlmalrqg6djx2gg61qq1a0nj87dm")))) + "1iijq8jmgdxr7961inal1ggs496ymxradm51m4sqx8vl983x14y8")))) (build-system gnu-build-system) (arguments `(#:tests? #f ; there are no tests that can be run automatically From f764947dab1b540cea30d9299e3b58ea622c5e8e Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Tue, 13 Dec 2022 13:41:16 +0100 Subject: [PATCH 117/790] gnu: kaldi: Remove trailing #T from build phases. * gnu/packages/machine-learning.scm (kaldi)[arguments]: Remove trailing #T from build phases. --- gnu/packages/machine-learning.scm | 8 +++----- 1 file changed, 3 insertions(+), 5 deletions(-) diff --git a/gnu/packages/machine-learning.scm b/gnu/packages/machine-learning.scm index 72458c3f66..f878cc8a36 100644 --- a/gnu/packages/machine-learning.scm +++ b/gnu/packages/machine-learning.scm @@ -1625,7 +1625,7 @@ discrete, and conditional dimensions.") #:phases (modify-phases %standard-phases (add-after 'unpack 'chdir - (lambda _ (chdir "src") #t)) + (lambda _ (chdir "src"))) (replace 'configure (lambda* (#:key build system inputs outputs #:allow-other-keys) (when (not (or (string-prefix? "x86_64" system) @@ -1671,8 +1671,7 @@ discrete, and conditional dimensions.") (invoke "make" "-C" "onlinebin" "depend") (invoke "make" "-C" "onlinebin") (invoke "make" "-C" "gst-plugin" "depend") - (invoke "make" "-C" "gst-plugin") - #t)) + (invoke "make" "-C" "gst-plugin"))) ;; TODO: also install the executables. (replace 'install (lambda* (#:key outputs #:allow-other-keys) @@ -1693,8 +1692,7 @@ discrete, and conditional dimensions.") (install-file file target-dir))) (find-files "." "\\.h")) (install-file "gst-plugin/libgstonlinegmmdecodefaster.so" - (string-append lib "/gstreamer-1.0")) - #t)))))) + (string-append lib "/gstreamer-1.0")))))))) (inputs (list alsa-lib `(,gfortran "lib") From 81841559f459e562c0e23b87fbdc6ed096d2b580 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Tue, 13 Dec 2022 13:44:39 +0100 Subject: [PATCH 118/790] gnu: kaldi: Update to 0-1.be22248. * gnu/packages/machine-learning.scm (kaldi): Update to 0-1.be22248. --- gnu/packages/machine-learning.scm | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/gnu/packages/machine-learning.scm b/gnu/packages/machine-learning.scm index f878cc8a36..75cc100851 100644 --- a/gnu/packages/machine-learning.scm +++ b/gnu/packages/machine-learning.scm @@ -1604,8 +1604,8 @@ discrete, and conditional dimensions.") ;; There have been no proper releases yet. (define-public kaldi - (let ((commit "dd107fd594ac58af962031c1689abfdc10f84452") - (revision "0") + (let ((commit "be22248e3a166d9ec52c78dac945f471e7c3a8aa") + (revision "1") (openfst openfst-1.7.3)) ;; Temporary bypass for upstream issues (package (name "kaldi") @@ -1618,7 +1618,7 @@ discrete, and conditional dimensions.") (file-name (git-file-name name version)) (sha256 (base32 - "0iqbzgn7gzmgwvjfzifpbwwidxx887qmlgmsjkg7b1yzyfv00l21")))) + "1wkxz3p0h68mxbg41i1wygir2r4rraxbb4672xkkvvs85r6c8r8i")))) (build-system gnu-build-system) (arguments `(#:test-target "test" From 2fb187ed7c2ae9b4c46ba128c105685e3adda2df Mon Sep 17 00:00:00 2001 From: Christopher Baines Date: Tue, 13 Dec 2022 13:11:40 +0000 Subject: [PATCH 119/790] gnu: guix-data-service: Update to 0.0.1-36.7b69611. * gnu/packages/web.scm (guix-data-service): Update to 0.0.1-36.7b69611. --- gnu/packages/web.scm | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/gnu/packages/web.scm b/gnu/packages/web.scm index d59a5c0a3c..dcb7b3872a 100644 --- a/gnu/packages/web.scm +++ b/gnu/packages/web.scm @@ -4659,8 +4659,8 @@ CDF, Atom 0.3, and Atom 1.0 feeds.") license:freebsd-doc)))) ; documentation (define-public guix-data-service - (let ((commit "95064d39a337da9f2eb7d5675e0e511301466f77") - (revision "34")) + (let ((commit "7b69611755ac3b9132710d83a1139b4c5606578d") + (revision "36")) (package (name "guix-data-service") (version (string-append "0.0.1-" revision "." (string-take commit 7))) @@ -4672,7 +4672,7 @@ CDF, Atom 0.3, and Atom 1.0 feeds.") (file-name (git-file-name name version)) (sha256 (base32 - "1nkasn2wk36jfnfan619lv604cjj6ppwvmiljckcyyr57yynqbr4")))) + "0lmvmalgfbc6q80f8dwqikdd5kna2vl4jlmf2li206hmcq2hzh6p")))) (build-system gnu-build-system) (arguments '(#:modules ((guix build utils) From 27efd3ed3ce325ef8a70e737b381259bccb9420c Mon Sep 17 00:00:00 2001 From: Martin Schmidt Date: Sat, 26 Nov 2022 18:35:54 +0100 Subject: [PATCH 120/790] gnu: Add gst-plugins-good-qt. * gnu/packages/gstreamer.scm (gst-plugins-good-qt): New variable. Signed-off-by: Christopher Baines --- gnu/packages/gstreamer.scm | 11 +++++++++++ 1 file changed, 11 insertions(+) diff --git a/gnu/packages/gstreamer.scm b/gnu/packages/gstreamer.scm index d846c79526..916ab2e990 100644 --- a/gnu/packages/gstreamer.scm +++ b/gnu/packages/gstreamer.scm @@ -734,6 +734,17 @@ model to base your own plug-in on, here it is.") (home-page "https://gstreamer.freedesktop.org/") (license license:lgpl2.0+))) +(define-public gst-plugins-good-qt + (package + (inherit gst-plugins-good) + (name "gst-plugins-good-qt") + (inputs + (modify-inputs (package-inputs gst-plugins-good) + (prepend qtbase-5 + qtdeclarative-5 + qtwayland-5 + qtx11extras))))) + (define-public gst-plugins-bad (package (name "gst-plugins-bad") From 34cf5e06a9acd021d1233587e140759bba452b35 Mon Sep 17 00:00:00 2001 From: Martin Schmidt Date: Sat, 26 Nov 2022 18:35:55 +0100 Subject: [PATCH 121/790] gnu: nheko: Support video calls. * gnu/packages/messaging.scm (nheko)[inputs]: Replace GST-PLUGINS-GOOD with GST-PLUGINS-GOOD-QT to fix video calls. Signed-off-by: Christopher Baines --- gnu/packages/messaging.scm | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/gnu/packages/messaging.scm b/gnu/packages/messaging.scm index fd7cbf921d..8b35480400 100644 --- a/gnu/packages/messaging.scm +++ b/gnu/packages/messaging.scm @@ -2459,7 +2459,7 @@ for the Matrix protocol. It is built on to of @code{Boost.Asio}.") curl gst-plugins-base gst-plugins-bad ; sdp & webrtc for voip - gst-plugins-good ; rtpmanager for voip + gst-plugins-good-qt ; rtpmanager for voip json-modern-cxx libevent libnice ; for voip From 36bd9121d670b6bfec19d6033d9d3e1bb3f3d884 Mon Sep 17 00:00:00 2001 From: "Paul A. Patience" Date: Sun, 27 Nov 2022 04:33:35 +0000 Subject: [PATCH 122/790] gnu: Add rust-csv-index-0.1. * gnu/packages/crates-io.scm (rust-csv-index-0.1): New variable. Signed-off-by: Christopher Baines --- gnu/packages/crates-io.scm | 24 ++++++++++++++++++++++++ 1 file changed, 24 insertions(+) diff --git a/gnu/packages/crates-io.scm b/gnu/packages/crates-io.scm index 24c6207d8d..f0f40207b9 100644 --- a/gnu/packages/crates-io.scm +++ b/gnu/packages/crates-io.scm @@ -30,6 +30,7 @@ ;;; Copyright © 2022 Gabriel Arazas ;;; Copyright © 2022 ( ;;; Copyright © 2022 Greg Hogan +;;; Copyright © 2022 Paul A. Patience ;;; ;;; This file is part of GNU Guix. ;;; @@ -14539,6 +14540,29 @@ processors.") "Bare bones CSV parsing with no_std support.") (license (list license:unlicense license:expat)))) +(define-public rust-csv-index-0.1 + (package + (name "rust-csv-index") + (version "0.1.6") + (source + (origin + (method url-fetch) + (uri (crate-uri "csv-index" version)) + (file-name (string-append name "-" version ".tar.gz")) + (sha256 + (base32 "01048y84y0bakqm0x4y1svjv6lzc753b9q598xp7xgcqrdgi6x7j")))) + (build-system cargo-build-system) + (arguments + `(#:cargo-inputs + (("rust-byteorder" ,rust-byteorder-1) + ("rust-csv" ,rust-csv-1)))) + (home-page "https://github.com/BurntSushi/rust-csv") + (synopsis "On-disk CSV indexing data structures") + (description + "A collection of data structures for indexing CSV data, with a focus on +data structures that can be easily serialized to and deserialized from disk.") + (license (list license:unlicense license:expat)))) + (define-public rust-cstr-core-0.2 (package (name "rust-cstr-core") From 866eb7fffbb4a011808d8231243c39c4d5e0f004 Mon Sep 17 00:00:00 2001 From: EuAndreh Date: Tue, 29 Nov 2022 21:29:00 -0300 Subject: [PATCH 123/790] gnu: Add tmux-plugin-resurrect. * gnu/packages/tmux.scm (tmux-plugin-resurrect): New variable. Signed-off-by: Christopher Baines --- gnu/packages/tmux.scm | 50 +++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 50 insertions(+) diff --git a/gnu/packages/tmux.scm b/gnu/packages/tmux.scm index 10b78cccf7..67ce18fea1 100644 --- a/gnu/packages/tmux.scm +++ b/gnu/packages/tmux.scm @@ -267,3 +267,53 @@ following features: @item Generate command lines from standard input (Pipe mode). @end itemize") (license license:expat))) + +(define-public tmux-plugin-resurrect + (let ((commit "a2ddfb96b94bb64a7a2e3f5fa2a7c57dce8ad579") + (revision "0")) + (package + (name "tmux-plugin-resurrect") + (version (git-version "0" revision commit)) + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/tmux-plugins/tmux-resurrect/") + (commit commit))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "1gc8z99na1d4scn2kq4alwyn43h3r7ykz9bkhcypjh8iri6dsl0c")))) + (build-system trivial-build-system) + (arguments + `(#:modules ((guix build utils)) + #:builder (begin + (use-modules (guix build utils)) + (let ((out (string-append %output + "/share/tmux-plugins/resurrect/"))) + (mkdir-p out) + (copy-recursively (assoc-ref %build-inputs "source") out))))) + (synopsis "Restore tmux environment after system restart") + (description + "This plugin goes to great lengths to save and restore all the details +from your tmux environment. Here's what's been taken care of: + +@itemize +@item all sessions, windows, panes and their order +@item current working directory for each pane +@item exact pane layouts within windows (even when zoomed) +@item active and alternative session +@item active and alternative window for each session +@item windows with focus +@item active pane for each window +@item \"grouped sessions\" (useful feature when using tmux with multiple monitors) +@item programs running within a pane! More details in the restoring programs doc. +@end itemize + +Optional: + +@itemize +@item restoring vim and neovim sessions +@item restoring pane contents +@end itemize") + (home-page "https://github.com/tmux-plugins/tmux-resurrect/") + (license license:expat)))) From 1a0dcc21123c0a9e8c16d0989df1db00092ac3e7 Mon Sep 17 00:00:00 2001 From: Sharlatan Hellseher Date: Sat, 3 Dec 2022 23:14:41 +0000 Subject: [PATCH 124/790] gnu: python-asdf-astropy: Update to 0.3.0. * gnu/packages/astronomy.scm (python-asdf-astropy): Update to 0.3.0. Signed-off-by: Christopher Baines --- gnu/packages/astronomy.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/astronomy.scm b/gnu/packages/astronomy.scm index f99dbcbf06..5f19fc4764 100644 --- a/gnu/packages/astronomy.scm +++ b/gnu/packages/astronomy.scm @@ -2505,13 +2505,13 @@ install an implementation package such as asdf-astropy.") (define-public python-asdf-astropy (package (name "python-asdf-astropy") - (version "0.2.2") + (version "0.3.0") (source (origin (method url-fetch) (uri (pypi-uri "asdf_astropy" version)) (sha256 - (base32 "1b0v4cl7xvly3x1k5k2rvc2l32jqgqp0iyf1j20fkvj450sx74f2")))) + (base32 "1gp5iav0a9g9q0zb22vhzi3v9vwk5wn2nxvr3mvi3bsdcdj3h23v")))) (build-system pyproject-build-system) (native-inputs (list python-coverage From 0682e7c2e36933c5447678549c8e61bd1271d92c Mon Sep 17 00:00:00 2001 From: Sharlatan Hellseher Date: Mon, 5 Dec 2022 22:59:12 +0000 Subject: [PATCH 125/790] gnu: python-h5netcdf: Update to 1.1.0. * gnu/packages/python-xyz.scm (python-h5netcdf): Update to 1.1.0. [build-system]: Use pyproject-build-system, to simplify package. [description]: Style content and add links to referenced projects. Signed-off-by: Christopher Baines --- gnu/packages/python-xyz.scm | 21 ++++++++------------- 1 file changed, 8 insertions(+), 13 deletions(-) diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index 2279503d63..3ea2763b49 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -1759,21 +1759,14 @@ NetCDF files can also be read and modified. Python-HDF4 is a fork of (define-public python-h5netcdf (package (name "python-h5netcdf") - (version "1.0.1") + (version "1.1.0") (source (origin (method url-fetch) (uri (pypi-uri "h5netcdf" version)) (sha256 - (base32 "1b2dcgf5rwy7pb7hr4prkc5vgcw9qc2was20dmnj90lbrpx08rvp")))) - (build-system python-build-system) - (arguments - (list #:phases - #~(modify-phases %standard-phases - (replace 'check - (lambda* (#:key tests? #:allow-other-keys) - (when tests? - (invoke "pytest" "-vv" "h5netcdf/tests"))))))) + (base32 "0mmzfr6k55zqxxpb64gvdqisak8s1zb2r04yzkmp0wzd7dbknb4k")))) + (build-system pyproject-build-system) (native-inputs (list python-netcdf4 python-pytest @@ -1782,9 +1775,11 @@ NetCDF files can also be read and modified. Python-HDF4 is a fork of (list python-h5py python-packaging)) (home-page "https://h5netcdf.org") (synopsis "Python interface for the netCDF4 file-format based on h5py") - (description "This package provides Python interface for the netCDF4 -file-format that reads and writes local or remote HDF5 files directly via h5py -or h5pyd, without relying on the Unidata netCDF library") + (description "This package provides a Python interface for the netCDF4 +file-format that reads and writes local or remote HDF5 files directly via +@url{h5py, https://www.h5py.org/} or @url{h5pyd, +https://github.com/HDFGroup/h5pyd}, without relying on the Unidata netCDF +library.") (license license:bsd-3))) (define-public python-h5py From 1810d67ad46355d299f0b9bf6cca6056ecaffa4d Mon Sep 17 00:00:00 2001 From: jgart Date: Fri, 9 Dec 2022 18:00:45 -0600 Subject: [PATCH 126/790] gnu: mercury-minimal: Update to 22.01.4. * gnu/packages/mercury.scm (mercury-minimal): Update to 22.01.4. [arguments]: Remove obsolete file path, update libatomic-ops, and update libgc-8. Signed-off-by: Christopher Baines --- gnu/packages/mercury.scm | 14 +++++++------- 1 file changed, 7 insertions(+), 7 deletions(-) diff --git a/gnu/packages/mercury.scm b/gnu/packages/mercury.scm index 1c7f5c5f55..8653e3977f 100644 --- a/gnu/packages/mercury.scm +++ b/gnu/packages/mercury.scm @@ -1,5 +1,6 @@ ;;; GNU Guix --- Functional package management for GNU ;;; Copyright © 2020 Brett Gilio +;;; Copyright © 2022 jgart ;;; ;;; This file is part of GNU Guix. ;;; @@ -56,7 +57,7 @@ (define-public mercury-minimal (package (name "mercury-minimal") - (version "20.06.1") + (version "22.01.4") (source (origin (method url-fetch) (uri (string-append @@ -64,7 +65,7 @@ version ".tar.gz")) (sha256 (base32 - "07qwkk871yxd4q1sw5xv26g8jrpvnpprmzvfd7zg7i142kl3l2gg")))) + "1vakjg4rqpplkxw7k91qv8jvlasrr6iwrzrylwqllbq088qs0mbp")))) (build-system gnu-build-system) (arguments `(#:modules ((guix build gnu-build-system) @@ -112,7 +113,6 @@ "scripts/Mmake.vars.in" "scripts/mdb.in" "scripts/rs6000_hack" - "scripts/fullarch" "scripts/mmc.in" "scripts/canonical_grade" "scripts/mprof.in" @@ -143,14 +143,14 @@ (gc-fork libatomic-ops "https://github.com/Mercury-Language/libatomic_ops.git" - "49b70d57f6922fd8be55a7dcb77955c8abfc9ae9" - "1flvwscsa6b2b8a38vhhcgl10bbkb5nnihw7s7iia60cinf7wcqm"))) + "95809e50a5ff6e765f1af2f589796970a73e9c00" + "0a1y795bvzwzk1v8d9g6wvifj7hvhmxlir1g581bq2slj16h95iz"))) ("libgc" ,(package-source (gc-fork libgc-7 "https://github.com/Mercury-Language/bdwgc.git" - "43ac2ea45261ba0a715534e9da41b2504904c46a" - "0bmzmbs7id0ndyhy9xli6fhfad1shrim6vmy2k8m1nqr5wb31q76"))) + "def741752f55f9068d4f469a14c4b2c168829730" + "07d94j5l9w6l2kjmcwblgn5lf77aw3r0zjn22pq4hbhknky6ny43"))) ("pkg-config" ,pkg-config))) (synopsis "Pure logic programming language (used only for bootstrapping dependent Mercury)") From 87638cdd48ccf9537e3e5bcc8156df7a38c1e54a Mon Sep 17 00:00:00 2001 From: jgart Date: Fri, 9 Dec 2022 18:00:46 -0600 Subject: [PATCH 127/790] gnu: mercury: Update to 22.01.4. * gnu/packages/mercury.scm (mercury-minimal): Update to 22.01.4. [arguments]: Remove obsolete and non-existent file from being patched. Signed-off-by: Christopher Baines --- gnu/packages/mercury.scm | 5 ++--- 1 file changed, 2 insertions(+), 3 deletions(-) diff --git a/gnu/packages/mercury.scm b/gnu/packages/mercury.scm index 8653e3977f..875e957c9f 100644 --- a/gnu/packages/mercury.scm +++ b/gnu/packages/mercury.scm @@ -171,7 +171,7 @@ separate compilation, and numerous optimization/time trade-offs.") (define-public mercury (package (inherit mercury-minimal) (name "mercury") - (version "20.06.1") + (version "22.01.4") (source (origin (method git-fetch) @@ -183,7 +183,7 @@ separate compilation, and numerous optimization/time trade-offs.") (file-name (git-file-name name version)) (sha256 (base32 - "1b6rmdinw8mj6n9sc7c75kkf42gd2k254rf51x4snlrqckxj7aaz")))) + "0ycy1j9a4rdj6d37x02dj6kyr00mykvc5kykci11fim906d92gzh")))) (arguments (substitute-keyword-arguments (package-arguments mercury-minimal) @@ -205,7 +205,6 @@ separate compilation, and numerous optimization/time trade-offs.") "scripts/Mmake.vars.in" "scripts/mdb.in" "scripts/rs6000_hack" - "scripts/fullarch" "scripts/mmc.in" "scripts/mprof.in" "scripts/gud.el" From 93b0c1e35e2e882b8e38ac2420f526ae941f2c8b Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Tue, 13 Dec 2022 10:11:20 -0500 Subject: [PATCH 128/790] gnu: Add rpi-imager. * gnu/packages/raspberry-pi.scm (rpi-imager): New variable. --- gnu/packages/raspberry-pi.scm | 88 +++++++++++++++++++++++++++++++++++ 1 file changed, 88 insertions(+) diff --git a/gnu/packages/raspberry-pi.scm b/gnu/packages/raspberry-pi.scm index 21bc9a3bd8..c0a2cb5bf2 100644 --- a/gnu/packages/raspberry-pi.scm +++ b/gnu/packages/raspberry-pi.scm @@ -1,6 +1,7 @@ ;;; GNU Guix --- Functional package management for GNU ;;; Copyright © 2020 Danny Milosavljevic ;;; Copyright © 2021 Stefan +;;; Copyright © 2022 Maxim Cournoyer ;;; ;;; This file is part of GNU Guix. ;;; @@ -23,18 +24,24 @@ #:use-module (gnu packages) #:use-module (gnu packages admin) #:use-module (gnu packages algebra) + #:use-module (gnu packages backup) #:use-module (gnu packages base) #:use-module (gnu packages bash) #:use-module (gnu packages bootloaders) #:use-module (gnu packages commencement) #:use-module (gnu packages cross-base) + #:use-module (gnu packages curl) #:use-module (gnu packages documentation) #:use-module (gnu packages embedded) #:use-module (gnu packages file) #:use-module (gnu packages gcc) + #:use-module (gnu packages guile) #:use-module (gnu packages linux) + #:use-module (gnu packages qt) + #:use-module (gnu packages tls) #:use-module (guix build-system copy) #:use-module (guix build-system gnu) + #:use-module (guix build-system qt) #:use-module (guix download) #:use-module (guix git-download) #:use-module ((guix licenses) #:prefix license:) @@ -367,3 +374,84 @@ argument of the function (modify-linux)." (make-raspi-defconfig "arm64" "bcmrpi3_defconfig" "1bfnl4p0ddx3200dg91kmh2pln36w95y05x1asc312kixv0jgd81")) + +(define-public rpi-imager + (package + (name "rpi-imager") + (version "1.7.3") + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/raspberrypi/rpi-imager") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (modules '((guix build utils) + (ice-9 ftw) + (srfi srfi-26))) + (snippet '(begin + ;; Remove all but the following bundled libraries, + ;; which are not yet packaged in Guix. + (define keep '("." ".." + "drivelist" + "mountutils" + "sha256crypt")) + (with-directory-excursion "src/dependencies" + (for-each delete-file-recursively + (scandir "." (negate + (cut member <> keep))))))) + (sha256 + (base32 + "0i7r1myhinhlgispq92nzvrjvbc48l87z8xfwc038l44qj1lsq8g")))) + (build-system qt-build-system) + (arguments + (list + #:tests? #f ;no test suite + #:configure-flags #~(list "-DENABLE_TELEMETRY=OFF") + #:phases + #~(modify-phases %standard-phases + (add-after 'unpack 'chdir + (lambda _ + (chdir "src"))) + (add-after 'chdir 'customize-os-list.json + ;; The default operating system JSON list contains non-FSDG + ;; systems. + (lambda _ + (let* ((datadir (string-append #$output + "/share/rpi-imager")) + (os-list.json (string-append datadir "/os-list.json"))) + (mkdir-p datadir) + #$(with-extensions (list guile-json-4) + #~(begin + (use-modules (json)) + (call-with-output-file os-list.json + ;; TODO: Register FSDG and RPi compatible OS + ;; images here. + (lambda (port) + (scm->json '() port))))) + (substitute* "config.h" + (("#define OSLIST_URL.*") + (string-append "#define OSLIST_URL \"file:///" + os-list.json "\"\n")))))) + (add-after 'chdir 'patch-cmake + (lambda _ + (substitute* "CMakeLists.txt" + ;; lsblk expects to have access to /sys/dev/block, + ;; which doesn't exist in the build container; + ;; prevent the check to fail the build. + (("ret EQUAL \"1\"") + "FALSE"))))))) + (inputs + (list gnutls + curl + libarchive + qtdeclarative-5 + qtquickcontrols2-5 + qtsvg-5 + qttools-5 + util-linux)) + (home-page "https://github.com/raspberrypi/rpi-imager/") + (synopsis "Raspberry Pi Imaging Utility") + (description "rpi-imager is graphical utility to easily provision and +flash a memory card with an operating system image suitable for the Raspberry +Pi single board computer.") + (license license:asl2.0))) From 6d2afaf25b40bc055374cc1a1bf85efa1fb2e6fb Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Tue, 13 Dec 2022 14:48:26 +0100 Subject: [PATCH 129/790] gnu: aragorn: Update to 1.2.41. * gnu/packages/bioinformatics.scm (aragorn): Update to 1.2.41. [source]: Fetch C source file from new location. [arguments]: Drop trailing #T in build phases; use gexp. [native-inputs]: Add origin for man page. [home-page]: Update to new home page. [license]: Update to GPLv3+. --- gnu/packages/bioinformatics.scm | 60 +++++++++++++++++---------------- 1 file changed, 31 insertions(+), 29 deletions(-) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 5e2e0796a0..9dcc5bc92c 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -172,47 +172,49 @@ (define-public aragorn (package (name "aragorn") - (version "1.2.38") + (version "1.2.41") (source (origin (method url-fetch) - (uri (string-append - "http://mbio-serv2.mbioekol.lu.se/ARAGORN/Downloads/aragorn" - version ".tgz")) + (uri (string-append "https://www.ansikte.se/ARAGORN/Downloads/" + "aragorn" version ".c")) (sha256 (base32 - "09i1rg716smlbnixfm7q1ml2mfpaa2fpn3hwjg625ysmfwwy712b")))) + "0jkzx7sqiarydvz3bwaxh790fpvpkfc926dhsza1dbdhq32ir8wj")))) (build-system gnu-build-system) (arguments - `(#:tests? #f ; there are no tests - #:phases - (modify-phases %standard-phases - (delete 'configure) - (replace 'build - (lambda _ - (invoke "gcc" - "-O3" - "-ffast-math" - "-finline-functions" - "-o" - "aragorn" - (string-append "aragorn" ,version ".c")) - #t)) - (replace 'install - (lambda* (#:key outputs #:allow-other-keys) - (let* ((out (assoc-ref outputs "out")) - (bin (string-append out "/bin")) - (man (string-append out "/share/man/man1"))) - (install-file "aragorn" bin) - (install-file "aragorn.1" man)) - #t))))) - (home-page "http://mbio-serv2.mbioekol.lu.se/ARAGORN") + (list + #:tests? #f ; there are no tests + #:phases + #~(modify-phases %standard-phases + (delete 'configure) + (replace 'build + (lambda _ + (invoke "gcc" "-O3" "-ffast-math" "-finline-functions" + "-o" "aragorn" #$source))) + (replace 'install + (lambda* (#:key inputs #:allow-other-keys) + (let ((bin (string-append #$output "/bin")) + (man (string-append #$output "/share/man/man1"))) + (install-file "aragorn" bin) + (mkdir-p man) + (copy-file (assoc-ref inputs "aragorn.1") + (string-append man "/aragorn.1")))))))) + (native-inputs + `(("aragorn.1" + ,(origin + (method url-fetch) + (uri "https://www.ansikte.se/ARAGORN/Downloads/aragorn.1") + (sha256 + (base32 + "0bn9lapa6f0cl07dbn2fjrapirv9d4bk7w248w39fhb4vbczcc3f")))))) + (home-page "https://www.ansikte.se/ARAGORN/") (synopsis "Detect tRNA, mtRNA and tmRNA genes in nucleotide sequences") (description "Aragorn identifies transfer RNA, mitochondrial RNA and transfer-messenger RNA from nucleotide sequences, based on homology to known tRNA consensus sequences and RNA structure. It also outputs the secondary structure of the predicted RNA.") - (license license:gpl2))) + (license license:gpl3+))) (define-public bamtools (package From 8cc22866c283f49c14f7b7419f57c40c8eee1f56 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Tue, 13 Dec 2022 14:53:03 +0100 Subject: [PATCH 130/790] gnu: bamtools: Update to 2.5.2. * gnu/packages/bioinformatics.scm (bamtools): Update to 2.5.2. [arguments]: Enable tests; remove extra phases. [inputs]: Add jsoncpp. [native-inputs]: Add pkg-config. --- gnu/packages/bioinformatics.scm | 19 ++++--------------- 1 file changed, 4 insertions(+), 15 deletions(-) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 9dcc5bc92c..0f3d8010af 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -219,7 +219,7 @@ structure of the predicted RNA.") (define-public bamtools (package (name "bamtools") - (version "2.5.1") + (version "2.5.2") (source (origin (method git-fetch) (uri (git-reference @@ -228,21 +228,10 @@ structure of the predicted RNA.") (file-name (git-file-name name version)) (sha256 (base32 - "0nfb2ypcx9959xnbz6wxh6py3xfizgmg8nrknxl95c507m9hmq8b")))) + "14lw571vbks138i0lj66qjdbk8iwa817x2zbpzij61vv1gdgfbn5")))) (build-system cmake-build-system) - (arguments - `(#:tests? #f ;no "check" target - #:phases - (modify-phases %standard-phases - (add-before - 'configure 'set-ldflags - (lambda* (#:key outputs #:allow-other-keys) - (setenv "LDFLAGS" - (string-append - "-Wl,-rpath=" - (assoc-ref outputs "out") "/lib/bamtools")) - #t))))) - (inputs (list zlib)) + (inputs (list jsoncpp zlib)) + (native-inputs (list pkg-config)) (home-page "https://github.com/pezmaster31/bamtools") (synopsis "C++ API and command-line toolkit for working with BAM data") (description From 4f1a36bd7b8febbcabbed76cdb9534e279445bd0 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Tue, 13 Dec 2022 15:12:14 +0100 Subject: [PATCH 131/790] gnu: bamutils: Update to 1.0.15. * gnu/packages/bioinformatics.scm (bamutils): Update to 1.0.15. [arguments]: Remove quasiquoting; remove USER_WARNINGS from make-flags. [native-inputs]: Update libstatgen. --- gnu/packages/bioinformatics.scm | 31 ++++++++++++++++--------------- 1 file changed, 16 insertions(+), 15 deletions(-) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 0f3d8010af..5291056dc8 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -242,7 +242,7 @@ BAM files.") (define-public bamutils (package (name "bamutils") - (version "1.0.14") + (version "1.0.15") (source (origin (method git-fetch) (uri (git-reference @@ -251,21 +251,22 @@ BAM files.") (file-name (git-file-name name version)) (sha256 (base32 - "0i2r332k1kz0jysyg89d858wqq59n16lw6dv5qmilcwshb77r9v7")))) + "1pxydf9qsr8667jh525bc2wiqn9nwk8rkg05kbyfmjs8d261fl9y")))) (build-system gnu-build-system) (arguments - `(#:tests? #f ; Unclear how to run tests - #:make-flags - ,#~(list "USER_WARNINGS=-std=gnu++98" ; - (string-append "INSTALLDIR=" #$output "/bin")) - #:phases - (modify-phases %standard-phases - (replace 'configure - (lambda* (#:key inputs #:allow-other-keys) - (substitute* "src/Makefile" ; - (("^DATE=.*") "DATE=\"1970-01-01\"\n")) - (copy-recursively (assoc-ref inputs "libstatgen") - "../libStatGen")))))) + (list + #:tests? #f ;fails to link debug libraries + #:test-target "test" + #:make-flags + #~(list (string-append "INSTALLDIR=" #$output "/bin")) + #:phases + #~(modify-phases %standard-phases + (replace 'configure + (lambda* (#:key inputs #:allow-other-keys) + (substitute* "src/Makefile" + (("^DATE=.*") "DATE=\"1970-01-01\"\n")) + (copy-recursively (assoc-ref inputs "libstatgen") + "../libStatGen")))))) (inputs (list zlib)) (native-inputs @@ -278,7 +279,7 @@ BAM files.") (file-name (git-file-name "libstatgen" version)) (sha256 (base32 - "0q9iyk046r4m7qnav8c3f28zsar25lj9nydiklwaswmzdijhi4p1")))))) + "0spvbpvnpxrgj8kajpkhf1mv7kdyvj723y9zh13jykvnjh8a15j3")))))) (home-page "https://genome.sph.umich.edu/wiki/BamUtil") (synopsis "Programs for working on SAM/BAM files") (description "This package provides several programs that perform From 53f65f7315c3f37d670a6164e72cf0c96cab6c2e Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Tue, 13 Dec 2022 15:13:57 +0100 Subject: [PATCH 132/790] gnu: bedtools: Remove unnecessary quasiquotation. * gnu/packages/bioinformatics.scm (bedtools)[arguments]: Remove quasiquote. [native-inputs]: Drop input label. --- gnu/packages/bioinformatics.scm | 13 +++++++------ 1 file changed, 7 insertions(+), 6 deletions(-) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 5291056dc8..1ead24dff1 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -435,14 +435,15 @@ computational cluster.") "1f2hh79l7dn147c2xyfgf5wfjvlqfw32kjfnnh2n1qy6rpzx2fik")))) (build-system gnu-build-system) (arguments - `(#:test-target "test" - #:make-flags - ,#~(list (string-append "prefix=" #$output)) - #:phases - (modify-phases %standard-phases + (list + #:test-target "test" + #:make-flags + #~(list (string-append "prefix=" #$output)) + #:phases + '(modify-phases %standard-phases (delete 'configure)))) (native-inputs - `(("python" ,python-wrapper))) + (list python-wrapper)) (inputs (list samtools zlib)) (home-page "https://github.com/arq5x/bedtools2") From 684d046e6c6198d7fadd2632ae9ca9ecfe7c3278 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Tue, 13 Dec 2022 15:26:11 +0100 Subject: [PATCH 133/790] gnu: pbcopper: Update to 2.0.0. * gnu/packages/bioinformatics.scm (pbcopper): Update to 2.0.0. --- gnu/packages/bioinformatics.scm | 61 ++++++++++++++++----------------- 1 file changed, 29 insertions(+), 32 deletions(-) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 1ead24dff1..039487ea80 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -496,39 +496,36 @@ BED, GFF/GTF, VCF.") (list samtools zlib)))) (define-public pbcopper - ;; This is the latest commit at the time of this writing. - (let ((commit "ad4143afd25a0bd6adc977c544865c992a515841") - (revision "1")) - (package - (name "pbcopper") - (version (git-version "1.9.0" revision commit)) - (source (origin - (method git-fetch) - (uri (git-reference - (url "https://github.com/PacificBiosciences/pbcopper") - (commit commit))) - (file-name (git-file-name name version)) - (sha256 - (base32 - "1qxkbpdkamfisnk36lpi1vdvf3p1lg2hdqna3xgd94pz52bwbmp7")))) - (build-system meson-build-system) - (arguments - `(#:phases - (modify-phases %standard-phases - (add-after 'unpack 'patch-meson-files - (lambda* (#:key inputs #:allow-other-keys) - (substitute* "meson.build" - (("-msse4.1") ""))))))) - (inputs - (list boost)) - (native-inputs - (list googletest pkg-config)) - (home-page "https://github.com/PacificBiosciences/pbcopper") - (synopsis "Data structures, algorithms, and utilities for PacBio C++ applications") - (description - "The pbcopper library provides a suite of data structures, algorithms, + (package + (name "pbcopper") + (version "2.0.0") + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/PacificBiosciences/pbcopper") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "04mgmla96bsmr9gijbn3ibspry625cv4kqqxv70z4jq4qc407jy3")))) + (build-system meson-build-system) + (arguments + `(#:phases + (modify-phases %standard-phases + (add-after 'unpack 'patch-meson-files + (lambda _ + (substitute* "meson.build" + (("-msse4.1") ""))))))) + (inputs + (list boost)) + (native-inputs + (list googletest pkg-config)) + (home-page "https://github.com/PacificBiosciences/pbcopper") + (synopsis "Data structures, algorithms, and utilities for PacBio C++ applications") + (description + "The pbcopper library provides a suite of data structures, algorithms, and utilities for PacBio C++ applications.") - (license license:bsd-3)))) + (license license:bsd-3))) (define-public r-btools (let ((commit "fa21d4ca01d37ea4d98b45582453f3bf95cbc2b5") From 8b2fdcb2c3977b2ff65a6584e6bdcfcdf95f1704 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Tue, 13 Dec 2022 15:43:56 +0100 Subject: [PATCH 134/790] gnu: pbbam: Update to 2.1.0. * gnu/packages/bioinformatics.scm (pbbam): Update to 2.1.0. --- gnu/packages/bioinformatics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 039487ea80..27f2473eb4 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -566,7 +566,7 @@ for all types of microbial diversity analyses.") (define-public pbbam (package (name "pbbam") - (version "1.7.0") + (version "2.1.0") (source (origin (method git-fetch) (uri (git-reference @@ -575,7 +575,7 @@ for all types of microbial diversity analyses.") (file-name (git-file-name name version)) (sha256 (base32 - "1avdm5hwhr5ls79017blyalx1npzbf1aa6dgb6j6lg8sq4nk9yyg")))) + "1iyazi3l7dswpfxh39k5j7ydi0ywja0579xz3r6l9kkwz2n1z6dc")))) (build-system meson-build-system) (arguments `(#:phases From eaf5198a5e40f54cfd3398bbf0c2df8a24fd51f7 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Tue, 13 Dec 2022 15:44:10 +0100 Subject: [PATCH 135/790] gnu: pbbam: Drop input labels. * gnu/packages/bioinformatics.scm (pbbam)[native-inputs]: Drop labels. --- gnu/packages/bioinformatics.scm | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 27f2473eb4..7a90cd1ac5 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -600,9 +600,9 @@ for all types of microbial diversity analyses.") (inputs (list boost samtools)) (native-inputs - `(("googletest" ,googletest) - ("pkg-config" ,pkg-config) - ("python" ,python-wrapper))) ; for tests + (list googletest + pkg-config + python-wrapper)) ;for tests (home-page "https://github.com/PacificBiosciences/pbbam") (synopsis "Work with PacBio BAM files") (description From 057579495f333c48b84454d7067977e19e680b2f Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Tue, 13 Dec 2022 15:56:21 +0100 Subject: [PATCH 136/790] gnu: blasr-libcpp: Remove trailing #T from build phases. * gnu/packages/bioinformatics.scm (blasr-libcpp)[arguments]: Remove trailing #T from build phases. --- gnu/packages/bioinformatics.scm | 6 ++---- 1 file changed, 2 insertions(+), 4 deletions(-) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 7a90cd1ac5..f07938d42f 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -673,8 +673,7 @@ speedup comes during compression.") m (format #f "cpp.find_library('hdf5', dirs : '~a'), \ cpp.find_library('hdf5_cpp', dirs : '~a'), " - hdf5 hdf5))))) - #t)) + hdf5 hdf5))))))) (add-after 'unpack 'find-googletest (lambda* (#:key inputs #:allow-other-keys) ;; It doesn't find gtest_main because there's no pkg-config file @@ -683,8 +682,7 @@ cpp.find_library('hdf5_cpp', dirs : '~a'), " (("libblasr_gtest_dep = dependency\\('gtest_main'.*") (format #f "cpp = meson.get_compiler('cpp') libblasr_gtest_dep = cpp.find_library('gtest_main', dirs : '~a')\n" - (assoc-ref inputs "googletest")))) - #t))) + (assoc-ref inputs "googletest"))))))) ;; TODO: unittest/libblasr_unittest cannot be linked ;; ld: ;; unittest/df08227@@libblasr_unittest@exe/alignment_utils_FileUtils_gtest.cpp.o: ;; undefined reference to symbol From de30c74b639c8739263973d0e49344b727b2c163 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Tue, 13 Dec 2022 15:59:21 +0100 Subject: [PATCH 137/790] gnu: bioawk: Use gexp. * gnu/packages/bioinformatics.scm (bioawk)[arguments]: Use gexp and simplify 'install phase. --- gnu/packages/bioinformatics.scm | 35 +++++++++++++++------------------ 1 file changed, 16 insertions(+), 19 deletions(-) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index f07938d42f..f9a51910d9 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -802,26 +802,23 @@ provides the Ribotaper pipeline.") (base32 "1pxc3zdnirxbf9a0az698hd8xdik7qkhypm7v6hn922x8y9qmspm")))) (build-system gnu-build-system) - (inputs - (list zlib)) - (native-inputs - (list bison)) + (inputs (list zlib)) + (native-inputs (list bison)) (arguments - `(#:tests? #f ; There are no tests to run. - ;; Bison must generate files, before other targets can build. - #:parallel-build? #f - #:phases - (modify-phases %standard-phases - (delete 'configure) ; There is no configure phase. - (replace 'install - (lambda* (#:key outputs #:allow-other-keys) - (let* ((out (assoc-ref outputs "out")) - (bin (string-append out "/bin")) - (man (string-append out "/share/man/man1"))) - (mkdir-p man) - (copy-file "awk.1" (string-append man "/bioawk.1")) - (install-file "bioawk" bin)) - #t))))) + (list + #:tests? #f ; There are no tests to run. + ;; Bison must generate files, before other targets can build. + #:parallel-build? #f + #:phases + #~(modify-phases %standard-phases + (delete 'configure) ; There is no configure phase. + (replace 'install + (lambda _ + (let ((bin (string-append #$output "/bin")) + (man (string-append #$output "/share/man/man1"))) + (mkdir-p man) + (copy-file "awk.1" (string-append man "/bioawk.1")) + (install-file "bioawk" bin))))))) (home-page "https://github.com/lh3/bioawk") (synopsis "AWK with bioinformatics extensions") (description "Bioawk is an extension to Brian Kernighan's awk, adding the From b339e181e1f9138c59934cdff330a73cc490cf32 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Tue, 13 Dec 2022 16:29:48 +0100 Subject: [PATCH 138/790] gnu: python-bx-python: Update to 0.9.0. * gnu/packages/bioinformatics.scm (python-bx-python): Update to 0.9.0. [build-system]: Use pyproject-build-system. [arguments]: Add phase 'build-extensions and 'disable-cython-doctests. [native-inputs]: Replace python-nose with python-pytest. --- gnu/packages/bioinformatics.scm | 21 ++++++++++++++++----- 1 file changed, 16 insertions(+), 5 deletions(-) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index f9a51910d9..1dae5982ea 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -2252,23 +2252,34 @@ off-target reads for a capture method that targets CpG-rich region.") (define-public python-bx-python (package (name "python-bx-python") - (version "0.8.12") + (version "0.9.0") (source (origin (method git-fetch) (uri (git-reference (url "https://github.com/bxlab/bx-python") - (commit "f4e6a5c93e719db69b5798b6fdd9b167da358316"))) + (commit "4f4a48d3f227ae390c1b22072867ba86e347bdef"))) (file-name (git-file-name name version)) (sha256 (base32 - "0mclahslz34vq9x424jmzsxk0nmpm1j716fa8h3zwr9ssvch7skc")))) - (build-system python-build-system) + "1c914rw8phiw7zwzngz9i9hdciz5lq53drwdbpl2bd2sf5bj2biy")))) + (build-system pyproject-build-system) + (arguments + (list + #:phases + '(modify-phases %standard-phases + (add-before 'check 'build-extensions + (lambda _ + ;; Cython extensions have to be built before running the tests. + (invoke "python" "setup.py" "build_ext" "--inplace"))) + ;; Unrecognized argument. + (add-after 'unpack 'disable-cython-doctests + (lambda _ (substitute* "pytest.ini" (("--doctest-cython") ""))))))) (propagated-inputs (list python-numpy)) (inputs (list zlib)) (native-inputs - (list python-lzo python-nose python-cython)) + (list python-cython python-lzo python-pytest)) (home-page "https://github.com/bxlab/bx-python") (synopsis "Tools for manipulating biological data") (description From 23322c2de8565f4bfc6787f154d6ae2a078ba097 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Tue, 13 Dec 2022 16:30:45 +0100 Subject: [PATCH 139/790] gnu: tophat: Remove trailing #T from build phases and snippet. * gnu/packages/bioinformatics.scm (tophat)[source]: Remove trailing #T from snippet. [arguments]: Remove trailing #T from build phases. --- gnu/packages/bioinformatics.scm | 9 +++------ 1 file changed, 3 insertions(+), 6 deletions(-) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 1dae5982ea..8236708391 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -2062,8 +2062,7 @@ genome (2.9 GB for paired-end).") '(begin ;; Remove bundled SeqAn and samtools (delete-file-recursively "src/SeqAn-1.4.2") - (delete-file-recursively "src/samtools-0.1.18") - #t)))) + (delete-file-recursively "src/samtools-0.1.18"))))) (build-system gnu-build-system) (arguments '(#:parallel-build? #f ; not supported @@ -2078,8 +2077,7 @@ genome (2.9 GB for paired-end).") (string-join (delete (string-append gcc "/include/c++") (string-split (getenv "CPLUS_INCLUDE_PATH") #\:)) - ":")) - #t))) + ":"))))) (add-after 'unpack 'use-system-samtools (lambda* (#:key inputs #:allow-other-keys) (substitute* "src/Makefile.in" @@ -2099,8 +2097,7 @@ genome (2.9 GB for paired-end).") "src/map2gtf.h" "src/align_status.h") (("#include ") "#include ") - (("#include ") "#include ")) - #t))))) + (("#include ") "#include "))))))) (native-inputs `(("gcc@5" ,gcc-5))) ;; doesn't build with later versions (inputs From a2f0297af0b53239cdcee62abe044532e80ca32b Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ludovic=20Court=C3=A8s?= Date: Tue, 13 Dec 2022 11:32:52 +0100 Subject: [PATCH 140/790] gnu: guile-gnutls: Add properties for the 'generic-git' updater. * gnu/packages/tls.scm (guile-gnutls)[properties]: New field. --- gnu/packages/tls.scm | 2 ++ 1 file changed, 2 insertions(+) diff --git a/gnu/packages/tls.scm b/gnu/packages/tls.scm index 1f40537b6a..a74b423ccf 100644 --- a/gnu/packages/tls.scm +++ b/gnu/packages/tls.scm @@ -416,6 +416,8 @@ required structures.") (inputs (list gnutls-latest guile-3.0)) + (properties '((release-tag-prefix . "v") + (release-tag-version-delimiter . "."))) (synopsis "Guile bindings to GnuTLS") (description "This package provides Guile bindings to GnuTLS, a library implementation From 052faadde70c44043d0db73bd254f664e1905ceb Mon Sep 17 00:00:00 2001 From: Lars-Dominik Braun Date: Fri, 9 Dec 2022 11:46:37 +0100 Subject: [PATCH 141/790] packages: Add 'package-upstream-name*'. MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * guix/packages.scm (package-upstream-name*): New procedure. * tests/packages.scm ("package-upstream-name*"): New test. Signed-off-by: Ludovic Courtès --- guix/packages.scm | 33 +++++++++++++++++++++++++++++++++ tests/packages.scm | 4 ++++ 2 files changed, 37 insertions(+) diff --git a/guix/packages.scm b/guix/packages.scm index 8f119d9fa7..6e61e16aa4 100644 --- a/guix/packages.scm +++ b/guix/packages.scm @@ -89,6 +89,7 @@ this-package package-name package-upstream-name + package-upstream-name* package-version package-full-name package-source @@ -691,6 +692,38 @@ it has in Guix." (or (assq-ref (package-properties package) 'upstream-name) (package-name package))) +(define (package-upstream-name* package) + "Return the upstream name of PACKAGE, accounting for commonly-used +package name prefixes in addition to the @code{upstream-name} property." + (let ((namespaces (list "cl-" + "ecl-" + "emacs-" + "ghc-" + "go-" + "guile-" + "java-" + "julia-" + "lua-" + "minetest-" + "node-" + "ocaml-" + "perl-" + "python-" + "r-" + "ruby-" + "rust-" + "sbcl-" + "texlive-")) + (name (package-name package))) + (or (assq-ref (package-properties package) 'upstream-name) + (let loop ((prefixes namespaces)) + (match prefixes + (() name) + ((prefix rest ...) + (if (string-prefix? prefix name) + (substring name (string-length prefix)) + (loop rest)))))))) + (define (hidden-package p) "Return a \"hidden\" version of P--i.e., one that 'fold-packages' and thus, user interfaces, ignores." diff --git a/tests/packages.scm b/tests/packages.scm index a5819d8de3..f58c47817b 100644 --- a/tests/packages.scm +++ b/tests/packages.scm @@ -626,6 +626,10 @@ (build-derivations %store (list drv)) (call-with-input-file output get-string-all))) +(test-equal "package-upstream-name*" + (package-upstream-name* (specification->package "guile-gcrypt")) + "gcrypt") + ;;; ;;; Source derivation with snippets. From bbcd06e56c06376e640a7ac81a7109e7135a20f2 Mon Sep 17 00:00:00 2001 From: Lars-Dominik Braun Date: Fri, 9 Dec 2022 12:01:31 +0100 Subject: [PATCH 142/790] ui: Take package upstream name into account when searching. MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * guix/ui.scm (%package-metrics): Add PACKAGE-UPSTREAM-NAME*. * tests/ui.scm ("package-relevance and upstream name"): New test. Co-authored-by: Ludovic Courtès --- guix/ui.scm | 1 + tests/ui.scm | 11 ++++++++++- 2 files changed, 11 insertions(+), 1 deletion(-) diff --git a/guix/ui.scm b/guix/ui.scm index 45eccb7335..3bca3b1e40 100644 --- a/guix/ui.scm +++ b/guix/ui.scm @@ -1668,6 +1668,7 @@ score, the more relevant OBJ is to REGEXPS." ;; Metrics used to compute the "relevance score" of a package against a set ;; of regexps. `((,package-name . 4) + (,package-upstream-name* . 2) ;; Match against uncommon outputs. (,(lambda (package) diff --git a/tests/ui.scm b/tests/ui.scm index 6a25a204ca..438acae525 100644 --- a/tests/ui.scm +++ b/tests/ui.scm @@ -1,5 +1,5 @@ ;;; GNU Guix --- Functional package management for GNU -;;; Copyright © 2013, 2014, 2015, 2016, 2017, 2019, 2020 Ludovic Courtès +;;; Copyright © 2013-2017, 2019-2020, 2022 Ludovic Courtès ;;; Copyright © 2022 Taiju HIGASHI ;;; ;;; This file is part of GNU Guix. @@ -294,6 +294,15 @@ Second line" 24)) (>0 (package-relevance libb2 (map rx '("crypto" "library"))))))) +(test-assert "package-relevance and upstream name" + ;; https://issues.guix.gnu.org/58136 + (let ((ggplot2 (specification->package "r-ggplot2")) + (ggstance (specification->package "r-ggstance")) + (rx (make-regexp "ggplot2" regexp/icase))) + (> (package-relevance ggplot2 (list rx)) + (package-relevance ggstance (list rx)) + 0))) + (define (make-empty-file directory file) ;; Create FILE in DIRECTORY. (close-port (open-output-file (in-vicinity directory file)))) From 22acc0b0291cc067a6a3ce36c7ca8e5f68fe4db6 Mon Sep 17 00:00:00 2001 From: Petr Hodina Date: Mon, 31 Oct 2022 16:12:38 +0100 Subject: [PATCH 143/790] services: nix: Add more configuration fields. MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * gnu/services/nix.scm ()[build-directory]: New field. (nix-service-etc, nix-shepherd-service): Take them into account. * doc/guix.texi (Nix): Update it. Signed-off-by: Ludovic Courtès --- doc/guix.texi | 9 +++++++++ gnu/services/nix.scm | 11 ++++++++--- 2 files changed, 17 insertions(+), 3 deletions(-) diff --git a/doc/guix.texi b/doc/guix.texi index aacf748838..b270964542 100644 --- a/doc/guix.texi +++ b/doc/guix.texi @@ -37209,6 +37209,15 @@ The Nix package to use. @item @code{sandbox} (default: @code{#t}) Specifies whether builds are sandboxed by default. +@item @code{build-directory} (default: @code{"/tmp"}) +The directory where build directory are stored during builds. +This is useful to change if, for example, the default location does not +have enough space to hold build trees for big packages. + +This is similar to setting the @env{TMPDIR} environment variable for +@command{guix-daemon}. @ref{Build Environment Setup, @env{TMPDIR}}, +for more info. + @item @code{build-sandbox-items} (default: @code{'()}) This is a list of strings or objects appended to the @code{build-sandbox-items} field of the configuration file. diff --git a/gnu/services/nix.scm b/gnu/services/nix.scm index df04a85c22..dcf994b603 100644 --- a/gnu/services/nix.scm +++ b/gnu/services/nix.scm @@ -54,6 +54,8 @@ (default nix)) (sandbox nix-configuration-sandbox ;boolean (default #t)) + (build-directory nix-configuration-build-directory ;string + (default "/tmp")) (build-sandbox-items nix-configuration-build-sandbox-items ;list of strings (default '())) (extra-config nix-configuration-extra-config ;list of strings @@ -106,7 +108,7 @@ GID." (define nix-service-etc (match-lambda - (($ package sandbox build-sandbox-items extra-config) + (($ package sandbox build-directory build-sandbox-items extra-config) (let ((ref-file (references-file package))) `(("nix/nix.conf" ,(computed-file @@ -130,7 +132,7 @@ GID." (define nix-shepherd-service ;; Return a for Nix. (match-lambda - (($ package _ _ _ extra-options) + (($ package _ build-directory _ _ extra-options) (list (shepherd-service (provision '(nix-daemon)) @@ -138,7 +140,10 @@ GID." (requirement '()) (start #~(make-forkexec-constructor (list (string-append #$package "/bin/nix-daemon") - #$@extra-options))) + #$@extra-options) + #:environment-variables + (list (string-append "TMPDIR=" build-directory) + "PATH=/run/current-system/profile/bin"))) (respawn? #f) (stop #~(make-kill-destructor))))))) From 3d2b2f12e590f7bb53864f567999c3b39bec92d4 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Tue, 13 Dec 2022 18:21:19 +0100 Subject: [PATCH 144/790] gnu: bedops: Update to 2.4.41. * gnu/packages/bioinformatics.scm (bedops): Update to 2.4.41. [arguments]: Remove trailing #T from build phases; do not set BINDIR in make-flags; set CC; replace 'install phase. [native-inputs]: Add diffutils, perl, and which. --- gnu/packages/bioinformatics.scm | 70 +++++++++++++++++++-------------- 1 file changed, 40 insertions(+), 30 deletions(-) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 8236708391..fa719e139f 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -364,7 +364,7 @@ transparently with both VCFs and BCFs, both uncompressed and BGZF-compressed.") (define-public bedops (package (name "bedops") - (version "2.4.35") + (version "2.4.41") (source (origin (method git-fetch) (uri (git-reference @@ -373,39 +373,49 @@ transparently with both VCFs and BCFs, both uncompressed and BGZF-compressed.") (file-name (git-file-name name version)) (sha256 (base32 - "0mmgsgwz5r9w76hzgxkxc9s9lkdhhaf7vr6i02b09vbswvs1fyqx")))) + "046037qdxsn01ln28rbrwnc7wq4a3xahmb2k74l0w75dby5ni42l")))) (build-system gnu-build-system) (arguments - '(#:tests? #f - #:make-flags (list (string-append "BINDIR=" %output "/bin")) - #:phases - (modify-phases %standard-phases - (add-after 'unpack 'unpack-tarballs - (lambda _ - ;; FIXME: Bedops includes tarballs of minimally patched upstream - ;; libraries jansson, zlib, and bzip2. We cannot just use stock - ;; libraries because at least one of the libraries (zlib) is - ;; patched to add a C++ function definition (deflateInit2cpp). - ;; Until the Bedops developers offer a way to link against system - ;; libraries we have to build the in-tree copies of these three - ;; libraries. + (list + ;; We cannot run the tests because the build system makes strange + ;; assumptions about where executables are located. + #:tests? #false + #:test-target "tests" + #:make-flags + #~(list (string-append "CC=" #$(cc-for-target))) + #:phases + #~(modify-phases %standard-phases + (add-after 'unpack 'unpack-tarballs + (lambda _ + ;; FIXME: Bedops includes tarballs of minimally patched upstream + ;; libraries jansson, zlib, and bzip2. We cannot just use stock + ;; libraries because at least one of the libraries (zlib) is + ;; patched to add a C++ function definition (deflateInit2cpp). + ;; Until the Bedops developers offer a way to link against system + ;; libraries we have to build the in-tree copies of these three + ;; libraries. - ;; See upstream discussion: - ;; https://github.com/bedops/bedops/issues/124 + ;; See upstream discussion: + ;; https://github.com/bedops/bedops/issues/124 - ;; Unpack the tarballs to benefit from shebang patching. - (with-directory-excursion "third-party" - (invoke "tar" "xvf" "jansson-2.6.tar.bz2") - (invoke "tar" "xvf" "zlib-1.2.7.tar.bz2") - (invoke "tar" "xvf" "bzip2-1.0.6.tar.bz2")) - ;; Disable unpacking of tarballs in Makefile. - (substitute* "system.mk/Makefile.linux" - (("^\tbzcat .*") "\t@echo \"not unpacking\"\n") - (("\\./configure") "CONFIG_SHELL=bash ./configure")) - (substitute* "third-party/zlib-1.2.7/Makefile.in" - (("^SHELL=.*$") "SHELL=bash\n")) - #t)) - (delete 'configure)))) + ;; Unpack the tarballs to benefit from shebang patching. + (with-directory-excursion "third-party" + (invoke "tar" "xvf" "jansson-2.6.tar.bz2") + (invoke "tar" "xvf" "zlib-1.2.7.tar.bz2") + (invoke "tar" "xvf" "bzip2-1.0.6.tar.bz2")) + ;; Disable unpacking of tarballs in Makefile. + (substitute* "system.mk/Makefile.linux" + (("^\tbzcat .*") "\t@echo \"not unpacking\"\n") + (("\\./configure") "CONFIG_SHELL=bash ./configure")) + (substitute* "third-party/zlib-1.2.7/Makefile.in" + (("^SHELL=.*$") "SHELL=bash\n")))) + (delete 'configure) + (replace 'install + (lambda _ + (invoke "make" "install" + (string-append "BINDIR=" #$output "/bin"))))))) + (native-inputs + (list diffutils perl which)) (home-page "https://github.com/bedops/bedops") (synopsis "Tools for high-performance genomic feature operations") (description From d83eef22b25a8717a62ba9d3432b7a8657b7b50b Mon Sep 17 00:00:00 2001 From: Mark H Weaver Date: Tue, 13 Dec 2022 02:22:37 -0500 Subject: [PATCH 145/790] gnu: icecat: Update to 102.6.0-guix0-preview1 [security fixes]. Includes fixes for CVE-2022-46872, CVE-2022-46874, CVE-2022-46875, CVE-2022-46878, CVE-2022-46880, CVE-2022-46881, and CVE-2022-46882. * gnu/packages/gnuzilla.scm (%icecat-version, %icecat-build-id): Update. (icecat-source): Update gnuzilla commit, base version, and hashes. --- gnu/packages/gnuzilla.scm | 12 ++++++------ 1 file changed, 6 insertions(+), 6 deletions(-) diff --git a/gnu/packages/gnuzilla.scm b/gnu/packages/gnuzilla.scm index ba910934be..1942fb0d8d 100644 --- a/gnu/packages/gnuzilla.scm +++ b/gnu/packages/gnuzilla.scm @@ -477,8 +477,8 @@ in C/C++.") ;; XXXX: Workaround 'snippet' limitations. (define computed-origin-method (@@ (guix packages) computed-origin-method)) -(define %icecat-version "102.5.0-guix0-preview1") -(define %icecat-build-id "20221115000000") ;must be of the form YYYYMMDDhhmmss +(define %icecat-version "102.6.0-guix0-preview1") +(define %icecat-build-id "20221213000000") ;must be of the form YYYYMMDDhhmmss ;; 'icecat-source' is a "computed" origin that generates an IceCat tarball ;; from the corresponding upstream Firefox ESR tarball, using the 'makeicecat' @@ -500,11 +500,11 @@ in C/C++.") "firefox-" upstream-firefox-version ".source.tar.xz")) (sha256 (base32 - "1n2pq165fxmvgcr5mv3hhaid2vn7lh3jg03lf13kz4c5295x8z81")))) + "1zhggzrk7lgip8jm37idh22qks76kmjy4yqy2qi63mvnv2j58cfj")))) - (upstream-icecat-base-version "102.5.0") ; maybe older than base-version + (upstream-icecat-base-version "102.6.0") ; maybe older than base-version ;;(gnuzilla-commit (string-append "v" upstream-icecat-base-version)) - (gnuzilla-commit "a8848cb35e4e47a344d40596f72d82d57bf5a6f1") + (gnuzilla-commit "b6260130b9808f550bdb35061af2d7962109a181") (gnuzilla-source (origin (method git-fetch) @@ -516,7 +516,7 @@ in C/C++.") (string-take gnuzilla-commit 8))) (sha256 (base32 - "0d0brzi7wmg70kvi9p3g24cyya17bvg2djgjn64g14hpnalg8icw")))) + "19v443w43jbcl9m5kl52nfai7hs4j07nf2ad9ggca7b2b0cz89b4")))) ;; 'search-patch' returns either a valid file name or #f, so wrap it ;; in 'assume-valid-file-name' to avoid 'local-file' warnings. From e4ab2ccb182fc75db2ba2789572ef58080e99ec8 Mon Sep 17 00:00:00 2001 From: dan Date: Mon, 12 Dec 2022 21:52:33 +0800 Subject: [PATCH 146/790] gnu: emacs-beancount: Update to 0.0.0-1.687775d. * gnu/packages/finance.scm (emacs-beancount): Update to 0.0.0-1.687775d. Signed-off-by: Nicolas Goaziou --- gnu/packages/finance.scm | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/gnu/packages/finance.scm b/gnu/packages/finance.scm index cc2d417003..828df0324e 100644 --- a/gnu/packages/finance.scm +++ b/gnu/packages/finance.scm @@ -1905,8 +1905,8 @@ generate a variety of reports from them, and provides a web interface.") (define-public emacs-beancount ;; Note that upstream has not made any release since this project moved ;; into its own repository (it was originally part of beancount itself) - (let ((commit "dbafe6a73d90c1f64d457b356b9dbb43499f70d5") - (revision "0")) + (let ((commit "687775da63784d153a3c1cfee9801090c6b51842") + (revision "1")) (package (name "emacs-beancount") (version (git-version "0.0.0" revision commit)) @@ -1918,7 +1918,7 @@ generate a variety of reports from them, and provides a web interface.") (commit commit))) (sha256 (base32 - "0v9bws2gv5b00x829p7hrcxqgdp7iwxvv1vhfjka81qrw6w1fvjw")) + "08383yqqanx29al1hg1r6ndx3gwjg6fj7kl340f1zz9m9cfiyvg3")) (file-name (git-file-name name version)))) (build-system emacs-build-system) (home-page "https://github.com/beancount/beancount-mode") From 89795dec983cee68350180586e5bf8cce3f10799 Mon Sep 17 00:00:00 2001 From: Nicolas Goaziou Date: Tue, 13 Dec 2022 16:35:35 +0100 Subject: [PATCH 147/790] gnu: emacs-project: Update to 0.9.3. * gnu/packages/emacs-xyz.scm (emacs-project): Update to 0.9.3. --- gnu/packages/emacs-xyz.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/emacs-xyz.scm b/gnu/packages/emacs-xyz.scm index 18d1989124..6abd1aa60e 100644 --- a/gnu/packages/emacs-xyz.scm +++ b/gnu/packages/emacs-xyz.scm @@ -915,13 +915,13 @@ buffer.") (define-public emacs-project (package (name "emacs-project") - (version "0.9.2") + (version "0.9.3") (source (origin (method url-fetch) (uri (string-append "https://elpa.gnu.org/packages/project-" version ".tar")) (sha256 - (base32 "0g4cnh771jjwjqhja0kwsv0162ff2xidpk8b6s3r5rzjc9inpcq7")))) + (base32 "0p2ivkmcx55xwmyg2vhj8qcqg4qd5y3myshn194ncy38lbvsj91h")))) (build-system emacs-build-system) (propagated-inputs (list emacs-xref)) (home-page "https://elpa.gnu.org/packages/project.html") From 98f7332aa8e3b453ff2e751350b93d295c804db7 Mon Sep 17 00:00:00 2001 From: Nicolas Goaziou Date: Tue, 13 Dec 2022 16:35:39 +0100 Subject: [PATCH 148/790] gnu: emacs-debbugs: Update to 0.35. * gnu/packages/emacs-xyz.scm (emacs-debbugs): Update to 0.35. --- gnu/packages/emacs-xyz.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/emacs-xyz.scm b/gnu/packages/emacs-xyz.scm index 6abd1aa60e..4e89fa0803 100644 --- a/gnu/packages/emacs-xyz.scm +++ b/gnu/packages/emacs-xyz.scm @@ -7426,14 +7426,14 @@ by a query, so both a link can refer to several mails.") (define-public emacs-debbugs (package (name "emacs-debbugs") - (version "0.34") + (version "0.35") (source (origin (method url-fetch) (uri (string-append "https://elpa.gnu.org/packages/debbugs-" version ".tar")) (sha256 - (base32 "06nxia4myhysiw12vsflgllrp9nyhmjnybrrcl1vyf4pw0fc6yrx")))) + (base32 "1w6y02ikjshfk12sdgbryfgj2z4yia2mpifa7g13ab7v9phpqpl1")))) (build-system emacs-build-system) (arguments '(#:include '("\\.el$" "\\.wsdl$" "\\.info$"))) (propagated-inputs From c922d935c37c9e7bdbf415c76c0b710a9179f8e7 Mon Sep 17 00:00:00 2001 From: Nicolas Goaziou Date: Tue, 13 Dec 2022 16:36:46 +0100 Subject: [PATCH 149/790] gnu: emacs-fountain-mode: Update to 3.6.1. * gnu/packages/emacs-xyz.scm (emacs-fountain-mode): Update to 3.6.1. --- gnu/packages/emacs-xyz.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/emacs-xyz.scm b/gnu/packages/emacs-xyz.scm index 4e89fa0803..21ba51d35b 100644 --- a/gnu/packages/emacs-xyz.scm +++ b/gnu/packages/emacs-xyz.scm @@ -5036,7 +5036,7 @@ files and directories.") (define-public emacs-fountain-mode (package (name "emacs-fountain-mode") - (version "3.6.0") + (version "3.6.1") (source (origin (method git-fetch) @@ -5045,7 +5045,7 @@ files and directories.") (commit (string-append "v" version)))) (file-name (git-file-name name version)) (sha256 - (base32 "14cb4r23pn98sxzh0qwjwpvm7k7q9hhpks8avydccwssm69x1s1w")))) + (base32 "1b1yjgink8psyggzkvqzwfnnimmawsv83yl34ccg9921z8bx27mb")))) (build-system emacs-build-system) (home-page "https://github.com/rnkn/fountain-mode") (synopsis "Major mode for screenwriting in Fountain markup") From 7d570036f0be065f658edc31555c4fc4645a5300 Mon Sep 17 00:00:00 2001 From: Nicolas Goaziou Date: Tue, 13 Dec 2022 16:38:17 +0100 Subject: [PATCH 150/790] gnu: emacs-pg: Update to 0.20. * gnu/packages/emacs-xyz.scm (emacs-pg): Update to 0.20. --- gnu/packages/emacs-xyz.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/emacs-xyz.scm b/gnu/packages/emacs-xyz.scm index 21ba51d35b..c60ae8833b 100644 --- a/gnu/packages/emacs-xyz.scm +++ b/gnu/packages/emacs-xyz.scm @@ -19653,7 +19653,7 @@ match and total match information in the mode-line in various search modes.") (define-public emacs-pg (package (name "emacs-pg") - (version "0.19") + (version "0.20") (source (origin (method git-fetch) (uri (git-reference (url "https://github.com/emarsden/pg-el") @@ -19661,7 +19661,7 @@ match and total match information in the mode-line in various search modes.") (file-name (git-file-name name version)) (sha256 (base32 - "13fkkpimhxh91hmsp551wzrdcic5ws7wj7vjwnh8l83hsrxmxz0y")))) + "0a38rvl5rwfb77p4xxmjhrs6s67pfkzjfm0pdxvf0b6xh7h404kh")))) (build-system emacs-build-system) (home-page "https://github.com/emarsden/pg-el") (synopsis "Emacs Lisp interface for PostgreSQL") From a67461f0e1a0caf98adf0396895ad4e45f46afd6 Mon Sep 17 00:00:00 2001 From: Konrad Hinsen Date: Tue, 13 Dec 2022 15:07:52 +0100 Subject: [PATCH 151/790] gnu: emacs-hyperbole: Add missing files. * gnu/packages/emacs-xyz.scm (emacs-hyperbole)[arguments]: Add a new INSTALL-DOC phase. Signed-off-by: Nicolas Goaziou --- gnu/packages/emacs-xyz.scm | 9 +++++++++ 1 file changed, 9 insertions(+) diff --git a/gnu/packages/emacs-xyz.scm b/gnu/packages/emacs-xyz.scm index c60ae8833b..1f24f9cbcb 100644 --- a/gnu/packages/emacs-xyz.scm +++ b/gnu/packages/emacs-xyz.scm @@ -708,6 +708,8 @@ uploading PlatformIO projects.") "DEMO-ROLO.otl" "HY-ABOUT" "man/hkey-help.txt" + "man/hyberbole.info" + "kotl/.*" "\\.kotl$" %default-include) #:phases @@ -724,6 +726,13 @@ uploading PlatformIO projects.") (("\\(hyperb:check-dir-user\\)") "")) (substitute* "hgnus.el" (("hmail ") "hmail hvar ")))) + (add-after 'install 'install-doc + (lambda _ + (install-file "man/hyperbole.info" + (string-append #$output "/share/info")) + (install-file "man/hkey-help.txt" + (string-append #$output "/share/doc/" + #$name "-" #$version)))) (add-after 'install 'install-images (lambda _ (let ((dir (string-append #$output "/share/info/im"))) From 688028931f0910a4688f7f5d2e44d71a70cf8092 Mon Sep 17 00:00:00 2001 From: Jelle Licht Date: Tue, 13 Dec 2022 18:49:52 +0100 Subject: [PATCH 152/790] gnu: emacs-pdf-tools: Update home page. * gnu/packages/emacs-xyz.scm (emacs-pdf-tools)[home-page]: Update. Signed-off-by: Nicolas Goaziou --- gnu/packages/emacs-xyz.scm | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/gnu/packages/emacs-xyz.scm b/gnu/packages/emacs-xyz.scm index 1f24f9cbcb..3286928f8d 100644 --- a/gnu/packages/emacs-xyz.scm +++ b/gnu/packages/emacs-xyz.scm @@ -4275,7 +4275,7 @@ during idle time, while Emacs is doing nothing else.") (list cairo glib libpng poppler zlib)) (propagated-inputs (list emacs-tablist)) - (home-page "https://github.com/politza/pdf-tools") + (home-page "https://github.com/vedang/pdf-tools") (synopsis "Emacs support library for PDF files") (description "PDF Tools is, among other things, a replacement of DocView for PDF From b0913931e97f0d7748009a9124c482efd717be77 Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Sun, 11 Dec 2022 01:00:01 +0100 Subject: [PATCH 153/790] gnu: realmd: Update to 0.17.1. * gnu/packages/admin.scm (realmd): Update to 0.17.1. --- gnu/packages/admin.scm | 5 ++--- 1 file changed, 2 insertions(+), 3 deletions(-) diff --git a/gnu/packages/admin.scm b/gnu/packages/admin.scm index 79f91d530d..5e46781efc 100644 --- a/gnu/packages/admin.scm +++ b/gnu/packages/admin.scm @@ -1802,7 +1802,7 @@ over ssh connections.") (define-public realmd (package (name "realmd") - (version "0.17.0") + (version "0.17.1") (source (origin (method git-fetch) @@ -1811,8 +1811,7 @@ over ssh connections.") (commit version))) (file-name (git-file-name name version)) (sha256 - (base32 - "1c6q2a86kk2f1akzc36nh52hfwsmmc0mbp6ayyjxj4zsyk9zx5bf")))) + (base32 "063cf4jkpfj548a7dxmffrpbh3j413nq3zy1zzj20lcfffnnaqwn")))) (build-system gnu-build-system) (arguments `(#:configure-flags '("--with-systemd-unit-dir=no" From 930b94809d463975f22496bf4af4d13d43326f0b Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Sun, 11 Dec 2022 01:00:01 +0100 Subject: [PATCH 154/790] gnu: libltc: Update to 1.3.2. * gnu/packages/audio.scm (libltc): Update to 1.3.2. --- gnu/packages/audio.scm | 5 ++--- 1 file changed, 2 insertions(+), 3 deletions(-) diff --git a/gnu/packages/audio.scm b/gnu/packages/audio.scm index 5e471d34e9..b1d3007b8c 100644 --- a/gnu/packages/audio.scm +++ b/gnu/packages/audio.scm @@ -5065,7 +5065,7 @@ stream to one or more IceCast and/or ShoutCast servers.") (define-public libltc (package (name "libltc") - (version "1.3.1") + (version "1.3.2") (source (origin (method url-fetch) @@ -5073,8 +5073,7 @@ stream to one or more IceCast and/or ShoutCast servers.") (string-append "https://github.com/x42/libltc/releases/download/v" version "/libltc-" version ".tar.gz")) (sha256 - (base32 - "173h9dgmain3nyrwk6q2d7yl4fnh4vacag4s2p01n5b7nyrkxrjh")))) + (base32 "0j8j7cnw02arh8122d13bwkps1c0mi2xqq55gyi2bs91dk6l4v8a")))) (build-system gnu-build-system) (arguments `(#:parallel-tests? #f)) ;tests fail otherwise From 2b7b0cac71978fb7c73a71cebfc83ddf70f1f5e4 Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Sun, 11 Dec 2022 01:00:00 +0100 Subject: [PATCH 155/790] gnu: fio: Update to 3.33. * gnu/packages/benchmark.scm (fio): Update to 3.33. --- gnu/packages/benchmark.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/benchmark.scm b/gnu/packages/benchmark.scm index e188b27789..e74d50c1a5 100644 --- a/gnu/packages/benchmark.scm +++ b/gnu/packages/benchmark.scm @@ -72,14 +72,14 @@ (define-public fio (package (name "fio") - (version "3.32") + (version "3.33") (source (origin (method url-fetch) (uri (string-append "https://brick.kernel.dk/snaps/" "fio-" version ".tar.bz2")) (sha256 (base32 - "0wlfzx6zwkp81fwqw0pqm9i7v0b89rpfbliwxdd8q4kp4mf3q2dv")))) + "083c1w8jqkvyw7wcy69142inlikzmk1k78mk973rnqdp3a7798qb")))) (build-system gnu-build-system) (arguments (list #:modules From aceb4e49d1d802cf428d8873dcb9dc3196996066 Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Sun, 11 Dec 2022 01:00:01 +0100 Subject: [PATCH 156/790] gnu: byacc: Update to 20221106. * gnu/packages/c.scm (byacc): Update to 20221106. --- gnu/packages/c.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/c.scm b/gnu/packages/c.scm index fb876eeb71..d03ad238b7 100644 --- a/gnu/packages/c.scm +++ b/gnu/packages/c.scm @@ -760,7 +760,7 @@ portability.") (define-public byacc (package (name "byacc") - (version "20220128") + (version "20221106") (source (origin (method url-fetch) (uri (string-append @@ -768,7 +768,7 @@ portability.") version ".tgz")) (sha256 (base32 - "173l5pdzgqk2ld6lf0ablii0iiw07sry2vrjfrm4wc99qmf81ha2")))) + "04lxggjarbidfq8ba5q6kwgqys4lhidbnz8gf3vrrb5wgcibx6d8")))) (build-system gnu-build-system) (home-page "https://invisible-island.net/byacc/byacc.html") (synopsis "Berkeley Yacc LALR parser generator") From 039bef4ac81ecc88f99434b8d414604281d4818d Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Sun, 11 Dec 2022 01:00:00 +0100 Subject: [PATCH 157/790] gnu: ccache: Update to 4.7.4. * gnu/packages/ccache.scm (ccache): Update to 4.7.4. --- gnu/packages/ccache.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/ccache.scm b/gnu/packages/ccache.scm index a2e5b35046..48f88c4b4b 100644 --- a/gnu/packages/ccache.scm +++ b/gnu/packages/ccache.scm @@ -35,14 +35,14 @@ (define-public ccache (package (name "ccache") - (version "4.7.2") + (version "4.7.4") (source (origin (method url-fetch) (uri (string-append "https://github.com/ccache/ccache/releases/download/v" version "/ccache-" version ".tar.xz")) (sha256 - (base32 "1bsf27dii1bm6bamvs6gi6vm5pjrd0956vf8597ix76lfyjpbjhp")))) + (base32 "0djfm138m863g772bnq7m2mfwh3y8sqxczc3yssg1yiybp8n836z")))) (build-system cmake-build-system) (arguments (list #:configure-flags From 816c7f4e843f6d21d3a3ac3db4d894ebc6561639 Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Sun, 11 Dec 2022 01:00:01 +0100 Subject: [PATCH 158/790] gnu: doctest: Update to 2.4.9. * gnu/packages/check.scm (doctest): Update to 2.4.9. --- gnu/packages/check.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/check.scm b/gnu/packages/check.scm index 9dd41e832b..a91a7e9d6d 100644 --- a/gnu/packages/check.scm +++ b/gnu/packages/check.scm @@ -750,7 +750,7 @@ and it supports a very flexible form of test discovery.") (define-public doctest (package (name "doctest") - (version "2.4.8") + (version "2.4.9") (home-page "https://github.com/onqtam/doctest") (source (origin (method git-fetch) @@ -759,7 +759,7 @@ and it supports a very flexible form of test discovery.") (file-name (git-file-name name version)) (sha256 (base32 - "057wdkv3gcz42mh1j284sgvm16i5fk1f9b1plgvavca70q4p52gz")))) + "1pkpwwvskcr21p00zrbnxpddv34p605mls86qirqqdwggmws82ds")))) (build-system cmake-build-system) (synopsis "C++ test framework") (description From 2ed751715f538ed99ab4feba60808f10ab0d7ed1 Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Sun, 11 Dec 2022 01:00:01 +0100 Subject: [PATCH 159/790] gnu: python-aiounittest: Update to 1.4.2. * gnu/packages/check.scm (python-aiounittest): Update to 1.4.2. --- gnu/packages/check.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/check.scm b/gnu/packages/check.scm index a91a7e9d6d..af0ad1c00f 100644 --- a/gnu/packages/check.scm +++ b/gnu/packages/check.scm @@ -3235,7 +3235,7 @@ system. The code under test requires no modification to work with pyfakefs.") (define-public python-aiounittest (package (name "python-aiounittest") - (version "1.4.1") + (version "1.4.2") ;; Pypi package lacks tests. (source (origin (method git-fetch) @@ -3245,7 +3245,7 @@ system. The code under test requires no modification to work with pyfakefs.") (file-name (git-file-name name version)) (sha256 (base32 - "10x7ds09b9415r92f7g9714gxixvvq3bm5mnh29ml9aba8blcb0n")))) + "0srahyzrk5awfh4rmppvqkblfmiavdklxl9i5mcr8gl7ahiwwl7f")))) (build-system python-build-system) (arguments '(#:phases (modify-phases %standard-phases From 885f18d750f950bfb930c47d9c8e30976dc361ef Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Sun, 11 Dec 2022 01:00:01 +0100 Subject: [PATCH 160/790] gnu: libdeflate: Update to 1.15. * gnu/packages/compression.scm (libdeflate): Update to 1.15. [build-system]: Use CMake. [arguments]: Remove #:make-flags and all custom phases. Add equivalent #:configure-flags and a custom 'check phase. --- gnu/packages/compression.scm | 17 +++++++---------- 1 file changed, 7 insertions(+), 10 deletions(-) diff --git a/gnu/packages/compression.scm b/gnu/packages/compression.scm index d2a1ed36f7..82b93e23b2 100644 --- a/gnu/packages/compression.scm +++ b/gnu/packages/compression.scm @@ -2695,7 +2695,7 @@ to their original, binary CD format.") (define-public libdeflate (package (name "libdeflate") - (version "1.14") + (version "1.15") (source (origin (method git-fetch) (uri (git-reference @@ -2704,19 +2704,16 @@ to their original, binary CD format.") (file-name (git-file-name name version)) (sha256 (base32 - "09y69mnbv3mprgjp53zvin5zqznqajginrk5b25xmi9y0b83bns8")))) - (build-system gnu-build-system) + "001l1xdc3k1dfjvl3ng480ydz0rnyvlhv54l5mshg2p9v4iz3v09")))) + (build-system cmake-build-system) (arguments - (list #:make-flags - #~(list (string-append "CC=" #$(cc-for-target)) - (string-append "PREFIX=" #$output)) + (list #:configure-flags + #~(list "-DLIBDEFLATE_BUILD_STATIC_LIB=NO") #:phases #~(modify-phases %standard-phases - (add-after 'unpack 'skip-static-library-installation + (replace 'check (lambda _ - (substitute* "Makefile" - (("install .*\\$\\(STATIC_LIB\\).*") "")))) - (delete 'configure)))) ; no configure script + (invoke "../source/scripts/run_tests.sh")))))) (inputs (list zlib)) (home-page "https://github.com/ebiggers/libdeflate") From 62cb0eae3e3312849c90c1bfaa59e18fa33af562 Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Sun, 11 Dec 2022 01:00:05 +0100 Subject: [PATCH 161/790] gnu: libhx: Update to 4.8. * gnu/packages/c.scm (libhx): Update to 4.8. --- gnu/packages/c.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/c.scm b/gnu/packages/c.scm index d03ad238b7..04c9fcdc62 100644 --- a/gnu/packages/c.scm +++ b/gnu/packages/c.scm @@ -425,14 +425,14 @@ whose behaviour is inconsistent across *NIX flavours.") (define-public libhx (package (name "libhx") - (version "4.3") + (version "4.8") (source (origin (method url-fetch) (uri (string-append "https://inai.de/files/libhx/" "libHX-" version ".tar.xz")) (sha256 - (base32 "06zkzaya6j3vaafz80qcgn5qcri047003bhmjisv5sbikcw97jqy")))) + (base32 "1mj6n4p0fs1jzj1dvk2xkyiyc1s7s5fxv27iciwn0xkwhasjmhxa")))) (build-system gnu-build-system) (home-page "https://inai.de/projects/libhx/") (synopsis "C library with common data structures and functions") From 187880b81479a912f6bf37500bc26642e1c93c28 Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Sun, 11 Dec 2022 01:00:00 +0100 Subject: [PATCH 162/790] gnu: global: Update to 6.6.9. * gnu/packages/code.scm (global): Update to 6.6.9. --- gnu/packages/code.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/code.scm b/gnu/packages/code.scm index 0ed978a768..4917c85a67 100644 --- a/gnu/packages/code.scm +++ b/gnu/packages/code.scm @@ -143,14 +143,14 @@ highlighting your own code that seemed comprehensible when you wrote it.") (define-public global ; a global variable (package (name "global") - (version "6.6.8") + (version "6.6.9") (source (origin (method url-fetch) (uri (string-append "mirror://gnu/global/global-" version ".tar.gz")) (sha256 (base32 - "1kaphc3gml89p8dpdgh2is8hj46wj05689kxj0bmh5q759rxk4vg")))) + "1mgss7ch4izz7ibb23xah6h4iva77g9dq4pkc9g69jk0ipxa1jxa")))) (build-system gnu-build-system) (arguments (list #:configure-flags From 885903e2f62e9660a05919fecc70503fafefb4ed Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Sun, 11 Dec 2022 01:00:01 +0100 Subject: [PATCH 163/790] gnu: botan: Update to 2.19.3. * gnu/packages/crypto.scm (botan): Update to 2.19.3. --- gnu/packages/crypto.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/crypto.scm b/gnu/packages/crypto.scm index 821e78d55a..cc633cb4bf 100644 --- a/gnu/packages/crypto.scm +++ b/gnu/packages/crypto.scm @@ -953,14 +953,14 @@ SHA256, SHA512, SHA3, AICH, ED2K, Tiger, DC++ TTH, BitTorrent BTIH, GOST R (define-public botan (package (name "botan") - (version "2.19.2") + (version "2.19.3") (source (origin (method url-fetch) (uri (string-append "https://botan.randombit.net/releases/" "Botan-" version ".tar.xz")) (sha256 (base32 - "0xad3fa96l6x3azxs2gbz5jfqm2drfv9y9idhf5wvdf62mvg3x9s")))) + "0m9dh00zibx13pbjij8lbncf86pix3cxklxmgl47z965k7rlgq6s")))) (build-system gnu-build-system) (arguments (list From 55e2b9b0a41b7d5789379ce77e7734eef4e2bc45 Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Sun, 11 Dec 2022 01:00:02 +0100 Subject: [PATCH 164/790] gnu: dash: Update to 0.5.12. * gnu/packages/shells.scm (dash): Update to 0.5.12. [arguments]: Don't explicitly return #t from phases. --- gnu/packages/shells.scm | 7 +++---- 1 file changed, 3 insertions(+), 4 deletions(-) diff --git a/gnu/packages/shells.scm b/gnu/packages/shells.scm index b607060716..f40e491535 100644 --- a/gnu/packages/shells.scm +++ b/gnu/packages/shells.scm @@ -84,14 +84,14 @@ (define-public dash (package (name "dash") - (version "0.5.11.5") + (version "0.5.12") (source (origin (method url-fetch) (uri (string-append "http://gondor.apana.org.au/~herbert/dash/files/" "dash-" version ".tar.gz")) (sha256 - (base32 "1g93w4lpn3jfwn2gaq17a1lxdig11x0j7gr9byc3fy8zi4882xyv")) + (base32 "12pjm2j0q0q88nvqbcyqjwr8s1c29ilxyq2cdj8k42wbdv24liva")) (modules '((guix build utils))) (snippet '(begin @@ -99,8 +99,7 @@ ;; This isn't the case on Guix or indeed most other GNU systems. (substitute* "src/dash.1" (("the standard command interpreter for the system") - "a command interpreter based on the original Bourne shell")) - #t)))) + "a command interpreter based on the original Bourne shell")))))) (build-system gnu-build-system) (inputs (list libedit)) From 992773d3a2af2e02eca920bf9ba6d8580b246e60 Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Sun, 11 Dec 2022 01:00:00 +0100 Subject: [PATCH 165/790] gnu: dash: Capitalise description sentences. MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * gnu/packages/shells.scm (dash)[description]: Capitalise ‘dash’. --- gnu/packages/shells.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/shells.scm b/gnu/packages/shells.scm index f40e491535..7cb57ed7ae 100644 --- a/gnu/packages/shells.scm +++ b/gnu/packages/shells.scm @@ -108,9 +108,9 @@ (home-page "http://gondor.apana.org.au/~herbert/dash") (synopsis "POSIX-compliant shell optimised for size") (description - "dash is a POSIX-compliant @command{/bin/sh} implementation that aims to be + "Dash is a POSIX-compliant @command{/bin/sh} implementation that aims to be as small as possible, often without sacrificing speed. It is faster than the -GNU Bourne-Again Shell (@command{bash}) at most scripted tasks. dash is a +GNU Bourne-Again Shell (@command{bash}) at most scripted tasks. Dash is a direct descendant of NetBSD's Almquist Shell (@command{ash}).") (license (list license:bsd-3 license:gpl2+)))) ; mksignames.c From 6c50e416a520ad6f118b84665f757b40ab74279f Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Sun, 11 Dec 2022 01:00:01 +0100 Subject: [PATCH 166/790] gnu: hyfetch: Update to 1.4.4. * gnu/packages/admin.scm (hyfetch): Update to 1.4.4. --- gnu/packages/admin.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/admin.scm b/gnu/packages/admin.scm index 5e46781efc..e8affe8d64 100644 --- a/gnu/packages/admin.scm +++ b/gnu/packages/admin.scm @@ -3918,13 +3918,13 @@ you are running, what theme or icon set you are using, etc.") (define-public hyfetch (package (name "hyfetch") - (version "1.4.1") + (version "1.4.4") (source (origin (method url-fetch) (uri (pypi-uri "HyFetch" version)) (sha256 - (base32 "18s8r63aqyah34vbahccgkiqw4008i2w5kvhqd9s8bdd4yvsrn4n")))) + (base32 "1k3pcl16y2czkk7wd79yk0w1kqpi4fp8h8szhjs5ywwy20nqmms8")))) (build-system python-build-system) (inputs (list python-hypy-utils python-typing-extensions)) (arguments `(#:phases (modify-phases %standard-phases From 2dfc21d9ce8c7aaf3dd1174d44f835b07496be7f Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Sun, 11 Dec 2022 01:00:01 +0100 Subject: [PATCH 167/790] gnu: inxi-minimal: Update to 3.3.24-1. * gnu/packages/admin.scm (inxi-minimal): Update to 3.3.24-1. --- gnu/packages/admin.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/admin.scm b/gnu/packages/admin.scm index e8affe8d64..b6154eee9f 100644 --- a/gnu/packages/admin.scm +++ b/gnu/packages/admin.scm @@ -4308,7 +4308,7 @@ Python loading in HPC environments.") (let ((real-name "inxi")) (package (name "inxi-minimal") - (version "3.3.23-1") + (version "3.3.24-1") (source (origin (method git-fetch) @@ -4317,7 +4317,7 @@ Python loading in HPC environments.") (commit version))) (file-name (git-file-name real-name version)) (sha256 - (base32 "0bpaffv4zqinfk46sbx82gic7572xsqiwb1lf894l1s6a6xi7zrd")))) + (base32 "1nai43251r791qvc1c4hhvcaa6hq7zcjlww7k3ip7br6zgxqjaxm")))) (build-system trivial-build-system) (inputs `(("bash" ,bash-minimal) From 932409da9c7ad25b1248e211ce8487f54f5c4607 Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Sun, 11 Dec 2022 01:00:07 +0100 Subject: [PATCH 168/790] gnu: inxi-minimal: Remove input labels. * gnu/packages/admin.scm (inxi-minimal)[inputs]: Remove input labels. --- gnu/packages/admin.scm | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/gnu/packages/admin.scm b/gnu/packages/admin.scm index b6154eee9f..4f39aa3350 100644 --- a/gnu/packages/admin.scm +++ b/gnu/packages/admin.scm @@ -4320,9 +4320,9 @@ Python loading in HPC environments.") (base32 "1nai43251r791qvc1c4hhvcaa6hq7zcjlww7k3ip7br6zgxqjaxm")))) (build-system trivial-build-system) (inputs - `(("bash" ,bash-minimal) - ("perl" ,perl) - ("procps" ,procps))) + (list bash-minimal + perl + procps)) (native-inputs (list gzip)) (arguments From bd268c21e531f0cc88f8920e0abcf1f33bf822b2 Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Sun, 11 Dec 2022 01:00:02 +0100 Subject: [PATCH 169/790] gnu: inxi-minimal: Reduce reliance on input names. * gnu/packages/admin.scm (inxi-minimal)[arguments]: Use SEARCH-INPUT-FILE. --- gnu/packages/admin.scm | 12 ++++++++---- 1 file changed, 8 insertions(+), 4 deletions(-) diff --git a/gnu/packages/admin.scm b/gnu/packages/admin.scm index 4f39aa3350..654fd55e17 100644 --- a/gnu/packages/admin.scm +++ b/gnu/packages/admin.scm @@ -4332,10 +4332,14 @@ Python loading in HPC environments.") (use-modules (guix build utils) (ice-9 match) (srfi srfi-26)) - (setenv "PATH" (string-append - (assoc-ref %build-inputs "bash") "/bin" ":" - (assoc-ref %build-inputs "gzip") "/bin" ":" - (assoc-ref %build-inputs "perl") "/bin" ":")) + (setenv "PATH" (string-join + (map (lambda (file) + (dirname (search-input-file %build-inputs + file))) + (list "bin/bash" + "bin/gzip" + "bin/perl")) + ":")) (copy-recursively (assoc-ref %build-inputs "source") ,(string-append real-name "-" version)) (with-directory-excursion ,(string-append real-name "-" version) From 2202fc90031419ff6928bcb39dfa7ddaa69c8063 Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Sun, 11 Dec 2022 01:00:01 +0100 Subject: [PATCH 170/790] gnu: nnn: Update to 4.7. * gnu/packages/admin.scm (nnn): Update to 4.7. --- gnu/packages/admin.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/admin.scm b/gnu/packages/admin.scm index 654fd55e17..a4d6473ea0 100644 --- a/gnu/packages/admin.scm +++ b/gnu/packages/admin.scm @@ -4084,14 +4084,14 @@ information tool.") (define-public nnn (package (name "nnn") - (version "4.6") + (version "4.7") (source (origin (method url-fetch) (uri (string-append "https://github.com/jarun/nnn/releases/download/v" version "/nnn-v" version ".tar.gz")) (sha256 - (base32 "0gvyvynw957yirvc1aj65flzni7niaj5bvyk82ka5dfgi2dazb0m")))) + (base32 "0dbm54m3iv8hzar38dsfxh77z4mlpjj649ga82s0wwms4vlrm5pg")))) (build-system gnu-build-system) (inputs (list ncurses readline)) From 54e7efd5cf803b46d5d8df776efd4f9d0e4a0c54 Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Sun, 11 Dec 2022 01:00:01 +0100 Subject: [PATCH 171/790] gnu: nmrpflash: Update to 0.9.19. * gnu/packages/admin.scm (nmrpflash): Update to 0.9.19. --- gnu/packages/admin.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/admin.scm b/gnu/packages/admin.scm index a4d6473ea0..756ca324cd 100644 --- a/gnu/packages/admin.scm +++ b/gnu/packages/admin.scm @@ -4856,7 +4856,7 @@ entries, providing commands to add, remove, comment, and search.") (define-public nmrpflash (package (name "nmrpflash") - (version "0.9.16") + (version "0.9.19") (source (origin (method git-fetch) @@ -4865,7 +4865,7 @@ entries, providing commands to add, remove, comment, and search.") (url "https://github.com/jclehner/nmrpflash") (commit (string-append "v" version)))) (sha256 - (base32 "0gp66l3a2wznjnlc2ljs8g38mfrf1b9a0qcfxqg2bczmfxnrsynj")) + (base32 "02r2z3mnbj8dfka7adw1l76zq1jh1l13mmkns93c54ychs44jz3d")) (file-name (git-file-name name version)))) (build-system gnu-build-system) (native-inputs From b853dbd0e2e7aedffb0054816564d1fd9e2a10ea Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Sun, 11 Dec 2022 01:00:00 +0100 Subject: [PATCH 172/790] gnu: nmrpflash: Rephrase synopsis. * gnu/packages/admin.scm (nmrpflash)[synopsis]: Rework awkward wording. --- gnu/packages/admin.scm | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/gnu/packages/admin.scm b/gnu/packages/admin.scm index 756ca324cd..0f2da3f18e 100644 --- a/gnu/packages/admin.scm +++ b/gnu/packages/admin.scm @@ -4884,7 +4884,7 @@ entries, providing commands to add, remove, comment, and search.") (lambda* (#:key outputs #:allow-other-keys) (mkdir-p (string-append (assoc-ref outputs "out") "/bin"))))))) (home-page "https://github.com/jclehner/nmrpflash") - (synopsis "Netgear unbrick utility") + (synopsis "Reflash (``unbrick'') Netgear devices with corrupted firmware") (description "This package provides a utility to flash a new firmware image to a Netgear device. It has been tested on Netgear EX2700, EX6120, EX6150v2, DNG3700v2, R6100, R6220, R7000, D7000, WNR3500, R6400, R6800, From 34242fe5c7af902b841481df0b66a88b1ca263c5 Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Sun, 11 Dec 2022 01:00:02 +0100 Subject: [PATCH 173/790] gnu: isc-dhcp: Update to 4.4.3-P1 [fixes CVE-2022-2928, CVE-2022-2929]. * gnu/packages/admin.scm (isc-dhcp): Update to 4.4.3-P1. --- gnu/packages/admin.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/admin.scm b/gnu/packages/admin.scm index 0f2da3f18e..62b52f8329 100644 --- a/gnu/packages/admin.scm +++ b/gnu/packages/admin.scm @@ -1409,14 +1409,14 @@ connection alive.") bind-release-version))) (package (name "isc-dhcp") - (version "4.4.3") + (version "4.4.3-P1") (source (origin (method url-fetch) (uri (string-append "https://ftp.isc.org/isc/dhcp/" version "/dhcp-" version ".tar.gz")) (sha256 (base32 - "062q2g8cj2zv0zv22x6pg21m21bdlscxkg3li0ac0pm0qasccghf")))) + "1ivkvhhvqxap6c51cli7pa6xn76ngxri1zbl45ishz4ranxidi0a")))) (build-system gnu-build-system) (arguments `(#:parallel-build? #f From 85dcea59f6bba846b93ab8f3df6817ad24a01152 Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Sun, 11 Dec 2022 01:00:00 +0100 Subject: [PATCH 174/790] gnu: isc-dhcp: Update description. * gnu/packages/admin.scm (isc-dhcp)[description]: Note EOL status. --- gnu/packages/admin.scm | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/gnu/packages/admin.scm b/gnu/packages/admin.scm index 62b52f8329..b9fd3dab27 100644 --- a/gnu/packages/admin.scm +++ b/gnu/packages/admin.scm @@ -1559,7 +1559,10 @@ connection alive.") (description "ISC's Dynamic Host Configuration Protocol (DHCP) distribution provides a reference implementation of all aspects of DHCP, through a suite of DHCP -tools: server, client, and relay agent.") +tools: server, client, and relay agent. + +This software is @emph{end-of-life}! ISC does not intend to issue any further +maintenance releases.") (license license:mpl2.0) (properties '((cpe-name . "dhcp")))))) From a312bc9cd8a80543cddd8a14295aa85a8102bc55 Mon Sep 17 00:00:00 2001 From: Bruno Victal Date: Wed, 30 Nov 2022 14:56:15 +0000 Subject: [PATCH 175/790] services: configuration: Remove orphan reference to example. MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit 'generic-serialize-alist' refers to (gnu home services version-control) for usage examples but there's no such module. * gnu/services/configuration.scm (generic-serialize-alist): Adjust docstring. Signed-off-by: Ludovic Courtès --- gnu/services/configuration.scm | 5 +---- 1 file changed, 1 insertion(+), 4 deletions(-) diff --git a/gnu/services/configuration.scm b/gnu/services/configuration.scm index 10cb933ed1..6b0291dc00 100644 --- a/gnu/services/configuration.scm +++ b/gnu/services/configuration.scm @@ -473,9 +473,6 @@ applied on the fields and values of FIELDS using the COMBINE is a procedure that takes one or more arguments and combines all the alist entries into one value, @code{string-append} or -@code{append} are usually good candidates for this. - -See the @code{serialize-alist} procedure in `@code{(gnu home services -version-control}' for an example usage.)}" +@code{append} are usually good candidates for this." (apply combine (map (generic-serialize-alist-entry serialize-field) fields))) From dcfd97b42ebfaf2f56050d3c0f777b0e539b3edc Mon Sep 17 00:00:00 2001 From: Bruno Victal Date: Tue, 29 Nov 2022 21:21:59 +0000 Subject: [PATCH 176/790] doc: Fix formatting for 'computed-file'. MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * doc/guix.texi (G-Expressions): Fix formatting for 'computed-file'. Signed-off-by: Ludovic Courtès --- doc/guix.texi | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/doc/guix.texi b/doc/guix.texi index b270964542..30674dab1e 100644 --- a/doc/guix.texi +++ b/doc/guix.texi @@ -11706,8 +11706,7 @@ This is the declarative counterpart of @code{text-file}. @end deffn @deffn {Scheme Procedure} computed-file @var{name} @var{gexp} @ - [#:local-build? #t] - [#:options '()] + [#:local-build? #t] [#:options '()] Return an object representing the store item @var{name}, a file or directory computed by @var{gexp}. When @var{local-build?} is true (the default), the derivation is built locally. @var{options} is a list of From 4eae37157fddecef7a732a66b77be5d3540948c8 Mon Sep 17 00:00:00 2001 From: Petr Hodina Date: Sun, 18 Jul 2021 12:11:55 +0200 Subject: [PATCH 177/790] gnu: Add bolt. MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * gnu/packages/linux.scm (bolt): New variable. Signed-off-by: Ludovic Courtès --- gnu/packages/linux.scm | 51 ++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 51 insertions(+) diff --git a/gnu/packages/linux.scm b/gnu/packages/linux.scm index 08e6d855eb..23008f1592 100644 --- a/gnu/packages/linux.scm +++ b/gnu/packages/linux.scm @@ -143,6 +143,7 @@ #:use-module (gnu packages perl) #:use-module (gnu packages pciutils) #:use-module (gnu packages pkg-config) + #:use-module (gnu packages polkit) #:use-module (gnu packages popt) #:use-module (gnu packages pulseaudio) #:use-module (gnu packages python) @@ -2868,6 +2869,56 @@ IPv6 packet filter. Both commands are targeted at system administrators.") (license license:gpl2+))) +(define-public bolt + (package + (name "bolt") + (version "0.9.2") + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://gitlab.freedesktop.org/bolt/bolt") + (commit version))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "1h48qmqxhjq9gxv5gf78cqm5wadmnhvc9bkd02zya77rh3pf6y3r")))) + (build-system meson-build-system) + (arguments + (list #:configure-flags '(list "--localstatedir=/var") + #:glib-or-gtk? #t ;To wrap binaries and/or compile schemas + #:phases #~(modify-phases %standard-phases + (add-after 'unpack 'replace-directories + (lambda* (#:key outputs #:allow-other-keys) + (substitute* "meson.build" + (("udev.get_pkgconfig_variable..udevdir..") + (string-append "'" + #$output "/lib/udev'"))) + (substitute* "scripts/meson-install.sh" + (("mkdir.*") + "")))) + (add-before 'install 'no-polkit-magic + (lambda* (#:key outputs #:allow-other-keys) + (setenv "PKEXEC_UID" "something")))))) + (native-inputs (list pkg-config + `(,glib "bin") python asciidoc umockdev)) + (inputs (list eudev dbus polkit)) + (synopsis "Thunderbolt 3 device manager") + (description + "This package provides @command{boltd}, a userspace daemon +for Thunderbolt devices, and @command{boltctl}, a command-line utility for +managing those devices. + +The daemon @command{boltd} exposes devices via D-Bus to clients. It also +stores a database of previously authorized devices and will, depending on the +policy set for the individual devices, automatically authorize newly connected +devices without user interaction. + +The command-line utility @command{boltctl} manages Thunderbolt devices via +@command{boltd}. It can list devices, monitor changes, and initiate +authorization of devices.") + (home-page "https://gitlab.freedesktop.org/bolt/bolt") + (license license:gpl2+))) + (define-public jitterentropy-rngd (package (name "jitterentropy-rngd") From 7e2b9dbe08b44f11a1d9ac8a921be7ca8fb60e72 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ludovic=20Court=C3=A8s?= Date: Wed, 14 Dec 2022 12:25:24 +0100 Subject: [PATCH 178/790] gnu: bolt: Update to 0.9.4. * gnu/packages/linux.scm (bolt): Update to 0.9.4. --- gnu/packages/linux.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/linux.scm b/gnu/packages/linux.scm index 23008f1592..73f3275838 100644 --- a/gnu/packages/linux.scm +++ b/gnu/packages/linux.scm @@ -2872,7 +2872,7 @@ Both commands are targeted at system administrators.") (define-public bolt (package (name "bolt") - (version "0.9.2") + (version "0.9.4") (source (origin (method git-fetch) (uri (git-reference @@ -2881,7 +2881,7 @@ Both commands are targeted at system administrators.") (file-name (git-file-name name version)) (sha256 (base32 - "1h48qmqxhjq9gxv5gf78cqm5wadmnhvc9bkd02zya77rh3pf6y3r")))) + "0w66shv7ra8yrhr0byifahbq25wi8qfsm3rifz0j31l7cmnys3js")))) (build-system meson-build-system) (arguments (list #:configure-flags '(list "--localstatedir=/var") From acab89748d07abaaa7b90a532f64d9c5780641fb Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Simen=20Endsj=C3=B8?= Date: Wed, 7 Dec 2022 10:43:41 +0100 Subject: [PATCH 179/790] gnu: Add aspell-dict-nb. MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * gnu/packages/aspell.scm (aspell-dict-nb): New variable. Signed-off-by: Ludovic Courtès --- gnu/packages/aspell.scm | 8 ++++++++ 1 file changed, 8 insertions(+) diff --git a/gnu/packages/aspell.scm b/gnu/packages/aspell.scm index ec0dafbc7a..9a5a9c6bcc 100644 --- a/gnu/packages/aspell.scm +++ b/gnu/packages/aspell.scm @@ -320,6 +320,14 @@ dictionaries, including personal ones.") (base32 "0w2k5l5rbqpliripgqwiqixz5ghnjf7i9ggbrc4ly4vy1ia10rmc"))) +(define-public aspell-dict-nb + (aspell-dictionary "nb" "Norwegian Bokmål" + #:version "0.50.1-2" + #:prefix "aspell-" + #:sha256 + (base32 + "1xvns7dwx2sc0msldj7r2hv0426913rg3dpnkxlrvnsyrxzjpbpc"))) + (define-public aspell-dict-pl (aspell-dictionary "pl" "Polish" #:version "0.51-0" From 8125c22ea2b61b1bbe7acb8741f8895b4d1f6f9f Mon Sep 17 00:00:00 2001 From: Bruno Victal Date: Tue, 6 Dec 2022 15:51:34 +0000 Subject: [PATCH 180/790] gnu: rasdaemon: Add missing inputs and rewrite using G-Exps. MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * gnu/packages/linux.scm (rasdaemon)[arguments]: Rewrite using G-Expressions. Add 'fix-dmidecode-and-modprobe' and 'wrap-rasdaemon' phases. [inputs]: Add perl-dbd-sqlite, dmidecode, and kmod. Signed-off-by: Ludovic Courtès --- gnu/packages/linux.scm | 50 +++++++++++++++++++++++++----------------- 1 file changed, 30 insertions(+), 20 deletions(-) diff --git a/gnu/packages/linux.scm b/gnu/packages/linux.scm index 73f3275838..e0129ac9de 100644 --- a/gnu/packages/linux.scm +++ b/gnu/packages/linux.scm @@ -9512,27 +9512,37 @@ provides user-space tools for creating EROFS file systems.") (sha256 (base32 "0r0339mg4rc12p63iiq2kwdqn1zjakyiv014i2a2l9s8v5rjik41")))) (native-inputs (list autoconf automake libtool)) - (inputs (list perl sqlite)) + (inputs (list perl perl-dbd-sqlite sqlite dmidecode kmod)) (arguments - `(#:configure-flags - (list "--enable-all" - ;; Don't install unused /etc/sysconfig/rasdaemon environment file. - "--with-sysconfdefdir=." - "--localstatedir=/var") - #:phases - (modify-phases %standard-phases - (add-before 'configure 'munge-autotools - (lambda _ - ;; For some reason upstream forces sysconfdir=/etc. This results - ;; in EPERM during the install phase. Removing the offending - ;; line lets sysconfdir correctly pick up DESTDIR. - (substitute* "configure.ac" - (("^test .* sysconfdir=/etc\n$") "")) - ;; Upstream tries to create /var/lib/rasdaemon at install time. - ;; This results in EPERM on guix. Instead, the service should - ;; create this at activation time. - (substitute* "Makefile.am" - (("^\\s*\\$\\(install_sh\\) -d .*@RASSTATEDIR@.*$") ""))))))) + (list + #:configure-flags + #~(list "--enable-all" + ;; Don't install unused /etc/sysconfig/rasdaemon environment file. + "--with-sysconfdefdir=." + "--localstatedir=/var") + #:phases + #~(modify-phases %standard-phases + (add-before 'configure 'munge-autotools + (lambda _ + ;; For some reason upstream forces sysconfdir=/etc. This results + ;; in EPERM during the install phase. Removing the offending + ;; line lets sysconfdir correctly pick up DESTDIR. + (substitute* "configure.ac" + (("^test .* sysconfdir=/etc\n$") "")) + ;; Upstream tries to create /var/lib/rasdaemon at install time. + ;; This results in EPERM on guix. Instead, the service should + ;; create this at activation time. + (substitute* "Makefile.am" + (("^\\s*\\$\\(install_sh\\) -d .*@RASSTATEDIR@.*$") "")))) + (add-after 'install 'fix-dmidecode-and-modprobe + (lambda _ + (substitute* (string-append #$output "/sbin/ras-mc-ctl") + (("find_prog \\(\"dmidecode\"\\).*$") (format #f "~s;~%" (string-append #$dmidecode "/sbin/dmidecode"))) + (("find_prog \\(\"modprobe\"\\).*$") (format #f "~s;~%" (string-append #$kmod "/bin/modprobe")))))) + (add-after 'wrap 'wrap-rasdaemon + (lambda _ + (wrap-program (string-append #$output "/sbin/ras-mc-ctl") + `("PERL5LIB" ":" prefix ,(string-split (getenv "PERL5LIB") #\:)))))))) (build-system gnu-build-system) (home-page "https://github.com/mchehab/rasdaemon") (synopsis "Platform Reliability, Availability, and Serviceability tools") From 1b6e251ed1bae7aa2f544e8ccb6b4aaf872e77e6 Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Tue, 13 Dec 2022 13:53:47 -0500 Subject: [PATCH 181/790] gnu: make-u-boot-package: Build verbosily. * gnu/packages/bootloaders.scm (make-u-boot-package) [arguments] : Add KBUILD_VERBOSE=1. --- gnu/packages/bootloaders.scm | 1 + 1 file changed, 1 insertion(+) diff --git a/gnu/packages/bootloaders.scm b/gnu/packages/bootloaders.scm index 0917095627..3c96453e5c 100644 --- a/gnu/packages/bootloaders.scm +++ b/gnu/packages/bootloaders.scm @@ -817,6 +817,7 @@ appended to the package description." #:test-target "test" #:make-flags (list "HOSTCC=gcc" + "KBUILD_VERBOSE=1" ,@(if (not (same-arch?)) `((string-append "CROSS_COMPILE=" ,triplet "-")) '())) From 627c56f5431b900b120a9fb25b36b7e077b20949 Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Sun, 11 Dec 2022 01:00:02 +0100 Subject: [PATCH 182/790] gnu: gulrak-filesystem: Update to 1.5.12. * gnu/packages/cpp.scm (gulrak-filesystem): Update to 1.5.12. --- gnu/packages/cpp.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/cpp.scm b/gnu/packages/cpp.scm index 210c76e482..a3df706f43 100644 --- a/gnu/packages/cpp.scm +++ b/gnu/packages/cpp.scm @@ -1901,7 +1901,7 @@ multi-threaded applications and network applications.") (define-public gulrak-filesystem (package (name "gulrak-filesystem") - (version "1.5.10") + (version "1.5.12") (source (origin (method git-fetch) (uri (git-reference @@ -1910,7 +1910,7 @@ multi-threaded applications and network applications.") (file-name (git-file-name name version)) (sha256 (base32 - "0dx1yvbz5rnisymkqap7z0b06ag9fcs6q6l82vgi8caylhkwsqs7")))) + "1qg10akvhp801xirkj4mqcpvcxj90z81ygpyg752xv110zj4914g")))) (build-system cmake-build-system) (synopsis "Header only C++ std::filesystem compatible library") (description "This package provides a header-only single-file From dbbca61bf0a83ac9cbb1cea12f11cb0ee3c28f2f Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Sun, 11 Dec 2022 01:00:00 +0100 Subject: [PATCH 183/790] gnu: nano: Update to 7.1. * gnu/packages/nano.scm (nano): Update to 7.1. --- gnu/packages/nano.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/nano.scm b/gnu/packages/nano.scm index b7654b9f9c..e386c78118 100644 --- a/gnu/packages/nano.scm +++ b/gnu/packages/nano.scm @@ -31,13 +31,13 @@ (define-public nano (package (name "nano") - (version "7.0") + (version "7.1") (source (origin (method url-fetch) (uri (string-append "mirror://gnu/nano/nano-" version ".tar.xz")) (sha256 - (base32 "0j91am8y8dy48dj1nf8p1lhpassgv2py3w414vc8d1rbig1ymmld")))) + (base32 "0dk8820w631ip6hpl7qc8kg5viw7wc154l7fvpvg06bmkcg7bfjp")))) (build-system gnu-build-system) (inputs (list gettext-minimal ncurses)) From 404d228319854a6b8f2a15ba00b06b621da8d97e Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Sun, 11 Dec 2022 01:00:01 +0100 Subject: [PATCH 184/790] gnu: memcached: Update to 1.6.17. * gnu/packages/databases.scm (memcached): Update to 1.6.17. --- gnu/packages/databases.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/databases.scm b/gnu/packages/databases.scm index 9d1eec5ea0..caa6a91702 100644 --- a/gnu/packages/databases.scm +++ b/gnu/packages/databases.scm @@ -487,14 +487,14 @@ mapping from string keys to string values.") (define-public memcached (package (name "memcached") - (version "1.6.16") + (version "1.6.17") (source (origin (method url-fetch) (uri (string-append "https://memcached.org/files/memcached-" version ".tar.gz")) (sha256 - (base32 "1nilmfhy8hc7zzlihnx3hmiqf7siyrpgz2g5s3r3l36xy4xsjl9h")))) + (base32 "090jpprdjhbr1v9ph15s077bj8ryrsnz1ydg54aw53rxc5ry6m90")))) (build-system gnu-build-system) (inputs (list libevent cyrus-sasl)) From 4a517a012f8cdaa4605ef2f49fd9347e7bc02ba5 Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Sun, 11 Dec 2022 01:00:03 +0100 Subject: [PATCH 185/790] gnu: libpqxx: Update to 7.7.4. * gnu/packages/databases.scm (libpqxx): Update to 7.7.4. --- gnu/packages/databases.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/databases.scm b/gnu/packages/databases.scm index caa6a91702..81a2581c0c 100644 --- a/gnu/packages/databases.scm +++ b/gnu/packages/databases.scm @@ -2844,7 +2844,7 @@ semantics.") (define-public libpqxx (package (name "libpqxx") - (version "7.7.3") + (version "7.7.4") (source (origin (method git-fetch) (uri (git-reference @@ -2853,7 +2853,7 @@ semantics.") (file-name (git-file-name name version)) (sha256 (base32 - "1mrhsih5bhiin0l3c4vp22l9p7c5035m0vvqpx18c0407fkzc7hp")))) + "1qwpfba8g55jjv0xnsk4hhf2cmhk7mdirxx115cvnjjw97ppy0z0")))) (build-system gnu-build-system) (native-inputs (list gcc-11 python-wrapper)) (inputs (list postgresql)) From 6cf6f423340f060e523c007205b691ec68120f50 Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Sun, 11 Dec 2022 01:00:00 +0100 Subject: [PATCH 186/790] guix-install.sh: Gracefully fail on | bash. * etc/guix-install.sh (welcome): Print an error message and a hint if the first read fails. --- etc/guix-install.sh | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/etc/guix-install.sh b/etc/guix-install.sh index fb9006b3e2..f008593d84 100755 --- a/etc/guix-install.sh +++ b/etc/guix-install.sh @@ -615,7 +615,10 @@ https://www.gnu.org/software/guix/ EOF # Don't use ‘read -p’ here! It won't display when run non-interactively. echo -n "Press return to continue..."$'\r' - read -r char + if ! read -r char; then + echo + die "Can't read standard input. Hint: don't pipe scripts into a shell." + fi if [ "$char" ]; then echo echo "...that ($char) was not a return!" From 7885b5be9bdedde417e46eb85e55b8ab98dd25df Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 14 Dec 2022 17:16:35 +0100 Subject: [PATCH 187/790] gnu: 389-ds-base: Drop input labels. * gnu/packages/openldap.scm (389-ds-base)[inputs]: Drop labels. [native-inputs]: Drop labels. --- gnu/packages/openldap.scm | 69 +++++++++++++++++++-------------------- 1 file changed, 34 insertions(+), 35 deletions(-) diff --git a/gnu/packages/openldap.scm b/gnu/packages/openldap.scm index 78f96e6190..cdacc99fa1 100644 --- a/gnu/packages/openldap.scm +++ b/gnu/packages/openldap.scm @@ -357,42 +357,41 @@ servers from Python programs.") "/bin/ds-logpipe.py" "/bin/ds-replcheck")))))))) (inputs - `(("bdb" ,bdb) - ("cracklib" ,cracklib) - ("cyrus-sasl" ,cyrus-sasl) - ("gnutls" ,gnutls) - ("httpd" ,httpd) - ("icu4c" ,icu4c) - ("iproute" ,iproute) - ("libevent" ,libevent) - ("libselinux" ,libselinux) - ("linux-pam" ,linux-pam) - ("mit-krb5" ,mit-krb5) - ("net-snmp" ,net-snmp) - ("nspr" ,nspr) - ("nss" ,nss) - ("nss:bin" ,nss "bin") ; for certutil - ("openldap" ,openldap) - ("openssl" ,openssl) ; #included by net-snmp - ("pcre" ,pcre) - ("perl" ,perl) - ("python" ,python) - ("python-pyasn1" ,python-pyasn1) - ("python-pyasn1-modules" ,python-pyasn1-modules) - ("python-pytest" ,python-pytest) - ("python-dateutil" ,python-dateutil) - ("python-six" ,python-six) - ("python-argcomplete" ,python-argcomplete) - ("python-argparse-manpage" ,python-argparse-manpage) - ("python-ldap" ,python-ldap))) + (list bdb + cracklib + cyrus-sasl + gnutls + httpd + icu4c + iproute + libevent + libselinux + linux-pam + mit-krb5 + net-snmp + nspr + nss + (list nss "bin") ; for certutil + openldap + openssl ; #included by net-snmp + pcre + python + python-pyasn1 + python-pyasn1-modules + python-pytest + python-dateutil + python-six + python-argcomplete + python-argparse-manpage + python-ldap)) (native-inputs - `(("autoconf" ,autoconf) - ("automake" ,automake) - ("doxygen" ,doxygen) - ("gettext" ,gettext-minimal) - ("libtool" ,libtool) - ("rsync" ,rsync) - ("pkg-config" ,pkg-config))) + (list autoconf + automake + doxygen + gettext-minimal + libtool + rsync + pkg-config)) (home-page "https://directory.fedoraproject.org") (synopsis "Enterprise-class LDAP server") (description "389ds is an enterprise-class LDAP server. It is hardened by From 2f707f9493df41632b8f1bd33a1a702a93dbc7a4 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 14 Dec 2022 17:17:29 +0100 Subject: [PATCH 188/790] gnu: 389-ds-base: Update to 1.4.5.0. * gnu/packages/openldap.scm (389-ds-base): Update to 1.4.5.0. [source]: Fetch from git. [arguments]: Remove unnecessary configure flags; update 'fix-references phase; update 'overwrite-default-locations phase. --- gnu/packages/openldap.scm | 37 ++++++++++++++----------------------- 1 file changed, 14 insertions(+), 23 deletions(-) diff --git a/gnu/packages/openldap.scm b/gnu/packages/openldap.scm index cdacc99fa1..b3b22d1709 100644 --- a/gnu/packages/openldap.scm +++ b/gnu/packages/openldap.scm @@ -2,7 +2,7 @@ ;;; Copyright © 2013, 2014, 2015, 2019, 2020 Ludovic Courtès ;;; Copyright © 2013 Andreas Enge ;;; Copyright © 2016, 2021 Leo Famulari -;;; Copyright © 2017, 2018, 2019, 2021 Ricardo Wurmus +;;; Copyright © 2017, 2018, 2019, 2021, 2022 Ricardo Wurmus ;;; Copyright © 2018 Tobias Geerinckx-Rice ;;; Copyright © 2019 Mathieu Othacehe ;;; Copyright © 2020 Lars-Dominik Braun @@ -58,6 +58,7 @@ #:use-module (guix gexp) #:use-module (guix utils) #:use-module (guix download) + #:use-module (guix git-download) #:use-module (guix build-system gnu) #:use-module (guix build-system python)) @@ -244,14 +245,16 @@ servers from Python programs.") (define-public 389-ds-base (package (name "389-ds-base") - (version "1.4.4.17") + (version "1.4.5.0") (source (origin - (method url-fetch) - (uri (string-append "https://github.com/389ds/389-ds-base/archive/" - "389-ds-base-" version ".tar.gz")) + (method git-fetch) + (uri (git-reference + (url "https://github.com/389ds/389-ds-base") + (commit (string-append "389-ds-base-" version)))) + (file-name (git-file-name name version)) (sha256 (base32 - "0i8m4crbnjjhfb7cq758rd0fxyz36i291yq6fykkprjykz9s3zv4")))) + "1s627w4kwrbszrkm6k6v32gx7jd27h4yqvs81kjkakiaq2lh1s1z")))) (build-system gnu-build-system) (arguments `(#:modules ((srfi srfi-1) @@ -264,26 +267,18 @@ servers from Python programs.") #:configure-flags (list (string-append "--with-db=" (assoc-ref %build-inputs "bdb")) - (string-append "--with-sasl=" - (assoc-ref %build-inputs "cyrus-sasl")) (string-append "--with-netsnmp=" (assoc-ref %build-inputs "net-snmp")) - (string-append "--with-pcre=" - (assoc-ref %build-inputs "pcre")) (string-append "--with-selinux=" (assoc-ref %build-inputs "libselinux")) "--localstatedir=/var" - "--with-instconfigdir=/etc/dirsrv" - ;; The Perl scripts are being removed in the 1.4.0 release. - ;; Building them would require packaging of the outdated Mozilla - ;; LDAP SDK (instead of OpenLDAP) and PerLDAP. - "--disable-perl") + "--with-instconfigdir=/etc/dirsrv") #:phases (modify-phases %standard-phases (add-after 'unpack 'fix-references (lambda _ - (substitute* "include/ldaputil/certmap.h" - (("nss3/cert.h") "nss/cert.h")) + (substitute* "ldap/servers/plugins/sync/sync_persist.c" + (("nspr4") "nspr")) (substitute* "src/lib389/lib389/utils.py" (("'/sbin/ip'") (string-append "'" (which "ip") "'"))) @@ -291,10 +286,7 @@ servers from Python programs.") (("'/usr/bin/certutil'") (string-append "'" (which "certutil") "'")) (("'/usr/bin/openssl'") - (string-append "'" (which "openssl") "'")) - (("'/usr/bin/c_rehash'") - (string-append "'" (which "perl") "', '" - (which "c_rehash") "'"))))) + (string-append "'" (which "openssl") "'"))))) (add-after 'unpack 'overwrite-default-locations (lambda* (#:key outputs #:allow-other-keys) (let ((out (assoc-ref outputs "out"))) @@ -309,8 +301,7 @@ servers from Python programs.") "initconfig_dir = /etc/dirsrv/registry\n")) ;; This is used to determine where to write certificate files ;; when installing new directory server instances. - (substitute* '("src/lib389/lib389/instance/setup.py" - "src/lib389/lib389/instance/remove.py") + (substitute* "src/lib389/lib389/instance/setup.py" (("etc_dirsrv_path = .*") "etc_dirsrv_path = '/etc/dirsrv/'\n"))))) (add-after 'unpack 'fix-install-location-of-python-tools From e5602a2747a56d8af46a3723034867facd54fb00 Mon Sep 17 00:00:00 2001 From: Guillaume Le Vaillant Date: Wed, 14 Dec 2022 17:03:43 +0100 Subject: [PATCH 189/790] gnu: hackrf: Update to 2022.09.1. * gnu/packages/radio.scm (hackrf): Update to 2022.09.1. --- gnu/packages/radio.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/radio.scm b/gnu/packages/radio.scm index 3834599cfc..3883f90f5d 100644 --- a/gnu/packages/radio.scm +++ b/gnu/packages/radio.scm @@ -1169,7 +1169,7 @@ for correctness.") (define-public hackrf (package (name "hackrf") - (version "2021.03.1") + (version "2022.09.1") (source (origin (method git-fetch) @@ -1178,7 +1178,7 @@ for correctness.") (commit (string-append "v" version)))) (file-name (git-file-name name version)) (sha256 - (base32 "12fkgimjy5ia291c1rn4y59pn9r5wdvz5x9z5xc8zr1xr96iyhfs")))) + (base32 "0m9j160q5zb3jimszv1lb6j76zf5lwijvpfl1k28d832rh847vvk")))) (build-system cmake-build-system) (arguments '(#:configure-flags From d94f7a7b5363c71bc9dbeaf6fff17b3a94c9fb18 Mon Sep 17 00:00:00 2001 From: Guillaume Le Vaillant Date: Wed, 14 Dec 2022 17:10:54 +0100 Subject: [PATCH 190/790] gnu: hackrf: Improve style. * gnu/packages/radio.scm (hackrf)[source]: Use new URL. [arguments]: Use gexps. Remove trailing booleans. --- gnu/packages/radio.scm | 40 ++++++++++++++++++---------------------- 1 file changed, 18 insertions(+), 22 deletions(-) diff --git a/gnu/packages/radio.scm b/gnu/packages/radio.scm index 3883f90f5d..ecca65391c 100644 --- a/gnu/packages/radio.scm +++ b/gnu/packages/radio.scm @@ -1174,34 +1174,30 @@ for correctness.") (origin (method git-fetch) (uri (git-reference - (url "https://github.com/mossmann/hackrf") + (url "https://github.com/greatscottgadgets/hackrf") (commit (string-append "v" version)))) (file-name (git-file-name name version)) (sha256 (base32 "0m9j160q5zb3jimszv1lb6j76zf5lwijvpfl1k28d832rh847vvk")))) (build-system cmake-build-system) (arguments - '(#:configure-flags - (list "-DUDEV_RULES_GROUP=dialout" - (string-append "-DUDEV_RULES_PATH=" - (assoc-ref %outputs "out") - "/lib/udev/rules.d")) - #:phases - (modify-phases %standard-phases - (add-before 'configure 'enter-source-directory - (lambda _ - (chdir "host") - #t)) - (add-after 'install 'delete-static-library - (lambda* (#:key outputs #:allow-other-keys) - (delete-file (string-append (assoc-ref outputs "out") - "/lib/libhackrf.a")) - #t)) - (add-before 'install-license-files 'leave-source-directory - (lambda _ - (chdir "..") - #t))) - #:tests? #f)) ; no test suite + (list #:configure-flags + #~(list "-DUDEV_RULES_GROUP=dialout" + (string-append "-DUDEV_RULES_PATH=" + #$output + "/lib/udev/rules.d")) + #:phases + #~(modify-phases %standard-phases + (add-before 'configure 'enter-source-directory + (lambda _ + (chdir "host"))) + (add-after 'install 'delete-static-library + (lambda _ + (delete-file (string-append #$output "/lib/libhackrf.a")))) + (add-before 'install-license-files 'leave-source-directory + (lambda _ + (chdir "..")))) + #:tests? #f)) ; no test suite (native-inputs (list pkg-config)) (inputs From d86c6cbd7b60d7e8cd0e30f8bb654d07b76e592b Mon Sep 17 00:00:00 2001 From: Guillaume Le Vaillant Date: Wed, 14 Dec 2022 17:32:42 +0100 Subject: [PATCH 191/790] gnu: soapyhackrf: Update to 0.3.4-1.6c0c33f. * gnu/packages/radio.scm (soapyhackrf): Update to 0.3.4-1.6c0c33f. --- gnu/packages/radio.scm | 47 ++++++++++++++++++++++-------------------- 1 file changed, 25 insertions(+), 22 deletions(-) diff --git a/gnu/packages/radio.scm b/gnu/packages/radio.scm index ecca65391c..51f9240a07 100644 --- a/gnu/packages/radio.scm +++ b/gnu/packages/radio.scm @@ -427,28 +427,31 @@ controls for certain tuners which may be paired with an audio device.") (license license:expat)))) (define-public soapyhackrf - (package - (name "soapyhackrf") - (version "0.3.4") - (source - (origin - (method git-fetch) - (uri (git-reference - (url "https://github.com/pothosware/SoapyHackRF") - (commit (string-append "soapy-hackrf-" version)))) - (file-name (git-file-name name version)) - (sha256 - (base32 "0wnnsm3c4ivwcbs1b68svbyds13aajws9mqk2xjc2pqgj0fdhcvz")))) - (build-system cmake-build-system) - (inputs - (list hackrf soapysdr)) - (arguments - `(#:tests? #f)) ; No test suite - (home-page "https://github.com/pothosware/SoapyHackRF/wiki") - (synopsis "SoapySDR HackRF module") - (description - "This package provides HackRF devices support to the SoapySDR library.") - (license license:expat))) + ;; Some fixes are not yet in a tagged release. + (let ((commit "6c0c33f0aa44c3080674e6bca0273184d3e9eb44") + (revision "1")) + (package + (name "soapyhackrf") + (version (git-version "0.3.4" revision commit)) + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/pothosware/SoapyHackRF") + (commit commit))) + (file-name (git-file-name name version)) + (sha256 + (base32 "1khplrp6iphdclj1wrybxs7pw42rf9112fhfhw7x2fvds8yiswm7")))) + (build-system cmake-build-system) + (inputs + (list hackrf soapysdr)) + (arguments + `(#:tests? #f)) ; No test suite + (home-page "https://github.com/pothosware/SoapyHackRF/wiki") + (synopsis "SoapySDR HackRF module") + (description + "This package provides HackRF devices support to the SoapySDR library.") + (license license:expat)))) (define-public soapyrtlsdr (package From 3a5940b82c8fbc5c69209d1ca76fe1f96cde296e Mon Sep 17 00:00:00 2001 From: Guillaume Le Vaillant Date: Wed, 14 Dec 2022 17:45:07 +0100 Subject: [PATCH 192/790] gnu: soapyrtlsdr: Update to 0.3.3. * gnu/packages/radio.scm (soapyrtlsdr): Update to 0.3.3. --- gnu/packages/radio.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/radio.scm b/gnu/packages/radio.scm index 51f9240a07..5b12cbfdfa 100644 --- a/gnu/packages/radio.scm +++ b/gnu/packages/radio.scm @@ -456,7 +456,7 @@ controls for certain tuners which may be paired with an audio device.") (define-public soapyrtlsdr (package (name "soapyrtlsdr") - (version "0.3.2") + (version "0.3.3") (source (origin (method git-fetch) @@ -465,7 +465,7 @@ controls for certain tuners which may be paired with an audio device.") (commit (string-append "soapy-rtl-sdr-" version)))) (file-name (git-file-name name version)) (sha256 - (base32 "1dlnryj6k20pk7w7v4v13y099r7ikhvlzbgzgphmi5cxkdv0shrd")))) + (base32 "0g1d69lpqw9c8hkir0h61nh40rgyz9p9x04xcfdih7iw26n5vai1")))) (build-system cmake-build-system) (inputs (list rtl-sdr soapysdr)) From 9764b1bb72ba4575bc9695da75686951a9c746ed Mon Sep 17 00:00:00 2001 From: Guillaume Le Vaillant Date: Wed, 14 Dec 2022 17:45:23 +0100 Subject: [PATCH 193/790] gnu: gqrx: Update to 2.15.9. * gnu/packages/radio.scm (gqrx): Update to 2.15.9. --- gnu/packages/radio.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/radio.scm b/gnu/packages/radio.scm index 5b12cbfdfa..25d9962bd1 100644 --- a/gnu/packages/radio.scm +++ b/gnu/packages/radio.scm @@ -988,7 +988,7 @@ satellites.") (define-public gqrx (package (name "gqrx") - (version "2.15.8") + (version "2.15.9") (source (origin (method git-fetch) @@ -997,7 +997,7 @@ satellites.") (commit (string-append "v" version)))) (file-name (git-file-name name version)) (sha256 - (base32 "1ph7fnjxfv7rfdlh17c8j4djvkfqjnalmcvnafhnq7agjy428727")))) + (base32 "1a70lmcidp5ccmpvlvpfk1g7pshyp8xq2k0kgxrplf8za5hns019")))) (build-system qt-build-system) (native-inputs (list pkg-config)) From 3796e8b4220f220e1e9b44407965306a3632cda0 Mon Sep 17 00:00:00 2001 From: Guillaume Le Vaillant Date: Wed, 14 Dec 2022 17:50:40 +0100 Subject: [PATCH 194/790] gnu: xnec2c: Update to 4.4.12. * gnu/packages/radio.scm (xnec2c): Update to 4.4.12. --- gnu/packages/radio.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/radio.scm b/gnu/packages/radio.scm index 25d9962bd1..fc46c32518 100644 --- a/gnu/packages/radio.scm +++ b/gnu/packages/radio.scm @@ -1515,14 +1515,14 @@ operators.") (define-public xnec2c (package (name "xnec2c") - (version "4.4.11") + (version "4.4.12") (source (origin (method url-fetch) (uri (string-append "https://www.xnec2c.org/releases/xnec2c-v" version ".tar.gz")) (sha256 - (base32 "13ybnb1v1y9wjmj49s8ir2rpfsz7h8r9jwv0qd4if9wsn44jg29k")))) + (base32 "1ibj2bjzn4dp988w0yayjsiccv44icsm02gr0g6gk389p7lg32p9")))) (build-system gnu-build-system) (native-inputs (list autoconf From c01b546d82266a585adb0dcf0ada2708573d50d4 Mon Sep 17 00:00:00 2001 From: Guillaume Le Vaillant Date: Wed, 14 Dec 2022 17:54:07 +0100 Subject: [PATCH 195/790] gnu: dump1090: Update to 8.2. * gnu/packages/radio.scm (dump1090): Update to 8.2. --- gnu/packages/radio.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/radio.scm b/gnu/packages/radio.scm index fc46c32518..f1533221f9 100644 --- a/gnu/packages/radio.scm +++ b/gnu/packages/radio.scm @@ -1561,7 +1561,7 @@ gain and standing wave ratio.") (define-public dump1090 (package (name "dump1090") - (version "7.1") + (version "8.2") (source (origin (method git-fetch) @@ -1570,7 +1570,7 @@ gain and standing wave ratio.") (commit (string-append "v" version)))) (file-name (git-file-name name version)) (sha256 - (base32 "1702qv5g27sgpqf98sj2qbg36sqzc7r3kssslzzgljqkr5jgrw6m")))) + (base32 "16ylywy2fdwf5kqr8kgl9lbzy1zwx4ckj9y122k3h86pfkswljs9")))) (build-system gnu-build-system) (native-inputs (list pkg-config)) From 181444e01cff184b34d10a82d3f5e1b6734ba52a Mon Sep 17 00:00:00 2001 From: Guillaume Le Vaillant Date: Wed, 14 Dec 2022 17:56:15 +0100 Subject: [PATCH 196/790] gnu: dump1090 : Improve style. * gnu/packages/radio.scm (dump1090)[arguments]: Use gexps. --- gnu/packages/radio.scm | 25 +++++++++++++------------ 1 file changed, 13 insertions(+), 12 deletions(-) diff --git a/gnu/packages/radio.scm b/gnu/packages/radio.scm index f1533221f9..9d651c0a1a 100644 --- a/gnu/packages/radio.scm +++ b/gnu/packages/radio.scm @@ -1577,18 +1577,19 @@ gain and standing wave ratio.") (inputs (list hackrf libusb ncurses rtl-sdr)) (arguments - `(#:test-target "test" - #:make-flags - (list (string-append "CC=" ,(cc-for-target)) - "BLADERF=no") - #:phases - (modify-phases %standard-phases - (delete 'configure) - (replace 'install - (lambda* (#:key outputs #:allow-other-keys) - (let ((bin (string-append (assoc-ref outputs "out") "/bin/"))) - (install-file "dump1090" bin) - (install-file "view1090" bin))))))) + (list + #:test-target "test" + #:make-flags + #~(list (string-append "CC=" #$(cc-for-target)) + "BLADERF=no") + #:phases + #~(modify-phases %standard-phases + (delete 'configure) + (replace 'install + (lambda _ + (let ((bin (string-append #$output "/bin/"))) + (install-file "dump1090" bin) + (install-file "view1090" bin))))))) (synopsis "Mode S decoder for rtl-sdr devices") (description "Dump1090 is a Mode S decoder specifically designed for rtl-sdr devices. From e2562d0408f5833664263afcea0d9c7ac2f4f605 Mon Sep 17 00:00:00 2001 From: Guillaume Le Vaillant Date: Wed, 14 Dec 2022 17:58:56 +0100 Subject: [PATCH 197/790] gnu: rtl-433: Update to 22.11. * gnu/packages/radio.scm (rtl-433): Update to 22.11. --- gnu/packages/radio.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/radio.scm b/gnu/packages/radio.scm index 9d651c0a1a..70147cc09f 100644 --- a/gnu/packages/radio.scm +++ b/gnu/packages/radio.scm @@ -1601,7 +1601,7 @@ their position, altitude, speed, etc.") (define-public rtl-433 (package (name "rtl-433") - (version "21.12") + (version "22.11") (source (origin (method git-fetch) @@ -1610,7 +1610,7 @@ their position, altitude, speed, etc.") (commit version))) (file-name (git-file-name name version)) (sha256 - (base32 "0ygxs35zvgnamhqdwk1akcwagcirzpi4wndzgf9d23faiv4cm01a")))) + (base32 "0qx89qmf0zn0qa05vraipny4ihx6lm72s830mbfyzw2znyk3wdm8")))) (build-system cmake-build-system) (native-inputs (list pkg-config)) From c96e41bd819c47e7622e74605658eb01917f8e04 Mon Sep 17 00:00:00 2001 From: Guillaume Le Vaillant Date: Wed, 14 Dec 2022 18:00:52 +0100 Subject: [PATCH 198/790] gnu: multimon-ng: Update to 1.2.0. * gnu/packages/radio.scm (multimon-ng): Update to 1.2.0. --- gnu/packages/radio.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/radio.scm b/gnu/packages/radio.scm index 70147cc09f..d323e18527 100644 --- a/gnu/packages/radio.scm +++ b/gnu/packages/radio.scm @@ -1626,7 +1626,7 @@ from devices on the 433 MHz, 868 MHz, 315 MHz, 345 MHz and 915 MHz ISM bands.") (define-public multimon-ng (package (name "multimon-ng") - (version "1.1.9") + (version "1.2.0") (source (origin (method git-fetch) @@ -1635,7 +1635,7 @@ from devices on the 433 MHz, 868 MHz, 315 MHz, 345 MHz and 915 MHz ISM bands.") (commit version))) (file-name (git-file-name name version)) (sha256 - (base32 "01716cfhxfzsab9zjply9giaa4nn4b7rm3p3vizrwi7n253yiwm2")))) + (base32 "0hm7391z1iz2sk4xkwfphqz8qvihqjzsh45csz14gb4jfs1p6ks2")))) (build-system cmake-build-system) (inputs (list libx11 pulseaudio)) From d06afc330ba92f8842c5ed516ca0323976fe4c27 Mon Sep 17 00:00:00 2001 From: Guillaume Le Vaillant Date: Wed, 14 Dec 2022 18:15:13 +0100 Subject: [PATCH 199/790] gnu: wfview: Update to 1.50. * gnu/packages/radio.scm (wfview): Update to 1.50. [inputs]: Add eigen, portaudio, pulseaudio and rtaudio. --- gnu/packages/radio.scm | 16 ++++++++++++---- 1 file changed, 12 insertions(+), 4 deletions(-) diff --git a/gnu/packages/radio.scm b/gnu/packages/radio.scm index d323e18527..11878c2983 100644 --- a/gnu/packages/radio.scm +++ b/gnu/packages/radio.scm @@ -2413,19 +2413,27 @@ software-defined radio receivers.") (define-public wfview (package (name "wfview") - (version "1.2d") + (version "1.50") (source (origin (method git-fetch) (uri (git-reference (url "https://gitlab.com/eliggett/wfview") - (commit version))) + (commit (string-append "v" version)))) (file-name (git-file-name name version)) (sha256 - (base32 "1kpkwxhcacgmprbr8xz840rj9a22513vxrh2q7d3js5i1dva8j2z")))) + (base32 "1djgn1z4hibzci53mrvskz47jfq6hk8lhhqckpa93pvsi9kadl4k")))) (build-system qt-build-system) (inputs - (list opus qcustomplot qtbase-5 qtmultimedia-5 qtserialport)) + (list eigen + opus + portaudio + pulseaudio + qcustomplot + qtbase-5 + qtmultimedia-5 + qtserialport + rtaudio)) (arguments `(#:tests? #f ; No test suite. #:phases From c50e3407070bc3f05401b9aaf43b1eea391171c9 Mon Sep 17 00:00:00 2001 From: Guillaume Le Vaillant Date: Wed, 14 Dec 2022 18:19:32 +0100 Subject: [PATCH 200/790] gnu: rfcat: Update to 1.9.6. * gnu/packages/radio.scm (rfcat): Update to 1.9.6. --- gnu/packages/radio.scm | 80 ++++++++++++++++++++---------------------- 1 file changed, 38 insertions(+), 42 deletions(-) diff --git a/gnu/packages/radio.scm b/gnu/packages/radio.scm index 11878c2983..1eb98fd1f8 100644 --- a/gnu/packages/radio.scm +++ b/gnu/packages/radio.scm @@ -2497,46 +2497,42 @@ Caller-ID.") (license license:gpl3+))) (define-public rfcat - ;; Use a commit for now because some fixes to make rfcat work with - ;; Python 3 instead of Python 2 are not in a release yet. - (let ((commit "725bf79af27d47cdec64107317c1c8fe3f7ad7b8") - (revision "1")) - (package - (name "rfcat") - (version (git-version "1.9.5" revision commit)) - (source - (origin - (method git-fetch) - (uri (git-reference - (url "https://github.com/atlas0fd00m/rfcat") - (commit commit))) - (file-name (git-file-name name version)) - (sha256 - (base32 "0dbc6n4pxsa73wzxny773khc73r1dn3ma5hi7xv76vcykjvzkdi3")))) - (build-system python-build-system) - (inputs - (list python-future - python-ipython - python-numpy - python-pyserial - python-pyside-2 - python-pyusb)) - (arguments - `(#:tests? #f ; Tests want to use a serial port - #:phases - (modify-phases %standard-phases - (add-after 'unpack 'fix-permissions - (lambda _ - (make-file-writable "rflib/rflib_version.py"))) - (add-after 'install 'install-udev-rules - (lambda* (#:key outputs #:allow-other-keys) - (install-file "etc/udev/rules.d/20-rfcat.rules" - (string-append (assoc-ref outputs "out") - "/lib/udev/rules.d"))))))) - (home-page "https://github.com/atlas0fd00m/rfcat") - (synopsis "Program to control some radio dongles") - (description - "@code{rfcat} is a program to control some radio dongles operating in + (package + (name "rfcat") + (version "1.9.6") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/atlas0fd00m/rfcat") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 "0zmgbgf1025ln2v6lc27dmkmwv8pxjgrmhmpk34rkkixhvnk69pf")))) + (build-system python-build-system) + (inputs + (list python-future + python-ipython + python-numpy + python-pyserial + python-pyside-2 + python-pyusb)) + (arguments + `(#:tests? #f ; Tests want to use a serial port + #:phases + (modify-phases %standard-phases + (add-after 'unpack 'fix-permissions + (lambda _ + (make-file-writable "rflib/rflib_version.py"))) + (add-after 'install 'install-udev-rules + (lambda* (#:key outputs #:allow-other-keys) + (install-file "etc/udev/rules.d/20-rfcat.rules" + (string-append (assoc-ref outputs "out") + "/lib/udev/rules.d"))))))) + (home-page "https://github.com/atlas0fd00m/rfcat") + (synopsis "Program to control some radio dongles") + (description + "@code{rfcat} is a program to control some radio dongles operating in ISM bands. Supported dongles: @@ -2549,8 +2545,8 @@ Supported dongles: To install the rfcat udev rules, you must extend @code{udev-service-type} with this package. E.g.: @code{(udev-rules-service 'rfcat rfcat)}") - (license (list license:bsd-3 - license:gpl2))))) + (license (list license:bsd-3 + license:gpl2)))) (define-public rx-tools ;; No tagged release since 2016, use commit instead. From e7b2433484d834dda5cd1ca857b9a445c40a337e Mon Sep 17 00:00:00 2001 From: Guillaume Le Vaillant Date: Wed, 14 Dec 2022 18:21:22 +0100 Subject: [PATCH 201/790] gnu: rfcat: Improve style. * gnu/packages/radio.scm (rfcat)[arguments]: Use gexp. --- gnu/packages/radio.scm | 22 +++++++++++----------- 1 file changed, 11 insertions(+), 11 deletions(-) diff --git a/gnu/packages/radio.scm b/gnu/packages/radio.scm index 1eb98fd1f8..9642f0e068 100644 --- a/gnu/packages/radio.scm +++ b/gnu/packages/radio.scm @@ -2518,17 +2518,17 @@ Caller-ID.") python-pyside-2 python-pyusb)) (arguments - `(#:tests? #f ; Tests want to use a serial port - #:phases - (modify-phases %standard-phases - (add-after 'unpack 'fix-permissions - (lambda _ - (make-file-writable "rflib/rflib_version.py"))) - (add-after 'install 'install-udev-rules - (lambda* (#:key outputs #:allow-other-keys) - (install-file "etc/udev/rules.d/20-rfcat.rules" - (string-append (assoc-ref outputs "out") - "/lib/udev/rules.d"))))))) + (list + #:tests? #f ; Tests want to use a serial port + #:phases + #~(modify-phases %standard-phases + (add-after 'unpack 'fix-permissions + (lambda _ + (make-file-writable "rflib/rflib_version.py"))) + (add-after 'install 'install-udev-rules + (lambda* _ + (install-file "etc/udev/rules.d/20-rfcat.rules" + (string-append #$output "/lib/udev/rules.d"))))))) (home-page "https://github.com/atlas0fd00m/rfcat") (synopsis "Program to control some radio dongles") (description From c6f81ff7a6a527b5a14189a2c359b981ddba43bc Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 14 Dec 2022 20:48:11 +0100 Subject: [PATCH 202/790] gnu: Add directory-server-service-type. * gnu/services/ldap.scm: New file. * gnu/local.mk (GNU_SYSTEM_MODULES): Add it. * doc/guix.texi (LDAP Services): Document it. --- doc/guix.texi | 185 ++++++++++++++++++++++++ gnu/local.mk | 1 + gnu/services/ldap.scm | 317 ++++++++++++++++++++++++++++++++++++++++++ 3 files changed, 503 insertions(+) create mode 100644 gnu/services/ldap.scm diff --git a/doc/guix.texi b/doc/guix.texi index 30674dab1e..f376fd2c9b 100644 --- a/doc/guix.texi +++ b/doc/guix.texi @@ -28452,6 +28452,8 @@ Local accounts with lower values will silently fail to authenticate. @node LDAP Services @subsection LDAP Services @cindex LDAP + +@subsubheading Authentication against LDAP with nslcd @cindex nslcd, LDAP service The @code{(gnu services authentication)} module provides the @@ -28928,6 +28930,189 @@ Defaults to @samp{()}. @c %end of generated documentation for nslcd-configuration +@subsubheading LDAP Directory Server +@cindex LDAP, server + +The @code{(gnu services ldap)} module provides the +@code{directory-server-service-type}, which can be used to create and +launch an LDAP server instance. + +Here is an example configuration of the +@code{directory-server-service-type}: + +@lisp +(use-service-modules ldap) + +... +(operating-system + ... + (services + (cons + (service directory-server-service-type + (directory-server-instance-configuration + (slapd + (slapd-configuration + (root-password "@{PBKDF2_SHA256@}AAAgAG@dots{}ABSOLUTELYSECRET"))))) + %base-services))) +@end lisp + +The root password should be generated with the @command{pwdhash} utility +that is provided by the @code{389-ds-base} package. + +Note that changes to the directory server configuration will not be +applied to existing instances. You will need to back up and restore +server data manually. Only new directory server instances will be +created upon system reconfiguration. + +@c %start of generated documentation for directory-server-instance-configuration +@deftp {Data Type} directory-server-instance-configuration +Available @code{directory-server-instance-configuration} fields are: + +@table @asis +@item @code{package} (default: @code{389-ds-base}) (type: file-like) +The @code{389-ds-base} package. + +@item @code{config-version} (default: @code{2}) (type: number) +Sets the format version of the configuration file. To use the INF file +with @command{dscreate}, this parameter must be 2. + +@item @code{full-machine-name} (default: @code{"localhost"}) (type: string) +Sets the fully qualified hostname (FQDN) of this system. + +@item @code{selinux} (default: @code{#false}) (type: boolean) +Enables SELinux detection and integration during the installation of +this instance. If set to @code{#true}, @command{dscreate} auto-detects +whether SELinux is enabled. + +@item @code{strict-host-checking} (default: @code{#true}) (type: boolean) +Sets whether the server verifies the forward and reverse record set in +the @code{full-machine-name} parameter. When installing this instance with +GSSAPI authentication behind a load balancer, set this parameter to +@code{#false}. + +@item @code{systemd} (default: @code{#false}) (type: boolean) +Enables systemd platform features. If set to @code{#true}, +@command{dscreate} auto-detects whether systemd is installed. + +@item @code{slapd} (type: slapd-configuration) +Configuration of slapd. + +@deftp {Data Type} slapd-configuration +Available @code{slapd-configuration} fields are: + +@table @asis +@item @code{instance-name} (default: @code{"localhost"}) (type: string) +Sets the name of the instance. You can refer to this value in other +parameters of this INF file using the @code{@{instance_name@}} variable. +Note that this name cannot be changed after the installation! + +@item @code{user} (default: @code{"dirsrv"}) (type: string) +Sets the user name the ns-slapd process will use after the service +started. + +@item @code{group} (default: @code{"dirsrv"}) (type: string) +Sets the group name the ns-slapd process will use after the service +started. + +@item @code{port} (default: @code{389}) (type: number) +Sets the TCP port the instance uses for LDAP connections. + +@item @code{secure-port} (default: @code{636}) (type: number) +Sets the TCP port the instance uses for TLS-secured LDAP connections +(LDAPS). + +@item @code{root-dn} (default: @code{"cn=Directory Manager"}) (type: string) +Sets the @dfn{Distinquished Name} (DN) of the administrator account for this +instance. + +@item @code{root-password} (default: @code{"@{invalid@}YOU-SHOULD-CHANGE-THIS"}) (type: string) +Sets the password of the account specified in the @code{root-dn} +parameter. You can either set this parameter to a plain text password +@command{dscreate} hashes during the installation or to a +"@{algorithm@}hash" string generated by the @command{pwdhash} utility. +Note that setting a plain text password can be a security risk if +unprivileged users can read this INF file! + +@item @code{self-sign-cert} (default: @code{#true}) (type: boolean) +Sets whether the setup creates a self-signed certificate and enables TLS +encryption during the installation. This is not suitable for +production, but it enables administrators to use TLS right after the +installation. You can replace the self-signed certificate with a +certificate issued by a certificate authority. + +@item @code{self-sign-cert-valid-months} (default: @code{24}) (type: number) +Set the number of months the issued self-signed certificate will be +valid. + +@item @code{backup-dir} (default: @code{"/var/lib/dirsrv/slapd-@{instance_name@}/bak"}) (type: string) +Set the backup directory of the instance. + +@item @code{cert-dir} (default: @code{"/etc/dirsrv/slapd-@{instance_name@}"}) (type: string) +Sets the directory of the instance's Network Security Services (NSS) +database. + +@item @code{config-dir} (default: @code{"/etc/dirsrv/slapd-@{instance_name@}"}) (type: string) +Sets the configuration directory of the instance. + +@item @code{db-dir} (default: @code{"/var/lib/dirsrv/slapd-@{instance_name@}/db"}) (type: string) +Sets the database directory of the instance. + +@item @code{initconfig-dir} (default: @code{"/etc/dirsrv/registry"}) (type: string) +Sets the directory of the operating system's rc configuration directory. + +@item @code{ldif-dir} (default: @code{"/var/lib/dirsrv/slapd-@{instance_name@}/ldif"}) (type: string) +Sets the LDIF export and import directory of the instance. + +@item @code{lock-dir} (default: @code{"/var/lock/dirsrv/slapd-@{instance_name@}"}) (type: string) +Sets the lock directory of the instance. + +@item @code{log-dir} (default: @code{"/var/log/dirsrv/slapd-@{instance_name@}"}) (type: string) +Sets the log directory of the instance. + +@item @code{run-dir} (default: @code{"/var/run/dirsrv"}) (type: string) +Sets PID directory of the instance. + +@item @code{schema-dir} (default: @code{"/etc/dirsrv/slapd-@{instance_name@}/schema"}) (type: string) +Sets schema directory of the instance. + +@item @code{tmp-dir} (default: @code{"/tmp"}) (type: string) +Sets the temporary directory of the instance. +@end table +@end deftp + +@item @code{backend-userroot} (type: backend-userroot-configuration) +Configuration of the userroot backend. + +@deftp {Data Type} backend-userroot-configuration +Available @code{backend-userroot-configuration} fields are: + +@table @asis +@item @code{create-suffix-entry?} (default: @code{#false}) (type: boolean) +Set this parameter to @code{#true} to create a generic root node entry +for the suffix in the database. + +@item @code{require-index?} (default: @code{#false}) (type: boolean) +Set this parameter to @code{#true} to refuse unindexed searches in this +database. + +@item @code{sample-entries} (default: @code{"no"}) (type: string) +Set this parameter to @code{"yes"} to add latest version of sample +entries to this database. Or, use @code{"001003006"} to use the 1.3.6 +version sample entries. Use this option, for example, to create a +database for testing purposes. + +@item @code{suffix} (type: maybe-string) +Sets the root suffix stored in this database. If you do not set the +suffix attribute the install process will not create the backend/suffix. +You can also create multiple backends/suffixes by duplicating this +section. + +@end table +@end deftp +@end table +@end deftp +@c end of generated documentation for directory-server + @node Web Services @subsection Web Services diff --git a/gnu/local.mk b/gnu/local.mk index 60a422fd7e..aae6e23e12 100644 --- a/gnu/local.mk +++ b/gnu/local.mk @@ -671,6 +671,7 @@ GNU_SYSTEM_MODULES = \ %D%/services/guix.scm \ %D%/services/hurd.scm \ %D%/services/kerberos.scm \ + %D%/services/ldap.scm \ %D%/services/lightdm.scm \ %D%/services/linux.scm \ %D%/services/lirc.scm \ diff --git a/gnu/services/ldap.scm b/gnu/services/ldap.scm new file mode 100644 index 0000000000..35f2735d40 --- /dev/null +++ b/gnu/services/ldap.scm @@ -0,0 +1,317 @@ +;;; GNU Guix --- Functional package management for GNU +;;; Copyright © 2018, 2019, 2022 Ricardo Wurmus +;;; +;;; This file is part of GNU Guix. +;;; +;;; GNU Guix is free software; you can redistribute it and/or modify it +;;; under the terms of the GNU General Public License as published by +;;; the Free Software Foundation; either version 3 of the License, or (at +;;; your option) any later version. +;;; +;;; GNU Guix is distributed in the hope that it will be useful, but +;;; WITHOUT ANY WARRANTY; without even the implied warranty of +;;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +;;; GNU General Public License for more details. +;;; +;;; You should have received a copy of thye GNU General Public License +;;; along with GNU Guix. If not, see . + +(define-module (gnu services ldap) + #:use-module (gnu packages admin) + #:use-module (gnu packages openldap) + #:use-module (gnu services) + #:use-module (gnu services configuration) + #:use-module (gnu services shepherd) + #:use-module (gnu system shadow) + #:use-module (guix gexp) + #:use-module (srfi srfi-1) + #:use-module (ice-9 match) + #:use-module (ice-9 string-fun) + #:export (directory-server-service-type + directory-server-shepherd-service + + directory-server-instance-configuration + slapd-configuration + backend-configuration)) + +(define (uglify-field-name name) + (let ((str (string-map (match-lambda + (#\- #\_) + (chr chr)) + (symbol->string name)))) + (if (string-suffix? "?" str) + (substring str 0 (1- (string-length str))) + str))) +(define (serialize-field field-name val) + (format #t "~a = ~a\n" (uglify-field-name field-name) val)) +(define serialize-string serialize-field) +(define-maybe string) +(define (serialize-boolean field-name val) + (serialize-field field-name (if val "True" "False"))) +(define (serialize-number field-name val) + (serialize-field field-name (number->string val))) + + +(define-configuration slapd-configuration + (instance-name + (string "localhost") + "Sets the name of the instance. You can refer to this value in other +parameters of this INF file using the \"{instance_name}\" variable. Note that +this name cannot be changed after the installation!") + (user + (string "dirsrv") + "Sets the user name the ns-slapd process will use after the service +started.") + (group + (string "dirsrv") + "Sets the group name the ns-slapd process will use after the service +started.") + (port + (number 389) + "Sets the TCP port the instance uses for LDAP connections.") + (secure-port + (number 636) + "Sets the TCP port the instance uses for TLS-secured LDAP +connections (LDAPS).") + (root-dn + (string "cn=Directory Manager") + "Sets the Distinquished Name (DN) of the administrator account for this +instance.") + (root-password + (string "{invalid}YOU-SHOULD-CHANGE-THIS") + "Sets the password of the account specified in the \"root-dn\" parameter. +You can either set this parameter to a plain text password dscreate hashes +during the installation or to a \"{algorithm}hash\" string generated by the +pwdhash utility. Note that setting a plain text password can be a security +risk if unprivileged users can read this INF file!") + (self-sign-cert + (boolean #t) + "Sets whether the setup creates a self-signed certificate and enables TLS +encryption during the installation. This is not suitable for production, but +it enables administrators to use TLS right after the installation. You can +replace the self-signed certificate with a certificate issued by a certificate +authority.") + (self-sign-cert-valid-months + (number 24) + "Set the number of months the issued self-signed certificate will be valid.") + (backup-dir + (string "/var/lib/dirsrv/slapd-{instance_name}/bak") + "Set the backup directory of the instance.") + (cert-dir + (string "/etc/dirsrv/slapd-{instance_name}") + "Sets the directory of the instance's Network Security Services (NSS) +database.") + (config-dir + (string "/etc/dirsrv/slapd-{instance_name}") + "Sets the configuration directory of the instance.") + (db-dir + (string "/var/lib/dirsrv/slapd-{instance_name}/db") + "Sets the database directory of the instance.") + (initconfig-dir + (string "/etc/dirsrv/registry") + "Sets the directory of the operating system's rc configuration directory.") + (ldif-dir + (string "/var/lib/dirsrv/slapd-{instance_name}/ldif") + "Sets the LDIF export and import directory of the instance.") + (lock-dir + (string "/var/lock/dirsrv/slapd-{instance_name}") + "Sets the lock directory of the instance.") + (log-dir + (string "/var/log/dirsrv/slapd-{instance_name}") + "Sets the log directory of the instance.") + (run-dir + (string "/var/run/dirsrv") + "Sets PID directory of the instance.") + (schema-dir + (string "/etc/dirsrv/slapd-{instance_name}/schema") + "Sets schema directory of the instance.") + (tmp-dir + (string "/tmp") + "Sets the temporary directory of the instance.")) + +(define (serialize-slapd-configuration field-name val) + #t) + + +(define-configuration backend-userroot-configuration + (create-suffix-entry? + (boolean #false) + "Set this parameter to #true to create a generic root node entry for the +suffix in the database.") + (require-index? + (boolean #false) + "Set this parameter to #true to refuse unindexed searches in this +database.") + (sample-entries + (string "no") + "Set this parameter to \"yes\" to add latest version of sample entries to +this database. Or, use \"001003006\" to use the 1.3.6 version sample entries. +Use this option, for example, to create a database for testing purposes.") + (suffix + maybe-string + "Sets the root suffix stored in this database. If you do not set the +suffix attribute the install process will not create the backend/suffix. You +can also create multiple backends/suffixes by duplicating this section.")) + +(define (serialize-backend-userroot-configuration field-name val) + #t) + + +(define-configuration directory-server-instance-configuration + (package + (file-like 389-ds-base) + "The 389-ds-base package.") + ;; General settings + (config-version + (number 2) + "Sets the format version of the configuration file. To use the INF file +with dscreate, this parameter must be 2.") + (full-machine-name + (string "localhost") + "Sets the fully qualified hostname (FQDN) of this system.") + (selinux + (boolean #false) + "Enables SELinux detection and integration during the installation of this +instance. If set to #T, dscreate auto-detects whether SELinux is enabled.") + (strict-host-checking + (boolean #t) + "Sets whether the server verifies the forward and reverse record set in the +\"full-machine-name\" parameter. When installing this instance with GSSAPI +authentication behind a load balancer, set this parameter to #F.") + (systemd + (boolean #false) + "Enables systemd platform features. If set to #T, dscreate auto-detects +whether systemd is installed.") + (slapd + (slapd-configuration (slapd-configuration)) + "Configuration of slapd.") + (backend-userroot + (backend-userroot-configuration (backend-userroot-configuration)) + "Configuration of the userroot backend.")) + +(define (serialize-directory-server-instance-configuration x) + (format #t "[general]\n") + (serialize-configuration + x + (filter (lambda (field) + (not (member (configuration-field-name field) + '(package slapd backend-userroot)))) + directory-server-instance-configuration-fields)) + ;; Do not start instance while running dscreate. Do this later with + ;; shepherd. + (format #t "start = False\n") + (format #t "\n[slapd]\n") + (serialize-configuration + (directory-server-instance-configuration-slapd x) + slapd-configuration-fields) + (format #t "\n[backend-userroot]\n") + (serialize-configuration + (directory-server-instance-configuration-backend-userroot x) + backend-userroot-configuration-fields)) + +(define (directory-server-instance-config-file config) + "Return an LDAP directory server instance configuration file." + (let* ((slapd (directory-server-instance-configuration-slapd config)) + (instance-name (slapd-configuration-instance-name slapd))) + (plain-file + (string-append "dirsrv-" instance-name ".inf") + (with-output-to-string + (lambda () + (serialize-directory-server-instance-configuration config)))))) + +(define (directory-server-shepherd-service config) + "Return a shepherd service for an LDAP directory server with CONFIG." + (let* ((389-ds-base (directory-server-instance-configuration-package config)) + (slapd (directory-server-instance-configuration-slapd config)) + (instance-name + (slapd-configuration-instance-name slapd))) + (list (shepherd-service + (documentation "Run an 389 directory server instance.") + (provision (list (symbol-append 'directory-server- + (string->symbol instance-name)))) + (requirement '()) + (start #~(make-forkexec-constructor + (list #$(file-append 389-ds-base "/sbin/dsctl") + #$instance-name "start") + #:pid-file + (string-append + #$(slapd-configuration-run-dir slapd) + "/slapd-" #$instance-name ".pid"))) + (stop #~(make-kill-destructor)))))) + +(define (directory-server-accounts config) + (let* ((slapd (directory-server-instance-configuration-slapd config)) + (user (slapd-configuration-user slapd)) + (group (slapd-configuration-group slapd))) + (list (user-group + (name group) + (system? #true)) + (user-account + (name user) + (group group) + (system? #true) + (comment "System user for the 389 directory server") + (home-directory "/var/empty") + (shell (file-append shadow "/sbin/nologin")))))) + +(define (directory-server-activation config) + (let* ((389-ds-base (directory-server-instance-configuration-package config)) + (config-file (directory-server-instance-config-file config)) + (slapd (directory-server-instance-configuration-slapd config)) + (instance-name (slapd-configuration-instance-name slapd)) + (user (slapd-configuration-user slapd)) + (group (slapd-configuration-group slapd)) + (instantiate (lambda (proc) + (string-replace-substring + (proc slapd) "{instance_name}" instance-name))) + (config-dir (instantiate slapd-configuration-config-dir)) + (all-dirs (delete-duplicates + (map (compose dirname instantiate) + (list slapd-configuration-backup-dir + slapd-configuration-cert-dir + slapd-configuration-db-dir + slapd-configuration-ldif-dir + slapd-configuration-lock-dir + slapd-configuration-log-dir + slapd-configuration-run-dir + slapd-configuration-schema-dir))))) + ;; 389-ds-base doesn't let us update an instance configuration, so bail + ;; out when the configuration directory already exists. + #~(begin + (use-modules (ice-9 match) + (guix build utils)) + (if (file-exists? #$config-dir) + (format #t + "directory-server: Instance configuration for `~a' already exists. Skipping.\n" + #$instance-name) + (let ((owner (getpwnam #$user))) + (for-each (lambda (dir) + (mkdir-p dir) + (chown dir (passwd:uid owner) (passwd:gid owner))) + (sort '#$all-dirs string<=)) + (system* #$(file-append 389-ds-base "/sbin/dscreate") + "from-file" #$config-file)))))) + +(define directory-server-service-type + (service-type (name 'directory-server) + (extensions + (list (service-extension shepherd-root-service-type + directory-server-shepherd-service) + (service-extension activation-service-type + directory-server-activation) + (service-extension account-service-type + directory-server-accounts))) + (default-value (directory-server-instance-configuration)) + (description + "Run a directory server instance."))) + +(define (generate-directory-server-documentation) + (generate-documentation + `((directory-server-instance-configuration + ,directory-server-instance-configuration-fields + (slapd slapd-configuration) + (backend-userroot backend-userroot-configuration)) + (slapd-configuration ,slapd-configuration-fields) + (backend-userroot-configuration + ,backend-userroot-configuration-fields)) + 'directory-server-instance-configuration)) From 042f169cc3952e7d1b717d1486c0cb50cea9d16c Mon Sep 17 00:00:00 2001 From: Nicolas Goaziou Date: Wed, 14 Dec 2022 18:09:02 +0100 Subject: [PATCH 203/790] gnu: flare-engine: Update to 1.14. * gnu/packages/games.scm (flare-engine): Update to 1.14. --- gnu/packages/games.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/games.scm b/gnu/packages/games.scm index 4c5f28a55c..c80eaa0c60 100644 --- a/gnu/packages/games.scm +++ b/gnu/packages/games.scm @@ -8885,7 +8885,7 @@ fight each other on an arena-like map.") (define-public flare-engine (package (name "flare-engine") - (version "1.13.04") + (version "1.14") (source (origin (method git-fetch) (uri (git-reference @@ -8894,7 +8894,7 @@ fight each other on an arena-like map.") (file-name (git-file-name name version)) (sha256 (base32 - "042n2r9whnd3kncf3k89dcl1srn7p2jk6kdc0lb2hbwff55iylnw")))) + "1gyaxr6zykwg5kg9xc3vlb5a6fas4z3zbk53y0zlfl35n4vqlh84")))) (build-system cmake-build-system) (arguments (list From ced3be2b562866b82f97a530cd66610c84c381f7 Mon Sep 17 00:00:00 2001 From: Nicolas Goaziou Date: Wed, 14 Dec 2022 18:15:00 +0100 Subject: [PATCH 204/790] gnu: flare-game: Update to 1.14. * gnu/packages/games.scm (flare-game): Update to 1.14. --- gnu/packages/games.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/games.scm b/gnu/packages/games.scm index c80eaa0c60..6064dabbaa 100644 --- a/gnu/packages/games.scm +++ b/gnu/packages/games.scm @@ -8914,7 +8914,7 @@ action RPGs.") (define-public flare-game (package (name "flare-game") - (version "1.13.04") + (version "1.14") (source (origin (method git-fetch) (uri (git-reference @@ -8923,7 +8923,7 @@ action RPGs.") (file-name (git-file-name name version)) (sha256 (base32 - "18rdrwv7p5rvmlah5pl9vbc09xlb8id75a7c73yn2sxkm6cf5c2l")))) + "1as9dsg0ddz14jjk4y5nj0ml20cwncrcnbdk10r1jaa2vss9bbn3")))) (build-system cmake-build-system) (arguments (list From 9f93bcd1862c76d7ff30da6f712c9bd2912b8346 Mon Sep 17 00:00:00 2001 From: Nicolas Goaziou Date: Wed, 14 Dec 2022 18:19:49 +0100 Subject: [PATCH 205/790] gnu: musescore: Update to 4.0. * gnu/packages/music.scm (musescore): Update to 4.0. [snippet]: Do not remove non-existing directories. [arguments]<#:configure-flags>: Do not mention non-existing flags. [native-inputs]: Add GIT-MINIMAL. [inputs]: Add PYTHON, QTNETWORKAUTH-5, QTX11EXTRAS. [license]: Switch to GPL3. --- gnu/packages/music.scm | 22 ++++++++++------------ 1 file changed, 10 insertions(+), 12 deletions(-) diff --git a/gnu/packages/music.scm b/gnu/packages/music.scm index e3cb67b413..0a472a6880 100644 --- a/gnu/packages/music.scm +++ b/gnu/packages/music.scm @@ -4775,7 +4775,7 @@ includes LV2 plugins and a JACK standalone client.") (define-public musescore (package (name "musescore") - (version "3.6.2") + (version "4.0") (source (origin (method git-fetch) @@ -4784,22 +4784,17 @@ includes LV2 plugins and a JACK standalone client.") (commit (string-append "v" version)))) (file-name (git-file-name name version)) (sha256 - (base32 "0szvb6mlzy9df9lrq546rrpixa480knzij1wgh6ilflxz87q048q")) + (base32 "16rcwr6fzghv8100syzicabqg8jqvng3zzsi6h3ja4zkp9hcbkcr")) (modules '((guix build utils))) (snippet ;; Remove unused libraries. '(begin (for-each delete-file-recursively - '("thirdparty/freetype" - "thirdparty/openssl" - "thirdparty/portmidi" - "thirdparty/qt-google-analytics")))))) + '("thirdparty/freetype")))))) (build-system qt-build-system) (arguments `(#:configure-flags - `("-DBUILD_TELEMETRY_MODULE=OFF" ;don't phone home - "-DBUILD_WEBENGINE=OFF" - "-DDOWNLOAD_SOUNDFONT=OFF" + `("-DDOWNLOAD_SOUNDFONT=OFF" "-DMUSESCORE_BUILD_CONFIG=release" "-DUSE_SYSTEM_FREETYPE=ON") ;; There are tests, but no simple target to run. The command used to @@ -4811,6 +4806,8 @@ includes LV2 plugins and a JACK standalone client.") ;; Basically, it requires to start a whole new build process. ;; So we simply skip them. #:tests? #f)) + (native-inputs + (list git-minimal pkg-config qttools-5)) (inputs (list alsa-lib freetype @@ -4823,15 +4820,16 @@ includes LV2 plugins and a JACK standalone client.") portaudio portmidi pulseaudio + python qtbase-5 qtdeclarative-5 qtgraphicaleffects + qtnetworkauth-5 qtquickcontrols2-5 qtscript qtsvg-5 + qtx11extras qtxmlpatterns)) - (native-inputs - (list pkg-config qttools-5)) (synopsis "Music composition and notation software") (description "MuseScore is a music score typesetter. Its main purpose is the creation @@ -4846,7 +4844,7 @@ appearance and layout are provided. MuseScore can also play back scores through the built-in sequencer and SoundFont sample library.") (home-page "https://musescore.org") - (license license:gpl2))) + (license license:gpl3))) (define-public muse-sequencer (package From b36375630602f8bf972e4576b2b5d4f93949f0f1 Mon Sep 17 00:00:00 2001 From: Nicolas Goaziou Date: Wed, 14 Dec 2022 18:41:27 +0100 Subject: [PATCH 206/790] gnu: rosegarden: Update to 22.12. * gnu/packages/music.scm (rosegarden): Update to 22.12. [inputs]: Add SHARED-MIME-INFO. --- gnu/packages/music.scm | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/gnu/packages/music.scm b/gnu/packages/music.scm index 0a472a6880..bf502e0e80 100644 --- a/gnu/packages/music.scm +++ b/gnu/packages/music.scm @@ -5008,7 +5008,7 @@ specification and header.") (define-public rosegarden (package (name "rosegarden") - (version "22.06") + (version "22.12") (source (origin (method url-fetch) @@ -5016,7 +5016,7 @@ specification and header.") (version-major+minor version) "/" "rosegarden-" version ".tar.bz2")) (sha256 - (base32 "1nzs6g8g36g37zi8dl7gznc77596418g6rzm9a5vxcgbam8q494h")))) + (base32 "061xy3flmj7bllibkp5wzdycvghfxvyzdr9g9yrr5q3m70a7wznz")))) (build-system cmake-build-system) (arguments `(#:configure-flags '("-DCMAKE_BUILD_TYPE=Release") @@ -5081,6 +5081,7 @@ specification and header.") lilypond lrdf qtbase-5 + shared-mime-info tar lirc wavpack From ef7ad7d451433d4f1505d265b623a1903525f03c Mon Sep 17 00:00:00 2001 From: Nicolas Goaziou Date: Wed, 14 Dec 2022 18:44:04 +0100 Subject: [PATCH 207/790] gnu: rosegarden: Improve package style. * gnu/packages/music.scm (rosegarden)[arguments]: Use G-expressions and SEARCH-INPUT-FILE. [inputs]: Use BASH-MINIMAL instead of BASH. --- gnu/packages/music.scm | 103 +++++++++++++++++++++-------------------- 1 file changed, 52 insertions(+), 51 deletions(-) diff --git a/gnu/packages/music.scm b/gnu/packages/music.scm index bf502e0e80..614eb57791 100644 --- a/gnu/packages/music.scm +++ b/gnu/packages/music.scm @@ -5019,58 +5019,59 @@ specification and header.") (base32 "061xy3flmj7bllibkp5wzdycvghfxvyzdr9g9yrr5q3m70a7wznz")))) (build-system cmake-build-system) (arguments - `(#:configure-flags '("-DCMAKE_BUILD_TYPE=Release") - #:phases - (modify-phases %standard-phases - (add-after 'unpack 'patch-tests - (lambda _ - (substitute* "CMakeLists.txt" - (("BUILD_TESTING OFF") "BUILD_TESTING ON") - ;; Make tests work. - ((" -fvisibility=hidden") "")))) - (add-after 'unpack 'fix-references - (lambda* (#:key inputs #:allow-other-keys) - (substitute* "src/gui/general/ProjectPackager.cpp" - (("\"flac\\>") - (string-append "\"" (assoc-ref inputs "flac") "/bin/flac")) - (("\"wavpack\\>") - (string-append "\"" (assoc-ref inputs "wavpack") "/bin/wavpack")) - (("\"wvunpack\\>") - (string-append "\"" (assoc-ref inputs "wavpack") "/bin/wvunpack")) - (("\"bash\\>") - (string-append "\"" (assoc-ref inputs "bash") "/bin/bash")) - (("\"tar\\>") - (string-append "\"" (assoc-ref inputs "tar") "/bin/tar"))) - (substitute* "src/gui/general/LilyPondProcessor.cpp" - (("\"convert-ly\\>") - (string-append "\"" (assoc-ref inputs "lilypond") "/bin/convert-ly")) - (("\"lilypond\\>") - (string-append "\"" (assoc-ref inputs "lilypond") "/bin/lilypond"))))) - (add-after 'unpack 'make-reproducible - (lambda _ - ;; Prevent Last-Modified from being written. - ;; The "*.qm" files that are used in locale.qrc would have a new - ;; mtime otherwise that is written into qrc_locale.cpp in the - ;; end - except when we disable it. - (substitute* "src/CMakeLists.txt" - (("COMMAND [$][{]QT_RCC_EXECUTABLE[}]") - "COMMAND ${QT_RCC_EXECUTABLE} --format-version 1") - ;; Extraneous. - ;;(("qt5_add_resources[(]rg_SOURCES ../data/data.qrc[)]") - ;; "qt5_add_resources(rg_SOURCES ../data/data.qrc OPTIONS --format-version 1)") - ) - ;; Make hashtable traversal order predicable. - (setenv "QT_RCC_TEST" "1"))) ; important - (add-before 'check 'prepare-check - (lambda _ - (setenv "QT_QPA_PLATFORM" "offscreen") - ;; Tests create files in $HOME/.local/share/rosegarden . - (mkdir-p "/tmp/foo") - (setenv "HOME" "/tmp/foo") - (setenv "XDG_RUNTIME_DIR" "/tmp/foo")))))) + (list + #:configure-flags #~(list "-DCMAKE_BUILD_TYPE=Release") + #:phases + #~(modify-phases %standard-phases + (add-after 'unpack 'patch-tests + (lambda _ + (substitute* "CMakeLists.txt" + (("BUILD_TESTING OFF") "BUILD_TESTING ON") + ;; Make tests work. + ((" -fvisibility=hidden") "")))) + (add-after 'unpack 'fix-references + (lambda* (#:key inputs #:allow-other-keys) + (substitute* "src/gui/general/ProjectPackager.cpp" + (("\"flac\\>") + (string-append "\"" (search-input-file inputs "/bin/flac"))) + (("\"wavpack\\>") + (string-append "\"" (search-input-file inputs "/bin/wavpack"))) + (("\"wvunpack\\>") + (string-append "\"" (search-input-file inputs "/bin/wvunpack"))) + (("\"bash\\>") + (string-append "\"" (search-input-file inputs "/bin/bash"))) + (("\"tar\\>") + (string-append "\"" (search-input-file inputs "/bin/tar")))) + (substitute* "src/gui/general/LilyPondProcessor.cpp" + (("\"convert-ly\\>") + (string-append "\"" (search-input-file inputs "/bin/convert-ly"))) + (("\"lilypond\\>") + (string-append "\"" (search-input-file inputs "/bin/lilypond")))))) + (add-after 'unpack 'make-reproducible + (lambda _ + ;; Prevent Last-Modified from being written. + ;; The "*.qm" files that are used in locale.qrc would have a new + ;; mtime otherwise that is written into qrc_locale.cpp in the + ;; end - except when we disable it. + (substitute* "src/CMakeLists.txt" + (("COMMAND [$][{]QT_RCC_EXECUTABLE[}]") + "COMMAND ${QT_RCC_EXECUTABLE} --format-version 1") + ;; Extraneous. + ;;(("qt5_add_resources[(]rg_SOURCES ../data/data.qrc[)]") + ;; "qt5_add_resources(rg_SOURCES ../data/data.qrc OPTIONS --format-version 1)") + ) + ;; Make hashtable traversal order predicable. + (setenv "QT_RCC_TEST" "1"))) ; important + (add-before 'check 'prepare-check + (lambda _ + (setenv "QT_QPA_PLATFORM" "offscreen") + ;; Tests create files in $HOME/.local/share/rosegarden . + (mkdir-p "/tmp/foo") + (setenv "HOME" "/tmp/foo") + (setenv "XDG_RUNTIME_DIR" "/tmp/foo")))))) (inputs (list alsa-lib - bash + bash-minimal dssi flac fftwf @@ -5087,7 +5088,7 @@ specification and header.") wavpack zlib)) (native-inputs - (list pkg-config qttools-5)) ;for qtlinguist + (list pkg-config qttools-5)) ;for qtlinguist (synopsis "Music composition and editing environment based around a MIDI sequencer") (description "Rosegarden is a music composition and editing environment From 838c1c4bd7b8be8976e2d0645727c376f8b37b21 Mon Sep 17 00:00:00 2001 From: Nicolas Goaziou Date: Wed, 14 Dec 2022 18:52:27 +0100 Subject: [PATCH 208/790] gnu: wireshark: Update to 4.0.2. * gnu/packages/networking.scm (wireshark): Update to 4.0.2. --- gnu/packages/networking.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/networking.scm b/gnu/packages/networking.scm index 751eb2b867..72af64b42d 100644 --- a/gnu/packages/networking.scm +++ b/gnu/packages/networking.scm @@ -1754,14 +1754,14 @@ of the same name.") (define-public wireshark (package (name "wireshark") - (version "4.0.1") + (version "4.0.2") (source (origin (method url-fetch) (uri (string-append "https://www.wireshark.org/download/src/wireshark-" version ".tar.xz")) (sha256 - (base32 "1hpxkw0ww6b8fnda5bhgpma2836bfarpxgnkkrzz9fqkkpwh5c5k")))) + (base32 "07a18jx88jaa2j1i949w9n1yb149xi02s80inbfji6rgkxliangk")))) (build-system cmake-build-system) (arguments `(#:phases From b81c4c449283e3ad9dc456ece92ea8c15a239f1c Mon Sep 17 00:00:00 2001 From: Nicolas Goaziou Date: Wed, 14 Dec 2022 18:55:04 +0100 Subject: [PATCH 209/790] gnu: xournalpp: Update to 1.1.3. * gnu/packages/pdf.scm (xournalpp): Update to 1.1.3. --- gnu/packages/pdf.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/pdf.scm b/gnu/packages/pdf.scm index 070dc59ac0..727fc20f36 100644 --- a/gnu/packages/pdf.scm +++ b/gnu/packages/pdf.scm @@ -951,7 +951,7 @@ using a stylus.") (define-public xournalpp (package (name "xournalpp") - (version "1.1.2") + (version "1.1.3") (source (origin (method git-fetch) @@ -960,7 +960,7 @@ using a stylus.") (commit (string-append "v" version)))) (file-name (git-file-name name version)) (sha256 - (base32 "13q3fsrszq828gki3z42lda9gghm9wsnsg7iylp1ypcbj7hd5zhk")))) + (base32 "17qq3clfmiyrcah89h8c5r6pc58xcskm5z1czbasv67bfq7chzhy")))) (build-system cmake-build-system) (arguments (list From 01279bb9bfeca6698e34f5a67134ee90df3c3caf Mon Sep 17 00:00:00 2001 From: Nicolas Goaziou Date: Wed, 14 Dec 2022 18:58:59 +0100 Subject: [PATCH 210/790] gnu: emacs-posframe: Update to 1.3.0. * gnu/packages/emacs-xyz.scm (emacs-posframe): Update to 1.3.0. --- gnu/packages/emacs-xyz.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/emacs-xyz.scm b/gnu/packages/emacs-xyz.scm index 3286928f8d..82d352b191 100644 --- a/gnu/packages/emacs-xyz.scm +++ b/gnu/packages/emacs-xyz.scm @@ -16340,14 +16340,14 @@ the center of the screen and not at the bottom.") (define-public emacs-posframe (package (name "emacs-posframe") - (version "1.2.0") + (version "1.3.0") (source (origin (method url-fetch) (uri (string-append "https://elpa.gnu.org/packages/" "posframe-" version ".tar")) (sha256 - (base32 "06xk6z3b5mqgcskjiwkl9viccvzriflr8y51aclyfdamh5qb6kqb")))) + (base32 "1w6hrxrnbh7c96n4am7igrxxy7w3xfcpqv3df13hd0cn6mh826ab")))) (build-system emacs-build-system) ;; emacs-minimal does not include the function font-info. (arguments From fa23fb86f7741570d194bba1f227016d9aa25881 Mon Sep 17 00:00:00 2001 From: Nicolas Goaziou Date: Wed, 14 Dec 2022 19:01:01 +0100 Subject: [PATCH 211/790] gnu: fet: Update to 6.7.6. * gnu/packages/education.scm (fet): Update to 6.7.6. --- gnu/packages/education.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/education.scm b/gnu/packages/education.scm index 0e3dd08c23..9a30abe8df 100644 --- a/gnu/packages/education.scm +++ b/gnu/packages/education.scm @@ -582,7 +582,7 @@ a pen-tablet display and a beamer.") (define-public fet (package (name "fet") - (version "6.7.1") + (version "6.7.6") (source (origin (method url-fetch) @@ -591,7 +591,7 @@ a pen-tablet display and a beamer.") (list (string-append directory base) (string-append directory "old/" base)))) (sha256 - (base32 "0vwddhmr9n21q4yhkcz6iakkff91hvjcfzhg84zvf1ap30xx09hk")))) + (base32 "0psvnplwp5n7v1j3ywxpq6vykjv1276n66f7ral7c70vjf4h7109")))) (build-system gnu-build-system) (arguments (list From 597685054b2b95cbf78e9dd9b32de5d44c57c2cd Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 14 Dec 2022 21:22:39 +0100 Subject: [PATCH 212/790] gnu: 389-ds-base: Update to 2.2.2. * gnu/packages/openldap.scm (389-ds-base): Update to 2.2.2. [inputs]: Add json-c and lmdb. --- gnu/packages/openldap.scm | 13 +++++++++---- 1 file changed, 9 insertions(+), 4 deletions(-) diff --git a/gnu/packages/openldap.scm b/gnu/packages/openldap.scm index b3b22d1709..ec5cbf43c6 100644 --- a/gnu/packages/openldap.scm +++ b/gnu/packages/openldap.scm @@ -30,6 +30,7 @@ #:use-module (gnu packages check) #:use-module (gnu packages compression) #:use-module (gnu packages cyrus-sasl) + #:use-module (gnu packages databases) #:use-module (gnu packages dbm) #:use-module (gnu packages documentation) #:use-module (gnu packages gettext) @@ -245,7 +246,9 @@ servers from Python programs.") (define-public 389-ds-base (package (name "389-ds-base") - (version "1.4.5.0") + ;; More recent versions require rust. That's not bad, but it's a + ;; challenge to integrate three build systems. + (version "2.2.2") (source (origin (method git-fetch) (uri (git-reference @@ -254,7 +257,7 @@ servers from Python programs.") (file-name (git-file-name name version)) (sha256 (base32 - "1s627w4kwrbszrkm6k6v32gx7jd27h4yqvs81kjkakiaq2lh1s1z")))) + "1sdvfbjfg0091f47562gw3gdc2vgvvhyhdi21lrpwnw9lqc8xdxk")))) (build-system gnu-build-system) (arguments `(#:modules ((srfi srfi-1) @@ -355,16 +358,18 @@ servers from Python programs.") httpd icu4c iproute + json-c libevent libselinux linux-pam + lmdb mit-krb5 net-snmp nspr nss - (list nss "bin") ; for certutil + (list nss "bin") ;for certutil openldap - openssl ; #included by net-snmp + openssl ;#included by net-snmp pcre python python-pyasn1 From b5bb44b260bb5758cfb0c42552652627c1b08295 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 14 Dec 2022 21:50:55 +0100 Subject: [PATCH 213/790] gnu: 389-ds-base: Use gexp. * gnu/packages/openldap.scm (389-ds-base)[arguments]: Use gexp; remove one obsolete substitution. --- gnu/packages/openldap.scm | 165 +++++++++++++++++++------------------- 1 file changed, 81 insertions(+), 84 deletions(-) diff --git a/gnu/packages/openldap.scm b/gnu/packages/openldap.scm index ec5cbf43c6..42808bbf79 100644 --- a/gnu/packages/openldap.scm +++ b/gnu/packages/openldap.scm @@ -260,96 +260,93 @@ servers from Python programs.") "1sdvfbjfg0091f47562gw3gdc2vgvvhyhdi21lrpwnw9lqc8xdxk")))) (build-system gnu-build-system) (arguments - `(#:modules ((srfi srfi-1) + (list + #:modules '((srfi srfi-1) (guix build gnu-build-system) ((guix build python-build-system) #:select (add-installed-pythonpath python-version)) (guix build utils)) - #:imported-modules ((guix build python-build-system) + #:imported-modules `((guix build python-build-system) ,@%gnu-build-system-modules) - #:configure-flags - (list (string-append "--with-db=" - (assoc-ref %build-inputs "bdb")) - (string-append "--with-netsnmp=" - (assoc-ref %build-inputs "net-snmp")) - (string-append "--with-selinux=" - (assoc-ref %build-inputs "libselinux")) - "--localstatedir=/var" - "--with-instconfigdir=/etc/dirsrv") - #:phases - (modify-phases %standard-phases - (add-after 'unpack 'fix-references - (lambda _ - (substitute* "ldap/servers/plugins/sync/sync_persist.c" - (("nspr4") "nspr")) - (substitute* "src/lib389/lib389/utils.py" - (("'/sbin/ip'") - (string-append "'" (which "ip") "'"))) - (substitute* "src/lib389/lib389/nss_ssl.py" - (("'/usr/bin/certutil'") - (string-append "'" (which "certutil") "'")) - (("'/usr/bin/openssl'") - (string-append "'" (which "openssl") "'"))))) - (add-after 'unpack 'overwrite-default-locations - (lambda* (#:key outputs #:allow-other-keys) - (let ((out (assoc-ref outputs "out"))) - (substitute* "src/lib389/lib389/paths.py" - (("/usr/share/dirsrv/inf/defaults.inf") - (string-append out "/share/dirsrv/inf/defaults.inf"))) - ;; This directory can only be specified relative to sysconfdir. This - ;; is used to determine where to look for installed directory - ;; servers, so in the absence of a search path it needs to be global. - (substitute* "ldap/admin/src/defaults.inf.in" - (("^initconfig_dir =.*") - "initconfig_dir = /etc/dirsrv/registry\n")) - ;; This is used to determine where to write certificate files - ;; when installing new directory server instances. - (substitute* "src/lib389/lib389/instance/setup.py" - (("etc_dirsrv_path = .*") - "etc_dirsrv_path = '/etc/dirsrv/'\n"))))) - (add-after 'unpack 'fix-install-location-of-python-tools - (lambda* (#:key inputs outputs #:allow-other-keys) - (let* ((out (assoc-ref outputs "out")) - (pythondir (string-append - out "/lib/python" - (python-version (assoc-ref inputs "python")) + #:configure-flags + #~(list (string-append "--with-db=" + #$(this-package-input "bdb")) + (string-append "--with-netsnmp=" + #$(this-package-input "net-snmp")) + (string-append "--with-selinux=" + #$(this-package-input "libselinux")) + "--localstatedir=/var" + "--with-instconfigdir=/etc/dirsrv") + #:phases + #~(modify-phases %standard-phases + (add-after 'unpack 'fix-references + (lambda _ + (substitute* "ldap/servers/plugins/sync/sync_persist.c" + (("nspr4") "nspr")) + (substitute* "src/lib389/lib389/utils.py" + (("'/sbin/ip'") + (string-append "'" (which "ip") "'"))) + (substitute* "src/lib389/lib389/nss_ssl.py" + (("'/usr/bin/certutil'") + (string-append "'" (which "certutil") "'")) + (("'/usr/bin/openssl'") + (string-append "'" (which "openssl") "'"))))) + (add-after 'unpack 'overwrite-default-locations + (lambda _ + (substitute* "src/lib389/lib389/paths.py" + (("/usr/share/dirsrv/inf/defaults.inf") + (string-append #$output "/share/dirsrv/inf/defaults.inf"))) + ;; This directory can only be specified relative to sysconfdir. This + ;; is used to determine where to look for installed directory + ;; servers, so in the absence of a search path it needs to be global. + (substitute* "ldap/admin/src/defaults.inf.in" + (("^initconfig_dir =.*") + "initconfig_dir = /etc/dirsrv/registry\n")) + ;; This is used to determine where to write certificate files + ;; when installing new directory server instances. + (substitute* "src/lib389/lib389/instance/setup.py" + (("etc_dirsrv_path = .*") + "etc_dirsrv_path = '/etc/dirsrv/'\n")))) + (add-after 'unpack 'fix-install-location-of-python-tools + (lambda* (#:key inputs outputs #:allow-other-keys) + (let ((pythondir (string-append + #$output "/lib/python" + (python-version #$(this-package-input "python")) "/site-packages/"))) - ;; Install directory must be on PYTHONPATH. - (add-installed-pythonpath inputs outputs) - ;; Install directory must exist. - (mkdir-p pythondir) - (substitute* "src/lib389/setup.py" - (("/usr") out)) - (substitute* "Makefile.am" - (("setup.py install --skip-build" m) - (string-append - m " --prefix=" out - " --root=/ --single-version-externally-managed")))))) - (add-after 'build 'build-python-tools - (lambda* (#:key make-flags #:allow-other-keys) - ;; Set DETERMINISTIC_BUILD to override the embedded mtime in pyc - ;; files. - (setenv "DETERMINISTIC_BUILD" "1") - ;; Use deterministic hashes for strings, bytes, and datetime - ;; objects. - (setenv "PYTHONHASHSEED" "0") - (apply invoke "make" "lib389" make-flags))) - (add-after 'install 'install-python-tools - (lambda* (#:key make-flags #:allow-other-keys) - (apply invoke "make" "lib389-install" make-flags))) - (add-after 'install-python-tools 'wrap-python-tools - (lambda* (#:key outputs #:allow-other-keys) - (let* ((out (assoc-ref outputs "out")) - (pythonpath (getenv "GUIX_PYTHONPATH"))) - (for-each (lambda (file) - (wrap-program (string-append out file) - `("GUIX_PYTHONPATH" ":" prefix (,pythonpath)))) - '("/sbin/dsconf" - "/sbin/dscreate" - "/sbin/dsctl" - "/sbin/dsidm" - "/bin/ds-logpipe.py" - "/bin/ds-replcheck")))))))) + ;; Install directory must be on PYTHONPATH. + (add-installed-pythonpath inputs outputs) + ;; Install directory must exist. + (mkdir-p pythondir) + (setenv "INSTALL_PREFIX" #$output) + (substitute* "Makefile.am" + (("setup.py install --skip-build" m) + (string-append + m " --prefix=" #$output + " --root=/ --single-version-externally-managed")))))) + (add-after 'build 'build-python-tools + (lambda* (#:key make-flags #:allow-other-keys) + ;; Set DETERMINISTIC_BUILD to override the embedded mtime in pyc + ;; files. + (setenv "DETERMINISTIC_BUILD" "1") + ;; Use deterministic hashes for strings, bytes, and datetime + ;; objects. + (setenv "PYTHONHASHSEED" "0") + (apply invoke "make" "lib389" make-flags))) + (add-after 'install 'install-python-tools + (lambda* (#:key make-flags #:allow-other-keys) + (apply invoke "make" "lib389-install" make-flags))) + (add-after 'install-python-tools 'wrap-python-tools + (lambda* (#:key outputs #:allow-other-keys) + (let ((pythonpath (getenv "GUIX_PYTHONPATH"))) + (for-each (lambda (file) + (wrap-program (string-append #$output file) + `("GUIX_PYTHONPATH" ":" prefix (,pythonpath)))) + '("/sbin/dsconf" + "/sbin/dscreate" + "/sbin/dsctl" + "/sbin/dsidm" + "/bin/ds-logpipe.py" + "/bin/ds-replcheck")))))))) (inputs (list bdb cracklib From e2bcd41ce35b051f311e36dfd104d36ce1145f8b Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 14 Dec 2022 21:51:58 +0100 Subject: [PATCH 214/790] gnu: 389-ds-base: Enable one test. * gnu/packages/openldap.scm (389-ds-base)[arguments]: Enable unit tests. [native-inputs]: Add cmocka. --- gnu/packages/openldap.scm | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/gnu/packages/openldap.scm b/gnu/packages/openldap.scm index 42808bbf79..73cb56c21b 100644 --- a/gnu/packages/openldap.scm +++ b/gnu/packages/openldap.scm @@ -269,7 +269,8 @@ servers from Python programs.") #:imported-modules `((guix build python-build-system) ,@%gnu-build-system-modules) #:configure-flags - #~(list (string-append "--with-db=" + #~(list "--enable-cmocka" + (string-append "--with-db=" #$(this-package-input "bdb")) (string-append "--with-netsnmp=" #$(this-package-input "net-snmp")) @@ -380,6 +381,7 @@ servers from Python programs.") (native-inputs (list autoconf automake + cmocka doxygen gettext-minimal libtool From 7b8cac86ba0bd7ddf02042ec8b9b46f13687d081 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 14 Dec 2022 22:46:21 +0100 Subject: [PATCH 215/790] gnu: 389-ds-base: Avoid dependency on systemd-detect-virt. * gnu/packages/openldap.scm (389-ds-base)[arguments]: Remove invocation of systemd-detect-virt. --- gnu/packages/openldap.scm | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/gnu/packages/openldap.scm b/gnu/packages/openldap.scm index 73cb56c21b..3f3015bd80 100644 --- a/gnu/packages/openldap.scm +++ b/gnu/packages/openldap.scm @@ -282,6 +282,10 @@ servers from Python programs.") #~(modify-phases %standard-phases (add-after 'unpack 'fix-references (lambda _ + ;; Avoid dependency on systemd-detect-virt + (substitute* "src/lib389/lib389/instance/setup.py" + (("container_result = subprocess.*") "container_result = 1\n") + (("container_result.returncode") "container_result")) (substitute* "ldap/servers/plugins/sync/sync_persist.c" (("nspr4") "nspr")) (substitute* "src/lib389/lib389/utils.py" From 1689215a30a24ed9b6eaf7743b0a6b240aefaf4e Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 14 Dec 2022 22:47:43 +0100 Subject: [PATCH 216/790] gnu: bedtools-2.18: Use gexp. * gnu/packages/bioinformatics.scm (bedtools-2.18)[arguments]: Use gexp. [native-inputs]: Drop package label. --- gnu/packages/bioinformatics.scm | 39 +++++++++++++++++---------------- 1 file changed, 20 insertions(+), 19 deletions(-) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index fa719e139f..e8da00d805 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -482,26 +482,27 @@ BED, GFF/GTF, VCF.") (base32 "11rvca19ncg03kxd0wzlfx5ws7r3nisd0z8s9j9n182d8ksp2pxz")))) (arguments - '(#:test-target "test" - #:phases - (modify-phases %standard-phases - (add-after 'unpack 'compatibility - (lambda _ - (substitute* "src/utils/fileType/FileRecordTypeChecker.h" - (("static const float PERCENTAGE") - "static constexpr float PERCENTAGE")) - (substitute* "src/utils/general/DualQueue.h" - (("template class CompareFunc>") - "template class CompareFunc>")))) - (delete 'configure) - (replace 'install - (lambda* (#:key outputs #:allow-other-keys) - (let ((bin (string-append (assoc-ref outputs "out") "/bin/"))) - (for-each (lambda (file) - (install-file file bin)) - (find-files "bin" ".*")))))))) + (list + #:test-target "test" + #:phases + #~(modify-phases %standard-phases + (add-after 'unpack 'compatibility + (lambda _ + (substitute* "src/utils/fileType/FileRecordTypeChecker.h" + (("static const float PERCENTAGE") + "static constexpr float PERCENTAGE")) + (substitute* "src/utils/general/DualQueue.h" + (("template class CompareFunc>") + "template class CompareFunc>")))) + (delete 'configure) + (replace 'install + (lambda _ + (let ((bin (string-append #$output "/bin/"))) + (for-each (lambda (file) + (install-file file bin)) + (find-files "bin" ".*")))))))) (native-inputs - `(("python" ,python-wrapper))) + (list python-wrapper)) (inputs (list samtools zlib)))) From 82c511dd5489bd7a2cbcd0313b9f54f9d7f166d2 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 14 Dec 2022 22:56:00 +0100 Subject: [PATCH 217/790] gnu: slapd-configuration: Update default for run-dir. * gnu/services/ldap.scm (slapd-configuration): Update default value for run-dir to match defaults of 389-ds-base package. * doc/guix.texi: Update documentation. --- doc/guix.texi | 2 +- gnu/services/ldap.scm | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/doc/guix.texi b/doc/guix.texi index f376fd2c9b..5cb5ae1dfe 100644 --- a/doc/guix.texi +++ b/doc/guix.texi @@ -29069,7 +29069,7 @@ Sets the lock directory of the instance. @item @code{log-dir} (default: @code{"/var/log/dirsrv/slapd-@{instance_name@}"}) (type: string) Sets the log directory of the instance. -@item @code{run-dir} (default: @code{"/var/run/dirsrv"}) (type: string) +@item @code{run-dir} (default: @code{"/run/dirsrv"}) (type: string) Sets PID directory of the instance. @item @code{schema-dir} (default: @code{"/etc/dirsrv/slapd-@{instance_name@}/schema"}) (type: string) diff --git a/gnu/services/ldap.scm b/gnu/services/ldap.scm index 35f2735d40..49a33fac08 100644 --- a/gnu/services/ldap.scm +++ b/gnu/services/ldap.scm @@ -120,7 +120,7 @@ database.") (string "/var/log/dirsrv/slapd-{instance_name}") "Sets the log directory of the instance.") (run-dir - (string "/var/run/dirsrv") + (string "/run/dirsrv") "Sets PID directory of the instance.") (schema-dir (string "/etc/dirsrv/slapd-{instance_name}/schema") From 8c8a7dc66c8fdf39d6d2d459022e32d376d9a562 Mon Sep 17 00:00:00 2001 From: Jonathan Brielmaier Date: Wed, 14 Dec 2022 23:16:32 +0100 Subject: [PATCH 218/790] gnu: icedove: Update to 102.6.0. * gnu/packages/gnuzilla.scm (icedove): Update to 102.6.0. --- gnu/packages/gnuzilla.scm | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/gnu/packages/gnuzilla.scm b/gnu/packages/gnuzilla.scm index 1942fb0d8d..b507ec0406 100644 --- a/gnu/packages/gnuzilla.scm +++ b/gnu/packages/gnuzilla.scm @@ -1097,8 +1097,8 @@ standards of the IceCat project.") (cpe-name . "firefox_esr") (cpe-version . ,(first (string-split version #\-))))))) -(define %icedove-build-id "20221201000000") ;must be of the form YYYYMMDDhhmmss -(define %icedove-version "102.5.1") +(define %icedove-build-id "20221213000000") ;must be of the form YYYYMMDDhhmmss +(define %icedove-version "102.6.0") ;; Provides the "comm" folder which is inserted into the icecat source. ;; Avoids the duplication of Icecat's source tarball. @@ -1107,11 +1107,11 @@ standards of the IceCat project.") (method hg-fetch) (uri (hg-reference (url "https://hg.mozilla.org/releases/comm-esr102") - (changeset "bbf216e50e6a8cb4362b2b77feeb8ca4a1d78914"))) + (changeset "d46a947ae837300f19cc45c75d473c7b1cf4ebb3"))) (file-name (string-append "thunderbird-" %icedove-version "-checkout")) (sha256 (base32 - "06fhdzpl72mihm97g2i76knbny1jj261isl2jy8085wdmriv2f8z")))) + "0klr6i2sbaiv2gc8q1cxrz87zd5cskdwa9qacp3dhfb8x17qwb41")))) (define-public icedove (package From f4dc53881b79b324ce7da731ac579a41c5078a48 Mon Sep 17 00:00:00 2001 From: Christopher Baines Date: Thu, 15 Dec 2022 10:13:24 +0000 Subject: [PATCH 219/790] services: nix: Fix nix-shepherd-service. * gnu/services/nix.scm (nix-shepherd-service): Un-gexp build-directory. --- gnu/services/nix.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/services/nix.scm b/gnu/services/nix.scm index dcf994b603..82853253f6 100644 --- a/gnu/services/nix.scm +++ b/gnu/services/nix.scm @@ -142,8 +142,8 @@ GID." (list (string-append #$package "/bin/nix-daemon") #$@extra-options) #:environment-variables - (list (string-append "TMPDIR=" build-directory) - "PATH=/run/current-system/profile/bin"))) + (list (string-append "TMPDIR=" #$build-directory) + "PATH=/run/current-system/profile/bin"))) (respawn? #f) (stop #~(make-kill-destructor))))))) From 3ad3869297fd327ef417b1ecb95c2c4caf53d2e6 Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Thu, 15 Dec 2022 12:29:12 +0200 Subject: [PATCH 220/790] gnu: rkdeveloptool: Fix build failure. This change was tested against a Pinebook Pro. * gnu/packages/hardware.scm (rkdeveloptool)[source]: Add snippet to fix build errors based on upstream pull request. --- gnu/packages/hardware.scm | 10 +++++++++- 1 file changed, 9 insertions(+), 1 deletion(-) diff --git a/gnu/packages/hardware.scm b/gnu/packages/hardware.scm index 65558ffe08..1b8ba9bc43 100644 --- a/gnu/packages/hardware.scm +++ b/gnu/packages/hardware.scm @@ -14,6 +14,7 @@ ;;; Copyright © 2022 Marius Bakke ;;; Copyright © 2022 Marcel Kupiec ;;; Copyright © 2022 Maxim Cournoyer +;;; Copyright © 2022 Efraim Flashner ;;; ;;; This file is part of GNU Guix. ;;; @@ -1132,7 +1133,14 @@ supported by the Linux kernel.") (commit commit))) (file-name (git-file-name name version)) (sha256 - (base32 "0zwrkqfxd671iy69v3q0844gfdpm1yk51i9qh2rqc969bd8glxga")))) + (base32 "0zwrkqfxd671iy69v3q0844gfdpm1yk51i9qh2rqc969bd8glxga")) + (snippet + #~(begin + ;; https://github.com/rockchip-linux/rkdeveloptool/pull/57 + (use-modules (guix build utils)) + (substitute* "main.cpp" + (("snprintf\\(buffer, sizeof\\(buffer\\), \"\\%s\", chip)") + "memccpy(buffer, chip, '\\0', sizeof(buffer))")))))) (build-system gnu-build-system) (native-inputs (list autoconf automake pkg-config)) From d3c32177e0ce28c0e38296d564673f0b29351c68 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 15 Dec 2022 13:32:25 +0100 Subject: [PATCH 221/790] gnu: Add gst-vosk. * gnu/packages/speech.scm (gst-vosk): New variable. --- gnu/packages/speech.scm | 49 ++++++++++++++++++++++++++++++++++++++++- 1 file changed, 48 insertions(+), 1 deletion(-) diff --git a/gnu/packages/speech.scm b/gnu/packages/speech.scm index 15fddd9895..d217d7ba01 100644 --- a/gnu/packages/speech.scm +++ b/gnu/packages/speech.scm @@ -4,7 +4,7 @@ ;;; Copyright © 2017 Leo Famulari ;;; Copyright © 2018, 2020–2022 Tobias Geerinckx-Rice ;;; Copyright © 2016 Kei Kebreau -;;; Copyright © 2019, 2021 Ricardo Wurmus +;;; Copyright © 2019, 2021, 2022 Ricardo Wurmus ;;; Copyright © 2020 Nicolas Goaziou ;;; Copyright © 2020 Efraim Flashner ;;; Copyright © 2021 qblade @@ -31,6 +31,7 @@ #:use-module (guix git-download) #:use-module (guix utils) #:use-module (guix build-system gnu) + #:use-module (guix build-system meson) #:use-module (gnu packages) #:use-module (gnu packages audio) #:use-module (gnu packages autotools) @@ -44,6 +45,7 @@ #:use-module (gnu packages glib) #:use-module (gnu packages gstreamer) #:use-module (gnu packages linux) + #:use-module (gnu packages machine-learning) #:use-module (gnu packages ncurses) #:use-module (gnu packages perl) #:use-module (gnu packages pkg-config) @@ -558,6 +560,51 @@ low level architecture and has a Scheme (SIOD) based command interpreter for control.") (license (license:non-copyleft "file://COPYING")))) +(define-public gst-vosk + (package + (name "gst-vosk") + (version "0.3.1") + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/PhilippeRo/gst-vosk") + (commit version))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "1zxifssh57a251af9x4ahglcipvmkgc1pmc67l59s805za9yvq3p")) + (modules '((guix build utils))) + (snippet + ;; Do not use prebuilt vosk library + '(begin + (delete-file-recursively "vosk") + (substitute* "meson.build" + (("subdir\\('vosk'\\)") "")) + (substitute* "src/meson.build" + (("vosk_libdir =.*") "") + ((", dirs : vosk_libdir") "") + (("include_directories : include_directories.*") "")) + (substitute* '("src/gstvosk.h" + "src/gstvosk.c") + (("vosk-api.h") "vosk_api.h")))))) + (build-system meson-build-system) + (arguments + (list + #:phases + '(modify-phases %standard-phases + (add-after 'unpack 'install-vosk-api-header + (lambda* (#:key inputs #:allow-other-keys) + (install-file (search-input-file inputs "src/vosk_api.h") + "src")))))) + (inputs + (list vosk-api gstreamer gobject-introspection)) + (native-inputs (list pkg-config gettext-minimal)) + (home-page "https://github.com/PhilippeRo/gst-vosk") + (synopsis "Gstreamer plugin for VOSK voice recognition engine") + (description "This package provides a Gstreamer plugin for the VOSK voice +recognition engine.") + (license license:gpl2+))) + (define-public ekho (package (name "ekho") From 7caf07f85195b21fbdc13cbe7a3b78865bd8e287 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 15 Dec 2022 15:15:26 +0100 Subject: [PATCH 222/790] gnu: Add ibus-speech-to-text. * gnu/packages/ibus.scm (ibus-speech-to-text): New variable. --- gnu/packages/ibus.scm | 76 ++++++++++++++++++++++++++++++++++++++++++- 1 file changed, 75 insertions(+), 1 deletion(-) diff --git a/gnu/packages/ibus.scm b/gnu/packages/ibus.scm index 29bfc44e4a..4c45671acc 100644 --- a/gnu/packages/ibus.scm +++ b/gnu/packages/ibus.scm @@ -1,5 +1,5 @@ ;;; GNU Guix --- Functional package management for GNU -;;; Copyright © 2015, 2016, 2017, 2018, 2019, 2020, 2021 Ricardo Wurmus +;;; Copyright © 2015, 2016, 2017, 2018, 2019, 2020, 2021, 2022 Ricardo Wurmus ;;; Copyright © 2015 Andreas Enge ;;; Copyright © 2016 Chris Marusich ;;; Copyright © 2017, 2018 Efraim Flashner @@ -36,6 +36,7 @@ #:use-module (guix build-system cmake) #:use-module (guix build-system gnu) #:use-module (guix build-system glib-or-gtk) + #:use-module (guix build-system meson) #:use-module (guix build-system python) #:use-module (guix utils) #:use-module (gnu packages) @@ -54,6 +55,7 @@ #:use-module (gnu packages gettext) #:use-module (gnu packages glib) #:use-module (gnu packages gnome) + #:use-module (gnu packages gstreamer) #:use-module (gnu packages gtk) #:use-module (gnu packages iso-codes) #:use-module (gnu packages logging) @@ -63,11 +65,13 @@ #:use-module (gnu packages python-xyz) #:use-module (gnu packages python-web) #:use-module (gnu packages serialization) + #:use-module (gnu packages speech) #:use-module (gnu packages sqlite) #:use-module (gnu packages textutils) #:use-module (gnu packages unicode) #:use-module (gnu packages xorg) #:use-module (gnu packages xdisorg) + #:use-module (gnu packages xml) #:use-module (srfi srfi-1)) (define-public ibus-minimal @@ -847,6 +851,76 @@ hanja dictionary and small hangul character classification.") "ibus-hangul is a Korean input method engine for IBus.") (license gpl2+))) +(define-public ibus-speech-to-text + (package + (name "ibus-speech-to-text") + (version "0.4.0") + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/PhilippeRo/IBus-Speech-To-Text") + (commit version))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "00p7jfv815dblg20hahch6151rdbxhkdhfj51i0yvvmg3irvf7nm")))) + (build-system meson-build-system) + (arguments + (list + #:glib-or-gtk? #true + #:phases + '(modify-phases %standard-phases + (add-after 'unpack 'skip-update-desktop-database + (lambda* (#:key inputs #:allow-other-keys) + (substitute* "meson.build" + (("update_desktop_database: true") + "update_desktop_database: false")))) + (add-after 'install 'wrap-with-additional-paths + (lambda* (#:key inputs outputs #:allow-other-keys) + ;; Make sure 'ibus-{setup,engine}-stt' find the gst-vosk plugin + ;; and run with the correct GUIX_PYTHONPATH and GI_TYPELIB_PATH. + (let ((out (assoc-ref outputs "out"))) + (for-each (lambda (prog) + (wrap-program prog + `("GST_PLUGIN_PATH" ":" prefix + (,(string-append (assoc-ref inputs "gst-vosk") + "/lib/gstreamer-1.0") + ,(getenv "GST_PLUGIN_SYSTEM_PATH"))) + `("GUIX_PYTHONPATH" ":" prefix + (,(getenv "GUIX_PYTHONPATH") + ,(string-append (assoc-ref inputs "ibus") + "/lib/girepository-1.0") + ,(string-append (assoc-ref outputs "out") + "/share/ibus-stt"))) + `("GI_TYPELIB_PATH" ":" prefix + (,(string-append (assoc-ref inputs "ibus") + "/lib/girepository-1.0") + ,(string-append (assoc-ref outputs "out") + "/share/ibus-stt"))))) + (list (string-append out "/libexec/ibus-engine-stt") + (string-append out "/libexec/ibus-setup-stt"))))))))) + (inputs + (list desktop-file-utils + (list glib "bin") + gobject-introspection + gst-vosk + gstreamer + gtk + ibus + libadwaita + python + python-babel + python-pygobject)) + (native-inputs + (list gettext-minimal libxml2 pkg-config)) + (home-page "https://github.com/PhilippeRo/IBus-Speech-To-Text") + (synopsis "Speech to text IBus engine using VOSK") + (description "This Input Method uses VOSK for voice recognition and allows +to dictate text in several languages in any application that supports IBus. +One of the main adavantages is that VOSK performs voice recognition locally +and does not rely on an online service.") + (license gpl3+))) + (define-public ibus-theme-tools (package (name "ibus-theme-tools") From b19f5bbac79522438bb9deca8bbb28fc0f751903 Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Thu, 15 Dec 2022 16:05:44 +0200 Subject: [PATCH 223/790] gnu: ncdu: Update to 1.18. * gnu/packages/ncdu.scm (ncdu): Update to 1.18. --- gnu/packages/ncdu.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/ncdu.scm b/gnu/packages/ncdu.scm index 5931ce7b84..a623cd5373 100644 --- a/gnu/packages/ncdu.scm +++ b/gnu/packages/ncdu.scm @@ -33,14 +33,14 @@ (define-public ncdu (package (name "ncdu") - (version "1.17") + (version "1.18") (source (origin (method url-fetch) (uri (string-append "https://dev.yorhel.nl/download/ncdu-" version ".tar.gz")) (sha256 (base32 - "1wfvdajln0iy7364nxkg4bpgdv8l3b6a9bnkhy67icqsxnl4a1w1")))) + "15czid6584j7vclwrw85ihahknghxv2w6b9mrk9cbjc0cnls2drw")))) (build-system gnu-build-system) (inputs (list ncurses)) (synopsis "Ncurses-based disk usage analyzer") From 407b4f5661ea806ddc1056b35722fd551237f87d Mon Sep 17 00:00:00 2001 From: Liliana Marie Prikler Date: Thu, 8 Dec 2022 09:31:42 +0100 Subject: [PATCH 224/790] gnu: Add catch2-3.1. * gnu/packages/check.scm (catch2-3.1): New variable. --- gnu/packages/check.scm | 79 ++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 79 insertions(+) diff --git a/gnu/packages/check.scm b/gnu/packages/check.scm index af0ad1c00f..aaa41777dc 100644 --- a/gnu/packages/check.scm +++ b/gnu/packages/check.scm @@ -580,6 +580,85 @@ It allows the specification of behaviour scenarios using a given-when-then pattern.") (license license:apsl2)))) +(define-public catch2-3.1 + (package + (name "catch2") + (version "3.1.1") + (home-page "https://github.com/catchorg/Catch2") + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/catchorg/Catch2") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "1qnr5b3zq8brh43f924rgnw5gmmjf9ax7kbq2crz1mlwgmdymxlp")))) + (outputs (list "out" "static")) + (build-system meson-build-system) + (arguments + (list + #:phases + #~(modify-phases %standard-phases + (add-after 'unpack 'patch-meson + (lambda _ + (substitute* "src/catch2/meson.build" + (("static_library") "both_libraries")))) + (add-after 'install 'install-cmake-config + (lambda* (#:key outputs #:allow-other-keys) + (define prefix (string-append (assoc-ref outputs "out") + "/lib/cmake/Catch2/")) + (mkdir-p prefix) + (call-with-output-file (string-append + prefix + "catch2-config-version.cmake") + (lambda (port) + (format + port + "set(PACKAGE_VERSION ~s)~@ + if(PACKAGE_FIND_VERSION STREQUAL PACKAGE_VERSION)~@ + set(PACKAGE_VERSION_EXACT TRUE)~@ + set(PACKAGE_VERSION_COMPATIBLE TRUE)~@ + elseif(PACKAGE_FIND_VERSION VERSION_LESS_EQUAL ~ + PACKAGE_VERSION)~@ + set(PACKAGE_VERSION_COMPATIBLE TRUE)~@ + else()~@ + set(PACKAGE_VERSION_COMPATIBLE FALSE)~@ + endif()" + #$version))) + (call-with-output-file (string-append prefix + "catch2-config.cmake") + (lambda (port) + (format + port + "include(FindPkgConfig)~@ + pkg_check_modules(CATCH2 IMPORTED_TARGET GLOBAL catch2)~@ + pkg_check_modules(CATCH2MAIN ~ + IMPORTED_TARGET GLOBAL ~ + catch2 catch2-with-main)~@ + if(CATCH2_FOUND)~@ + add_library(Catch2::Catch2 ALIAS PkgConfig::CATCH2)~@ + endif()~@ + if(CATCH2MAIN_FOUND)~@ + add_library(Catch2::Catch2WithMain ~ + ALIAS PkgConfig::CATCH2MAIN)~@ + endif()"))))) + (add-after 'install 'move-static-libraries + (lambda* (#:key outputs #:allow-other-keys) + (let ((out (assoc-ref outputs "out")) + (static (assoc-ref outputs "static"))) + (for-each + (lambda (file) + (install-file file (string-append static "/lib")) + (delete-file file)) + (find-files (string-append out "/lib") + "\\.a$")))))))) + (inputs (list python-wrapper)) + (synopsis "Automated test framework for C++ and Objective-C") + (description "Catch2 stands for C++ Automated Test Cases in Headers and is +a multi-paradigm automated test framework for C++ and Objective-C.") + (license license:boost1.0))) + (define-public cmdtest (package (name "cmdtest") From 188269f06252d746e5015b3e4c80db7cfd7018e1 Mon Sep 17 00:00:00 2001 From: Liliana Marie Prikler Date: Thu, 8 Dec 2022 09:33:05 +0100 Subject: [PATCH 225/790] gnu: clingo: Update to 5.6.2. MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * gnu/packages/maths.scm (clingo): Update to 5.6.2. [source]: Unbundle clasp and catch. [arguments]<#:configure-flags>: Add “-DCLINGO_USE_LOCAL_CLASP=off” and “-DCLINGO_USE_LOCAL_CATCH=off”. [inputs]: Add catch2-3.1. [native-inputs]: Add pkg-config. --- gnu/packages/maths.scm | 23 ++++++++++++----------- 1 file changed, 12 insertions(+), 11 deletions(-) diff --git a/gnu/packages/maths.scm b/gnu/packages/maths.scm index aee050735e..147d3ac0ac 100644 --- a/gnu/packages/maths.scm +++ b/gnu/packages/maths.scm @@ -2626,27 +2626,30 @@ satisfiability checking (SAT).") (define-public clingo (package (name "clingo") - (version "5.5.0") + (version "5.6.2") (source (origin (method git-fetch) (uri (git-reference (url "https://github.com/potassco/clingo") (commit (string-append "v" version)))) (file-name (git-file-name name version)) + (modules '((guix build utils))) + (snippet + #~(begin + (delete-file-recursively "clasp") + ;; TODO: Unvendor other third-party stuff + (delete-file-recursively "third_party/catch"))) (sha256 (base32 - "0rfjwkcwm0mmf3r4i7asyjwb6cia4i7px7fn2kdbi9j85qvas4pb")))) + "19s59ndcm2yj0kxlikfxnx2bmp6b7n31wq1zvwc7hyk37rqarwys")))) (build-system cmake-build-system) (arguments `(#:configure-flags `("-DCLINGO_BUILD_TESTS=on" "-DCLINGO_INSTALL_LIB=on" "-DCLINGO_BUILD_STATIC=off" "-DCLINGO_BUILD_SHARED=on" - ;; XXX: Clingo requries private headers and - ;; sources from clasp - ,(string-append - "-DCLASP_SOURCE_DIR=" - (assoc-ref %build-inputs "clasp-src"))) + "-DCLINGO_USE_LOCAL_CLASP=off" + "-DCLINGO_USE_LOCAL_CATCH=off") #:phases (modify-phases %standard-phases (add-after 'unpack 'patch-cmake @@ -2678,10 +2681,8 @@ satisfiability checking (SAT).") "unpool-ast-v2" "parse_term" "propagator" "propgator-sequence-mining" "symbol" "visitor")))))))))) - (inputs - (list clasp libpotassco)) - (native-inputs - `(("clasp-src" ,(package-source clasp)))) + (inputs (list catch2-3.1 clasp libpotassco)) + (native-inputs (list pkg-config)) (home-page "https://potassco.org/") (synopsis "Grounder and solver for logic programs") (description "Clingo computes answer sets for a given logic program.") From 25e3e0c6eca0b78875f01904a95659aeddbbd4cd Mon Sep 17 00:00:00 2001 From: Liliana Marie Prikler Date: Thu, 8 Dec 2022 09:47:52 +0100 Subject: [PATCH 226/790] gnu: clingo: Use G-Expressions. * gnu/packages/maths.scm (clingo)[arguments]: Convert to list of G-Expressions. --- gnu/packages/maths.scm | 75 +++++++++++++++++++++--------------------- 1 file changed, 38 insertions(+), 37 deletions(-) diff --git a/gnu/packages/maths.scm b/gnu/packages/maths.scm index 147d3ac0ac..e524b63699 100644 --- a/gnu/packages/maths.scm +++ b/gnu/packages/maths.scm @@ -2644,43 +2644,44 @@ satisfiability checking (SAT).") "19s59ndcm2yj0kxlikfxnx2bmp6b7n31wq1zvwc7hyk37rqarwys")))) (build-system cmake-build-system) (arguments - `(#:configure-flags `("-DCLINGO_BUILD_TESTS=on" - "-DCLINGO_INSTALL_LIB=on" - "-DCLINGO_BUILD_STATIC=off" - "-DCLINGO_BUILD_SHARED=on" - "-DCLINGO_USE_LOCAL_CLASP=off" - "-DCLINGO_USE_LOCAL_CATCH=off") - #:phases - (modify-phases %standard-phases - (add-after 'unpack 'patch-cmake - (lambda _ - (substitute* "CMakeLists.txt" - (("add_subdirectory\\(clasp\\)") - "find_package(clasp REQUIRED)")) - (substitute* "libclingo/CMakeLists.txt" - (("\"cmake/Clingo\"") "\"cmake/clingo\"") - (("ClingoConfig\\.cmake") "clingo-config.cmake") - (("ClingoConfigVersion\\.cmake") - "clingo-config-version.cmake")) - (substitute* "cmake/ClingoConfig.cmake.in" - (("find_package\\(Clasp") "find_package(clasp")) - (rename-file "cmake/ClingoConfig.cmake.in" - "cmake/clingo-config.cmake.in"))) - (add-after 'unpack 'skip-failing-tests - (lambda _ - (with-directory-excursion "libclingo/tests" - (substitute* "CMakeLists.txt" - (("COMMAND test_clingo" all) - (string-append all - " -f " - "\"${CMAKE_CURRENT_SOURCE_DIR}/good.txt\""))) - (call-with-output-file "good.txt" - (lambda (port) - (for-each (lambda (test) (format port "~s~%" test)) - '("parse-ast-v2" "add-ast-v2" "build-ast-v2" - "unpool-ast-v2" "parse_term" - "propagator" "propgator-sequence-mining" - "symbol" "visitor")))))))))) + (list + #:configure-flags #~`("-DCLINGO_BUILD_TESTS=on" + "-DCLINGO_INSTALL_LIB=on" + "-DCLINGO_BUILD_STATIC=off" + "-DCLINGO_BUILD_SHARED=on" + "-DCLINGO_USE_LOCAL_CLASP=off" + "-DCLINGO_USE_LOCAL_CATCH=off") + #:phases + #~(modify-phases %standard-phases + (add-after 'unpack 'patch-cmake + (lambda _ + (substitute* "CMakeLists.txt" + (("add_subdirectory\\(clasp\\)") + "find_package(clasp REQUIRED)")) + (substitute* "libclingo/CMakeLists.txt" + (("\"cmake/Clingo\"") "\"cmake/clingo\"") + (("ClingoConfig\\.cmake") "clingo-config.cmake") + (("ClingoConfigVersion\\.cmake") + "clingo-config-version.cmake")) + (substitute* "cmake/ClingoConfig.cmake.in" + (("find_package\\(Clasp") "find_package(clasp")) + (rename-file "cmake/ClingoConfig.cmake.in" + "cmake/clingo-config.cmake.in"))) + (add-after 'unpack 'skip-failing-tests + (lambda _ + (with-directory-excursion "libclingo/tests" + (substitute* "CMakeLists.txt" + (("COMMAND test_clingo" all) + (string-append all + " -f " + "\"${CMAKE_CURRENT_SOURCE_DIR}/good.txt\""))) + (call-with-output-file "good.txt" + (lambda (port) + (for-each (lambda (test) (format port "~s~%" test)) + '("parse-ast-v2" "add-ast-v2" "build-ast-v2" + "unpool-ast-v2" "parse_term" + "propagator" "propgator-sequence-mining" + "symbol" "visitor")))))))))) (inputs (list catch2-3.1 clasp libpotassco)) (native-inputs (list pkg-config)) (home-page "https://potassco.org/") From 1339623a42174c7cdfea07dc796908fae5ad047f Mon Sep 17 00:00:00 2001 From: Liliana Marie Prikler Date: Thu, 8 Dec 2022 09:48:53 +0100 Subject: [PATCH 227/790] gnu: Add python-clingo. * gnu/packages/maths.scm (python-clingo): New variable. --- gnu/packages/maths.scm | 29 +++++++++++++++++++++++++++++ 1 file changed, 29 insertions(+) diff --git a/gnu/packages/maths.scm b/gnu/packages/maths.scm index e524b63699..64fa725184 100644 --- a/gnu/packages/maths.scm +++ b/gnu/packages/maths.scm @@ -127,6 +127,7 @@ #:use-module (gnu packages image) #:use-module (gnu packages java) #:use-module (gnu packages less) + #:use-module (gnu packages libffi) #:use-module (gnu packages lisp) #:use-module (gnu packages linux) #:use-module (gnu packages llvm) @@ -2689,6 +2690,34 @@ satisfiability checking (SAT).") (description "Clingo computes answer sets for a given logic program.") (license license:expat))) +(define-public python-clingo + (package + (inherit clingo) + (name "python-clingo") + (arguments + (substitute-keyword-arguments (package-arguments clingo) + ((#:configure-flags flags #~'()) + #~(cons* "-DCLINGO_BUILD_WITH_PYTHON=pip" + "-DCLINGO_USE_LIB=yes" + #$flags)) + ((#:phases phases #~%standard-phases) + #~(modify-phases #$phases + (add-after 'unpack 'fix-failing-tests + (lambda _ + (substitute* "libpyclingo/clingo/tests/test_conf.py" + (("ctl\\.solve\\(on_statistics=on_statistics\\)" all) + (string-append + all + "; self.skipTest(\"You shall not fail.\")"))))))))) + (inputs (list clingo python-wrapper)) + (propagated-inputs (list python-cffi)) + (native-inputs (modify-inputs (package-native-inputs clingo) + (prepend python-scikit-build))) + (synopsis "Python bindings for clingo") + (description "This package provides Python bindings to the clingo package, +making it so that you can write @acronym{ASPs, Answer Set Programs} through +Python code."))) + (define-public ceres (package (name "ceres-solver") From 4f94156452f8c9292c802686f099c2830a205312 Mon Sep 17 00:00:00 2001 From: Liliana Marie Prikler Date: Thu, 8 Dec 2022 09:49:07 +0100 Subject: [PATCH 228/790] gnu: Add python-telingo. * gnu/packages/patches/python-telingo-fix-comparison.patch: New file. * gnu/local.mk (dist_patch_DATA): Register it. * gnu/packages/maths.scm (python-telingo): New variable. --- gnu/local.mk | 1 + gnu/packages/maths.scm | 23 +++++++++++++++++++ .../python-telingo-fix-comparison.patch | 19 +++++++++++++++ 3 files changed, 43 insertions(+) create mode 100644 gnu/packages/patches/python-telingo-fix-comparison.patch diff --git a/gnu/local.mk b/gnu/local.mk index aae6e23e12..5b8944f568 100644 --- a/gnu/local.mk +++ b/gnu/local.mk @@ -1643,6 +1643,7 @@ dist_patch_DATA = \ %D%/packages/patches/python-louvain-fix-test.patch \ %D%/packages/patches/python-random2-getrandbits-test.patch \ %D%/packages/patches/python-poppler-qt5-fix-build.patch \ + %D%/packages/patches/python-telingo-fix-comparison.patch \ %D%/packages/patches/python-w3lib-fix-test-failure.patch \ %D%/packages/patches/sdcc-disable-non-free-code.patch \ %D%/packages/patches/sdl-pango-api_additions.patch \ diff --git a/gnu/packages/maths.scm b/gnu/packages/maths.scm index 64fa725184..050450e12c 100644 --- a/gnu/packages/maths.scm +++ b/gnu/packages/maths.scm @@ -93,6 +93,7 @@ #:use-module (guix build-system ocaml) #:use-module (guix build-system perl) #:use-module (guix build-system python) + #:use-module (guix build-system pyproject) #:use-module (guix build-system ruby) #:use-module (gnu packages algebra) #:use-module (gnu packages audio) @@ -2718,6 +2719,28 @@ satisfiability checking (SAT).") making it so that you can write @acronym{ASPs, Answer Set Programs} through Python code."))) +(define-public python-telingo + (package + (name "python-telingo") + (version "2.1.1") + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/potassco/telingo") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (patches (search-patches "python-telingo-fix-comparison.patch")) + (sha256 + (base32 + "0g3khxfdzc2hc7dkiyyqhb399h6h21m5wkp6wy8w71n0m32fiy53")))) + (build-system pyproject-build-system) + (propagated-inputs (list python-clingo)) + (home-page "https://potassco.org/") + (synopsis "Solve dynamic temporal logic programs") + (description "This package provides a system to solve dynamic temporal +logic programs based on clingo.") + (license license:expat))) + (define-public ceres (package (name "ceres-solver") diff --git a/gnu/packages/patches/python-telingo-fix-comparison.patch b/gnu/packages/patches/python-telingo-fix-comparison.patch new file mode 100644 index 0000000000..6d05048dcb --- /dev/null +++ b/gnu/packages/patches/python-telingo-fix-comparison.patch @@ -0,0 +1,19 @@ +Index: source/telingo/transformers/head.py +=================================================================== +--- source.orig/telingo/transformers/head.py ++++ source/telingo/transformers/head.py +@@ -564,10 +564,12 @@ class HeadTransformer: + cond = [] + diff = _ast.BinaryOperation(loc, _ast.BinaryOperator.Minus, param, shift) + if lhs.ast_type != _ast.ASTType.SymbolicTerm or lhs.symbol.type != _clingo.SymbolType.Number or lhs.symbol.number > 0: +- cond.append(_ast.Literal(loc, _ast.Sign.NoSign, _ast.Comparison(_ast.ComparisonOperator.LessEqual, lhs, diff))) ++ cond.append(_ast.Literal(loc, _ast.Sign.NoSign, ++ _ast.Comparison(lhs, [_ast.Guard(_ast.ComparisonOperator.LessEqual, diff)]))) + + if rhs.ast_type != _ast.ASTType.SymbolicTerm or rhs.symbol.type != _clingo.SymbolType.Supremum: +- cond.append(_ast.Literal(loc, _ast.Sign.NoSign, _ast.Comparison(_ast.ComparisonOperator.LessEqual, diff, rhs))) ++ cond.append(_ast.Literal(loc, _ast.Sign.NoSign, ++ _ast.Comparison(diff, [_ast.Guard(_ast.ComparisonOperator.LessEqual, rhs)]))) + + elems.extend([_ast.ConditionalLiteral(loc, _ast.Literal(loc, _ast.Sign.NoSign, head), cond) for head in heads]) + From f19d49e69cce1a962cdd77b3cb7e1dcbe0d22240 Mon Sep 17 00:00:00 2001 From: Liliana Marie Prikler Date: Sat, 3 Dec 2022 11:20:45 +0100 Subject: [PATCH 229/790] gnu: Add orf-dl. * gnu/packages/video.scm (orf-dl): New variable. --- gnu/packages/video.scm | 33 +++++++++++++++++++++++++++++++++ 1 file changed, 33 insertions(+) diff --git a/gnu/packages/video.scm b/gnu/packages/video.scm index a15c86ee07..e32186f5ce 100644 --- a/gnu/packages/video.scm +++ b/gnu/packages/video.scm @@ -167,6 +167,7 @@ #:use-module (gnu packages perl) #:use-module (gnu packages perl-check) #:use-module (gnu packages perl-web) + #:use-module (gnu packages php) #:use-module (gnu packages photo) #:use-module (gnu packages pkg-config) #:use-module (gnu packages popt) @@ -2444,6 +2445,38 @@ To load this plugin, specify the following option when starting mpv: (base32 "1x12f2bd4jqd532rnixmwvcx8d29yxiacpcxqqh86qczc49la8gm")))))) +(define-public orf-dl + (let ((commit "2dbbe7ef4e0efe0f3c1d59c503108e22d9065999") + (revision "1")) + (package + (name "orf-dl") + (version (git-version "0" revision commit)) + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/tpoechtrager/orf_dl") + (commit commit))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "1w413miy01cm7rzb5c6wwfdnc2sqv87cvxwikafgrkswpimvdjsk")))) + (build-system copy-build-system) + (arguments + (list #:install-plan #~`(("orf_dl.php" "bin/orf-dl")) + #:phases + #~(modify-phases %standard-phases + (add-after 'unpack 'patch-source + (lambda* (#:key inputs #:allow-other-keys) + (substitute* "orf_dl.php" + (("ffmpeg") + (search-input-file inputs "bin/ffmpeg")))))))) + (inputs (list php ffmpeg)) + (home-page "https://github.com/tpoechtrager/orf_dl") + (synopsis "Download videos from tvthek.orf.at") + (description "This package provides a PHP-based command line application +to download videos from Austria's national television broadcaster.") + (license license:gpl2+)))) + (define-public youtube-dl (package (name "youtube-dl") From 2cf232d1cd38ff619547484ceb222a7223db3d43 Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Sun, 11 Dec 2022 01:00:01 +0100 Subject: [PATCH 230/790] gnu: knot: Update to 3.2.4. * gnu/packages/dns.scm (knot): Update to 3.2.4. --- gnu/packages/dns.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/dns.scm b/gnu/packages/dns.scm index 3762e093a2..4f25147d00 100644 --- a/gnu/packages/dns.scm +++ b/gnu/packages/dns.scm @@ -871,7 +871,7 @@ Extensions} (DNSSEC).") (define-public knot (package (name "knot") - (version "3.2.3") + (version "3.2.4") (source (origin (method git-fetch) @@ -880,7 +880,7 @@ Extensions} (DNSSEC).") (commit (string-append "v" version)))) (file-name (git-file-name name version)) (sha256 - (base32 "117q8jllaakd6gv0mfkq45sigy5c8j8jbyxiwna3wan0mjx81fhv")) + (base32 "0b6fnrdy5zqn3mnn5cl92j0m7k9l6hh4gnr92qpirqf54bl2lfm2")) (modules '((guix build utils))) (snippet '(begin From b51c5c1997450a8b6caffb366c9ec53facf9104f Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Sun, 11 Dec 2022 01:00:01 +0100 Subject: [PATCH 231/790] gnu: rizin: Update to 0.4.1. * gnu/packages/engineering.scm (rizin): Update to 0.4.1. --- gnu/packages/engineering.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/engineering.scm b/gnu/packages/engineering.scm index ee224ad173..0426762dbd 100644 --- a/gnu/packages/engineering.scm +++ b/gnu/packages/engineering.scm @@ -3886,7 +3886,7 @@ form, numpad. (define-public rizin (package (name "rizin") - (version "0.4.0") + (version "0.4.1") (source (origin (method url-fetch) (uri (string-append @@ -3894,7 +3894,7 @@ form, numpad. version "/rizin-src-v" version ".tar.xz")) (sha256 (base32 - "0nkb6v9lks25w5sv5s6p2ghgqnnnsf39md8nlx1cy4z89xlaisq9")))) + "1f5zzlnr2na4hkvcwn4n9cjlk6595945vwrw89pa683qk5mrb7b6")))) (build-system meson-build-system) (arguments (list From 4283b867a189cdbea8d07c39ffd576556c8b7c16 Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Sun, 11 Dec 2022 01:00:02 +0100 Subject: [PATCH 232/790] gnu: hw-probe: Update to 1.6.5. * gnu/packages/hardware.scm (hw-probe): Update to 1.6.5. [inputs]: Add edac-utils. --- gnu/packages/hardware.scm | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/gnu/packages/hardware.scm b/gnu/packages/hardware.scm index 1b8ba9bc43..f73896460b 100644 --- a/gnu/packages/hardware.scm +++ b/gnu/packages/hardware.scm @@ -135,7 +135,7 @@ sets, and tools to deal with register databases.") (define-public hw-probe (package (name "hw-probe") - (version "1.6.4") + (version "1.6.5") (source (origin (method git-fetch) @@ -145,7 +145,7 @@ sets, and tools to deal with register databases.") (commit version))) (file-name (git-file-name name version)) (sha256 - (base32 "028wnhrbn10lfxwmcpzdbz67ygldimv7z1k1bm64ggclykvg5aim")))) + (base32 "1sbp0scdi54zwgvb1s3ki3cw8xnxaxzm5cicq2nn3a2b6n1d4ljs")))) (build-system perl-build-system) (arguments (list @@ -264,6 +264,7 @@ sets, and tools to deal with register databases.") ddcutil dmidecode dpkg + edac-utils edid-decode efibootmgr efivar From 1cec2b9aa524e6312dbf97d44a6d914e1fc70091 Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Sun, 11 Dec 2022 01:00:01 +0100 Subject: [PATCH 233/790] gnu: ne: Update to 3.3.2. * gnu/packages/text-editors.scm (ne): Update to 3.3.2. [arguments]: Disable parallel builds. --- gnu/packages/text-editors.scm | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/gnu/packages/text-editors.scm b/gnu/packages/text-editors.scm index a95cf37011..854a424b8a 100644 --- a/gnu/packages/text-editors.scm +++ b/gnu/packages/text-editors.scm @@ -1148,7 +1148,7 @@ card. It offers: (define-public ne (package (name "ne") - (version "3.3.1") + (version "3.3.2") (source (origin (method git-fetch) (uri (git-reference @@ -1157,7 +1157,7 @@ card. It offers: (file-name (git-file-name name version)) (sha256 (base32 - "0sg2f6lxq6cjkpd3dvlxxns82hvq826rjnams5in97pssmknr77g")))) + "16hzja0x41xz6028d8qij9rh1vkiil8qkswd8yznwlcwyl4h04wr")))) (build-system gnu-build-system) (native-inputs (list perl texinfo)) @@ -1165,6 +1165,7 @@ card. It offers: (list ncurses)) (arguments `(#:tests? #f + #:parallel-build? #f ; or enums.h may not yet be generated #:make-flags (list "STRIP=true" ; don't (string-append "CC=" ,(cc-for-target)) From 142a938afd48f1d4fa407a7d800bb52994ba361f Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Sun, 11 Dec 2022 01:00:02 +0100 Subject: [PATCH 234/790] gnu: oil: Update to 0.12.9. * gnu/packages/shells.scm (oil): Update to 0.12.9. --- gnu/packages/shells.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/shells.scm b/gnu/packages/shells.scm index 7cb57ed7ae..128e557a21 100644 --- a/gnu/packages/shells.scm +++ b/gnu/packages/shells.scm @@ -848,7 +848,7 @@ Shell (pdksh).") (define-public oil (package (name "oil") - (version "0.12.7") + (version "0.12.9") (source ;; oil's sources contain a modified version of CPython 2.7.13. ;; According to https://www.oilshell.org/blog/2017/05/05.html @@ -861,7 +861,7 @@ Shell (pdksh).") (uri (string-append "https://www.oilshell.org/download/oil-" version ".tar.gz")) (sha256 - (base32 "02p8w2rpwb8i4lwl2ah5whchn0lihc6hgbmnp0yr0jv4f0r3mgby")))) + (base32 "047gjar5lkbms4gdp3063njnqc6fl6p0dcx8bbpi1cdn1956yh1s")))) (build-system gnu-build-system) (arguments (list #:strip-binaries? #f ; strip breaks the binary From a44ca60684b2dd91907a09063ecc72571c3600d3 Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Sun, 11 Dec 2022 01:00:01 +0100 Subject: [PATCH 235/790] gnu: eid-mw: Update to 5.1.8. * gnu/packages/security-token.scm (eid-mw): Update to 5.1.8. --- gnu/packages/security-token.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/security-token.scm b/gnu/packages/security-token.scm index 16099a4da7..619be42305 100644 --- a/gnu/packages/security-token.scm +++ b/gnu/packages/security-token.scm @@ -121,7 +121,7 @@ readers and is needed to communicate with such devices through the (define-public eid-mw (package (name "eid-mw") - (version "5.1.6") + (version "5.1.8") (source (origin (method git-fetch) @@ -130,7 +130,7 @@ readers and is needed to communicate with such devices through the (commit (string-append "v" version)))) (file-name (git-file-name name version)) (sha256 - (base32 "19sq9bs1580zrjw0cxykdvrm1rwfw8n0vbvy9kdjnykjjnb7g6g1")))) + (base32 "11jf828ag8y5iykcfjmjc3n8g5mchpl3fxkr110civ3qqbdiw882")))) (build-system glib-or-gtk-build-system) (native-inputs (list autoconf From ed2b7c854d5a2ffb7bd0afc1be80ff85756bda86 Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Sun, 11 Dec 2022 01:00:03 +0100 Subject: [PATCH 236/790] gnu: pdfarranger: Update to 1.9.2. * gnu/packages/pdf.scm (pdfarranger): Update to 1.9.2. --- gnu/packages/pdf.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/pdf.scm b/gnu/packages/pdf.scm index 727fc20f36..19e10649f3 100644 --- a/gnu/packages/pdf.scm +++ b/gnu/packages/pdf.scm @@ -1276,7 +1276,7 @@ manage or manipulate PDFs.") (define-public pdfarranger (package (name "pdfarranger") - (version "1.9.1") + (version "1.9.2") (source (origin (method git-fetch) @@ -1285,7 +1285,7 @@ manage or manipulate PDFs.") (commit version))) (file-name (git-file-name name version)) (sha256 - (base32 "1s0ysg8kfbrvwcr80vrsx7150ixa9v7pb4xm49s97nkiq5k69hal")))) + (base32 "1zj1fdaqih9d878yxy96ivgqyg4j31slvh2gqsyz2l2vj3s8z54x")))) (build-system python-build-system) (arguments (list From d33dec8976714b5e1e8dd970680c8756387b0cdd Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Sun, 11 Dec 2022 01:00:01 +0100 Subject: [PATCH 237/790] gnu: hwdata: Update to 0.365. * gnu/packages/pciutils.scm (hwdata): Update to 0.365. --- gnu/packages/pciutils.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/pciutils.scm b/gnu/packages/pciutils.scm index 91e3fad33b..ec6bb76d5d 100644 --- a/gnu/packages/pciutils.scm +++ b/gnu/packages/pciutils.scm @@ -39,7 +39,7 @@ (define-public hwdata (package (name "hwdata") - (version "0.357") ;updated monthly + (version "0.365") ;updated monthly (source (origin (method git-fetch) (uri (git-reference @@ -48,7 +48,7 @@ (file-name (git-file-name name version)) (sha256 (base32 - "0kvxpdx14w2myqm3dikjvr2mr4j6767y4v5j8v7kffwvcv0ga9gv")))) + "00gqx24dyy9l98ygnvx8i087xq8pl9d2393h4d2cm4d5nnvr51d4")))) (build-system gnu-build-system) (outputs '("out" "iab" "oui" "pci" "pnp" "usb")) (arguments From 8c5b49cd26209a1f2a03275c6d4672f368b63a8c Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Sun, 11 Dec 2022 01:00:01 +0100 Subject: [PATCH 238/790] gnu: exfatprogs: Update to 1.2.0. * gnu/packages/file-systems.scm (exfatprogs): Update to 1.2.0. --- gnu/packages/file-systems.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/file-systems.scm b/gnu/packages/file-systems.scm index 4b1c1cebe8..85454cada3 100644 --- a/gnu/packages/file-systems.scm +++ b/gnu/packages/file-systems.scm @@ -599,7 +599,7 @@ from the bcachefs-tools package. It is meant to be used in initrds.") (define-public exfatprogs (package (name "exfatprogs") - (version "1.1.3") + (version "1.2.0") (source (origin (method git-fetch) @@ -608,7 +608,7 @@ from the bcachefs-tools package. It is meant to be used in initrds.") (commit version))) (file-name (git-file-name name version)) (sha256 - (base32 "14lgwvbg6jibsdpzpcj484p9q4ixawyjxi9hw23w89c6870gglw9")))) + (base32 "02a6178brikg12wl80h9qgxyhpm6mly0jnml0rs9phb7lkbv9kzh")))) (build-system gnu-build-system) (arguments `(#:configure-flags From a35ca7148481d0308ed75bf9206e5c0ecf132f62 Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Sun, 11 Dec 2022 01:00:01 +0100 Subject: [PATCH 239/790] gnu: python-pylibmc: Update to 1.6.3. * gnu/packages/databases.scm (python-pylibmc): Update to 1.6.3. [native-inputs]: Replace python-nose with python-pytest. --- gnu/packages/databases.scm | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/gnu/packages/databases.scm b/gnu/packages/databases.scm index 81a2581c0c..504d6ff5f8 100644 --- a/gnu/packages/databases.scm +++ b/gnu/packages/databases.scm @@ -577,13 +577,13 @@ the API, and provides features such as: (define-public python-pylibmc (package (name "python-pylibmc") - (version "1.6.1") + (version "1.6.3") (source (origin (method url-fetch) (uri (pypi-uri "pylibmc" version)) (sha256 - (base32 "1sg7d9j0v6g3xg3finf4l1hb72c13vcyyi6rqrc9shbx903d93ca")))) + (base32 "1q06696lxpqn155sydg3z6dksimks6n35q72zdjsvarpal8ldypf")))) (build-system python-build-system) (arguments '(#:phases @@ -593,7 +593,7 @@ the API, and provides features such as: (lambda _ (invoke "memcached" "-d")))))) (native-inputs - (list memcached python-nose)) + (list memcached python-pytest)) (inputs (list libmemcached zlib cyrus-sasl)) (home-page "http://sendapatch.se/projects/pylibmc/") From dcbd6461399835ab4bbbe6f040f8d500b31b1e7f Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Sun, 11 Dec 2022 01:00:01 +0100 Subject: [PATCH 240/790] gnu: python-psycopg2: Update to 2.9.5. * gnu/packages/databases.scm (python-psycopg2): Update to 2.9.5. --- gnu/packages/databases.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/databases.scm b/gnu/packages/databases.scm index 504d6ff5f8..37ecc7ea81 100644 --- a/gnu/packages/databases.scm +++ b/gnu/packages/databases.scm @@ -3686,13 +3686,13 @@ managers for automatically closing connections.") (define-public python-psycopg2 (package (name "python-psycopg2") - (version "2.9.3") + (version "2.9.5") (source (origin (method url-fetch) (uri (pypi-uri "psycopg2" version)) (sha256 - (base32 "1099as8ind9kpz30rmqzc3nir668fmpkxwayrj2sjka3ycdiv14f")))) + (base32 "0ni4kq6p7hbkm2qsky998q36q5gq5if4nwd8hwhjx5rsd0p6s955")))) (build-system python-build-system) (arguments ;; Tests would require a postgresql database "psycopg2_test" From daaaa4ba03b50cddd220a46d855b68e8147e271f Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Sun, 11 Dec 2022 01:00:01 +0100 Subject: [PATCH 241/790] gnu: python-rq: Update to 1.11.1. * gnu/packages/databases.scm (python-rq): Update to 1.11.1. --- gnu/packages/databases.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/databases.scm b/gnu/packages/databases.scm index 37ecc7ea81..fc2146516e 100644 --- a/gnu/packages/databases.scm +++ b/gnu/packages/databases.scm @@ -4008,7 +4008,7 @@ reasonable substitute.") (define-public python-rq (package (name "python-rq") - (version "1.11") + (version "1.11.1") (source (origin (method git-fetch) @@ -4017,7 +4017,7 @@ reasonable substitute.") (commit (string-append "v" version)))) (file-name (git-file-name name version)) (sha256 - (base32 "1dj3m8dh9vf1qiq1drjhfw5xbr975v1kpzn4fwja83cfd7jrpzvy")))) + (base32 "0dnjm2s036l4j4ypq0h903vh132dp2wiwjrn8jicz1nw829dqpzf")))) (build-system python-build-system) (arguments '(#:phases (modify-phases %standard-phases From 02ddd4410d795b75626c112ae6b60ed70978d9f3 Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Sun, 11 Dec 2022 01:00:00 +0100 Subject: [PATCH 242/790] gnu: python-sqlparse: Update to 0.4.3. * gnu/packages/databases.scm (python-sqlparse): Update to 0.4.3. --- gnu/packages/databases.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/databases.scm b/gnu/packages/databases.scm index fc2146516e..cc8f6eac2a 100644 --- a/gnu/packages/databases.scm +++ b/gnu/packages/databases.scm @@ -4105,13 +4105,13 @@ is designed to have a low barrier to entry.") (define-public python-sqlparse (package (name "python-sqlparse") - (version "0.4.2") + (version "0.4.3") (source (origin (method url-fetch) (uri (pypi-uri "sqlparse" version)) (sha256 (base32 - "1bkx52c2jh28c528b69qfk2ijfzw1laxx6lim7jr8fi6fh67600c")))) + "0s3jyllg0ka0n7pgqfng1hzvh39li853dr40qcp4s4dv8r481jk9")))) (build-system python-build-system) (arguments `(#:phases From 417ccba3bb689eb0bc9403dca5024c5b89c4f567 Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Sun, 11 Dec 2022 01:00:00 +0100 Subject: [PATCH 243/790] gnu: python-sqlalchemy-utils: Update to 0.38.3. * gnu/packages/databases.scm (python-sqlalchemy-utils): Update to 0.38.3. --- gnu/packages/databases.scm | 5 ++--- 1 file changed, 2 insertions(+), 3 deletions(-) diff --git a/gnu/packages/databases.scm b/gnu/packages/databases.scm index cc8f6eac2a..a76e034306 100644 --- a/gnu/packages/databases.scm +++ b/gnu/packages/databases.scm @@ -3452,14 +3452,13 @@ framework.") (define-public python-sqlalchemy-utils (package (name "python-sqlalchemy-utils") - (version "0.38.2") + (version "0.38.3") (source (origin (method url-fetch) (uri (pypi-uri "SQLAlchemy-Utils" version)) (sha256 - (base32 - "1d6fq81489kqzxmk3l6f39sinw206lzs392frmpr5lsjzg9xc0cy")))) + (base32 "0k8z0mjhvdv302kn0nhci8b2dgw4cn2akprsf37ma1540ykgp6lz")))) (build-system python-build-system) (arguments '(#:tests? #f)) ; FIXME: Many tests require a running database server. From 25ffb738b5cd1a31a7f83d4e947e1e8be0fc3e99 Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Sun, 11 Dec 2022 01:00:01 +0100 Subject: [PATCH 244/790] gnu: python-asyncmy: Update to 0.2.5. * gnu/packages/databases.scm (python-asyncmy): Update to 0.2.5. --- gnu/packages/databases.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/databases.scm b/gnu/packages/databases.scm index a76e034306..a5479363f2 100644 --- a/gnu/packages/databases.scm +++ b/gnu/packages/databases.scm @@ -2986,13 +2986,13 @@ with Python's asyncio framework.") (define-public python-asyncmy (package (name "python-asyncmy") - (version "0.2.3") + (version "0.2.5") (source (origin (method url-fetch) (uri (pypi-uri "asyncmy" version)) (sha256 - (base32 "19p81jd4w7m7v2x1jdrwibp67wzqx1a7rdw5n4qqmch3iffp97vn")))) + (base32 "0i18zxy6xvzv6dk791xifn2sw2q4zvqwpzrzy8qx51d3mp8z6gng")))) (build-system python-build-system) (native-inputs (list python-cython)) (home-page "https://github.com/long2ice/asyncmy") From 0cf2cb51b9b932857932e43a23348cb2f4d5e255 Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Sun, 11 Dec 2022 01:00:00 +0100 Subject: [PATCH 245/790] gnu: python-pyodbc: Update to 4.0.35. * gnu/packages/databases.scm (python-pyodbc): Update to 4.0.35. --- gnu/packages/databases.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/databases.scm b/gnu/packages/databases.scm index a5479363f2..387755b8ec 100644 --- a/gnu/packages/databases.scm +++ b/gnu/packages/databases.scm @@ -3138,13 +3138,13 @@ or languages. It uses only Python's built-in data types.") (define-public python-pyodbc (package (name "python-pyodbc") - (version "4.0.32") + (version "4.0.35") (source (origin (method url-fetch) (uri (pypi-uri "pyodbc" version)) (sha256 - (base32 "0sqs0x2l5mk3yv0wwz3ya8yh5f4babihyhc8hjbf2m86b71z1rcv")) + (base32 "1j7577acd2f16zifw49ajg0aw7vm0pdg6jxrr1dlaa5rx14azfcj")) (modules '((guix build utils))) (snippet ;; Delete precompiled binaries. The corresponding source is included. From 3ad8bcae5db82ccbb44b70902f70d6a0e78d328b Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Sun, 11 Dec 2022 01:00:01 +0100 Subject: [PATCH 246/790] gnu: plfit: Update to 0.9.4. * gnu/packages/graph.scm (plfit): Update to 0.9.4. --- gnu/packages/graph.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/graph.scm b/gnu/packages/graph.scm index 02c80f0682..52c63c8654 100644 --- a/gnu/packages/graph.scm +++ b/gnu/packages/graph.scm @@ -67,7 +67,7 @@ (define-public plfit (package (name "plfit") - (version "0.9.3") + (version "0.9.4") (source (origin (method git-fetch) (uri (git-reference @@ -76,7 +76,7 @@ (file-name (git-file-name name version)) (sha256 (base32 - "03x5jbvg8vwr92682swy58ljxrhqwmga1xzd0cpfbfmda41gm2fb")))) + "042b60cnsz5wy27sz026xs0mnn9p58j46crgs78skncgkvzqyyc6")))) (build-system cmake-build-system) (arguments '(#:configure-flags (list "-DBUILD_SHARED_LIBS=ON"))) From 21b322a05ee064c98e558b3f5a5afcba3fa057cf Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Sun, 11 Dec 2022 01:00:01 +0100 Subject: [PATCH 247/790] gnu: dpkg: Update to 1.21.12. * gnu/packages/debian.scm (dpkg): Update to 1.21.12. --- gnu/packages/debian.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/debian.scm b/gnu/packages/debian.scm index 67b66be38d..4319d3a518 100644 --- a/gnu/packages/debian.scm +++ b/gnu/packages/debian.scm @@ -339,7 +339,7 @@ distributions such as Debian and Trisquel.") (define-public dpkg (package (name "dpkg") - (version "1.21.8") + (version "1.21.12") (source (origin (method git-fetch) @@ -348,7 +348,7 @@ distributions such as Debian and Trisquel.") (commit version))) (file-name (git-file-name name version)) (sha256 - (base32 "1whb78pywdlm4v1ablgvvplqjn15b6qrwqkj0pihw5j77aakyz2s")))) + (base32 "08a72lhkgz4iiimdkqlmf58m31zrwqcs0741nbxxq1x3s9phc25m")))) (build-system gnu-build-system) (arguments `(#:phases From ad3df339b4858ac7d45ba1086b47a8d37bb85e34 Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Sun, 11 Dec 2022 01:00:02 +0100 Subject: [PATCH 248/790] gnu: reprotest: Update to 0.7.22. * gnu/packages/diffoscope.scm (reprotest): Update to 0.7.22. [arguments]: Don't explicitly return #t from phases. --- gnu/packages/diffoscope.scm | 8 +++----- 1 file changed, 3 insertions(+), 5 deletions(-) diff --git a/gnu/packages/diffoscope.scm b/gnu/packages/diffoscope.scm index f05f60f016..f730d976fe 100644 --- a/gnu/packages/diffoscope.scm +++ b/gnu/packages/diffoscope.scm @@ -245,7 +245,7 @@ install.") (define-public reprotest (package (name "reprotest") - (version "0.7.21") + (version "0.7.22") (source (origin (method git-fetch) @@ -254,8 +254,7 @@ install.") (commit version))) (file-name (git-file-name name version)) (sha256 - (base32 - "1jmnp6dwd91w00vfvph89cvgxwk0nvij8his9az5b72265jf9bxz")))) + (base32 "0qpjg37x2ha7lb113fb5cic5if3zv30zqijsmkq91ld909x30ggd")))) (inputs (list python-debian python-distro python-libarchive-c python-rstr)) (native-inputs @@ -296,8 +295,7 @@ install.") (install-file "doc/reprotest.1" mandir1) (mkdir-p docdir) (install-file "./README.rst" docdir) - (install-file "./README-dev.rst" docdir)) - #t))))) + (install-file "./README-dev.rst" docdir))))))) (home-page "https://salsa.debian.org/reproducible-builds/reprotest") (synopsis "Build software and check it for reproducibility") (description "Reprotest builds the same source code twice in different From a39034cdbdfae1b662b0530c23a1daca48c6d74b Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Sun, 11 Dec 2022 01:00:01 +0100 Subject: [PATCH 249/790] gnu: dnsmasq: Update to 2.88. * gnu/packages/dns.scm (dnsmasq): Update to 2.88. --- gnu/packages/dns.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/dns.scm b/gnu/packages/dns.scm index 4f25147d00..a34d5cbdd1 100644 --- a/gnu/packages/dns.scm +++ b/gnu/packages/dns.scm @@ -290,7 +290,7 @@ prompt the user with the option to go with insecure DNS only.") (define-public dnsmasq (package (name "dnsmasq") - (version "2.87") + (version "2.88") (source (origin (method url-fetch) (uri (string-append @@ -298,7 +298,7 @@ prompt the user with the option to go with insecure DNS only.") version ".tar.xz")) (sha256 (base32 - "0ynyi4mixhxhbfxb2bivinkrjc5zgj9lj5bzgvymc8vz98vc0a02")))) + "1cy1zci6vyhzczy6ncc5m9d7zsnnzs9mmwd6pr9w0h03l7nlsm13")))) (build-system gnu-build-system) (native-inputs (list pkg-config)) From 269dcdd304008543c43c62997626afe2536cf4c8 Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Sun, 11 Dec 2022 01:00:00 +0100 Subject: [PATCH 250/790] gnu: nsd: Update to 4.6.1. * gnu/packages/dns.scm (nsd): Update to 4.6.1. --- gnu/packages/dns.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/dns.scm b/gnu/packages/dns.scm index a34d5cbdd1..e4aa1f242a 100644 --- a/gnu/packages/dns.scm +++ b/gnu/packages/dns.scm @@ -544,14 +544,14 @@ asynchronous fashion.") (define-public nsd (package (name "nsd") - (version "4.4.0") + (version "4.6.1") (source (origin (method url-fetch) (uri (string-append "https://www.nlnetlabs.nl/downloads/nsd/nsd-" version ".tar.gz")) (sha256 - (base32 "0dl8iriy0mscppfa6ar5qcglgvxw87140abwxyksak1lk7fnzkfg")))) + (base32 "0ym2fgkjar94y99lyvp93p7jpj33ysprvqd7py28xxn37shs6q1z")))) (build-system gnu-build-system) (arguments `(#:configure-flags From ceeef9a923065d3f0ae45535112b9055223d59ca Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Sun, 11 Dec 2022 01:00:01 +0100 Subject: [PATCH 251/790] gnu: alembic: Update to 1.8.4. * gnu/packages/graphics.scm (alembic): Update to 1.8.4. --- gnu/packages/graphics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/graphics.scm b/gnu/packages/graphics.scm index 4642dfbe36..0132f4fe66 100644 --- a/gnu/packages/graphics.scm +++ b/gnu/packages/graphics.scm @@ -957,7 +957,7 @@ other vector formats such as: (define-public alembic (package (name "alembic") - (version "1.8.3") + (version "1.8.4") (source (origin (method git-fetch) @@ -966,7 +966,7 @@ other vector formats such as: (commit version))) (file-name (git-file-name name version)) (sha256 - (base32 "0glfx3cm7r8zn3cn7j4x4ch1ab6igfis0i2lcy23jc56q87r8yj2")))) + (base32 "04cvzr87zqx55si4j3dqiidbmfx92ja3mc1dj0v6ddvl0cwj3m7i")))) (build-system cmake-build-system) (arguments `(#:configure-flags (list "-DUSE_HDF5=ON"))) From 43595cfc788ecada54c67944b1fde498e54507f5 Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Sun, 11 Dec 2022 01:00:03 +0100 Subject: [PATCH 252/790] gnu: libofx: Update to 0.10.9. * gnu/packages/finance.scm (libofx): Update to 0.10.9. --- gnu/packages/finance.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/finance.scm b/gnu/packages/finance.scm index 828df0324e..8554a67764 100644 --- a/gnu/packages/finance.scm +++ b/gnu/packages/finance.scm @@ -1645,7 +1645,7 @@ a client based on Qt. This is a fork of Bitcoin Core.") (define-public libofx (package (name "libofx") - (version "0.10.7") + (version "0.10.9") (source (origin (method git-fetch) (uri (git-reference @@ -1654,7 +1654,7 @@ a client based on Qt. This is a fork of Bitcoin Core.") (file-name (git-file-name name version)) (sha256 (base32 - "1k3ygavyb9b3f1ra62dsa46iiia0a1588yn3zy7bh7w4vfcrbd6d")))) + "120hyhs4fkxrgpvd2p0hpf5v8dq0jjql2fzllk77m33m1c82pr18")))) (build-system gnu-build-system) (arguments (list From a78e2675925c93b1bded910880d48379a365675e Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Sun, 11 Dec 2022 01:00:08 +0100 Subject: [PATCH 253/790] gnu: libofx: Don't build static library. * gnu/packages/finance.scm (libofx)[arguments]: Add "--disable-static" to #:configure-flags. --- gnu/packages/finance.scm | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/gnu/packages/finance.scm b/gnu/packages/finance.scm index 8554a67764..f9ee7acaa1 100644 --- a/gnu/packages/finance.scm +++ b/gnu/packages/finance.scm @@ -1660,7 +1660,8 @@ a client based on Qt. This is a fork of Bitcoin Core.") (list #:parallel-build? #f ;fails with -j64 #:configure-flags - #~(list (string-append "--with-opensp-includes=" + #~(list "--disable-static" + (string-append "--with-opensp-includes=" (search-input-directory %build-inputs "include/OpenSP"))))) (native-inputs From d1c3681e38a3ea70d1ce4df1077fba11fb88508b Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Sun, 11 Dec 2022 01:00:00 +0100 Subject: [PATCH 254/790] =?UTF-8?q?gnu:=20olm:=20Drop=20custom=20=E2=80=98?= =?UTF-8?q?lib-=E2=80=99=20prefix.?= MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * gnu/packages/crypto.scm (olm): New variable, renamed from… (libolm): …this one, which is now a DEPRECATED-PACKAGE alias of olm. Adjust all users. [synopsis, description]: Adjust. Capitalise proper nouns. (python-olm)[description]: Remove implementation detail. --- gnu/packages/crypto.scm | 18 ++++++++++-------- gnu/packages/messaging.scm | 6 +++--- 2 files changed, 13 insertions(+), 11 deletions(-) diff --git a/gnu/packages/crypto.scm b/gnu/packages/crypto.scm index cc633cb4bf..791de39368 100644 --- a/gnu/packages/crypto.scm +++ b/gnu/packages/crypto.scm @@ -1293,9 +1293,9 @@ signatures include trusted comments in addition to untrusted comments. Trusted comments are signed, thus verified, before being displayed.") (license license:isc))) -(define-public libolm +(define-public olm (package - (name "libolm") + (name "olm") (version "3.2.12") (source (origin (method git-fetch) @@ -1319,13 +1319,16 @@ Trusted comments are signed, thus verified, before being displayed.") (when tests? (with-directory-excursion "tests" (invoke "ctest" ".")))))))) - (synopsis "Implementation of the olm and megolm cryptographic ratchets") - (description "The libolm library implements the Double Ratchet + (synopsis "Implementation of the Olm and Megolm cryptographic ratchets") + (description "The Olm library implements the Double Ratchet cryptographic ratchet. It is written in C and C++11, and exposed as a C API.") (home-page "https://matrix.org/docs/projects/other/olm/") (license license:asl2.0))) +(define-public libolm + (deprecated-package "libolm" olm)) + (define-public python-olm (package ;; python-olm is part of libolm and must be updated at the same time. @@ -1351,10 +1354,9 @@ API.") (list python-cffi python-future)) (native-inputs (list python-pytest python-pytest-benchmark python-aspectlib)) - (synopsis "Python bindings for libolm") - (description "The libolm library implements the Double Ratchet -cryptographic ratchet. It is written in C and C++11, and exposed as a C -API. This package contains its Python bindings."))) + (synopsis "Python bindings for Olm") + (description "The Olm library implements the Double Ratchet +cryptographic ratchet. This package contains its Python bindings."))) (define-public hash-extender (let ((commit "cb8aaee49f93e9c0d2f03eb3cafb429c9eed723d") diff --git a/gnu/packages/messaging.scm b/gnu/packages/messaging.scm index 8b35480400..27a68439ef 100644 --- a/gnu/packages/messaging.scm +++ b/gnu/packages/messaging.scm @@ -2380,7 +2380,7 @@ QMatrixClient project.") curl json-modern-cxx libevent - libolm + olm libsodium openssl spdlog @@ -2463,7 +2463,7 @@ for the Matrix protocol. It is built on to of @code{Boost.Asio}.") json-modern-cxx libevent libnice ; for voip - libolm + olm lmdb lmdbxx mtxclient @@ -2884,7 +2884,7 @@ validating international phone numbers.") libgcrypt libgee libhandy - libolm + olm libphonenumber modem-manager pidgin From d6df6363d6b8342eefa1bbce62a4aa76d758b460 Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Sun, 11 Dec 2022 01:00:01 +0100 Subject: [PATCH 255/790] gnu: olm: Update to 3.2.14. * gnu/packages/crypto.scm (olm): Update to 3.2.14. --- gnu/packages/crypto.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/crypto.scm b/gnu/packages/crypto.scm index 791de39368..ad31ff8a8b 100644 --- a/gnu/packages/crypto.scm +++ b/gnu/packages/crypto.scm @@ -1296,7 +1296,7 @@ Trusted comments are signed, thus verified, before being displayed.") (define-public olm (package (name "olm") - (version "3.2.12") + (version "3.2.14") (source (origin (method git-fetch) (uri (git-reference @@ -1304,7 +1304,7 @@ Trusted comments are signed, thus verified, before being displayed.") (commit version))) (sha256 (base32 - "1k8v9ig32vmjm58rbris621d7mvp4q91qa5p79vc51p41sz91yhj")) + "0pj7gs32ixhlls792wah7xf49j5pra0avp7dpvy9cndkdkg6biq5")) (file-name (git-file-name name version)) ;; Delete the bundled blob. It's free, but unauditable, ;; and apparently only required for android. From ae60376b3068a61e96dcf3acc2bab4fa2abbfe3d Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Sun, 11 Dec 2022 01:00:01 +0100 Subject: [PATCH 256/790] gnu: assimp: Update to 5.2.5. * gnu/packages/graphics.scm (assimp): Update to 5.2.5. --- gnu/packages/graphics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/graphics.scm b/gnu/packages/graphics.scm index 0132f4fe66..f23fad7c50 100644 --- a/gnu/packages/graphics.scm +++ b/gnu/packages/graphics.scm @@ -570,7 +570,7 @@ and export to various formats including the format used by Magicavoxel.") (define-public assimp (package (name "assimp") - (version "5.2.2") + (version "5.2.5") (source (origin (method git-fetch) (uri (git-reference @@ -579,7 +579,7 @@ and export to various formats including the format used by Magicavoxel.") (file-name (git-file-name name version)) (sha256 (base32 - "1kjifakjnpm89410pw27wq21fn975gfq46kn9zs3h8bryldvvlgk")))) + "0j0pd279n6xyy95x782ha8j75kbx0ck7vs5wv3krhbyfim9bw64l")))) (build-system cmake-build-system) (inputs (list zlib)) From 1febafb4af8dbe8a68ef501d7d28e56e49d172f8 Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Wed, 14 Dec 2022 15:42:12 -0500 Subject: [PATCH 257/790] guix-install.sh: Add missing "useradd" command. * etc/guix-install.sh: (REQUIRE): Add missing "useradd" command. --- etc/guix-install.sh | 1 + 1 file changed, 1 insertion(+) diff --git a/etc/guix-install.sh b/etc/guix-install.sh index f008593d84..b8ea9e54c3 100755 --- a/etc/guix-install.sh +++ b/etc/guix-install.sh @@ -53,6 +53,7 @@ REQUIRE=( "chmod" "uname" "groupadd" + "useradd" "tail" "tr" "xz" From 7ce9b7e7062eee406e269bc40a20247973732be2 Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Wed, 14 Dec 2022 10:35:54 -0500 Subject: [PATCH 258/790] guix-install.sh: Directly exit in case of errors in chk_require. * etc/guix-install.sh (chk_require): Directly exit in case of errors in chk_require, instead of relying on 'set -e'. --- etc/guix-install.sh | 6 ++---- 1 file changed, 2 insertions(+), 4 deletions(-) diff --git a/etc/guix-install.sh b/etc/guix-install.sh index b8ea9e54c3..3ce9affc06 100755 --- a/etc/guix-install.sh +++ b/etc/guix-install.sh @@ -121,10 +121,8 @@ chk_require() command -v "$c" &>/dev/null || warn+=("$c") done - [ "${#warn}" -ne 0 ] && - { _err "${ERR}Missing commands: ${warn[*]}."; - return 1; } - + [ "${#warn}" -ne 0 ] && die "Missing commands: ${warn[*]}." + _msg "${PAS}verification of required commands completed" } From 8548ba5847417eabe14aa08fa9861f91743bd3a1 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Fri, 16 Dec 2022 15:34:31 +0100 Subject: [PATCH 259/790] gnu: Add python-tbb. * gnu/packages/tbb.scm (python-tbb): New variable. --- gnu/packages/tbb.scm | 45 ++++++++++++++++++++++++++++++++++++++++++-- 1 file changed, 43 insertions(+), 2 deletions(-) diff --git a/gnu/packages/tbb.scm b/gnu/packages/tbb.scm index 4ce7c1cf49..f22282264c 100644 --- a/gnu/packages/tbb.scm +++ b/gnu/packages/tbb.scm @@ -1,5 +1,5 @@ ;;; GNU Guix --- Functional package management for GNU -;;; Copyright © 2015, 2016 Ricardo Wurmus +;;; Copyright © 2015, 2016, 2022 Ricardo Wurmus ;;; Copyright © 2016 Nikita ;;; Copyright © 2019 Tobias Geerinckx-Rice ;;; Copyright © 2021 Guillaume Le Vaillant @@ -23,11 +23,14 @@ (define-module (gnu packages tbb) #:use-module (guix packages) #:use-module (guix licenses) + #:use-module (guix gexp) #:use-module (guix git-download) #:use-module (guix utils) #:use-module (guix build-system cmake) #:use-module (guix build-system gnu) - #:use-module (gnu packages)) + #:use-module (gnu packages) + #:use-module (gnu packages python) + #:use-module (gnu packages swig)) (define-public tbb (package @@ -56,6 +59,44 @@ implementation work. It provides parallel loop constructs, asynchronous tasks, synchronization primitives, atomic operations, and more.") (license asl2.0))) +(define-public python-tbb + (package + (inherit tbb) + (name "python-tbb") + (arguments + (list + #:configure-flags + #~(list "-DTBB_STRICT=OFF" + "-DTBB4PY_BUILD=ON") + #:phases + #~(modify-phases %standard-phases + (add-after 'unpack 'patch-python-install-directory + (lambda _ + (substitute* "python/CMakeLists.txt" + (("\\$\\{PYTHON_BUILD_WORK_DIR\\}/build") + #$output)) + (substitute* "python/setup.py" + (("extra_link_args=tbb_flag,") + (string-append "extra_link_args=['-Wl,-rpath=" + #$(this-package-input "tbb") "/lib" + "', '-Wl,-rpath=" #$output "/lib'] + tbb_flag,"))))) + (replace 'build + (lambda _ + (setenv "PYTHONHASHSEED" "0") + (setenv "PYTHONDONTWRITEBYTECODE" "1") + (invoke "make" "python_build"))) + ;; The 'build phase already installs the modules + (replace 'install + (lambda _ + (with-directory-excursion "python/rml" + (invoke "make" "install")))) + (replace 'check + (lambda* (#:key tests? #:allow-other-keys) + (when tests? + (invoke "ctest" "-R" "python_test" "--output-on-failure"))))))) + (inputs (list python tbb)) + (native-inputs (list swig)))) + (define-public tbb-2020 (package (name "tbb") From 587716149913a4c88612884c709c44d3736d5769 Mon Sep 17 00:00:00 2001 From: jgart Date: Wed, 14 Dec 2022 09:04:07 -0600 Subject: [PATCH 260/790] gnu: Add emacs-pydoc. * gnu/packages/emacs-xyz.scm (emacs-pydoc): New variable. Signed-off-by: Nicolas Goaziou --- gnu/packages/emacs-xyz.scm | 41 ++++++++++++++++++++++++++++++++++++++ 1 file changed, 41 insertions(+) diff --git a/gnu/packages/emacs-xyz.scm b/gnu/packages/emacs-xyz.scm index 82d352b191..4a93093cdb 100644 --- a/gnu/packages/emacs-xyz.scm +++ b/gnu/packages/emacs-xyz.scm @@ -196,6 +196,7 @@ #:use-module (gnu packages linux) #:use-module (gnu packages libevent) #:use-module (gnu packages lisp-xyz) + #:use-module (gnu packages lsof) #:use-module (gnu packages lua) #:use-module (gnu packages music) #:use-module (gnu packages version-control) @@ -8637,6 +8638,46 @@ autocomplete style popup menu.") windows Emacs produces, while still keeping them within arm’s reach.") (license license:gpl3+)))) +(define-public emacs-pydoc + ;; https://github.com/statmobile/pydoc/issues/31 + (let ((commit "c8b667e17bfe3e63221f822c5c4d58c8fb4fea90") + (revision "0")) + (package + (name "emacs-pydoc") + (version (git-version "0.2" revision commit)) + (source + (origin + (uri (git-reference + (url "https://github.com/statmobile/pydoc") + (commit commit))) + (method git-fetch) + (sha256 + (base32 "082ar5w28dknaa63mf587vdzr78xlnvh8lbxqq3hk6qa2c72akam")) + (file-name (git-file-name name version)))) + (build-system emacs-build-system) + (arguments + (list + #:phases + #~(modify-phases %standard-phases + (add-after 'unpack 'patch-python-executable + (lambda* (#:key outputs #:allow-other-keys) + (emacs-substitute-variables "pydoc.el" + ("pydoc-python-command" + (search-input-file outputs "bin/python"))))) + (add-after 'unpack 'patch-lsof-executable + (lambda* (#:key inputs #:allow-other-keys) + (substitute* "pydoc.el" + (("\"lsof") + ;; Replace removed double quote in parsing of lsof executable. + (string-append "\"" (search-input-file inputs "bin/lsof"))))))))) + (inputs (list lsof python-wrapper)) + (propagated-inputs (list python-jedi)) + (home-page "https://github.com/statmobile/pydoc") + (synopsis "Navigate Python documentation in Emacs") + (description "This package provides an Emacs mode for navigating +Python documentation with @code{pydoc} in Emacs.") + (license license:gpl3+)))) + (define-public emacs-python-black (package (name "emacs-python-black") From ba48c89ab96044ff60b8ed2310dc08cc84409c29 Mon Sep 17 00:00:00 2001 From: jgart Date: Fri, 16 Dec 2022 00:09:19 -0600 Subject: [PATCH 261/790] gnu: Add emacs-eglot-tempel. * gnu/packages/emacs-xyz.scm (emacs-eglot-tempel): New variable. Signed-off-by: Nicolas Goaziou --- gnu/packages/emacs-xyz.scm | 23 +++++++++++++++++++++++ 1 file changed, 23 insertions(+) diff --git a/gnu/packages/emacs-xyz.scm b/gnu/packages/emacs-xyz.scm index 4a93093cdb..839668e848 100644 --- a/gnu/packages/emacs-xyz.scm +++ b/gnu/packages/emacs-xyz.scm @@ -10234,6 +10234,29 @@ provides a front-end interface for the workspace/symbols LSP procedure call.") (license license:gpl3+))) +(define-public emacs-eglot-tempel + (let ((commit "e08b203d6a7c495d4b91ed4537506b5f1ea8a84f") + (revision "0")) + (package + (name "emacs-eglot-tempel") + (version (git-version "0.1" revision commit)) + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/fejfighter/eglot-tempel") + (commit commit))) + (file-name (git-file-name name version)) + (sha256 + (base32 "0f4m0bb1f91x9jqfc0ny95a3pfh1mzzjzdjpa6f548hynq8j34ib")))) + (build-system emacs-build-system) + (propagated-inputs (list emacs-eglot emacs-tempel)) + (home-page "https://github.com/fejfighter/eglot-tempel") + (synopsis "Bridge for Tempel templates with Eglot") + (description "This package is an adapter to use the Tempel templating +library with Eglot instead of Yasnippet.") + (license license:gpl3+)))) + (define-public emacs-consult-yasnippet (let ((commit "ae0450889484f23dc4ec37518852a2c61b89f184") (revision "0")) From 48a2f54dc20d4cabfede18fda4fa5267ea618725 Mon Sep 17 00:00:00 2001 From: Nicolas Goaziou Date: Fri, 16 Dec 2022 18:06:16 +0100 Subject: [PATCH 262/790] gnu: emacs-eglot-tempel: Run tests. * gnu/packages/emacs-xyz.scm (emacs-eglot-tempel)[arguments]: Run tests. [native-inputs]: Add EMACS-ERT-RUNNER. --- gnu/packages/emacs-xyz.scm | 7 +++++++ 1 file changed, 7 insertions(+) diff --git a/gnu/packages/emacs-xyz.scm b/gnu/packages/emacs-xyz.scm index 839668e848..455317b15d 100644 --- a/gnu/packages/emacs-xyz.scm +++ b/gnu/packages/emacs-xyz.scm @@ -10250,6 +10250,13 @@ call.") (sha256 (base32 "0f4m0bb1f91x9jqfc0ny95a3pfh1mzzjzdjpa6f548hynq8j34ib")))) (build-system emacs-build-system) + (arguments + (list + #:tests? #true + #:test-command #~(list "emacs" "-Q" "-batch" + "-l" "eglot-tempel-tests.el" + "-f" "ert-run-tests-batch-and-exit"))) + (native-inputs (list emacs-ert-runner)) (propagated-inputs (list emacs-eglot emacs-tempel)) (home-page "https://github.com/fejfighter/eglot-tempel") (synopsis "Bridge for Tempel templates with Eglot") From b770ecb57e06b3db5c05773b9125afd61f291a40 Mon Sep 17 00:00:00 2001 From: Joeke Date: Fri, 16 Dec 2022 14:05:43 +0100 Subject: [PATCH 263/790] gnu: Add emacs-islisp-mode. * gnu/packages/emacs-xyz.scm (emacs-islisp-mode): New variable. Signed-off-by: Nicolas Goaziou --- gnu/packages/emacs-xyz.scm | 50 ++++++++++++++++++++++++++++++++++++++ 1 file changed, 50 insertions(+) diff --git a/gnu/packages/emacs-xyz.scm b/gnu/packages/emacs-xyz.scm index 455317b15d..9069b452ea 100644 --- a/gnu/packages/emacs-xyz.scm +++ b/gnu/packages/emacs-xyz.scm @@ -118,6 +118,7 @@ ;;; Copyright © 2022 Hilton Chain ;;; Copyright © 2022 Nicolas Graves ;;; Copyright © 2022 Thiago Jung Bauermann +;;; Copyright © 2022 Joeke de Graaf ;;; ;;; This file is part of GNU Guix. ;;; @@ -195,6 +196,7 @@ #:use-module (gnu packages image) #:use-module (gnu packages linux) #:use-module (gnu packages libevent) + #:use-module (gnu packages lisp) #:use-module (gnu packages lisp-xyz) #:use-module (gnu packages lsof) #:use-module (gnu packages lua) @@ -13253,6 +13255,54 @@ you a @code{helm} selection of directory Makefile's targets. Selecting a target will call @code{compile} on it.") (license license:gpl3+)))) +(define-public emacs-islisp-mode + (package + (name "emacs-islisp-mode") + (version "0.3.1") + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://gitlab.com/sasanidas/islisp-mode") + (commit version))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "1s6alrv1hfi1plj5lh826j0h71xvm2v092kglj3yvy34g73dgrna")))) + (build-system emacs-build-system) + (arguments + (list + #:include #~(cons "\\.lsp$" %default-include) + #:phases + #~(modify-phases %standard-phases + ;; Move the extensions source files to the top level, which is + ;; included in the EMACSLOADPATH. + (add-after 'unpack 'move-source-files + (lambda _ + (for-each (lambda (dir) + (let ((files (find-files dir "\\.(lsp|el)$"))) + (for-each (lambda (f) + (rename-file f (basename f))) + files))) + '("advance" "implementations/easy-islisp")))) + (add-after 'move-source-files 'patch-eisl-variables + (lambda* (#:key inputs #:allow-other-keys) + (emacs-substitute-variables "easy-islisp.el" + ("easy-islisp-executable" + (search-input-file inputs "/bin/eisl")) + ("easy-islisp-library-directory" + `(or (getenv "EASY_ISLISP") + ,(search-input-directory inputs "share/eisl/library"))))))))) + (inputs (list eisl)) + (home-page "https://gitlab.com/sasanidas/islisp-mode") + (synopsis "ISLisp support for Emacs") + (description + "This package provides support for programming with ISLisp in Emacs. It +features a major mode with syntax highlighting, symbol autocompletion and +documentation search, among other features. It also includes an inferior mode +with REPL integration. Currently it only supports the Easy ISLisp (eisl) +implementation.") + (license license:gpl3+))) + (define-public emacs-cider (package (name "emacs-cider") From 6887a645931e7332983747b1c75fd56ea6aff5c9 Mon Sep 17 00:00:00 2001 From: Nicolas Goaziou Date: Fri, 16 Dec 2022 18:24:52 +0100 Subject: [PATCH 264/790] gnu: emacs-islisp-mode: Run tests. * gnu/packages/emacs-xyz.scm (emacs-islisp-mode)[arguments]: Run tests. [native-inputs]: Add EMACS-ERT-RUNNER. --- gnu/packages/emacs-xyz.scm | 3 +++ 1 file changed, 3 insertions(+) diff --git a/gnu/packages/emacs-xyz.scm b/gnu/packages/emacs-xyz.scm index 9069b452ea..5dd275b7b2 100644 --- a/gnu/packages/emacs-xyz.scm +++ b/gnu/packages/emacs-xyz.scm @@ -13272,6 +13272,8 @@ target will call @code{compile} on it.") (arguments (list #:include #~(cons "\\.lsp$" %default-include) + #:tests? #true + #:test-command #~(list "ert-runner") #:phases #~(modify-phases %standard-phases ;; Move the extensions source files to the top level, which is @@ -13292,6 +13294,7 @@ target will call @code{compile} on it.") ("easy-islisp-library-directory" `(or (getenv "EASY_ISLISP") ,(search-input-directory inputs "share/eisl/library"))))))))) + (native-inputs (list emacs-ert-runner)) (inputs (list eisl)) (home-page "https://gitlab.com/sasanidas/islisp-mode") (synopsis "ISLisp support for Emacs") From 59eb7d8bc120185a3f91929f207a274314b90fe3 Mon Sep 17 00:00:00 2001 From: Nicolas Goaziou Date: Fri, 16 Dec 2022 18:28:32 +0100 Subject: [PATCH 265/790] gnu: emacs-posframe: Update to 1.3.1. * gnu/packages/emacs-xyz.scm (emacs-posframe): Update to 1.3.1. --- gnu/packages/emacs-xyz.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/emacs-xyz.scm b/gnu/packages/emacs-xyz.scm index 5dd275b7b2..dc5503ba57 100644 --- a/gnu/packages/emacs-xyz.scm +++ b/gnu/packages/emacs-xyz.scm @@ -16464,14 +16464,14 @@ the center of the screen and not at the bottom.") (define-public emacs-posframe (package (name "emacs-posframe") - (version "1.3.0") + (version "1.3.1") (source (origin (method url-fetch) (uri (string-append "https://elpa.gnu.org/packages/" "posframe-" version ".tar")) (sha256 - (base32 "1w6hrxrnbh7c96n4am7igrxxy7w3xfcpqv3df13hd0cn6mh826ab")))) + (base32 "0j5nchfpbrf9fsr82lnvhnq6vi33gv3glsbqn18knnby8m7sxzci")))) (build-system emacs-build-system) ;; emacs-minimal does not include the function font-info. (arguments From fb9ddff29ebafc13389c9a2975006b42748fc580 Mon Sep 17 00:00:00 2001 From: Nicolas Goaziou Date: Fri, 16 Dec 2022 18:29:44 +0100 Subject: [PATCH 266/790] gnu: emacs-denote: Update to 1.2.0. * gnu/packages/emacs-xyz.scm (emacs-denote): Update to 1.2.0. --- gnu/packages/emacs-xyz.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/emacs-xyz.scm b/gnu/packages/emacs-xyz.scm index dc5503ba57..b2d14ad5b8 100644 --- a/gnu/packages/emacs-xyz.scm +++ b/gnu/packages/emacs-xyz.scm @@ -14922,7 +14922,7 @@ you to deal with multiple log levels.") (define-public emacs-denote (package (name "emacs-denote") - (version "1.1.0") + (version "1.2.0") (source (origin (method git-fetch) @@ -14931,7 +14931,7 @@ you to deal with multiple log levels.") (commit version))) (file-name (git-file-name name version)) (sha256 - (base32 "05ckjx1a2cydp46pd8y36safhj95pqi6lm4vs0vr6q3a858bxf8b")))) + (base32 "0cglzccbqpcppb9s3phhszskkxp2wd0582jv85qhawxabfzyzkj3")))) (build-system emacs-build-system) (native-inputs (list texinfo)) (home-page "https://protesilaos.com/emacs/denote/") From c193b5203b31246a6d74270c8086c45851561947 Mon Sep 17 00:00:00 2001 From: Nicolas Goaziou Date: Fri, 16 Dec 2022 18:32:49 +0100 Subject: [PATCH 267/790] gnu: emacs-prescient: Update to 6.1. * gnu/packages/emacs-xyz.scm (emacs-prescient): Update to 6.1. [propagated-inputs]: Add EMACS-CORFU and EMACS-VERTICO. --- gnu/packages/emacs-xyz.scm | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/gnu/packages/emacs-xyz.scm b/gnu/packages/emacs-xyz.scm index b2d14ad5b8..819a7ccdec 100644 --- a/gnu/packages/emacs-xyz.scm +++ b/gnu/packages/emacs-xyz.scm @@ -10015,7 +10015,7 @@ include installing, removing or visiting the homepage.") (define-public emacs-prescient (package (name "emacs-prescient") - (version "6.0") + (version "6.1") (source (origin (method git-fetch) @@ -10024,10 +10024,10 @@ include installing, removing or visiting the homepage.") (commit (string-append "v" version)))) (file-name (git-file-name name version)) (sha256 - (base32 "0156sbs4b535mcwm44qjr8lx48svmjvdqh8c8hr6d0l709f27yq3")))) + (base32 "1mc9pjb80bxcmzaylfwh0sgpvwbx3h35jalznwz464hw3vqfff83")))) (build-system emacs-build-system) (propagated-inputs - (list emacs-company emacs-ivy emacs-selectrum)) + (list emacs-company emacs-corfu emacs-ivy emacs-selectrum emacs-vertico)) (home-page "https://github.com/raxod502/prescient.el/") (synopsis "Emacs library for sorting and filtering candidates") (description From 447015dac267536e3667c9beaab41e52511aecf0 Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Sun, 11 Dec 2022 01:00:02 +0100 Subject: [PATCH 268/790] gnu: hashcat: Update to 6.2.6. * gnu/packages/password-utils.scm (hashcat): Update to 6.2.6. --- gnu/packages/password-utils.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/password-utils.scm b/gnu/packages/password-utils.scm index aab0a3f2a4..410c92d268 100644 --- a/gnu/packages/password-utils.scm +++ b/gnu/packages/password-utils.scm @@ -1252,14 +1252,14 @@ your online accounts makes it necessary.") (define-public hashcat (package (name "hashcat") - (version "6.2.5") + (version "6.2.6") (source (origin (method url-fetch) (uri (string-append "https://hashcat.net/files/hashcat-" version ".tar.gz")) (sha256 (base32 - "0sc96xcsc20xd4fyby3i45nm9as3hl4nhk9snkvmk5l9mpbrjs3g")) + "0akv1cgbmwyw8h8zbw5w5ixh92y95sdadh8qiz60hjgkpivi0pmj")) (modules '((guix build utils))) ;; Delete bundled libraries. (snippet From e7233d38337e257fb3209cd47d3cc7db96cd0ca1 Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Sun, 11 Dec 2022 01:00:01 +0100 Subject: [PATCH 269/790] gnu: libostree: Update to 2022.7. * gnu/packages/package-management.scm (libostree): Update to 2022.7. --- gnu/packages/package-management.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/package-management.scm b/gnu/packages/package-management.scm index 5a09b1fcf8..27a42a0189 100644 --- a/gnu/packages/package-management.scm +++ b/gnu/packages/package-management.scm @@ -1865,7 +1865,7 @@ for packaging and deployment of cross-compiled Windows applications.") (define-public libostree (package (name "libostree") - (version "2022.6") + (version "2022.7") (source (origin (method url-fetch) @@ -1873,7 +1873,7 @@ for packaging and deployment of cross-compiled Windows applications.") "https://github.com/ostreedev/ostree/releases/download/v" (version-major+minor version) "/libostree-" version ".tar.xz")) (sha256 - (base32 "135dzxqzy19a8hkxm25mriy7zf72sbxz1mzzfw6a2d8bk9yz8pl3")))) + (base32 "07s14awf9ynlp84s08dkbwj9i18g93y0yf0k87nbks4l3hkakqlb")))) (build-system gnu-build-system) (arguments '(#:phases From 81f3f31b3c29001d353fdca91e34523e0c2110bd Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Sun, 11 Dec 2022 01:00:00 +0100 Subject: [PATCH 270/790] gnu: direnv: Update to 2.32.2. * gnu/packages/shellutils.scm (direnv): Update to 2.32.2. --- gnu/packages/shellutils.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/shellutils.scm b/gnu/packages/shellutils.scm index 3fd98ecba8..0f7616616e 100644 --- a/gnu/packages/shellutils.scm +++ b/gnu/packages/shellutils.scm @@ -428,7 +428,7 @@ are already there.") (define-public direnv (package (name "direnv") - (version "2.32.1") + (version "2.32.2") (source (origin (method git-fetch) (uri (git-reference @@ -437,7 +437,7 @@ are already there.") (file-name (git-file-name name version)) (sha256 (base32 - "1i473j7j4sx8p83zqlnakskqk0jyd3byajp7jmv2gym9s4k841y7")))) + "17nn4qg1fj4i9rh1gdpbddn2nky71h9dkxyz5a4jsdq25bsx0ps2")))) (build-system go-build-system) (arguments '(#:import-path "github.com/direnv/direnv" From 1752e30f0253cda49bade267e931beaf37a2ab5b Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Sun, 11 Dec 2022 01:00:01 +0100 Subject: [PATCH 271/790] gnu: grml-zsh-config: Update to 0.19.5. * gnu/packages/shellutils.scm (grml-zsh-config): Update to 0.19.5. --- gnu/packages/shellutils.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/shellutils.scm b/gnu/packages/shellutils.scm index 0f7616616e..b1c1373376 100644 --- a/gnu/packages/shellutils.scm +++ b/gnu/packages/shellutils.scm @@ -275,7 +275,7 @@ particularly in catching syntax errors.") (define-public grml-zsh-config (package (name "grml-zsh-config") - (version "0.19.3") + (version "0.19.5") (source (origin (method url-fetch) (uri (string-append @@ -283,7 +283,7 @@ particularly in catching syntax errors.") version ".tar.gz")) (sha256 (base32 - "05fri77028znjnvmh8mz3424rn8ilysj7hn8br2hk1qwkp4zzwp9")))) + "0ifw490z3v9ljccbmm04adz39fj2dmx8mjgayxqj0a9ln90yfdc4")))) (build-system copy-build-system) (arguments (list From bfa8238ed8039979648de8dc51eb526ba74cc94c Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Sun, 11 Dec 2022 01:00:01 +0100 Subject: [PATCH 272/790] gnu: skalibs: Update to 2.12.0.1. * gnu/packages/skarnet.scm (skalibs): Update to 2.12.0.1. --- gnu/packages/skarnet.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/skarnet.scm b/gnu/packages/skarnet.scm index 31349e858b..5f4dfdc4f4 100644 --- a/gnu/packages/skarnet.scm +++ b/gnu/packages/skarnet.scm @@ -30,14 +30,14 @@ (define-public skalibs (package (name "skalibs") - (version "2.11.0.0") + (version "2.12.0.1") (source (origin (method url-fetch) (uri (string-append "https://skarnet.org/software/skalibs/skalibs-" version ".tar.gz")) (sha256 - (base32 "1n9l7mb54dlb0iijjaf446jba6nmq1ql9n39s095ngrk5ahcipwq")))) + (base32 "1182ldnz5dj266gqhzkygd17jdvd3n46c2jfdizw324dy5r8y8iy")))) (build-system gnu-build-system) (arguments '(#:tests? #f ; no tests exist From 6b6a81f0871d515d70fc5f11e75f8ca7217654f2 Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Sun, 11 Dec 2022 01:00:00 +0100 Subject: [PATCH 273/790] gnu: execline: Update to 2.9.0.1. * gnu/packages/skarnet.scm (execline): Update to 2.9.0.1. --- gnu/packages/skarnet.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/skarnet.scm b/gnu/packages/skarnet.scm index 5f4dfdc4f4..199e4fedc2 100644 --- a/gnu/packages/skarnet.scm +++ b/gnu/packages/skarnet.scm @@ -61,14 +61,14 @@ and file system operations. It is used by all skarnet.org software.") (define-public execline (package (name "execline") - (version "2.8.1.0") + (version "2.9.0.1") (source (origin (method url-fetch) (uri (string-append "https://skarnet.org/software/execline/execline-" version ".tar.gz")) (sha256 - (base32 "0msmzf5zwjcsgjlvvq28rd2i0fkdb2skmv8ii0ix8dhyckwwjmav")))) + (base32 "1xiijn3r2rqji2pwhm9v0frkk7pv9m3ylmdajhmcmyqgz350y9h1")))) (build-system gnu-build-system) (inputs (list skalibs)) (arguments From 6f21376ff5ade0380ef79665fa2d847e0141ab52 Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Sun, 11 Dec 2022 01:00:01 +0100 Subject: [PATCH 274/790] gnu: s6: Update to 2.11.1.2. * gnu/packages/skarnet.scm (s6): Update to 2.11.1.2. --- gnu/packages/skarnet.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/skarnet.scm b/gnu/packages/skarnet.scm index 199e4fedc2..0341a0e7fe 100644 --- a/gnu/packages/skarnet.scm +++ b/gnu/packages/skarnet.scm @@ -103,14 +103,14 @@ complexity."))) (define-public s6 (package (name "s6") - (version "2.11.0.0") + (version "2.11.1.2") (source (origin (method url-fetch) (uri (string-append "https://skarnet.org/software/s6/s6-" version ".tar.gz")) (sha256 - (base32 "1a3lj0xfhn1w3a4ygqsxy8q4dr3n48hnwml4xzdpz3nrikhy8if5")))) + (base32 "18h38piz117ilx7ch9f7hl6bxm2w06z7lc7f5hwsr7c87sz7853c")))) (build-system gnu-build-system) (inputs (list skalibs execline)) (arguments From b290fb14a432cc2ccc38717206dbb0fd5202cec7 Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Sun, 11 Dec 2022 01:00:01 +0100 Subject: [PATCH 275/790] gnu: s6-dns: Update to 2.3.5.4. * gnu/packages/skarnet.scm (s6-dns): Update to 2.3.5.4. --- gnu/packages/skarnet.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/skarnet.scm b/gnu/packages/skarnet.scm index 0341a0e7fe..aded8232fa 100644 --- a/gnu/packages/skarnet.scm +++ b/gnu/packages/skarnet.scm @@ -147,14 +147,14 @@ functionality with a very small amount of code."))) (define-public s6-dns (package (name "s6-dns") - (version "2.3.5.2") + (version "2.3.5.4") (source (origin (method url-fetch) (uri (string-append "https://skarnet.org/software/s6-dns/s6-dns-" version ".tar.gz")) (sha256 - (base32 "0nczzjprvp6wirzycgf5h32dlgx4r8grzkqhif27n3ii6f5g78yw")))) + (base32 "0hyvyi8qwgs6529hafl3yvkb3qaw4mad76n5rn1lyxf4f8j25bvn")))) (build-system gnu-build-system) (inputs (list skalibs)) (arguments From 0619a63db65b2902715cc985ce6c75f237b96299 Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Sun, 11 Dec 2022 01:00:01 +0100 Subject: [PATCH 276/790] gnu: s6-networking: Update to 2.5.1.1. * gnu/packages/skarnet.scm (s6-networking): Update to 2.5.1.1. --- gnu/packages/skarnet.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/skarnet.scm b/gnu/packages/skarnet.scm index aded8232fa..f1e9f5b62e 100644 --- a/gnu/packages/skarnet.scm +++ b/gnu/packages/skarnet.scm @@ -176,14 +176,14 @@ as an alternative to the BIND, djbdns or other DNS clients."))) (define-public s6-networking (package (name "s6-networking") - (version "2.5.0.0") + (version "2.5.1.1") (source (origin (method url-fetch) (uri (string-append "https://skarnet.org/software/s6-networking/" "s6-networking-" version ".tar.gz")) (sha256 - (base32 "1fn3g9gkwgmnxallhk82f5rly81pnkilj7n49g5fbfmaalsq96mh")))) + (base32 "0624ls5d9iwx9nc05m99fbxd0jp0qjbp9as4whr3bhfrwd6rvivs")))) (build-system gnu-build-system) (inputs (list skalibs execline s6 s6-dns)) (arguments From 45f9783c708709316b736de5e85b66184b2a9885 Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Sun, 11 Dec 2022 01:00:01 +0100 Subject: [PATCH 277/790] gnu: s6-rc: Update to 0.5.3.2. * gnu/packages/skarnet.scm (s6-rc): Update to 0.5.3.2. --- gnu/packages/skarnet.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/skarnet.scm b/gnu/packages/skarnet.scm index f1e9f5b62e..123e7bf445 100644 --- a/gnu/packages/skarnet.scm +++ b/gnu/packages/skarnet.scm @@ -216,14 +216,14 @@ clock synchronization."))) (define-public s6-rc (package (name "s6-rc") - (version "0.5.2.3") + (version "0.5.3.2") (source (origin (method url-fetch) (uri (string-append "https://skarnet.org/software/s6-rc/s6-rc-" version ".tar.gz")) (sha256 - (base32 "1xyaplwzvqnb53mg59a7jklakzwsiqivp6qggsry3sbaw4hf3d5j")))) + (base32 "0f70sswqcmihynks3cs6kk97nywcp2lzr2hspp9578sadaba892g")))) (build-system gnu-build-system) (inputs (list skalibs execline s6)) (arguments From 217e369656b2496dfcdc1c9701b67f06a35f85c3 Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Sun, 11 Dec 2022 01:00:01 +0100 Subject: [PATCH 278/790] gnu: s6-portable-utils: Update to 2.2.5.0. * gnu/packages/skarnet.scm (s6-portable-utils): Update to 2.2.5.0. --- gnu/packages/skarnet.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/skarnet.scm b/gnu/packages/skarnet.scm index 123e7bf445..1c833bda07 100644 --- a/gnu/packages/skarnet.scm +++ b/gnu/packages/skarnet.scm @@ -255,7 +255,7 @@ environment."))) (define-public s6-portable-utils (package (name "s6-portable-utils") - (version "2.2.3.3") + (version "2.2.5.0") (source (origin (method url-fetch) @@ -263,7 +263,7 @@ environment."))) "https://skarnet.org/software/s6-portable-utils/s6-portable-utils-" version ".tar.gz")) (sha256 - (base32 "132jj5qk8x40kw6lrrn7jiqhvqj9d2h6g6mhl8zma1sp37bg0i84")))) + (base32 "0dkfj6ymi5pxs981hh84kwg2ph2dv6xn2bim65fz4dpx6j4rzczb")))) (build-system gnu-build-system) (inputs (list skalibs)) (arguments From db69afc21da493863e75e17e3bf1d54bacea75d1 Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Sun, 11 Dec 2022 01:00:01 +0100 Subject: [PATCH 279/790] gnu: s6-linux-init: Update to 1.0.8.0. * gnu/packages/skarnet.scm (s6-linux-init): Update to 1.0.8.0. --- gnu/packages/skarnet.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/skarnet.scm b/gnu/packages/skarnet.scm index 1c833bda07..ecaf9c3162 100644 --- a/gnu/packages/skarnet.scm +++ b/gnu/packages/skarnet.scm @@ -287,7 +287,7 @@ systems and other constrained environments, but they work everywhere."))) (define-public s6-linux-init (package (name "s6-linux-init") - (version "1.0.6.4") + (version "1.0.8.0") (source (origin (method url-fetch) @@ -295,7 +295,7 @@ systems and other constrained environments, but they work everywhere."))) "https://skarnet.org/software/s6-linux-init/s6-linux-init-" version ".tar.gz")) (sha256 - (base32 "0grqk111d6aqym1c4l9j26fdqcgra1hvwb9vdgylrfbvn1c3hlpb")))) + (base32 "1iixih6iwd618qqy06w2cig7rvlj4cn4m5mdcr060rngciwml1cj")))) (build-system gnu-build-system) (inputs (list execline s6 skalibs)) From 3a56a55b0643e9763a75f35f2949619fbfcdbfa7 Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Sun, 11 Dec 2022 01:00:02 +0100 Subject: [PATCH 280/790] gnu: s6-linux-utils: Update to 2.6.0.0. * gnu/packages/skarnet.scm (s6-linux-utils): Update to 2.6.0.0. --- gnu/packages/skarnet.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/skarnet.scm b/gnu/packages/skarnet.scm index ecaf9c3162..5b70a1e042 100644 --- a/gnu/packages/skarnet.scm +++ b/gnu/packages/skarnet.scm @@ -331,7 +331,7 @@ all the details."))) (define-public s6-linux-utils (package (name "s6-linux-utils") - (version "2.5.1.6") + (version "2.6.0.0") (source (origin (method url-fetch) @@ -339,7 +339,7 @@ all the details."))) "https://skarnet.org/software/s6-linux-utils/s6-linux-utils-" version ".tar.gz")) (sha256 - (base32 "0hr49nl0d7a6i5w8cfg43xzvzayb8kpqij9xg7bmw2fyvc2z338z")))) + (base32 "0ngd8ckak2xg6c63q0m8cvbrfnhpkx30r4g65q08g0hc99rk4wbc")))) (build-system gnu-build-system) (inputs (list skalibs)) (arguments From 06e088cc67e64e800365bb1b5b1fcec592b006e1 Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Sun, 11 Dec 2022 01:00:00 +0100 Subject: [PATCH 281/790] gnu: bird: Update to 2.0.11. * gnu/packages/networking.scm (bird): Update to 2.0.11. --- gnu/packages/networking.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/networking.scm b/gnu/packages/networking.scm index 72af64b42d..10cafa1c01 100644 --- a/gnu/packages/networking.scm +++ b/gnu/packages/networking.scm @@ -3852,14 +3852,14 @@ protocol daemons for BGP, IS-IS, LDP, OSPF, PIM, and RIP.") (define-public bird (package (name "bird") - (version "2.0.10") + (version "2.0.11") (source (origin (method url-fetch) (uri (string-append "ftp://bird.network.cz/pub/bird/bird-" version ".tar.gz")) (sha256 (base32 - "0npx3zgbjnhm4905zmj2qkz3d13s8hakassq6sbzm1ywv3fl3lvy")))) + "1mjm7w5zkbc5q2v4bdn7mcqzcq94s7fiz8a5lz98kl5rcwxvi9v0")))) (inputs (list libssh readline)) (native-inputs From 52ffc0c44fd66b47591fb4dcc9f22ed9cc4c56d3 Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Sun, 11 Dec 2022 01:00:02 +0100 Subject: [PATCH 282/790] gnu: arp-scan: Update to 1.9.8. * gnu/packages/networking.scm (arp-scan): Update to 1.9.8. --- gnu/packages/networking.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/networking.scm b/gnu/packages/networking.scm index 10cafa1c01..41ea34dfbd 100644 --- a/gnu/packages/networking.scm +++ b/gnu/packages/networking.scm @@ -196,7 +196,7 @@ runs on top of IP or UDP, and supports both v4 and v6 versions.") (define-public arp-scan (package (name "arp-scan") - (version "1.9.7") + (version "1.9.8") (source (origin (method git-fetch) @@ -206,7 +206,7 @@ runs on top of IP or UDP, and supports both v4 and v6 versions.") (commit version))) (file-name (git-file-name name version)) (sha256 - (base32 "1mf7a4f9vzvnkiavc87aqyciswggsb4fpy7j05jxnvjyyxv3l7gp")))) + (base32 "18pck3hi7caykpkry5ri16w4w8m11g8gvh3qx5rhwsc6d9xa2a6d")))) (build-system gnu-build-system) (inputs (list libpcap)) From 6e336a8721b113b76d70e033443c69e21cae012a Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Sun, 11 Dec 2022 01:00:03 +0100 Subject: [PATCH 283/790] gnu: httping: Fix DESTDIR. * gnu/packages/networking.scm (httping)[arguments]: Set PREFIX. --- gnu/packages/networking.scm | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/gnu/packages/networking.scm b/gnu/packages/networking.scm index 41ea34dfbd..ac6cfb2a32 100644 --- a/gnu/packages/networking.scm +++ b/gnu/packages/networking.scm @@ -1972,8 +1972,7 @@ transmission protocol (SCTP) in a Go application.") (list fftw ncurses openssl)) (arguments `(#:make-flags (list ,(string-append "CC=" (cc-for-target)) - (string-append "DESTDIR=" (assoc-ref %outputs "out")) - "PREFIX=") + (string-append "PREFIX=" (assoc-ref %outputs "out"))) #:tests? #f)) ; no tests (home-page "https://www.vanheusden.com/httping/") (synopsis "Web server latency and throughput monitor") From ca9cf7b1002b1821b19a65d77fb7736a03232433 Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Sun, 11 Dec 2022 01:00:00 +0100 Subject: [PATCH 284/790] gnu: httping: Remove input labels. * gnu/packages/networking.scm (httping)[native-inputs]: Remove input labels. --- gnu/packages/networking.scm | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/gnu/packages/networking.scm b/gnu/packages/networking.scm index ac6cfb2a32..77284c05e1 100644 --- a/gnu/packages/networking.scm +++ b/gnu/packages/networking.scm @@ -1966,14 +1966,14 @@ transmission protocol (SCTP) in a Go application.") (base32 "1y7sbgkhgadmd93x1zafqc4yp26ssiv16ni5bbi9vmvvdl55m29y")))) (build-system gnu-build-system) - (native-inputs - `(("gettext" ,gettext-minimal))) - (inputs - (list fftw ncurses openssl)) (arguments `(#:make-flags (list ,(string-append "CC=" (cc-for-target)) (string-append "PREFIX=" (assoc-ref %outputs "out"))) #:tests? #f)) ; no tests + (native-inputs + (list gettext-minimal)) + (inputs + (list fftw ncurses openssl)) (home-page "https://www.vanheusden.com/httping/") (synopsis "Web server latency and throughput monitor") (description From 56a0cb50e1e89b27c441e3287436d6ab49011c11 Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Sun, 11 Dec 2022 01:00:01 +0100 Subject: [PATCH 285/790] gnu: httping: Use G-expressions. * gnu/packages/networking.scm (httping)[arguments]: Rewrite as G-expressions. --- gnu/packages/networking.scm | 7 ++++--- 1 file changed, 4 insertions(+), 3 deletions(-) diff --git a/gnu/packages/networking.scm b/gnu/packages/networking.scm index 77284c05e1..f85d1e6fc0 100644 --- a/gnu/packages/networking.scm +++ b/gnu/packages/networking.scm @@ -1967,9 +1967,10 @@ transmission protocol (SCTP) in a Go application.") "1y7sbgkhgadmd93x1zafqc4yp26ssiv16ni5bbi9vmvvdl55m29y")))) (build-system gnu-build-system) (arguments - `(#:make-flags (list ,(string-append "CC=" (cc-for-target)) - (string-append "PREFIX=" (assoc-ref %outputs "out"))) - #:tests? #f)) ; no tests + (list #:make-flags + #~(list (string-append "CC=" #$(cc-for-target)) + (string-append "PREFIX=" #$output)) + #:tests? #f)) ; no test suite (native-inputs (list gettext-minimal)) (inputs From a4e98faa1e852c0e25bddd915a7dd8c8bed26a04 Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Sun, 11 Dec 2022 01:00:01 +0100 Subject: [PATCH 286/790] gnu: ncdu2: Do not use the illegal instructions. * gnu/packages/ncdu.scm (ncdu-2)[arguments]: Compile for a baseline CPU. --- gnu/packages/ncdu.scm | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/gnu/packages/ncdu.scm b/gnu/packages/ncdu.scm index a623cd5373..6f541878fc 100644 --- a/gnu/packages/ncdu.scm +++ b/gnu/packages/ncdu.scm @@ -71,7 +71,9 @@ ncurses installed.") (list #:make-flags #~(list (string-append "PREFIX=" #$output) - (string-append "CC=" #$(cc-for-target))) + (string-append "CC=" #$(cc-for-target)) + ;; XXX By default, zig builds with -march=native! + (string-append "ZIG_FLAGS=-Drelease-fast -Dcpu=baseline")) #:phases #~(modify-phases %standard-phases (delete 'configure) ; No configure script. From 7951892d39211aaeccefeab9a5971ec08572cce8 Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Sun, 11 Dec 2022 01:00:06 +0100 Subject: [PATCH 287/790] gnu: ncdu2: Delete pregenerated man page from source. * gnu/packages/ncdu.scm (ncdu2)[source]: Add a snippet. [arguments]: Adjust 'build-manpage phase accordingly. --- gnu/packages/ncdu.scm | 8 ++++++-- 1 file changed, 6 insertions(+), 2 deletions(-) diff --git a/gnu/packages/ncdu.scm b/gnu/packages/ncdu.scm index 6f541878fc..6b802aafa0 100644 --- a/gnu/packages/ncdu.scm +++ b/gnu/packages/ncdu.scm @@ -66,7 +66,12 @@ ncurses installed.") version ".tar.gz")) (sha256 (base32 - "0hfimrr7z9zrfkiyj09i8nh4a1rjn7d00y9xzpc7mkyqpkvghjjy")))) + "0hfimrr7z9zrfkiyj09i8nh4a1rjn7d00y9xzpc7mkyqpkvghjjy")) + (modules '((guix build utils))) + (snippet + #~(begin + ;; Delete a pregenerated man page. We'll build it ourselves. + (delete-file "ncdu.1"))))) (arguments (list #:make-flags @@ -83,7 +88,6 @@ ncurses installed.") (mkdtemp "/tmp/zig-cache-XXXXXX")))) (add-after 'build 'build-manpage (lambda _ - (delete-file "ncdu.1") (invoke "make" "doc"))) (replace 'check (lambda* (#:key tests? #:allow-other-keys) From d0d06d81682ed88e4ba59b02cedbf52f58af8155 Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Sun, 11 Dec 2022 01:00:00 +0100 Subject: [PATCH 288/790] gnu: ncdu: Use upstream name. MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * gnu/packages/ncdu.scm (ncdu-1): New variable, renamed from… (ncdu): …this one, itself renamed from the old ncdu-2. Simple! [name]: Drop suffix. [properties]: Remove obsolete 'upstream-name. (ncdu-2): Redefine as a DEPRECATED-PACKAGE alias of ncdu. --- gnu/packages/ncdu.scm | 17 +++++++++++------ 1 file changed, 11 insertions(+), 6 deletions(-) diff --git a/gnu/packages/ncdu.scm b/gnu/packages/ncdu.scm index 6b802aafa0..feea8f8819 100644 --- a/gnu/packages/ncdu.scm +++ b/gnu/packages/ncdu.scm @@ -30,7 +30,10 @@ #:use-module (gnu packages perl) #:use-module (gnu packages zig)) -(define-public ncdu +(define-public ncdu-1 + ;; This old version is ‘LTS’. Version 2 works fine and has more features, + ;; but Zig is still a fast-moving target and doesn't support cross-compilation + ;; yet, so we'll keep both for just a little longer. (package (name "ncdu") (version "1.18") @@ -55,10 +58,10 @@ ncurses installed.") version))) (home-page "https://dev.yorhel.nl/ncdu"))) -(define-public ncdu-2 +(define-public ncdu (package - (inherit ncdu) - (name "ncdu2") ; To destinguish it from the C based version. + (inherit ncdu-1) + (name "ncdu") (version "2.2.1") (source (origin (method url-fetch) @@ -94,5 +97,7 @@ ncurses installed.") (when tests? (invoke "zig" "test" "build.zig"))))))) (native-inputs - (list perl zig)) - (properties `((upstream-name . "ncdu"))))) + (list perl zig)))) + +(define-public ncdu-2 + (deprecated-package "ncdu2" ncdu)) From e0039b858c94fa71478ac4eec71bd80ff53efa3a Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Sun, 11 Dec 2022 01:00:01 +0100 Subject: [PATCH 289/790] gnu: lldpd: Update to 1.0.16. * gnu/packages/networking.scm (lldpd): Update to 1.0.16. --- gnu/packages/networking.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/networking.scm b/gnu/packages/networking.scm index f85d1e6fc0..8a2a7322ca 100644 --- a/gnu/packages/networking.scm +++ b/gnu/packages/networking.scm @@ -4257,14 +4257,14 @@ realistic with today's hardware.") (define-public lldpd (package (name "lldpd") - (version "1.0.15") + (version "1.0.16") (source (origin (method url-fetch) (uri (string-append "https://media.luffy.cx/files/lldpd/lldpd-" version ".tar.gz")) (sha256 - (base32 "09iidaan6gq384n7ykdwwsll3vmq6q7zd7j7j721k2p91c9kmzpp")) + (base32 "1ab5hkgi2iwqpfw6xy2wxjhqmz6pnkynfkg85zm7r9kv1ijr3cz3")) (modules '((guix build utils))) (snippet '(begin From 994b10f481521fd1444f75bbd3a41e01c9a8c9d8 Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Sun, 11 Dec 2022 01:00:02 +0100 Subject: [PATCH 290/790] gnu: libnetfilter-conntrack: Update to 1.0.9. * gnu/packages/linux.scm (libnetfilter-conntrack): Update to 1.0.9. --- gnu/packages/linux.scm | 5 ++--- 1 file changed, 2 insertions(+), 3 deletions(-) diff --git a/gnu/packages/linux.scm b/gnu/packages/linux.scm index e0129ac9de..38f14452de 100644 --- a/gnu/packages/linux.scm +++ b/gnu/packages/linux.scm @@ -7694,7 +7694,7 @@ userspace queueing component and the logging subsystem.") (define-public libnetfilter-conntrack (package (name "libnetfilter-conntrack") - (version "1.0.8") + (version "1.0.9") (source (origin (method url-fetch) @@ -7703,8 +7703,7 @@ userspace queueing component and the logging subsystem.") "libnetfilter_conntrack-" version ".tar.bz2")) (sha256 - (base32 - "1ky1mqgnplw2h9jf0kn0a69d94jkydhbiipng9l2hdcj13h3pl8c")))) + (base32 "1a3rnpsba64dzy97wwjrxal89wr0nf9znvag2j18nkp3kzs9vgb7")))) (build-system gnu-build-system) (native-inputs (list pkg-config)) (inputs (list libnfnetlink libmnl)) From 9e35951dc8198c4aac9da4e025badaceb5ff6315 Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Sun, 11 Dec 2022 01:00:01 +0100 Subject: [PATCH 291/790] gnu: libnetfilter-cttimeout: Update to 1.0.1. * gnu/packages/linux.scm (libnetfilter-cttimeout): Update to 1.0.1. --- gnu/packages/linux.scm | 5 ++--- 1 file changed, 2 insertions(+), 3 deletions(-) diff --git a/gnu/packages/linux.scm b/gnu/packages/linux.scm index 38f14452de..c3a6d42a5d 100644 --- a/gnu/packages/linux.scm +++ b/gnu/packages/linux.scm @@ -7721,7 +7721,7 @@ conntrack-tools among many other applications.") (define-public libnetfilter-cttimeout (package (name "libnetfilter-cttimeout") - (version "1.0.0") + (version "1.0.1") (source (origin (method url-fetch) @@ -7729,8 +7729,7 @@ conntrack-tools among many other applications.") "libnetfilter_cttimeout/files/" "libnetfilter_cttimeout-" version ".tar.bz2")) (sha256 - (base32 - "1fpyz1zlvcq80244knvyvy87909xjqlj02lmw8yblz2m9xsi5axf")))) + (base32 "0983cpyvxyycbnzqlrzml80pph2z51r6s7sxp06ciq8468pxln8b")))) (build-system gnu-build-system) (native-inputs (list pkg-config)) (inputs (list libmnl)) From 8bdb5b195a65d478e8514f82f63c682a7de02ca2 Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Sun, 11 Dec 2022 01:00:00 +0100 Subject: [PATCH 292/790] gnu: libnetfilter-cthelper: Update to 1.0.1. * gnu/packages/linux.scm (libnetfilter-cthelper): Update to 1.0.1. --- gnu/packages/linux.scm | 5 ++--- 1 file changed, 2 insertions(+), 3 deletions(-) diff --git a/gnu/packages/linux.scm b/gnu/packages/linux.scm index c3a6d42a5d..1c6b572708 100644 --- a/gnu/packages/linux.scm +++ b/gnu/packages/linux.scm @@ -7747,7 +7747,7 @@ by conntrack-tools.") (define-public libnetfilter-cthelper (package (name "libnetfilter-cthelper") - (version "1.0.0") + (version "1.0.1") (source (origin (method url-fetch) @@ -7755,8 +7755,7 @@ by conntrack-tools.") "libnetfilter_cthelper/files/" "libnetfilter_cthelper-" version ".tar.bz2")) (sha256 - (base32 - "0gfgzkc1fjniqwk4jxds72c0lcgfhq2591hrvjrvd9nrqiqqwq87")))) + (base32 "04n95ngil5l8m8v64dfjm1dwq0wd3kf4vw1zblsrff13hxa3s1ql")))) (build-system gnu-build-system) (native-inputs (list pkg-config)) (inputs (list libmnl)) From 7f58c1be47f9fe53bd53bb6fe9f6e4f16d0a1e78 Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Sun, 11 Dec 2022 01:00:01 +0100 Subject: [PATCH 293/790] gnu: mu: Update to 1.8.13. * gnu/packages/mail.scm (mu): Update to 1.8.13. --- gnu/packages/mail.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/mail.scm b/gnu/packages/mail.scm index a0e6510fda..82620442b8 100644 --- a/gnu/packages/mail.scm +++ b/gnu/packages/mail.scm @@ -1164,7 +1164,7 @@ security functionality including PGP, S/MIME, SSH, and SSL.") (define-public mu (package (name "mu") - (version "1.8.11") + (version "1.8.13") (source (origin (method git-fetch) (uri (git-reference @@ -1173,7 +1173,7 @@ security functionality including PGP, S/MIME, SSH, and SSL.") (file-name (git-file-name name version)) (sha256 (base32 - "0b5h5kdalv62z31aqyipymiqhazfssbx4c7ww96nn41a0l0g0ir0")))) + "0y4f5p7pwmaj8733rjzg29038dw33057qlsbsq2wapvp24wcjymr")))) (build-system meson-build-system) (native-inputs (list pkg-config From 5a957ca6b231f79d596c54c50a67245d4b480be2 Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Sun, 11 Dec 2022 01:00:01 +0100 Subject: [PATCH 294/790] gnu: opensmtpd-filter-dkimsign: Update to 0.6. * gnu/packages/mail.scm (opensmtpd-filter-dkimsign): Update to 0.6. --- gnu/packages/mail.scm | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/gnu/packages/mail.scm b/gnu/packages/mail.scm index 82620442b8..72ee3a2a40 100644 --- a/gnu/packages/mail.scm +++ b/gnu/packages/mail.scm @@ -3294,7 +3294,7 @@ writing OpenSMTPd filters.") (define-public opensmtpd-filter-dkimsign (package (name "opensmtpd-filter-dkimsign") - (version "0.5") + (version "0.6") (source (origin (method url-fetch) @@ -3303,7 +3303,7 @@ writing OpenSMTPd filters.") (string-append "https://distfiles.sigtrap.nl/" "filter-dkimsign-" version ".tar.gz"))) (sha256 - (base32 "0jwp47ixibnz8rghn193bk2hxh1j1zfrnidml18j7d7cylxfrd55")))) + (base32 "1hrn31hayr0hb32km5c42hhbaxw7g3jcgm59p0v0ydlj1fs0sprv")))) (build-system gnu-build-system) (arguments `(#:make-flags @@ -3324,8 +3324,8 @@ writing OpenSMTPd filters.") (list mandoc)) ; silently installs empty man page without (inputs (list libevent libopensmtpd - ;; XXX Our OpenSMTPd package uses libressl, but this package currently - ;; supports HAVE_ED25519 only with openssl. Switch back when possible. + ;; Our OpenSMTPd package uses libressl, but this package currently + ;; supports HAVE_ED25519 only with openssl. openssl)) (home-page "http://imperialat.at/dev/filter-dkimsign/") (synopsis "OpenSMTPd filter for signing mail with DKIM") From 875ff18ccd3b9347a6c68f6daec8eff1922f7b79 Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Sun, 11 Dec 2022 01:00:02 +0100 Subject: [PATCH 295/790] gnu: rspamd: Update to 3.4. * gnu/packages/mail.scm (rspamd): Update to 3.4. --- gnu/packages/mail.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/mail.scm b/gnu/packages/mail.scm index 72ee3a2a40..172c3e55e7 100644 --- a/gnu/packages/mail.scm +++ b/gnu/packages/mail.scm @@ -4471,7 +4471,7 @@ on RFC 3501 and original @code{imaplib} module.") (define-public rspamd (package (name "rspamd") - (version "3.2") + (version "3.4") (source (origin (method git-fetch) @@ -4479,7 +4479,7 @@ on RFC 3501 and original @code{imaplib} module.") (url "https://github.com/rspamd/rspamd") (commit version))) (sha256 - (base32 "122d5m1nfxxz93bhsk8lm4dazvdknzphb0a1188m7bsa4iynbfv2")) + (base32 "0jgmi8wqzsnwvfj6w4njzhxhcawbafsdxjkx1ym8r2jx8k4hwhi8")) (file-name (git-file-name name version)))) (build-system cmake-build-system) (arguments From 36cfb61d21239cdc0a6a40269e2449f8b9d3b08e Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Sun, 11 Dec 2022 01:00:01 +0100 Subject: [PATCH 296/790] gnu: man-pages: Update to 6.01. * gnu/packages/man.scm (man-pages): Update to 6.01. --- gnu/packages/man.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/man.scm b/gnu/packages/man.scm index 5d4643d842..ae9fe87a2f 100644 --- a/gnu/packages/man.scm +++ b/gnu/packages/man.scm @@ -270,7 +270,7 @@ PostScript, and PDF. Additional tools include the @command{man} viewer, and (define-public man-pages (package (name "man-pages") - (version "6.00") + (version "6.01") (source (origin (method url-fetch) @@ -280,7 +280,7 @@ PostScript, and PDF. Additional tools include the @command{man} viewer, and (string-append "mirror://kernel.org/linux/docs/man-pages/Archive/" "man-pages-" version ".tar.xz"))) (sha256 - (base32 "1252c1356z5spya3yl0lcmmymglx3bmfwmamiz1y5l13xqpwbnwy")))) + (base32 "02swrdim3wq4ppsfv0zdxbnn9apz0bb4fyaihjlq1i484xxigrcb")))) (build-system gnu-build-system) (arguments (list From da26c3975e0bc6c96c7030f67fe13fd6cddcfec2 Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Sun, 11 Dec 2022 01:00:00 +0100 Subject: [PATCH 297/790] gnu: man-pages-posix: Note that updates may be illegal to distribute. * gnu/packages/man.scm (man-pages-posix): Add comment. --- gnu/packages/man.scm | 1 + 1 file changed, 1 insertion(+) diff --git a/gnu/packages/man.scm b/gnu/packages/man.scm index ae9fe87a2f..4fdd06e214 100644 --- a/gnu/packages/man.scm +++ b/gnu/packages/man.scm @@ -316,6 +316,7 @@ Linux kernel and C library interfaces employed by user-space programs.") (define-public man-pages-posix (package (name "man-pages-posix") + ;; Make sure that updates are still legally distributable. 2017-a is not. (version "2013-a") (source (origin From 0b3743c059f4e02a33cdaba332fad71728c088f8 Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Sun, 11 Dec 2022 01:00:04 +0100 Subject: [PATCH 298/790] gnu: ii: Update to 2.0. * gnu/packages/irc.scm (ii): Update to 2.0. --- gnu/packages/irc.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/irc.scm b/gnu/packages/irc.scm index 495645236e..a6edc103fe 100644 --- a/gnu/packages/irc.scm +++ b/gnu/packages/irc.scm @@ -387,14 +387,14 @@ highlighted. (define-public ii (package (name "ii") - (version "1.9") + (version "2.0") (source (origin (method url-fetch) (uri (string-append "http://dl.suckless.org/tools/" name "-" version ".tar.gz")) (sha256 (base32 - "05wcaszm9hap5gqf58bciqm3ad1kfgp976fs3fsn3ll3nliv6345")))) + "0ns2wpzkk7qzhv7addgr0w5as0m7jwag5nxai2dr61wc436syrsg")))) (build-system gnu-build-system) (arguments `(#:tests? #f ; no tests From e3e4c46644b014bb7ccb41aaa9b5f50d7636a432 Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Sun, 11 Dec 2022 01:00:01 +0100 Subject: [PATCH 299/790] gnu: ii: Use G-expressions. * gnu/packages/irc.scm (ii)[arguments]: Rewrite as G-expressions. --- gnu/packages/irc.scm | 13 +++++++------ 1 file changed, 7 insertions(+), 6 deletions(-) diff --git a/gnu/packages/irc.scm b/gnu/packages/irc.scm index a6edc103fe..0a6c28980d 100644 --- a/gnu/packages/irc.scm +++ b/gnu/packages/irc.scm @@ -397,12 +397,13 @@ highlighted. "0ns2wpzkk7qzhv7addgr0w5as0m7jwag5nxai2dr61wc436syrsg")))) (build-system gnu-build-system) (arguments - `(#:tests? #f ; no tests - #:make-flags (list (string-append "PREFIX=" %output) - ,(string-append "CC=" (cc-for-target))) - #:phases - (modify-phases %standard-phases - (delete 'configure)))) ; no configure + (list #:tests? #f ; no tests + #:make-flags + #~(list (string-append "PREFIX=" #$output) + (string-append "CC=" #$(cc-for-target))) + #:phases + #~(modify-phases %standard-phases + (delete 'configure)))) ; no configure script (home-page "https://tools.suckless.org/ii/") (synopsis "FIFO and file system based IRC client") (description From 145747f64fbe8ce38229639c9b3da4aa1fda2ba3 Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Sun, 11 Dec 2022 01:00:01 +0100 Subject: [PATCH 300/790] gnu: ipset: Update to 7.16. * gnu/packages/linux.scm (ipset): Update to 7.16. --- gnu/packages/linux.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/linux.scm b/gnu/packages/linux.scm index 1c6b572708..69466d0ae2 100644 --- a/gnu/packages/linux.scm +++ b/gnu/packages/linux.scm @@ -9397,14 +9397,14 @@ receiving. It is dedicated to the PL011 UART of the Raspberry Pi.") (define-public ipset (package (name "ipset") - (version "7.15") + (version "7.16") (source (origin (method url-fetch) (uri (string-append "https://ipset.netfilter.org/" "ipset-" version ".tar.bz2")) (sha256 - (base32 "0l8pcaym6057hq3a4zwnk53p5y6xg1m3d3c83wn18h5nmnm4am8a")))) + (base32 "1l4nybq17gr2ick7bbb5gq46bsqiw4rxmrvi0qfkvpm1yk6xkcc7")))) (build-system gnu-build-system) (inputs (list libmnl)) From 6d16ae4af962ab0e14edd2336ef05b128f31ba39 Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Sun, 11 Dec 2022 01:00:00 +0100 Subject: [PATCH 301/790] gnu: cpuid: Update to 20221201. * gnu/packages/linux.scm (cpuid): Update to 20221201. --- gnu/packages/linux.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/linux.scm b/gnu/packages/linux.scm index 69466d0ae2..b1c940938e 100644 --- a/gnu/packages/linux.scm +++ b/gnu/packages/linux.scm @@ -8162,14 +8162,14 @@ available in the kernel Linux.") (define-public cpuid (package (name "cpuid") - (version "20221003") + (version "20221201") (source (origin (method url-fetch) (uri (string-append "http://www.etallen.com/cpuid/cpuid-" version ".src.tar.gz")) (sha256 (base32 - "01w318kxcksfbjwjnnc9ly12g0yp4vm6xjgfl8mmi0jndg0cbi33")))) + "0vlg5zc0dayyn9bzyb25fcaxid9svrsjjza11afplrhh50wdrzh8")))) (build-system gnu-build-system) (arguments (list #:make-flags From 54bf243bae630641a9cf884490074e9133175d1f Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Sun, 11 Dec 2022 01:00:01 +0100 Subject: [PATCH 302/790] gnu: powerstat: Update to 0.02.28. * gnu/packages/linux.scm (powerstat): Update to 0.02.28. --- gnu/packages/linux.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/linux.scm b/gnu/packages/linux.scm index b1c940938e..acdbacc146 100644 --- a/gnu/packages/linux.scm +++ b/gnu/packages/linux.scm @@ -1934,7 +1934,7 @@ It provides the commands @code{powercap-info} and @code{powercap-set}.") (define-public powerstat (package (name "powerstat") - (version "0.02.27") + (version "0.02.28") (source (origin (method git-fetch) @@ -1943,7 +1943,7 @@ It provides the commands @code{powercap-info} and @code{powercap-set}.") (commit (string-append "V" version)))) (file-name (git-file-name name version)) (sha256 - (base32 "1ik5yv2bhz2hvyga4h1m28rf0xpi20zpqm4swhvskyf1g6qf381z")))) + (base32 "1wydjxmb6qf7rqarpl8rblg4biq3r2kfcx7p3pzvsr0w1xwdiisd")))) (build-system gnu-build-system) (arguments `(#:make-flags From 4681e01bdccecccc90721147ad1fa7bb7fa2be72 Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Sun, 11 Dec 2022 01:00:01 +0100 Subject: [PATCH 303/790] gnu: mcelog: Update to 190. * gnu/packages/linux.scm (mcelog): Update to 190. --- gnu/packages/linux.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/linux.scm b/gnu/packages/linux.scm index acdbacc146..d4a6c1ef39 100644 --- a/gnu/packages/linux.scm +++ b/gnu/packages/linux.scm @@ -6947,7 +6947,7 @@ the @code{mce-inject} module loaded if it exists.") (define-public mcelog (package (name "mcelog") - (version "189") + (version "190") (source (origin (method git-fetch) @@ -6956,7 +6956,7 @@ the @code{mce-inject} module loaded if it exists.") (commit (string-append "v" version)))) (file-name (git-file-name name version)) (sha256 - (base32 "0ml12xmmmljp22a89fw23c6gmba4dngavgnisv665w67kbnv5085")) + (base32 "1466zkbxgjg8ik0gd9vwsjiwg0yg7g8ra4bw3lg3ypla2kiydy4q")) (modules '((guix build utils))) (snippet `(begin From 7ff99f7a56e169591d271d4da6aadd0f7048efff Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Sun, 11 Dec 2022 01:00:01 +0100 Subject: [PATCH 304/790] gnu: mtd-utils: Update to 2.1.5. * gnu/packages/linux.scm (mtd-utils): Update to 2.1.5. --- gnu/packages/linux.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/linux.scm b/gnu/packages/linux.scm index d4a6c1ef39..f39a77d6d0 100644 --- a/gnu/packages/linux.scm +++ b/gnu/packages/linux.scm @@ -6992,7 +6992,7 @@ exceeded.") (define-public mtd-utils (package (name "mtd-utils") - (version "2.1.4") + (version "2.1.5") (source (origin (method url-fetch) (uri (string-append @@ -7000,7 +7000,7 @@ exceeded.") "mtd-utils-" version ".tar.bz2")) (sha256 (base32 - "168vyzpfa0n66i8lcf626b9jczjr81rqbdk7735lfb18bp8i2rrc")))) + "0ilz8hkcyvfcnqpy25kbr8fb71x9vl28wbmw56vvd68n2byjfviq")))) (arguments (list #:configure-flags (if (%current-target-system) ; When cross-compiling. From 1077b0b73de75f3609410d321947e73896417d6c Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Sun, 11 Dec 2022 01:00:01 +0100 Subject: [PATCH 305/790] gnu: mtd-utils: Remove input labels. * gnu/packages/linux.scm (mtd-utils)[inputs]: Remove input labels. --- gnu/packages/linux.scm | 12 ++++++------ 1 file changed, 6 insertions(+), 6 deletions(-) diff --git a/gnu/packages/linux.scm b/gnu/packages/linux.scm index f39a77d6d0..d3904a601e 100644 --- a/gnu/packages/linux.scm +++ b/gnu/packages/linux.scm @@ -7011,12 +7011,12 @@ exceeded.") (native-inputs (list cmocka pkg-config)) (inputs - `(("acl" ,acl) ; extended attributes (xattr) - ("libuuid" ,util-linux "lib") - ("lzo" ,lzo) - ("openssl" ,openssl) ; optional crypto support - ("zlib" ,zlib) - ("zstd" ,zstd "lib"))) + (list acl ; extended attributes (xattr) + lzo + openssl ; optional crypto support + `(,util-linux "lib") + zlib + `(,zstd "lib"))) (build-system gnu-build-system) (synopsis "MTD Flash Storage Utilities") (description "This package provides utilities for testing, partitioning, etc From 69509c56f8c5c031defd52122bf0f71b66e85692 Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Sun, 11 Dec 2022 01:00:01 +0100 Subject: [PATCH 306/790] gnu: liburing: Update to 2.3. * gnu/packages/linux.scm (liburing): Update to 2.3. --- gnu/packages/linux.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/linux.scm b/gnu/packages/linux.scm index d3904a601e..9858871540 100644 --- a/gnu/packages/linux.scm +++ b/gnu/packages/linux.scm @@ -9436,7 +9436,7 @@ then IP sets may be the proper tool for you.") (define-public liburing (package (name "liburing") - (version "2.2") + (version "2.3") (source (origin (method git-fetch) (uri (git-reference @@ -9445,7 +9445,7 @@ then IP sets may be the proper tool for you.") (file-name (git-file-name name version)) (sha256 (base32 - "1677zqqbd9nw9hrdaxqbd1zwy54cxfsv2z0bjipn23mrkz2xzy1k")))) + "1ngg5640adlinkal8b28x5snrbab9yr8jw1w539h39k4pqnsbpmw")))) (build-system gnu-build-system) (arguments `(;; Tests are dependent on kernel version and features From 819c2256ecc1025ca57f467cd58c1edf3edde8e7 Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Sun, 11 Dec 2022 01:00:00 +0100 Subject: [PATCH 307/790] gnu: libnftnl: Update to 1.2.4. * gnu/packages/linux.scm (libnftnl): Update to 1.2.4. --- gnu/packages/linux.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/linux.scm b/gnu/packages/linux.scm index 9858871540..c3834a5211 100644 --- a/gnu/packages/linux.scm +++ b/gnu/packages/linux.scm @@ -7611,14 +7611,14 @@ re-use code and to avoid re-inventing the wheel.") (define-public libnftnl (package (name "libnftnl") - (version "1.2.3") + (version "1.2.4") (source (origin (method url-fetch) (uri (string-append "mirror://netfilter.org/libnftnl/" "libnftnl-" version ".tar.bz2")) (sha256 - (base32 "0m82bmh8i24hwxmz7rxwxjll4904ghd2b1x1p5h8algrg6dyl5p9")))) + (base32 "0zs7c8swlirxnbhl8q1b0p8g3jrzns7fyxsrglz71zfdwhxj7zn0")))) (build-system gnu-build-system) (native-inputs (list pkg-config)) From 6dcd6fecba3691658b49751d21fe3bb1aa43183e Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Sun, 11 Dec 2022 01:00:01 +0100 Subject: [PATCH 308/790] gnu: bpftrace: Update to 0.16.0. * gnu/packages/linux.scm (bpftrace): Update to 0.16.0. --- gnu/packages/linux.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/linux.scm b/gnu/packages/linux.scm index c3834a5211..18d53d3e5c 100644 --- a/gnu/packages/linux.scm +++ b/gnu/packages/linux.scm @@ -9331,7 +9331,7 @@ and above.") (define-public bpftrace (package (name "bpftrace") - (version "0.15.0") + (version "0.16.0") (source (origin (method git-fetch) @@ -9340,7 +9340,7 @@ and above.") (commit (string-append "v" version)))) (file-name (git-file-name name version)) (sha256 - (base32 "022fg0kiz0liahj82wvlxmivkwyp86shs5fwr2v4blx7lh05k9zm")) + (base32 "0v1376wfk4gy5rrjdsck6r3347nb0bgbj70998z1bkx9z95wm3ab")) (patches (search-patches "bpftrace-disable-bfd-disasm.patch")))) (build-system cmake-build-system) (native-inputs From bd3e72b79ffde6ffc65a4bbfab9a365477e80c55 Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Sun, 11 Dec 2022 01:00:03 +0100 Subject: [PATCH 309/790] gnu: earlyoom: Update to 1.7. * gnu/packages/linux.scm (earlyoom): Update to 1.7. --- gnu/packages/linux.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/linux.scm b/gnu/packages/linux.scm index 18d53d3e5c..409b034f58 100644 --- a/gnu/packages/linux.scm +++ b/gnu/packages/linux.scm @@ -4024,7 +4024,7 @@ from the module-init-tools project.") (define-public earlyoom (package (name "earlyoom") - (version "1.6.2") + (version "1.7") (source (origin (method git-fetch) (uri (git-reference @@ -4033,7 +4033,7 @@ from the module-init-tools project.") (file-name (git-file-name name version)) (sha256 (base32 - "16iyn51xlrsbshc7p5xl2338yyfzknaqc538sa7mamgccqwgyvvq")))) + "1xqrs6wz59ks76hdgfd4vaj010kbvllilgam2xxyn0g56kai71zi")))) (build-system gnu-build-system) (arguments (list From 208006b4107205504fadda4a5322ae9281d046a4 Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Sun, 11 Dec 2022 01:00:01 +0100 Subject: [PATCH 310/790] gnu: fakeroot: Update to 1.30.1. * gnu/packages/linux.scm (fakeroot): Update to 1.30.1. --- gnu/packages/linux.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/linux.scm b/gnu/packages/linux.scm index 409b034f58..db21d05b5c 100644 --- a/gnu/packages/linux.scm +++ b/gnu/packages/linux.scm @@ -8833,7 +8833,7 @@ the superuser to make device nodes.") (define-public fakeroot (package (name "fakeroot") - (version "1.28") + (version "1.30.1") (source (origin ;; There are no tags in the repository, so take this snapshot. @@ -8842,7 +8842,7 @@ the superuser to make device nodes.") "fakeroot/fakeroot_" version ".orig.tar.gz")) (file-name (string-append name "-" version ".tar.gz")) (sha256 - (base32 "1hlh77b6m2cfm42lcav372mbjni5akbgs25yg4wgi1gndzihbm2n")) + (base32 "0xba5gfh7ygv6na8n1ckqd2jnpdr9q88qan385qxp85c47sb3srj")) (modules '((guix build utils) (ice-9 ftw))) (snippet From 37cce5599c7b324c57db67802a742c9636820b24 Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Sun, 11 Dec 2022 01:00:01 +0100 Subject: [PATCH 311/790] gnu: fakeroot: Remove input labels. * gnu/packages/linux.scm (fakeroot)[native-inputs]: Remove input labels. --- gnu/packages/linux.scm | 12 ++---------- 1 file changed, 2 insertions(+), 10 deletions(-) diff --git a/gnu/packages/linux.scm b/gnu/packages/linux.scm index db21d05b5c..720ad43375 100644 --- a/gnu/packages/linux.scm +++ b/gnu/packages/linux.scm @@ -8904,16 +8904,8 @@ the superuser to make device nodes.") (substitute* "test/compare-tar" (("tar -tvf") "tar --numeric-owner -tvf"))))))) (native-inputs - `(;; For bootstrapping the package. - ("autoconf" ,autoconf-2.71) - ("automake" ,automake) - ("libtool" ,libtool) - ("gettext" ,gettext-minimal) - ("po4a" ,po4a) - - ;; For tests. - ("sharutils" ,sharutils) - ("xz" ,xz))) + (list autoconf-2.71 automake gettext-minimal libtool po4a + sharutils xz)) ; for tests (inputs (list acl libcap util-linux sed coreutils)) (synopsis "Run commands in an environment with fake root privileges") From bba76198c587559a8d68ccf024b491364e0ee7a7 Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Sun, 11 Dec 2022 01:00:01 +0100 Subject: [PATCH 312/790] gnu: mpd: Update to 0.23.11. * gnu/packages/mpd.scm (mpd): Update to 0.23.11. --- gnu/packages/mpd.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/mpd.scm b/gnu/packages/mpd.scm index b9b6924451..63fb9bc974 100644 --- a/gnu/packages/mpd.scm +++ b/gnu/packages/mpd.scm @@ -116,7 +116,7 @@ interfacing MPD in the C, C++ & Objective C languages.") (define-public mpd (package (name "mpd") - (version "0.23.10") + (version "0.23.11") (source (origin (method url-fetch) (uri @@ -125,7 +125,7 @@ interfacing MPD in the C, C++ & Objective C languages.") "/mpd-" version ".tar.xz")) (sha256 (base32 - "1a764k504nh9vqmsd92qh8sg03fwns19d7mypm618j6c8bmqqp30")))) + "1afwvw2670yz3kxzlqjlg9r8ra8fjihj97hgc6skiwnzz6lfgd7d")))) (build-system meson-build-system) (arguments (list From 90a2b8c64a0155a1cd663ee5408dc6bb09d64123 Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Sun, 11 Dec 2022 01:00:00 +0100 Subject: [PATCH 313/790] install: Add lvm2-static system package. * gnu/system/install.scm (%installer-disk-utilities): Add lvm2-static. --- gnu/system/install.scm | 2 ++ 1 file changed, 2 insertions(+) diff --git a/gnu/system/install.scm b/gnu/system/install.scm index f6f1923121..3f5352be87 100644 --- a/gnu/system/install.scm +++ b/gnu/system/install.scm @@ -465,6 +465,8 @@ Access documentation at any time by pressing Alt-F2.\x1b[0m ;; A well-rounded set of packages for interacting with disks, partitions and ;; file systems, included with the Guix installation image. (list parted gptfdisk ddrescue + ;; Use the static LVM2 because it's already pulled in by the installer. + lvm2-static ;; We used to provide fdisk from GNU fdisk, but as of version 2.0.0a ;; it pulls Guile 1.8, which takes unreasonable space; furthermore ;; util-linux's fdisk is already available, in %base-packages-linux. From 491bddfa276cc9775adf325c07e5f82638f330e7 Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Thu, 15 Dec 2022 13:39:35 -0500 Subject: [PATCH 314/790] system: examples: Add mode prop line. * gnu/system/examples/asus-c201.tmpl: Add a mode prop line. * gnu/system/examples/bare-bones.tmpl: Likewise. * gnu/system/examples/beaglebone-black.tmpl: Likewise. * gnu/system/examples/desktop.tmpl: Likewise. * gnu/system/examples/docker-image.tmpl: Likewise. * gnu/system/examples/lightweight-desktop.tmpl: Likewise. * gnu/system/examples/raspberry-pi-64-nfs-root.tmpl: Likewise. * gnu/system/examples/raspberry-pi-64.tmpl: Likewise. * gnu/system/examples/vm-image.tmpl: Likewise. --- gnu/system/examples/asus-c201.tmpl | 1 + gnu/system/examples/bare-bones.tmpl | 1 + gnu/system/examples/beaglebone-black.tmpl | 1 + gnu/system/examples/desktop.tmpl | 1 + gnu/system/examples/docker-image.tmpl | 1 + gnu/system/examples/lightweight-desktop.tmpl | 1 + gnu/system/examples/raspberry-pi-64-nfs-root.tmpl | 1 + gnu/system/examples/raspberry-pi-64.tmpl | 1 + gnu/system/examples/vm-image.tmpl | 1 + 9 files changed, 9 insertions(+) diff --git a/gnu/system/examples/asus-c201.tmpl b/gnu/system/examples/asus-c201.tmpl index 6b6aa706fa..019111c167 100644 --- a/gnu/system/examples/asus-c201.tmpl +++ b/gnu/system/examples/asus-c201.tmpl @@ -1,3 +1,4 @@ +;; -*- mode: scheme; -*- ;; This is an operating system configuration template ;; for a "bare bones" setup for an ASUS C201PA. diff --git a/gnu/system/examples/bare-bones.tmpl b/gnu/system/examples/bare-bones.tmpl index 687d4c1573..45b4995574 100644 --- a/gnu/system/examples/bare-bones.tmpl +++ b/gnu/system/examples/bare-bones.tmpl @@ -1,3 +1,4 @@ +;; -*- mode: scheme; -*- ;; This is an operating system configuration template ;; for a "bare bones" setup, with no X11 display server. diff --git a/gnu/system/examples/beaglebone-black.tmpl b/gnu/system/examples/beaglebone-black.tmpl index 90dab62062..40d0a76a37 100644 --- a/gnu/system/examples/beaglebone-black.tmpl +++ b/gnu/system/examples/beaglebone-black.tmpl @@ -1,3 +1,4 @@ +;; -*- mode: scheme; -*- ;; This is an operating system configuration template ;; for a "bare bones" setup on BeagleBone Black board. diff --git a/gnu/system/examples/desktop.tmpl b/gnu/system/examples/desktop.tmpl index 7055a8f92d..10d0e54fa7 100644 --- a/gnu/system/examples/desktop.tmpl +++ b/gnu/system/examples/desktop.tmpl @@ -1,3 +1,4 @@ +;; -*- mode: scheme; -*- ;; This is an operating system configuration template ;; for a "desktop" setup with GNOME and Xfce where the ;; root partition is encrypted with LUKS, and a swap file. diff --git a/gnu/system/examples/docker-image.tmpl b/gnu/system/examples/docker-image.tmpl index bdc6afa6f0..7123917af4 100644 --- a/gnu/system/examples/docker-image.tmpl +++ b/gnu/system/examples/docker-image.tmpl @@ -1,3 +1,4 @@ +;; -*- mode: scheme; -*- ;; This is an operating system configuration template for a "Docker image" ;; setup, so it has barely any services at all. diff --git a/gnu/system/examples/lightweight-desktop.tmpl b/gnu/system/examples/lightweight-desktop.tmpl index d4330ecc8e..4cb3c38311 100644 --- a/gnu/system/examples/lightweight-desktop.tmpl +++ b/gnu/system/examples/lightweight-desktop.tmpl @@ -1,3 +1,4 @@ +;; -*- mode: scheme; -*- ;; This is an operating system configuration template ;; for a "desktop" setup without full-blown desktop ;; environments. diff --git a/gnu/system/examples/raspberry-pi-64-nfs-root.tmpl b/gnu/system/examples/raspberry-pi-64-nfs-root.tmpl index 8c47c650f6..2203375270 100644 --- a/gnu/system/examples/raspberry-pi-64-nfs-root.tmpl +++ b/gnu/system/examples/raspberry-pi-64-nfs-root.tmpl @@ -1,3 +1,4 @@ +;; -*- mode: scheme; -*- ;; This is an operating-system configuration template of a ;; 64-bit minimal system for a Raspberry Pi with an NFS root file-system. diff --git a/gnu/system/examples/raspberry-pi-64.tmpl b/gnu/system/examples/raspberry-pi-64.tmpl index 3ad588207c..185d25c412 100644 --- a/gnu/system/examples/raspberry-pi-64.tmpl +++ b/gnu/system/examples/raspberry-pi-64.tmpl @@ -1,3 +1,4 @@ +;; -*- mode: scheme; -*- ;; This is an operating-system configuration template of a ;; 64-bit minimal system for a Raspberry Pi with local storage. diff --git a/gnu/system/examples/vm-image.tmpl b/gnu/system/examples/vm-image.tmpl index d46a27978c..343287eaf6 100644 --- a/gnu/system/examples/vm-image.tmpl +++ b/gnu/system/examples/vm-image.tmpl @@ -1,3 +1,4 @@ +;; -*- mode: scheme; -*- ;; This is an operating system configuration for a VM image. ;; Modify it as you see fit and instantiate the changes by running: ;; From 88908c6edce845b8737a18dda415f162d699384a Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Wed, 14 Dec 2022 20:43:38 +0100 Subject: [PATCH 315/790] services: ganeti: Add support for cluster hooks. * gnu/services/ganeti.scm (): Add HOOKS. (hooks->directory): Rename to ... (debootstrap-hooks->directory): ... this, for clarity. (debootstrap-configuration-compiler): Adjust accordingly. (ganeti-directory): Add HOOKS when set. (ganeti-etc-service): Pass HOOKS. * doc/guix.texi (Virtualization Services): Mention it. --- doc/guix.texi | 4 ++++ gnu/services/ganeti.scm | 14 ++++++++++---- 2 files changed, 14 insertions(+), 4 deletions(-) diff --git a/doc/guix.texi b/doc/guix.texi index 5cb5ae1dfe..eb37d4d393 100644 --- a/doc/guix.texi +++ b/doc/guix.texi @@ -34249,6 +34249,10 @@ To override a setting, you must use the configuration type for that service: @item @code{file-storage-paths} (default: @code{'()}) List of allowed directories for file storage backend. +@item @code{hooks} (default: @code{#f}) +When set, this should be a file-like object containing a directory with +@url{https://docs.ganeti.org/docs/ganeti/3.0/html/hooks.html,cluster execution hooks}. + @item @code{os} (default: @code{%default-ganeti-os}) List of @code{} records. @end table diff --git a/gnu/services/ganeti.scm b/gnu/services/ganeti.scm index d9770b1a29..f8127e8721 100644 --- a/gnu/services/ganeti.scm +++ b/gnu/services/ganeti.scm @@ -777,6 +777,8 @@ than 21 days from @file{/var/lib/ganeti/queue/archive}."))) (default (ganeti-cleaner-configuration))) (file-storage-paths ganeti-configuration-file-storage-paths ;list of strings | gexp (default '())) + (hooks ganeti-configuration-hooks ; | #f + (default #f)) (os ganeti-configuration-os ;list of (default '()))) @@ -910,7 +912,7 @@ trap - EXIT (partition-alignment debootstrap-configuration-partition-alignment ;#f | integer (default 2048))) -(define (hooks->directory hooks) +(define (debootstrap-hooks->directory hooks) (match hooks ((? file-like?) hooks) @@ -918,7 +920,7 @@ trap - EXIT (let ((names (map car hooks)) (files (map cdr hooks))) (with-imported-modules '((guix build utils)) - (computed-file "hooks-union" + (computed-file "debootstrap-hooks" #~(begin (use-modules (guix build utils) (ice-9 match)) @@ -942,7 +944,7 @@ trap - EXIT (($ hooks proxy mirror arch suite extra-pkgs components generate-cache? clean-cache partition-style partition-alignment) - (let ((customize-dir (hooks->directory hooks))) + (let ((customize-dir (debootstrap-hooks->directory hooks))) (gexp->derivation "debootstrap-variant" #~(call-with-output-file (ungexp output "out") @@ -1034,7 +1036,7 @@ in /etc/ganeti/instance-$os for OS." (computed-file (string-append name "-os") builder #:local-build? #t))) -(define (ganeti-directory file-storage-file os) +(define (ganeti-directory file-storage-file hooks os) (let ((dirs (map ganeti-os->directory os)) (names (map ganeti-os-name os))) (define builder @@ -1044,6 +1046,9 @@ in /etc/ganeti/instance-$os for OS." (when #$file-storage-file (symlink #$file-storage-file (string-append #$output "/file-storage-paths"))) + (when #$hooks + (symlink #$hooks + (string-append #$output "/hooks"))) (for-each (match-lambda ((name dest) (symlink dest @@ -1063,6 +1068,7 @@ in /etc/ganeti/instance-$os for OS." (list `("ganeti" ,(ganeti-directory (file-storage-file (ganeti-configuration-file-storage-paths config)) + (ganeti-configuration-hooks config) (ganeti-configuration-os config))))) (define (debootstrap-os variants) From 4d94cdf69889043dd8d9b1305f5f3946ec0f8ff6 Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Thu, 15 Dec 2022 16:28:14 +0100 Subject: [PATCH 316/790] activation: Firmware activation handles missing support in kernel. * gnu/build/activation.scm (activate-firmware): Check if firmware loading is enabled before attempting to use it. --- gnu/build/activation.scm | 11 ++++++++--- 1 file changed, 8 insertions(+), 3 deletions(-) diff --git a/gnu/build/activation.scm b/gnu/build/activation.scm index 10c9045740..eea2233563 100644 --- a/gnu/build/activation.scm +++ b/gnu/build/activation.scm @@ -363,9 +363,14 @@ second element is the name it should appear at, such as: "Tell the kernel to look for device firmware under DIRECTORY. This mechanism bypasses udev: it allows Linux to handle firmware loading directly by itself, without having to resort to a \"user helper\"." - (call-with-output-file "/sys/module/firmware_class/parameters/path" - (lambda (port) - (display directory port)))) + + ;; If the kernel was built without firmware loading support, this file + ;; does not exist. Do nothing in that case. + (let ((firmware-path "/sys/module/firmware_class/parameters/path")) + (when (file-exists? firmware-path) + (call-with-output-file firmware-path + (lambda (port) + (display directory port)))))) (define (activate-ptrace-attach) "Allow users to PTRACE_ATTACH their own processes. From 95692ffa8bcb1fec56039b6a4e5a2a368e7dfdbe Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Fri, 16 Dec 2022 17:41:58 +0100 Subject: [PATCH 317/790] gnu: ungoogled-chromium: Update to 108.0.5359.124-1. * gnu/packages/chromium.scm (%chromium-version): Set to 108.0.5359.124. (%ungoogled-origin, ungoogled-chromium): Update hashes. --- gnu/packages/chromium.scm | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/gnu/packages/chromium.scm b/gnu/packages/chromium.scm index 299a4edcbe..ed6dd9dfd1 100644 --- a/gnu/packages/chromium.scm +++ b/gnu/packages/chromium.scm @@ -317,7 +317,7 @@ ;; run the Blink performance tests, just remove everything to save ~70MiB. '("third_party/blink/perf_tests")) -(define %chromium-version "108.0.5359.98") +(define %chromium-version "108.0.5359.124") (define %ungoogled-revision (string-append %chromium-version "-1")) (define %debian-revision "debian/102.0.5005.61-1") (define %arch-revision "4de5019014aeb77187a517c5ca6db8723d622a40") @@ -330,7 +330,7 @@ (file-name (git-file-name "ungoogled-chromium" %ungoogled-revision)) (sha256 (base32 - "16rc15qsndrsj52p56ma3hg94jslkfy2f91ryr3qss73r2rkjf8j")))) + "18sz2ksawyb08h4kbxzkf1zhxs832z8mwvndm43nykz01wxk20bp")))) (define %debian-origin (origin @@ -491,7 +491,7 @@ %chromium-version ".tar.xz")) (sha256 (base32 - "07jnhd5y7k4zp2ipz052isw7llagxn8l8rbz8x3jkjz3f5wi7dk0")) + "0x9ac6m4xdccjdrk2bmq4y7bhfpgf2dv0q7lsbbsa50vlv1gm3fl")) (modules '((guix build utils))) (snippet (force ungoogled-chromium-snippet)))) (build-system gnu-build-system) From 287f997489a504c7f62b408ef8be8a2cf3617671 Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Sat, 17 Dec 2022 01:07:05 +0100 Subject: [PATCH 318/790] gnu: SeaBIOS: Update to 1.16.1. * gnu/packages/firmware.scm (seabios): Update to 1.16.1. --- gnu/packages/firmware.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/firmware.scm b/gnu/packages/firmware.scm index e9bb3ed450..09a6a1a909 100644 --- a/gnu/packages/firmware.scm +++ b/gnu/packages/firmware.scm @@ -402,7 +402,7 @@ executing in M-mode.") (define-public seabios (package (name "seabios") - (version "1.15.0") + (version "1.16.1") (source (origin (method git-fetch) @@ -411,7 +411,7 @@ executing in M-mode.") (commit (string-append "rel-" version)))) (file-name (git-file-name name version)) (sha256 - (base32 "0gnsfmbgcvihsap8sz8c2n3qs439q44i3pwrms2nv3xcnf1sclj9")))) + (base32 "0gph1hf70jjpx55qc0lzx2yghkipg9dnsin07i4jajk0p1jpd2d0")))) (build-system gnu-build-system) (native-inputs (list python-wrapper)) (arguments From f7793ce0e0d4e45459ed1cd485c7ff39f3bcd90d Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Sat, 17 Dec 2022 01:09:16 +0100 Subject: [PATCH 319/790] gnu: SeaBIOS: Build verbosely. * gnu/packages/firmware.scm (seabios)[arguments]: Add "V=1" to #:make-flags. --- gnu/packages/firmware.scm | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/gnu/packages/firmware.scm b/gnu/packages/firmware.scm index 09a6a1a909..781d8ae004 100644 --- a/gnu/packages/firmware.scm +++ b/gnu/packages/firmware.scm @@ -416,7 +416,8 @@ executing in M-mode.") (native-inputs (list python-wrapper)) (arguments `(#:tests? #f ; no check target - #:make-flags '("EXTRAVERSION=-guix") ;upstream wants distros to set this + #:make-flags '("EXTRAVERSION=-guix" ;upstream wants distros to set this + "V=1") ;build verbosely #:modules (,@%gnu-build-system-modules (ice-9 match)) #:phases From ec76f45d30ad24f76a4274d92e79231c3d9bc7de Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Sat, 17 Dec 2022 01:12:40 +0100 Subject: [PATCH 320/790] gnu: SeaBIOS: Simplify build. * gnu/packages/firmware.scm (seabios)[arguments]: Don't install bios.bin twice. Drop redundant append step. --- gnu/packages/firmware.scm | 4 +--- 1 file changed, 1 insertion(+), 3 deletions(-) diff --git a/gnu/packages/firmware.scm b/gnu/packages/firmware.scm index 781d8ae004..a4e43e71ec 100644 --- a/gnu/packages/firmware.scm +++ b/gnu/packages/firmware.scm @@ -450,7 +450,7 @@ executing in M-mode.") (string-drop-right entry 2)) (format port "CONFIG_~a~%" entry))) (cons "BUILD_VGABIOS=y" config)))) - (apply invoke "make" (append flags '("oldnoconfig"))) + (apply invoke "make" "oldnoconfig" flags) (apply invoke "make" flags) (link (string-append target "/bios.bin") (string-append "out/" target ".bin"))))) @@ -469,8 +469,6 @@ executing in M-mode.") (lambda* (#:key outputs #:allow-other-keys) (let* ((out (assoc-ref outputs "out")) (fmw (string-append out "/share/firmware"))) - (mkdir-p fmw) - (copy-file "out/bios.bin" (string-append fmw "/bios.bin")) (for-each (lambda (bios) (install-file bios fmw)) (find-files "out" "\\.bin$")) From 810b455013037f44801cf1048c81796e77577962 Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Sat, 17 Dec 2022 01:46:23 +0100 Subject: [PATCH 321/790] gnu: QEMU: Update to 7.2.0. * gnu/packages/virtualization.scm (qemu): Update to 7.2.0. [source](snippet): Don't remove slirp, as it's no longer bundled. [arguments]: Remove related configure-flag. Specify Meson path. [native-inputs]: Change from MESON to MESON-0.63. --- gnu/packages/virtualization.scm | 11 ++++++----- 1 file changed, 6 insertions(+), 5 deletions(-) diff --git a/gnu/packages/virtualization.scm b/gnu/packages/virtualization.scm index 1218112a20..6890f13233 100644 --- a/gnu/packages/virtualization.scm +++ b/gnu/packages/virtualization.scm @@ -160,7 +160,7 @@ (define-public qemu (package (name "qemu") - (version "7.1.0") + (version "7.2.0") (source (origin (method url-fetch) @@ -168,7 +168,7 @@ version ".tar.xz")) (sha256 (base32 - "1rmvrgqjhrvcmchnz170dxvrrf14n6nm39y8ivrprmfydd9lwqx0")) + "0mr1xd78bgp1l61281sdx0338ji0aa68j2p9994sskblhwkcwjav")) (patches (search-patches "qemu-build-info-manual.patch" "qemu-disable-aarch64-migration-test.patch" "qemu-fix-agent-paths.patch")) @@ -178,7 +178,7 @@ ;; Delete bundled code that we provide externally. ;; TODO: Unbundle SeaBIOS! (for-each delete-file-recursively - '("dtc" "meson" "slirp")))))) + '("dtc" "meson")))))) (outputs '("out" "static" "doc")) ;5.3 MiB of HTML docs (build-system gnu-build-system) (arguments @@ -195,7 +195,8 @@ (string-append "--host-cc=" gcc) (string-append "--prefix=" out) "--sysconfdir=/etc" - "--enable-slirp=system" + (string-append "--meson=" (search-input-file %build-inputs + "bin/meson")) "--enable-fdt=system" (string-append "--smbd=" out "/libexec/samba-wrapper") "--disable-debug-info" ;for space considerations @@ -371,7 +372,7 @@ exec smbd $@"))) perl flex bison - meson + meson-0.63 ninja pkg-config python-wrapper From c3a25e90f249d39a1d5916fcf4009f9320d41f03 Mon Sep 17 00:00:00 2001 From: Leo Famulari Date: Fri, 16 Dec 2022 21:56:29 -0500 Subject: [PATCH 322/790] gnu: linux-libre: Update to 6.0.13. * gnu/packages/linux.scm (linux-libre-6.0-version): Update to 6.0.13. (linux-libre-6.0-pristine-source): Update hash. --- gnu/packages/linux.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/linux.scm b/gnu/packages/linux.scm index 720ad43375..a113be63e6 100644 --- a/gnu/packages/linux.scm +++ b/gnu/packages/linux.scm @@ -478,7 +478,7 @@ corresponding UPSTREAM-SOURCE (an origin), using the given DEBLOB-SCRIPTS." ;; The current "stable" kernels. That is, the most recently released major ;; versions that are still supported upstream. -(define-public linux-libre-6.0-version "6.0.12") +(define-public linux-libre-6.0-version "6.0.13") (define-public linux-libre-6.0-gnu-revision "gnu") (define deblob-scripts-6.0 (linux-libre-deblob-scripts @@ -488,7 +488,7 @@ corresponding UPSTREAM-SOURCE (an origin), using the given DEBLOB-SCRIPTS." (base32 "16g2bin3xay30zfss1vlb7pwcss5giaxaksp4v1gk05wn51wjrqr"))) (define-public linux-libre-6.0-pristine-source (let ((version linux-libre-6.0-version) - (hash (base32 "00ag63lnxw2gijw3b6v29lhrlv480m12954q5zh4jawlz3nk1dw9"))) + (hash (base32 "191dlxcmbx8vy6z2k04jq2kr6hwnaknsnsyycvqnjmvmdf6i3lq8"))) (make-linux-libre-source version (%upstream-linux-source version hash) deblob-scripts-6.0))) From ddcae98539302e5010daf3166b319ab938bb100c Mon Sep 17 00:00:00 2001 From: Leo Famulari Date: Fri, 16 Dec 2022 21:56:54 -0500 Subject: [PATCH 323/790] gnu: linux-libre 5.15: Update to 5.15.83. * gnu/packages/linux.scm (linux-libre-5.15-version): Update to 5.15.83. (linux-libre-5.15-pristine-source): Update hash. --- gnu/packages/linux.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/linux.scm b/gnu/packages/linux.scm index a113be63e6..55b23fd6a0 100644 --- a/gnu/packages/linux.scm +++ b/gnu/packages/linux.scm @@ -496,7 +496,7 @@ corresponding UPSTREAM-SOURCE (an origin), using the given DEBLOB-SCRIPTS." ;; The "longterm" kernels — the older releases with long-term upstream support. ;; Here are the support timelines: ;; -(define-public linux-libre-5.15-version "5.15.82") +(define-public linux-libre-5.15-version "5.15.83") (define-public linux-libre-5.15-gnu-revision "gnu") (define deblob-scripts-5.15 (linux-libre-deblob-scripts @@ -506,7 +506,7 @@ corresponding UPSTREAM-SOURCE (an origin), using the given DEBLOB-SCRIPTS." (base32 "1m73pgx8v047xb2gck2g7j7khniis8c9akn9vhzgsdfglrf8p6fj"))) (define-public linux-libre-5.15-pristine-source (let ((version linux-libre-5.15-version) - (hash (base32 "0r8v7113favmch2x6br7jk6idihza99l9qyd7ik99i5sg6xzdvpw"))) + (hash (base32 "1wvzfhzqq9dps508wmp2gblfz93ipppnjzqm0n8pi1acq11hhna0"))) (make-linux-libre-source version (%upstream-linux-source version hash) deblob-scripts-5.15))) From 9d4b9838ee7b16719ef0e6e2f4cf3d6d4dcdcf4a Mon Sep 17 00:00:00 2001 From: Leo Famulari Date: Fri, 16 Dec 2022 21:57:10 -0500 Subject: [PATCH 324/790] gnu: linux-libre 5.10: Update to 5.10.159. * gnu/packages/linux.scm (linux-libre-5.10-version): Update to 5.10.159. (linux-libre-5.10-pristine-source): Update hash. --- gnu/packages/linux.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/linux.scm b/gnu/packages/linux.scm index 55b23fd6a0..09179fb75e 100644 --- a/gnu/packages/linux.scm +++ b/gnu/packages/linux.scm @@ -511,7 +511,7 @@ corresponding UPSTREAM-SOURCE (an origin), using the given DEBLOB-SCRIPTS." (%upstream-linux-source version hash) deblob-scripts-5.15))) -(define-public linux-libre-5.10-version "5.10.158") +(define-public linux-libre-5.10-version "5.10.159") (define-public linux-libre-5.10-gnu-revision "gnu1") (define deblob-scripts-5.10 (linux-libre-deblob-scripts @@ -521,7 +521,7 @@ corresponding UPSTREAM-SOURCE (an origin), using the given DEBLOB-SCRIPTS." (base32 "0a96g4pjdgwvxn2wpz6rfc8nwdlkw138r9pp66kvfrrn08i313ii"))) (define-public linux-libre-5.10-pristine-source (let ((version linux-libre-5.10-version) - (hash (base32 "1rq7lyp41fydybs53rcdjhiy271arh95xch16s5s3jhhanxj82hy"))) + (hash (base32 "19yfi5vknxnw0cb8274q3pb5zjs6ny04n16m8xjdfdmznrbvza8v"))) (make-linux-libre-source version (%upstream-linux-source version hash) deblob-scripts-5.10))) From 3bf77e65f0cce2ab2065b4a0d8f85b29a6835fcc Mon Sep 17 00:00:00 2001 From: Leo Famulari Date: Fri, 16 Dec 2022 21:57:24 -0500 Subject: [PATCH 325/790] gnu: linux-libre 5.4: Update to 5.4.227. * gnu/packages/linux.scm (linux-libre-5.4-version): Update to 5.4.227. (linux-libre-5.4-pristine-source): Update hash. --- gnu/packages/linux.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/linux.scm b/gnu/packages/linux.scm index 09179fb75e..e9cf286e7e 100644 --- a/gnu/packages/linux.scm +++ b/gnu/packages/linux.scm @@ -526,7 +526,7 @@ corresponding UPSTREAM-SOURCE (an origin), using the given DEBLOB-SCRIPTS." (%upstream-linux-source version hash) deblob-scripts-5.10))) -(define-public linux-libre-5.4-version "5.4.226") +(define-public linux-libre-5.4-version "5.4.227") (define-public linux-libre-5.4-gnu-revision "gnu1") (define deblob-scripts-5.4 (linux-libre-deblob-scripts @@ -536,7 +536,7 @@ corresponding UPSTREAM-SOURCE (an origin), using the given DEBLOB-SCRIPTS." (base32 "1bgblfkcnrabnr9hpdl07qgps57h6bq4v5pjrxs798vq43db66va"))) (define-public linux-libre-5.4-pristine-source (let ((version linux-libre-5.4-version) - (hash (base32 "0i4s1hl5q0ax55z7m5krzyw1zj9v03q8jcfksknb6qrg3lm5a7qc"))) + (hash (base32 "14q5gy48j78vwnqivrgpdhj778n2jq5l7yiw5na1rwqmfh1wbvsy"))) (make-linux-libre-source version (%upstream-linux-source version hash) deblob-scripts-5.4))) From ca0600b01a8a71eef353b14a98771a2f65d7ac5e Mon Sep 17 00:00:00 2001 From: Leo Famulari Date: Fri, 16 Dec 2022 21:57:41 -0500 Subject: [PATCH 326/790] gnu: linux-libre 4.19: Update to 4.19.269. * gnu/packages/linux.scm (linux-libre-4.19-version): Update to 4.19.269. (linux-libre-4.19-pristine-source): Update hash. --- gnu/packages/linux.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/linux.scm b/gnu/packages/linux.scm index e9cf286e7e..5581d1225c 100644 --- a/gnu/packages/linux.scm +++ b/gnu/packages/linux.scm @@ -541,7 +541,7 @@ corresponding UPSTREAM-SOURCE (an origin), using the given DEBLOB-SCRIPTS." (%upstream-linux-source version hash) deblob-scripts-5.4))) -(define-public linux-libre-4.19-version "4.19.268") +(define-public linux-libre-4.19-version "4.19.269") (define-public linux-libre-4.19-gnu-revision "gnu1") (define deblob-scripts-4.19 (linux-libre-deblob-scripts @@ -551,7 +551,7 @@ corresponding UPSTREAM-SOURCE (an origin), using the given DEBLOB-SCRIPTS." (base32 "0g1yhzxm3ixfll6n630v7lddcyvf888sg114nimh0lkvzd180s99"))) (define-public linux-libre-4.19-pristine-source (let ((version linux-libre-4.19-version) - (hash (base32 "0kr0di4gr6p57c8h6ybcli01kazq235npbh6qrpx0hpmqcdcx6r1"))) + (hash (base32 "02mjb16xxfj984vibpxvhjl84y5yg0jgzjccjdxnn8db4k9aa2vf"))) (make-linux-libre-source version (%upstream-linux-source version hash) deblob-scripts-4.19))) From 2634b303c0c7c938d24a5267a927dbbfea6d913f Mon Sep 17 00:00:00 2001 From: Leo Famulari Date: Fri, 16 Dec 2022 21:57:56 -0500 Subject: [PATCH 327/790] gnu: linux-libre 4.14: Update to 4.14.302. * gnu/packages/linux.scm (linux-libre-4.14-version): Update to 4.14.302. (linux-libre-4.14-pristine-source): Update hash. --- gnu/packages/linux.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/linux.scm b/gnu/packages/linux.scm index 5581d1225c..53a634b28c 100644 --- a/gnu/packages/linux.scm +++ b/gnu/packages/linux.scm @@ -556,7 +556,7 @@ corresponding UPSTREAM-SOURCE (an origin), using the given DEBLOB-SCRIPTS." (%upstream-linux-source version hash) deblob-scripts-4.19))) -(define-public linux-libre-4.14-version "4.14.301") +(define-public linux-libre-4.14-version "4.14.302") (define-public linux-libre-4.14-gnu-revision "gnu1") (define deblob-scripts-4.14 (linux-libre-deblob-scripts @@ -566,7 +566,7 @@ corresponding UPSTREAM-SOURCE (an origin), using the given DEBLOB-SCRIPTS." (base32 "00i91lx938nqlgy63hiricqd0fnbbf26vgya9c5lb7m1f4x324im"))) (define-public linux-libre-4.14-pristine-source (let ((version linux-libre-4.14-version) - (hash (base32 "16zrpfadsnznpl37crbq5g1hz1ch0zfp2a75yzlqy2fs0f7fxlmc"))) + (hash (base32 "102c9h0byr9v4bxzkdh7mnw1grm47ji6lf6l1gjlwah7f46j6ap3"))) (make-linux-libre-source version (%upstream-linux-source version hash) deblob-scripts-4.14))) From 34e8cd1e4ce2a778dc04675a01e049910766543a Mon Sep 17 00:00:00 2001 From: Leo Famulari Date: Fri, 16 Dec 2022 21:58:13 -0500 Subject: [PATCH 328/790] gnu: linux-libre 4.9: Update to 4.9.336. * gnu/packages/linux.scm (linux-libre-4.9-version): Update to 4.9.336. (linux-libre-4.9-pristine-source): Update hash. --- gnu/packages/linux.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/linux.scm b/gnu/packages/linux.scm index 53a634b28c..a025c51dab 100644 --- a/gnu/packages/linux.scm +++ b/gnu/packages/linux.scm @@ -571,7 +571,7 @@ corresponding UPSTREAM-SOURCE (an origin), using the given DEBLOB-SCRIPTS." (%upstream-linux-source version hash) deblob-scripts-4.14))) -(define-public linux-libre-4.9-version "4.9.335") +(define-public linux-libre-4.9-version "4.9.336") (define-public linux-libre-4.9-gnu-revision "gnu1") (define deblob-scripts-4.9 (linux-libre-deblob-scripts @@ -581,7 +581,7 @@ corresponding UPSTREAM-SOURCE (an origin), using the given DEBLOB-SCRIPTS." (base32 "0bib3641dbcqdkx3anna3caxnsg3nw9cnmhcklq0s93g3m57041h"))) (define-public linux-libre-4.9-pristine-source (let ((version linux-libre-4.9-version) - (hash (base32 "0agb1avdqxbmb0z751f5c4d6s7k9zb6dq04z82gx0v4zzrhxhkzd"))) + (hash (base32 "032hgfvn7za2v49jjc3pdzx0cfglrmjkbl2d3pz857yc0q9y2v8z"))) (make-linux-libre-source version (%upstream-linux-source version hash) deblob-scripts-4.9))) From 5f3082084daf4968879a30747eafd23c1206d88a Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Sun, 11 Dec 2022 01:00:00 +0100 Subject: [PATCH 329/790] teams: Add Tobias Geerinckx-Rice. * etc/teams.scm.in: Add Tobias Geerinckx-Rice. --- etc/teams.scm.in | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/etc/teams.scm.in b/etc/teams.scm.in index 57d4357900..aa38a3b798 100644 --- a/etc/teams.scm.in +++ b/etc/teams.scm.in @@ -428,6 +428,10 @@ importer." "andreas@enge.fr") science) +(define-member (person "Tobias Geerinckx-Rice" + "me@tobias.gr") + core kernel mentors) + (define-member (person "Björn Höfling" "bjoern.hoefling@bjoernhoefling.de") java) From f28ca2447c5e2eef1ba6a3a11587380a665b0e26 Mon Sep 17 00:00:00 2001 From: Simon South Date: Sat, 17 Dec 2022 13:12:05 -0500 Subject: [PATCH 330/790] gnu: flashrom: Fix build on AArch64. * gnu/packages/patches/flashrom-fix-building-on-aarch64.patch: New file. * gnu/local.mk (dist_patch_DATA): Add it. * gnu/packages/flashing-tools.scm (flashrom)[source]: Apply it. Signed-off-by: Tobias Geerinckx-Rice --- gnu/local.mk | 1 + gnu/packages/flashing-tools.scm | 4 +- .../flashrom-fix-building-on-aarch64.patch | 89 +++++++++++++++++++ 3 files changed, 93 insertions(+), 1 deletion(-) create mode 100644 gnu/packages/patches/flashrom-fix-building-on-aarch64.patch diff --git a/gnu/local.mk b/gnu/local.mk index 5b8944f568..56634e090c 100644 --- a/gnu/local.mk +++ b/gnu/local.mk @@ -1112,6 +1112,7 @@ dist_patch_DATA = \ %D%/packages/patches/firebird-riscv64-support-pt1.patch \ %D%/packages/patches/firebird-riscv64-support-pt2.patch \ %D%/packages/patches/flann-cmake-3.11.patch \ + %D%/packages/patches/flashrom-fix-building-on-aarch64.patch \ %D%/packages/patches/flatpak-fix-path.patch \ %D%/packages/patches/flatpak-unset-gdk-pixbuf-for-sandbox.patch \ %D%/packages/patches/fontconfig-cache-ignore-mtime.patch \ diff --git a/gnu/packages/flashing-tools.scm b/gnu/packages/flashing-tools.scm index 08300cb860..e7165efe79 100644 --- a/gnu/packages/flashing-tools.scm +++ b/gnu/packages/flashing-tools.scm @@ -66,7 +66,9 @@ version ".tar.bz2")) (sha256 (base32 - "0ax4kqnh7kd3z120ypgp73qy1knz47l6qxsqzrfkd97mh5cdky71")))) + "0ax4kqnh7kd3z120ypgp73qy1knz47l6qxsqzrfkd97mh5cdky71")) + (patches + (search-patches "flashrom-fix-building-on-aarch64.patch")))) (build-system gnu-build-system) (inputs (list dmidecode pciutils libusb libftdi)) (native-inputs (list pkg-config)) diff --git a/gnu/packages/patches/flashrom-fix-building-on-aarch64.patch b/gnu/packages/patches/flashrom-fix-building-on-aarch64.patch new file mode 100644 index 0000000000..9f54305b47 --- /dev/null +++ b/gnu/packages/patches/flashrom-fix-building-on-aarch64.patch @@ -0,0 +1,89 @@ +commit da6b3b70cb852dd8e9f9e21aef95fa83e7f7ab0d +Author: Pyry Kontio +Date: Mon Jul 6 12:57:35 2020 +0900 + + Makefile: Fix building on AArch64 NixOS + + The parsing of the output of archtest.c produced an unexpected + value on AArch64 NixOS. For example, the make variable ARCH was set to: + + ``` + bit outside of fd_set selected + arm + ``` + + This made the arch and OS checks fail. + + This commit simplifies the parsing, making it more robust. + + The C files archtest.c, endiantest.c and os.h used to set the + TARGET_OS, ARCH and ENDIAN variables, respectively, output + the result of the test as the final line, so just extracting + the final line and removing double quoting is enough. + + This commit also fixes a bug with debug_shell lacking escaping + single quotes, which prevented using the single quote in the + debug_shell calls. It used to work by accident before this fix; + the line in the call happened to contain a balanced pair of double + quotes and lacked other characters that needed escaping, which + didn't break the debug_shell, but this was accidental and very + brittle. + + Signed-off-by: Pyry Kontio + Change-Id: Iaa4477a71e758cf9ecad2c22f3b77bc6508a3510 + Reviewed-on: https://review.coreboot.org/c/flashrom/+/43140 + Tested-by: build bot (Jenkins) + Reviewed-by: Angel Pons + +diff --git a/Makefile b/Makefile +index f3f7717e..e475cbdb 100644 +--- a/Makefile ++++ b/Makefile +@@ -83,7 +83,8 @@ dummy_for_make_3_80:=$(shell printf "Build started on %s\n\n" "$$(date)" >$(BUIL + + # Provide an easy way to execute a command, print its output to stdout and capture any error message on stderr + # in the build details file together with the original stdout output. +-debug_shell = $(shell export LC_ALL=C ; { echo 'exec: export LC_ALL=C ; { $(1) ; }' >&2; { $(1) ; } | tee -a $(BUILD_DETAILS_FILE) ; echo >&2 ; } 2>>$(BUILD_DETAILS_FILE)) ++debug_shell = $(shell export LC_ALL=C ; { echo 'exec: export LC_ALL=C ; { $(subst ','\'',$(1)) ; }' >&2; \ ++ { $(1) ; } | tee -a $(BUILD_DETAILS_FILE) ; echo >&2 ; } 2>>$(BUILD_DETAILS_FILE)) + + ############################################################################### + # General OS-specific settings. +@@ -106,7 +107,8 @@ endif + # IMPORTANT: The following line must be placed before TARGET_OS is ever used + # (of course), but should come after any lines setting CC because the line + # below uses CC itself. +-override TARGET_OS := $(strip $(call debug_shell,$(CC) $(CPPFLAGS) -E os.h 2>/dev/null | grep -v '^\#' | grep '"' | cut -f 2 -d'"')) ++override TARGET_OS := $(strip $(call debug_shell,$(CC) $(CPPFLAGS) -E os.h 2>/dev/null \ ++ | tail -1 | cut -f 2 -d'"')) + + ifeq ($(TARGET_OS), Darwin) + override CPPFLAGS += -I/opt/local/include -I/usr/local/include +@@ -490,8 +492,10 @@ endif + # IMPORTANT: The following line must be placed before ARCH is ever used + # (of course), but should come after any lines setting CC because the line + # below uses CC itself. +-override ARCH := $(strip $(call debug_shell,$(CC) $(CPPFLAGS) -E archtest.c 2>/dev/null | grep -v '^\#' | grep '"' | cut -f 2 -d'"')) +-override ENDIAN := $(strip $(call debug_shell,$(CC) $(CPPFLAGS) -E endiantest.c 2>/dev/null | grep -v '^\#')) ++override ARCH := $(strip $(call debug_shell,$(CC) $(CPPFLAGS) -E archtest.c 2>/dev/null \ ++ | tail -1 | cut -f 2 -d'"')) ++override ENDIAN := $(strip $(call debug_shell,$(CC) $(CPPFLAGS) -E endiantest.c 2>/dev/null \ ++ | tail -1)) + + # Disable the internal programmer on unsupported architectures (everything but x86 and mipsel) + ifneq ($(ARCH)-little, $(filter $(ARCH),x86 mips)-$(ENDIAN)) +@@ -1299,12 +1303,12 @@ compiler: featuresavailable + @printf "Target arch is " + @# FreeBSD wc will output extraneous whitespace. + @echo $(ARCH)|wc -w|grep -q '^[[:blank:]]*1[[:blank:]]*$$' || \ +- ( echo "unknown. Aborting."; exit 1) ++ ( echo "unknown (\"$(ARCH)\"). Aborting."; exit 1) + @printf "%s\n" '$(ARCH)' + @printf "Target OS is " + @# FreeBSD wc will output extraneous whitespace. + @echo $(TARGET_OS)|wc -w|grep -q '^[[:blank:]]*1[[:blank:]]*$$' || \ +- ( echo "unknown. Aborting."; exit 1) ++ ( echo "unknown (\"$(TARGET_OS)\"). Aborting."; exit 1) + @printf "%s\n" '$(TARGET_OS)' + ifeq ($(TARGET_OS), libpayload) + @$(CC) --version 2>&1 | grep -q coreboot || \ From da2f7868f8816d801d485d7d73206161d69aa8e9 Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Sun, 11 Dec 2022 01:00:01 +0100 Subject: [PATCH 331/790] gnu: coturn: Update to 4.6.1. * gnu/packages/telephony.scm (coturn): Update to 4.6.1. --- gnu/packages/telephony.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/telephony.scm b/gnu/packages/telephony.scm index 302b351fbb..81621e9d4d 100644 --- a/gnu/packages/telephony.scm +++ b/gnu/packages/telephony.scm @@ -904,7 +904,7 @@ telephony functionality into custom Telegram clients.") (define-public coturn (package (name "coturn") - (version "4.6.0") + (version "4.6.1") (source (origin (method git-fetch) @@ -913,7 +913,7 @@ telephony functionality into custom Telegram clients.") (commit version))) (file-name (git-file-name name version)) (sha256 - (base32 "152v2lnjj9b3w61d8aak7hmi9riw9cjs5g54g1gfpzlyk4c2jw21")))) + (base32 "04d3c2lxc496zxx3nzqr9fskm2w57kqijdfq3wsa0yp2dp28yjkj")))) (inputs (list openssl sqlite From 0335499876d08b12c63057f386535695f1b65597 Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Sun, 11 Dec 2022 01:00:30 +0100 Subject: [PATCH 332/790] gnu: ecryptfs-utils: Wrap scripts. This should fix #59850, although there might be other binaries I missed. * gnu/packages/linux.scm (ecryptfs-utils)[arguments]: Add a new 'wrap-scripts phase to do what it says. [inputs]: Add coreutils, findutils, gawk, grep, keyutils, lsof, rsync, sed, and which. --- gnu/packages/linux.scm | 43 +++++++++++++++++++++++++++++++++++++++--- 1 file changed, 40 insertions(+), 3 deletions(-) diff --git a/gnu/packages/linux.scm b/gnu/packages/linux.scm index a025c51dab..f8b29d4d46 100644 --- a/gnu/packages/linux.scm +++ b/gnu/packages/linux.scm @@ -130,6 +130,7 @@ #:use-module (gnu packages libunwind) #:use-module (gnu packages libusb) #:use-module (gnu packages llvm) + #:use-module (gnu packages lsof) #:use-module (gnu packages lua) #:use-module (gnu packages man) #:use-module (gnu packages maths) @@ -150,6 +151,7 @@ #:use-module (gnu packages python-xyz) #:use-module (gnu packages readline) #:use-module (gnu packages rrdtool) + #:use-module (gnu packages rsync) #:use-module (gnu packages samba) #:use-module (gnu packages sdl) #:use-module (gnu packages serialization) @@ -6762,6 +6764,10 @@ not as a replacement for it.") (build-system gnu-build-system) (arguments `(#:configure-flags (list "--disable-pywrap") + #:modules (,@%gnu-build-system-modules + (ice-9 binary-ports) + (rnrs bytevectors) + (srfi srfi-26)) #:phases (modify-phases %standard-phases (add-after 'patch-source-shebangs 'patch-hardcoded-paths @@ -6799,17 +6805,48 @@ not as a replacement for it.") (("/sbin/unix_chkpwd") (string-append linux-pam "/sbin/unix_chkpwd")) (("/sbin/dmsetup") - (string-append lvm2 "/sbin/dmsetup"))))))))) + (string-append lvm2 "/sbin/dmsetup")))))) + (add-after 'install 'wrap-scripts + (lambda* (#:key inputs outputs #:allow-other-keys) + (let* ((out (assoc-ref outputs "out")) + (bin (string-append out "/bin")) + (add (map (lambda (bin) + (dirname (search-input-file + inputs (string-append "bin/" bin)))) + ;; For simplicity, we wrap all scripts the same. + (list "awk" "find" "gettext" "grep" "keyctl" "ls" + "lsof" "mount" "rsync" "sed" "which"))) + (script? (lambda (file) + (call-with-input-file file + (lambda (port) + (bytevector=? (string->utf8 "#!") + (get-bytevector-n port 2))))))) + (for-each (lambda (file) + (when (script? file) + (wrap-program file + ;; '= would be better than 'suffix but break + ;; setuid binaries. + `("PATH" ":" suffix (,@add + ,(string-append bin)))))) + (find-files bin ".")))))))) (native-inputs (list intltool perl ; for pod2man pkg-config)) (inputs - `(("keyutils" ,keyutils) + `(("coreutils" ,coreutils) + ("findutils" ,findutils) + ("gawk" ,gawk) + ("grep" ,grep) + ("keyutils" ,keyutils) ("linux-pam" ,linux-pam) + ("lsof" ,lsof) ("utils-linux" ,util-linux) ("cryptsetup" ,cryptsetup) ("lvm2" ,lvm2) - ("nss" ,nss))) + ("nss" ,nss) + ("rsync", rsync) + ("sed" ,sed) + ("which" ,which))) (home-page "https://ecryptfs.org/") (synopsis "eCryptfs cryptographic file system utilities") (description From 2472015c36f333657c5a223150e3e809f01ad1af Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Sun, 11 Dec 2022 01:00:01 +0100 Subject: [PATCH 333/790] gnu: ecryptfs-utils: Remove input labels. MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * gnu/packages/linux.scm (ecryptfs-utils)[inputs]: Remove input labels. [arguments]: Fix ‘utils-linux’ typo. --- gnu/packages/linux.scm | 34 +++++++++++++++++----------------- 1 file changed, 17 insertions(+), 17 deletions(-) diff --git a/gnu/packages/linux.scm b/gnu/packages/linux.scm index f8b29d4d46..41fb24f82a 100644 --- a/gnu/packages/linux.scm +++ b/gnu/packages/linux.scm @@ -6773,7 +6773,7 @@ not as a replacement for it.") (add-after 'patch-source-shebangs 'patch-hardcoded-paths (lambda* (#:key inputs outputs #:allow-other-keys) (let ((out (assoc-ref outputs "out")) - (utils-linux (assoc-ref inputs "utils-linux")) + (util-linux (assoc-ref inputs "util-linux")) (cryptsetup (assoc-ref inputs "cryptsetup")) (linux-pam (assoc-ref inputs "linux-pam")) (lvm2 (assoc-ref inputs "lvm2"))) @@ -6787,9 +6787,9 @@ not as a replacement for it.") "src/desktop/ecryptfs-mount-private.desktop.in" "src/desktop/ecryptfs-setup-private.desktop.in") (("/bin/mount") - (string-append utils-linux "/bin/mount")) + (string-append util-linux "/bin/mount")) (("/bin/umount") - (string-append utils-linux "/bin/umount")) + (string-append util-linux "/bin/umount")) (("/sbin/mount.ecryptfs_private") (string-append out "/sbin/mount.ecryptfs_private")) (("/sbin/umount.ecryptfs_private") @@ -6833,20 +6833,20 @@ not as a replacement for it.") (list intltool perl ; for pod2man pkg-config)) (inputs - `(("coreutils" ,coreutils) - ("findutils" ,findutils) - ("gawk" ,gawk) - ("grep" ,grep) - ("keyutils" ,keyutils) - ("linux-pam" ,linux-pam) - ("lsof" ,lsof) - ("utils-linux" ,util-linux) - ("cryptsetup" ,cryptsetup) - ("lvm2" ,lvm2) - ("nss" ,nss) - ("rsync", rsync) - ("sed" ,sed) - ("which" ,which))) + (list coreutils + cryptsetup + findutils + gawk + grep + keyutils + linux-pam + lsof + lvm2 + nss + rsync + sed + util-linux + which)) (home-page "https://ecryptfs.org/") (synopsis "eCryptfs cryptographic file system utilities") (description From 09b984b77d060e6fd37833541b828f73238cf2be Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ludovic=20Court=C3=A8s?= Date: Wed, 14 Dec 2022 09:50:38 +0100 Subject: [PATCH 334/790] doc: Verify the release with my own OpenPGP key. * doc/guix.texi (OPENPGP-SIGNING-KEY-ID, OPENPGP-SIGNING-KEY-URL): Switch to my key. --- doc/guix.texi | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/doc/guix.texi b/doc/guix.texi index e547d469f4..84bfa390f7 100644 --- a/doc/guix.texi +++ b/doc/guix.texi @@ -10,8 +10,8 @@ @include version.texi @c Identifier of the OpenPGP key used to sign tarballs and such. -@set OPENPGP-SIGNING-KEY-ID 27D586A4F8900854329FF09F1260E46482E63562 -@set OPENPGP-SIGNING-KEY-URL https://sv.gnu.org/people/viewgpg.php?user_id=127547 +@set OPENPGP-SIGNING-KEY-ID 3CE464558A84FDC69DB40CFB090B11993D9AEBB5 +@set OPENPGP-SIGNING-KEY-URL https://sv.gnu.org/people/viewgpg.php?user_id=15145 @c Base URL for downloads. @set BASE-URL https://ftp.gnu.org/gnu/guix From 2cf16f2c31e5e124754ec8c400f22ad9fe4a506b Mon Sep 17 00:00:00 2001 From: Bruno Victal Date: Tue, 29 Nov 2022 21:21:59 +0000 Subject: [PATCH 335/790] doc: Fix formatting for 'computed-file'. MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * doc/guix.texi (G-Expressions): Fix formatting for 'computed-file'. Signed-off-by: Ludovic Courtès --- doc/guix.texi | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/doc/guix.texi b/doc/guix.texi index 84bfa390f7..2fc73b8f3e 100644 --- a/doc/guix.texi +++ b/doc/guix.texi @@ -11706,8 +11706,7 @@ This is the declarative counterpart of @code{text-file}. @end deffn @deffn {Scheme Procedure} computed-file @var{name} @var{gexp} @ - [#:local-build? #t] - [#:options '()] + [#:local-build? #t] [#:options '()] Return an object representing the store item @var{name}, a file or directory computed by @var{gexp}. When @var{local-build?} is true (the default), the derivation is built locally. @var{options} is a list of From 047ae5c3458d03bea4926e6cc1760bcfce1e2ab4 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ludovic=20Court=C3=A8s?= Date: Thu, 15 Dec 2022 00:12:43 +0100 Subject: [PATCH 336/790] doc: Use VM image file name consistently. Previously, what "/tmp/qemu-image" refers to could be unclear at first. * doc/guix.texi (Running Guix in a VM): Use the original image file name instead of /tmp/qemu-image. * po/doc/guix-manual.de.po, po/doc/guix-manual.es.po, po/doc/guix-manual.fr.po, po/doc/guix-manual.pt_BR.po, po/doc/guix-manual.ru.po, po/doc/guix-manual.zh_CN.po: Adjust accordingly. --- doc/guix.texi | 7 ++++--- po/doc/guix-manual.de.po | 4 ++-- po/doc/guix-manual.es.po | 4 ++-- po/doc/guix-manual.fr.po | 4 ++-- po/doc/guix-manual.pt_BR.po | 4 ++-- po/doc/guix-manual.ru.po | 4 ++-- po/doc/guix-manual.zh_CN.po | 4 ++-- 7 files changed, 16 insertions(+), 15 deletions(-) diff --git a/doc/guix.texi b/doc/guix.texi index 2fc73b8f3e..784114f0bb 100644 --- a/doc/guix.texi +++ b/doc/guix.texi @@ -39223,7 +39223,7 @@ $ qemu-system-x86_64 \ -nic user,model=virtio-net-pci \ -enable-kvm -m 2048 \ -device virtio-blk,drive=myhd \ - -drive if=none,file=/tmp/qemu-image,id=myhd + -drive if=none,file=guix-system-vm-image-@value{VERSION}.x86_64-linux.qcow2,id=myhd @end example Here is what each of these options means: @@ -39259,8 +39259,9 @@ better performance than if it were emulating a complete disk drive. See the QEMU and KVM documentation for more info. @item -drive if=none,file=/tmp/qemu-image,id=myhd -Use our QCOW image, the @file{/tmp/qemu-image} file, as the backing -store of the ``myhd'' drive. +Use our QCOW image, the +@file{guix-system-vm-image-@value{VERSION}.x86_64-linux.qcow2} file, as +the backing store of the ``myhd'' drive. @end table The default @command{run-vm.sh} script that is returned by an invocation of diff --git a/po/doc/guix-manual.de.po b/po/doc/guix-manual.de.po index e8b2de6943..b33bce32e9 100644 --- a/po/doc/guix-manual.de.po +++ b/po/doc/guix-manual.de.po @@ -13,7 +13,7 @@ msgstr "" "Project-Id-Version: guix-manual 1.2.0-pre3\n" "Report-Msgid-Bugs-To: bug-guix@gnu.org\n" "POT-Creation-Date: 2022-12-02 03:18+0000\n" -"PO-Revision-Date: 2022-12-03 17:33+0000\n" +"PO-Revision-Date: 2022-12-15 00:11+0100\n" "Last-Translator: Florian Pelz \n" "Language-Team: German \n" "Language: de\n" @@ -73899,7 +73899,7 @@ msgstr "-drive if=none,file=/tmp/qemu-image,id=myhd" #. type: table #: guix-git/doc/guix.texi:39296 -msgid "Use our QCOW image, the @file{/tmp/qemu-image} file, as the backing store of the ``myhd'' drive." +msgid "Use our QCOW image, the @file{guix-system-vm-image-@value{VERSION}.x86_64-linux.qcow2} file, as the backing store of the ``myhd'' drive." msgstr "Unser QCOW-Abbild in der Datei @file{/tmp/qemu-image} soll als Inhalt des „myhd“-Laufwerks herhalten." #. type: Plain text diff --git a/po/doc/guix-manual.es.po b/po/doc/guix-manual.es.po index ec048f03e3..a7441941b9 100644 --- a/po/doc/guix-manual.es.po +++ b/po/doc/guix-manual.es.po @@ -55,7 +55,7 @@ msgstr "" "Project-Id-Version: guix-manual 1.2.0-pre3\n" "Report-Msgid-Bugs-To: bug-guix@gnu.org\n" "POT-Creation-Date: 2022-12-02 03:18+0000\n" -"PO-Revision-Date: 2022-11-04 11:27+0000\n" +"PO-Revision-Date: 2022-12-15 00:11+0100\n" "Last-Translator: Julien Lepiller \n" "Language-Team: Spanish \n" "Language: es\n" @@ -77483,7 +77483,7 @@ msgstr "-drive if=none,file=/tmp/imagen-qemu,id=midisco" #. type: table #: guix-git/doc/guix.texi:39296 -msgid "Use our QCOW image, the @file{/tmp/qemu-image} file, as the backing store of the ``myhd'' drive." +msgid "Use our QCOW image, the @file{guix-system-vm-image-@value{VERSION}.x86_64-linux.qcow2} file, as the backing store of the ``myhd'' drive." msgstr "Usa nuestra imagen QCOW, el archivo @file{/tmp/imagen-qemu}, como almacenamiento físico para la unidad ``midisco''." #. type: Plain text diff --git a/po/doc/guix-manual.fr.po b/po/doc/guix-manual.fr.po index bec07beebf..aed8e16128 100644 --- a/po/doc/guix-manual.fr.po +++ b/po/doc/guix-manual.fr.po @@ -46,7 +46,7 @@ msgstr "" "Project-Id-Version: guix-manual 1.2.0-pre3\n" "Report-Msgid-Bugs-To: bug-guix@gnu.org\n" "POT-Creation-Date: 2022-12-02 03:18+0000\n" -"PO-Revision-Date: 2022-12-03 17:33+0000\n" +"PO-Revision-Date: 2022-12-15 00:11+0100\n" "Last-Translator: Julien Lepiller \n" "Language-Team: French \n" "Language: fr\n" @@ -74054,7 +74054,7 @@ msgstr "-drive if=none,file=/tmp/qemu-image,id=myhd" #. type: table #: guix-git/doc/guix.texi:39296 -msgid "Use our QCOW image, the @file{/tmp/qemu-image} file, as the backing store of the ``myhd'' drive." +msgid "Use our QCOW image, the @file{guix-system-vm-image-@value{VERSION}.x86_64-linux.qcow2} file, as the backing store of the ``myhd'' drive." msgstr "Utilise notre image QCOW, le fichier @file{/tmp/qemu-image}, comme stockage pour le lecteur « myhd »." #. type: Plain text diff --git a/po/doc/guix-manual.pt_BR.po b/po/doc/guix-manual.pt_BR.po index bfe3e98eb1..0372dc2c13 100644 --- a/po/doc/guix-manual.pt_BR.po +++ b/po/doc/guix-manual.pt_BR.po @@ -10,7 +10,7 @@ msgstr "" "Project-Id-Version: guix manual checkout\n" "Report-Msgid-Bugs-To: bug-guix@gnu.org\n" "POT-Creation-Date: 2022-12-02 03:18+0000\n" -"PO-Revision-Date: 2022-01-25 15:16+0000\n" +"PO-Revision-Date: 2022-12-15 00:11+0100\n" "Last-Translator: Fábio Rodrigues Ribeiro \n" "Language-Team: Portuguese (Brazil) \n" "Language: pt_BR\n" @@ -71324,7 +71324,7 @@ msgstr "" #. type: table #: guix-git/doc/guix.texi:39296 -msgid "Use our QCOW image, the @file{/tmp/qemu-image} file, as the backing store of the ``myhd'' drive." +msgid "Use our QCOW image, the @file{guix-system-vm-image-@value{VERSION}.x86_64-linux.qcow2} file, as the backing store of the ``myhd'' drive." msgstr "" #. type: Plain text diff --git a/po/doc/guix-manual.ru.po b/po/doc/guix-manual.ru.po index 2efbce94c1..9738d516c6 100644 --- a/po/doc/guix-manual.ru.po +++ b/po/doc/guix-manual.ru.po @@ -16,7 +16,7 @@ msgstr "" "Project-Id-Version: guix-manual 1.2.0-pre2\n" "Report-Msgid-Bugs-To: bug-guix@gnu.org\n" "POT-Creation-Date: 2022-12-02 03:18+0000\n" -"PO-Revision-Date: 2021-12-11 23:16+0000\n" +"PO-Revision-Date: 2022-12-15 00:11+0100\n" "Last-Translator: Nikolay Korotkiy \n" "Language-Team: Russian \n" "Language: ru\n" @@ -72867,7 +72867,7 @@ msgstr "" #. type: table #: guix-git/doc/guix.texi:39296 -msgid "Use our QCOW image, the @file{/tmp/qemu-image} file, as the backing store of the ``myhd'' drive." +msgid "Use our QCOW image, the @file{guix-system-vm-image-@value{VERSION}.x86_64-linux.qcow2} file, as the backing store of the ``myhd'' drive." msgstr "" #. type: Plain text diff --git a/po/doc/guix-manual.zh_CN.po b/po/doc/guix-manual.zh_CN.po index 7e53f0f41d..f5abe54b11 100644 --- a/po/doc/guix-manual.zh_CN.po +++ b/po/doc/guix-manual.zh_CN.po @@ -16,7 +16,7 @@ msgstr "" "Project-Id-Version: guix-manual 1.0.1-pre1\n" "Report-Msgid-Bugs-To: bug-guix@gnu.org\n" "POT-Creation-Date: 2022-12-02 03:18+0000\n" -"PO-Revision-Date: 2022-09-22 13:19+0000\n" +"PO-Revision-Date: 2022-12-15 00:11+0100\n" "Last-Translator: Yang Yulin \n" "Language-Team: Chinese (Simplified) \n" "Language: zh_CN\n" @@ -71148,7 +71148,7 @@ msgstr "" #. type: table #: guix-git/doc/guix.texi:39296 -msgid "Use our QCOW image, the @file{/tmp/qemu-image} file, as the backing store of the ``myhd'' drive." +msgid "Use our QCOW image, the @file{guix-system-vm-image-@value{VERSION}.x86_64-linux.qcow2} file, as the backing store of the ``myhd'' drive." msgstr "" #. type: Plain text From b1aef25453067004279c4267cf25e8d6d365890d Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ludovic=20Court=C3=A8s?= Date: Thu, 15 Dec 2022 23:54:10 +0100 Subject: [PATCH 337/790] install: Make sure uvesafb can be loaded. Fixes . Reported by pelzflorian (Florian Pelz) . Previously, the 'modprobe' executable would try and fail to load the module from /lib/modules/*. Set 'LINUX_MODULE_DIRECTORY' to make sure 'modprobe' looks for the module in the right place. * gnu/system/install.scm (uvesafb-shepherd-service)[modprobe]: New variable. In 'start' method, invoke it instead of KMOD/bin/modprobe. --- gnu/system/install.scm | 13 ++++++++++++- 1 file changed, 12 insertions(+), 1 deletion(-) diff --git a/gnu/system/install.scm b/gnu/system/install.scm index f6f1923121..3dd9e0e87b 100644 --- a/gnu/system/install.scm +++ b/gnu/system/install.scm @@ -284,13 +284,24 @@ templates under @file{/etc/configuration}."))) ;; appropriate options. The GUI installer needs it when the machine does not ;; support Kernel Mode Setting. Otherwise kmscon is missing /dev/fb0. (define (uvesafb-shepherd-service _) + (define modprobe + (program-file "modprobe-wrapper" + #~(begin + ;; Use a wrapper because shepherd 0.9.3 won't let us + ;; pass environment variables to the child process: + ;; . + (setenv "LINUX_MODULE_DIRECTORY" + "/run/booted-system/kernel/lib/modules") + (apply execl #$(file-append kmod "/bin/modprobe") + "modprobe" (cdr (command-line)))))) + (list (shepherd-service (documentation "Load the uvesafb kernel module if needed.") (provision '(maybe-uvesafb)) (requirement '(file-systems)) (start #~(lambda () (or (file-exists? "/dev/fb0") - (invoke #+(file-append kmod "/bin/modprobe") + (invoke #+modprobe "uvesafb" (string-append "v86d=" #$v86d "/sbin/v86d") "mode_option=1024x768")))) From 239bfe2ec1fa3b4305500211e6cade6e4bda2a62 Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Sat, 17 Dec 2022 19:15:50 +0100 Subject: [PATCH 338/790] Update NEWS. --- NEWS | 11 +++++++++-- 1 file changed, 9 insertions(+), 2 deletions(-) diff --git a/NEWS b/NEWS index c35f1266cf..3d89138fa0 100644 --- a/NEWS +++ b/NEWS @@ -80,9 +80,10 @@ Please send Guix bug reports to bug-guix@gnu.org. *** The init RAM disk honors more arguments—e.g. ‘root’ and ‘rootflags’ *** ‘guix system image’ can now generate WSL images *** The mcron task scheduler logs now contain the jobs exit statuses +*** Chromium extensions are now built in a deterministic fashion ** Programming interfaces -*** Package input fields can now plain package lists +*** Package input fields can now be plain package lists *** G-expressions can now be used in build phases *** New ‘modify-inputs’ macro to ease customizing a list of package inputs *** New ‘this-package-input’ and ‘this-package-native-input’ macros @@ -92,7 +93,7 @@ Please send Guix bug reports to bug-guix@gnu.org. *** ‘texlive-union’ is now deprecated in favor of ‘texlive-updmap.cfg’ *** New (guix cpu) module *** New (guix least-authority) module -*** New (guix plaform) module +*** New (guix platform) module *** New (guix read-print) module It provides a comment-preserving reader and a comment-preserving @@ -103,6 +104,12 @@ pretty-printer smarter than (ice-9 pretty-print). This build system lets you build Guix instances from channel specifications, similar to how 'guix time-machine' would do it, as regular packages. +*** New ‘pyproject-build-system’ + +This is an extension of ‘python-build-system’ with support for PEP-517 and +‘pyproject.toml’ files. It may eventually get merged back into +‘python-build-system’. + *** New ‘elm-build-system’ *** New ‘rebar-build-system’ *** New services From 2d4d26769d6a3be1b21302b0bb2bd099fd55ccf8 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ludovic=20Court=C3=A8s?= Date: Sat, 17 Dec 2022 12:25:47 +0100 Subject: [PATCH 339/790] daemon: Make "opening file" error messages distinguishable. * nix/libstore/build.cc (DerivationGoal::openLogFile): Customize "opening file" error message. * nix/libutil/hash.cc (hashFile): Likewise. * nix/libutil/util.cc (readFile, writeFile): Likewise. --- nix/libstore/build.cc | 2 +- nix/libutil/hash.cc | 2 +- nix/libutil/util.cc | 4 ++-- 3 files changed, 4 insertions(+), 4 deletions(-) diff --git a/nix/libstore/build.cc b/nix/libstore/build.cc index 10a6093bd5..c5383bc756 100644 --- a/nix/libstore/build.cc +++ b/nix/libstore/build.cc @@ -2576,7 +2576,7 @@ Path DerivationGoal::openLogFile() closeOnExec(fd); if (!(fLogFile = fdopen(fd.borrow(), "w"))) - throw SysError(format("opening file `%1%'") % logFileName); + throw SysError(format("opening log file `%1%'") % logFileName); int err; if (!(bzLogFile = BZ2_bzWriteOpen(&err, fLogFile, 9, 0, 0))) diff --git a/nix/libutil/hash.cc b/nix/libutil/hash.cc index 7853acdd49..9ba604eb85 100644 --- a/nix/libutil/hash.cc +++ b/nix/libutil/hash.cc @@ -244,7 +244,7 @@ Hash hashFile(HashType ht, const Path & path) start(ht, ctx); AutoCloseFD fd = open(path.c_str(), O_RDONLY); - if (fd == -1) throw SysError(format("opening file `%1%'") % path); + if (fd == -1) throw SysError(format("computing hash of file `%1%'") % path); unsigned char buf[8192]; ssize_t n; diff --git a/nix/libutil/util.cc b/nix/libutil/util.cc index 4d3780e3c2..82eac72120 100644 --- a/nix/libutil/util.cc +++ b/nix/libutil/util.cc @@ -264,7 +264,7 @@ string readFile(const Path & path, bool drain) { AutoCloseFD fd = open(path.c_str(), O_RDONLY); if (fd == -1) - throw SysError(format("opening file `%1%'") % path); + throw SysError(format("reading file `%1%'") % path); return drain ? drainFD(fd) : readFile(fd); } @@ -273,7 +273,7 @@ void writeFile(const Path & path, const string & s) { AutoCloseFD fd = open(path.c_str(), O_WRONLY | O_TRUNC | O_CREAT, 0666); if (fd == -1) - throw SysError(format("opening file '%1%'") % path); + throw SysError(format("writing file '%1%'") % path); writeFull(fd, s); } From a8f9579348aae58b68b25004cfd28aa7407db802 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ludovic=20Court=C3=A8s?= Date: Sat, 17 Dec 2022 22:39:37 +0100 Subject: [PATCH 340/790] Update NEWS. --- NEWS | 21 ++++++++++++++++++--- 1 file changed, 18 insertions(+), 3 deletions(-) diff --git a/NEWS b/NEWS index 3d89138fa0..47545f6bae 100644 --- a/NEWS +++ b/NEWS @@ -81,6 +81,24 @@ Please send Guix bug reports to bug-guix@gnu.org. *** ‘guix system image’ can now generate WSL images *** The mcron task scheduler logs now contain the jobs exit statuses *** Chromium extensions are now built in a deterministic fashion +*** The ‘rsync’ service lets you specify individual “modules” +*** New services + +anonip, bitmask, fail2ban, gitile, greetd, jami, lightdm, log-cleanup, +nar-herder, opendht, rasdaemon, samba, seatd, strongswan, wsdd + +*** 5311 new packages + +*** 6573 package updates + +Noteworthy updates: +bash 5.1.8, binutils 2.37, clojure 1.11.1, cups 2.3.3op2, emacs 28.2, +enlightenment 0.25.4, gcc-toolchain 12.2.0, gdb 12.1, ghc 8.10.7, +gimp 2.10.32, glibc 2.33, gnome 42.4, gnupg 2.2.32, go 1.19.1, guile 3.0.8, +icecat 102.5.0-guix0-preview1, icedtea 3.19.0, inkscape 1.2.1, julia 1.6.7, +libreoffice 7.4.3.2, linux-libre 6.0.10, ocaml 4.14.0, octave 7.2.0, +openjdk 18, perl 5.34.0, python2 2.7.18, python 3.9.9, racket 8.7, +rust 1.60.0, r 4.2.2, sbcl 2.2.10, shepherd 0.9.3, xorg-server 21.1.4 ** Programming interfaces *** Package input fields can now be plain package lists @@ -112,9 +130,6 @@ This is an extension of ‘python-build-system’ with support for PEP-517 and *** New ‘elm-build-system’ *** New ‘rebar-build-system’ -*** New services -anonip, bitmask, fail2ban, gitile, greetd, jami, lightdm, log-cleanup, -nar-herder, opendht, rasdaemon, samba, seatd, strongswan, wsdd ** Noteworthy bug fixes *** Fall back to Software Heritage when cloning a channel From 9b6703eabee07068328a5e489deb3d532f242daa Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ludovic=20Court=C3=A8s?= Date: Sat, 17 Dec 2022 23:36:02 +0100 Subject: [PATCH 341/790] installer: final: Stop guix-daemon before accessing store database. As part of fixing , make sure /var/guix/db.sqlite is only copied while guix-daemon is stopped. * gnu/installer/final.scm (call-with-mnt-container): Add FIXME comment. (install-system): Copy DATABASE-FILE and SAVED-DATABASE only when 'guix-daemon' is stopped. Add logging lines. --- gnu/installer/final.scm | 22 ++++++++++++++++------ 1 file changed, 16 insertions(+), 6 deletions(-) diff --git a/gnu/installer/final.scm b/gnu/installer/final.scm index 044f79372b..f5601d8649 100644 --- a/gnu/installer/final.scm +++ b/gnu/installer/final.scm @@ -1,6 +1,6 @@ ;;; GNU Guix --- Functional package management for GNU ;;; Copyright © 2018, 2020 Mathieu Othacehe -;;; Copyright © 2019, 2020 Ludovic Courtès +;;; Copyright © 2019, 2020, 2022 Ludovic Courtès ;;; ;;; This file is part of GNU Guix. ;;; @@ -114,6 +114,8 @@ it can interact with the rest of the system." ;; Catch SIGINT and kill the container process. (sigaction SIGINT (lambda (signum) + ;: FIXME: Use of SIGKILL prevents the dynamic-wind exit handler of + ;; THUNK to run. (false-if-exception (kill pid SIGKILL)))) @@ -196,14 +198,16 @@ or #f. Return #t on success and #f on failure." ;; the loaded cow-store locale files will prevent umounting. (install-locale locale) - ;; Save the database, so that it can be restored once the - ;; cow-store is umounted. + ;; Stop the daemon and save the database, so that it can be + ;; restored once the cow-store is umounted. + (stop-service 'guix-daemon) (copy-file database-file saved-database) + + (installer-log-line "mounting copy-on-write store") (mount-cow-store (%installer-target-dir) backing-directory)) (lambda () ;; We need to drag the guix-daemon to the container MNT ;; namespace, so that it can operate on the cow-store. - (stop-service 'guix-daemon) (start-service 'guix-daemon (list (number->string (getpid)))) (setvbuf (current-output-port) 'none) @@ -213,11 +217,17 @@ or #f. Return #t on success and #f on failure." (set! ret (run-command install-command #:tty? #t))) (lambda () - ;; Restart guix-daemon so that it does no keep the MNT namespace + ;; Stop guix-daemon so that it does no keep the MNT namespace ;; alive. - (restart-service 'guix-daemon) + (stop-service 'guix-daemon) + + ;; Restore the database and restart it. + (installer-log-line "restoring store database from '~a'" + saved-database) (copy-file saved-database database-file) + (start-service 'guix-daemon) ;; Finally umount the cow-store and exit the container. + (installer-log-line "unmounting copy-on-write store") (unmount-cow-store (%installer-target-dir) backing-directory) (assert-exit ret)))))))) From 495c50008be91429ebea3805e161a1e385a2a572 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ludovic=20Court=C3=A8s?= Date: Sun, 18 Dec 2022 00:35:21 +0100 Subject: [PATCH 342/790] installer: final: Delete SQLite WAL and shm files upon completion. Previously, db.sqlite-{wal,shm} could be left behind after stopping guix-daemon. When resuming installation, SQLite could end up behaving as if transactions visible in the WAL file had been committed, in spite of having restored SAVED-DATABASE. Fixes . Reported by pelzflorian (Florian Pelz) . * gnu/installer/final.scm (install-system): Before restarting guix-daemon, delete db.sqlite-{wal,shm}. --- gnu/installer/final.scm | 10 +++++++++- 1 file changed, 9 insertions(+), 1 deletion(-) diff --git a/gnu/installer/final.scm b/gnu/installer/final.scm index f5601d8649..069426a3b8 100644 --- a/gnu/installer/final.scm +++ b/gnu/installer/final.scm @@ -221,10 +221,18 @@ or #f. Return #t on success and #f on failure." ;; alive. (stop-service 'guix-daemon) - ;; Restore the database and restart it. + ;; Restore the database and restart it. As part of restoring the + ;; database, remove the WAL and shm files in case they were left + ;; behind after guix-daemon was stopped. Failing to do so, + ;; sqlite might behave as if transactions that appear in the WAL + ;; file were committed. (See .) (installer-log-line "restoring store database from '~a'" saved-database) (copy-file saved-database database-file) + (for-each (lambda (suffix) + (false-if-exception + (delete-file (string-append database-file suffix)))) + '("-wal" "-shm")) (start-service 'guix-daemon) ;; Finally umount the cow-store and exit the container. From d7d049fdcd80e27a42b31766890f589f482a4f23 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ludovic=20Court=C3=A8s?= Date: Sun, 18 Dec 2022 13:08:04 +0100 Subject: [PATCH 343/790] services: kmsconf: Load GNU Freefont. This provides glyphs for additional fonts such as Amharic that were otherwise missing. Fixes . Reported by Wolf . * gnu/services/base.scm (kmscon-service-type): In 'start' method, pass #:environment-variables to set 'XDG_DATA_DIRS'. --- gnu/services/base.scm | 11 ++++++++++- 1 file changed, 10 insertions(+), 1 deletion(-) diff --git a/gnu/services/base.scm b/gnu/services/base.scm index 2b1974d77e..565e8d9e98 100644 --- a/gnu/services/base.scm +++ b/gnu/services/base.scm @@ -72,6 +72,7 @@ #:select (dosfstools)) #:use-module ((gnu packages file-systems) #:select (bcachefs-tools exfat-utils jfsutils zfs)) + #:use-module (gnu packages fonts) #:use-module (gnu packages terminals) #:use-module ((gnu packages wm) #:select (sway)) #:use-module ((gnu build file-systems) @@ -2487,7 +2488,15 @@ notably to select, copy, and paste text. The default options use the (documentation "kmscon virtual terminal") (requirement '(user-processes udev dbus-system)) (provision (list (symbol-append 'term- (string->symbol virtual-terminal)))) - (start #~(make-forkexec-constructor #$kmscon-command)) + (start #~(make-forkexec-constructor + #$kmscon-command + + ;; The installer needs to be able to display glyphs from + ;; various scripts, so give it access to freefont. + ;; TODO: Make this configurable. + #:environment-variables + (list (string-append "XDG_DATA_DIRS=" + #$font-gnu-freefont "/share")))) (stop #~(make-kill-destructor))))) (description "Start the @command{kmscon} virtual terminal emulator for the Linux @dfn{kernel mode setting} (KMS)."))) From 6aebf864a724184a7073982c2dff6db945a29579 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sun, 18 Dec 2022 15:19:27 +0100 Subject: [PATCH 344/790] gnu: python-multivelo: Simplify with pyproject-build-system. * gnu/packages/bioinformatics.scm (python-multivelo)[build-system]: Use pyproject-build-system. [arguments]: Remove custom 'build and 'install phases. --- gnu/packages/bioinformatics.scm | 15 +-------------- 1 file changed, 1 insertion(+), 14 deletions(-) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index e8da00d805..1d3c5d6312 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -10847,25 +10847,12 @@ API services.") (sha256 (base32 "1b4qyngwagh5sc2ygyfqyirg63myzh1g1glk03a1ykxfii32cjlp")))) - (build-system python-build-system) + (build-system pyproject-build-system) (arguments (list #:tests? #f ;pypi source does not contain tests #:phases #~(modify-phases %standard-phases - (replace 'build - (lambda _ - ;; ZIP does not support timestamps before 1980. - (setenv "SOURCE_DATE_EPOCH" "315532800") - (invoke "python" "-m" "build" "--wheel" "--no-isolation" "."))) - (replace 'install - (lambda _ - (for-each - (lambda (wheel) - (format #t wheel) - (invoke "python" "-m" "pip" "install" - wheel (string-append "--prefix=" #$output))) - (find-files "dist" "\\.whl$")))) (add-before 'sanity-check 'set-env (lambda _ ;; numba RuntimeError: cannot cache function 'rdist' From 9cb42f725a2a652bb41e38988d03d7020ccf2aa1 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sun, 18 Dec 2022 15:28:20 +0100 Subject: [PATCH 345/790] gnu: python-scanpy: Use pyproject-build-system. * gnu/packages/bioinformatics.scm (python-scanpy)[build-system]: Use pyproject-build-system. [arguments]: Remove custom 'build and 'install phases; move pytest arguments to #:test-flags; add 'pretend-version phase; replace custom 'check phase with 'delete-bad-tests phase. --- gnu/packages/bioinformatics.scm | 79 ++++++++++++++------------------- 1 file changed, 33 insertions(+), 46 deletions(-) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 1d3c5d6312..c41cdfbd86 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -12802,32 +12802,35 @@ implementation differs in these ways: (sha256 (base32 "0k524xnx3dvpz5yx65p316wghvi01zs17is8w2m3w2qywiswk0sl")))) - (build-system python-build-system) + (build-system pyproject-build-system) (arguments - `(#:phases - (modify-phases %standard-phases - (replace 'build - (lambda _ - (setenv "SETUPTOOLS_SCM_PRETEND_VERSION" ,version) - ;; ZIP does not support timestamps before 1980. - (setenv "SOURCE_DATE_EPOCH" "315532800") - (invoke "flit" "build"))) - (replace 'install - (lambda* (#:key inputs outputs #:allow-other-keys) - (add-installed-pythonpath inputs outputs) - (let ((out (assoc-ref outputs "out"))) - (for-each (lambda (wheel) - (format #true wheel) - (invoke "python" "-m" "pip" "install" - wheel (string-append "--prefix=" out))) - (find-files "dist" "\\.whl$"))))) - ;; Numba needs a writable dir to cache functions. - (add-before 'check 'set-numba-cache-dir - (lambda _ - (setenv "NUMBA_CACHE_DIR" "/tmp"))) - (replace 'check - (lambda* (#:key tests? inputs #:allow-other-keys) - (when tests? + (list + #:test-flags + '(list "-k" + ;; Plot tests that fail. + (string-append "not test_dotplot_matrixplot_stacked_violin" + " and not test_violin_without_raw" + " and not test_correlation" + " and not test_scatterplots" + " and not test_scatter_embedding_add_outline_vmin_vmax_norm" + " and not test_paga" + " and not test_paga_compare" + " and not test_clustermap" + + ;; These try to connect to the network + " and not test_scrublet_plots" + " and not test_plot_rank_genes_groups_gene_symbols" + " and not test_pca_n_pcs" + " and not test_pca_chunked" + " and not test_pca_sparse" + " and not test_pca_reproducible")) + #:phases + #~(modify-phases %standard-phases + (add-after 'unpack 'pretend-version + (lambda _ + (setenv "SETUPTOOLS_SCM_PRETEND_VERSION" #$version))) + (add-after 'unpack 'delete-bad-tests + (lambda _ ;; These tests require Internet access. (delete-file-recursively "scanpy/tests/notebooks") (delete-file "scanpy/tests/test_clustering.py") @@ -12854,27 +12857,11 @@ implementation differs in these ways: (setenv "PYTHONPATH" (string-append (getcwd) ":" - (assoc-ref inputs "python-anndata:source") ":" - (getenv "GUIX_PYTHONPATH"))) - (invoke "pytest" "-vv" - "-k" - ;; Plot tests that fail. - (string-append "not test_dotplot_matrixplot_stacked_violin" - " and not test_violin_without_raw" - " and not test_correlation" - " and not test_scatterplots" - " and not test_scatter_embedding_add_outline_vmin_vmax_norm" - " and not test_paga" - " and not test_paga_compare" - " and not test_clustermap" - - ;; These try to connect to the network - " and not test_scrublet_plots" - " and not test_plot_rank_genes_groups_gene_symbols" - " and not test_pca_n_pcs" - " and not test_pca_chunked" - " and not test_pca_sparse" - " and not test_pca_reproducible")))))))) + #$(this-package-native-input "python-anndata:source") ":" + (getenv "GUIX_PYTHONPATH"))))) + ;; Numba needs a writable dir to cache functions. + (add-before 'check 'set-numba-cache-dir + (lambda _ (setenv "NUMBA_CACHE_DIR" "/tmp")))))) (propagated-inputs (list python-anndata python-dask From b77b4c7c3a5ac180f5aed0983be50ffbe6832f87 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ludovic=20Court=C3=A8s?= Date: Sun, 18 Dec 2022 15:53:43 +0100 Subject: [PATCH 346/790] doc: Add guile-netlink to 'htmlxref.cnf'. * doc/htmlxref.cnf: Add guile-netlink. --- doc/htmlxref.cnf | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/doc/htmlxref.cnf b/doc/htmlxref.cnf index 21efbe2ddc..d961c91c56 100644 --- a/doc/htmlxref.cnf +++ b/doc/htmlxref.cnf @@ -1,7 +1,7 @@ # htmlxref.cnf - reference file for free Texinfo manuals on the web. # Modified by Ludovic Courtès for the GNU Guix manual. -htmlxrefversion=2022-08-04.13; # UTC +htmlxrefversion=2022-12-18.14; # UTC # Copyright 2010-2020, 2022 Free Software Foundation, Inc. # @@ -409,6 +409,8 @@ GUILE_GNOME = ${GS}/guile-gnome/docs guile-gtk node ${GS}/guile-gtk/docs/guile-gtk/ +guile-netlink mono https://git.lepiller.eu/guile-netlink/manual/manual.html + guile-rpc mono ${GS}/guile-rpc/manual/guile-rpc.html guile-rpc node ${GS}/guile-rpc/manual/html_node/ From 8e2f32cee982d42a79e53fc1e9aa7b8ff0514714 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ludovic=20Court=C3=A8s?= Date: Sun, 18 Dec 2022 16:01:32 +0100 Subject: [PATCH 347/790] doc: Update URLs for the manual and cookbook translations. * doc/htmlxref.cnf: Update URLs for "guix" and "guix-cookbook". --- doc/htmlxref.cnf | 10 +++++++--- 1 file changed, 7 insertions(+), 3 deletions(-) diff --git a/doc/htmlxref.cnf b/doc/htmlxref.cnf index d961c91c56..d8a7aa12c9 100644 --- a/doc/htmlxref.cnf +++ b/doc/htmlxref.cnf @@ -1,7 +1,7 @@ # htmlxref.cnf - reference file for free Texinfo manuals on the web. # Modified by Ludovic Courtès for the GNU Guix manual. -htmlxrefversion=2022-12-18.14; # UTC +htmlxrefversion=2022-12-18.15; # UTC # Copyright 2010-2020, 2022 Free Software Foundation, Inc. # @@ -422,6 +422,8 @@ GUIX = ${GUIX_ROOT}/manual guix.es node ${GUIX}/es/html_node/ guix.fr mono ${GUIX}/fr/guix.fr.html guix.fr node ${GUIX}/fr/html_node/ + guix.pt_BR mono ${GUIX}/pt-br/guix.pt_BR.html + guix.pt_BR node ${GUIX}/pt-br/html_node/ guix.ru mono ${GUIX}/ru/guix.ru.html guix.ru node ${GUIX}/ru/html_node/ guix.zh_CN mono ${GUIX}/zh-cn/guix.zh_CN.html @@ -430,10 +432,12 @@ GUIX = ${GUIX_ROOT}/manual guix node ${GUIX}/en/html_node/ GUIX_COOKBOOK = ${GUIX_ROOT}/cookbook - guix-cookbook.de mono ${GUIX_COOKBOOK}/de/guix-cookbook.html + guix-cookbook.de mono ${GUIX_COOKBOOK}/de/guix-cookbook.de.html guix-cookbook.de node ${GUIX_COOKBOOK}/de/html_node/ - guix-cookbook.fr mono ${GUIX_COOKBOOK}/fr/guix-cookbook.html + guix-cookbook.fr mono ${GUIX_COOKBOOK}/fr/guix-cookbook.fr.html guix-cookbook.fr node ${GUIX_COOKBOOK}/fr/html_node/ + guix-cookbook.sk mono ${GUIX_COOKBOOK}/sk/guix-cookbook.sk.html + guix-cookbook.sk node ${GUIX_COOKBOOK}/sk/html_node/ guix-cookbook mono ${GUIX_COOKBOOK}/en/guix-cookbook.html guix-cookbook node ${GUIX_COOKBOOK}/en/html_node/ From 989a3916dc8967bcb7275f10452f89bc6c3389cc Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ludovic=20Court=C3=A8s?= Date: Sun, 18 Dec 2022 16:30:58 +0100 Subject: [PATCH 348/790] gnu: guix: Update to 1.4.0. --- gnu/packages/package-management.scm | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/gnu/packages/package-management.scm b/gnu/packages/package-management.scm index 5a09b1fcf8..5ab6f60763 100644 --- a/gnu/packages/package-management.scm +++ b/gnu/packages/package-management.scm @@ -164,8 +164,8 @@ ;; Latest version of Guix, which may or may not correspond to a release. ;; Note: the 'update-guix-package.scm' script expects this definition to ;; start precisely like this. - (let ((version "1.4.0rc2") - (commit "7866294e32f1e758d06fce4e1b1035eca3a7d772") + (let ((version "1.4.0") + (commit "8e2f32cee982d42a79e53fc1e9aa7b8ff0514714") (revision 0)) (package (name "guix") @@ -182,7 +182,7 @@ (commit commit))) (sha256 (base32 - "0np4fw5kq882nrkfgsvvwgcxqwvm6bzn3dbdf8p48nr7mfrm3rz9")) + "042mipw2bp9lc75m9g5q6rdifrp8483cmk57kwrdps0i3vd590dl")) (file-name (string-append "guix-" version "-checkout")))) (build-system gnu-build-system) (arguments From 47348b85f67d23b074d8d624450eaf1d443c101a Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Sun, 18 Dec 2022 21:44:10 +0200 Subject: [PATCH 349/790] gnu: git-annex: Update to 10.20221212. * gnu/packages/haskell-apps.scm (git-annex): Update to 10.20221212. --- gnu/packages/haskell-apps.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/haskell-apps.scm b/gnu/packages/haskell-apps.scm index b9e9050814..a2405796ca 100644 --- a/gnu/packages/haskell-apps.scm +++ b/gnu/packages/haskell-apps.scm @@ -304,14 +304,14 @@ to @code{cabal repl}).") (define-public git-annex (package (name "git-annex") - (version "10.20221103") + (version "10.20221212") (source (origin (method url-fetch) (uri (string-append "https://hackage.haskell.org/package/" "git-annex/git-annex-" version ".tar.gz")) (sha256 - (base32 "0fwg74ldw2paq9dr052hqjz2x219zkkramvm8jskpnnnch9c6jgm")))) + (base32 "0afnl2w29w4j0229rsla93dzkmhcjlp8dv76sr861n186ywv8rzg")))) (build-system haskell-build-system) (arguments `(#:configure-flags From c81f2118d21f02e6b978b0eff70f9cfab324c6cb Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Sun, 18 Dec 2022 21:44:14 +0200 Subject: [PATCH 350/790] gnu: khard: Update to 0.18.0. * gnu/packages/mail.scm (khard): Update to 0.18.0. --- gnu/packages/mail.scm | 7 +++---- 1 file changed, 3 insertions(+), 4 deletions(-) diff --git a/gnu/packages/mail.scm b/gnu/packages/mail.scm index 172c3e55e7..a31c6a51a6 100644 --- a/gnu/packages/mail.scm +++ b/gnu/packages/mail.scm @@ -2566,13 +2566,13 @@ maintained.") (define-public khard (package (name "khard") - (version "0.17.0") + (version "0.18.0") (source (origin (method url-fetch) (uri (pypi-uri name version)) (sha256 (base32 - "062nv4xkfsjc11k9m52dh6xjn9z68a4a6x1s8z05wwv4jbp1lkhn")))) + "05860fdayqap128l7i6bcmi9kdyi2gx02g2pmh88d56xgysd927y")))) (build-system python-build-system) (arguments `(#:phases @@ -2581,8 +2581,7 @@ maintained.") (lambda* (#:key outputs #:allow-other-keys) (let* ((out (assoc-ref outputs "out")) (zsh (string-append out "/share/zsh/site-functions"))) - (copy-recursively "misc/zsh" zsh) - #t)))))) + (copy-recursively "misc/zsh" zsh))))))) (native-inputs (list python-setuptools-scm)) (inputs From 710c8f159f314e58c3328eae076ae84a5b4960c4 Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Sun, 18 Dec 2022 21:44:15 +0200 Subject: [PATCH 351/790] gnu: toot: Update to 0.32.1. * gnu/packages/mastodon.scm (toot): Update to 0.32.1. --- gnu/packages/mastodon.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/mastodon.scm b/gnu/packages/mastodon.scm index e8c31fb168..cad2cac690 100644 --- a/gnu/packages/mastodon.scm +++ b/gnu/packages/mastodon.scm @@ -42,13 +42,13 @@ (define-public toot (package (name "toot") - (version "0.30.1") + (version "0.32.1") (source (origin (method url-fetch) (uri (pypi-uri "toot" version)) (sha256 - (base32 "0r9f2frlwfxkcv6c9lh36maph90v2yp6s7phynbrb3m7v35xzaxz")))) + (base32 "0diskgvqmnkjl4k6sdda8f1sfz0c4w0j8ppv1q7p84phh9vgml6g")))) (build-system python-build-system) (arguments '(#:phases From 471c94ae175d1dfe9919b9ac81d31230b765e3a1 Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Sun, 18 Dec 2022 21:44:15 +0200 Subject: [PATCH 352/790] gnu: vim: Update to 9.0.1073. * gnu/packages/vim.scm (vim): Update to 9.0.1073. --- gnu/packages/vim.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/vim.scm b/gnu/packages/vim.scm index 9a4a2ce235..1451bf80a3 100644 --- a/gnu/packages/vim.scm +++ b/gnu/packages/vim.scm @@ -78,7 +78,7 @@ (define-public vim (package (name "vim") - (version "9.0.0954") + (version "9.0.1073") (source (origin (method git-fetch) (uri (git-reference @@ -87,7 +87,7 @@ (file-name (git-file-name name version)) (sha256 (base32 - "098fiqw6hz0cc5zzy934alqxgwp01180vz3v9wm9i6x6fhdnhxxn")))) + "0vifinbxjcs7j3zs290q91009cdqijn2awyva2332if7qbx48ssw")))) (build-system gnu-build-system) (arguments `(#:test-target "test" From 391712648419551bb085e8dd197eeee0bbf83520 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sun, 18 Dec 2022 20:00:41 +0100 Subject: [PATCH 353/790] gnu: guile-webutils: Update to 0.1-1.d309d65. * gnu/packages/guile-xyz.scm (guile-webutils): Update to 0.1-1.d309d65. [source]: Remove snippet. --- gnu/packages/guile-xyz.scm | 14 +++----------- 1 file changed, 3 insertions(+), 11 deletions(-) diff --git a/gnu/packages/guile-xyz.scm b/gnu/packages/guile-xyz.scm index 9fc6344491..bbf0f08c9a 100644 --- a/gnu/packages/guile-xyz.scm +++ b/gnu/packages/guile-xyz.scm @@ -4076,8 +4076,8 @@ gnome-keyring, and many more.") (license license:expat))) (define-public guile-webutils - (let ((commit "8541904f761066dc9c27b1153e9a838be9a55299") - (revision "0")) + (let ((commit "d309d65a85247e4f3cea63a17defd1e6d35d821f") + (revision "1")) (package (name "guile-webutils") (version (git-version "0.1" revision commit)) @@ -4089,15 +4089,7 @@ gnome-keyring, and many more.") (file-name (git-file-name name version)) (sha256 (base32 - "1s9n3hbxd7lfpdi0x8wr0cfvlsf6g62ird9gbspxdrp5p05rbi64")) - (modules '((guix build utils))) - (snippet - '(begin - ;; Allow builds with Guile 3.0. - (substitute* "configure.ac" - (("2\\.2 2\\.0") - "3.0 2.2 2.0")) - #t)))) + "1a3bblk5zaldkkxn0a94s544drqm0w2i5fsjpghagd64m149blf0")))) (build-system gnu-build-system) (native-inputs (list autoconf automake pkg-config texinfo)) From 422e571d4a967c42149512acb29dc5e6025d65fc Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sun, 18 Dec 2022 22:36:14 +0100 Subject: [PATCH 354/790] gnu: Add guile-8sync-for-pubstrate. * gnu/packages/guile-xyz.scm (guile-8sync-for-pubstrate): New variable. --- gnu/packages/guile-xyz.scm | 38 ++++++++++++++++++++++++++++++++++++++ 1 file changed, 38 insertions(+) diff --git a/gnu/packages/guile-xyz.scm b/gnu/packages/guile-xyz.scm index bbf0f08c9a..e3c4d7c10f 100644 --- a/gnu/packages/guile-xyz.scm +++ b/gnu/packages/guile-xyz.scm @@ -564,6 +564,44 @@ library for GNU Guile based on the actor model.") (properties '((upstream-name . "8sync"))) (license license:lgpl3+)))) +(define guile-8sync-for-pubstrate + (let ((commit "7972787723d08a491379b63e6e5dc1cc6a3fac87") + (revision "0")) + (package + (inherit guile-8sync) + (name "guile-8sync-for-pubstrate") + (version (git-version "0.4.2" revision commit)) + (source (origin + (method git-fetch) + (uri (git-reference + (commit commit) + (url "https://git.savannah.gnu.org/git/8sync.git"))) + (sha256 + (base32 + "0m3k3cizi89frnw58dws3g4jcssck6jf1ahpadxxg3ncclqzad8r")) + (file-name (git-file-name name version)) + (modules '((guix build utils))) + (snippet + '(substitute* "Makefile.am" + (("2.2") "3.0"))))) + (build-system gnu-build-system) + (arguments + (list + #:make-flags + '(list "GUILE_AUTO_COMPILE=0") + #:phases + '(modify-phases %standard-phases + ;; See commit ee371103855e5bfe8aae3debe442a24c6353e172 + (add-after 'unpack 'fix-srfi64-tests + (lambda _ + (substitute* '("tests/test-actors.scm" + "tests/test-rmeta-slot.scm") + (("\\(test-exit\\)") "") + (("\\(test-end.*" m) + (string-append "(test-exit)" m)))))))) + (native-inputs (list autoconf automake guile-3.0 pkg-config texinfo)) + (propagated-inputs (list guile-fibers))))) + (define-public guile-daemon (package (name "guile-daemon") From d083809c8048a64f71a40f0657c217c9dd230428 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sun, 18 Dec 2022 22:36:41 +0100 Subject: [PATCH 355/790] gnu: Add guile-pubstrate. * gnu/packages/guile-xyz.scm (guile-pubstrate): New variable. --- gnu/packages/guile-xyz.scm | 66 ++++++++++++++++++++++++++++++++++++++ 1 file changed, 66 insertions(+) diff --git a/gnu/packages/guile-xyz.scm b/gnu/packages/guile-xyz.scm index e3c4d7c10f..745c7b3217 100644 --- a/gnu/packages/guile-xyz.scm +++ b/gnu/packages/guile-xyz.scm @@ -337,6 +337,72 @@ to UNIX pipes (@code{|}), Clojure's threading macros (@code{->} and @code{->>}).") (license license:gpl3+)))) +(define-public guile-pubstrate + (let ((commit "b11b7df5e7ffefa45c5859b868d8125c4d939418") + (revision "1")) + (package + (name "guile-pubstrate") + (version (git-version "0.1.dev" revision commit)) + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://gitlab.com/dustyweb/pubstrate") + (commit commit))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "1qk45b3hjhzzq3dim699jrbmlc7ryr4s1fiz99ljz16rag2rr5p4")))) + (build-system gnu-build-system) + (arguments + (list + #:make-flags + '(list "GUILE_AUTO_COMPILE=0") + #:phases + '(modify-phases %standard-phases + (add-after 'unpack 'fix-build-system + (lambda _ + (substitute* "configure.ac" + (("GUILE_PROGS" m) + (string-append m " +guilemoduledir=\"${datarootdir}/guile/site/${GUILE_EFFECTIVE_VERSION}\" +AC_SUBST([guilemoduledir]) +AC_SUBST([GUILE_EFFECTIVE_VERSION]) +"))) + ;; The user.scm line is doubled + (substitute* "Makefile.am" + ((".*pubstrate/webapp/user.scm.*") "") + ((".*pubstrate/webapp/app.scm.*" m) + (string-append m "pubstrate/webapp/user.scm \\\n")) + (("/ccache") "/site-ccache")))) + (add-after 'unpack 'fix-srfi64-tests + (lambda _ + (substitute* (find-files "tests/" "test-.*\\.scm$") + (("\\(test-exit\\)") "") + (("\\(test-end.*" m) + (string-append "(test-exit)" m)))))))) + (native-inputs + (list autoconf + automake + pkg-config + texinfo)) + (inputs + (list guile-3.0 + libgcrypt)) + (propagated-inputs + (list gnutls + guile-8sync-for-pubstrate + guile-gcrypt + guile-gdbm-ffi + guile-irregex + guile-lib + guile-sjson + guile-webutils)) + (home-page "https://gitlab.com/dustyweb/pubstrate/") + (synopsis "ActivityStreams and ActivityPub implementation in Guile") + (description "This package provides an implementation of ActivityStreams +and ActivityPub in Guile. It includes a full (currently demo) web server.") + (license license:gpl3+)))) + (define-public guile-f-scm (package (name "guile-f-scm") From 553f46a094951df99eb1fb6b1a4d3ca1df91adfd Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ludovic=20Court=C3=A8s?= Date: Sat, 17 Dec 2022 16:55:07 +0100 Subject: [PATCH 356/790] doc: Tweak cross-ref Texinfo command. * doc/guix.texi (Swap Space): Use @pxref instead of @xref at the end of a sentence. --- doc/guix.texi | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/doc/guix.texi b/doc/guix.texi index eb37d4d393..b4ca211e61 100644 --- a/doc/guix.texi +++ b/doc/guix.texi @@ -17059,7 +17059,7 @@ I/O faster, and thus paging out unused portions of program memory will expand the RAM available for such caching. For a more detailed description of how memory is managed from the -viewpoint of a monolithic kernel, @xref{Memory +viewpoint of a monolithic kernel, @pxref{Memory Concepts,,, libc, The GNU C Library Reference Manual}. The Linux kernel has support for swap partitions and swap files: the From 1679dec45b535d831e4c3a1ec8605d8e9e2f8ab0 Mon Sep 17 00:00:00 2001 From: Vagrant Cascadian Date: Sun, 18 Dec 2022 15:41:32 -0800 Subject: [PATCH 357/790] gnu: r-gson: Fix typo. * gnu/packages/cran.scm (r-gson)[description]: Fix pluralized "This package". --- gnu/packages/cran.scm | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 340a63cab1..5a76c76c6e 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -634,7 +634,7 @@ the output locally.") (home-page "https://cran.r-project.org/package=gson") (synopsis "Base Class and Methods for 'gson' Format") (description - "This packages proposes a new file format named @code{gson} for storing + "This package proposes a new file format named @code{gson} for storing gene set and related information, and provides read, write and other utilities to process this file format.") (license license:artistic2.0))) From 5d48d9b90575b126911cb942f7894ebd93770903 Mon Sep 17 00:00:00 2001 From: Vagrant Cascadian Date: Sun, 18 Dec 2022 15:52:20 -0800 Subject: [PATCH 358/790] gnu: kdebugsettings: Fix typo. * gnu/packages/kde-utils.scm (kdebugsettings)[description]: Remove use of "allows to". --- gnu/packages/kde-utils.scm | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/gnu/packages/kde-utils.scm b/gnu/packages/kde-utils.scm index 2742d6b846..5774fa9910 100644 --- a/gnu/packages/kde-utils.scm +++ b/gnu/packages/kde-utils.scm @@ -423,7 +423,7 @@ Kate's features include: (home-page "https://invent.kde.org/utilities/kdebugsettings") (synopsis "Choose which QLoggingCategory are displayed") (description - "This package allows to select which QLoggingCategory are displayed.") + "This package selects which QLoggingCategory are displayed.") (license license:lgpl2.0+))) (define-public kbackup From abd478690ce30a4898bdfc2399e67cbccc8955e1 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Mon, 19 Dec 2022 11:01:26 +0100 Subject: [PATCH 359/790] gnu: Add guile-aws. * gnu/packages/guile-xyz.scm (guile-aws): New variable. --- gnu/packages/guile-xyz.scm | 30 ++++++++++++++++++++++++++++++ 1 file changed, 30 insertions(+) diff --git a/gnu/packages/guile-xyz.scm b/gnu/packages/guile-xyz.scm index 745c7b3217..3fa75b26d1 100644 --- a/gnu/packages/guile-xyz.scm +++ b/gnu/packages/guile-xyz.scm @@ -1281,6 +1281,36 @@ non-mutating insert, delete, and search operations, with support for convenient nested tree operations.") (license license:gpl3+))) +(define-public guile-aws + (let ((commit "f32bea12333e1054b97ab50e58a72636edabb5b7") + (revision "1")) + (package + (name "guile-aws") + (version (git-version "0.1.0" revision commit)) + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://git.elephly.net/software/guile-aws.git") + (commit commit))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "0z2mrjw1dry14vjqsh9xi199bavlmy6cajshnv015n7p5my0cx9z")))) + (build-system gnu-build-system) + (native-inputs + (list autoconf automake pkg-config)) + (inputs + (list guile-3.0)) + (propagated-inputs + (list guile-json-4 guile-gcrypt)) + (home-page "https://git.elephly.net/software/guile-aws.git") + (synopsis "Scheme DSL for the AWS APIs") + (description + "This package provides a DSL for a number of @dfn{Amazon Web +Services} (AWS) APIs, including EFS, EC2, Route53, and more. Guile AWS uses +the Guile compiler tower to generate the DSL from AWS JSON specifications.") + (license license:gpl3+)))) + (define-public guile-simple-zmq (let ((commit "ff0b39aec9312517fb48681564e261bd000aaf63") (revision "10")) From 3dde5f4df496a2b1415990e138877e71945f557b Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Tue, 6 Dec 2022 09:23:27 +0200 Subject: [PATCH 360/790] gnu: Add nilfs-utils. * gnu/packages/file-systems.scm (nilfs-utils): New variable. --- gnu/packages/file-systems.scm | 35 +++++++++++++++++++++++++++++++++++ 1 file changed, 35 insertions(+) diff --git a/gnu/packages/file-systems.scm b/gnu/packages/file-systems.scm index 85454cada3..57a25a0d90 100644 --- a/gnu/packages/file-systems.scm +++ b/gnu/packages/file-systems.scm @@ -752,6 +752,41 @@ transaction log. from the jfsutils package. It is meant to be used in initrds.") (license (package-license jfsutils)))) +(define-public nilfs-utils + (package + (name "nilfs-utils") + (version "2.2.9") + (source + (origin + (method url-fetch) + (uri (string-append "https://nilfs.sourceforge.io/download" + "/nilfs-utils-" version ".tar.bz2")) + (sha256 + (base32 "15vsayvzr8nc29n939sz9ddq46vpn53rp8h8qv484h88qac3kxjx")))) + (build-system gnu-build-system) + (arguments + (list + #:configure-flags + #~(list "--enable-static=no") + #:phases + #~(modify-phases %standard-phases + (add-before 'bootstrap 'force-bootstrap + (lambda _ + (delete-file "configure") + (substitute* "configure.ac" + (("\\[/etc\\]") "[${prefix}/etc]") + (("\\[/sbin\\]") "[${prefix}/sbin]"))))))) + (inputs + (list (list util-linux "lib"))) + (native-inputs (list autoconf automake libtool)) + (home-page "https://nilfs.sourceforge.io/") + (synopsis "Continuous Snapshotting Filesystem") + (description + "NILFS is a log-structured file system supporting versioning of the entire +file system and continuous snapshotting, which allows users to even restore +files mistakenly overwritten or destroyed just a few seconds ago.") + (license license:gpl3+))) + (define-public disorderfs (package (name "disorderfs") From 3a9653166462a961eb4c2d140bd2440ec9cadd25 Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Mon, 19 Dec 2022 12:42:25 +0200 Subject: [PATCH 361/790] gnu: tor: Update to 0.4.7.12. * gnu/packages/tor.scm (tor): Update to 0.4.7.12. --- gnu/packages/tor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/tor.scm b/gnu/packages/tor.scm index fc98481740..5b0ea278ba 100644 --- a/gnu/packages/tor.scm +++ b/gnu/packages/tor.scm @@ -61,14 +61,14 @@ (define-public tor (package (name "tor") - (version "0.4.7.11") + (version "0.4.7.12") (source (origin (method url-fetch) (uri (string-append "https://dist.torproject.org/tor-" version ".tar.gz")) (sha256 (base32 - "0vhk5bingy0m70wri44jzynmw00as7b783jlq38mzg5xxnzayg6g")))) + "15g3p42hnccpz8zyk4bi8pm9fnpi7qs19wr8s0dqary42abrcp9v")))) (build-system gnu-build-system) (arguments (list #:configure-flags From 77ef82ce93e088e3d810b394b7cacd33f0d2de85 Mon Sep 17 00:00:00 2001 From: Andrew Tropin Date: Mon, 19 Dec 2022 15:02:20 +0400 Subject: [PATCH 362/790] home: xdg: Make it possible to extend user-directories service. * gnu/home/services/xdg.scm (home-xdg-user-directories-service-type): Make it possible to override user-directories configuration by extending. --- gnu/home/services/xdg.scm | 2 ++ 1 file changed, 2 insertions(+) diff --git a/gnu/home/services/xdg.scm b/gnu/home/services/xdg.scm index 865f8b81d7..fb2dbb393e 100644 --- a/gnu/home/services/xdg.scm +++ b/gnu/home/services/xdg.scm @@ -245,6 +245,8 @@ pre-populated content.") home-activation-service-type home-xdg-user-directories-activation-service))) (default-value (home-xdg-user-directories-configuration)) + (compose identity) + (extend last-extension-or-cfg) (description "Configure XDG user directories. To disable a directory, point it to the $HOME."))) From 061609ee57a201157a21d8d2c237f4f0be067bba Mon Sep 17 00:00:00 2001 From: jgart Date: Tue, 6 Dec 2022 23:57:09 -0600 Subject: [PATCH 363/790] guix: packages: Add type hint comment to home-page record field. * guix/packages.scm (package)[home-page]: Add type comment. Signed-off-by: Andrew Tropin --- guix/packages.scm | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/guix/packages.scm b/guix/packages.scm index 6e61e16aa4..041a872f9d 100644 --- a/guix/packages.scm +++ b/guix/packages.scm @@ -8,6 +8,7 @@ ;;; Copyright © 2020, 2021 Maxim Cournoyer ;;; Copyright © 2021 Chris Marusich ;;; Copyright © 2022 Maxime Devos +;;; Copyright © 2022 jgart ;;; ;;; This file is part of GNU Guix. ;;; @@ -610,7 +611,7 @@ Texinfo. Otherwise, return the string." (sanitize validate-texinfo)) ; one or two paragraphs (license package-license ; (list of) (sanitize validate-license)) - (home-page package-home-page) + (home-page package-home-page) ; string (supported-systems package-supported-systems ; list of strings (default %supported-systems)) From debfbdefda777d36a625f071d3e17faa89c10545 Mon Sep 17 00:00:00 2001 From: cage Date: Tue, 13 Dec 2022 21:19:33 +0100 Subject: [PATCH 364/790] gnu: cl-croatoan: Update to 0.0.1-6.35c92fc. * gnu/packages/lisp-xyz.scm (sbcl-croatoan): Update to 0.0.1-6.35c92fc. Signed-off-by: Guillaume Le Vaillant --- gnu/packages/lisp-xyz.scm | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/gnu/packages/lisp-xyz.scm b/gnu/packages/lisp-xyz.scm index 364be8c7a5..8f68e88e9b 100644 --- a/gnu/packages/lisp-xyz.scm +++ b/gnu/packages/lisp-xyz.scm @@ -16872,8 +16872,8 @@ protocol for Mastodon.") (sbcl-package->cl-source-package sbcl-tooter)) (define-public sbcl-croatoan - (let ((commit "5d0949d57a12e7fece8828e089daa339b260da96") - (revision "5")) + (let ((commit "35c92fcc6c4458339c7e27bdf16f7fa908d95eb8") + (revision "6")) (package (name "sbcl-croatoan") (version (git-version "0.0.1" revision commit)) @@ -16885,7 +16885,7 @@ protocol for Mastodon.") (commit commit))) (file-name (git-file-name "cl-croatoan" version)) (sha256 - (base32 "0qsnz10hri95al73vhpqrs7mapz2px0dbwgfn52sbi93gwk5aki9")))) + (base32 "0v1lrdjd29krjb6pr0mql9hjj5c2lv760xwpr17dbsw263vx29xz")))) (build-system asdf-build-system/sbcl) (arguments '(#:phases From 89a8534b425817640c3e168399543b7f6e10b5a7 Mon Sep 17 00:00:00 2001 From: Charles Jackson Date: Tue, 13 Dec 2022 22:56:23 -0600 Subject: [PATCH 365/790] gnu: sbcl-triads: Add bin output. * gnu/packages/lisp-xyz.scm (sbcl-triads)[arguments]: Add 'build-binary' phase to build and install the binary executable. (ecl-triads): Remove the build-binary phase because this program has not been tested on ECL upstream. Signed-off-by: Guillaume Le Vaillant --- gnu/packages/lisp-xyz.scm | 29 +++++++++++++++++++++++++++-- 1 file changed, 27 insertions(+), 2 deletions(-) diff --git a/gnu/packages/lisp-xyz.scm b/gnu/packages/lisp-xyz.scm index 8f68e88e9b..bf1ee39c98 100644 --- a/gnu/packages/lisp-xyz.scm +++ b/gnu/packages/lisp-xyz.scm @@ -26264,8 +26264,25 @@ Zombie Raptor game engine project.") (sha256 (base32 "146mwshynhdw82m2nxrcjvf1nk0z3fn6ywcd2vqxkly5qricc53w")))) (build-system asdf-build-system/sbcl) + (outputs '("out" "bin")) (arguments - '(#:asd-systems '("charje.triads"))) + '(#:asd-systems '("charje.triads") + #:phases + (modify-phases %standard-phases + (add-after 'create-asdf-configuration 'build-binary + (lambda* (#:key outputs #:allow-other-keys) + (setenv "HOME" (getcwd)) + (invoke + "sbcl" "--eval" "(require :asdf)" "--eval" + (format + #f "~S" + `(progn + (require "charje.triads" + ,(string-append (getcwd) "/charje.triads.asd")) + (asdf:make "charje.triads")))) + (install-file + (string-append (getcwd) "/triads") + (string-append (assoc-ref outputs "bin") "/bin"))))))) (inputs (list sbcl-cl-str sbcl-serapeum @@ -26282,7 +26299,15 @@ roman numeral given in the key.") (sbcl-package->cl-source-package sbcl-triads)) (define-public ecl-triads - (sbcl-package->ecl-package sbcl-triads)) + (let ((ecl-package (sbcl-package->ecl-package sbcl-triads))) + (package + (inherit ecl-package) + (outputs '("out")) + (arguments + (substitute-keyword-arguments (package-arguments ecl-package) + ((#:phases phases) + `(modify-phases ,phases + (delete 'build-binary)))))))) (define-public sbcl-closure-template ;; There are no releases since 2015. From 8fe9a4ca1ff8cf2686a7ea4b58eaed5429a46e48 Mon Sep 17 00:00:00 2001 From: cage Date: Wed, 14 Dec 2022 10:50:30 +0100 Subject: [PATCH 366/790] gnu: cl-i18n: Update to 0.5.3-2.5b569f3. * gnu/packages/lisp-xyz.scm (sbcl-cl-i18n): Update to 0.5.3-2.5b569f3. Signed-off-by: Guillaume Le Vaillant --- gnu/packages/lisp-xyz.scm | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/gnu/packages/lisp-xyz.scm b/gnu/packages/lisp-xyz.scm index bf1ee39c98..2ebf2c23a9 100644 --- a/gnu/packages/lisp-xyz.scm +++ b/gnu/packages/lisp-xyz.scm @@ -17011,11 +17011,11 @@ dynamically.") (sbcl-package->cl-source-package sbcl-sxql-composer)) (define-public sbcl-cl-i18n - (let ((commit "5b569f3fe4c76d600fafecac507ac4f50e4cc1d1") - (revision "1")) + (let ((commit "66b02dc2cff3ab97f924329aaf965807fe18aa20") + (revision "2")) (package (name "sbcl-cl-i18n") - (version (git-version "0.5.2" revision commit)) + (version (git-version "0.5.3" revision commit)) (source (origin (method git-fetch) @@ -17024,7 +17024,7 @@ dynamically.") (commit commit))) (file-name (git-file-name "cl-i18n" version)) (sha256 - (base32 "0kj1wfvlbi7qwq61b0rcdxa0bmb4sfsnh1bj3n5jxp24sdib73w2")))) + (base32 "06ij1wxancsym87gg63nvjh7vfzjipi1f02h4fb2ypip60vw06lc")))) (build-system asdf-build-system/sbcl) (inputs (list sbcl-alexandria sbcl-babel sbcl-cl-ppcre-unicode)) From d9c6f14af1bc38cb15b6b108e8a7f7c99ab39ced Mon Sep 17 00:00:00 2001 From: cage Date: Wed, 14 Dec 2022 12:26:27 +0100 Subject: [PATCH 367/790] gnu: tinmop: Update to 0.9.9.14. * gnu/packages/web-browsers.scm (tinmop): Update to 0.9.9.14. [inputs]: Add imagemagick. Signed-off-by: Guillaume Le Vaillant --- gnu/packages/web-browsers.scm | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) diff --git a/gnu/packages/web-browsers.scm b/gnu/packages/web-browsers.scm index a2d6e399e9..a126902395 100644 --- a/gnu/packages/web-browsers.scm +++ b/gnu/packages/web-browsers.scm @@ -72,6 +72,7 @@ #:use-module (gnu packages gnupg) #:use-module (gnu packages gtk) #:use-module (gnu packages image) + #:use-module (gnu packages imagemagick) #:use-module (gnu packages libevent) #:use-module (gnu packages libidn) #:use-module (gnu packages libunistring) @@ -829,7 +830,7 @@ http, and https via third-party applications.") (define-public tinmop (package (name "tinmop") - (version "0.9.9") + (version "0.9.9.14") (source (origin (method git-fetch) @@ -838,12 +839,13 @@ http, and https via third-party applications.") (commit (string-append "v" version)))) (file-name (git-file-name name version)) (sha256 - (base32 "0s73587wf29jzymlqrgcnci7w6wsfj1vcs7szxshsmaiszf0skwk")))) + (base32 "0xpqakqg4827wv92vvzwcvkqzr8d523fvnyjvnj4ac83d4w6nnls")))) (build-system gnu-build-system) (native-inputs (list autoconf automake gnu-gettext + imagemagick mandoc nano openssl From 2565616ab3635eae1161a97974e80928400ae624 Mon Sep 17 00:00:00 2001 From: "Paul A. Patience" Date: Sun, 18 Dec 2022 03:43:16 +0000 Subject: [PATCH 368/790] gnu: Add cl-coleslaw. * gnu/packages/lisp-xyz.scm (sbcl-coleslaw, cl-coleslaw, ecl-coleslaw): New variables. Signed-off-by: Guillaume Le Vaillant --- gnu/packages/lisp-xyz.scm | 66 +++++++++++++++++++++++++++++++++++++++ 1 file changed, 66 insertions(+) diff --git a/gnu/packages/lisp-xyz.scm b/gnu/packages/lisp-xyz.scm index 2ebf2c23a9..bb5e9ef041 100644 --- a/gnu/packages/lisp-xyz.scm +++ b/gnu/packages/lisp-xyz.scm @@ -104,6 +104,7 @@ #:use-module (gnu packages python) #:use-module (gnu packages python-xyz) #:use-module (gnu packages readline) + #:use-module (gnu packages rsync) #:use-module (gnu packages sdl) #:use-module (gnu packages serialization) #:use-module (gnu packages sqlite) @@ -894,6 +895,71 @@ Features: (define-public ecl-cl-irc (sbcl-package->ecl-package sbcl-cl-irc)) +(define-public sbcl-coleslaw + (let ((commit "e7e68ce6020d13b14bf212890a7d8973d7af3b40") + (revision "0")) + (package + (name "sbcl-coleslaw") + (version (git-version "0.9.7" revision commit)) + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/coleslaw-org/coleslaw") + (commit commit))) + (file-name (git-file-name "cl-coleslaw" version)) + (sha256 + (base32 "1w21a272q4x7nlr4kbmwwvkjvb4hpnw869byvy47vv361y7pimws")))) + (build-system asdf-build-system/sbcl) + (outputs '("out" "bin")) + (arguments + '(#:asd-systems '("coleslaw" "coleslaw-cli") + #:phases + (modify-phases %standard-phases + (add-after 'unpack 'fix-paths + (lambda _ + (substitute* "plugins/publish-gh-pages.sh" + (("^rsync\\b") (which "rsync"))) + (substitute* '("plugins/rsync.lisp" + "src/coleslaw.lisp") + (("\\brun-program \"rsync\\b") + (string-append "run-program \"" (which "rsync")))))) + (add-after 'create-asdf-configuration 'build-program + (lambda* (#:key outputs #:allow-other-keys) + (build-program + (string-append (assoc-ref outputs "bin") "/bin/coleslaw") + outputs + #:dependencies '("coleslaw-cli") + #:entry-program '((apply (function coleslaw-cli::main) + arguments)) + #:compress? #t)))))) + (native-inputs + (list sbcl-prove)) + (inputs + (list rsync + sbcl-3bmd + sbcl-alexandria + sbcl-cl-fad + sbcl-cl-ppcre + sbcl-cl-unicode + sbcl-clack + sbcl-closer-mop + sbcl-closure-template + sbcl-inferior-shell + sbcl-local-time + sbcl-trivia)) + (home-page "https://github.com/coleslaw-org/coleslaw") + (synopsis "Static site generator") + (description + "Coleslaw is a static site generator written in Common Lisp.") + (license license:bsd-2)))) + +(define-public cl-coleslaw + (sbcl-package->cl-source-package sbcl-coleslaw)) + +(define-public ecl-coleslaw + (sbcl-package->ecl-package sbcl-coleslaw)) + (define-public sbcl-tripod (let ((commit "bcea16610b4961a927e417e4413fffe686d71c83") (revision "0")) From d9f3567abb593cd89632dd4bb03d5bb2a5b4764c Mon Sep 17 00:00:00 2001 From: "Paul A. Patience" Date: Mon, 19 Dec 2022 14:12:36 +0100 Subject: [PATCH 369/790] gnu: cl-tripod: Update to 0.0.1-1.b019a27. * gnu/packages/lisp-xyz.scm (sbcl-tripod): Update to 0.0.1-1.b019a27. [outputs, arguments]: New fields. [inputs]: Add sbcl-local-time, sbcl-nactivitypub and sbcl-njson, and reindent. Signed-off-by: Guillaume Le Vaillant --- gnu/packages/lisp-xyz.scm | 36 ++++++++++++++++++++++++------------ 1 file changed, 24 insertions(+), 12 deletions(-) diff --git a/gnu/packages/lisp-xyz.scm b/gnu/packages/lisp-xyz.scm index bb5e9ef041..b37c9e4224 100644 --- a/gnu/packages/lisp-xyz.scm +++ b/gnu/packages/lisp-xyz.scm @@ -961,8 +961,8 @@ Features: (sbcl-package->ecl-package sbcl-coleslaw)) (define-public sbcl-tripod - (let ((commit "bcea16610b4961a927e417e4413fffe686d71c83") - (revision "0")) + (let ((commit "b019a27cd7eb895870f84b0eb6c3edc5d7b05928") + (revision "1")) (package (name "sbcl-tripod") (version (git-version "0.0.1" revision commit)) @@ -974,17 +974,30 @@ Features: (commit commit))) (file-name (git-file-name "cl-tripod" version)) (sha256 - (base32 "07czbwzfqg8n1q4dsfmrdp2zmp90xgsg8q26hkrniyvkylq4nn1z")))) + (base32 "0y8sns6njq9x7km58vpj7gx4cia9zkcpng3d38300xk0nnk2kz8w")))) (build-system asdf-build-system/sbcl) + (outputs '("out" "bin")) + (arguments + (list #:phases + #~(modify-phases %standard-phases + (add-after 'create-asdf-configuration 'build-program + (lambda* (#:key outputs #:allow-other-keys) + (build-program (string-append #$output:bin "/bin/tripod") + outputs + #:entry-program '((tripod:entry-point)) + #:compress? #t)))))) (inputs - (list sbcl-alexandria - sbcl-cl-gopher - sbcl-cl-markdown - sbcl-clss - sbcl-hunchentoot - sbcl-phos - sbcl-plump - sbcl-trivial-mimes)) + (list sbcl-alexandria + sbcl-cl-gopher + sbcl-cl-markdown + sbcl-clss + sbcl-hunchentoot + sbcl-local-time + sbcl-nactivitypub + sbcl-njson + sbcl-phos + sbcl-plump + sbcl-trivial-mimes)) (home-page "https://aartaka.me/blog/tripod") (synopsis "Common Lisp web server aiming to ease website hosting") (description @@ -998,7 +1011,6 @@ and Gopher website hosting.") (define-public ecl-tripod (sbcl-package->ecl-package sbcl-tripod)) - (define-public sbcl-trivial-timeout (let ((commit "feb869357f40f5e109570fb40abad215fb370c6c") (revision "1")) From 513ab9956ddfd54cfb411c73cfd0838b78b47fc4 Mon Sep 17 00:00:00 2001 From: "Paul A. Patience" Date: Mon, 19 Dec 2022 02:35:34 +0000 Subject: [PATCH 370/790] gnu: Add cl-germinal. * gnu/packages/lisp-xyz.scm (sbcl-germinal, cl-germinal, ecl-germinal): New variables. Signed-off-by: Guillaume Le Vaillant --- gnu/packages/lisp-xyz.scm | 44 +++++++++++++++++++++++++++++++++++++++ 1 file changed, 44 insertions(+) diff --git a/gnu/packages/lisp-xyz.scm b/gnu/packages/lisp-xyz.scm index b37c9e4224..a41eb845df 100644 --- a/gnu/packages/lisp-xyz.scm +++ b/gnu/packages/lisp-xyz.scm @@ -23334,6 +23334,50 @@ Lisp. A subsystem offers an experimental GUI Gemini client.") (define-public ecl-phos (sbcl-package->ecl-package sbcl-phos)) +(define-public sbcl-germinal + (let ((commit "5bfb371ea57dae8985c0e1c6f184f0338487d684") + (revision "0")) + (package + (name "sbcl-germinal") + (version (git-version "1.0.0" revision commit)) + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://git.carcosa.net/jmcbray/germinal") + (commit commit))) + (file-name (git-file-name "cl-germinal" version)) + (sha256 + (base32 "12jypa8m10825lp5yxfcm1fyk3r4ziwcri7ndxa0m5dz0y7hggck")))) + (build-system asdf-build-system/sbcl) + (inputs + (list sbcl-alexandria + sbcl-babel + sbcl-bordeaux-threads + sbcl-cl+ssl + sbcl-cl-fad + sbcl-cl-interpol + sbcl-cl-ppcre + sbcl-cl-str + sbcl-local-time + sbcl-osicat + sbcl-ppath + sbcl-quri + sbcl-trivial-mimes + sbcl-uax-15 + sbcl-usocket)) + (home-page "https://git.carcosa.net/jmcbray/germinal") + (synopsis "Gemini protocol server") + (description "Germinal is a server for the Gemini protocol, written in +Common Lisp.") + (license license:agpl3)))) + +(define-public cl-germinal + (sbcl-package->cl-source-package sbcl-germinal)) + +(define-public ecl-germinal + (sbcl-package->ecl-package sbcl-germinal)) + (define-public sbcl-css-lite (let ((commit "6ee4e6212ed56943d665df163d2a834b122e6273") (revision "0")) From dc33a21fc099909c076029081cafc8338cf14b8b Mon Sep 17 00:00:00 2001 From: Nicolas Goaziou Date: Mon, 19 Dec 2022 15:52:53 +0100 Subject: [PATCH 371/790] gnu: emacs-clojure-mode: Update to 5.16.0. * gnu/packages/emacs-xyz.scm (emacs-clojure-mode): Update to 5.16.0. --- gnu/packages/emacs-xyz.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/emacs-xyz.scm b/gnu/packages/emacs-xyz.scm index 819a7ccdec..6cd5d686cd 100644 --- a/gnu/packages/emacs-xyz.scm +++ b/gnu/packages/emacs-xyz.scm @@ -11342,7 +11342,7 @@ allowing unprefixed keys to insert their respective characters as expected.") (define-public emacs-clojure-mode (package (name "emacs-clojure-mode") - (version "5.15.1") + (version "5.16.0") (source (origin (method git-fetch) @@ -11351,7 +11351,7 @@ allowing unprefixed keys to insert their respective characters as expected.") (commit (string-append "v" version)))) (file-name (git-file-name name version)) (sha256 - (base32 "12m3yjhy4q0x3ri4xxb9raqg9lmw4hk4jgn436d9zvsk4fr3h1nd")))) + (base32 "0s09b9gbmjmk56jm9hcbk06zfa96kqhgx58d98w13yy01yx0pych")))) (build-system emacs-build-system) (native-inputs (list emacs-buttercup emacs-dash emacs-paredit emacs-s)) From 71bc9d195a110e014b86c7738e63ecd4a4edaabd Mon Sep 17 00:00:00 2001 From: Nicolas Goaziou Date: Mon, 19 Dec 2022 16:02:15 +0100 Subject: [PATCH 372/790] gnu: Add emacs-external-completion. * gnu/packages/emacs-xyz.scm (emacs-external-completion): New variable. --- gnu/packages/emacs-xyz.scm | 27 +++++++++++++++++++++++++++ 1 file changed, 27 insertions(+) diff --git a/gnu/packages/emacs-xyz.scm b/gnu/packages/emacs-xyz.scm index 6cd5d686cd..10b7229878 100644 --- a/gnu/packages/emacs-xyz.scm +++ b/gnu/packages/emacs-xyz.scm @@ -4527,6 +4527,33 @@ create an Extempore REPL, connect the current @code{extempore-mode} buffer to a running Extempore process, and more.") (license license:bsd-2)))) +(define-public emacs-external-completion + (package + (name "emacs-external-completion") + (version "0.1") + (source (origin + (method url-fetch) + (uri (string-append + "https://elpa.gnu.org/packages/external-completion-" version + ".tar")) + (sha256 + (base32 + "12pddwp5jby2icshj77w4kwxv75zi00jdxw18f721d7zx3l7q668")))) + (build-system emacs-build-system) + (home-page "https://elpa.gnu.org/packages/external-completion.html") + (synopsis "Let external tools control Emacs completion style") + (description + "The @code{external} completion style is used with a ``programmable +completion'' table that gathers completions from an external tool such as +a shell utility, an inferior process, an HTTP server. The table and external +tool are fully in control of the matching of the pattern string to the +potential candidates of completion. When @code{external} is in use, the usual +styles configured by the user or other in @code{completion-styles} are +ignored. This compromise is for speed: all other styles need the full data +set to be available in Emacs addressing space, which is often slow if not +completely unfeasible.") + (license license:gpl3+))) + (define-public emacs-kakoune ;; Package has no release. Version is extracted from "Version:" keyword in ;; main file. From 1d893c3a97457be5861f129d666d4a6b9c390a5a Mon Sep 17 00:00:00 2001 From: Nicolas Goaziou Date: Mon, 19 Dec 2022 16:06:32 +0100 Subject: [PATCH 373/790] gnu: emacs-eglot: Update to 1.10. * gnu/packages/emacs-xyz.scm (emacs-eglot): Update to 1.10. [source]: Use GNU ELPA as upstream since the project as been merged into Emacs and the GitHub repository is no longer up-to-date. [arguments]: Remove tests, which do not exist in the tarball. [propagated-inputs]: Add EMACS-EXTERNAL-COMPLETION, EMACS-SEQ, EMACS-XREF. --- gnu/packages/emacs-xyz.scm | 26 +++++++++++--------------- 1 file changed, 11 insertions(+), 15 deletions(-) diff --git a/gnu/packages/emacs-xyz.scm b/gnu/packages/emacs-xyz.scm index 10b7229878..5cd518c5c4 100644 --- a/gnu/packages/emacs-xyz.scm +++ b/gnu/packages/emacs-xyz.scm @@ -17050,27 +17050,23 @@ Emacs.") (define-public emacs-eglot (package (name "emacs-eglot") - (version "1.9") + (version "1.10") (source (origin - (method git-fetch) - (uri (git-reference - (url "https://github.com/joaotavora/eglot") - (commit version))) - (file-name (git-file-name name version)) + (method url-fetch) + (uri (string-append "https://elpa.gnu.org/packages/eglot-" version + ".tar")) (sha256 (base32 - "030837yak24ymjawsfr1hgyfdjy3k30ld1ca0cgnrxhgxc7p8hwv")))) + "0iw1jnfsjd2yq73ic3cld8m51wyxdwn3kjv9ala28krvsvb4h3y4")))) (build-system emacs-build-system) - (arguments - (list - #:tests? #t - #:test-command #~(list "emacs" "--batch" - "-l" "eglot.el" - "-l" "eglot-tests.el" - "-f" "ert-run-tests-batch-and-exit"))) (propagated-inputs - (list emacs-eldoc emacs-jsonrpc emacs-project)) + (list emacs-external-completion + emacs-eldoc + emacs-jsonrpc + emacs-project + emacs-seq + emacs-xref)) (home-page "https://github.com/joaotavora/eglot") (synopsis "Client for Language Server Protocol (LSP) servers") (description From 5aff27b68e41e9b821832863d67abe82c780196f Mon Sep 17 00:00:00 2001 From: Nicolas Goaziou Date: Mon, 19 Dec 2022 16:08:54 +0100 Subject: [PATCH 374/790] gnu: emacs-engine-mode: Update to 2.2.1. * gnu/packages/emacs-xyz.scm (emacs-engine-mode): Update to 2.2.1. --- gnu/packages/emacs-xyz.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/emacs-xyz.scm b/gnu/packages/emacs-xyz.scm index 5cd518c5c4..4e971c6545 100644 --- a/gnu/packages/emacs-xyz.scm +++ b/gnu/packages/emacs-xyz.scm @@ -18077,7 +18077,7 @@ the nick color and the background color (define-public emacs-engine-mode (package (name "emacs-engine-mode") - (version "2.1.1") + (version "2.2.1") (source (origin (method git-fetch) @@ -18086,7 +18086,7 @@ the nick color and the background color (commit (string-append "v" version)))) (file-name (git-file-name name version)) (sha256 - (base32 "1xka8i4cdvp5r2v2mkli1zz17x1sdsnmszbhqav2rf94v656d91i")))) + (base32 "11ls3wrvfmcz61pps438x772nk06rqff91s3xi5rzc3n2hkl1ayb")))) (build-system emacs-build-system) (synopsis "Minor mode for defining and querying search engines") (description "@code{engine-mode} is a global minor mode for Emacs. It From cf1e1ec9e29e4102c5115e76222f729bede0d9de Mon Sep 17 00:00:00 2001 From: Nicolas Goaziou Date: Mon, 19 Dec 2022 16:10:54 +0100 Subject: [PATCH 375/790] gnu: emacs-subed: Update to 1.0.27. * gnu/packages/emacs-xyz.scm (emacs-subed): Update to 1.0.27. --- gnu/packages/emacs-xyz.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/emacs-xyz.scm b/gnu/packages/emacs-xyz.scm index 4e971c6545..d7b062c583 100644 --- a/gnu/packages/emacs-xyz.scm +++ b/gnu/packages/emacs-xyz.scm @@ -7343,14 +7343,14 @@ user.") (define-public emacs-subed (package (name "emacs-subed") - (version "1.0.26") + (version "1.0.27") (source (origin (method url-fetch) (uri (string-append "https://elpa.nongnu.org/nongnu/subed-" version ".tar")) (sha256 (base32 - "1vssgrchjgf36qxm6bm574wvvcjxmcfhlpziwilzixkxw48hh0ym")))) + "0nyhrlpvvglc3gd2wv20j34mws6f6s2j7q73b4lf3j0mw9yq1cgf")))) (arguments (list #:tests? #t From 7d0c6da52227add6076f84365b6fa31ed4c9d44e Mon Sep 17 00:00:00 2001 From: Nicolas Goaziou Date: Mon, 19 Dec 2022 16:10:58 +0100 Subject: [PATCH 376/790] gnu: emacs-vertico-posframe: Update to 0.5.9. * gnu/packages/emacs-xyz.scm (emacs-vertico-posframe): Update to 0.5.9. --- gnu/packages/emacs-xyz.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/emacs-xyz.scm b/gnu/packages/emacs-xyz.scm index d7b062c583..949cacfb83 100644 --- a/gnu/packages/emacs-xyz.scm +++ b/gnu/packages/emacs-xyz.scm @@ -34649,7 +34649,7 @@ across sessions.") (define-public emacs-vertico-posframe (package (name "emacs-vertico-posframe") - (version "0.5.5") + (version "0.5.9") (source (origin (method url-fetch) (uri (string-append @@ -34657,7 +34657,7 @@ across sessions.") ".tar")) (sha256 (base32 - "1rfji5x7rb787xzm9g268z7khvrby0plvas97q8wfshl96md8svx")))) + "1d1b8lfhr8zxa0dwsiqb1wzawx90l6lrr26jl17gpj85iyj3imq6")))) (build-system emacs-build-system) (propagated-inputs (list emacs-posframe emacs-vertico)) (home-page "https://github.com/tumashu/vertico-posframe") From 164c3151b4c9595439f7f9ed41197d8efa74a701 Mon Sep 17 00:00:00 2001 From: Nicolas Goaziou Date: Mon, 19 Dec 2022 16:28:25 +0100 Subject: [PATCH 377/790] gnu: emacs-jsonrpc: Update to 1.0.16. * gnu/packages/emacs-xyz.scm (emacs-jsonrpc): Update to 1.0.16. [source]: Remove ".git" suffix from URL. --- gnu/packages/emacs-xyz.scm | 9 ++++----- 1 file changed, 4 insertions(+), 5 deletions(-) diff --git a/gnu/packages/emacs-xyz.scm b/gnu/packages/emacs-xyz.scm index 949cacfb83..f63c09fba1 100644 --- a/gnu/packages/emacs-xyz.scm +++ b/gnu/packages/emacs-xyz.scm @@ -17344,21 +17344,20 @@ highlighting.") ;; Commit refers to a commit in the Emacs repository, as jsonrpc.el was ;; upstreamed. By convention, it should refer to a commit in which ;; jsonrpc.el was actually touched. - (let ((commit "50654cf0b1bf6210fc8f46d8e7ae13bbeeccecb5") - (revision "0")) ; Currently a version bump + (let ((commit "8bf4cdcf79bc3254a9169f28f68922ab83bd4e78")) ;version bump (package (name "emacs-jsonrpc") - (version (git-version "1.0.15" revision commit)) + (version "1.0.16") (source (origin (method git-fetch) (uri (git-reference - (url "https://git.savannah.gnu.org/git/emacs.git") + (url "https://git.savannah.gnu.org/git/emacs") (commit commit))) (file-name (git-file-name name version)) (sha256 (base32 - "0srwb171dxha1nfzppk6x9v4bdj3lk74pksqnhalw8jw9c67b72y")))) + "1mka35kparv7z52kknh9nam4wyczcp73glp48q24v05gm42a8xxr")))) (build-system emacs-build-system) (arguments (list #:phases From 423ba27c85cd318098bb55f7aa36dd992497d0cc Mon Sep 17 00:00:00 2001 From: Nicolas Goaziou Date: Mon, 19 Dec 2022 16:32:28 +0100 Subject: [PATCH 378/790] gnu: emacs-package-build: Update to 4.0.0. * gnu/packages/emacs-xyz.scm (emacs-package-build): Update to 4.0.0. --- gnu/packages/emacs-xyz.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/emacs-xyz.scm b/gnu/packages/emacs-xyz.scm index f63c09fba1..09f001169b 100644 --- a/gnu/packages/emacs-xyz.scm +++ b/gnu/packages/emacs-xyz.scm @@ -803,7 +803,7 @@ comparing large files in batches.") (define-public emacs-package-build (package (name "emacs-package-build") - (version "3.2") + (version "4.0.0") (source (origin (method git-fetch) (uri (git-reference @@ -812,7 +812,7 @@ comparing large files in batches.") (file-name (git-file-name name version)) (sha256 (base32 - "02ngllr9lilpjsgdpk4628kdp0nwdlrkxj78bvi4jlhnbk4chh1c")))) + "165gbrc1h1yj764kn3qq2y1551y04lqnklfa0k87gqgd38q5v985")))) (build-system emacs-build-system) (home-page "https://github.com/melpa/package-build") (synopsis "Tools for assembling an Emacs package archive") From 05e4efe0c83c09929d15a0f5faa23a9afc0079e4 Mon Sep 17 00:00:00 2001 From: Nicolas Goaziou Date: Mon, 19 Dec 2022 16:35:36 +0100 Subject: [PATCH 379/790] gnu: giac: Update to 1.9.0-33. * gnu/packages/algebra.scm (giac): Update to 1.9.0-33. --- gnu/packages/algebra.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/algebra.scm b/gnu/packages/algebra.scm index a2e17e84a3..3ceef8ecd2 100644 --- a/gnu/packages/algebra.scm +++ b/gnu/packages/algebra.scm @@ -327,7 +327,7 @@ precision.") (define-public giac (package (name "giac") - (version "1.9.0-29") + (version "1.9.0-33") (source (origin (method url-fetch) @@ -339,7 +339,7 @@ precision.") "~parisse/debian/dists/stable/main/source/" "giac_" version ".tar.gz")) (sha256 - (base32 "03hbg5b0xmdfp919mxn5lsard1mwg1kcm9xrm8gk7wnmr9r1adgn")))) + (base32 "00hdfakys4xpvmf2v851dr4hf3j6483pwwkfy5i63s5hs10mjsq5")))) (build-system gnu-build-system) (arguments (list From 5281bcc858a435338d326837ea3c821b3601547c Mon Sep 17 00:00:00 2001 From: Liliana Marie Prikler Date: Fri, 16 Dec 2022 00:31:00 +0100 Subject: [PATCH 380/790] gnu: musescore: Fix build. MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * gnu/packages/music.scm (musescore)[snippet]: Remove crashpad_handler and associated install actions. [arguments]<#:configure-flags>: Add “-DBUILD_DIAGNOSTICS=OFF”. [inputs]: Add qtquickcontrols-5. Co-authored-by: Vivien Kraus Signed-off-by: Nicolas Goaziou --- gnu/packages/music.scm | 10 ++++++++-- 1 file changed, 8 insertions(+), 2 deletions(-) diff --git a/gnu/packages/music.scm b/gnu/packages/music.scm index 614eb57791..bde01cb312 100644 --- a/gnu/packages/music.scm +++ b/gnu/packages/music.scm @@ -4787,14 +4787,19 @@ includes LV2 plugins and a JACK standalone client.") (base32 "16rcwr6fzghv8100syzicabqg8jqvng3zzsi6h3ja4zkp9hcbkcr")) (modules '((guix build utils))) (snippet - ;; Remove unused libraries. '(begin + ;; Remove unused libraries... (for-each delete-file-recursively - '("thirdparty/freetype")))))) + '("thirdparty/freetype")) + ;; ... and precompiled binaries. + (delete-file-recursively "src/diagnostics/crashpad_handler") + (substitute* "src/diagnostics/CMakeLists.txt" + (("install") "#install")))))) (build-system qt-build-system) (arguments `(#:configure-flags `("-DDOWNLOAD_SOUNDFONT=OFF" + "-DBUILD_DIAGNOSTICS=OFF" "-DMUSESCORE_BUILD_CONFIG=release" "-DUSE_SYSTEM_FREETYPE=ON") ;; There are tests, but no simple target to run. The command used to @@ -4825,6 +4830,7 @@ includes LV2 plugins and a JACK standalone client.") qtdeclarative-5 qtgraphicaleffects qtnetworkauth-5 + qtquickcontrols-5 qtquickcontrols2-5 qtscript qtsvg-5 From df822dffb37a72886a49bc66be59b46dc018c27c Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Mon, 19 Dec 2022 13:47:08 +0100 Subject: [PATCH 381/790] gnu: r-vctrs: Remove r-knitr from native inputs. * gnu/packages/cran.scm (r-vctrs)[native-inputs]: Remove. --- gnu/packages/cran.scm | 3 +++ 1 file changed, 3 insertions(+) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 5a76c76c6e..f928403bd6 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -7736,6 +7736,9 @@ estimated from a given sample.") (build-system r-build-system) (propagated-inputs (list r-cli r-glue r-lifecycle r-rlang)) + ;; We can't have r-knitr among the inputs here, because r-vctrs ends up + ;; being an eventual input to r-knitr. + #; (native-inputs (list r-knitr)) (home-page "https://github.com/r-lib/vctrs") From 839a8fc59e9e0aed9e01dff1b25ddfd02df1be65 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Mon, 19 Dec 2022 13:47:53 +0100 Subject: [PATCH 382/790] gnu: r-lifecycle: Remove r-knitr from native inputs. * gnu/packages/cran.scm (r-lifecycle)[native-inputs]: Remove r-knitr. --- gnu/packages/cran.scm | 3 +++ 1 file changed, 3 insertions(+) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index f928403bd6..0ee670b3bb 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -22918,6 +22918,9 @@ atmospheric physics.") (build-system r-build-system) (propagated-inputs (list r-cli r-glue r-rlang)) + ;; We can't add this here because via r-stringr this package ends up being + ;; an input to r-knitr. + #; (native-inputs (list r-knitr)) ; for vignettes (home-page "https://github.com/r-lib/lifecycle") From 71c3179ba3da1b493a098efcd64e4a8840c4a22e Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Mon, 19 Dec 2022 13:48:44 +0100 Subject: [PATCH 383/790] gnu: r-stringr: Update to 1.5.0. * gnu/packages/statistics.scm (r-stringr): Update to 1.5.0. [propagated-inputs]: Add r-cli, r-lifecycle, r-rlang, and r-vctrs. --- gnu/packages/statistics.scm | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm index 4c7609683b..0fd1cc8cd7 100644 --- a/gnu/packages/statistics.scm +++ b/gnu/packages/statistics.scm @@ -1187,16 +1187,16 @@ transliteration, concatenation, date-time formatting and parsing, etc.") (define-public r-stringr (package (name "r-stringr") - (version "1.4.1") + (version "1.5.0") (source (origin (method url-fetch) (uri (cran-uri "stringr" version)) (sha256 - (base32 "1cfw1lv64lzg16zb04c0fcmd3gx8vq9x73hqikqhgqd3ra88w3gc")))) + (base32 "0fk34ql5ak57f06l10ai300kxay6r7kkkyfanh8r24qaf3bmkcaj")))) (build-system r-build-system) (propagated-inputs - (list r-glue r-magrittr r-stringi)) + (list r-cli r-glue r-lifecycle r-magrittr r-rlang r-stringi r-vctrs)) ;; We can't add r-knitr here, because this package ends up being an input ;; to r-knitr. #; From 3724396a8f2d4f12da27e8cc20ac25a44254d4de Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Mon, 19 Dec 2022 13:49:49 +0100 Subject: [PATCH 384/790] gnu: r-bslib: Update to 0.4.2. * gnu/packages/cran.scm (r-bslib): Update to 0.4.2. [source]: Update snippet. [propagated-inputs]: Add r-base64enc and r-mime. [native-inputs]: Update bootstrap5 from 5.1.3 to 5.2.2. --- gnu/packages/cran.scm | 13 +++++++------ 1 file changed, 7 insertions(+), 6 deletions(-) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 0ee670b3bb..2ee551d892 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -3177,18 +3177,17 @@ expression estimates for all genes.") (define-public r-bslib (package (name "r-bslib") - (version "0.4.1") + (version "0.4.2") (source (origin (method url-fetch) (uri (cran-uri "bslib" version)) (sha256 (base32 - "0bz6w34shk2pijq5hvjv2bg8xhhg4yazn4wcix7436yi9k41zgaf")) + "069ghbzp0bsmbw2nzw28cmbym65i3a90v50y7qksy2g4pfhvfh4s")) (snippet '(for-each delete-file '("inst/lib/bs-a11y-p/plugins/js/bootstrap-accessibility.min.js" - "inst/lib/bs-colorpicker/js/bootstrap-colorpicker.min.js" "inst/lib/bs3/assets/javascripts/bootstrap.min.js" "inst/lib/bs4/dist/js/bootstrap.bundle.min.js" "inst/lib/bs5/dist/js/bootstrap.bundle.min.js"))))) @@ -3224,11 +3223,13 @@ expression estimates for all genes.") (string-append "--outfile=" target))) sources targets))))))))) (propagated-inputs - (list r-cachem + (list r-base64enc + r-cachem r-htmltools r-jquerylib r-jsonlite r-memoise + r-mime r-rlang r-sass)) (native-inputs @@ -3243,10 +3244,10 @@ expression estimates for all genes.") ("js-bootstrap5-bundle" ,(origin (method url-fetch) - (uri "https://raw.githubusercontent.com/twbs/bootstrap/v5.1.3/dist/js/bootstrap.bundle.js") + (uri "https://raw.githubusercontent.com/twbs/bootstrap/v5.2.2/dist/js/bootstrap.bundle.js") (sha256 (base32 - "116979i2vr1y9i6g7n5iir19p85xwr642scbl9jcqdr0w9801nw6")))))) + "1ibfb1lwwm50did0b4fvxaqc7xyljmp20f3qb1ybdlvcy22mk8bg")))))) (home-page "https://rstudio.github.io/bslib/") (synopsis "Custom Bootstrap Sass themes for shiny and rmarkdown") (description From 2f346d33ca24bbc586484b03dbc2938eada0a26c Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Mon, 19 Dec 2022 13:51:43 +0100 Subject: [PATCH 385/790] gnu: r-htmlwidgets: Update to 1.6.0. * gnu/packages/cran.scm (r-htmlwidgets): Update to 1.6.0. [propagated-inputs]: Add r-knitr and r-rmarkdown. --- gnu/packages/cran.scm | 8 +++++--- 1 file changed, 5 insertions(+), 3 deletions(-) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 2ee551d892..db1e4e24b2 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -2838,16 +2838,18 @@ a list of p-values.") (define-public r-htmlwidgets (package (name "r-htmlwidgets") - (version "1.5.4") + (version "1.6.0") (source (origin (method url-fetch) (uri (cran-uri "htmlwidgets" version)) (sha256 (base32 - "1hgz8sx8xrvfcdwa4q15k942w4qsqg8lyxbbf7qyfzbi807wcgqs")))) + "06prjx6ic2bddaw50ksz6l7hsidkzwb69m85vzc0apxvwaygz0gh")))) (build-system r-build-system) (propagated-inputs - (list r-htmltools r-jsonlite r-yaml)) + (list r-htmltools r-jsonlite + r-knitr r-rmarkdown + r-yaml)) (native-inputs (list r-knitr)) (home-page "https://github.com/ramnathv/htmlwidgets") From 5a1a5677cd6123a5b1771bd8933a6af33870567b Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Mon, 19 Dec 2022 17:03:04 +0100 Subject: [PATCH 386/790] import/cran: Add more mappings from sysnames to Guix package names. * guix/import/cran.scm (transform-sysname): Add more mappings. --- guix/import/cran.scm | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/guix/import/cran.scm b/guix/import/cran.scm index a02e746417..48fbc1dccb 100644 --- a/guix/import/cran.scm +++ b/guix/import/cran.scm @@ -410,7 +410,11 @@ empty list when the FIELD cannot be found." ("tcl/tk" "tcl") ("booktabs" "texlive-booktabs") ("freetype2" "freetype") + ("mariadb-devel" "mariadb") + ("mysql56_dev" "mariadb") ("sqlite3" "sqlite") + ("udunits-2" "udunits") + ("x11" "libx11") (_ sysname))) (define cran-guix-name (cut guix-name "r-" <>)) From 9035903370e594393385f1784a86d58418545f80 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Mon, 19 Dec 2022 17:07:15 +0100 Subject: [PATCH 387/790] gnu: r-datawizard: Update to 0.6.5. * gnu/packages/cran.scm (r-datawizard): Update to 0.6.5. --- gnu/packages/cran.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index db1e4e24b2..6fe0ccff8d 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -307,14 +307,14 @@ etc.") (define-public r-datawizard (package (name "r-datawizard") - (version "0.6.4") + (version "0.6.5") (source (origin (method url-fetch) (uri (cran-uri "datawizard" version)) (sha256 (base32 - "0iv3h08bzmijrxyv2jz70jf53i2bk14kh0vq9a93fms5z08jv19p")))) + "0il98vmy8l4wrisqz9xli7iki2ajdlsxyhh4k4grrd28gzkj8lgb")))) (properties `((upstream-name . "datawizard"))) (build-system r-build-system) (propagated-inputs From deaffeb197f37bcf62e03e8c92a31e2660434db6 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Mon, 19 Dec 2022 17:07:15 +0100 Subject: [PATCH 388/790] gnu: r-ggpp: Update to 0.5.0. * gnu/packages/cran.scm (r-ggpp): Update to 0.5.0. --- gnu/packages/cran.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 6fe0ccff8d..e499cbefb2 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -1369,14 +1369,14 @@ variables.") (define-public r-ggpp (package (name "r-ggpp") - (version "0.4.5") + (version "0.5.0") (source (origin (method url-fetch) (uri (cran-uri "ggpp" version)) (sha256 (base32 - "02inwvfz2zxsj7bq0nz11c5spnyaf8zhjnlfllpwfjfy46qrx2p9")))) + "0zmxnzsdmwv9v77fifgiknalwif59261kslq8848x1xch8f82l77")))) (properties `((upstream-name . "ggpp"))) (build-system r-build-system) (propagated-inputs From 50f69ad7ba63a17c1aa61b9840a0ba2c52357c76 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Mon, 19 Dec 2022 17:07:15 +0100 Subject: [PATCH 389/790] gnu: r-ggpmisc: Update to 0.5.2. * gnu/packages/cran.scm (r-ggpmisc): Update to 0.5.2. --- gnu/packages/cran.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index e499cbefb2..704f32e1f3 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -1574,13 +1574,13 @@ axis} (SMA), and @dfn{ranged major axis} (RMA).") (define-public r-ggpmisc (package (name "r-ggpmisc") - (version "0.5.1") + (version "0.5.2") (source (origin (method url-fetch) (uri (cran-uri "ggpmisc" version)) (sha256 (base32 - "18085n6id5v3g3w1z1010im85i4yii4wib2cmcxwqk7qvk9rsrqi")))) + "1zvq580vi1h2afdgxaqabjhfsphvmdchwiaahqvvhljxmpmh82q6")))) (build-system r-build-system) (propagated-inputs (list r-confintr From 96e1f10e66356b37521712a02c9c63498dab115b Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Mon, 19 Dec 2022 17:07:16 +0100 Subject: [PATCH 390/790] gnu: r-ggside: Update to 0.2.2. * gnu/packages/cran.scm (r-ggside): Update to 0.2.2. [propagated-inputs]: Add r-vctrs. --- gnu/packages/cran.scm | 7 ++++--- 1 file changed, 4 insertions(+), 3 deletions(-) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 704f32e1f3..dbde36c225 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -1609,13 +1609,13 @@ respecting the grammar of its graphics paradigm.") (define-public r-ggside (package (name "r-ggside") - (version "0.2.1") + (version "0.2.2") (source (origin (method url-fetch) (uri (cran-uri "ggside" version)) (sha256 (base32 - "1vl7kzgmi5xxxsqvyg4cm4xwd3lfjgysay1lw6hri5vj22mnga5h")))) + "1z50z4xpxfpqdz26hja6xw3q403p00cr5qawjxl0qg4jixl7j65p")))) (properties `((upstream-name . "ggside"))) (build-system r-build-system) (propagated-inputs @@ -1624,7 +1624,8 @@ respecting the grammar of its graphics paradigm.") r-gtable r-rlang r-scales - r-tibble)) + r-tibble + r-vctrs)) (native-inputs (list r-knitr)) (home-page "https://cran.r-project.org/package=ggside") (synopsis "Side grammar graphics that extends @code{ggplot2}") From 5ff58253ae73d75763f94bfb863a9f7777261878 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Mon, 19 Dec 2022 17:07:16 +0100 Subject: [PATCH 391/790] gnu: r-httpuv: Update to 1.6.7. * gnu/packages/cran.scm (r-httpuv): Update to 1.6.7. --- gnu/packages/cran.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index dbde36c225..c608ee0bce 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -2703,13 +2703,13 @@ Zucchini.") (define-public r-httpuv (package (name "r-httpuv") - (version "1.6.6") + (version "1.6.7") (source (origin (method url-fetch) (uri (cran-uri "httpuv" version)) (sha256 (base32 - "14qjf7bpl7pay89b7vi2vccl342q8xs6101a9x6qijy54k9myfa1")) + "0jjb2w59x8a4k24j9rc4rjm37h1ccrfq1nzd40inbnd6kcqf3lkm")) ;; Unvendor bundled libraries. As of 1.5.4 the vendored libuv ;; only contains fixes for building on Solaris. (patches (search-patches "r-httpuv-1.6.6-unvendor-libuv.patch")) From fb53f7f483d4d2533ae67b3c6f436a8f1f952f48 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Mon, 19 Dec 2022 17:07:16 +0100 Subject: [PATCH 392/790] gnu: r-jsonlite: Update to 1.8.4. * gnu/packages/cran.scm (r-jsonlite): Update to 1.8.4. --- gnu/packages/cran.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index c608ee0bce..ec30c94835 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -2750,13 +2750,13 @@ particularly easy to create complete web applications using httpuv alone.") (define-public r-jsonlite (package (name "r-jsonlite") - (version "1.8.3") + (version "1.8.4") (source (origin (method url-fetch) (uri (cran-uri "jsonlite" version)) (sha256 (base32 - "1w685bwhvqxh8y3b4rmzmbbxsj0sqrdad4rni7dxbiqzd2piszy5")))) + "0y0jzf74c3q1sghgarvwmrkvxs7yahywd342m8c0jsr28bhapskr")))) (build-system r-build-system) (native-inputs (list r-knitr)) From 8e133b08e480b6739b548ba6eae1fe78e1a61bd4 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Mon, 19 Dec 2022 17:07:17 +0100 Subject: [PATCH 393/790] gnu: r-htmltools: Update to 0.5.4. * gnu/packages/cran.scm (r-htmltools): Update to 0.5.4. [propagated-inputs]: Add r-ellipsis. --- gnu/packages/cran.scm | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index ec30c94835..83289650ef 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -2820,16 +2820,16 @@ a list of p-values.") (define-public r-htmltools (package (name "r-htmltools") - (version "0.5.3") + (version "0.5.4") (source (origin (method url-fetch) (uri (cran-uri "htmltools" version)) (sha256 (base32 - "0krjyz99q7zvdfg60b128c0zwr36h54gb05jw9c874d8kqv1ni9c")))) + "0zij9zrgsi82q5c65sf4pbidnzrkfr763g0n4ypdhf8dd6l2i0h0")))) (build-system r-build-system) (propagated-inputs - (list r-base64enc r-digest r-fastmap r-rlang)) + (list r-base64enc r-digest r-ellipsis r-fastmap r-rlang)) (home-page "https://cran.r-project.org/web/packages/htmltools") (synopsis "R tools for HTML") (description From 5f7d9401bc882aeee46e364f1f9c38fd9e50667e Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Mon, 19 Dec 2022 17:07:17 +0100 Subject: [PATCH 394/790] gnu: r-ggtern: Update to 3.4.1. * gnu/packages/cran.scm (r-ggtern): Update to 3.4.1. --- gnu/packages/cran.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 83289650ef..2cf8cd9b0a 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -3797,13 +3797,13 @@ annotation data to keep updated.") (define-public r-ggtern (package (name "r-ggtern") - (version "3.4.0") + (version "3.4.1") (source (origin (method url-fetch) (uri (cran-uri "ggtern" version)) (sha256 - (base32 "01j1rvff3vz72vwqsy3bh81aav7gfymg4sbvc267vg0r3a16ywcg")))) + (base32 "0w0kg6755kfpczqpaly251fgqv31js9gdzr17x734l2adycji3yr")))) (properties `((upstream-name . "ggtern"))) (build-system r-build-system) (propagated-inputs From 2b184f70e0850147657f7c8181c17f4a43204f62 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Mon, 19 Dec 2022 17:07:17 +0100 Subject: [PATCH 395/790] gnu: r-progressr: Update to 0.12.0. * gnu/packages/cran.scm (r-progressr): Update to 0.12.0. --- gnu/packages/cran.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 2cf8cd9b0a..3ef35b67f7 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -5946,13 +5946,13 @@ available in a vignette.") (define-public r-progressr (package (name "r-progressr") - (version "0.11.0") + (version "0.12.0") (source (origin (method url-fetch) (uri (cran-uri "progressr" version)) (sha256 - (base32 "1nbc6vvsyqa1gvh1a1m4prnvng88wsa0r35i9fiwq84a6j18qrnq")))) + (base32 "0nahvfcnx45n0q24r4j9cjqmmgh302ra3207izs6fzfda7sqn25q")))) (properties `((upstream-name . "progressr"))) (build-system r-build-system) (propagated-inputs From efdd3ef2f0b0efd5709dbc7d06ca090c3e264bcb Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Mon, 19 Dec 2022 17:07:17 +0100 Subject: [PATCH 396/790] gnu: r-timedate: Update to 4021.107. * gnu/packages/cran.scm (r-timedate): Update to 4021.107. --- gnu/packages/cran.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 3ef35b67f7..b8e75b3100 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -6088,14 +6088,14 @@ included in this package.") (define-public r-timedate (package (name "r-timedate") - (version "4021.106") + (version "4021.107") (source (origin (method url-fetch) (uri (cran-uri "timeDate" version)) (sha256 (base32 - "1qhh1d85s8r4wkcf4fljfm67lnkj8flnx9iz4hdg305xdkng3b8l")))) + "1i54a425r5hi08yl9rb2qh1nynh29ppv9b4h46cxyzn1ybqlr9sg")))) (properties `((upstream-name . "timeDate"))) (build-system r-build-system) (home-page "https://www.rmetrics.org") From 837fabf0dce70fa353ce5fa7303a1ff17510ab54 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Mon, 19 Dec 2022 17:07:18 +0100 Subject: [PATCH 397/790] gnu: r-rmysql: Update to 0.10.25. * gnu/packages/cran.scm (r-rmysql): Update to 0.10.25. --- gnu/packages/cran.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index b8e75b3100..28b3c26676 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -6132,14 +6132,14 @@ dimensioned arrays.") (define-public r-rmysql (package (name "r-rmysql") - (version "0.10.24") + (version "0.10.25") (source (origin (method url-fetch) (uri (cran-uri "RMySQL" version)) (sha256 (base32 - "0hbjcf0gzkkg8h50msj4a6ymax9s3j4aw44jl1mqcxkdmfn9l6ya")))) + "1527ba5vqg4ss6rqxrkxa1a66r1m9h4zmdnv9xdzva8fv2dhy4zd")))) (properties `((upstream-name . "RMySQL"))) (build-system r-build-system) (inputs From bf43c373f146c6b701d88c9fc26c10434b73ced1 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Mon, 19 Dec 2022 17:07:18 +0100 Subject: [PATCH 398/790] gnu: r-broom: Update to 1.0.2. * gnu/packages/cran.scm (r-broom): Update to 1.0.2. [propagated-inputs]: Remove r-ggplot2. --- gnu/packages/cran.scm | 5 ++--- 1 file changed, 2 insertions(+), 3 deletions(-) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 28b3c26676..165e134ca7 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -6393,21 +6393,20 @@ by base R methods related to model fitting.") (define-public r-broom (package (name "r-broom") - (version "1.0.1") + (version "1.0.2") (source (origin (method url-fetch) (uri (cran-uri "broom" version)) (sha256 (base32 - "14i8729m38nxf5q344isgq4006p3b50wi3q8jgckxqphhnj5lpjb")))) + "13hj4y3ajrn7x8hvirp2vfh1c8j2pdrz3dnxc5f0dr7jyfhp4dcy")))) (build-system r-build-system) (propagated-inputs (list r-backports r-dplyr r-ellipsis r-generics - r-ggplot2 r-glue r-purrr r-rlang From 482b3f3890e22cceefce77e86469eb6c165da278 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Mon, 19 Dec 2022 17:07:18 +0100 Subject: [PATCH 399/790] gnu: r-vioplot: Update to 0.4.0. * gnu/packages/cran.scm (r-vioplot): Update to 0.4.0. --- gnu/packages/cran.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 165e134ca7..dd04cfcc46 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -7015,14 +7015,14 @@ structure.") (define-public r-vioplot (package (name "r-vioplot") - (version "0.3.7") + (version "0.4.0") (source (origin (method url-fetch) (uri (cran-uri "vioplot" version)) (sha256 (base32 - "1dmdasp3jldc41233z6r08w3j76vyyp9m3jrj7n4ahk48yd5siq6")))) + "1db7g0378jbcd6ssb7afff4y4r0v472qnb625hfwixx4wf1v8aap")))) (build-system r-build-system) (propagated-inputs (list r-sm r-zoo)) From bb7051b5498db0a257f565abf103a8cbdf8e02c6 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Mon, 19 Dec 2022 17:07:18 +0100 Subject: [PATCH 400/790] gnu: r-aricode: Update to 1.0.2. * gnu/packages/cran.scm (r-aricode): Update to 1.0.2. --- gnu/packages/cran.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index dd04cfcc46..64b13960fc 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -7407,13 +7407,13 @@ script.") (define-public r-aricode (package (name "r-aricode") - (version "1.0.1") + (version "1.0.2") (source (origin (method url-fetch) (uri (cran-uri "aricode" version)) (sha256 (base32 - "0772l9gyrih48l1kymih0mb7szjqqnwcm4lzj0yzp4cs8l2mdf4f")))) + "1w5jnql49f0wd5h4b89l69s7qldp7qm90p4jm0j4kz9w0vvm2kjz")))) (properties `((upstream-name . "aricode"))) (build-system r-build-system) (propagated-inputs (list r-matrix r-rcpp)) From 17adace60baf85082af9ced56e6e9c9083fccee5 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Mon, 19 Dec 2022 17:07:19 +0100 Subject: [PATCH 401/790] gnu: r-tinytex: Update to 0.43. * gnu/packages/cran.scm (r-tinytex): Update to 0.43. --- gnu/packages/cran.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 64b13960fc..34f2457fbe 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -7835,14 +7835,14 @@ packages that work with genomic data.") (define-public r-tinytex (package (name "r-tinytex") - (version "0.42") + (version "0.43") (source (origin (method url-fetch) (uri (cran-uri "tinytex" version)) (sha256 (base32 - "1c925r62h84mhwd7v5j35ckdldf6cwb3wzczdn5s72hig0cplpr0")))) + "01183i6z6jyyqmmxri3xmscn7k6hswi2q7r0b5ix0s7pd1cz57jq")))) (build-system r-build-system) (propagated-inputs (list r-xfun)) From c9f9ad5832c01a5f28c909ccf8f39ca3c0b47259 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Mon, 19 Dec 2022 17:07:19 +0100 Subject: [PATCH 402/790] gnu: r-maptools: Update to 1.1-6. * gnu/packages/cran.scm (r-maptools): Update to 1.1-6. --- gnu/packages/cran.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 34f2457fbe..fed742cf7c 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -9681,14 +9681,14 @@ simple method for converting between file types.") (define-public r-maptools (package (name "r-maptools") - (version "1.1-5") + (version "1.1-6") (source (origin (method url-fetch) (uri (cran-uri "maptools" version)) (sha256 (base32 - "1p155w26hpmqc589kxha0xgw5b4x6610a3im7ap4mjx1sfavvn9w")))) + "024kyq81gwpl7shil63nng1z6pgqcwy6j6wj44gj7ch3vd9dz9fn")))) (build-system r-build-system) (propagated-inputs (list r-foreign r-lattice r-sp)) From bf9e3e0b644d8229eb23e138aa156c6c9e1030e5 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Mon, 19 Dec 2022 17:07:19 +0100 Subject: [PATCH 403/790] gnu: r-factominer: Update to 2.7. * gnu/packages/cran.scm (r-factominer): Update to 2.7. --- gnu/packages/cran.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index fed742cf7c..0330c720e0 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -10583,14 +10583,14 @@ clustering.") (define-public r-factominer (package (name "r-factominer") - (version "2.6") + (version "2.7") (source (origin (method url-fetch) (uri (cran-uri "FactoMineR" version)) (sha256 (base32 - "0xcg4vjs5v9k28hhxhkfkks7nvpxpp2cvim00kh67f4pq041c9l1")))) + "03952kcnwrm61kn5im55ky1j91nm5x4i4f5gs115li6gck63xf17")))) (properties `((upstream-name . "FactoMineR"))) (build-system r-build-system) (propagated-inputs From 90ebc6612c069a212504db3587fe3011569fd507 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Mon, 19 Dec 2022 17:07:19 +0100 Subject: [PATCH 404/790] gnu: r-rbibutils: Update to 2.2.11. * gnu/packages/cran.scm (r-rbibutils): Update to 2.2.11. --- gnu/packages/cran.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 0330c720e0..8f9a99f99e 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -10880,14 +10880,14 @@ hierarchical models using Markov Chain Monte Carlo (MCMC) simulation.") (define-public r-rbibutils (package (name "r-rbibutils") - (version "2.2.10") + (version "2.2.11") (source (origin (method url-fetch) (uri (cran-uri "rbibutils" version)) (sha256 (base32 - "1xqpij07d19nvg18kyikpm37r3fharkdmxzm0cjddmqwv757lim6")))) + "10g3fv8ninihjldhvh00yrp260dczhz3q519000jm3wp5w47b945")))) (properties `((upstream-name . "rbibutils"))) (build-system r-build-system) (home-page "https://geobosh.github.io/rbibutils/") From 245301440562ee06faddb4eb7faafceffe36487e Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Mon, 19 Dec 2022 17:07:20 +0100 Subject: [PATCH 405/790] gnu: r-argparse: Update to 2.2.1. * gnu/packages/cran.scm (r-argparse): Update to 2.2.1. --- gnu/packages/cran.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 8f9a99f99e..0f4cf4bae5 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -11486,14 +11486,14 @@ matches version and feature constraints.") (define-public r-argparse (package (name "r-argparse") - (version "2.1.6") + (version "2.2.1") (source (origin (method url-fetch) (uri (cran-uri "argparse" version)) (sha256 (base32 - "14p57nm0w3siqd473snzhpmnvsgl72x92pdcd64vhy2qg6nzmmra")))) + "193pjjy4vkmzmsc1w69szafgrisvn08gddilbxcg671sdk0dxd7k")))) (build-system r-build-system) (inputs (list python)) (propagated-inputs From 88682e87c1013de6082e47dbcae21612f88b5bbd Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Mon, 19 Dec 2022 17:07:20 +0100 Subject: [PATCH 406/790] gnu: r-doby: Update to 4.6.15. * gnu/packages/cran.scm (r-doby): Update to 4.6.15. --- gnu/packages/cran.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 0f4cf4bae5..da910779cd 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -11580,14 +11580,14 @@ the work.") (define-public r-doby (package (name "r-doby") - (version "4.6.14") + (version "4.6.15") (source (origin (method url-fetch) (uri (cran-uri "doBy" version)) (sha256 (base32 - "1ps6r7yxs0a6rpfi2yzrb9j41862za3gdl1aq9vw3j5cmgrk8w1n")))) + "14asz3bpyvxakvpap2aajk6f5j2d3d6vrvrgnlixg5q6gdbh465m")))) (properties `((upstream-name . "doBy"))) (build-system r-build-system) (propagated-inputs From 706efcc632b8f14981332c750e8f91458d0b03e6 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Mon, 19 Dec 2022 17:07:20 +0100 Subject: [PATCH 407/790] gnu: r-emmeans: Update to 1.8.3. * gnu/packages/cran.scm (r-emmeans): Update to 1.8.3. [propagated-inputs]: Remove r-xtable. --- gnu/packages/cran.scm | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index da910779cd..66bf61b142 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -13536,17 +13536,17 @@ the differences were not significantly different.") (define-public r-emmeans (package (name "r-emmeans") - (version "1.8.2") + (version "1.8.3") (source (origin (method url-fetch) (uri (cran-uri "emmeans" version)) (sha256 (base32 - "02fj957f67m1ik9n31h1p726hjnlhwlvd1wz93glfrcagm2p6nbq")))) + "004fd6kzky44xixd87q2nl1sn37krmqfas5gsylbc1cbrwnjzxlz")))) (build-system r-build-system) (propagated-inputs - (list r-estimability r-mvtnorm r-numderiv r-xtable)) + (list r-estimability r-mvtnorm r-numderiv)) (native-inputs (list r-knitr)) (home-page "https://github.com/rvlenth/emmeans") From 94793d19d79ba42cb6b1c5f552937dea11c1ec13 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Mon, 19 Dec 2022 17:07:20 +0100 Subject: [PATCH 408/790] gnu: r-gert: Update to 1.9.2. * gnu/packages/cran.scm (r-gert): Update to 1.9.2. --- gnu/packages/cran.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 66bf61b142..e4541cbee8 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -14105,14 +14105,14 @@ user credentials.") (define-public r-gert (package (name "r-gert") - (version "1.9.1") + (version "1.9.2") (source (origin (method url-fetch) (uri (cran-uri "gert" version)) (sha256 (base32 - "1p8z5qap06qf680r25y78wgnprzl9ib3xp3kvsw01bh819v1h7bm")))) + "0pk6mf300kh6wwzvaqymwzlikkbf8zj0xpslgyydn7zvr95ipjj2")))) (properties `((upstream-name . "gert"))) (build-system r-build-system) (inputs From e694144c10d5b93079f4dd8edaccb0cfd44932f2 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Mon, 19 Dec 2022 17:07:21 +0100 Subject: [PATCH 409/790] gnu: r-ncdf4: Update to 1.20. * gnu/packages/cran.scm (r-ncdf4): Update to 1.20. --- gnu/packages/cran.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index e4541cbee8..f03a9b3c90 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -14830,14 +14830,14 @@ other values.") (define-public r-ncdf4 (package (name "r-ncdf4") - (version "1.19") + (version "1.20") (source (origin (method url-fetch) (uri (cran-uri "ncdf4" version)) (sha256 (base32 - "0qzvin2fjzcb7h2knlnw14s6043pwi1nm7yf6p27ax7w269173fb")))) + "1kpi5xygx1nj8ybxrn9z0jxi3lbcibdvc7mjgyvm6f9plwjlxjvq")))) (build-system r-build-system) (inputs (list netcdf zlib)) From 3b626e859643c8cf6094517f8e038941bf754302 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Mon, 19 Dec 2022 17:07:21 +0100 Subject: [PATCH 410/790] gnu: r-tm: Update to 0.7-10. * gnu/packages/cran.scm (r-tm): Update to 0.7-10. --- gnu/packages/cran.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index f03a9b3c90..0631298287 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -15439,14 +15439,14 @@ Processing.") (define-public r-tm (package (name "r-tm") - (version "0.7-9") + (version "0.7-10") (source (origin (method url-fetch) (uri (cran-uri "tm" version)) (sha256 (base32 - "0a3ylj9735i21fh6iz63fkh1pnf2hs8ipp8wjdj25dahl18yhlyv")))) + "15lxaqlgkl9chiz0aw05l55bvlh48jwdgplfl8f2d8xsaq4gmbvc")))) (properties `((upstream-name . "tm"))) (build-system r-build-system) (propagated-inputs From 41cd18b3b8eedb4dd359fe74b59e9bba0302aac6 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Mon, 19 Dec 2022 17:07:21 +0100 Subject: [PATCH 411/790] gnu: r-tidytree: Update to 0.4.2. * gnu/packages/cran.scm (r-tidytree): Update to 0.4.2. [propagated-inputs]: Add r-cli. --- gnu/packages/cran.scm | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 0631298287..4f9d3472a1 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -15559,16 +15559,17 @@ maps.") (define-public r-tidytree (package (name "r-tidytree") - (version "0.4.1") + (version "0.4.2") (source (origin (method url-fetch) (uri (cran-uri "tidytree" version)) (sha256 - (base32 "1sq982x0pqvrn4d77m6v5xbbr9c8dkrwvw3as1pc5cg12x6kdi7v")))) + (base32 "0phmvbpsxx85fvw4000d160qh8njrgmzpr3ja0gy59dgv1k1m0yb")))) (build-system r-build-system) (propagated-inputs (list r-ape + r-cli r-dplyr r-lazyeval r-magrittr From e00df6abd4becdf089c880dbcefcd664b501f04d Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Mon, 19 Dec 2022 17:07:22 +0100 Subject: [PATCH 412/790] gnu: r-rnexml: Update to 2.4.9. * gnu/packages/cran.scm (r-rnexml): Update to 2.4.9. --- gnu/packages/cran.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 4f9d3472a1..004c938456 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -16036,13 +16036,13 @@ useful for building large phylogenies using multiple markers.") (define-public r-rnexml (package (name "r-rnexml") - (version "2.4.8") + (version "2.4.9") (source (origin (method url-fetch) (uri (cran-uri "RNeXML" version)) (sha256 (base32 - "0l5qpg6f107k927vnnki7g9yfs20xkpd7c5pkvbj8bpybbwjkm16")))) + "180w7c8n4xcn3x7haymi1fl3fpnklqfgmaki6jkxpm3hdiffmbsd")))) (build-system r-build-system) (propagated-inputs (list r-ape From fe858e93969eac4ae4733e82f269710a923b574a Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Mon, 19 Dec 2022 17:07:22 +0100 Subject: [PATCH 413/790] gnu: r-gmp: Update to 0.6-9. * gnu/packages/cran.scm (r-gmp): Update to 0.6-9. --- gnu/packages/cran.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 004c938456..f8e23bdc34 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -16533,14 +16533,14 @@ preparing, executing, and processing HTTP requests.") (define-public r-gmp (package (name "r-gmp") - (version "0.6-8") + (version "0.6-9") (source (origin (method url-fetch) (uri (cran-uri "gmp" version)) (sha256 (base32 - "0fba80f28fcb2w2spiy6wg7dr5cz7w6gf9z3yrkc6p60zbxdaccf")))) + "00zh0phr8axva2y2c10nla7n9mgh3wvwvsyyd3y43jpb3xim6lv6")))) (build-system r-build-system) (arguments '(#:phases From 80ed92310b9770022037260c45cc975f4b9732db Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Mon, 19 Dec 2022 17:07:22 +0100 Subject: [PATCH 414/790] gnu: r-survivalroc: Update to 1.0.3.1. * gnu/packages/cran.scm (r-survivalroc): Update to 1.0.3.1. --- gnu/packages/cran.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index f8e23bdc34..6aed94c9aa 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -17191,14 +17191,14 @@ package \"boot\".") (define-public r-survivalroc (package (name "r-survivalroc") - (version "1.0.3") + (version "1.0.3.1") (source (origin (method url-fetch) (uri (cran-uri "survivalROC" version)) (sha256 (base32 - "0wnd65ff5w679hxa1zrpfrx9qg47q21pjxppsga6m3h4iq1yfj8l")))) + "0p6irjs8a9xxgxwax0y9fzapcib237if3iy8g6lzv793mzmsyx41")))) (properties `((upstream-name . "survivalROC"))) (build-system r-build-system) (home-page "https://cran.r-project.org/web/packages/survivalROC") From 24dbabb23cdc645725b2b1dccc5d09cd2cb3f545 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Mon, 19 Dec 2022 17:07:22 +0100 Subject: [PATCH 415/790] gnu: r-listenv: Update to 0.9.0. * gnu/packages/cran.scm (r-listenv): Update to 0.9.0. --- gnu/packages/cran.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 6aed94c9aa..332a3fc6d5 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -17584,14 +17584,14 @@ by change of variable.") (define-public r-listenv (package (name "r-listenv") - (version "0.8.0") + (version "0.9.0") (source (origin (method url-fetch) (uri (cran-uri "listenv" version)) (sha256 (base32 - "0ps8bk7zlhbviawrw7vw25skjq81hkk3ijyi6g74dmfqy8zsyapx")))) + "11s8cy259al6x98xcz93jw6p87si01gcgzccnxhx69879zh42a1m")))) (build-system r-build-system) (arguments `(#:phases From 46d00e5d99657cbddf243b17ceb0a0d1681328ca Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Mon, 19 Dec 2022 17:07:23 +0100 Subject: [PATCH 416/790] gnu: r-parallelly: Update to 1.33.0. * gnu/packages/cran.scm (r-parallelly): Update to 1.33.0. --- gnu/packages/cran.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 332a3fc6d5..abb5ef906f 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -17636,14 +17636,14 @@ them in distributed compute environments.") (define-public r-parallelly (package (name "r-parallelly") - (version "1.32.1") + (version "1.33.0") (source (origin (method url-fetch) (uri (cran-uri "parallelly" version)) (sha256 (base32 - "146a9i999vrflr4g1fph1pgkl4bq0dw102bjw8pp1zy7kbsqbiii")))) + "0ymrpcxp2fnk1fpfig0kd1q3whzh7sykgcl91k53c2w20v2wwfpw")))) (properties `((upstream-name . "parallelly"))) (build-system r-build-system) (home-page "https://github.com/HenrikBengtsson/parallelly") From c2f9e5ac17f2bffc8eef3d948fc56deeef1201a9 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Mon, 19 Dec 2022 17:07:23 +0100 Subject: [PATCH 417/790] gnu: r-future: Update to 1.30.0. * gnu/packages/cran.scm (r-future): Update to 1.30.0. --- gnu/packages/cran.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index abb5ef906f..1e8653fa25 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -17664,14 +17664,14 @@ port-forwarding to your local computer.") (define-public r-future (package (name "r-future") - (version "1.29.0") + (version "1.30.0") (source (origin (method url-fetch) (uri (cran-uri "future" version)) (sha256 (base32 - "0ws3jp82qjpnvgn5xrxdq7hg7r97rkylj329f9jqr69g3paiyvc5")))) + "1njmgnq0qz7b9yvcp6351yz7ydz9hj8bnnaf1ys3md66v9mg1xf7")))) (build-system r-build-system) (arguments `(#:phases From 8400a8d7364d581f3664e17955f893ea20ce8c6f Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Mon, 19 Dec 2022 17:07:23 +0100 Subject: [PATCH 418/790] gnu: r-dorng: Update to 1.8.3. * gnu/packages/cran.scm (r-dorng): Update to 1.8.3. --- gnu/packages/cran.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 1e8653fa25..3c9c00656b 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -17806,14 +17806,14 @@ heuristics.") (define-public r-dorng (package (name "r-dorng") - (version "1.8.2") + (version "1.8.3") (source (origin (method url-fetch) (uri (cran-uri "doRNG" version)) (sha256 (base32 - "1jff27zzrvd1fd61x2m9468h8xn3s1c9f6wibviy5zdhj5dx9s9k")))) + "1aqzy646c6aggscmwninr1hz0z4nkxibmrg1mm77p2jnf1lh914c")))) (properties `((upstream-name . "doRNG"))) (build-system r-build-system) (propagated-inputs From 06261e05a7308dd09fcf40367b22db219241511b Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Mon, 19 Dec 2022 17:07:23 +0100 Subject: [PATCH 419/790] gnu: r-bayesm: Update to 3.1-5. * gnu/packages/cran.scm (r-bayesm): Update to 3.1-5. [native-inputs]: Add r-knitr. --- gnu/packages/cran.scm | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 3c9c00656b..c2e6cdd78c 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -18037,16 +18037,17 @@ identifying outliers.") (define-public r-bayesm (package (name "r-bayesm") - (version "3.1-4") + (version "3.1-5") (source (origin (method url-fetch) (uri (cran-uri "bayesm" version)) (sha256 - (base32 "154glks7rsjkza0sfi1kj7wj727py9sl1ba6sswflwmwc9n226q6")))) + (base32 "18j7h32nq4hx1qnxfgfgz3q39q35lmvsq3im90xjkphyli60f8zj")))) (build-system r-build-system) (propagated-inputs (list r-rcpp r-rcpparmadillo)) + (native-inputs (list r-knitr)) (home-page "http://www.perossi.org/home/bsm-1") (synopsis "Bayesian inference for marketing/micro-econometrics") (description From 16a5e39f1d0bc4e22555215f36c9ec4d2ed9109f Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Mon, 19 Dec 2022 17:07:24 +0100 Subject: [PATCH 420/790] gnu: r-lemon: Update to 0.4.6. * gnu/packages/cran.scm (r-lemon): Update to 0.4.6. [propagated-inputs]: Remove r-rlang. --- gnu/packages/cran.scm | 5 ++--- 1 file changed, 2 insertions(+), 3 deletions(-) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index c2e6cdd78c..32b0835cb8 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -18813,14 +18813,14 @@ can be used with function approximation, eligibility traces (Singh & Sutton, (define-public r-lemon (package (name "r-lemon") - (version "0.4.5") + (version "0.4.6") (source (origin (method url-fetch) (uri (cran-uri "lemon" version)) (sha256 (base32 - "1y3ljidhqdakxlya2npj2w0az820g8kw6gl1cfm4f0cxvzgd1ly4")))) + "0v1kbyk64yzsk92h6yq03kp9alc9632qprznsws61r8firiskim5")))) (build-system r-build-system) (propagated-inputs (list r-ggplot2 @@ -18829,7 +18829,6 @@ can be used with function approximation, eligibility traces (Singh & Sutton, r-knitr r-lattice r-plyr - r-rlang r-scales)) (native-inputs (list r-knitr)) From a53f3da11150b2e77e8ef45ec4d511b43c2f46b6 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Mon, 19 Dec 2022 17:07:24 +0100 Subject: [PATCH 421/790] gnu: r-units: Update to 0.8-1. * gnu/packages/cran.scm (r-units): Update to 0.8-1. --- gnu/packages/cran.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 32b0835cb8..bd4a823d4d 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -19076,14 +19076,14 @@ utilities for sequence data management under the ACNUC system.") (define-public r-units (package (name "r-units") - (version "0.8-0") + (version "0.8-1") (source (origin (method url-fetch) (uri (cran-uri "units" version)) (sha256 (base32 - "06mjprqi06xprj6185k5cmrrdl025x0pd1r6a4x3s74ciq9zwilw")))) + "16ndhl4hkcll9r5vh8flp2bc3mavddfz8g6sqddj15scdcjbmqfk")))) (build-system r-build-system) (inputs (list udunits)) From 5986d8dc711aff00b90cae06cf522fa478fc9d72 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Mon, 19 Dec 2022 17:07:24 +0100 Subject: [PATCH 422/790] gnu: r-wk: Update to 0.7.1. * gnu/packages/cran.scm (r-wk): Update to 0.7.1. --- gnu/packages/cran.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index bd4a823d4d..14b94b20f6 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -19225,14 +19225,14 @@ tessellation.") (define-public r-wk (package (name "r-wk") - (version "0.7.0") + (version "0.7.1") (source (origin (method url-fetch) (uri (cran-uri "wk" version)) (sha256 (base32 - "1pm2293xqcgjckghbf6q9sk7jh74njiynq3wqq1dbwigiz9jfhz2")))) + "116kvg2a9gga14agqvmvj2rbgfpdyasbkjnfjcsw9a9dk0n7g9g5")))) (properties `((upstream-name . "wk"))) (build-system r-build-system) (home-page "https://paleolimbot.github.io/wk/") From 76a8bc9b157a2bb200ff49fcf514d7644b382d17 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Mon, 19 Dec 2022 17:07:25 +0100 Subject: [PATCH 423/790] gnu: r-bookdown: Update to 0.31. * gnu/packages/cran.scm (r-bookdown): Update to 0.31. --- gnu/packages/cran.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 14b94b20f6..7d35d50974 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -19792,13 +19792,13 @@ SELECT or UPDATE queries to an end-point.") (define-public r-bookdown (package (name "r-bookdown") - (version "0.30") + (version "0.31") (source (origin (method url-fetch) (uri (cran-uri "bookdown" version)) (sha256 (base32 - "1i54sbrdv2c9l6pcm3229wlwdnhn0x6f2918adszm5k8qdp0h74i")))) + "0rkapx3zz0vwggnrpk0ns8bpqsblkp08xpr0srz93c3kzlsjdiac")))) (build-system r-build-system) (propagated-inputs (list r-htmltools From d4e02af4358ccb2b0d4ea298f82bb5618d19637b Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Mon, 19 Dec 2022 17:07:25 +0100 Subject: [PATCH 424/790] gnu: r-eulerr: Update to 7.0.0. * gnu/packages/cran.scm (r-eulerr): Update to 7.0.0. --- gnu/packages/cran.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 7d35d50974..a30ecf344a 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -20496,13 +20496,13 @@ that fills this gap.") (define-public r-eulerr (package (name "r-eulerr") - (version "6.1.1") + (version "7.0.0") (source (origin (method url-fetch) (uri (cran-uri "eulerr" version)) (sha256 (base32 - "0lldp2319qd08y87f862gx8a77rvikcnkmdl9xgx4glynfs3hk19")))) + "16a84a2xgv1iqsir0hzn6qclljni4f3prpycb7qpp06vrd0yn8lw")))) (properties `((upstream-name . "eulerr"))) (build-system r-build-system) (propagated-inputs From fb22cc0655990dfb3715d4e09726aff6b7658e5f Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Mon, 19 Dec 2022 17:07:25 +0100 Subject: [PATCH 425/790] gnu: r-arrow: Update to 10.0.1. * gnu/packages/cran.scm (r-arrow): Update to 10.0.1. --- gnu/packages/cran.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index a30ecf344a..59545e0849 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -21323,14 +21323,14 @@ colored by the number of neighboring points. This is useful to visualize the (define-public r-arrow (package (name "r-arrow") - (version "10.0.0") + (version "10.0.1") (source (origin (method url-fetch) (uri (cran-uri "arrow" version)) (sha256 (base32 - "04qsj68zsqcwkv1ryp4l0is474siyi1b64dy41fr74ryj7mbamg8")))) + "0dwdi9sq7wv34ia6kg446pqf5za75hl6zrb2ly51p2zdr4g69p0y")))) (properties `((upstream-name . "arrow"))) (build-system r-build-system) (inputs From 9b7703016a61bfbb4ee40507a4b5bed0582c9c2c Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Mon, 19 Dec 2022 17:07:25 +0100 Subject: [PATCH 426/790] gnu: r-terra: Update to 1.6-47. * gnu/packages/cran.scm (r-terra): Update to 1.6-47. --- gnu/packages/cran.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 59545e0849..fa76c16950 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -22708,14 +22708,14 @@ emphasize hidden group structures in networks or focus on specific nodes.") (define-public r-terra (package (name "r-terra") - (version "1.6-41") + (version "1.6-47") (source (origin (method url-fetch) (uri (cran-uri "terra" version)) (sha256 (base32 - "0n0si3b6l88w0svvpc999slqack1djdd96jc0m8fdkwp0nwi3hkc")))) + "13n6rxrrkn4wgcgq2kyyhn5nxw099hy9fbzxg78waxa6cxapwpmh")))) (properties `((upstream-name . "terra"))) (build-system r-build-system) (inputs From 8b367602f8d965adcfa8bc8adddf0508b2369fad Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Mon, 19 Dec 2022 17:07:26 +0100 Subject: [PATCH 427/790] gnu: r-rgdal: Update to 1.6-3. * gnu/packages/cran.scm (r-rgdal): Update to 1.6-3. --- gnu/packages/cran.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index fa76c16950..96ffdb56b3 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -22857,13 +22857,13 @@ effect size.") (define-public r-rgdal (package (name "r-rgdal") - (version "1.6-2") + (version "1.6-3") (source (origin (method url-fetch) (uri (cran-uri "rgdal" version)) (sha256 - (base32 "0g83r9lzq79hs7mk31kqym1sjqnmk53j3nikrn2vk257v854pavy")))) + (base32 "0snz5m158as39h6zdcdrydwm5n2r2vayv3xy8n3g5mmkbxyyx7i2")))) (properties `((upstream-name . "rgdal"))) (build-system r-build-system) (inputs From eddf2dbb25e0a0647f5cad3d47d1b83db775fe4c Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Mon, 19 Dec 2022 17:07:26 +0100 Subject: [PATCH 428/790] gnu: r-lhs: Update to 1.1.6. * gnu/packages/cran.scm (r-lhs): Update to 1.1.6. --- gnu/packages/cran.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 96ffdb56b3..6abf30c564 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -24051,14 +24051,14 @@ See e.g. Gentle (2003) @url{doi:10.1007/b97336}.") (define-public r-lhs (package (name "r-lhs") - (version "1.1.5") + (version "1.1.6") (source (origin (method url-fetch) (uri (cran-uri "lhs" version)) (sha256 (base32 - "0fb3bc3s5pbwg92qkjbg7v8ah36wm6qs05vf098hwjakr7f6yg3s")))) + "0gyjdic714pqvq2jv1v0vh7hl9s83sg2zxx2gdkp38z6xx2cwzz3")))) (properties `((upstream-name . "lhs"))) (build-system r-build-system) (propagated-inputs (list r-rcpp)) From c6b2b5fb57100b85108ec0fe4d5d79e0e495683f Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Mon, 19 Dec 2022 17:07:26 +0100 Subject: [PATCH 429/790] gnu: r-imager: Update to 0.42.16. * gnu/packages/cran.scm (r-imager): Update to 0.42.16. --- gnu/packages/cran.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 6abf30c564..2d9f23cbc6 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -25431,14 +25431,14 @@ number embedded in the file rather than the file extension.") (define-public r-imager (package (name "r-imager") - (version "0.42.13") + (version "0.42.16") (source (origin (method url-fetch) (uri (cran-uri "imager" version)) (sha256 (base32 - "0zygnmxwbbmj5i2l2affzdz90xvsa7b5pbkzkhjbm40is69rh2nr")))) + "00q2v000xanp03bzscmj3q9qnlhc97b1lgr4l19s9jmbf0hf9c5c")))) (properties `((upstream-name . "imager"))) (build-system r-build-system) (inputs From 55743b0ee973b367c2ae77f96dad660b93a50b03 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Mon, 19 Dec 2022 17:07:26 +0100 Subject: [PATCH 430/790] gnu: r-forestplot: Update to 3.1.1. * gnu/packages/cran.scm (r-forestplot): Update to 3.1.1. --- gnu/packages/cran.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 2d9f23cbc6..c5013b6206 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -26629,13 +26629,13 @@ space models and automatic ARIMA modelling.") (define-public r-forestplot (package (name "r-forestplot") - (version "3.1.0") + (version "3.1.1") (source (origin (method url-fetch) (uri (cran-uri "forestplot" version)) (sha256 (base32 - "0xk30mpb87sab2afnk2j474qjjf4j6x1ifh9j5n7w690f481iqqb")))) + "0jf7sl7z963r92l5r2irvnakmbmx554vbprg51smj6qns5a6dfcj")))) (properties `((upstream-name . "forestplot"))) (build-system r-build-system) (propagated-inputs From 61c9fc76831e52a0011fa34dbd2a0049805f0f20 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Mon, 19 Dec 2022 17:07:27 +0100 Subject: [PATCH 431/790] gnu: r-quanteda: Update to 3.2.4. * gnu/packages/cran.scm (r-quanteda): Update to 3.2.4. --- gnu/packages/cran.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index c5013b6206..ab8c55f124 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -26819,14 +26819,14 @@ Norwegian, Portuguese, Romanian, Russian, Spanish, Swedish and Turkish.") (define-public r-quanteda (package (name "r-quanteda") - (version "3.2.3") + (version "3.2.4") (source (origin (method url-fetch) (uri (cran-uri "quanteda" version)) (sha256 (base32 - "1blk9nhydvqyyz0kzhph7nh7ahcjzflmgyr4sv8fx5bpmn4hwjzk")))) + "1yg3lgckh6fncmw037p4gaa2bab59yh6izqix1cgyysjg4jpcw62")))) (properties `((upstream-name . "quanteda"))) (build-system r-build-system) (propagated-inputs From f63f93767383fe80b6324743ec1b0f96998f376a Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Mon, 19 Dec 2022 17:07:27 +0100 Subject: [PATCH 432/790] gnu: r-topicmodels: Update to 0.2-13. * gnu/packages/cran.scm (r-topicmodels): Update to 0.2-13. --- gnu/packages/cran.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index ab8c55f124..bd479859ba 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -26858,14 +26858,14 @@ machine learning, visually representing text and text analyses, and more.") (define-public r-topicmodels (package (name "r-topicmodels") - (version "0.2-12") + (version "0.2-13") (source (origin (method url-fetch) (uri (cran-uri "topicmodels" version)) (sha256 (base32 - "1d6iizmn042b59q2y6qc82z19wq3xm0zvgkf8iqf8fdzh51kmn5g")))) + "16mw0l7wm5idc831csxlk176c42a5xw8qm8xhbnmmdl2hjk0cqbx")))) (properties `((upstream-name . "topicmodels"))) (build-system r-build-system) (inputs From 53967550f2864a52320e51e7354cdae0657b7b5f Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Mon, 19 Dec 2022 17:07:27 +0100 Subject: [PATCH 433/790] gnu: r-bdgraph: Update to 2.71. * gnu/packages/cran.scm (r-bdgraph): Update to 2.71. --- gnu/packages/cran.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index bd479859ba..d69d3fcf12 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -27330,14 +27330,14 @@ output in R.") (define-public r-bdgraph (package (name "r-bdgraph") - (version "2.70") + (version "2.71") (source (origin (method url-fetch) (uri (cran-uri "BDgraph" version)) (sha256 (base32 - "1s148fvvg1c0n4swsvcinlwckj86jys5nvwp4wlyzh3aw9siyqz7")))) + "1lihsbliq7f91ywdq5cabzd5fbyhb10h62ss3n2l7i2fdglb77d1")))) (properties `((upstream-name . "BDgraph"))) (build-system r-build-system) (propagated-inputs From 2f23edcab8d9bd15ef606b87d717044bac8a3332 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Mon, 19 Dec 2022 17:07:27 +0100 Subject: [PATCH 434/790] gnu: r-qgraph: Update to 1.9.3. * gnu/packages/cran.scm (r-qgraph): Update to 1.9.3. --- gnu/packages/cran.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index d69d3fcf12..31ac534fbf 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -27397,14 +27397,14 @@ network, tree, dendrogram, and Sankey graphs from R using data frames.") (define-public r-qgraph (package (name "r-qgraph") - (version "1.9.2") + (version "1.9.3") (source (origin (method url-fetch) (uri (cran-uri "qgraph" version)) (sha256 (base32 - "0r225b7rnsv6wz41ij0msmqr1xy0iqxh9dbsvjixbi1hvgv91wds")))) + "14azjxlvb02wlbskbsv5x3a6gpfb8hfyijfpbay6fimnsaqnmbj6")))) (properties `((upstream-name . "qgraph"))) (build-system r-build-system) (propagated-inputs From 55b2498ed18f810e9723a28aecd849b9930ba73f Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Mon, 19 Dec 2022 17:07:28 +0100 Subject: [PATCH 435/790] gnu: r-lightgbm: Update to 3.3.4. * gnu/packages/cran.scm (r-lightgbm): Update to 3.3.4. --- gnu/packages/cran.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 31ac534fbf..ae0169f59a 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -29243,14 +29243,14 @@ input.") (define-public r-lightgbm (package (name "r-lightgbm") - (version "3.3.3") + (version "3.3.4") (source (origin (method url-fetch) (uri (cran-uri "lightgbm" version)) (sha256 (base32 - "1a4nacdpsqd5mr7jnw1g9nyn8w7p0hskfm07cy8yrj3h8a5hmcz8")))) + "12hcq2idjgggs8l9a5aaxbw1wsfz6byzaxqn9k6afvkf3v5srp65")))) (properties `((upstream-name . "lightgbm"))) (build-system r-build-system) (propagated-inputs From 238ee9154f0cf39e00329f6022435c2530ad4c1a Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Mon, 19 Dec 2022 17:07:28 +0100 Subject: [PATCH 436/790] gnu: r-gaston: Update to 1.5.8. * gnu/packages/cran.scm (r-gaston): Update to 1.5.8. --- gnu/packages/cran.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index ae0169f59a..9b5f473ef0 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -29935,14 +29935,14 @@ formal inference.") (define-public r-gaston (package (name "r-gaston") - (version "1.5.7") + (version "1.5.8") (source (origin (method url-fetch) (uri (cran-uri "gaston" version)) (sha256 (base32 - "14z94dpln4dvgrv2w7w9ik7h6rpvbf02qhq1hqzx8c2cndzxr21i")))) + "1pv37csq3gvkld7hfxgbq72n35gx1wg3bvrcvzzzf0qsfb6g42cc")))) (properties `((upstream-name . "gaston"))) (build-system r-build-system) (inputs (list zlib)) From 8c98ffffca998cfa08b320a669cd1fa1ac93db05 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Mon, 19 Dec 2022 17:07:28 +0100 Subject: [PATCH 437/790] gnu: r-clusterr: Update to 1.2.9. * gnu/packages/cran.scm (r-clusterr): Update to 1.2.9. --- gnu/packages/cran.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 9b5f473ef0..47859d93b4 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -30081,14 +30081,14 @@ model.") (define-public r-clusterr (package (name "r-clusterr") - (version "1.2.7") + (version "1.2.9") (source (origin (method url-fetch) (uri (cran-uri "ClusterR" version)) (sha256 (base32 - "1sl218scrf5s02v54bmmk2sz1vrnlq16c14c0lcg1n7x8d76sgk6")))) + "04aswnmxzpffc1fj2hf85pc5b10fh418k29a1x5cs1f1y7b3zav3")))) (properties `((upstream-name . "ClusterR"))) (build-system r-build-system) (propagated-inputs From fb907546b9bf1ce79ef6e7c2912e46bbe3445042 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Mon, 19 Dec 2022 17:07:29 +0100 Subject: [PATCH 438/790] gnu: r-rsample: Update to 1.1.1. * gnu/packages/cran.scm (r-rsample): Update to 1.1.1. [propagated-inputs]: Remove r-ellipsis. --- gnu/packages/cran.scm | 5 ++--- 1 file changed, 2 insertions(+), 3 deletions(-) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 47859d93b4..fd9e3d5bc8 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -30917,19 +30917,18 @@ pipeline friendly so that data processing with lists can be chained.") (define-public r-rsample (package (name "r-rsample") - (version "1.1.0") + (version "1.1.1") (source (origin (method url-fetch) (uri (cran-uri "rsample" version)) (sha256 (base32 - "1iy61riwjch9z4m6k7whsrkl80sk9sww5lf1np4iq4vdfq6w01jb")))) + "1fmqfk1yihmh7lkszsf7pvn6zf67lpgff46hv2lpnfbssa3axllh")))) (properties `((upstream-name . "rsample"))) (build-system r-build-system) (propagated-inputs (list r-dplyr - r-ellipsis r-furrr r-generics r-glue From b5c0cb4a469a81bdb3b5523ed2dcca3351ef9aef Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Mon, 19 Dec 2022 17:07:29 +0100 Subject: [PATCH 439/790] gnu: r-infer: Update to 1.0.4. * gnu/packages/cran.scm (r-infer): Update to 1.0.4. --- gnu/packages/cran.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index fd9e3d5bc8..f315e5ab21 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -31373,14 +31373,14 @@ functions or computational engines (e.g. R, Spark, Stan, etc).") (define-public r-infer (package (name "r-infer") - (version "1.0.3") + (version "1.0.4") (source (origin (method url-fetch) (uri (cran-uri "infer" version)) (sha256 (base32 - "1m5srhcmkh8wq12pvy57g3g703wilkl8r3gmm5s7lbj103iz7v8b")))) + "1s4q0nslykl0pb2w1i6ni6hkpp7awvp0wks79br3gk5wa1qkvs19")))) (properties `((upstream-name . "infer"))) (build-system r-build-system) (propagated-inputs From 0874c5f9062d044356d539c52bc40df435f281cf Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Mon, 19 Dec 2022 17:07:29 +0100 Subject: [PATCH 440/790] gnu: r-qtl: Update to 1.54. * gnu/packages/cran.scm (r-qtl): Update to 1.54. --- gnu/packages/cran.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index f315e5ab21..5b7a404ce5 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -31676,14 +31676,14 @@ covariate (usually group indicator) and the scores.") (define-public r-qtl (package (name "r-qtl") - (version "1.52") + (version "1.54") (source (origin (method url-fetch) (uri (cran-uri "qtl" version)) (sha256 (base32 - "0q49g3ar1451whsl6ig7kz4mg8s9zxlcvgkj4ivyw4995wbwc2ij")))) + "1rzkxkmcgd6drxbgqp6w6jab5bs7vla2x2ndv3l4nlbcwzi41jw0")))) (build-system r-build-system) (home-page "https://rqtl.org/") (synopsis "R package for analyzing QTL experiments in genetics") From e9464e207da4a8531662014f8a7cc88f60bc3d21 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Mon, 19 Dec 2022 17:07:29 +0100 Subject: [PATCH 441/790] gnu: r-qtl2: Update to 0.30. * gnu/packages/cran.scm (r-qtl2): Update to 0.30. --- gnu/packages/cran.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 5b7a404ce5..6cf66834e3 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -31699,12 +31699,12 @@ genome scans.") (define-public r-qtl2 (package (name "r-qtl2") - (version "0.28") + (version "0.30") (source (origin (method url-fetch) (uri (cran-uri "qtl2" version)) (sha256 - (base32 "0ppc6dzlq77mppxc6bczai9gi40jrbxd1466y2cn2s8a4ah1jg9y")))) + (base32 "0c9v5hwfmlchrdzdysvmi6dsxyclc15sqbp65l4x6zwpd0828h6c")))) (build-system r-build-system) (propagated-inputs (list r-data-table From e863cf42036cd8d06e96fe29068eb0309e895e43 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Mon, 19 Dec 2022 17:07:30 +0100 Subject: [PATCH 442/790] gnu: r-bbotk: Update to 0.7.2. * gnu/packages/cran.scm (r-bbotk): Update to 0.7.2. --- gnu/packages/cran.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 6cf66834e3..51f872fc60 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -32469,14 +32469,14 @@ vector machines, and gradient boosting.") (define-public r-bbotk (package (name "r-bbotk") - (version "0.7.0") + (version "0.7.2") (source (origin (method url-fetch) (uri (cran-uri "bbotk" version)) (sha256 (base32 - "0g3x3r1dkp9w57arpqc6iccvsawjdf7vlv8c27cb1r36b0z45fi6")))) + "1gw0rkbiv93ifl9110r9sr0p9g4vg7qc11mznmmjq0a5vzmqgpm9")))) (properties `((upstream-name . "bbotk"))) (build-system r-build-system) (propagated-inputs From 627246b1347553bdd0764f7d09774253cc353fe7 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Mon, 19 Dec 2022 17:07:30 +0100 Subject: [PATCH 443/790] gnu: r-mlr3tuning: Update to 0.17.1. * gnu/packages/cran.scm (r-mlr3tuning): Update to 0.17.1. --- gnu/packages/cran.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 51f872fc60..3f367577c2 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -32499,13 +32499,13 @@ annealing.") (define-public r-mlr3tuning (package (name "r-mlr3tuning") - (version "0.17.0") + (version "0.17.1") (source (origin (method url-fetch) (uri (cran-uri "mlr3tuning" version)) (sha256 (base32 - "1dg02qyyymflgws47sly3b7wd8nj4i9vv7ybx42hgvd55al3smdp")))) + "03habi7dm5xgwfb4zjn9nhvyym46qcljy31jz32fxalsap1mk9jb")))) (build-system r-build-system) (propagated-inputs (list r-bbotk From 27d16e79d07bb0cd186912620e921ea071304b36 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Mon, 19 Dec 2022 17:07:30 +0100 Subject: [PATCH 444/790] gnu: r-pkgdown: Update to 2.0.7. * gnu/packages/cran.scm (r-pkgdown): Update to 2.0.7. --- gnu/packages/cran.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 3f367577c2..4817ca092c 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -32853,14 +32853,14 @@ in output to the equivalent HTML.") (define-public r-pkgdown (package (name "r-pkgdown") - (version "2.0.6") + (version "2.0.7") (source (origin (method url-fetch) (uri (cran-uri "pkgdown" version)) (sha256 (base32 - "0sbz3kzd0hbdnszylsb281arldn2z1c9yxifhj4zv2dilp46b6nj")))) + "0sim3fwayf4mpxqi8y9v7clnkzs56amhxsc75lc1k0zskn374f7k")))) (properties `((upstream-name . "pkgdown"))) (build-system r-build-system) (inputs (list pandoc)) From 0345854b823c4274070471ec8c2f4ba76918afe4 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Mon, 19 Dec 2022 17:07:30 +0100 Subject: [PATCH 445/790] gnu: r-rgeos: Update to 0.6-1. * gnu/packages/cran.scm (r-rgeos): Update to 0.6-1. --- gnu/packages/cran.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 4817ca092c..876476cae1 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -34313,14 +34313,14 @@ object to and from disk.") (define-public r-rgeos (package (name "r-rgeos") - (version "0.5-9") + (version "0.6-1") (source (origin (method url-fetch) (uri (cran-uri "rgeos" version)) (sha256 (base32 - "1m73y0nwrdwsjrl48c4fg1kdqnh79835brnmxv9ak01ndbzcp45b")))) + "1wppxr9iibb0gi1hr6qzda9dc8spf6297lkfddl41j78q14bs3a2")))) (properties `((upstream-name . "rgeos"))) (build-system r-build-system) (inputs From b422ab4a245b09b8feccdbb054c6b4701c30ba24 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Mon, 19 Dec 2022 17:07:31 +0100 Subject: [PATCH 446/790] gnu: r-paws-common: Update to 0.5.3. * gnu/packages/cran.scm (r-paws-common): Update to 0.5.3. --- gnu/packages/cran.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 876476cae1..72caa05721 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -34698,14 +34698,14 @@ fully reproducible.") (define-public r-paws-common (package (name "r-paws-common") - (version "0.5.1") + (version "0.5.3") (source (origin (method url-fetch) (uri (cran-uri "paws.common" version)) (sha256 (base32 - "17cfvx2ma0zcrj3grpsadx8p5r97s2z6c23qqmzry7ys9mn6k9f1")))) + "090csb0wjnsfhkphws5anrnml18y1k54yi48lxav8wp5kqj4wlb6")))) (properties `((upstream-name . "paws.common"))) (build-system r-build-system) (propagated-inputs From 0d37363e37c95158be3e9a8f1a9754914e173757 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Mon, 19 Dec 2022 17:07:31 +0100 Subject: [PATCH 447/790] gnu: r-fasterize: Update to 1.0.4. * gnu/packages/cran.scm (r-fasterize): Update to 1.0.4. --- gnu/packages/cran.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 72caa05721..fccf0002a7 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -35759,13 +35759,13 @@ formatting and delivering log messages with low overhead.") (define-public r-fasterize (package (name "r-fasterize") - (version "1.0.3") + (version "1.0.4") (source (origin (method url-fetch) (uri (cran-uri "fasterize" version)) (sha256 - (base32 "10bzl77c1b9jhcn1xp467qzp2n8c7s3wpxn53qjh1nwvbri5kd32")))) + (base32 "1ckxi2iyxdahhgbliblcrkzziblfagzr54srjk27yp1lcgivvvs4")))) (properties `((upstream-name . "fasterize"))) (build-system r-build-system) (propagated-inputs From 7db010ad70540902ca037a20b7c77dda6493eeb2 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Mon, 19 Dec 2022 17:07:31 +0100 Subject: [PATCH 448/790] gnu: r-foreign: Update to 0.8-84. * gnu/packages/statistics.scm (r-foreign): Update to 0.8-84. --- gnu/packages/statistics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm index 0fd1cc8cd7..5b2e53289b 100644 --- a/gnu/packages/statistics.scm +++ b/gnu/packages/statistics.scm @@ -592,14 +592,14 @@ code for possible problems.") (define-public r-foreign (package (name "r-foreign") - (version "0.8-83") + (version "0.8-84") (source (origin (method url-fetch) (uri (cran-uri "foreign" version)) (sha256 (base32 - "06vj61h52idbjbgmbd6ml9541q3vr38j2gjvlkqbqsqbg0zygsl7")))) + "0jc5r5wiqqbkni2xjdd24hic1xvfi151m9lnqhni52jnqw1g7v8p")))) (build-system r-build-system) (home-page "https://cran.r-project.org/web/packages/foreign") (synopsis "Read data stored by other statistics software") From 4f2159f534e2789cfd7026c989787f412acf0f7b Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Mon, 19 Dec 2022 17:07:31 +0100 Subject: [PATCH 449/790] gnu: r-nlme: Update to 3.1-161. * gnu/packages/statistics.scm (r-nlme): Update to 3.1-161. --- gnu/packages/statistics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm index 5b2e53289b..6d1b63f413 100644 --- a/gnu/packages/statistics.scm +++ b/gnu/packages/statistics.scm @@ -678,13 +678,13 @@ and operations on them using LAPACK and SuiteSparse.") (define-public r-nlme (package (name "r-nlme") - (version "3.1-160") + (version "3.1-161") (source (origin (method url-fetch) (uri (cran-uri "nlme" version)) (sha256 - (base32 "024a1pfdbv5dp1cbfk424n1rwfxw4g92yrjcfy1v0xj834ilcifl")))) + (base32 "0pw9kwhac6a01zcchl4xxy2rk3ghzc9kxxn6kjkh2z4iq41a1z9a")))) (build-system r-build-system) (propagated-inputs (list r-lattice)) From c9a449ae6384fb8fb86a6ac25f66250d11742179 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Mon, 19 Dec 2022 17:07:31 +0100 Subject: [PATCH 450/790] gnu: r-digest: Update to 0.6.31. * gnu/packages/statistics.scm (r-digest): Update to 0.6.31. --- gnu/packages/statistics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm index 6d1b63f413..5c817543f8 100644 --- a/gnu/packages/statistics.scm +++ b/gnu/packages/statistics.scm @@ -945,13 +945,13 @@ effects of different types of color-blindness.") (define-public r-digest (package (name "r-digest") - (version "0.6.30") + (version "0.6.31") (source (origin (method url-fetch) (uri (cran-uri "digest" version)) (sha256 - (base32 "19va0z7blshsai1jjys9vdahpfz1klicrpv8682sdnz77fa5k03v")))) + (base32 "1f9isi4i2502f88c2sh4l461hgyary2aa02zd47pb9mc1r4lya2s")))) (build-system r-build-system) ;; Vignettes require r-knitr, which requires r-digest, so we have to ;; disable them and the tests. From cdb7da5f00423a26de0657d7f71f55412b93a9aa Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Mon, 19 Dec 2022 17:07:31 +0100 Subject: [PATCH 451/790] gnu: r-evaluate: Update to 0.19. * gnu/packages/statistics.scm (r-evaluate): Update to 0.19. --- gnu/packages/statistics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm index 5c817543f8..d61806c165 100644 --- a/gnu/packages/statistics.scm +++ b/gnu/packages/statistics.scm @@ -1430,13 +1430,13 @@ for template use among CRAN packages.") (define-public r-evaluate (package (name "r-evaluate") - (version "0.18") + (version "0.19") (source (origin (method url-fetch) (uri (cran-uri "evaluate" version)) (sha256 (base32 - "0dmznan8zajzb5f31yabcgpkinlqczz59i1rg9f6sa5cjzffqkkz")))) + "1k36mpb12nvcr5bv3n6591shhr38d6zpfwgj643cgprd8l0kvk39")))) (build-system r-build-system) (home-page "https://github.com/hadley/evaluate") (synopsis "Parsing and evaluation tools for R") From 02ceaa592586dbd39014082cd2b2b9084eb4f6fe Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Mon, 19 Dec 2022 17:07:32 +0100 Subject: [PATCH 452/790] gnu: r-testthat: Update to 3.1.6. * gnu/packages/statistics.scm (r-testthat): Update to 3.1.6. --- gnu/packages/statistics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm index d61806c165..213e90c601 100644 --- a/gnu/packages/statistics.scm +++ b/gnu/packages/statistics.scm @@ -1703,13 +1703,13 @@ R packages that praise their users.") (define-public r-testthat (package (name "r-testthat") - (version "3.1.5") + (version "3.1.6") (source (origin (method url-fetch) (uri (cran-uri "testthat" version)) (sha256 (base32 - "1z5pyp4cmyn8ms243zav5wfbwbh45zzq432m1g1xyv904sa6pxd8")))) + "1bndjkwv6f9x3a0wklwnf7bymn655yhw6cmazb285hbmci0qrjx7")))) (build-system r-build-system) (propagated-inputs (list r-brio From d72dd70180cf53aa44fc7f930051772fe36a7fc2 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Mon, 19 Dec 2022 17:07:32 +0100 Subject: [PATCH 453/790] gnu: r-whisker: Update to 0.4.1. * gnu/packages/statistics.scm (r-whisker): Update to 0.4.1. --- gnu/packages/statistics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm index 213e90c601..8b62d7e0fd 100644 --- a/gnu/packages/statistics.scm +++ b/gnu/packages/statistics.scm @@ -2233,13 +2233,13 @@ previous R versions and their release dates.") (define-public r-whisker (package (name "r-whisker") - (version "0.4") + (version "0.4.1") (source (origin (method url-fetch) (uri (cran-uri "whisker" version)) (sha256 (base32 - "1a7vz0dk95xfjvi38wbpw8vmf5qn3g8p490msz2rw0piwidmk1ks")))) + "1g7jy6dnc5igs7yqy1n7cmy0ia8dm2yi3qj1mil2y0q88m4m2ldz")))) (build-system r-build-system) (home-page "https://github.com/edwindj/whisker") (synopsis "Logicless mustache templating for R") From 5e73dc3fa35e946ef67e52b3fa2bd157a042a932 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Mon, 19 Dec 2022 17:07:32 +0100 Subject: [PATCH 454/790] gnu: r-roxygen2: Update to 7.2.3. * gnu/packages/statistics.scm (r-roxygen2): Update to 7.2.3. [propagated-inputs]: Remove r-digest. --- gnu/packages/statistics.scm | 5 ++--- 1 file changed, 2 insertions(+), 3 deletions(-) diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm index 8b62d7e0fd..da4c29fed6 100644 --- a/gnu/packages/statistics.scm +++ b/gnu/packages/statistics.scm @@ -2437,13 +2437,13 @@ tables, autolinks and strikethrough text.") (define-public r-roxygen2 (package (name "r-roxygen2") - (version "7.2.2") + (version "7.2.3") (source (origin (method url-fetch) (uri (cran-uri "roxygen2" version)) (sha256 (base32 - "07pijickz5kgd31xzn2z11xqiym4sscj742qwbc5bjh7mayhhmki")))) + "1nhn0jhnxzlyqx0qnpd7k7q3azzngyn0j4zs8awmlmyjfywzli6q")))) (build-system r-build-system) (propagated-inputs (list r-brew @@ -2451,7 +2451,6 @@ tables, autolinks and strikethrough text.") r-commonmark r-cpp11 r-desc - r-digest r-knitr r-pkgload r-purrr From 7b2ef36a5c9cda3b0bed71f729ddd86f2f27d56c Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Mon, 19 Dec 2022 17:07:32 +0100 Subject: [PATCH 455/790] gnu: r-openssl: Update to 2.0.5. * gnu/packages/statistics.scm (r-openssl): Update to 2.0.5. --- gnu/packages/statistics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm index da4c29fed6..0bc42367d3 100644 --- a/gnu/packages/statistics.scm +++ b/gnu/packages/statistics.scm @@ -2472,14 +2472,14 @@ collation, and NAMESPACE files.") (define-public r-openssl (package (name "r-openssl") - (version "2.0.4") + (version "2.0.5") (source (origin (method url-fetch) (uri (cran-uri "openssl" version)) (sha256 (base32 - "1v2w19sffwqkgi9nj593ga46l9qp716lyb3gnjihq3624x8wd9d1")))) + "1lw60yq20r42l7y1wbp79s3mk3dwg62v0dh7jx1cdd7rb46i9hla")))) (build-system r-build-system) (arguments (list From 01998e39db0065af1ecb985780c314c9a1ee0237 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Mon, 19 Dec 2022 17:07:32 +0100 Subject: [PATCH 456/790] gnu: r-rmarkdown: Update to 2.19. * gnu/packages/statistics.scm (r-rmarkdown): Update to 2.19. --- gnu/packages/statistics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm index 0bc42367d3..2d6d1358cf 100644 --- a/gnu/packages/statistics.scm +++ b/gnu/packages/statistics.scm @@ -2851,13 +2851,13 @@ certain criterion, e.g., it contains a certain regular file.") (define-public r-rmarkdown (package (name "r-rmarkdown") - (version "2.18") + (version "2.19") (source (origin (method url-fetch) (uri (cran-uri "rmarkdown" version)) (sha256 - (base32 "08lgzb7n7lll1ff7flcyilnz9afj60npi882c035pyyy4vk7majg")))) + (base32 "14lvvdq3n95qbl7nrqlym1lp05i17m6f9mx3ly35iip83p2s9hir")))) (properties `((upstream-name . "rmarkdown"))) (build-system r-build-system) (propagated-inputs From d854b069ef87fb5b0bfe3b90e9eec953c1971c25 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Mon, 19 Dec 2022 17:07:32 +0100 Subject: [PATCH 457/790] gnu: r-xml: Update to 3.99-0.13. * gnu/packages/statistics.scm (r-xml): Update to 3.99-0.13. --- gnu/packages/statistics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm index 2d6d1358cf..0e78407c6a 100644 --- a/gnu/packages/statistics.scm +++ b/gnu/packages/statistics.scm @@ -3040,13 +3040,13 @@ ldap, and also supports cookies, redirects, authentication, etc.") (define-public r-xml (package (name "r-xml") - (version "3.99-0.12") + (version "3.99-0.13") (source (origin (method url-fetch) (uri (cran-uri "XML" version)) (sha256 (base32 - "053dlc1762qjqmqiq0sb9qnrpg8rx1a8inizq1fl1gw6r0jr886b")))) + "0fppx0jnqxx3l7y8ivb56sq0fjcqv3fn226i4s03mi7hwak6iic5")))) (properties `((upstream-name . "XML"))) (build-system r-build-system) From 468cdf02caddede161a6c35b3dad919b942749d8 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Mon, 19 Dec 2022 17:07:33 +0100 Subject: [PATCH 458/790] gnu: r-segmented: Update to 1.6-2. * gnu/packages/statistics.scm (r-segmented): Update to 1.6-2. --- gnu/packages/statistics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm index 0e78407c6a..4d248d6b8e 100644 --- a/gnu/packages/statistics.scm +++ b/gnu/packages/statistics.scm @@ -3161,14 +3161,14 @@ statements.") (define-public r-segmented (package (name "r-segmented") - (version "1.6-1") + (version "1.6-2") (source (origin (method url-fetch) (uri (cran-uri "segmented" version)) (sha256 (base32 - "0vym03p04jf66fdpx3kzy727b8bay2fpvd3n0xxmm94c3hqwl2gn")))) + "0livckkhci3w1x9xai2m0a30fj06qsks2qds7y5jr9vwx03jqg21")))) (build-system r-build-system) (propagated-inputs (list r-mass r-nlme)) (home-page "https://cran.r-project.org/web/packages/segmented") From 82d77d567bba86e9786c7ff5bed9d4e2c2786b4f Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Mon, 19 Dec 2022 17:07:33 +0100 Subject: [PATCH 459/790] gnu: r-ggbeeswarm: Update to 0.7.1. * gnu/packages/statistics.scm (r-ggbeeswarm): Update to 0.7.1. [propagated-inputs]: Add r-lifecycle. --- gnu/packages/statistics.scm | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm index 4d248d6b8e..f7f6729246 100644 --- a/gnu/packages/statistics.scm +++ b/gnu/packages/statistics.scm @@ -4995,16 +4995,16 @@ representation of R code.") (define-public r-ggbeeswarm (package (name "r-ggbeeswarm") - (version "0.6.0") + (version "0.7.1") (source (origin (method url-fetch) (uri (cran-uri "ggbeeswarm" version)) (sha256 (base32 - "0crk29p5vi1r3a988kms4y7r0iqwgwzsikgvh18r9wbzyr98bb5v")))) + "14mc00i107rww3al5q3rrqmd1v0ck06jipfhzqi23g29a4rm05gl")))) (build-system r-build-system) (propagated-inputs - (list r-beeswarm r-ggplot2 r-vipor)) + (list r-beeswarm r-ggplot2 r-lifecycle r-vipor)) (home-page "https://github.com/eclarke/ggbeeswarm") (synopsis "Categorical scatter (violin point) plots") (description From 227e35f58787d609172b04851cef347f378eef39 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Mon, 19 Dec 2022 17:07:33 +0100 Subject: [PATCH 460/790] gnu: r-mixtools: Update to 2.0.0. * gnu/packages/statistics.scm (r-mixtools): Update to 2.0.0. [propagated-inputs]: Add r-plotly and r-scales. --- gnu/packages/statistics.scm | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm index f7f6729246..52d081b47a 100644 --- a/gnu/packages/statistics.scm +++ b/gnu/packages/statistics.scm @@ -5157,17 +5157,17 @@ letters, as is often required for scientific publications.") (define-public r-mixtools (package (name "r-mixtools") - (version "1.2.0") + (version "2.0.0") (source (origin (method url-fetch) (uri (cran-uri "mixtools" version)) (sha256 (base32 - "08whic8hmmzi55b7azwj11l2x5r9s5qbyrv7s9jr08156vqkw0zg")))) + "03by64xi7yka0hzc1qyz1jdqzah6isvr3cdsc7g5v6hb4f178kl5")))) (build-system r-build-system) (propagated-inputs - (list r-mass r-kernlab r-segmented r-survival)) + (list r-mass r-kernlab r-plotly r-scales r-segmented r-survival)) (home-page "https://cran.r-project.org/web/packages/mixtools") (synopsis "Tools for analyzing finite mixture models") (description From 608694f918d33b12bcfaa3fc8cf82d76e7d4e86e Mon Sep 17 00:00:00 2001 From: Nicolas Goaziou Date: Mon, 19 Dec 2022 18:40:10 +0100 Subject: [PATCH 461/790] gnu: emacs-org-transclusion: Update to 1.3.1. * gnu/packages/emacs-xyz.scm (emacs-org-transclusion): Update to 1.3.1. --- gnu/packages/emacs-xyz.scm | 53 +++++++++++++++++++------------------- 1 file changed, 27 insertions(+), 26 deletions(-) diff --git a/gnu/packages/emacs-xyz.scm b/gnu/packages/emacs-xyz.scm index 09f001169b..f97775ce95 100644 --- a/gnu/packages/emacs-xyz.scm +++ b/gnu/packages/emacs-xyz.scm @@ -17193,37 +17193,38 @@ running tests easier.") (license license:gpl3+))) (define-public emacs-org-transclusion - (package - (name "emacs-org-transclusion") - (version "1.3.0") - (source - (origin - (method git-fetch) - (uri (git-reference - (url "https://github.com/nobiot/org-transclusion") - (commit (string-append "v" version)))) - (file-name (git-file-name name version)) - (sha256 - (base32 "0pjk6686ss50s9ws014if9mnixsf9m53z1d7bvkbx09lq3jqa7ry")))) - (build-system emacs-build-system) - (arguments - (list - #:tests? #true - #:test-command #~(list "emacs" "--batch" - "-l" "org-transclusion.el" - "-l" "test/unit-tests.el" - "-f" "ert-run-tests-batch-and-exit"))) - (native-inputs - (list emacs-ert-runner)) - (home-page "https://nobiot.github.io/org-transclusion/") - (synopsis "Enable transclusion with Org Mode") - (description "Org-transclusion lets you insert a copy of text content via + (let ((commit "cf51df7b87e0d32ba13ac5380557e81d9845d81b")) ;version bump + (package + (name "emacs-org-transclusion") + (version "1.3.1") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/nobiot/org-transclusion") + (commit commit))) + (file-name (git-file-name name version)) + (sha256 + (base32 "0ix5l8cjcafw8lqhkmwa3cpdw6cbpx65k0iww426nxya849y61yx")))) + (build-system emacs-build-system) + (arguments + (list + #:tests? #true + #:test-command #~(list "emacs" "--batch" + "-l" "org-transclusion.el" + "-l" "test/unit-tests.el" + "-f" "ert-run-tests-batch-and-exit"))) + (native-inputs + (list emacs-ert-runner)) + (home-page "https://nobiot.github.io/org-transclusion/") + (synopsis "Enable transclusion with Org Mode") + (description "Org-transclusion lets you insert a copy of text content via a file link or ID link within an Org file. It lets you have the same content present in different buffers at the same time without copy-and-pasting it. Edit the source of the content, and you can refresh the transcluded copies to the up-to-date state. Org-transclusion keeps your files clear of the transcluded copies, leaving only the links to the original content.") - (license license:gpl3+))) + (license license:gpl3+)))) (define-public emacs-disable-mouse (package From 97ef08c20719b608560dc969549aed220a98f453 Mon Sep 17 00:00:00 2001 From: zimoun Date: Mon, 19 Dec 2022 16:03:41 +0100 Subject: [PATCH 462/790] gnu: Add r-cardelino. * gnu/packages/bioconductor.scm (r-cardelino): New variable. --- gnu/packages/bioconductor.scm | 38 +++++++++++++++++++++++++++++++++++ 1 file changed, 38 insertions(+) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index ec1bbb99d1..29768dc7c2 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -3480,6 +3480,44 @@ of Bioconductor.") packages.") (license license:artistic2.0))) +(define-public r-cardelino + (package + (name "r-cardelino") + (version "1.0.0") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "cardelino" version)) + (sha256 + (base32 + "1ma4clkrkrjvy12ln2d2smyzzsz9y9554f5wgwmh9kv6s4xc66qs")))) + (properties `((upstream-name . "cardelino"))) + (build-system r-build-system) + (propagated-inputs (list r-combinat + r-genomeinfodb + r-genomicranges + r-ggplot2 + r-ggtree + r-matrix + r-matrixstats + r-pheatmap + r-s4vectors + r-snpstats + r-variantannotation + r-vcfr)) + (native-inputs (list r-knitr)) + (home-page "https://github.com/single-cell-genetics/cardelino") + (synopsis "Clone identification from single cell data") + (description + "This package provides methods to infer clonal tree configuration for a +population of cells using single-cell RNA-seq data (scRNA-seq), and possibly +other data modalities. Methods are also provided to assign cells to inferred +clones and explore differences in gene expression between clones. These +methods can flexibly integrate information from imperfect clonal trees +inferred based on bulk exome-seq data, and sparse variant alleles expressed in +scRNA-seq data. A flexible beta-binomial error model that accounts for +stochastic dropout events as well as systematic allelic imbalance is used.") + (license license:gpl3))) + (define-public r-coverageview (package (name "r-coverageview") From d03b6fb0e3f0b81b35a9b35b89c213c144c59fe6 Mon Sep 17 00:00:00 2001 From: Roman Scherer Date: Sat, 3 Dec 2022 12:14:53 +0100 Subject: [PATCH 463/790] gnu: Add libaec. * gnu/packages/geo.scm (libaec): New variable. Signed-off-by: Guillaume Le Vaillant --- gnu/packages/geo.scm | 24 ++++++++++++++++++++++++ 1 file changed, 24 insertions(+) diff --git a/gnu/packages/geo.scm b/gnu/packages/geo.scm index b3a5c0df3f..c0d5dcf7cd 100644 --- a/gnu/packages/geo.scm +++ b/gnu/packages/geo.scm @@ -128,6 +128,30 @@ #:use-module (gnu packages xml) #:use-module (gnu packages xorg)) +(define-public libaec + (package + (name "libaec") + (version "1.0.6") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://gitlab.dkrz.de/k202009/libaec") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 "14myrmmiz9z6wgxqywf3a63cq514vrzsd6z4zvpwigvawlk30iip")))) + (build-system cmake-build-system) + (home-page "https://gitlab.dkrz.de/k202009/libaec") + (synopsis "Adaptive Entropy Coding library") + (description "Libaec provides fast lossless compression of 1 up to 32 bit +wide signed or unsigned integers (samples). The library achieves best results +for low entropy data as often encountered in space imaging instrument data or +numerical model output from weather or climate simulations. While floating +point representations are not directly supported, they can also be efficiently +coded by grouping exponents and mantissa.") + (license license:bsd-2))) + (define-public cdo (package (name "cdo") From 1504edd84f1a0b4afda11cab99edc602d82085c1 Mon Sep 17 00:00:00 2001 From: Roman Scherer Date: Mon, 19 Dec 2022 15:18:43 +0100 Subject: [PATCH 464/790] gnu: Add eccodes. * gnu/packages/geo.scm (eccodes): New variable. Signed-off-by: Guillaume Le Vaillant --- gnu/packages/geo.scm | 30 ++++++++++++++++++++++++++++++ 1 file changed, 30 insertions(+) diff --git a/gnu/packages/geo.scm b/gnu/packages/geo.scm index c0d5dcf7cd..4e872f6846 100644 --- a/gnu/packages/geo.scm +++ b/gnu/packages/geo.scm @@ -79,6 +79,7 @@ #:use-module (gnu packages flex) #:use-module (gnu packages fonts) #:use-module (gnu packages fontutils) + #:use-module (gnu packages gcc) #:use-module (gnu packages gettext) #:use-module (gnu packages gl) #:use-module (gnu packages glib) @@ -152,6 +153,35 @@ point representations are not directly supported, they can also be efficiently coded by grouping exponents and mantissa.") (license license:bsd-2))) +(define-public eccodes + (package + (name "eccodes") + (version "2.27.0") + (source + (origin + (method url-fetch) + (uri (string-append + "https://confluence.ecmwf.int/download/attachments/45757960/" + "eccodes-" version "-Source.tar.gz")) + (sha256 + (base32 "16cw4v2d0kjq6gq04paqny0sh5jymn70w449mig7m5h3spzv7rgd")))) + (build-system cmake-build-system) + (arguments + `(#:configure-flags '("-DENABLE_MEMFS=ON" "-DENABLE_PNG=ON") + #:validate-runpath? #f)) + (inputs + (list jasper libaec libjpeg-turbo libpng netcdf openjpeg)) + (native-inputs + (list gfortran perl pkg-config python)) + (home-page "https://confluence.ecmwf.int/display/ECC") + (synopsis "Library for handling the GRIB, BUFR and GTS file formats") + (description "ecCodes is a package developed by @acronym{ECMWF, European +Centre for Medium-Range Weather Forecasts} which provides an application +programming interface and a set of tools for decoding and encoding messages in +the @acronym{WMO, World Meteorological Organization} FM-92 GRIB, WMO FM-94 +BUFR and WMO GTS abbreviated header formats.") + (license license:asl2.0))) + (define-public cdo (package (name "cdo") From d241517d2cadac3122301b6260c0dfc9f3b383d6 Mon Sep 17 00:00:00 2001 From: Roman Scherer Date: Sat, 3 Dec 2022 13:17:57 +0100 Subject: [PATCH 465/790] gnu: cdo: Update to 2.1.0. * gnu/packages/geo.scm (cdo): Update to 2.1.0. [inputs]: Add curl, eccodes, fftw, hdf5, libxml2, proj and udunits. Signed-off-by: Guillaume Le Vaillant --- gnu/packages/geo.scm | 41 +++++++++++++++++++++++++++++------------ 1 file changed, 29 insertions(+), 12 deletions(-) diff --git a/gnu/packages/geo.scm b/gnu/packages/geo.scm index 4e872f6846..cefe973f4a 100644 --- a/gnu/packages/geo.scm +++ b/gnu/packages/geo.scm @@ -65,6 +65,7 @@ #:use-module (gnu packages bison) #:use-module (gnu packages boost) #:use-module (gnu packages build-tools) + #:use-module (gnu packages c) #:use-module (gnu packages check) #:use-module (gnu packages cmake) #:use-module (gnu packages compression) @@ -185,22 +186,38 @@ BUFR and WMO GTS abbreviated header formats.") (define-public cdo (package (name "cdo") - (version "2.0.5") - (source (origin - (method url-fetch) - (uri (string-append - "https://code.mpimet.mpg.de/attachments/download/26823/cdo-" - version ".tar.gz")) - (sha256 - (base32 - "1khdbd5cmnn7qm6hcqg4md5wbq14fs6brrns8b3g18diqgqvpvpd")))) + (version "2.1.0") + (source + (origin + (method url-fetch) + (uri (string-append + "https://code.mpimet.mpg.de/attachments/download/27481/cdo-" + version ".tar.gz")) + (sha256 + (base32 "1k18llghpf3jnjn0xcnhmbg7arb1fiy854qqn9m5c1abjin38wdq")))) (build-system gnu-build-system) (arguments (list #:configure-flags - #~(list (string-append "--with-netcdf=" - #$(this-package-input "netcdf"))))) + #~(list (string-append "--with-curl=" + #$(this-package-input "curl")) + (string-append "--with-eccodes=" + #$(this-package-input "eccodes")) + (string-append "--with-fftw3=" + #$(this-package-input "fftw")) + (string-append "--with-hdf5=" + #$(this-package-input "hdf5")) + (string-append "--with-netcdf=" + #$(this-package-input "netcdf")) + (string-append "--with-proj=" + #$(this-package-input "proj")) + (string-append "--with-udunits2=" + #$(this-package-input "udunits")) + (string-append "--with-libxml2=" + #$(this-package-input "libxml2"))) + ;; Some tests can fail on machines with many threads. + #:parallel-tests? #f)) (inputs - (list netcdf)) + (list curl eccodes fftw hdf5 libxml2 netcdf proj udunits)) (native-inputs (list pkg-config)) (home-page "https://code.mpimet.mpg.de/projects/cdo") From 6ea7d25396e51fcd8f2a54f1f7460efbf5f93dbd Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Sat, 17 Dec 2022 20:06:46 +0100 Subject: [PATCH 466/790] gnu: SeaBIOS: Use G-expression. * gnu/packages/firmware.scm (seabios)[arguments]: Rewrite as gexp. --- gnu/packages/firmware.scm | 119 +++++++++++++++++++------------------- 1 file changed, 60 insertions(+), 59 deletions(-) diff --git a/gnu/packages/firmware.scm b/gnu/packages/firmware.scm index a4e43e71ec..79e0577077 100644 --- a/gnu/packages/firmware.scm +++ b/gnu/packages/firmware.scm @@ -415,66 +415,67 @@ executing in M-mode.") (build-system gnu-build-system) (native-inputs (list python-wrapper)) (arguments - `(#:tests? #f ; no check target - #:make-flags '("EXTRAVERSION=-guix" ;upstream wants distros to set this - "V=1") ;build verbosely - #:modules (,@%gnu-build-system-modules + (list + #:tests? #f ;no tests + #:make-flags + #~'("EXTRAVERSION=-guix" ;upstream wants distros to set this + "V=1") ;build verbosely + #:modules `(,@%gnu-build-system-modules (ice-9 match)) - #:phases - (modify-phases %standard-phases - (replace 'configure - (lambda _ - ;; Create the ".version" file that is present in release tarballs. - ;; Otherwise this will be regarded as an "unclean" build, and the - ;; build system ends up encoding the build date in the binaries. - (call-with-output-file ".version" - (lambda (port) - (format port ,(package-version this-package)))) - (setenv "CC" "gcc"))) - (add-after 'build 'build-vgabios - (lambda* (#:key (make-flags ''()) #:allow-other-keys) - (for-each - (match-lambda - ((target . config) - (let* ((dot-config (string-append (getcwd) "/" target "/.config")) - (flags (append make-flags - (list (string-append "KCONFIG_CONFIG=" - dot-config) - (string-append "OUT=" target "/"))))) - (mkdir target) - (call-with-output-file dot-config - (lambda (port) - (for-each (lambda (entry) - (if (string-suffix? "=n" entry) - (format port "# CONFIG_~a is not set~%" - (string-drop-right entry 2)) - (format port "CONFIG_~a~%" entry))) - (cons "BUILD_VGABIOS=y" config)))) - (apply invoke "make" "oldnoconfig" flags) - (apply invoke "make" flags) - (link (string-append target "/bios.bin") - (string-append "out/" target ".bin"))))) - ;; These tuples are modelled after Debians packaging: - ;; https://salsa.debian.org/qemu-team/seabios/-/blob/master/debian/rules - '(("ati" . ("VGA_ATI=y" "VGA_PCI=y")) - ("bochs-display" . ("DISPLAY_BOCHS=y" "VGA_PCI=y")) - ("cirrus" . ("VGA_CIRRUS=y" "VGA_PCI=y")) - ("stdvga" . ("VGA_BOCHS=y" "VGA_PCI=y")) - ("virtio" . ("VGA_BOCHS_VIRTIO=y" "VGA_PCI=y")) - ("vmware" . ("VGA_BOCHS_VMWARE=y" "VGA_PCI=y")) - ("qxl" . ("VGA_BOCHS_QXL=y" "VGA_PCI=y")) - ("isavga" . ("VGA_BOCHS=y" "VGA_PCI=n")) - ("ramfb" . ("VGA_RAMFB=y" "VGA_PCI=n")))))) - (replace 'install - (lambda* (#:key outputs #:allow-other-keys) - (let* ((out (assoc-ref outputs "out")) - (fmw (string-append out "/share/firmware"))) - (for-each (lambda (bios) - (install-file bios fmw)) - (find-files "out" "\\.bin$")) - (with-directory-excursion fmw - ;; QEMU 1.7 and later looks only for the latter. - (symlink "bios.bin" "bios-256k.bin")))))))) + #:phases + #~(modify-phases %standard-phases + (replace 'configure + (lambda _ + ;; Create the ".version" file that is present in release tarballs. + ;; Otherwise this will be regarded as an "unclean" build, and the + ;; build system ends up encoding the build date in the binaries. + (call-with-output-file ".version" + (lambda (port) + (format port #$(package-version this-package)))) + (setenv "CC" "gcc"))) + (add-after 'build 'build-vgabios + (lambda* (#:key (make-flags #~'()) #:allow-other-keys) + (for-each + (match-lambda + ((target . config) + (let* ((dot-config (string-append (getcwd) "/" target "/.config")) + (flags (append make-flags + (list (string-append "KCONFIG_CONFIG=" + dot-config) + (string-append "OUT=" target "/"))))) + (mkdir target) + (call-with-output-file dot-config + (lambda (port) + (for-each (lambda (entry) + (if (string-suffix? "=n" entry) + (format port "# CONFIG_~a is not set~%" + (string-drop-right entry 2)) + (format port "CONFIG_~a~%" entry))) + (cons "BUILD_VGABIOS=y" config)))) + (apply invoke "make" "oldnoconfig" flags) + (apply invoke "make" flags) + (link (string-append target "/bios.bin") + (string-append "out/" target ".bin"))))) + ;; These tuples are modelled after Debians packaging: + ;; https://salsa.debian.org/qemu-team/seabios/-/blob/master/debian/rules + '(("ati" . ("VGA_ATI=y" "VGA_PCI=y")) + ("bochs-display" . ("DISPLAY_BOCHS=y" "VGA_PCI=y")) + ("cirrus" . ("VGA_CIRRUS=y" "VGA_PCI=y")) + ("stdvga" . ("VGA_BOCHS=y" "VGA_PCI=y")) + ("virtio" . ("VGA_BOCHS_VIRTIO=y" "VGA_PCI=y")) + ("vmware" . ("VGA_BOCHS_VMWARE=y" "VGA_PCI=y")) + ("qxl" . ("VGA_BOCHS_QXL=y" "VGA_PCI=y")) + ("isavga" . ("VGA_BOCHS=y" "VGA_PCI=n")) + ("ramfb" . ("VGA_RAMFB=y" "VGA_PCI=n")))))) + (replace 'install + (lambda _ + (let ((fmw (string-append #$output "/share/firmware"))) + (for-each (lambda (bios) + (install-file bios fmw)) + (find-files "out" "\\.bin$")) + (with-directory-excursion fmw + ;; QEMU 1.7 and later looks only for the latter. + (symlink "bios.bin" "bios-256k.bin")))))))) (home-page "https://www.seabios.org/SeaBIOS") (synopsis "x86 BIOS implementation") (description "SeaBIOS is an implementation of a 16bit x86 BIOS. SeaBIOS From 16f2cc5a8f258b37530e2ced75765bf354d769bc Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Sun, 18 Dec 2022 19:12:41 +0100 Subject: [PATCH 467/790] gnu: SeaBIOS: Remove pre-generated code. * gnu/packages/firmware.scm (seabios)[source](modules, snippet): New fields. [native-inputs]: Add ACPICA. [arguments]: Add build-iasl phase. --- gnu/packages/firmware.scm | 15 +++++++++++++-- 1 file changed, 13 insertions(+), 2 deletions(-) diff --git a/gnu/packages/firmware.scm b/gnu/packages/firmware.scm index 79e0577077..623e60f2b1 100644 --- a/gnu/packages/firmware.scm +++ b/gnu/packages/firmware.scm @@ -411,9 +411,14 @@ executing in M-mode.") (commit (string-append "rel-" version)))) (file-name (git-file-name name version)) (sha256 - (base32 "0gph1hf70jjpx55qc0lzx2yghkipg9dnsin07i4jajk0p1jpd2d0")))) + (base32 "0gph1hf70jjpx55qc0lzx2yghkipg9dnsin07i4jajk0p1jpd2d0")) + (modules '((guix build utils))) + (snippet + #~(begin + ;; Delete IASL-generated files. + (for-each delete-file (find-files "." "\\.hex$")))))) (build-system gnu-build-system) - (native-inputs (list python-wrapper)) + (native-inputs (list acpica python-wrapper)) (arguments (list #:tests? #f ;no tests @@ -433,6 +438,12 @@ executing in M-mode.") (lambda (port) (format port #$(package-version this-package)))) (setenv "CC" "gcc"))) + (add-before 'build 'build-description-tables + (lambda _ + ;; Regenerate the ACPI description tables. + (invoke "make" "iasl") + ;; Clear temporary files added by the iasl target. + (invoke "make" "clean"))) (add-after 'build 'build-vgabios (lambda* (#:key (make-flags #~'()) #:allow-other-keys) (for-each From 5877dc88a2a1cecce2eeb76ca3ce997c277551f3 Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Mon, 19 Dec 2022 01:23:25 +0100 Subject: [PATCH 468/790] gnu: SeaBIOS: Build more BIOSen. * gnu/packages/firmware.scm (seabios)[arguments]: Build the "128k" and "microvm" BIOSen expected by QEMU. Fix installation of vgabios. --- gnu/packages/firmware.scm | 103 ++++++++++++++++++++++++-------------- 1 file changed, 65 insertions(+), 38 deletions(-) diff --git a/gnu/packages/firmware.scm b/gnu/packages/firmware.scm index 623e60f2b1..79d4442487 100644 --- a/gnu/packages/firmware.scm +++ b/gnu/packages/firmware.scm @@ -444,49 +444,76 @@ executing in M-mode.") (invoke "make" "iasl") ;; Clear temporary files added by the iasl target. (invoke "make" "clean"))) - (add-after 'build 'build-vgabios + (replace 'build (lambda* (#:key (make-flags #~'()) #:allow-other-keys) - (for-each - (match-lambda - ((target . config) - (let* ((dot-config (string-append (getcwd) "/" target "/.config")) - (flags (append make-flags - (list (string-append "KCONFIG_CONFIG=" - dot-config) - (string-append "OUT=" target "/"))))) - (mkdir target) - (call-with-output-file dot-config - (lambda (port) - (for-each (lambda (entry) - (if (string-suffix? "=n" entry) - (format port "# CONFIG_~a is not set~%" - (string-drop-right entry 2)) - (format port "CONFIG_~a~%" entry))) - (cons "BUILD_VGABIOS=y" config)))) - (apply invoke "make" "oldnoconfig" flags) - (apply invoke "make" flags) - (link (string-append target "/bios.bin") - (string-append "out/" target ".bin"))))) - ;; These tuples are modelled after Debians packaging: - ;; https://salsa.debian.org/qemu-team/seabios/-/blob/master/debian/rules - '(("ati" . ("VGA_ATI=y" "VGA_PCI=y")) - ("bochs-display" . ("DISPLAY_BOCHS=y" "VGA_PCI=y")) - ("cirrus" . ("VGA_CIRRUS=y" "VGA_PCI=y")) - ("stdvga" . ("VGA_BOCHS=y" "VGA_PCI=y")) - ("virtio" . ("VGA_BOCHS_VIRTIO=y" "VGA_PCI=y")) - ("vmware" . ("VGA_BOCHS_VMWARE=y" "VGA_PCI=y")) - ("qxl" . ("VGA_BOCHS_QXL=y" "VGA_PCI=y")) - ("isavga" . ("VGA_BOCHS=y" "VGA_PCI=n")) - ("ramfb" . ("VGA_RAMFB=y" "VGA_PCI=n")))))) + ;; Note: These BIOS configurations are taken from QEMUs roms/ + ;; directory. + (let ((biosen + '(;; The standard BIOS using default options. + ("bios-256k" . ("QEMU=y" "ROM_SIZE=256" "ATA_DMA=n")) + ;; A minimal BIOS for old QEMU machine types. + ("bios-128k" + . ("QEMU=y" "ROM_SIZE=128" "ATA_DMA=n" "BOOTSPLASH=n" + "XEN=n" "USB_OHCI=n" "USB_XHCI=n" "USB_UAS=n" + "SDCARD=n" "TCGBIOS=n" "MPT_SCSI=n" "ESP_SCSI=n" + "MEGASAS=n" "PVSCSI=n" "NVME=n" "USE_SMM=n" + "VGAHOOKS=n" "HOST_BIOS_GEOMETRY=n" "ACPI_PARSE=n")) + ;; Minimal BIOS for the "microvm" machine type. + ("bios-microvm" + . ("QEMU=y" "ROM_SIZE=128" "XEN=n" "BOOTSPLASH=n" "ATA=n" + "AHCI=n" "SDCARD=n" "PVSCSI=n" "ESP_SCSI=n" "LSI_SCSI=n" + "MEGASAS=n" "MPT_SCSI=n" "FLOPPY=n" "FLASH_FLOPPY=n" + "NVME=n" "PS2PORT=n" "USB=n" "LPT=n" "RTC_TIMER=n" + "USE_SMM=n" "PMTIMER=n" "TCGBIOS=n" "HARDWARE_IRQ=n" + "ACPI_PARSE=y")))) + (vgabiosen + '(("ati" . ("VGA_ATI=y" "VGA_PCI=y")) + ("bochs-display" . ("DISPLAY_BOCHS=y" "VGA_PCI=y")) + ("cirrus" . ("VGA_CIRRUS=y" "VGA_PCI=y")) + ("stdvga" . ("VGA_BOCHS=y" "VGA_PCI=y")) + ("virtio" . ("VGA_BOCHS=y" "VGA_BOCHS_VIRTIO=y" "VGA_PCI=y")) + ("vmware" . ("VGA_BOCHS=y" "VGA_BOCHS_VMWARE=y" "VGA_PCI=y")) + ("qxl" . ("VGA_BOCHS=y" "VGA_BOCHS_QXL=y" "VGA_PCI=y")) + ("isavga" . ("VGA_BOCHS=y" "VGA_PCI=n")) + ("ramfb" . ("VGA_RAMFB=y" "VGA_PCI=n"))))) + (mkdir "out") + (for-each + (match-lambda + ((target . config) + (let* ((dot-config (string-append (getcwd) "/" target + "/.config")) + (flags (append make-flags + (list (string-append "KCONFIG_CONFIG=" + dot-config) + (string-append "OUT=" target "/"))))) + (mkdir target) + (call-with-output-file dot-config + (lambda (port) + (for-each (lambda (entry) + (format port "CONFIG_~a~%" entry)) + config))) + (apply invoke "make" "oldnoconfig" flags) + (apply invoke "make" flags) + (link (string-append target "/" + (if (string-prefix? "vgabios" target) + "vgabios.bin" "bios.bin")) + (string-append "out/" target ".bin"))))) + (append biosen + (map (lambda (pair) + `(,(string-append "vgabios-" (car pair)) + . + ,(cons "BUILD_VGABIOS=y" (cdr pair)))) + vgabiosen)))))) (replace 'install (lambda _ - (let ((fmw (string-append #$output "/share/firmware"))) + (let ((firmware (string-append #$output "/share/firmware"))) (for-each (lambda (bios) - (install-file bios fmw)) + (install-file bios firmware)) (find-files "out" "\\.bin$")) - (with-directory-excursion fmw - ;; QEMU 1.7 and later looks only for the latter. - (symlink "bios.bin" "bios-256k.bin")))))))) + (with-directory-excursion firmware + ;; Compatibility symlinks for QEMU. + (symlink "bios-128k.bin" "bios.bin") + (symlink "vgabios-isavga.bin" "vgabios.bin")))))))) (home-page "https://www.seabios.org/SeaBIOS") (synopsis "x86 BIOS implementation") (description "SeaBIOS is an implementation of a 16bit x86 BIOS. SeaBIOS From 145aa7f04b1c61e52f61bca039350e898e20aac8 Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Mon, 19 Dec 2022 07:46:47 +0100 Subject: [PATCH 469/790] gnu: SeaBIOS: Build in parallel. * gnu/packages/firmware.scm (seabios)[arguments]: Use N-PAR-FOR-EACH to build the various targets. --- gnu/packages/firmware.scm | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/gnu/packages/firmware.scm b/gnu/packages/firmware.scm index 79d4442487..7239b85cb2 100644 --- a/gnu/packages/firmware.scm +++ b/gnu/packages/firmware.scm @@ -426,6 +426,7 @@ executing in M-mode.") #~'("EXTRAVERSION=-guix" ;upstream wants distros to set this "V=1") ;build verbosely #:modules `(,@%gnu-build-system-modules + (ice-9 threads) (ice-9 match)) #:phases #~(modify-phases %standard-phases @@ -477,7 +478,7 @@ executing in M-mode.") ("isavga" . ("VGA_BOCHS=y" "VGA_PCI=n")) ("ramfb" . ("VGA_RAMFB=y" "VGA_PCI=n"))))) (mkdir "out") - (for-each + (n-par-for-each (parallel-job-count) (match-lambda ((target . config) (let* ((dot-config (string-append (getcwd) "/" target From b2fc209b2ce5b6f18f1cf9d8c599f52e608ace42 Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Mon, 19 Dec 2022 01:29:53 +0100 Subject: [PATCH 470/790] gnu: SeaBIOS: Prettify version string. * gnu/packages/firmware.scm (seabios)[arguments]: Display version as "1.16.1/GNU Guix" instead of "1.16.1-guix". --- gnu/packages/firmware.scm | 10 ++++++---- 1 file changed, 6 insertions(+), 4 deletions(-) diff --git a/gnu/packages/firmware.scm b/gnu/packages/firmware.scm index 7239b85cb2..8c8949a5da 100644 --- a/gnu/packages/firmware.scm +++ b/gnu/packages/firmware.scm @@ -423,7 +423,10 @@ executing in M-mode.") (list #:tests? #f ;no tests #:make-flags - #~'("EXTRAVERSION=-guix" ;upstream wants distros to set this + ;; If EXTRAVERSION is not set the build system will embed the current + ;; date in binaries. Use this opportunity to personalize as recommended + ;; by Build_overview.md. + #~'("EXTRAVERSION=/GNU Guix" "V=1") ;build verbosely #:modules `(,@%gnu-build-system-modules (ice-9 threads) @@ -432,9 +435,8 @@ executing in M-mode.") #~(modify-phases %standard-phases (replace 'configure (lambda _ - ;; Create the ".version" file that is present in release tarballs. - ;; Otherwise this will be regarded as an "unclean" build, and the - ;; build system ends up encoding the build date in the binaries. + ;; Ensure this file is present in case we're building from a git + ;; checkout instead of release tarball. (call-with-output-file ".version" (lambda (port) (format port #$(package-version this-package)))) From 814214c369851da50e7006266f718b2d9324ada0 Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Sat, 17 Dec 2022 23:26:09 +0100 Subject: [PATCH 471/790] gnu: QEMU: Unbundle SeaBIOS. * gnu/packages/virtualization.scm (qemu)[source](snippet): Delete SeaBIOS ROMs and source code. [arguments]: Add replace-firmwares and delete-firmwares phases. [inputs]: Add SEABIOS. [native-inputs]: Add ACPICA. While here, sort inputs. --- gnu/packages/virtualization.scm | 69 +++++++++++++++++++++++++++++---- 1 file changed, 61 insertions(+), 8 deletions(-) diff --git a/gnu/packages/virtualization.scm b/gnu/packages/virtualization.scm index 6890f13233..d0f5fd5af4 100644 --- a/gnu/packages/virtualization.scm +++ b/gnu/packages/virtualization.scm @@ -175,10 +175,13 @@ (modules '((guix build utils))) (snippet '(begin + ;; TODO: Scrub all firmwares from this directory! + (with-directory-excursion "pc-bios" + ;; Delete firmwares provided by SeaBIOS. + (for-each delete-file (find-files "." "^(bios|vgabios).*\\.bin$"))) ;; Delete bundled code that we provide externally. - ;; TODO: Unbundle SeaBIOS! (for-each delete-file-recursively - '("dtc" "meson")))))) + '("dtc" "meson" "roms/seabios")))))) (outputs '("out" "static" "doc")) ;5.3 MiB of HTML docs (build-system gnu-build-system) (arguments @@ -189,15 +192,20 @@ (not (string=? "i686-linux" (%current-system)))) #:configure-flags #~(let ((gcc (search-input-file %build-inputs "/bin/gcc")) + (meson (search-input-file %build-inputs "bin/meson")) + (seabios (search-input-file %build-inputs + "share/firmware/bios.bin")) (out #$output)) (list (string-append "--cc=" gcc) ;; Some architectures insist on using HOST_CC. (string-append "--host-cc=" gcc) + (string-append "--meson=" meson) (string-append "--prefix=" out) + "--sysconfdir=/etc" - (string-append "--meson=" (search-input-file %build-inputs - "bin/meson")) "--enable-fdt=system" + (string-append "--firmwarepath=" out "/share/qemu:" + (dirname seabios)) (string-append "--smbd=" out "/libexec/samba-wrapper") "--disable-debug-info" ;for space considerations ;; The binaries need to be linked against -lrt. @@ -211,6 +219,33 @@ ,@%gnu-build-system-modules) #:phases #~(modify-phases %standard-phases + ;; Since we removed the bundled firmwares above, many tests + ;; can't work. Re-add them here. + (add-after 'unpack 'replace-firmwares + (lambda* (#:key inputs #:allow-other-keys) + (let* ((seabios (dirname (search-input-file + inputs "share/firmware/bios.bin"))) + (seabios-firmwares (find-files seabios "\\.bin$")) + (allowed-differences + ;; Ignore minor differences (addresses etc) in the firmware + ;; data tables compared to what the test suite expects. + '("tests/data/acpi/pc/SSDT.dimmpxm" + "tests/data/acpi/pc/DSDT.dimmpxm" + "tests/data/acpi/pc/ERST.acpierst" + "tests/data/acpi/q35/ERST.acpierst" + "tests/data/acpi/q35/DSDT.cxl")) + (allowed-differences-whitelist + (open-file "tests/qtest/bios-tables-test-allowed-diff.h" + "a"))) + (with-directory-excursion "pc-bios" + (for-each (lambda (file) + (symlink file (basename file))) + seabios-firmwares)) + (for-each (lambda (file) + (format allowed-differences-whitelist + "\"~a\",~%" file)) + allowed-differences) + (close-port allowed-differences-whitelist)))) (add-after 'unpack 'extend-test-time-outs (lambda _ ;; These tests can time out on heavily-loaded and/or slow storage. @@ -277,17 +312,22 @@ (mkdir-p "b/qemu") (chdir "b/qemu") (apply invoke "../../configure" configure-flags))) + ;; Configure, build and install QEMU user-emulation static binaries. (add-after 'configure 'configure-user-static (lambda* (#:key inputs outputs #:allow-other-keys) (let* ((static (assoc-ref outputs "static")) (gcc (search-input-file inputs "/bin/gcc")) + (seabios (search-input-file inputs "/share/firmware/bios.bin")) ;; This is the common set of configure flags; it is ;; duplicated here to isolate this phase from manipulations ;; to the #:configure-flags build argument, as done in ;; derived packages such as qemu-minimal. (configure-flags (list (string-append "--cc=" gcc) (string-append "--host-cc=" gcc) + (string-append "--firmwarepath=" + #$output "/share/qemu:" + (dirname seabios)) "--sysconfdir=/etc" "--disable-debug-info"))) (mkdir-p "../user-static") @@ -313,6 +353,15 @@ (scandir "." (cut string-suffix? "-linux-user" <>)))))))) + + (add-after 'install 'delete-firmwares + (lambda _ + ;; Delete firmares that are accessible on --firmwarepath. + ;; For some reason tests fail if we simply remove them from + ;; pc-bios/meson.build, hence this roundabout way. + (with-directory-excursion (string-append #$output "/share/qemu") + (for-each delete-file + (find-files "." "^(vga)?bios(-[a-z0-9-]+)?\\.bin$"))))) ;; Create a wrapper for Samba. This allows QEMU to use Samba without ;; pulling it in as an input. Note that you need to explicitly install ;; Samba in your Guix profile for Samba support. @@ -357,6 +406,7 @@ exec smbd $@"))) pixman pulseaudio sdl2 + seabios spice usbredir util-linux @@ -367,13 +417,16 @@ exec smbd $@"))) zlib `(,zstd "lib"))) (native-inputs - (list gettext-minimal - `(,glib "bin") ;gtester, etc. - perl - flex + ;; Note: acpica is here only to pretty-print firmware differences with IASL + ;; (see the replace-firmwares phase above). + (list acpica bison + flex + gettext-minimal + `(,glib "bin") ;gtester, etc. meson-0.63 ninja + perl pkg-config python-wrapper python-sphinx From 416f9141dbf5230689b1dabddb63f80097c9dd3d Mon Sep 17 00:00:00 2001 From: Leo Famulari Date: Mon, 19 Dec 2022 19:51:30 -0500 Subject: [PATCH 472/790] gnu: linux-libre: Update to 6.0.14. * gnu/packages/linux.scm (linux-libre-6.0-version): Update to 6.0.14. (linux-libre-6.0-pristine-source): Update hash. --- gnu/packages/linux.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/linux.scm b/gnu/packages/linux.scm index 41fb24f82a..d7e7361bca 100644 --- a/gnu/packages/linux.scm +++ b/gnu/packages/linux.scm @@ -480,7 +480,7 @@ corresponding UPSTREAM-SOURCE (an origin), using the given DEBLOB-SCRIPTS." ;; The current "stable" kernels. That is, the most recently released major ;; versions that are still supported upstream. -(define-public linux-libre-6.0-version "6.0.13") +(define-public linux-libre-6.0-version "6.0.14") (define-public linux-libre-6.0-gnu-revision "gnu") (define deblob-scripts-6.0 (linux-libre-deblob-scripts @@ -490,7 +490,7 @@ corresponding UPSTREAM-SOURCE (an origin), using the given DEBLOB-SCRIPTS." (base32 "16g2bin3xay30zfss1vlb7pwcss5giaxaksp4v1gk05wn51wjrqr"))) (define-public linux-libre-6.0-pristine-source (let ((version linux-libre-6.0-version) - (hash (base32 "191dlxcmbx8vy6z2k04jq2kr6hwnaknsnsyycvqnjmvmdf6i3lq8"))) + (hash (base32 "0862g1djm2hlcw44ks08494pbsd44syb7k0z8dqjbynggxz8zway"))) (make-linux-libre-source version (%upstream-linux-source version hash) deblob-scripts-6.0))) From 6490835e4a9e362d4f75a684eecba6d0f4aad4fa Mon Sep 17 00:00:00 2001 From: Leo Famulari Date: Mon, 19 Dec 2022 19:51:50 -0500 Subject: [PATCH 473/790] gnu: linux-libre 5.15: Update to 5.15.84. * gnu/packages/linux.scm (linux-libre-5.15-version): Update to 5.15.84. (linux-libre-5.15-pristine-source): Update hash. --- gnu/packages/linux.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/linux.scm b/gnu/packages/linux.scm index d7e7361bca..c0fa38835d 100644 --- a/gnu/packages/linux.scm +++ b/gnu/packages/linux.scm @@ -498,7 +498,7 @@ corresponding UPSTREAM-SOURCE (an origin), using the given DEBLOB-SCRIPTS." ;; The "longterm" kernels — the older releases with long-term upstream support. ;; Here are the support timelines: ;; -(define-public linux-libre-5.15-version "5.15.83") +(define-public linux-libre-5.15-version "5.15.84") (define-public linux-libre-5.15-gnu-revision "gnu") (define deblob-scripts-5.15 (linux-libre-deblob-scripts @@ -508,7 +508,7 @@ corresponding UPSTREAM-SOURCE (an origin), using the given DEBLOB-SCRIPTS." (base32 "1m73pgx8v047xb2gck2g7j7khniis8c9akn9vhzgsdfglrf8p6fj"))) (define-public linux-libre-5.15-pristine-source (let ((version linux-libre-5.15-version) - (hash (base32 "1wvzfhzqq9dps508wmp2gblfz93ipppnjzqm0n8pi1acq11hhna0"))) + (hash (base32 "05w29fh1k40iwsm7h67i86lv6jw075micav5b5dy7hjrn06c739i"))) (make-linux-libre-source version (%upstream-linux-source version hash) deblob-scripts-5.15))) From 0e0f54416fc3f85b9702b137e09feb1a87d7cb39 Mon Sep 17 00:00:00 2001 From: Leo Famulari Date: Mon, 19 Dec 2022 19:52:13 -0500 Subject: [PATCH 474/790] gnu: linux-libre 5.10: Update to 5.10.160. * gnu/packages/linux.scm (linux-libre-5.10-version): Update to 5.10.160. (linux-libre-5.10-pristine-source): Update hash. --- gnu/packages/linux.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/linux.scm b/gnu/packages/linux.scm index c0fa38835d..f1504af480 100644 --- a/gnu/packages/linux.scm +++ b/gnu/packages/linux.scm @@ -513,7 +513,7 @@ corresponding UPSTREAM-SOURCE (an origin), using the given DEBLOB-SCRIPTS." (%upstream-linux-source version hash) deblob-scripts-5.15))) -(define-public linux-libre-5.10-version "5.10.159") +(define-public linux-libre-5.10-version "5.10.160") (define-public linux-libre-5.10-gnu-revision "gnu1") (define deblob-scripts-5.10 (linux-libre-deblob-scripts @@ -523,7 +523,7 @@ corresponding UPSTREAM-SOURCE (an origin), using the given DEBLOB-SCRIPTS." (base32 "0a96g4pjdgwvxn2wpz6rfc8nwdlkw138r9pp66kvfrrn08i313ii"))) (define-public linux-libre-5.10-pristine-source (let ((version linux-libre-5.10-version) - (hash (base32 "19yfi5vknxnw0cb8274q3pb5zjs6ny04n16m8xjdfdmznrbvza8v"))) + (hash (base32 "02w4mapfhds26ahqy5ijm5a6mlh9a5f4q3488l898qz8r9m0gm9h"))) (make-linux-libre-source version (%upstream-linux-source version hash) deblob-scripts-5.10))) From bd6d76b8a44bb14dedaed070b7056f2f56c2e161 Mon Sep 17 00:00:00 2001 From: Leo Famulari Date: Mon, 19 Dec 2022 19:52:27 -0500 Subject: [PATCH 475/790] gnu: linux-libre 5.4: Update to 5.4.228. * gnu/packages/linux.scm (linux-libre-5.4-version): Update to 5.4.228. (linux-libre-5.4-pristine-source): Update hash. --- gnu/packages/linux.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/linux.scm b/gnu/packages/linux.scm index f1504af480..4cb97d1b82 100644 --- a/gnu/packages/linux.scm +++ b/gnu/packages/linux.scm @@ -528,7 +528,7 @@ corresponding UPSTREAM-SOURCE (an origin), using the given DEBLOB-SCRIPTS." (%upstream-linux-source version hash) deblob-scripts-5.10))) -(define-public linux-libre-5.4-version "5.4.227") +(define-public linux-libre-5.4-version "5.4.228") (define-public linux-libre-5.4-gnu-revision "gnu1") (define deblob-scripts-5.4 (linux-libre-deblob-scripts @@ -538,7 +538,7 @@ corresponding UPSTREAM-SOURCE (an origin), using the given DEBLOB-SCRIPTS." (base32 "1bgblfkcnrabnr9hpdl07qgps57h6bq4v5pjrxs798vq43db66va"))) (define-public linux-libre-5.4-pristine-source (let ((version linux-libre-5.4-version) - (hash (base32 "14q5gy48j78vwnqivrgpdhj778n2jq5l7yiw5na1rwqmfh1wbvsy"))) + (hash (base32 "0935dq7zbpf0fkppl3q96a2gh1zrmq01h1nivzgmdhjlmhn3n9c0"))) (make-linux-libre-source version (%upstream-linux-source version hash) deblob-scripts-5.4))) From bbd11199e6856ded8d75468a16789715b6817b45 Mon Sep 17 00:00:00 2001 From: Florian Pelz Date: Mon, 19 Dec 2022 17:38:37 +0100 Subject: [PATCH 476/790] =?UTF-8?q?services:=C2=B7kmscon:=C2=B7Display?= =?UTF-8?q?=C2=B7CJK=C2=B7characters.?= MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Follow-up·to d7d049fdcd80e27a42b31766890f589f482a4f23. * gnu/services/base.scm·(kmscon-service-type):·Use·GNU·Unifont, which bundles CJK glyphs from WenQuanYi and elsewhere. --- gnu/services/base.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/services/base.scm b/gnu/services/base.scm index 52b94e060b..6993e1f174 100644 --- a/gnu/services/base.scm +++ b/gnu/services/base.scm @@ -2494,11 +2494,11 @@ notably to select, copy, and paste text. The default options use the #$kmscon-command ;; The installer needs to be able to display glyphs from - ;; various scripts, so give it access to freefont. + ;; various scripts, so give it access to unifont. ;; TODO: Make this configurable. #:environment-variables (list (string-append "XDG_DATA_DIRS=" - #$font-gnu-freefont "/share")))) + #$font-gnu-unifont "/share")))) (stop #~(make-kill-destructor))))) (description "Start the @command{kmscon} virtual terminal emulator for the Linux @dfn{kernel mode setting} (KMS)."))) From 2ad9bf1661a38ab0f74241f2d9ba9e87a4534815 Mon Sep 17 00:00:00 2001 From: Nicolas Goaziou Date: Tue, 20 Dec 2022 10:58:29 +0100 Subject: [PATCH 477/790] gnu: sfizz: Update to 1.2.0. * gnu/packages/music.scm (sfizz): Update to 1.2.0. [arguments]<#:configure-flags>: Use system Pugixml. --- gnu/packages/music.scm | 15 +++++++++------ 1 file changed, 9 insertions(+), 6 deletions(-) diff --git a/gnu/packages/music.scm b/gnu/packages/music.scm index bde01cb312..a14719f89a 100644 --- a/gnu/packages/music.scm +++ b/gnu/packages/music.scm @@ -4730,7 +4730,7 @@ standalone JACK client and an LV2 plugin is also available.") (define-public sfizz (package (name "sfizz") - (version "1.0.0") + (version "1.2.0") (source (origin (method url-fetch) (uri (string-append "https://github.com/sfztools/sfizz" @@ -4738,16 +4738,15 @@ standalone JACK client and an LV2 plugin is also available.") "/sfizz-" version ".tar.gz")) (sha256 (base32 - "1pk67xvyqkvhjz2q5hbj5v0mnfvdvvl8vl5bsh6ymwiq3glkd41l")) + "1wsr3dpn7a7whqn480m02kp6n4raamnfi3imhf2q8k58md1yn9jw")) (modules '((guix build utils))) (snippet - ;; TODO: pugixml is bundled, but can only be removed in - ;; versions after 1.0.0. '(for-each delete-file-recursively '("external/abseil-cpp" "external/simde" "plugins/editor/external/vstgui4" - "plugins/vst"))))) + "plugins/vst" + "src/external/pugixml"))))) (build-system cmake-build-system) (arguments `(#:configure-flags @@ -4755,7 +4754,11 @@ standalone JACK client and an LV2 plugin is also available.") "-DSFIZZ_VST=OFF" "-DSFIZZ_VST2=OFF" "-DSFIZZ_TESTS=ON" - "-DSFIZZ_USE_SYSTEM_ABSEIL=ON"))) + "-DSFIZZ_USE_SYSTEM_ABSEIL=ON" + "-DSFIZZ_USE_SYSTEM_PUGIXML=ON" + ;; XXX: Guix SIMDe version 0.7.2 is not enough. + ;; "-DSFIZZ_USE_SYSTEM_SIMDE=ON" + ))) (native-inputs (list pkg-config)) (inputs From 851fbac0a99f7659d1bc1c9486d2505855b0daa8 Mon Sep 17 00:00:00 2001 From: Nicolas Goaziou Date: Tue, 20 Dec 2022 11:01:57 +0100 Subject: [PATCH 478/790] gnu: sfizz: Improve package style. * gnu/packages/music.scm (sfizz)[arguments]: Use G-expressions. [inputs]: Remove input labels. --- gnu/packages/music.scm | 35 ++++++++++++++++++----------------- 1 file changed, 18 insertions(+), 17 deletions(-) diff --git a/gnu/packages/music.scm b/gnu/packages/music.scm index a14719f89a..5be767a138 100644 --- a/gnu/packages/music.scm +++ b/gnu/packages/music.scm @@ -4749,26 +4749,27 @@ standalone JACK client and an LV2 plugin is also available.") "src/external/pugixml"))))) (build-system cmake-build-system) (arguments - `(#:configure-flags - (list "-DSFIZZ_LV2_UI=OFF" - "-DSFIZZ_VST=OFF" - "-DSFIZZ_VST2=OFF" - "-DSFIZZ_TESTS=ON" - "-DSFIZZ_USE_SYSTEM_ABSEIL=ON" - "-DSFIZZ_USE_SYSTEM_PUGIXML=ON" - ;; XXX: Guix SIMDe version 0.7.2 is not enough. - ;; "-DSFIZZ_USE_SYSTEM_SIMDE=ON" - ))) + (list + #:configure-flags + #~(list "-DSFIZZ_LV2_UI=OFF" + "-DSFIZZ_VST=OFF" + "-DSFIZZ_VST2=OFF" + "-DSFIZZ_TESTS=ON" + "-DSFIZZ_USE_SYSTEM_ABSEIL=ON" + "-DSFIZZ_USE_SYSTEM_PUGIXML=ON" + ;; XXX: Guix SIMDe version 0.7.2 is not enough. + ;; "-DSFIZZ_USE_SYSTEM_SIMDE=ON" + ))) (native-inputs (list pkg-config)) (inputs - `(("abseil-cpp" ,abseil-cpp) - ("glib" ,glib) - ("jack" ,jack-2) - ("lv2" ,lv2) - ("libsamplerate" ,libsamplerate) - ("pugixml" ,pugixml) - ("simde" ,simde))) + (list abseil-cpp + glib + jack-2 + lv2 + libsamplerate + pugixml + simde)) (home-page "https://sfz.tools/sfizz/") (synopsis "SFZ parser and synth library") (description "Sfizz provides an SFZ parser and synth C++ library. It From 49b68c984278c6af2df347f79faf0a13c30d1b13 Mon Sep 17 00:00:00 2001 From: Nicolas Goaziou Date: Tue, 20 Dec 2022 11:06:57 +0100 Subject: [PATCH 479/790] gnu: emacs-eldev: Update to 1.3.1. * gnu/packages/emacs-xyz.scm (emacs-eldev): Update to 1.3.1. --- gnu/packages/emacs-xyz.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/emacs-xyz.scm b/gnu/packages/emacs-xyz.scm index f97775ce95..d7fac08b7d 100644 --- a/gnu/packages/emacs-xyz.scm +++ b/gnu/packages/emacs-xyz.scm @@ -20413,7 +20413,7 @@ according to a parsing expression grammar.") (define-public emacs-eldev (package (name "emacs-eldev") - (version "1.3") + (version "1.3.1") (source (origin (method git-fetch) @@ -20422,7 +20422,7 @@ according to a parsing expression grammar.") (commit version))) (file-name (git-file-name name version)) (sha256 - (base32 "112jv9rz6brglffwsablnhafhhnfnq89k9vh8xzbbi6i4xz2l1ak")))) + (base32 "14rrh5ycwd3r5k3df8aif4jii645m5jgplxky3hrjgr8vxd951h8")))) (build-system emacs-build-system) (arguments (list From 9dbd12f629f2ceb227e196b5ef7a65fe228e00f3 Mon Sep 17 00:00:00 2001 From: jgart via Guix-patches via Date: Mon, 19 Dec 2022 21:29:16 -0600 Subject: [PATCH 480/790] gnu: Add emacs-fzf. * gnu/packages/emacs-xyz.scm (emacs-fzf): New variable. Signed-off-by: Nicolas Goaziou --- gnu/packages/emacs-xyz.scm | 32 ++++++++++++++++++++++++++++++++ 1 file changed, 32 insertions(+) diff --git a/gnu/packages/emacs-xyz.scm b/gnu/packages/emacs-xyz.scm index d7fac08b7d..dca9bb5b95 100644 --- a/gnu/packages/emacs-xyz.scm +++ b/gnu/packages/emacs-xyz.scm @@ -1283,6 +1283,38 @@ leveraging built-in functionality.") (license (list license:gpl3+ license:fdl1.3+)))) ; GFDLv1.3+ for the manual +(define-public emacs-fzf + (let ((commit "21912ebc7e1084aa88c9d8b7715e782a3978ed23") + (revision "0")) + (package + (name "emacs-fzf") + (version (git-version "0.0.2" revision commit)) + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/bling/fzf.el") + (commit commit))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "0gdqjh8996hb06bnnyhi94k69mjfrzyfgq00a9s4wwagv28sqmkj")))) + (build-system emacs-build-system) + (arguments + (list + #:tests? #f ;no tests + #:phases + #~(modify-phases %standard-phases + (add-after 'unpack 'patch-fzf-executable + (lambda* (#:key inputs #:allow-other-keys) + (emacs-substitute-variables "fzf.el" + ("fzf/executable" (search-input-file inputs "/bin/fzf")))))))) + (inputs (list fzf)) + (home-page "https://github.com/bling/fzf.el") + (synopsis "Emacs front-end for Fzf finder") + (description "This package provides an Emacs front-end for Fzf general +purpose finder.") + (license license:gpl3+)))) + (define-public emacs-minions (package (name "emacs-minions") From 326d485c296e7af20cde15d8b0825e7bf3ed4c2c Mon Sep 17 00:00:00 2001 From: Nicolas Goaziou Date: Tue, 20 Dec 2022 11:56:27 +0100 Subject: [PATCH 481/790] gnu: emacs-posframe: Update to 1.3.2. * gnu/packages/emacs-xyz.scm (emacs-posframe): Update to 1.3.2. --- gnu/packages/emacs-xyz.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/emacs-xyz.scm b/gnu/packages/emacs-xyz.scm index dca9bb5b95..efec88dc76 100644 --- a/gnu/packages/emacs-xyz.scm +++ b/gnu/packages/emacs-xyz.scm @@ -16523,14 +16523,14 @@ the center of the screen and not at the bottom.") (define-public emacs-posframe (package (name "emacs-posframe") - (version "1.3.1") + (version "1.3.2") (source (origin (method url-fetch) (uri (string-append "https://elpa.gnu.org/packages/" "posframe-" version ".tar")) (sha256 - (base32 "0j5nchfpbrf9fsr82lnvhnq6vi33gv3glsbqn18knnby8m7sxzci")))) + (base32 "05qkwb3ys05chn0maz7q19kp539m7p5acb8di4rni4vjjlkpx2bj")))) (build-system emacs-build-system) ;; emacs-minimal does not include the function font-info. (arguments From f5d53ac4ae5a2e45be05e25891a1507a313bcae8 Mon Sep 17 00:00:00 2001 From: Nicolas Goaziou Date: Tue, 20 Dec 2022 11:56:42 +0100 Subject: [PATCH 482/790] gnu: emacs-rec-mode: Update to 1.9.1. * gnu/packages/databases.scm (emacs-rec-mode): Update to 1.9.1. --- gnu/packages/databases.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/databases.scm b/gnu/packages/databases.scm index 387755b8ec..83515ad17e 100644 --- a/gnu/packages/databases.scm +++ b/gnu/packages/databases.scm @@ -1621,14 +1621,14 @@ types are supported, as is encryption.") (define-public emacs-rec-mode (package (name "emacs-rec-mode") - (version "1.9.0") + (version "1.9.1") (source (origin (method url-fetch) (uri (string-append "https://elpa.gnu.org/packages/" "rec-mode-" version ".tar")) (sha256 (base32 - "1w1q6kh567fd8xismq9i6wr1y893lypd30l452yvydi1qjiq1n6x")) + "0f60bw07l6kk1kkjjxsk30p6rxj9mpngaxqy8piyabnijfgjzd3s")) (snippet #~(begin (delete-file "rec-mode.info"))))) (build-system emacs-build-system) (arguments From 50024eeef103aa67ba5c9282a9731a3a9be8e6ac Mon Sep 17 00:00:00 2001 From: Nicolas Goaziou Date: Tue, 20 Dec 2022 11:56:47 +0100 Subject: [PATCH 483/790] gnu: emacs-vertico-posframe: Update to 0.6.0. * gnu/packages/emacs-xyz.scm (emacs-vertico-posframe): Update to 0.6.0. --- gnu/packages/emacs-xyz.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/emacs-xyz.scm b/gnu/packages/emacs-xyz.scm index efec88dc76..ae7522a07b 100644 --- a/gnu/packages/emacs-xyz.scm +++ b/gnu/packages/emacs-xyz.scm @@ -34681,7 +34681,7 @@ across sessions.") (define-public emacs-vertico-posframe (package (name "emacs-vertico-posframe") - (version "0.5.9") + (version "0.6.0") (source (origin (method url-fetch) (uri (string-append @@ -34689,7 +34689,7 @@ across sessions.") ".tar")) (sha256 (base32 - "1d1b8lfhr8zxa0dwsiqb1wzawx90l6lrr26jl17gpj85iyj3imq6")))) + "1cwi26jz9dn8la6zxxai2pfkcpz8lwf4cd8hr44lak6x0ca9bwr3")))) (build-system emacs-build-system) (propagated-inputs (list emacs-posframe emacs-vertico)) (home-page "https://github.com/tumashu/vertico-posframe") From 260743991f3388267a805f8c15877f75082de8fb Mon Sep 17 00:00:00 2001 From: Nicolas Goaziou Date: Tue, 20 Dec 2022 11:57:49 +0100 Subject: [PATCH 484/790] gnu: emacs-bfuture: Update to 1.0.2. * gnu/packages/emacs-xyz.scm (emacs-bfuture): Update to 1.0.2. --- gnu/packages/emacs-xyz.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/emacs-xyz.scm b/gnu/packages/emacs-xyz.scm index ae7522a07b..f40c767944 100644 --- a/gnu/packages/emacs-xyz.scm +++ b/gnu/packages/emacs-xyz.scm @@ -27119,7 +27119,7 @@ Debug server.") (define-public emacs-bfuture (package (name "emacs-bfuture") - (version "1.0.1") + (version "1.0.2") (source (origin (method git-fetch) @@ -27128,7 +27128,7 @@ Debug server.") (commit (string-append "v" version)))) (sha256 (base32 - "1m4v4xbsvg26z7nvg2c8q7x1nvv7v4ajm56l0nbkwcbdbrgahpva")) + "1qflkyr7fafw84mksxs25mka133y8ak8nsga3al29014pshbvzxn")) (file-name (git-file-name name version)))) (build-system emacs-build-system) (arguments From 69dade5bbfd870856557513f72ea36fecf7a6711 Mon Sep 17 00:00:00 2001 From: Nicolas Goaziou Date: Tue, 20 Dec 2022 11:58:54 +0100 Subject: [PATCH 485/790] gnu: emacs-citeproc-el: Update to 0.9.2. * gnu/packages/emacs-xyz.scm (emacs-citeproc-el): Update to 0.9.2. --- gnu/packages/emacs-xyz.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/emacs-xyz.scm b/gnu/packages/emacs-xyz.scm index f40c767944..aa95c90762 100644 --- a/gnu/packages/emacs-xyz.scm +++ b/gnu/packages/emacs-xyz.scm @@ -3613,7 +3613,7 @@ Its features are: (define-public emacs-citeproc-el (package (name "emacs-citeproc-el") - (version "0.9.1") + (version "0.9.2") (source (origin (method git-fetch) @@ -3622,7 +3622,7 @@ Its features are: (commit version))) (file-name (git-file-name name version)) (sha256 - (base32 "0rkwqn9pcimfcyq19wlrcij0kcjyhbwisla7vwbhjj8ang0bq9rm")))) + (base32 "0p9gch5iijia5pm9rzlv50xcad2g9mis9mc90nvh31in9xjcccpz")))) (build-system emacs-build-system) (arguments `(#:emacs ,emacs)) ;need libxml support From 1102b5de69d428b6a1495d18f5500932b244c84c Mon Sep 17 00:00:00 2001 From: Nicolas Goaziou Date: Tue, 20 Dec 2022 12:00:03 +0100 Subject: [PATCH 486/790] gnu: emacs-consult-notmuch: Update to 0.8.1. * gnu/packages/emacs-xyz.scm (emacs-consult-notmuch): Update to 0.8.1. --- gnu/packages/emacs-xyz.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/emacs-xyz.scm b/gnu/packages/emacs-xyz.scm index aa95c90762..cd2bc08352 100644 --- a/gnu/packages/emacs-xyz.scm +++ b/gnu/packages/emacs-xyz.scm @@ -10228,7 +10228,7 @@ replaced with the directory you choose.") (define-public emacs-consult-notmuch (package (name "emacs-consult-notmuch") - (version "0.8") + (version "0.8.1") (source (origin (method git-fetch) @@ -10237,7 +10237,7 @@ replaced with the directory you choose.") (commit version))) (file-name (git-file-name name version)) (sha256 - (base32 "18r47cj89qli534irah3lwwzsnik5bcf61clnrkhafqv9y51m67z")))) + (base32 "0gcd69i99prnskh1na7clydqgh1y9rbzkdc6dy9zmin9hfdrw1yd")))) (build-system emacs-build-system) (propagated-inputs (list emacs-consult emacs-notmuch)) From f4e4e82483a02a6158dd1979cc5fc9487a6446f5 Mon Sep 17 00:00:00 2001 From: Nicolas Goaziou Date: Tue, 20 Dec 2022 12:06:56 +0100 Subject: [PATCH 487/790] gnu: emacs-org-contrib: Update to 0.4.1. * gnu/packages/emacs-xyz.scm (emacs-org-contrib): Update to 0.4.1. --- gnu/packages/emacs-xyz.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/emacs-xyz.scm b/gnu/packages/emacs-xyz.scm index cd2bc08352..6313192978 100644 --- a/gnu/packages/emacs-xyz.scm +++ b/gnu/packages/emacs-xyz.scm @@ -14468,7 +14468,7 @@ programming and reproducible research.") (define-public emacs-org-contrib (package (name "emacs-org-contrib") - (version "0.4") + (version "0.4.1") (source (origin (method git-fetch) @@ -14477,7 +14477,7 @@ programming and reproducible research.") (commit (string-append "release_" version)))) (file-name (git-file-name name version)) (sha256 - (base32 "06b1rpywj596nnnap6pj6fnmcq8fcc4i30zv7qsvs3ryxciw01fb")))) + (base32 "0f3zjy3ybkqmvvlx04251add0vcz248qibxy5akal96l8bdhjajx")))) (build-system emacs-build-system) (arguments `(#:phases From 64ed2e8380eff18628c03a75a5fcdbb383e6f38a Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Mon, 19 Dec 2022 22:59:44 +0100 Subject: [PATCH 488/790] gnu: r-ancombc: Update to 2.0.2. * gnu/packages/bioconductor.scm (r-ancombc): Update to 2.0.2. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 29768dc7c2..11d5a3c0cb 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -2334,13 +2334,13 @@ analysis, modelling, and visualization of spike-in controls.") (define-public r-ancombc (package (name "r-ancombc") - (version "2.0.1") + (version "2.0.2") (source (origin (method url-fetch) (uri (bioconductor-uri "ANCOMBC" version)) (sha256 (base32 - "1bwzvi6j3s66dcll1lb4xy25j4nfn1ln6mc3flh0wgy13l26x8m6")))) + "0dlinv4vhxgni8ygzvfw8pbc6d1v9x5chhrpxblhs2c65bkgyxz5")))) (properties `((upstream-name . "ANCOMBC"))) (build-system r-build-system) (propagated-inputs From d7fda903543a0299f8f0b12522dc42d57e820eb2 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Mon, 19 Dec 2022 22:59:56 +0100 Subject: [PATCH 489/790] gnu: r-bambu: Update to 3.0.5. * gnu/packages/bioconductor.scm (r-bambu): Update to 3.0.5. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 11d5a3c0cb..41f8cd8cc4 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -3292,13 +3292,13 @@ Various visual and textual types of output are available.") (define-public r-bambu (package (name "r-bambu") - (version "3.0.2") + (version "3.0.5") (source (origin (method url-fetch) (uri (bioconductor-uri "bambu" version)) (sha256 (base32 - "0246cn5l1kxysjrzy4prfdxn71vc47a8kciqw384nm2mi3vsy4vx")))) + "12rcbspy4ly714cyxbgd5v2m92vasksxm19m6hd4avasrhcr4d6l")))) (properties `((upstream-name . "bambu"))) (build-system r-build-system) (propagated-inputs From 72f9c4312be3dde0e94153c4c388176a4c61cb9d Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Mon, 19 Dec 2022 22:59:56 +0100 Subject: [PATCH 490/790] gnu: r-bandits: Update to 1.14.1. * gnu/packages/bioconductor.scm (r-bandits): Update to 1.14.1. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 41f8cd8cc4..daa6eeab45 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -3335,13 +3335,13 @@ usage.") (define-public r-bandits (package (name "r-bandits") - (version "1.14.0") + (version "1.14.1") (source (origin (method url-fetch) (uri (bioconductor-uri "BANDITS" version)) (sha256 (base32 - "18xq8gg1j07gbbxy7r0cc34zwn40mh4fr39zzi8l3z0cymw73qs8")))) + "0dbiz7zgdl3bqrwf4ffb73sc2dd8ygh76fakx5887a14azj8pk8x")))) (properties `((upstream-name . "BANDITS"))) (build-system r-build-system) (propagated-inputs From d2666970d16cbbcc40f321ca827777831c381865 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Mon, 19 Dec 2022 22:59:56 +0100 Subject: [PATCH 491/790] gnu: r-damefinder: Update to 1.10.1. * gnu/packages/bioconductor.scm (r-damefinder): Update to 1.10.1. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index daa6eeab45..0f0a5bc57b 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -3600,13 +3600,13 @@ factorial microarray data.") (define-public r-damefinder (package (name "r-damefinder") - (version "1.10.0") + (version "1.10.1") (source (origin (method url-fetch) (uri (bioconductor-uri "DAMEfinder" version)) (sha256 (base32 - "0ygsgg51473sycsh367rf8plca6zb1jg2l39zcprwvgpiln8mjdg")))) + "1cgykb70mxnhilwwp1jr4dr523zvjxpix173s4ldfh49064gzwc1")))) (properties `((upstream-name . "DAMEfinder"))) (build-system r-build-system) (propagated-inputs From e757936b96ce519a0ad08c8c57945343b4692ec7 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Mon, 19 Dec 2022 22:59:56 +0100 Subject: [PATCH 492/790] gnu: r-deconvr: Update to 1.4.3. * gnu/packages/bioconductor.scm (r-deconvr): Update to 1.4.3. [propagated-inputs]: Add r-minfi. --- gnu/packages/bioconductor.scm | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 0f0a5bc57b..21986a70c0 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -3914,13 +3914,13 @@ negative control samples.") (define-public r-deconvr (package (name "r-deconvr") - (version "1.4.2") + (version "1.4.3") (source (origin (method url-fetch) (uri (bioconductor-uri "deconvR" version)) (sha256 (base32 - "1wa8l9zxdwx32122slnzqyk32klyznxnbziwn98jbp5fxmjka92l")))) + "1jz7q4rv3m85bcvarjhqsyc2330fynb0wr5ajd2qffznczk846xb")))) (properties `((upstream-name . "deconvR"))) (build-system r-build-system) (propagated-inputs @@ -3936,6 +3936,7 @@ negative control samples.") r-mass r-matrixstats r-methylkit + r-minfi r-nnls r-quadprog r-rsq From 74be5ec3e85ed02aaa4eeb22413c201961ad95c8 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Mon, 19 Dec 2022 22:59:57 +0100 Subject: [PATCH 493/790] gnu: r-biocparallel: Update to 1.32.4. * gnu/packages/bioconductor.scm (r-biocparallel): Update to 1.32.4. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 21986a70c0..51ccb1a6f1 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -4997,13 +4997,13 @@ only one command.") (define-public r-biocparallel (package (name "r-biocparallel") - (version "1.32.3") + (version "1.32.4") (source (origin (method url-fetch) (uri (bioconductor-uri "BiocParallel" version)) (sha256 (base32 - "0z2g3p6ip4g865na9bmqaa7w2s52769pmjr3hpiv6x8bhifh3nm5")))) + "1m4i27zx3ajwygwp38lrxf36rs575dkaxxc6jawpj1kzn7whi5ym")))) (properties `((upstream-name . "BiocParallel"))) (build-system r-build-system) From db6ae57157506b1396641c9f6360483ec226d54c Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Mon, 19 Dec 2022 22:59:57 +0100 Subject: [PATCH 494/790] gnu: r-deseq2: Update to 1.38.2. * gnu/packages/bioconductor.scm (r-deseq2): Update to 1.38.2. [propagated-inputs]: Remove r-genefilter; add r-matrixstats. --- gnu/packages/bioconductor.scm | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 51ccb1a6f1..f1e875633f 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -5364,26 +5364,26 @@ distribution.") (define-public r-deseq2 (package (name "r-deseq2") - (version "1.38.1") + (version "1.38.2") (source (origin (method url-fetch) (uri (bioconductor-uri "DESeq2" version)) (sha256 (base32 - "0xp3rfhwn8k1bqzqnjzjqlaq8lqyad7kqjhb29vkbxgzjvafvxmk")))) + "1m81yvcl63h5m7kbbxpjk7hzygxmn4l9mlgqrdmnnls56183h3b4")))) (properties `((upstream-name . "DESeq2"))) (build-system r-build-system) (propagated-inputs (list r-biobase r-biocgenerics r-biocparallel - r-genefilter r-geneplotter r-genomicranges r-ggplot2 r-iranges r-locfit + r-matrixstats r-rcpp r-rcpparmadillo r-s4vectors From 6af97fcc0eef7e8577b3d5ceafe7be2c7592bb6e Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Mon, 19 Dec 2022 22:59:57 +0100 Subject: [PATCH 495/790] gnu: r-edger: Update to 3.40.1. * gnu/packages/bioconductor.scm (r-edger): Update to 3.40.1. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index f1e875633f..9557cb736a 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -5596,13 +5596,13 @@ global-scaling and full-quantile normalization.") (define-public r-edger (package (name "r-edger") - (version "3.40.0") + (version "3.40.1") (source (origin (method url-fetch) (uri (bioconductor-uri "edgeR" version)) (sha256 (base32 - "18vap3qp9blncr4sdl9q1szb4qhm46gldhxy3k3abw9fckcvggwg")))) + "1a0rmczlqmqmip2ix28m4iwcpfj04p6nrcl562bjgaifvgyjqhzg")))) (properties `((upstream-name . "edgeR"))) (build-system r-build-system) (propagated-inputs From a71a89ac39f81ab8b6902f25ff12e9d1bb4fb7d2 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Mon, 19 Dec 2022 22:59:57 +0100 Subject: [PATCH 496/790] gnu: r-genefilter: Update to 1.80.2. * gnu/packages/bioconductor.scm (r-genefilter): Update to 1.80.2. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 9557cb736a..790eef98d7 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -5721,14 +5721,14 @@ analysis using other methods.") (define-public r-genefilter (package (name "r-genefilter") - (version "1.80.0") + (version "1.80.2") (source (origin (method url-fetch) (uri (bioconductor-uri "genefilter" version)) (sha256 (base32 - "0swdqdyz956gx44crbx3qai0qx7n7yazg3yw7i93djcgahyz3kk7")))) + "0f25z0hqmrkimv14j03pgjsxpq5rz9ymk151rlg4j4vpc06n73cq")))) (build-system r-build-system) (native-inputs (list gfortran r-knitr)) From 86fcb20aa839c069c553b3dcb5c2ca4f9be3ee24 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Mon, 19 Dec 2022 22:59:57 +0100 Subject: [PATCH 497/790] gnu: r-genomeinfodb: Update to 1.34.4. * gnu/packages/bioconductor.scm (r-genomeinfodb): Update to 1.34.4. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 790eef98d7..86b9dc0123 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -5811,13 +5811,13 @@ genomic intervals. In addition, it can use BAM or BigWig files as input.") (define-public r-genomeinfodb (package (name "r-genomeinfodb") - (version "1.34.3") + (version "1.34.4") (source (origin (method url-fetch) (uri (bioconductor-uri "GenomeInfoDb" version)) (sha256 (base32 - "1pw8ml6b33z7zh7h592xl23l8dy32nqq4lzq20p57n9f0krqj1iv")))) + "1nskqmlar85zg96c1fbacl7dqg6r0gl814rc7yh482y4wgmwyg0r")))) (properties `((upstream-name . "GenomeInfoDb"))) (build-system r-build-system) From a4362f4599fd8f7a0912b74830608d5c7f2d2604 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Mon, 19 Dec 2022 22:59:58 +0100 Subject: [PATCH 498/790] gnu: r-genomicfeatures: Update to 1.50.3. * gnu/packages/bioconductor.scm (r-genomicfeatures): Update to 1.50.3. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 86b9dc0123..1f648012bb 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -5871,13 +5871,13 @@ alignments.") (define-public r-genomicfeatures (package (name "r-genomicfeatures") - (version "1.50.2") + (version "1.50.3") (source (origin (method url-fetch) (uri (bioconductor-uri "GenomicFeatures" version)) (sha256 (base32 - "10w15j107hy9qb0lh6jmyw7rinfvy3ca34xsskxw3wf25mh6vhzz")))) + "14pn7lngayascj5k84g2g748assbivpiakss247cdj9ngzx5sfwz")))) (properties `((upstream-name . "GenomicFeatures"))) (build-system r-build-system) From b035f07cc2eaf5c5955a949862844fc74fbb6269 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Mon, 19 Dec 2022 22:59:58 +0100 Subject: [PATCH 499/790] gnu: r-genomicranges: Update to 1.50.2. * gnu/packages/bioconductor.scm (r-genomicranges): Update to 1.50.2. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 1f648012bb..97d36bac9d 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -5949,13 +5949,13 @@ provide added flexibility for data combination and manipulation.") (define-public r-genomicranges (package (name "r-genomicranges") - (version "1.50.1") + (version "1.50.2") (source (origin (method url-fetch) (uri (bioconductor-uri "GenomicRanges" version)) (sha256 (base32 - "14m4pvvd9m8kpc7k905km9vib7giq0i9g11bxc1ygw30ifi96966")))) + "13b6bm6nrxx1vgzrzpf59c2lq5w8kjq9hsch5h037f0p9w3w5z9p")))) (properties `((upstream-name . "GenomicRanges"))) (build-system r-build-system) From 53fb765c85601cd35b8d73f28d77536b3127ad62 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Mon, 19 Dec 2022 22:59:58 +0100 Subject: [PATCH 500/790] gnu: r-impute: Update to 1.72.2. * gnu/packages/bioconductor.scm (r-impute): Update to 1.72.2. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 97d36bac9d..91d62d4b30 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -6112,13 +6112,13 @@ of other R packages who wish to make use of HTSlib.") (define-public r-impute (package (name "r-impute") - (version "1.72.1") + (version "1.72.2") (source (origin (method url-fetch) (uri (bioconductor-uri "impute" version)) (sha256 (base32 - "0862mpbmznizcq5bgnp85dl9q0bip76jkga45gssdrv90wsi2192")))) + "1k697pqlkrwmfszipl9irbzmwhk1vz97j3rh0k5nj2mrj3dr71mv")))) (native-inputs (list gfortran)) (build-system r-build-system) From 5fc338637b08a4791b3bc84897c1d227c80011c7 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Mon, 19 Dec 2022 22:59:58 +0100 Subject: [PATCH 501/790] gnu: r-lfa: Update to 1.28.1. * gnu/packages/bioconductor.scm (r-lfa): Update to 1.28.1. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 91d62d4b30..a6e39f986a 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -6181,13 +6181,13 @@ Shiny-based display methods for Bioconductor objects.") (define-public r-lfa (package (name "r-lfa") - (version "1.28.0") + (version "1.28.1") (source (origin (method url-fetch) (uri (bioconductor-uri "lfa" version)) (sha256 - (base32 "1l3ip0bsvbz9nagzv47qjh5hf7qf8ffk4hlnkwagngiwyq84vyp1")))) + (base32 "0047wspvarbnbawrwvfjfz5y6i36l2r2k2501zjya09rjpiq101m")))) (properties `((upstream-name . "lfa"))) (build-system r-build-system) (propagated-inputs (list r-corpcor)) From dc6f9ab3ab3f64a26af7c99f86b5f7bc20f48957 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Mon, 19 Dec 2022 22:59:59 +0100 Subject: [PATCH 502/790] gnu: r-scmap: Update to 1.20.1. * gnu/packages/bioconductor.scm (r-scmap): Update to 1.20.1. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index a6e39f986a..24e166fd18 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -7314,13 +7314,13 @@ comprehensive scDblFinder method.") (define-public r-scmap (package (name "r-scmap") - (version "1.20.0") + (version "1.20.1") (source (origin (method url-fetch) (uri (bioconductor-uri "scmap" version)) (sha256 - (base32 "14vyjvfs2n4h0xsy25xg4zdmc8dqbg5vyl3qns6f0rh4bsshqdlm")))) + (base32 "0rq185ynk874vgw4a5s2n92381dj6kxxnx2fcx2v7b2ahr3ybys7")))) (properties `((upstream-name . "scmap"))) (build-system r-build-system) (propagated-inputs From 9e18e3a372d738f9cc7722613db1e876dbfe9e4a Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Mon, 19 Dec 2022 22:59:59 +0100 Subject: [PATCH 503/790] gnu: r-tximport: Update to 1.26.1. * gnu/packages/bioconductor.scm (r-tximport): Update to 1.26.1. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 24e166fd18..90df6bac1e 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -7861,13 +7861,13 @@ dependencies between GO terms can be implemented and applied.") (define-public r-tximport (package (name "r-tximport") - (version "1.26.0") + (version "1.26.1") (source (origin (method url-fetch) (uri (bioconductor-uri "tximport" version)) (sha256 (base32 - "1w1m6r85a5nvcfxbkq5dmczaar8vf3vbrgrmxqkjqhlpcq58z5ng")))) + "1r67q4nb2bx9nqycyr2gnfmh4gizl0c7l510vmlcdvplv3yi73yn")))) (build-system r-build-system) (native-inputs (list r-knitr)) From a13f5a52d05ec94ed0d788ec586ad979276fa34e Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Mon, 19 Dec 2022 22:59:59 +0100 Subject: [PATCH 504/790] gnu: r-oligo: Update to 1.62.1. * gnu/packages/bioconductor.scm (r-oligo): Update to 1.62.1. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 90df6bac1e..8a38836afe 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -8234,14 +8234,14 @@ packages.") (define-public r-oligo (package (name "r-oligo") - (version "1.62.0") + (version "1.62.1") (source (origin (method url-fetch) (uri (bioconductor-uri "oligo" version)) (sha256 (base32 - "0l6yb58frh4c080k6h8wyipc5kiz4qi7jimnr62jg8d737rrvnk2")))) + "1rhzav57d092ip9qjsmskj3l8h4xyq8cpa2a2jl8g32fwh0dyvsz")))) (properties `((upstream-name . "oligo"))) (build-system r-build-system) (inputs (list zlib)) From c47fd0c47c3dbe523af9bdf109d3ea47d24dd53c Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Mon, 19 Dec 2022 22:59:59 +0100 Subject: [PATCH 505/790] gnu: r-diffbind: Update to 3.8.3. * gnu/packages/bioconductor.scm (r-diffbind): Update to 3.8.3. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 8a38836afe..81241f85de 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -8379,14 +8379,14 @@ signal in the input, that lead to spurious peaks during peak calling.") (define-public r-diffbind (package (name "r-diffbind") - (version "3.8.1") + (version "3.8.3") (source (origin (method url-fetch) (uri (bioconductor-uri "DiffBind" version)) (sha256 (base32 - "1wgnrd1xpl49pdxxjzzl0v9535naapwp3ayqzvrx3z4m6iai2awj")))) + "039gy9ll6ingh3y5h2hp3rhbh2imaryjxzgf8ysk87irlbpnx1qs")))) (properties `((upstream-name . "DiffBind"))) (build-system r-build-system) (propagated-inputs From 96508fa43aa5f122a84c5b8ed1f41fabceada197 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Mon, 19 Dec 2022 23:00:00 +0100 Subject: [PATCH 506/790] gnu: r-glmgampoi: Update to 1.10.1. * gnu/packages/bioconductor.scm (r-glmgampoi): Update to 1.10.1. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 81241f85de..19379d95b9 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -9097,13 +9097,13 @@ information.") (define-public r-glmgampoi (package (name "r-glmgampoi") - (version "1.10.0") + (version "1.10.1") (source (origin (method url-fetch) (uri (bioconductor-uri "glmGamPoi" version)) (sha256 (base32 - "12jbqigg4k2ngrk2anbrrxrwkp57bbzdz492lg8lc6w1gygp5yip")))) + "1qxzbh5i208cpghmysailachj8xpx4g4iqk8552xjpjkn54pkpbd")))) (properties `((upstream-name . "glmGamPoi"))) (build-system r-build-system) (propagated-inputs From b51001141bd36d939bcd60ac9f6b1bc459562545 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Mon, 19 Dec 2022 23:00:00 +0100 Subject: [PATCH 507/790] gnu: r-dnacopy: Update to 1.72.2. * gnu/packages/bioconductor.scm (r-dnacopy): Update to 1.72.2. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 19379d95b9..397fb788a0 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -9624,14 +9624,14 @@ penalized least squares regression method.") (define-public r-dnacopy (package (name "r-dnacopy") - (version "1.72.0") + (version "1.72.2") (source (origin (method url-fetch) (uri (bioconductor-uri "DNAcopy" version)) (sha256 (base32 - "0z2hl68f5f6d2w6gbhax4531g3zbgiihj99h32sa44hp29al38ld")))) + "1f6ilfwhli7bdnr48y2ijdydvw7kjbyz701kgbsw3w7inr6x6ayr")))) (properties `((upstream-name . "DNAcopy"))) (build-system r-build-system) (native-inputs (list gfortran)) From 2eb81c0888a3784658e7d7cfe4426994863280a5 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Mon, 19 Dec 2022 23:00:00 +0100 Subject: [PATCH 508/790] gnu: r-lpsymphony: Update to 1.26.2. * gnu/packages/bioconductor.scm (r-lpsymphony): Update to 1.26.2. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 397fb788a0..8afed238c5 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -9782,14 +9782,14 @@ coordinates.") (define-public r-lpsymphony (package (name "r-lpsymphony") - (version "1.26.0") + (version "1.26.2") (source (origin (method url-fetch) (uri (bioconductor-uri "lpsymphony" version)) (sha256 (base32 - "0ryl48zxscb35s1gizyspxg48dlqg1j51h9iw2flq16y7y63ppzi")))) + "167zpf7k7gn7gw2cxkqx89y322qinyzjr1naracp5axj4q2qagm3")))) (build-system r-build-system) (arguments (list From ceffbc313fa945be32fe5702227b93a497657f9c Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Mon, 19 Dec 2022 23:00:00 +0100 Subject: [PATCH 509/790] gnu: r-linnorm: Update to 2.22.1. * gnu/packages/bioconductor.scm (r-linnorm): Update to 2.22.1. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 8afed238c5..2da844b822 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -10671,14 +10671,14 @@ especially Illumina Infinium methylation microarrays.") (define-public r-linnorm (package (name "r-linnorm") - (version "2.22.0") + (version "2.22.1") (source (origin (method url-fetch) (uri (bioconductor-uri "Linnorm" version)) (sha256 (base32 - "0ndhvdd9gkqyayxqgj5320sgj15di7ji945lpdi3rj5lwldh7na0")))) + "16d7viyidqbsy3mbr2cpq9p291yf362a4blhvs05qxcwm3fjllij")))) (properties `((upstream-name . "Linnorm"))) (build-system r-build-system) (propagated-inputs From 72053845339db0237107c18ee3d85aa68aadf49c Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Mon, 19 Dec 2022 23:00:01 +0100 Subject: [PATCH 510/790] gnu: r-sigpathway: Update to 1.66.1. * gnu/packages/bioconductor.scm (r-sigpathway): Update to 1.66.1. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 2da844b822..ac9d49db73 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -11019,14 +11019,14 @@ the data set is suitable for such analysis.") (define-public r-sigpathway (package (name "r-sigpathway") - (version "1.66.0") + (version "1.66.1") (source (origin (method url-fetch) (uri (bioconductor-uri "sigPathway" version)) (sha256 (base32 - "0vb6v61ak8z3hx7d65lr1hrxk89n36j0zi3x0pp828khdyh3zvag")))) + "1ln1n4zwmjw1ils45vix93q3h19xlg4q894yhhxkphgyj0qcy00b")))) (properties `((upstream-name . "sigPathway"))) (build-system r-build-system) (home-page "https://www.pnas.org/cgi/doi/10.1073/pnas.0506577102") From 2e10df101f76154b6d5a64f9c295c2402b01ad18 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Mon, 19 Dec 2022 23:00:01 +0100 Subject: [PATCH 511/790] gnu: r-enrichplot: Update to 1.18.3. * gnu/packages/bioconductor.scm (r-enrichplot): Update to 1.18.3. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index ac9d49db73..b1c5b7db3c 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -11141,14 +11141,14 @@ data.") (define-public r-enrichplot (package (name "r-enrichplot") - (version "1.18.1") + (version "1.18.3") (source (origin (method url-fetch) (uri (bioconductor-uri "enrichplot" version)) (sha256 (base32 - "1x84wlkqisq1x2zniy4mp02zlsp4v85kxbflalmq0pixlkagq0vr")))) + "0nzcr23m58z3h0n0frxf26z14j7ilcl4fjy7rqm7f2i1wyld70zl")))) (build-system r-build-system) (propagated-inputs (list r-aplot From da24c1c9495ba414d786cf69c6c73009ce2a4756 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Mon, 19 Dec 2022 23:00:01 +0100 Subject: [PATCH 512/790] gnu: r-clusterexperiment: Update to 2.18.1. * gnu/packages/bioconductor.scm (r-clusterexperiment): Update to 2.18.1. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index b1c5b7db3c..457e988b80 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -11219,13 +11219,13 @@ profiles (GO and KEGG) of gene and gene clusters.") (define-public r-clusterexperiment (package (name "r-clusterexperiment") - (version "2.18.0") + (version "2.18.1") (source (origin (method url-fetch) (uri (bioconductor-uri "clusterExperiment" version)) (sha256 (base32 - "04kdiwz8qzr7cr1an1c7a684wqv9pkca0iaym5f069pdjhqvvq0a")))) + "1f3f56d88yiqyj45rhcwqb04wbxr9m4fxhbbckw1j7nykm8100ps")))) (build-system r-build-system) (native-inputs (list r-knitr)) From 7f45db2df8b6ad47a4da0ef9f6a25bb4d887213d Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Mon, 19 Dec 2022 23:00:01 +0100 Subject: [PATCH 513/790] gnu: r-aucell: Update to 1.20.2. * gnu/packages/bioconductor.scm (r-aucell): Update to 1.20.2. [propagated-inputs]: Add r-matrix. --- gnu/packages/bioconductor.scm | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 457e988b80..050650de87 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -11988,14 +11988,14 @@ investigation using RNA-seq data.") (define-public r-aucell (package (name "r-aucell") - (version "1.20.1") + (version "1.20.2") (source (origin (method url-fetch) (uri (bioconductor-uri "AUCell" version)) (sha256 (base32 - "0bq729kavqkam2s4dmfzixgznsys61j0lvj5pk3b70gxv44gmpsh")))) + "1qb13qd5xzgrpx6jlg3ll0ff5spz3y06ji31vvqzm759almg2w3s")))) (properties `((upstream-name . "AUCell"))) (build-system r-build-system) (propagated-inputs @@ -12004,6 +12004,7 @@ investigation using RNA-seq data.") r-delayedarray r-delayedmatrixstats r-gseabase + r-matrix r-mixtools r-r-utils r-shiny From 90b10b37e8ef9cd9b1409be74bd0d45d9b3cc1ab Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Mon, 19 Dec 2022 23:00:01 +0100 Subject: [PATCH 514/790] gnu: r-iclusterplus: Update to 1.34.2. * gnu/packages/bioconductor.scm (r-iclusterplus): Update to 1.34.2. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 050650de87..5b684a4e64 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -12825,14 +12825,14 @@ and data files used across sessions.") (define-public r-iclusterplus (package (name "r-iclusterplus") - (version "1.34.0") + (version "1.34.2") (source (origin (method url-fetch) (uri (bioconductor-uri "iClusterPlus" version)) (sha256 (base32 - "01bl1gmc1v1b4lh88sdazjvm8pl7383dgzxnhmzpxwz7lkcxi1h2")))) + "05y4jmbf8sxl32f3g5lw9ycxky0rw69gax3n2z0kif7xcb5qf3qv")))) (properties `((upstream-name . "iClusterPlus"))) (build-system r-build-system) (native-inputs (list gfortran)) From 5ac36a82e86a179c4b851cac1045fa2bdac3dc02 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Mon, 19 Dec 2022 23:00:02 +0100 Subject: [PATCH 515/790] gnu: r-rsubread: Update to 2.12.2. * gnu/packages/bioconductor.scm (r-rsubread): Update to 2.12.2. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 5b684a4e64..db3faf7efe 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -13265,14 +13265,14 @@ annotations.") (define-public r-rsubread (package (name "r-rsubread") - (version "2.12.0") + (version "2.12.2") (source (origin (method url-fetch) (uri (bioconductor-uri "Rsubread" version)) (sha256 (base32 - "0iha7xln7l3mrmka8rcmmlp74f5km9rc88k9nv6bxw0krr03089n")))) + "1gvd8vmglvzc3bixqxrm4k7yikl2as5l4x6bvvvnwsgx2i7vz7dm")))) (properties `((upstream-name . "Rsubread"))) (build-system r-build-system) (inputs (list zlib)) From 7edcbf84bf2fae8e1d58d086f645fb7c21fb65aa Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Mon, 19 Dec 2022 23:00:02 +0100 Subject: [PATCH 516/790] gnu: r-ggcyto: Update to 1.26.4. * gnu/packages/bioconductor.scm (r-ggcyto): Update to 1.26.4. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index db3faf7efe..761a878cdb 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -13498,14 +13498,14 @@ manipulation of flow cytometry data.") (define-public r-ggcyto (package (name "r-ggcyto") - (version "1.26.0") + (version "1.26.4") (source (origin (method url-fetch) (uri (bioconductor-uri "ggcyto" version)) (sha256 (base32 - "0phhm54wcqihj62a0jk46whmf6wwg7wj3306wvnszy7yik4z857w")))) + "1pj1v0bhvckvwn1p826phskqz9lv71c1913cz5w0fd87dzdbpzpj")))) (properties `((upstream-name . "ggcyto"))) (build-system r-build-system) (propagated-inputs From 031dbcbd0e32208574b770700a35fef2138a5719 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Mon, 19 Dec 2022 23:00:02 +0100 Subject: [PATCH 517/790] gnu: r-opencyto: Update to 2.10.1. * gnu/packages/bioconductor.scm (r-opencyto): Update to 2.10.1. [propagated-inputs]: Remove r-clue, r-flowstats, r-gtools, r-ks, r-lattice, r-mass, r-plyr, r-r-utils, r-rcpp, and r-rrcov; add r-bh and r-cpp11. --- gnu/packages/bioconductor.scm | 20 ++++++-------------- 1 file changed, 6 insertions(+), 14 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 761a878cdb..90ae32877a 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -13721,38 +13721,30 @@ package.") (define-public r-opencyto (package (name "r-opencyto") - (version "2.10.0") + (version "2.10.1") (source (origin (method url-fetch) (uri (bioconductor-uri "openCyto" version)) (sha256 (base32 - "1pkpm98fs17zqdvyymd58sl4cib7gdi7drvdkagilrafjcrpq31m")))) + "16wsa9dhnz8gz1siyhfxvnbfg142g7fmhxiqxr7n69qpq9w8yhr0")))) (properties `((upstream-name . "openCyto"))) (build-system r-build-system) (propagated-inputs - (list r-biobase + (list r-bh + r-biobase r-biocgenerics - r-clue + r-cpp11 r-data-table r-flowclust r-flowcore - r-flowstats r-flowviz r-flowworkspace r-graph - r-gtools - r-ks - r-lattice - r-mass r-ncdfflow - r-plyr - r-r-utils r-rbgl - r-rcolorbrewer - r-rcpp - r-rrcov)) + r-rcolorbrewer)) (native-inputs (list r-knitr)) (home-page "https://bioconductor.org/packages/openCyto") From fc617e70e655470101b6c599cc0be11b5b672e00 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Mon, 19 Dec 2022 23:00:02 +0100 Subject: [PATCH 518/790] gnu: r-rcistarget: Update to 1.18.2. * gnu/packages/bioconductor.scm (r-rcistarget): Update to 1.18.2. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 90ae32877a..679b6dc183 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -13944,14 +13944,14 @@ data, to only emphasize the data that actually matters.") (define-public r-rcistarget (package (name "r-rcistarget") - (version "1.17.0") + (version "1.18.2") (source (origin (method url-fetch) (uri (bioconductor-uri "RcisTarget" version)) (sha256 (base32 - "1anwin5476q2n0zgywrmp3nj6sgy07i6pw1lczydvn4h1a8n1rvk")))) + "02lz2m2zhwy1dvmjvlss6qg0dh574qhnvn7al3wx7ck1hkz0dgi2")))) (properties `((upstream-name . "RcisTarget"))) (build-system r-build-system) (propagated-inputs From 18468f775e49a32df89a39f9a808d5c1880d8364 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Mon, 19 Dec 2022 23:00:03 +0100 Subject: [PATCH 519/790] gnu: r-biocviews: Update to 1.66.1. * gnu/packages/bioconductor.scm (r-biocviews): Update to 1.66.1. [native-inputs]: Add r-knitr. --- gnu/packages/bioconductor.scm | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 679b6dc183..730e3b417f 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -15614,13 +15614,13 @@ functionality.") (define-public r-biocviews (package (name "r-biocviews") - (version "1.66.0") + (version "1.66.1") (source (origin (method url-fetch) (uri (bioconductor-uri "biocViews" version)) (sha256 (base32 - "1rgn0agw5m4y8838lxzq1r658h1pblaidmm444yfimjffa8znj23")))) + "1xplkzm29v6aysfhb6kf2nnmvc37jmcvv6vsgbx8z8qccn96jk02")))) (properties `((upstream-name . "biocViews"))) (build-system r-build-system) @@ -15632,6 +15632,7 @@ functionality.") r-rcurl r-xml r-runit)) + (native-inputs (list r-knitr)) (home-page "https://bioconductor.org/packages/biocViews") (synopsis "Bioconductor package categorization helper") (description "The purpose of biocViews is to create HTML pages that From e895da0406bb5053cdc85b374938b091f7db79df Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Mon, 19 Dec 2022 23:00:03 +0100 Subject: [PATCH 520/790] gnu: r-preprocesscore: Update to 1.60.1. * gnu/packages/bioconductor.scm (r-preprocesscore): Update to 1.60.1. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 730e3b417f..764af84960 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -16201,14 +16201,14 @@ generated.") (define-public r-preprocesscore (package (name "r-preprocesscore") - (version "1.60.0") + (version "1.60.1") (source (origin (method url-fetch) (uri (bioconductor-uri "preprocessCore" version)) (sha256 (base32 - "1l0m591scln024jdpib47fndhx2wfp9jgkj3mdmwd9nkc5y0qjda")))) + "1rwr31jp4dh3xcfx1kx8rz5xvyx1mrwy85hqrjrfr4m6h0qv28k1")))) (properties `((upstream-name . "preprocessCore"))) (build-system r-build-system) From 68701917b8c8458cff6e41e78ebcea5d45b9875e Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Mon, 19 Dec 2022 23:00:03 +0100 Subject: [PATCH 521/790] gnu: r-s4vectors: Update to 0.36.1. * gnu/packages/bioconductor.scm (r-s4vectors): Update to 0.36.1. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 764af84960..7af0634daa 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -16222,13 +16222,13 @@ routines.") (define-public r-s4vectors (package (name "r-s4vectors") - (version "0.36.0") + (version "0.36.1") (source (origin (method url-fetch) (uri (bioconductor-uri "S4Vectors" version)) (sha256 (base32 - "05al4diwdbsa9b37i8msxnp79fxk7k24dk2vhh131s3snb89jvfs")))) + "16lssnmhy3klqp4sw1328f38cixkjh9317gdyikcrmsbcwg2ak6v")))) (properties `((upstream-name . "S4Vectors"))) (build-system r-build-system) From c4cbfa40d8d9b3619b987a360322ee105c78f76e Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Mon, 19 Dec 2022 23:00:03 +0100 Subject: [PATCH 522/790] gnu: r-chromvar: Update to 1.20.1. * gnu/packages/bioconductor.scm (r-chromvar): Update to 1.20.1. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 7af0634daa..34e11fc28f 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -16712,13 +16712,13 @@ This package wraps C++ code from the MOODS motif calling library.") (define-public r-chromvar (package (name "r-chromvar") - (version "1.20.0") + (version "1.20.1") (source (origin (method url-fetch) (uri (bioconductor-uri "chromVAR" version)) (sha256 - (base32 "1rwgbicbmszdkr05ksxfsisyhk0a4pvc3jrxbzjyc13jj5h6m5kp")))) + (base32 "1nhhpqhpvmw6b0nwxdwsjnakmfpxzpii8fmabwwg9bk8ni3zj5dq")))) (properties `((upstream-name . "chromVAR"))) (build-system r-build-system) (propagated-inputs From 71c115fd943fc20de6112904a523c3c72993c08d Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Mon, 19 Dec 2022 23:00:04 +0100 Subject: [PATCH 523/790] gnu: r-scuttle: Update to 1.8.3. * gnu/packages/bioconductor.scm (r-scuttle): Update to 1.8.3. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 34e11fc28f..b55f11a741 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -16819,14 +16819,14 @@ cell types to infer the cell of origin of each single cell independently.") (define-public r-scuttle (package (name "r-scuttle") - (version "1.8.1") + (version "1.8.3") (source (origin (method url-fetch) (uri (bioconductor-uri "scuttle" version)) (sha256 (base32 - "10wk46zgi57m9q9ab6wlmljcss3fph2r9yp1bp01s9yv7sd749b2")))) + "1wgh28rj8m5dz89s9y4rzfy68d8ign6pcnnwj9g7h4sc3jfsg56i")))) (properties `((upstream-name . "scuttle"))) (build-system r-build-system) (propagated-inputs From cfa8d448bcc1c4aa83b61797ed45e4560894356f Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Mon, 19 Dec 2022 23:00:04 +0100 Subject: [PATCH 524/790] gnu: r-scran: Update to 1.26.1. * gnu/packages/bioconductor.scm (r-scran): Update to 1.26.1. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index b55f11a741..c1e6c4c002 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -16899,14 +16899,14 @@ quality control.") (define-public r-scran (package (name "r-scran") - (version "1.26.0") + (version "1.26.1") (source (origin (method url-fetch) (uri (bioconductor-uri "scran" version)) (sha256 (base32 - "11iwpw44600pfx01vqil97k728m1wf4dljr27k2ak4s7z75kxfih")))) + "1sqc8pf1qzm24kf1l45da12wbzv0nxsy6l3v9fc8srmnvk37p04p")))) (build-system r-build-system) (propagated-inputs (list r-beachmat From fd4ca4a2661cba23e7ee688628a1a4a0ee1d943f Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Mon, 19 Dec 2022 23:00:04 +0100 Subject: [PATCH 525/790] gnu: r-kegggraph: Update to 1.58.3. * gnu/packages/bioconductor.scm (r-kegggraph): Update to 1.58.3. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index c1e6c4c002..53c7d048c9 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -17501,13 +17501,13 @@ EMBL-EBI GWAS catalog.") (define-public r-kegggraph (package (name "r-kegggraph") - (version "1.58.0") + (version "1.58.3") (source (origin (method url-fetch) (uri (bioconductor-uri "KEGGgraph" version)) (sha256 - (base32 "0hpsb009qmhy9p67d5wd0cl60smhgjlhxsz5f52i1c6qy4jk1niq")))) + (base32 "1s5j7zdp8ck4vhca81i4b6qclhwi56gmz8brawrxj3szvwmxf3y6")))) (properties `((upstream-name . "KEGGgraph"))) (build-system r-build-system) (propagated-inputs From 4651d380b4737e66ae328a44c15f3ae1c70c29cb Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Tue, 20 Dec 2022 11:13:15 +0100 Subject: [PATCH 526/790] gnu: p2c: Update to 2.02. * gnu/packages/pascal.scm (p2c): Update to 2.02. [arguments]: Use gexp. [native-inputs]: Add unzip. --- gnu/packages/pascal.scm | 58 ++++++++++++++++++++--------------------- 1 file changed, 28 insertions(+), 30 deletions(-) diff --git a/gnu/packages/pascal.scm b/gnu/packages/pascal.scm index 8c193830fd..f563f077dc 100644 --- a/gnu/packages/pascal.scm +++ b/gnu/packages/pascal.scm @@ -3,6 +3,7 @@ ;;; Copyright © 2017 Kei Kebreau ;;; Copyright © 2020 Eric Bavier ;;; Copyright © 2021 Maxim Cournoyer +;;; Copyright © 2022 Ricardo Wurmus ;;; ;;; This file is part of GNU Guix. ;;; @@ -23,6 +24,7 @@ #:use-module ((guix licenses) #:prefix license:) #:use-module (guix packages) #:use-module (guix download) + #:use-module (guix gexp) #:use-module (guix utils) #:use-module (guix build-system gnu) #:use-module (gnu packages) @@ -229,43 +231,39 @@ many useful extensions to the Pascal programming language.") (define-public p2c (package (name "p2c") - (version "2.01") + (version "2.02") (source (origin (method url-fetch) - (uri (string-append "https://alum.mit.edu/www/toms/p2c/p2c-" - version ".tar.gz")) + (uri (string-append "http://users.fred.net/tds/lab/p2c/p2c-" + version ".zip")) (sha256 (base32 - "03x72lv6jrvikbrpz4kfq1xp61l2jw5ki6capib71lxs65zndajn")))) + "17q6s0vbz298pks80bxf4r6gm8kwbrml1q3vfs6g6yj75sqj58xs")))) (build-system gnu-build-system) (arguments - `(#:make-flags - (let ((out (assoc-ref %outputs "out"))) - (list (string-append "CC=" ,(cc-for-target)) - (string-append "HOMEDIR=" out "/lib/p2c") - (string-append "INCDIR=" out "/include/p2c") - (string-append "BINDIR=" out "/bin") - (string-append "LIBDIR=" out "/lib") - (string-append "MANDIR=" out "/share/man/man1") - "MANFILE=p2c.man.inst")) - #:test-target "test" - #:phases - (modify-phases %standard-phases - (delete 'configure) - (add-before 'build 'mkdir - (lambda* (#:key outputs #:allow-other-keys) - (let ((out (assoc-ref outputs "out"))) - (mkdir-p (string-append out "/share/man")) - (mkdir-p (string-append out "/lib")) - (mkdir-p (string-append out "/bin")) - (mkdir-p (string-append out "/include"))) - #t)) - (add-before 'build 'chdir - (lambda* (#:key make-flags #:allow-other-keys) - (chdir "src") - #t))))) + (list + #:make-flags + #~(list (string-append "CC=" #$(cc-for-target)) + (string-append "HOMEDIR=" #$output "/lib/p2c") + (string-append "INCDIR=" #$output "/include/p2c") + (string-append "BINDIR=" #$output "/bin") + (string-append "LIBDIR=" #$output "/lib") + (string-append "MANDIR=" #$output "/share/man/man1") + "MANFILE=p2c.man.inst") + #:test-target "test" + #:phases + #~(modify-phases %standard-phases + (delete 'configure) + (add-before 'build 'mkdir + (lambda _ + (mkdir-p (string-append #$output "/share/man")) + (mkdir-p (string-append #$output "/lib")) + (mkdir-p (string-append #$output "/bin")) + (mkdir-p (string-append #$output "/include")))) + (add-before 'build 'chdir + (lambda _ (chdir "src")))))) (native-inputs - (list perl which)) + (list perl unzip which)) (synopsis "p2c converts Pascal programs to C programs") (description "This package provides @command{p2c}, a program to convert Pascal source code to C source code, and @command{p2cc}, a compiler for From e2b8cdde37eec971cd3fa1ca5fc97160de56fbd3 Mon Sep 17 00:00:00 2001 From: Nicolas Goaziou Date: Tue, 20 Dec 2022 15:26:01 +0100 Subject: [PATCH 527/790] gnu: emacs-fzf: Fix version. * gnu/packages/emacs-xyz.scm (emacs-fzf)[version]: Set to 0.2. Last tagged version and Version keyword from main file differ. We use the highest one (the tag). --- gnu/packages/emacs-xyz.scm | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/gnu/packages/emacs-xyz.scm b/gnu/packages/emacs-xyz.scm index 6313192978..6e1d05dceb 100644 --- a/gnu/packages/emacs-xyz.scm +++ b/gnu/packages/emacs-xyz.scm @@ -1288,7 +1288,7 @@ leveraging built-in functionality.") (revision "0")) (package (name "emacs-fzf") - (version (git-version "0.0.2" revision commit)) + (version (git-version "0.2" revision commit)) (source (origin (method git-fetch) (uri (git-reference From 040c43d78a3514773925ed3a3bcd70aca8c21cab Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Tue, 20 Dec 2022 14:22:40 +0100 Subject: [PATCH 528/790] gnu: Add edk2-tools. * gnu/packages/firmware.scm (edk2-tools): New variable. --- gnu/packages/firmware.scm | 64 +++++++++++++++++++++++++++++++++++++++ 1 file changed, 64 insertions(+) diff --git a/gnu/packages/firmware.scm b/gnu/packages/firmware.scm index 8c8949a5da..8972b84f51 100644 --- a/gnu/packages/firmware.scm +++ b/gnu/packages/firmware.scm @@ -530,6 +530,70 @@ coreboot.") ;; cpl with a linking exception. license:cpl1.0)))) +(define-public edk2-tools + (package + (name "edk2-tools") + (version "202211") + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/tianocore/edk2") + (commit (string-append "edk2-stable" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "1264542mm0mffjcmw5sw34h94n405swz5z56rw1ragp3j62144iy")))) + (build-system gnu-build-system) + (arguments + (list #:make-flags + #~(list (string-append "BUILD_CC=" #$(cc-for-target))) + #:test-target "Tests" + #:phases + #~(modify-phases %standard-phases + (add-after 'unpack 'change-directory + (lambda _ + (chdir "BaseTools"))) + (add-after 'change-directory 'disable-some-tools + (lambda _ + ;; Disable building brotli and xz, since we package them + ;; separately, and it would require fetching submodules. + (substitute* "Source/C/GNUmakefile" + (("^[[:blank:]]+BrotliCompress[[:blank:]]+\\\\") + "\\") + (("^[[:blank:]]+LzmaCompress[[:blank:]]+\\\\") + "\\")))) + (replace 'build + (lambda* (#:key (make-flags #~'()) #:allow-other-keys) + ;; The default build target also runs tests. + (apply invoke "make" "-C" "Source/C" make-flags))) + (delete 'configure) + (replace 'install + (lambda _ + (mkdir #$output) + (copy-recursively "Source/C/bin" + (string-append #$output "/bin"))))))) + (native-inputs + (list python-wrapper)) + (inputs + (list `(,util-linux "lib"))) ;for libuuid + (home-page + "https://github.com/tianocore/tianocore.github.io/wiki/EDK-II-Tools-List") + (synopsis "EFI development tools") + (description + "This package contains tools for processing UEFI firmware content. +Executables included are: + +@itemize +@item @code{EfiRom}: Build Option ROM images. +@item @code{GenFfs}: Generate FFS files. +@item @code{GenFv}: Generate a PI firmware volume image. +@item @code{GenFw}: Get image data from PE32 files. +@item @code{GenSec}: Generate EFI_SECTION type files. +@item @code{VfrCompile}: Parse preprocessed UEFI and Framework VFR files. +@item @code{VolInfo}: Display the contents of a firmware volume. +@end itemize") + (license license:bsd-2))) + (define-public ovmf (let ((commit "13a50a6fe1dcfa6600c38456ee24e0f9ecf51b5f") (revision "1")) From 2f2a9aca4b4e5199b1196bbee0ba81237d09f4be Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Tue, 20 Dec 2022 15:24:25 +0100 Subject: [PATCH 529/790] gnu: Add ipxe-qemu. * gnu/packages/bootloaders.scm (ipxe-qemu): New variable. --- gnu/packages/bootloaders.scm | 58 +++++++++++++++++++++++++++++++++++- 1 file changed, 57 insertions(+), 1 deletion(-) diff --git a/gnu/packages/bootloaders.scm b/gnu/packages/bootloaders.scm index 3c96453e5c..b968ecd441 100644 --- a/gnu/packages/bootloaders.scm +++ b/gnu/packages/bootloaders.scm @@ -3,7 +3,7 @@ ;;; Copyright © 2015, 2018 Mark H Weaver ;;; Copyright © 2015 Leo Famulari ;;; Copyright © 2016, 2020 Jan (janneke) Nieuwenhuizen -;;; Copyright © 2016, 2017, 2018, 2021 Marius Bakke +;;; Copyright © 2016-2018, 2021-2022 Marius Bakke ;;; Copyright © 2016, 2017 Danny Milosavljevic ;;; Copyright © 2016, 2017 David Craven ;;; Copyright © 2017, 2018, 2020, 2021, 2022 Efraim Flashner @@ -1532,3 +1532,59 @@ existing PXE ROM on your network card, or you can chainload into iPXE to obtain the features of iPXE without the hassle of reflashing.") (license license:gpl2+)))) +(define-public ipxe-qemu + (package/inherit ipxe + (name "ipxe-qemu") + (native-inputs + (modify-inputs (package-native-inputs ipxe) + (prepend edk2-tools))) + (arguments + (let ((roms + ;; Alist of ROM -> (VID . DID) entries. This list and below + ;; build steps are taken from QEMUs roms/Makefile. + '(("e1000" . ("8086" . "100e")) + ("e1000e" . ("8086" . "10d3")) + ("eepro100" . ("8086" . "1209")) + ("ne2k_pci" . ("1050" . "0940")) + ("pcnet" . ("1022" . "2000")) + ("rtl8139" . ("10ec" . "8139")) + ("virtio" . ("1af4" . "1000")) + ("vmxnet3" . ("15ad" . "07b0"))))) + (substitute-keyword-arguments (package-arguments ipxe) + ((#:modules modules) + `((ice-9 match) ,@modules)) + ((#:make-flags flags) + #~(append (delete "everything" #$flags) + '("CONFIG=qemu") + (map (match-lambda + ((_ . (vid . did)) + (string-append "bin/" vid did ".rom"))) + '#$roms) + (map (match-lambda + ((_ . (vid . did)) + (string-append "bin-efi/" + vid did ".efidrv"))) + '#$roms))) + ((#:phases phases) + #~(modify-phases #$phases + (replace 'install + (lambda _ + (let ((firmware (string-append #$output "/share/firmware"))) + (mkdir-p firmware) + (for-each + (match-lambda + ((name . (vid . did)) + (let ((rom (string-append "bin/" vid did ".rom"))) + (copy-file rom + (string-append firmware + "/pxe-" name ".rom")) + (invoke "EfiRom" + "-b" rom + "-l" "0x02" + "-f" (string-append "0x" vid) + "-i" (string-append "0x" did) + "-ec" (string-append "bin-efi/" + vid did ".efidrv") + "-o" (string-append firmware + "/efi-" name ".rom"))))) + '#$roms))))))))))) From 04665f267398307f7d682335a46fbf7222345276 Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Sun, 18 Dec 2022 01:00:00 +0100 Subject: [PATCH 530/790] gnu: audacity: Be less alpha. * gnu/packages/audio.scm (audacity)[arguments]: Set AUDACITY_BUILD_LEVEL in the #:configure-flags. --- gnu/packages/audio.scm | 15 +++++---------- 1 file changed, 5 insertions(+), 10 deletions(-) diff --git a/gnu/packages/audio.scm b/gnu/packages/audio.scm index b1d3007b8c..fdbb6f4ac9 100644 --- a/gnu/packages/audio.scm +++ b/gnu/packages/audio.scm @@ -856,15 +856,6 @@ engineers, musicians, soundtrack editors and composers.") (version "3.2.1") (source (origin - ;; If built from the release tag, Audacity will describe itself - ;; as an "Alpha test version" and suggest to users that they use - ;; the "latest stable released version". - ;; XXX: For 3.2.1 we rebelliously use a git tag anyway because the only - ;; "processed" download is a .zip containing a .tar.gz which does not - ;; fare well with the patch and snippet machinery: - ;; https://github.com/audacity/audacity/issues/3811 - ;; TODO: Find a way to control the "alpha" status even when using git - ;; so we're not reliant on preprocessed source code. (method git-fetch) (uri (git-reference (url "https://github.com/audacity/audacity") @@ -940,7 +931,11 @@ engineers, musicians, soundtrack editors and composers.") ;; TODO: enable this flag once we've packaged all dependencies ;; "-Daudacity_obey_system_dependencies=on" ;; disable crash reports, updates, ..., anything that phones home - "-Daudacity_has_networking=off") + "-Daudacity_has_networking=off" + ;; When building from Git — even from a release tag — this is undefined, + ;; and Audacity assumes that is is an ‘alpha’ version and includes debug + ;; symbols and extra code. Force level 2, ‘release’. + "-DAUDACITY_BUILD_LEVEL=2") #:imported-modules ((guix build glib-or-gtk-build-system) ,@%cmake-build-system-modules) #:modules From 1a3d8b922863c22f612ea679d9419bb457874fdf Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Sun, 11 Dec 2022 01:00:01 +0100 Subject: [PATCH 531/790] gnu: audacity: Update to 3.2.2. * gnu/packages/audio.scm (audacity): Update to 3.2.2. --- gnu/packages/audio.scm | 5 ++--- 1 file changed, 2 insertions(+), 3 deletions(-) diff --git a/gnu/packages/audio.scm b/gnu/packages/audio.scm index fdbb6f4ac9..b1a16ef3d3 100644 --- a/gnu/packages/audio.scm +++ b/gnu/packages/audio.scm @@ -853,7 +853,7 @@ engineers, musicians, soundtrack editors and composers.") (define-public audacity (package (name "audacity") - (version "3.2.1") + (version "3.2.2") (source (origin (method git-fetch) @@ -862,8 +862,7 @@ engineers, musicians, soundtrack editors and composers.") (commit (string-append "Audacity-" version)))) (file-name (git-file-name name version)) (sha256 - (base32 - "00mal30jxbcacs1ka4yb5s8xq81zm7mv3y8l5hvg77abkyvfvdzf")) + (base32 "1akp9marc4y2g9mwwgfnl43q0gbb2dv7vhsnybh8wdn8ql30hfdw")) (patches (search-patches "audacity-ffmpeg-fallback.patch")) (modules '((guix build utils))) (snippet From f667aeb642c5deab342fe42f3744eb9a7fccc003 Mon Sep 17 00:00:00 2001 From: Greg Hogan Date: Mon, 12 Dec 2022 21:19:32 +0000 Subject: [PATCH 532/790] gnu: openjdk11: Update to 11.0.17. * gnu/packages/java.scm (openjdk11): Update to 11.0.17. [source]: Fix source file-name. [native-inputs]: Add bash. Signed-off-by: Efraim Flashner --- gnu/packages/java.scm | 7 ++++--- 1 file changed, 4 insertions(+), 3 deletions(-) diff --git a/gnu/packages/java.scm b/gnu/packages/java.scm index f80406cab9..fa4d2d3bd0 100644 --- a/gnu/packages/java.scm +++ b/gnu/packages/java.scm @@ -1761,15 +1761,15 @@ new Date();")) (define-public openjdk11 (package (name "openjdk") - (version "11.0.15") + (version "11.0.17") (source (origin (method url-fetch) (uri (string-append "https://openjdk-sources.osci.io/openjdk11/openjdk-" version "-ga.tar.xz")) - (file-name (string-append name "-" version ".tar.bz2")) + (file-name (string-append name "-" version ".tar.xz")) (sha256 (base32 - "0di91nnms2iq1svgq72r5y17am17r4vh2lq43k0bkcwpc84d6nd8")) + "1prvqy0ysz0999wrhsrbz6vrknpqfihl9l74l16ph93g89dqi5ia")) (modules '((guix build utils))) (snippet '(for-each delete-file (find-files "." ".*.(bin|exe|jar)$"))))) @@ -2019,6 +2019,7 @@ new Date();")) libxtst)) (native-inputs (list autoconf + bash ; not bash-minimal, needs ulimit openjdk10 `(,openjdk10 "jdk") gnu-make-4.2 From c8ebfa0dd9514affbc30ca56f9f8cce0fc7550dc Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Mon, 19 Dec 2022 16:00:23 +0200 Subject: [PATCH 533/790] gnu: openjdk11: Fix find-files syntax. * gnu/packages/java.scm (openjdk11)[source]: Remove extra characters from find-files invocation. [arguments]: Remove extra characters from find-files invocations in multiple phases. --- gnu/packages/java.scm | 15 +++++++-------- 1 file changed, 7 insertions(+), 8 deletions(-) diff --git a/gnu/packages/java.scm b/gnu/packages/java.scm index fa4d2d3bd0..e06020eedf 100644 --- a/gnu/packages/java.scm +++ b/gnu/packages/java.scm @@ -1772,7 +1772,7 @@ new Date();")) "1prvqy0ysz0999wrhsrbz6vrknpqfihl9l74l16ph93g89dqi5ia")) (modules '((guix build utils))) (snippet - '(for-each delete-file (find-files "." ".*.(bin|exe|jar)$"))))) + '(for-each delete-file (find-files "." "\\.(bin|exe|jar)$"))))) (build-system gnu-build-system) (outputs '("out" "jdk" "doc")) (arguments @@ -1851,8 +1851,7 @@ new Date();")) (format (current-error-port) "warning: failed to substitute: ~a~%" file)))) - (find-files "." - "\\.c$|\\.h$"))))) + (find-files "." "\\.c$|\\.h$"))))) (add-before 'build 'write-source-revision-file (lambda _ (with-output-to-file ".src-rev" @@ -1879,7 +1878,7 @@ new Date();")) ,@make-flags)))) (replace 'install (lambda _ - (let ((images (car (find-files "build" ".*-server-release" + (let ((images (car (find-files "build" "-server-release" #:directories? #t)))) (copy-recursively (string-append images "/images/jdk") #$output:jdk) @@ -1913,7 +1912,7 @@ new Date();")) (invoke "unzip" archive)) (delete-file archive) (with-directory-excursion dir - (let ((char-data-files (find-files "." "CharacterData.*"))) + (let ((char-data-files (find-files "." "CharacterData"))) (for-each (lambda (file) (substitute* file (((string-append "This file was generated " @@ -1924,7 +1923,7 @@ new Date();")) "file")))) char-data-files))) (with-directory-excursion dir - (let ((files (find-files "." ".*" #:directories? #t))) + (let ((files (find-files "." #:directories? #t))) (apply invoke "zip" "-0" "-X" archive files)))))) (add-after 'strip-character-data-timestamps 'remove-extraneous-files (lambda* (#:key outputs #:allow-other-keys) @@ -1949,7 +1948,7 @@ new Date();")) (invoke "unzip" archive)) (delete-file archive) (for-each (compose repack-archive canonicalize-path) - (find-files dir "(ct.sym|\\.jar)$")) + (find-files dir "(ct\\.sym|\\.jar)$")) (let ((reset-file-timestamp (lambda (file) (let ((s (lstat file))) @@ -1959,7 +1958,7 @@ new Date();")) (for-each reset-file-timestamp (find-files dir #:directories? #t))) (with-directory-excursion dir - (let ((files (find-files "." ".*" #:directories? #t))) + (let ((files (find-files "." #:directories? #t))) (apply invoke "zip" "-0" "-X" archive files))))))) (for-each repack-archive (find-files #$output:doc "\\.zip$")) From 8a6316ef9ea9e993f0c46cbda2a9ae2aaf26a4d2 Mon Sep 17 00:00:00 2001 From: Greg Hogan Date: Mon, 12 Dec 2022 21:19:33 +0000 Subject: [PATCH 534/790] gnu: openjdk13: Update to 13.0.13. * gnu/packages/java.scm (openjdk13): Update to 13.0.13. Signed-off-by: Efraim Flashner --- gnu/packages/java.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/java.scm b/gnu/packages/java.scm index e06020eedf..e71c70753d 100644 --- a/gnu/packages/java.scm +++ b/gnu/packages/java.scm @@ -2100,8 +2100,8 @@ blacklisted.certs.pem" "#! java BlacklistedCertsConverter SHA-256\n")))))))))) (define-public openjdk13 - (make-openjdk openjdk12 "13.0.7" - "0wrrr0d7lz1v8qqm752mn4gz5l2vpl2kmx4ac3ysvk4mljc924hp")) + (make-openjdk openjdk12 "13.0.13" + "0pxf4dlig61k0pg7amg4mi919hzam7nzwckry01avgq1wj8ambji")) (define-public openjdk14 (make-openjdk From 0175b93199b0e0e863e7d6037c3581b4025c22ac Mon Sep 17 00:00:00 2001 From: Greg Hogan Date: Mon, 12 Dec 2022 21:19:34 +0000 Subject: [PATCH 535/790] gnu: openjdk15: Update to 15.0.9. * gnu/packages/java.scm (openjdk15): Update to 15.0.9. Signed-off-by: Efraim Flashner --- gnu/packages/java.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/java.scm b/gnu/packages/java.scm index e71c70753d..04c16ba2e9 100644 --- a/gnu/packages/java.scm +++ b/gnu/packages/java.scm @@ -2119,8 +2119,8 @@ blacklisted.certs.pem" (define-public openjdk15 (make-openjdk - openjdk14 "15.0.3" - "168cr08nywp0q3vyj8njkhsmmnyd8rz9r58hk4xhzdzc6bdfkl1i" + openjdk14 "15.0.9" + "1k3x06fv89l84ysjsyw8s89q8blghq85m6xjzv373x6297ln8n7a" (source (origin (inherit (package-source base)) (modules '()) From 7cf6e66548615c5debee71351b214af7783610c7 Mon Sep 17 00:00:00 2001 From: Greg Hogan Date: Mon, 12 Dec 2022 21:19:35 +0000 Subject: [PATCH 536/790] gnu: openjdk16: Update to 16.0.2. * gnu/packages/java.scm (openjdk16): Update to 16.0.2. Signed-off-by: Efraim Flashner --- gnu/packages/java.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/java.scm b/gnu/packages/java.scm index 04c16ba2e9..97e4eb2c31 100644 --- a/gnu/packages/java.scm +++ b/gnu/packages/java.scm @@ -2137,8 +2137,8 @@ blacklisted.certs.pem" (append `(,openjdk14 "jdk")))))) (define-public openjdk16 - (make-openjdk openjdk15 "16.0.1" - "1ggddsbsar4dj2fycfqqqagqil7prhb30afvq6933rz7pa9apm2f")) + (make-openjdk openjdk15 "16.0.2" + "0587px2qbz07g3xi4a3ya6m630p72dvkxcn0bj1813pxnwvcgigz")) (define-public openjdk17 (make-openjdk From a49e4087a14125923dd39e847f8a7eb0978e2370 Mon Sep 17 00:00:00 2001 From: Greg Hogan Date: Mon, 12 Dec 2022 21:19:36 +0000 Subject: [PATCH 537/790] gnu: openjdk17: Update to 17.0.5. * gnu/packages/java.scm (openjdk17): Update to 17.0.5. Signed-off-by: Efraim Flashner --- gnu/packages/java.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/java.scm b/gnu/packages/java.scm index 97e4eb2c31..a5a0495916 100644 --- a/gnu/packages/java.scm +++ b/gnu/packages/java.scm @@ -2142,8 +2142,8 @@ blacklisted.certs.pem" (define-public openjdk17 (make-openjdk - openjdk16 "17.0.3" - "0slmd6ww947gxpp4yr2wmr5z975bg86qh7zqfp2radf2q77ql65b" + openjdk16 "17.0.5" + "1asnysg6kxdkrmb88y6qihdr12ljsyxv0mg6hlcs7cwxgsdlqkfs" (arguments (substitute-keyword-arguments (package-arguments openjdk16) ((#:phases phases) From fc4eef75067747696d1f9c3104e5f725b1434351 Mon Sep 17 00:00:00 2001 From: Greg Hogan Date: Mon, 12 Dec 2022 21:19:37 +0000 Subject: [PATCH 538/790] gnu: openjdk18: Update to 18.0.2. * gnu/packages/java.scm (openjdk18): Update to 18.0.2. Signed-off-by: Efraim Flashner --- gnu/packages/java.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/java.scm b/gnu/packages/java.scm index a5a0495916..fc7ea120a8 100644 --- a/gnu/packages/java.scm +++ b/gnu/packages/java.scm @@ -2155,8 +2155,8 @@ blacklisted.certs.pem" (("^#!.*") "#! java BlockedCertsConverter SHA-256\n")))))))))) (define-public openjdk18 - (make-openjdk openjdk17 "18" - "1bv6bdhkmwvn10l0xy8yi9xibds640hs5zsvx0jp7wrxa3qw4qy8")) + (make-openjdk openjdk17 "18.0.2" + "1yimfdkwpinhg5cf1mcrzk9xvjwnray3cx762kypb9jcwbranjwx")) ;;; Convenience alias to point to the latest version of OpenJDK. (define-public openjdk openjdk18) From 35530133ae38ba7ba85a52ba769802e1c4fec6d1 Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Tue, 20 Dec 2022 17:10:17 +0200 Subject: [PATCH 539/790] Revert "gnu: QEMU: Unbundle SeaBIOS." This reverts commit 814214c369851da50e7006266f718b2d9324ada0. SeaBIOS is only buildable on i686-linux machines and has flags set to force building for i386 so that it works from x86_64-linux. This commit breaks qemu and qemu-minimal on all other architectures. --- gnu/packages/virtualization.scm | 69 ++++----------------------------- 1 file changed, 8 insertions(+), 61 deletions(-) diff --git a/gnu/packages/virtualization.scm b/gnu/packages/virtualization.scm index d0f5fd5af4..6890f13233 100644 --- a/gnu/packages/virtualization.scm +++ b/gnu/packages/virtualization.scm @@ -175,13 +175,10 @@ (modules '((guix build utils))) (snippet '(begin - ;; TODO: Scrub all firmwares from this directory! - (with-directory-excursion "pc-bios" - ;; Delete firmwares provided by SeaBIOS. - (for-each delete-file (find-files "." "^(bios|vgabios).*\\.bin$"))) ;; Delete bundled code that we provide externally. + ;; TODO: Unbundle SeaBIOS! (for-each delete-file-recursively - '("dtc" "meson" "roms/seabios")))))) + '("dtc" "meson")))))) (outputs '("out" "static" "doc")) ;5.3 MiB of HTML docs (build-system gnu-build-system) (arguments @@ -192,20 +189,15 @@ (not (string=? "i686-linux" (%current-system)))) #:configure-flags #~(let ((gcc (search-input-file %build-inputs "/bin/gcc")) - (meson (search-input-file %build-inputs "bin/meson")) - (seabios (search-input-file %build-inputs - "share/firmware/bios.bin")) (out #$output)) (list (string-append "--cc=" gcc) ;; Some architectures insist on using HOST_CC. (string-append "--host-cc=" gcc) - (string-append "--meson=" meson) (string-append "--prefix=" out) - "--sysconfdir=/etc" + (string-append "--meson=" (search-input-file %build-inputs + "bin/meson")) "--enable-fdt=system" - (string-append "--firmwarepath=" out "/share/qemu:" - (dirname seabios)) (string-append "--smbd=" out "/libexec/samba-wrapper") "--disable-debug-info" ;for space considerations ;; The binaries need to be linked against -lrt. @@ -219,33 +211,6 @@ ,@%gnu-build-system-modules) #:phases #~(modify-phases %standard-phases - ;; Since we removed the bundled firmwares above, many tests - ;; can't work. Re-add them here. - (add-after 'unpack 'replace-firmwares - (lambda* (#:key inputs #:allow-other-keys) - (let* ((seabios (dirname (search-input-file - inputs "share/firmware/bios.bin"))) - (seabios-firmwares (find-files seabios "\\.bin$")) - (allowed-differences - ;; Ignore minor differences (addresses etc) in the firmware - ;; data tables compared to what the test suite expects. - '("tests/data/acpi/pc/SSDT.dimmpxm" - "tests/data/acpi/pc/DSDT.dimmpxm" - "tests/data/acpi/pc/ERST.acpierst" - "tests/data/acpi/q35/ERST.acpierst" - "tests/data/acpi/q35/DSDT.cxl")) - (allowed-differences-whitelist - (open-file "tests/qtest/bios-tables-test-allowed-diff.h" - "a"))) - (with-directory-excursion "pc-bios" - (for-each (lambda (file) - (symlink file (basename file))) - seabios-firmwares)) - (for-each (lambda (file) - (format allowed-differences-whitelist - "\"~a\",~%" file)) - allowed-differences) - (close-port allowed-differences-whitelist)))) (add-after 'unpack 'extend-test-time-outs (lambda _ ;; These tests can time out on heavily-loaded and/or slow storage. @@ -312,22 +277,17 @@ (mkdir-p "b/qemu") (chdir "b/qemu") (apply invoke "../../configure" configure-flags))) - ;; Configure, build and install QEMU user-emulation static binaries. (add-after 'configure 'configure-user-static (lambda* (#:key inputs outputs #:allow-other-keys) (let* ((static (assoc-ref outputs "static")) (gcc (search-input-file inputs "/bin/gcc")) - (seabios (search-input-file inputs "/share/firmware/bios.bin")) ;; This is the common set of configure flags; it is ;; duplicated here to isolate this phase from manipulations ;; to the #:configure-flags build argument, as done in ;; derived packages such as qemu-minimal. (configure-flags (list (string-append "--cc=" gcc) (string-append "--host-cc=" gcc) - (string-append "--firmwarepath=" - #$output "/share/qemu:" - (dirname seabios)) "--sysconfdir=/etc" "--disable-debug-info"))) (mkdir-p "../user-static") @@ -353,15 +313,6 @@ (scandir "." (cut string-suffix? "-linux-user" <>)))))))) - - (add-after 'install 'delete-firmwares - (lambda _ - ;; Delete firmares that are accessible on --firmwarepath. - ;; For some reason tests fail if we simply remove them from - ;; pc-bios/meson.build, hence this roundabout way. - (with-directory-excursion (string-append #$output "/share/qemu") - (for-each delete-file - (find-files "." "^(vga)?bios(-[a-z0-9-]+)?\\.bin$"))))) ;; Create a wrapper for Samba. This allows QEMU to use Samba without ;; pulling it in as an input. Note that you need to explicitly install ;; Samba in your Guix profile for Samba support. @@ -406,7 +357,6 @@ exec smbd $@"))) pixman pulseaudio sdl2 - seabios spice usbredir util-linux @@ -417,16 +367,13 @@ exec smbd $@"))) zlib `(,zstd "lib"))) (native-inputs - ;; Note: acpica is here only to pretty-print firmware differences with IASL - ;; (see the replace-firmwares phase above). - (list acpica - bison - flex - gettext-minimal + (list gettext-minimal `(,glib "bin") ;gtester, etc. + perl + flex + bison meson-0.63 ninja - perl pkg-config python-wrapper python-sphinx From 7fb27b5441bf3d9884422cd93447737723124407 Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Tue, 20 Dec 2022 17:12:07 +0200 Subject: [PATCH 540/790] gnu: seabios: Limit to i686-linux and x86_64-linux. * gnu/packages/firmware.scm (seabios)[supported-systems]: New field. --- gnu/packages/firmware.scm | 1 + 1 file changed, 1 insertion(+) diff --git a/gnu/packages/firmware.scm b/gnu/packages/firmware.scm index 8972b84f51..2e2b48162f 100644 --- a/gnu/packages/firmware.scm +++ b/gnu/packages/firmware.scm @@ -522,6 +522,7 @@ executing in M-mode.") (description "SeaBIOS is an implementation of a 16bit x86 BIOS. SeaBIOS can run in an emulator or it can run natively on X86 hardware with the use of coreboot.") + (supported-systems '("i686-linux" "x86_64-linux")) ;; Dual licensed. (license (list license:gpl3+ license:lgpl3+ ;; src/fw/acpi-dsdt.dsl is lgpl2 From 680970490c556ae0029aa1ba2b0faba162118186 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ludovic=20Court=C3=A8s?= Date: Tue, 20 Dec 2022 10:26:16 +0100 Subject: [PATCH 541/790] tests: Adjust 'guix package' test to latest package search metrics. With commit bbcd06e56c06376e640a7ac81a7109e7135a20f2, the command "guix package -s '^fileutils$'" would match the 'ocaml-fileutils' package, because its 'package-upstream-name*' is "fileutils". Work around it. Reported by Vagrant Cascadian. * tests/guix-package.sh: Change "fileutils" example to use a different package name. --- tests/guix-package.sh | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/tests/guix-package.sh b/tests/guix-package.sh index dedba2fd74..cc416ec6a1 100644 --- a/tests/guix-package.sh +++ b/tests/guix-package.sh @@ -149,11 +149,11 @@ cat > "$module_dir/foo.scm"< Date: Tue, 20 Dec 2022 10:33:03 +0100 Subject: [PATCH 542/790] doc: Avoid 'match' on the record. Fixes . Reported by MANCINI Raffael . * doc/guix.texi (Service Types and Services): Change 'udev-configuration' example to avoid 'match'. --- doc/guix.texi | 9 ++++----- 1 file changed, 4 insertions(+), 5 deletions(-) diff --git a/doc/guix.texi b/doc/guix.texi index c031c8d880..6478deba1d 100644 --- a/doc/guix.texi +++ b/doc/guix.texi @@ -39719,11 +39719,10 @@ The service type for an @emph{extensible} service looks like this: (compose concatenate) ;concatenate the list of rules (extend (lambda (config rules) - (match config - (($ udev initial-rules) - (udev-configuration - (udev udev) ;the udev package to use - (rules (append initial-rules rules))))))))) + (udev-configuration + (inherit config) + (rules (append (udev-configuration-rules config) + rules))))))) @end lisp This is the service type for the From 2880dc3046170e9129437caca586f13956d0d811 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ludovic=20Court=C3=A8s?= Date: Tue, 20 Dec 2022 10:35:37 +0100 Subject: [PATCH 543/790] cpio: Skip test on inode numbers that don't fit on 32 bits. Fixes . Reported by Christopher Baines . * tests/cpio.scm (%test-file): New variable. ("file->cpio-header + write-cpio-header + read-cpio-header"): Use it. Skip test when the inode number of %TEST-FILE is too big. --- tests/cpio.scm | 12 +++++++++--- 1 file changed, 9 insertions(+), 3 deletions(-) diff --git a/tests/cpio.scm b/tests/cpio.scm index 516de0655b..832101d1bb 100644 --- a/tests/cpio.scm +++ b/tests/cpio.scm @@ -1,5 +1,5 @@ ;;; GNU Guix --- Functional package management for GNU -;;; Copyright © 2015 Ludovic Courtès +;;; Copyright © 2015, 2022 Ludovic Courtès ;;; ;;; This file is part of GNU Guix. ;;; @@ -31,12 +31,18 @@ (define %cpio-program (which "cpio")) +(define %test-file + (search-path %load-path "guix.scm")) + (test-begin "cpio") +;; The cpio format expects 'ino' to fit in 32 bits. If we have a bigger inode +;; number, skip this test. +(test-skip + (if (>= (stat:ino (lstat %test-file)) (expt 2 32)) 1 0)) (test-assert "file->cpio-header + write-cpio-header + read-cpio-header" - (let* ((file (search-path %load-path "guix.scm")) - (header (file->cpio-header file))) + (let* ((header (file->cpio-header %test-file))) (call-with-values (lambda () (open-bytevector-output-port)) From 3011e8ae11f6fce87ee5c7f9c702f9d2e10a0e54 Mon Sep 17 00:00:00 2001 From: Bruno Victal Date: Tue, 6 Dec 2022 16:52:09 +0000 Subject: [PATCH 544/790] services: opensmtpd: Use 'match-record' instead of 'match'. MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * gnu/services/mail.scm (opensmtpd-shepherd-service) (opensmtpd-activation) (opensmtpd-set-gids): Use 'match-record' instead of 'match'. Signed-off-by: Ludovic Courtès --- gnu/services/mail.scm | 117 ++++++++++++++++++++---------------------- 1 file changed, 57 insertions(+), 60 deletions(-) diff --git a/gnu/services/mail.scm b/gnu/services/mail.scm index 2dc235a585..dc4a7986b6 100644 --- a/gnu/services/mail.scm +++ b/gnu/services/mail.scm @@ -1666,18 +1666,17 @@ action outbound relay match from local for any action outbound ")) -(define opensmtpd-shepherd-service - (match-lambda - (($ package config-file) - (list (shepherd-service - (provision '(smtpd)) - (requirement '(loopback)) - (documentation "Run the OpenSMTPD daemon.") - (start (let ((smtpd (file-append package "/sbin/smtpd"))) - #~(make-forkexec-constructor - (list #$smtpd "-f" #$config-file) - #:pid-file "/var/run/smtpd.pid"))) - (stop #~(make-kill-destructor))))))) +(define (opensmtpd-shepherd-service config) + (match-record config (package config-file) + (list (shepherd-service + (provision '(smtpd)) + (requirement '(loopback)) + (documentation "Run the OpenSMTPD daemon.") + (start (let ((smtpd (file-append package "/sbin/smtpd"))) + #~(make-forkexec-constructor + (list #$smtpd "-f" #$config-file) + #:pid-file "/var/run/smtpd.pid"))) + (stop #~(make-kill-destructor)))))) (define %opensmtpd-accounts (list (user-group @@ -1698,58 +1697,56 @@ match from local for any action outbound (home-directory "/var/empty") (shell (file-append shadow "/sbin/nologin"))))) -(define opensmtpd-activation - (match-lambda - (($ package config-file) - (let ((smtpd (file-append package "/sbin/smtpd"))) - #~(begin - (use-modules (guix build utils)) - ;; Create mbox and spool directories. - (mkdir-p "/var/mail") - (mkdir-p "/var/spool/smtpd") - (chmod "/var/spool/smtpd" #o711) - (mkdir-p "/var/spool/mail") - (chmod "/var/spool/mail" #o711)))))) +(define (opensmtpd-activation config) + (match-record config (package config-file) + (let ((smtpd (file-append package "/sbin/smtpd"))) + #~(begin + (use-modules (guix build utils)) + ;; Create mbox and spool directories. + (mkdir-p "/var/mail") + (mkdir-p "/var/spool/smtpd") + (chmod "/var/spool/smtpd" #o711) + (mkdir-p "/var/spool/mail") + (chmod "/var/spool/mail" #o711))))) (define %opensmtpd-pam-services (list (unix-pam-service "smtpd"))) -(define opensmtpd-set-gids - (match-lambda - (($ package config-file set-gids?) - (if set-gids? - (list - (setuid-program - (program (file-append package "/sbin/smtpctl")) - (setuid? #false) - (setgid? #true) - (group "smtpq")) - (setuid-program - (program (file-append package "/sbin/sendmail")) - (setuid? #false) - (setgid? #true) - (group "smtpq")) - (setuid-program - (program (file-append package "/sbin/send-mail")) - (setuid? #false) - (setgid? #true) - (group "smtpq")) - (setuid-program - (program (file-append package "/sbin/makemap")) - (setuid? #false) - (setgid? #true) - (group "smtpq")) - (setuid-program - (program (file-append package "/sbin/mailq")) - (setuid? #false) - (setgid? #true) - (group "smtpq")) - (setuid-program - (program (file-append package "/sbin/newaliases")) - (setuid? #false) - (setgid? #true) - (group "smtpq"))) - '())))) +(define (opensmtpd-set-gids config) + (match-record config (package config-file setgid-commands?) + (if setgid-commands? + (list + (setuid-program + (program (file-append package "/sbin/smtpctl")) + (setuid? #false) + (setgid? #true) + (group "smtpq")) + (setuid-program + (program (file-append package "/sbin/sendmail")) + (setuid? #false) + (setgid? #true) + (group "smtpq")) + (setuid-program + (program (file-append package "/sbin/send-mail")) + (setuid? #false) + (setgid? #true) + (group "smtpq")) + (setuid-program + (program (file-append package "/sbin/makemap")) + (setuid? #false) + (setgid? #true) + (group "smtpq")) + (setuid-program + (program (file-append package "/sbin/mailq")) + (setuid? #false) + (setgid? #true) + (group "smtpq")) + (setuid-program + (program (file-append package "/sbin/newaliases")) + (setuid? #false) + (setgid? #true) + (group "smtpq"))) + '()))) (define opensmtpd-service-type (service-type From 00f48860e9df4e83ed9527e3a9f267787ddefee5 Mon Sep 17 00:00:00 2001 From: Bruno Victal Date: Tue, 6 Dec 2022 16:52:10 +0000 Subject: [PATCH 545/790] services: opensmtpd: Add 'shepherd-requirement' field. MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * gnu/services/mail.scm ()[shepherd-requirement]: New field. (opensmtpd-shepherd-service): Honor it. * doc/guix.texi (Mail Services): Document it. Signed-off-by: Ludovic Courtès --- doc/guix.texi | 5 +++++ gnu/services/mail.scm | 7 +++++-- 2 files changed, 10 insertions(+), 2 deletions(-) diff --git a/doc/guix.texi b/doc/guix.texi index 6478deba1d..fd03da8c97 100644 --- a/doc/guix.texi +++ b/doc/guix.texi @@ -25729,6 +25729,11 @@ Data type representing the configuration of opensmtpd. @item @code{package} (default: @var{opensmtpd}) Package object of the OpenSMTPD SMTP server. +@item @code{shepherd-requirement} (default: @code{'()}) +This option can be used to provide a list of symbols naming Shepherd services +that this service will depend on, such as @code{'networking} +if you want to configure OpenSMTPD to listen on non-loopback interfaces. + @item @code{config-file} (default: @code{%default-opensmtpd-config-file}) File-like object of the OpenSMTPD configuration file to use. By default it listens on the loopback network interface, and allows for mail from diff --git a/gnu/services/mail.scm b/gnu/services/mail.scm index dc4a7986b6..6f588679b1 100644 --- a/gnu/services/mail.scm +++ b/gnu/services/mail.scm @@ -1651,6 +1651,8 @@ by @code{dovecot-configuration}. @var{config} may also be created by opensmtpd-configuration? (package opensmtpd-configuration-package (default opensmtpd)) + (shepherd-requirement opensmtpd-configuration-shepherd-requirement + (default '())) ; list of symbols (config-file opensmtpd-configuration-config-file (default %default-opensmtpd-config-file)) (setgid-commands? opensmtpd-setgid-commands? (default #t))) @@ -1667,10 +1669,11 @@ match from local for any action outbound ")) (define (opensmtpd-shepherd-service config) - (match-record config (package config-file) + (match-record config + (package config-file shepherd-requirement) (list (shepherd-service (provision '(smtpd)) - (requirement '(loopback)) + (requirement `(loopback ,@shepherd-requirement)) (documentation "Run the OpenSMTPD daemon.") (start (let ((smtpd (file-append package "/sbin/smtpd"))) #~(make-forkexec-constructor From fcc4e51e61d1982765a4e86c95fbc9a8179e21f3 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ludovic=20Court=C3=A8s?= Date: Tue, 20 Dec 2022 16:51:14 +0100 Subject: [PATCH 546/790] read-print: Add special forms. * guix/read-print.scm (%special-forms): Add 'define-configuration' and 'match-record'. --- guix/read-print.scm | 2 ++ 1 file changed, 2 insertions(+) diff --git a/guix/read-print.scm b/guix/read-print.scm index a6aaa149e4..8a720ef2ef 100644 --- a/guix/read-print.scm +++ b/guix/read-print.scm @@ -288,11 +288,13 @@ expressions and blanks that were read." ('define-gexp-compiler 2) ('define-record-type 2) ('define-record-type* 4) + ('define-configuration 2) ('let 2) ('let* 2) ('letrec 2) ('letrec* 2) ('match 2) + ('match-record 3) ('when 2) ('unless 2) ('package 1) From 990da1af79afa4c33385508f32f79878a4a67966 Mon Sep 17 00:00:00 2001 From: Felix Gruber Date: Sat, 17 Dec 2022 11:42:55 +0000 Subject: [PATCH 547/790] gnu: proj: Update to 9.1.1. * gnu/packages/geo.scm (proj): Update to 9.1.1. Signed-off-by: Guillaume Le Vaillant --- gnu/packages/geo.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/geo.scm b/gnu/packages/geo.scm index cefe973f4a..c7071f1559 100644 --- a/gnu/packages/geo.scm +++ b/gnu/packages/geo.scm @@ -599,7 +599,7 @@ fully fledged Spatial SQL capabilities.") (define-public proj (package (name "proj") - (version "9.1.0") + (version "9.1.1") (source (origin (method url-fetch) @@ -607,7 +607,7 @@ fully fledged Spatial SQL capabilities.") version ".tar.gz")) (sha256 (base32 - "0593vd9sac0c98j1f4rammd90d4xnhygbr6d49i8il6ajjdj7cl1")))) + "0fbd1vj4cj19kwh03vdn0a4hr0xaacvi876yyyw5xfsj1q0x8g00")))) (build-system cmake-build-system) (native-inputs (list googletest pkg-config)) (propagated-inputs (list curl libtiff sqlite)) ;required by proj.pc From 12586fd0b843c942f87f3afad4be422bf5f1e6cb Mon Sep 17 00:00:00 2001 From: Felix Gruber Date: Sat, 17 Dec 2022 11:42:56 +0000 Subject: [PATCH 548/790] gnu: libgeotiff: Apply patch for building against proj 9.1.1. * gnu/packages/patches/libgeotiff-fix-tests-with-proj-9.1.1.patch: New file. * gnu/local.mk (dist_patch_DATA): Register it. * gnu/packages/geo.scm (libgeotiff): Apply it. Signed-off-by: Guillaume Le Vaillant --- gnu/local.mk | 1 + gnu/packages/geo.scm | 1 + ...libgeotiff-fix-tests-with-proj-9.1.1.patch | 100 ++++++++++++++++++ 3 files changed, 102 insertions(+) create mode 100644 gnu/packages/patches/libgeotiff-fix-tests-with-proj-9.1.1.patch diff --git a/gnu/local.mk b/gnu/local.mk index 56634e090c..faad95d902 100644 --- a/gnu/local.mk +++ b/gnu/local.mk @@ -1381,6 +1381,7 @@ dist_patch_DATA = \ %D%/packages/patches/julia-tracker-16-compat.patch \ %D%/packages/patches/libffi-3.3-powerpc-fixes.patch \ %D%/packages/patches/libffi-float128-powerpc64le.patch \ + %D%/packages/patches/libgeotiff-fix-tests-with-proj-9.1.1.patch \ %D%/packages/patches/libobjc2-unbundle-robin-map.patch \ %D%/packages/patches/librime-fix-build-with-gcc10.patch \ %D%/packages/patches/libvirt-add-install-prefix.patch \ diff --git a/gnu/packages/geo.scm b/gnu/packages/geo.scm index c7071f1559..66280ff18b 100644 --- a/gnu/packages/geo.scm +++ b/gnu/packages/geo.scm @@ -409,6 +409,7 @@ and driving.") (method url-fetch) (uri (string-append "http://download.osgeo.org/geotiff/libgeotiff/libgeotiff-" version ".tar.gz")) + (patches (search-patches "libgeotiff-fix-tests-with-proj-9.1.1.patch")) (sha256 (base32 "1mjmgv48x51ppax5dnb6lq7z600czxll53bx6jbzqwd4m93i7aq5")) (modules '((guix build utils))) diff --git a/gnu/packages/patches/libgeotiff-fix-tests-with-proj-9.1.1.patch b/gnu/packages/patches/libgeotiff-fix-tests-with-proj-9.1.1.patch new file mode 100644 index 0000000000..b4bf292c1e --- /dev/null +++ b/gnu/packages/patches/libgeotiff-fix-tests-with-proj-9.1.1.patch @@ -0,0 +1,100 @@ +From: Even Rouault +Date: Sat, 26 Nov 2022 13:23:12 +0100 +Subject: Fix test failures with PROJ 9.1.1 + +https://github.com/OSGeo/libgeotiff/pull/82 +--- + bin/listgeo.c | 7 ++++++- + test/testlistgeo | 4 ++-- + test/testlistgeo_out.dist | 14 -------------- + 3 files changed, 8 insertions(+), 17 deletions(-) + +diff --git a/bin/listgeo.c b/bin/listgeo.c +index 06c45f70..acad54c6 100644 +--- a/bin/listgeo.c ++++ b/bin/listgeo.c +@@ -29,6 +29,7 @@ void Usage() + " -tfw: Generate a .tfw (ESRI TIFF World) file for the target file.\n" + " -proj4: Report PROJ.4 equivalent projection definition.\n" + " -no_norm: Don't report 'normalized' parameter values.\n" ++ " -no_corners: Don't report corner coordinates.\n" + " filename: Name of the GeoTIFF file to report on.\n" ); + + exit( 1 ); +@@ -42,6 +43,7 @@ int main(int argc, char *argv[]) + int i, norm_print_flag = 1, proj4_print_flag = 0; + int tfw_flag = 0, inv_flag = 0, dec_flag = 0; + int st_test_flag = 0; ++ int corners = 1; + + /* + * Handle command line options. +@@ -50,6 +52,8 @@ int main(int argc, char *argv[]) + { + if( strcmp(argv[i],"-no_norm") == 0 ) + norm_print_flag = 0; ++ else if( strcmp(argv[i],"-no_corners") == 0 ) ++ corners = 0; + else if( strcmp(argv[i],"-tfw") == 0 ) + tfw_flag = 1; + else if( strcmp(argv[i],"-proj4") == 0 ) +@@ -130,7 +134,8 @@ int main(int argc, char *argv[]) + + TIFFGetField( tif, TIFFTAG_IMAGEWIDTH, &xsize ); + TIFFGetField( tif, TIFFTAG_IMAGELENGTH, &ysize ); +- GTIFPrintCorners( gtif, &defn, stdout, xsize, ysize, inv_flag, dec_flag ); ++ if( corners ) ++ GTIFPrintCorners( gtif, &defn, stdout, xsize, ysize, inv_flag, dec_flag ); + } + + } +diff --git a/test/testlistgeo b/test/testlistgeo +index 596301b4..9a41e74f 100755 +--- a/test/testlistgeo ++++ b/test/testlistgeo +@@ -59,11 +59,11 @@ $EXE ${DATA_DIR}/ProjLinearUnitsGeoKey_9036.tif >>${OUT} + echo "" >>${OUT} + + echo "Testing listgeo ProjectedCSTypeGeoKey_28191_cassini_soldner.tif" >> ${OUT} +-$EXE ${DATA_DIR}/ProjectedCSTypeGeoKey_28191_cassini_soldner.tif >>${OUT} ++$EXE -no_corners ${DATA_DIR}/ProjectedCSTypeGeoKey_28191_cassini_soldner.tif >>${OUT} + echo "" >>${OUT} + + echo "Testing listgeo cassini_soldner.tif" >> ${OUT} +-$EXE ${DATA_DIR}/cassini_soldner.tif >>${OUT} ++$EXE -no_corners ${DATA_DIR}/cassini_soldner.tif >>${OUT} + echo "" >>${OUT} + + echo "Testing listgeo ProjectedCSTypeGeoKey_27200_new_zealand_mapping_grid.tif" >> ${OUT} +diff --git a/test/testlistgeo_out.dist b/test/testlistgeo_out.dist +index 742f0fce..20221cec 100644 +--- a/test/testlistgeo_out.dist ++++ b/test/testlistgeo_out.dist +@@ -299,13 +299,6 @@ Ellipsoid: 7010/Clarke 1880 (Benoit) (6378300.79,6356566.43) + Prime Meridian: 8901/Greenwich (0.000000/ 0d 0' 0.00"E) + Projection Linear Units: 9001/metre (1.000000m) + +-Corner Coordinates: +-Upper Left ( 440720.000, 3751320.000) ( 40d47'28.08"E, 64d13'29.57"N) +-Lower Left ( 440720.000, 3751260.000) ( 40d47'27.69"E, 64d13'27.64"N) +-Upper Right ( 440780.000, 3751320.000) ( 40d47'32.51"E, 64d13'29.40"N) +-Lower Right ( 440780.000, 3751260.000) ( 40d47'32.12"E, 64d13'27.47"N) +-Center ( 440750.000, 3751290.000) ( 40d47'30.10"E, 64d13'28.52"N) +- + Testing listgeo cassini_soldner.tif + Geotiff_Information: + Version: 1 +@@ -348,13 +341,6 @@ Projection Method: CT_CassiniSoldner + ProjFalseNorthingGeoKey: 126867.909000 m + Projection Linear Units: 9001/metre (1.000000m) + +-Corner Coordinates: +-Upper Left ( 440720.000, 3751320.000) ( 40d47'28.08"E, 64d13'29.57"N) +-Lower Left ( 440720.000, 3751260.000) ( 40d47'27.69"E, 64d13'27.64"N) +-Upper Right ( 440780.000, 3751320.000) ( 40d47'32.51"E, 64d13'29.40"N) +-Lower Right ( 440780.000, 3751260.000) ( 40d47'32.12"E, 64d13'27.47"N) +-Center ( 440750.000, 3751290.000) ( 40d47'30.10"E, 64d13'28.52"N) +- + Testing listgeo ProjectedCSTypeGeoKey_27200_new_zealand_mapping_grid.tif + Geotiff_Information: + Version: 1 From 9c5c432f407d6717c85c25a09910d600a69d38da Mon Sep 17 00:00:00 2001 From: Felix Gruber Date: Sat, 17 Dec 2022 11:42:57 +0000 Subject: [PATCH 549/790] gnu: python-pyproj: Update to 3.4.0. * gnu/packages/geo.scm (python-pyproj): Update to 3.4.0. Signed-off-by: Guillaume Le Vaillant --- gnu/packages/geo.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/geo.scm b/gnu/packages/geo.scm index 66280ff18b..b157678eba 100644 --- a/gnu/packages/geo.scm +++ b/gnu/packages/geo.scm @@ -702,14 +702,14 @@ projections.") (define-public python-pyproj (package (name "python-pyproj") - (version "3.3.1") + (version "3.4.0") (source (origin (method url-fetch) (uri (pypi-uri "pyproj" version)) (sha256 (base32 - "1gjg63irs44djyqbp9gg7s02d0y5i9cd1a83phyzp5fcj56y3n5k")))) + "0czbfl5dd7jckbwvinfwiwdb99sxj796gfn3a9zqbsdc4xcl8257")))) (build-system python-build-system) (arguments `(#:phases From f912be4c12ec4c3200dccca642c7021aa872d3c2 Mon Sep 17 00:00:00 2001 From: Felix Gruber Date: Sat, 17 Dec 2022 11:42:58 +0000 Subject: [PATCH 550/790] gnu: python-cartopy: Update to 0.21.0. * gnu/packages/geo.scm (python-cartopy): Update to 0.21.0. [inputs]: Remove proj. [native-inputs]: Add python-pytest-mpl. Signed-off-by: Guillaume Le Vaillant --- gnu/packages/geo.scm | 15 +++++++-------- 1 file changed, 7 insertions(+), 8 deletions(-) diff --git a/gnu/packages/geo.scm b/gnu/packages/geo.scm index b157678eba..897d5ecee6 100644 --- a/gnu/packages/geo.scm +++ b/gnu/packages/geo.scm @@ -1178,13 +1178,13 @@ utilities for data translation and processing.") (package (name "python-cartopy") ;; This is a post-release fix that adds build_ext to setup.py. - (version "0.20.3") + (version "0.21.0") (source (origin (method url-fetch) (uri (pypi-uri "Cartopy" version)) (sha256 - (base32 "01lhnkhw22jp6hnrs5qvgkq4fqcni2sx7ydiyv8w8xxx5wpglq0d")))) + (base32 "0hnfs75dcnz12ximah5xn9566r8zz189lxikmj4lrs9jl4l3l7ff")))) (build-system python-build-system) (arguments `(#:phases @@ -1207,13 +1207,12 @@ utilities for data translation and processing.") python-scipy python-shapely)) (inputs - (list geos - ;; cartopy's setup.py looks for the proj executable. - ;; Not sure if it actually makes use of it since it - ;; probably uses proj only through pyproj. - proj)) + (list geos)) (native-inputs - (list python-cython python-flufl-lock python-pytest)) + (list python-cython + python-flufl-lock + python-pytest + python-pytest-mpl)) (home-page "https://scitools.org.uk/cartopy/docs/latest/") (synopsis "Cartographic library for visualisation") (description From d30ad6ff5c4c4fbcaa9821f4e04a90d601642506 Mon Sep 17 00:00:00 2001 From: Felix Gruber Date: Sat, 17 Dec 2022 12:24:10 +0000 Subject: [PATCH 551/790] gnu: geos: Update to 3.11.1. * gnu/packages/geo.scm (geos): Update to 3.11.1. Signed-off-by: Guillaume Le Vaillant --- gnu/packages/geo.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/geo.scm b/gnu/packages/geo.scm index 897d5ecee6..cc537ee179 100644 --- a/gnu/packages/geo.scm +++ b/gnu/packages/geo.scm @@ -293,7 +293,7 @@ OpenStreetMap written in C using eXpat, Cairo and GLib.") (define-public geos (package (name "geos") - (version "3.11.0") + (version "3.11.1") (source (origin (method url-fetch) (uri (string-append "http://download.osgeo.org/geos/geos-" @@ -301,7 +301,7 @@ OpenStreetMap written in C using eXpat, Cairo and GLib.") ".tar.bz2")) (sha256 (base32 - "12l59pxawyizmc4wn20dvjn7aifqwkim4ysmc78h91mayjmqravr")))) + "1qhbirv1rbznv99ha0pa0zybvcsn0dsz2xfc65vr8bgrm77v63kd")))) (build-system cmake-build-system) (arguments `(#:phases (modify-phases %standard-phases From d8231432c57a3d8d8def39c2effd45221794bb6f Mon Sep 17 00:00:00 2001 From: Felix Gruber Date: Sat, 17 Dec 2022 13:12:37 +0000 Subject: [PATCH 552/790] gnu: gdal: Update to 3.6.1. * gnu/packages/geo.scm (gdal): Update to 3.6.1. [inputs]: Add libjxl. Signed-off-by: Guillaume Le Vaillant --- gnu/packages/geo.scm | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/gnu/packages/geo.scm b/gnu/packages/geo.scm index cc537ee179..78427f03eb 100644 --- a/gnu/packages/geo.scm +++ b/gnu/packages/geo.scm @@ -1046,7 +1046,7 @@ development.") (define-public gdal (package (name "gdal") - (version "3.5.1") + (version "3.6.1") (source (origin (method url-fetch) (uri (string-append @@ -1054,7 +1054,7 @@ development.") version ".tar.gz")) (sha256 (base32 - "1l93q7xf6qx9ck5axfkf3ygmvclxkvrjd8x00ckn7j0d0750ci3w")) + "1qckwnygszxkkq40bf87s3m1sab6jj9jyakdvskh0qf7dq8zjarf")) (modules '((guix build utils))) (snippet `(begin @@ -1084,6 +1084,7 @@ development.") json-c libgeotiff libjpeg-turbo + libjxl libpng libtiff libwebp From 3c6f7b53cea7ea5dc8176fec02271bc3770d7fc1 Mon Sep 17 00:00:00 2001 From: Roman Scherer Date: Sat, 3 Dec 2022 18:59:02 +0100 Subject: [PATCH 553/790] gnu: gdal: Add support for lz4 and openjpeg. * gnu/packages/geo.scm (gdal)[inputs]: Add lz4 and openjpeg. Signed-off-by: Guillaume Le Vaillant --- gnu/packages/geo.scm | 2 ++ 1 file changed, 2 insertions(+) diff --git a/gnu/packages/geo.scm b/gnu/packages/geo.scm index 78427f03eb..02259c2f6c 100644 --- a/gnu/packages/geo.scm +++ b/gnu/packages/geo.scm @@ -1088,8 +1088,10 @@ development.") libpng libtiff libwebp + lz4 netcdf openssl + openjpeg pcre2 postgresql ; libpq proj From 25f702449c8683b3ec78b2e4a5728e700462e5a2 Mon Sep 17 00:00:00 2001 From: Guillaume Le Vaillant Date: Tue, 20 Dec 2022 17:01:41 +0100 Subject: [PATCH 554/790] gnu: Merge gdal and python-gdal packages. * gnu/packages/geo.scm (gdal)[inputs]: Add swig and zstd. [native-inputs]: Add python. [propagated-inputs]: Add python-numpy. (python-gdal): Remove variable. (qgis)[inputs]: Remove python-gdal. [arguments]: Disable a flaky test. --- gnu/packages/geo.scm | 30 ++++++++---------------------- 1 file changed, 8 insertions(+), 22 deletions(-) diff --git a/gnu/packages/geo.scm b/gnu/packages/geo.scm index 02259c2f6c..2185af7a98 100644 --- a/gnu/packages/geo.scm +++ b/gnu/packages/geo.scm @@ -1097,9 +1097,14 @@ development.") proj qhull sqlite - zlib)) + swig + zlib + zstd)) (native-inputs - (list pkg-config)) + (list pkg-config + python)) + (propagated-inputs + (list python-numpy)) (home-page "https://gdal.org/") (synopsis "Raster and vector geospatial data format library") (description "GDAL is a translator library for raster and vector geospatial @@ -1128,25 +1133,6 @@ utilities for data translation and processing.") ;; frmts/mrf/libLERC license:asl2.0)))) -(define-public python-gdal - (package (inherit gdal) - (name "python-gdal") - (build-system python-build-system) - (arguments - '(#:tests? #f ; no tests - #:phases - (modify-phases %standard-phases - (add-before 'build 'chdir - (lambda _ - (chdir "swig/python") - #t))))) - (native-inputs '()) - (propagated-inputs - (list python-numpy)) - (inputs - (list gdal)) - (synopsis "GDAL (Geospatial Data Abstraction Library) python bindings"))) - (define-public python-pyshp (package (name "python-pyshp") @@ -2554,6 +2540,7 @@ growing set of geoscientific methods.") "ProcessingQgisAlgorithmsTestPt2" "ProcessingQgisAlgorithmsTestPt3" "ProcessingQgisAlgorithmsTestPt4" + "ProcessingGdalAlgorithmsRasterTest" "ProcessingGdalAlgorithmsVectorTest" "ProcessingGrass7AlgorithmsImageryTest" "ProcessingGrass7AlgorithmsRasterTestPt1" @@ -2671,7 +2658,6 @@ growing set of geoscientific methods.") python-chardet python-dateutil python-future - python-gdal python-jinja2 python-numpy python-owslib From b0943d3d2e5b896ef974381e6298895b41490607 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 21 Dec 2022 00:29:33 +0100 Subject: [PATCH 555/790] gnu: mumi: Update to 0.0.3-1.350b2df. * gnu/packages/mail.scm (mumi): Update to 0.0.3-1.350b2df. [arguments]: Use gexp; add phase 'install-picocss. [native-inputs]: Add sassc and picocss sources. --- gnu/packages/mail.scm | 60 ++++++++++++++++++++++++++----------------- 1 file changed, 37 insertions(+), 23 deletions(-) diff --git a/gnu/packages/mail.scm b/gnu/packages/mail.scm index a31c6a51a6..6ce961e2c8 100644 --- a/gnu/packages/mail.scm +++ b/gnu/packages/mail.scm @@ -4026,11 +4026,11 @@ It is a replacement for the @command{urlview} program.") (license license:gpl2+))) (define-public mumi - (let ((commit "4590e4822dda792f59f69b764824aa148d92dad0") - (revision "2")) + (let ((commit "350b2dfbe22bea82ca2d5739d5aebbf9277fe7b7") + (revision "1")) (package (name "mumi") - (version (git-version "0.0.2" revision commit)) + (version (git-version "0.0.3" revision commit)) (source (origin (method git-fetch) (uri (git-reference @@ -4039,33 +4039,38 @@ It is a replacement for the @command{urlview} program.") (file-name (git-file-name name version)) (sha256 (base32 - "16brl1dk92kppzvxx8q5hcqiywg863s4sz5wb64hz8a37xa4hkyr")))) + "1i728cf5shsh0rcv38z244855s2jhifj91prq7c2zk99fsiadw50")))) (build-system gnu-build-system) (arguments - `(#:modules ((guix build gnu-build-system) + (list + #:modules '((guix build gnu-build-system) ((guix build guile-build-system) #:select (target-guile-effective-version)) (guix build utils)) - #:imported-modules ((guix build guile-build-system) + #:imported-modules `((guix build guile-build-system) ,@%gnu-build-system-modules) - #:configure-flags '("--localstatedir=/var") + #:configure-flags '(list "--localstatedir=/var") - #:phases - (modify-phases %standard-phases - (add-after 'install 'wrap-executable - (lambda* (#:key outputs #:allow-other-keys) - (let* ((out (assoc-ref outputs "out")) - (bin (string-append out "/bin")) - (version (target-guile-effective-version)) - (scm (string-append out "/share/guile/site/" version)) - (go (string-append out "/lib/guile/" version - "/site-ccache"))) - (wrap-program (string-append bin "/mumi") - `("GUILE_LOAD_PATH" ":" prefix - (,scm ,(getenv "GUILE_LOAD_PATH"))) - `("GUILE_LOAD_COMPILED_PATH" ":" prefix - (,go ,(getenv "GUILE_LOAD_COMPILED_PATH")))))))))) + #:phases + #~(modify-phases %standard-phases + (add-after 'unpack 'install-picocss + (lambda* (#:key inputs #:allow-other-keys) + (let ((pico (dirname (search-input-file inputs "/scss/pico.scss")))) + (mkdir-p "assets/pico/scss") + (copy-recursively pico "assets/pico/scss")))) + (add-after 'install 'wrap-executable + (lambda _ + (let* ((bin (string-append #$output "/bin")) + (version (target-guile-effective-version)) + (scm (string-append #$output "/share/guile/site/" version)) + (go (string-append #$output "/lib/guile/" version + "/site-ccache"))) + (wrap-program (string-append bin "/mumi") + `("GUILE_LOAD_PATH" ":" prefix + (,scm ,(getenv "GUILE_LOAD_PATH"))) + `("GUILE_LOAD_COMPILED_PATH" ":" prefix + (,go ,(getenv "GUILE_LOAD_COMPILED_PATH")))))))))) (inputs (list guile-email-latest guile-fibers @@ -4079,7 +4084,16 @@ It is a replacement for the @command{urlview} program.") guile-3.0 mailutils)) (native-inputs - (list autoconf automake pkg-config)) + (list autoconf automake pkg-config sassc + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/picocss/pico.git") + (commit "3052db4bd3439e236479dc0f98069f7d3b559486"))) + (file-name (git-file-name "pico" "1.5.6")) + (sha256 + (base32 + "1gs1li48hqizx7lc4n2fdxn9i2v4vafkqpza7svvfpcamfz29jpi"))))) (home-page "https://git.elephly.net/software/mumi.git") (synopsis "Debbugs web interface") (description "Mumi is a Debbugs web interface.") From 4a4f2d226e6fbbb303bc03b77fc4031f3db8e058 Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Tue, 20 Dec 2022 17:36:39 -0500 Subject: [PATCH 556/790] gnu: u-boot-tools: Delete trailing #t. * gnu/packages/bootloaders.scm (u-boot-tools) [phases]: Delete trailing #t. --- gnu/packages/bootloaders.scm | 6 ++---- 1 file changed, 2 insertions(+), 4 deletions(-) diff --git a/gnu/packages/bootloaders.scm b/gnu/packages/bootloaders.scm index b968ecd441..3e8607f61a 100644 --- a/gnu/packages/bootloaders.scm +++ b/gnu/packages/bootloaders.scm @@ -728,8 +728,7 @@ def test_ctrl_c")) ;; This test requires a sound system, which is un-used ;; in u-boot-tools. (("CONFIG_SOUND=y") "CONFIG_SOUND=n"))) - (find-files "configs" "sandbox_.*defconfig$|tools-only_defconfig")) - #t)) + (find-files "configs" "sandbox_.*defconfig$|tools-only_defconfig")))) (replace 'configure (lambda* (#:key make-flags #:allow-other-keys) (apply invoke "make" "tools-only_defconfig" make-flags))) @@ -754,8 +753,7 @@ def test_ctrl_c")) "tools/proftool" "tools/fdtgrep" "tools/env/fw_printenv" - "tools/sunxi-spl-image-builder")) - #t))) + "tools/sunxi-spl-image-builder"))))) (delete 'check) (add-after 'install 'check (lambda* (#:key make-flags test-target #:allow-other-keys) From d368210af5760d81fcb9964d3cd88c590c36407f Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Tue, 20 Dec 2022 16:34:22 -0500 Subject: [PATCH 557/790] kconfig: Move pair->config-string up. * guix/build/kconfig.scm (pair->config-string): Move earlier, to match the natural dependency of declarations (useful when experimenting at the REPL). --- guix/build/kconfig.scm | 20 ++++++++++---------- 1 file changed, 10 insertions(+), 10 deletions(-) diff --git a/guix/build/kconfig.scm b/guix/build/kconfig.scm index d0189f558f..192bc17c21 100644 --- a/guix/build/kconfig.scm +++ b/guix/build/kconfig.scm @@ -31,6 +31,16 @@ ;; ;; Code: +(define (pair->config-string pair) + "Convert a PAIR back to a config-string." + (let* ((key (first pair)) + (value (cdr pair))) + (if (string? key) + (if (string? value) + (string-append key "=" value) + (string-append "# " key " is not set")) + value))) + (define (config-string->pair config-string) "Parse a configuration string like \"CONFIG_EXAMPLE=m\" into a key-value pair. An error is thrown for invalid configurations. @@ -77,16 +87,6 @@ An error is thrown for invalid configurations. (cons #f config-string) ;keep valid comments (error "Invalid configuration" config-string))))) -(define (pair->config-string pair) - "Convert a PAIR back to a config-string." - (let* ((key (first pair)) - (value (cdr pair))) - (if (string? key) - (if (string? value) - (string-append key "=" value) - (string-append "# " key " is not set")) - value))) - (define (defconfig->alist defconfig) "Convert the content of a DEFCONFIG (or .config) file into an alist." (with-input-from-file defconfig From 1d448662802309b0cb4886afefe8a91c2315ffa0 Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Tue, 20 Dec 2022 16:35:37 -0500 Subject: [PATCH 558/790] kconfig: Mostly preserve keys ordering of original defconfig. * guix/build/kconfig.scm (defconfig->alist): Reverse the results of lists constructed with cons. --- guix/build/kconfig.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/guix/build/kconfig.scm b/guix/build/kconfig.scm index 192bc17c21..7c1f128ffd 100644 --- a/guix/build/kconfig.scm +++ b/guix/build/kconfig.scm @@ -102,10 +102,10 @@ An error is thrown for invalid configurations. ;; The search for duplicates is done. ;; Return the alist or throw an error on duplicates. (if (null? duplicates) - alist + (reverse alist) (error (format #f "duplicate configurations in ~a" defconfig) - duplicates)) + (reverse duplicates))) ;; Continue the search for duplicates. (loop (cdr keys) (if (member (first keys) (cdr keys)) From 68330e7797821bb5196c31cef8bf82a90b41a06c Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Tue, 20 Dec 2022 16:37:53 -0500 Subject: [PATCH 559/790] kconfig: Streamline comment in 'modify-defconfig'. * guix/build/kconfig.scm (modify-defconfig): Streamline comment. --- guix/build/kconfig.scm | 6 ++---- 1 file changed, 2 insertions(+), 4 deletions(-) diff --git a/guix/build/kconfig.scm b/guix/build/kconfig.scm index 7c1f128ffd..0c9ef6baff 100644 --- a/guix/build/kconfig.scm +++ b/guix/build/kconfig.scm @@ -133,10 +133,8 @@ DEFCONFIG: \"CONFIG_F\") Instead of a list, CONFIGS can be a string with one configuration per line." - (let* (;; Split the configs into a list of single configurations. Both a - ;; string and or a list of strings is supported, each with newlines - ;; to separate configurations. - (config-pairs (map config-string->pair + ;; Normalize CONFIGS to a list of configuration pairs. + (let* ((config-pairs (map config-string->pair (append-map (cut string-split <> #\newline) (if (string? configs) (list configs) From 57abc2b7b262d34dd07d1d495c765de75af7ea9b Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Tue, 20 Dec 2022 20:47:00 -0500 Subject: [PATCH 560/790] gnu: u-boot: Add pkg-config to native inputs. * gnu/packages/bootloaders.scm (u-boot) [native-inputs]: Add pkg-config. --- gnu/packages/bootloaders.scm | 1 + 1 file changed, 1 insertion(+) diff --git a/gnu/packages/bootloaders.scm b/gnu/packages/bootloaders.scm index 3e8607f61a..bd9f7bb577 100644 --- a/gnu/packages/bootloaders.scm +++ b/gnu/packages/bootloaders.scm @@ -655,6 +655,7 @@ tree binary files. These are board description files used by Linux and BSD.") lz4 ncurses/tinfo perl + pkg-config ;for 'make menuconfig' python python-coverage python-pycryptodomex From c04528d2a2597d79278833f3607c806278253446 Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Tue, 20 Dec 2022 21:25:27 -0500 Subject: [PATCH 561/790] gnu: u-boot-am335x-evm-boneblack: Fix variable name. * gnu/packages/bootloaders.scm (u-boot-am335x-boneblack): Rename to... (u-boot-am335x-evm-boneblack), to match the package name. * gnu/bootloader/u-boot.scm (u-boot-beaglebone-black-bootloader): Adjust accordingly. --- gnu/bootloader/u-boot.scm | 2 +- gnu/packages/bootloaders.scm | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/bootloader/u-boot.scm b/gnu/bootloader/u-boot.scm index 6cad33b741..de3a43ed70 100644 --- a/gnu/bootloader/u-boot.scm +++ b/gnu/bootloader/u-boot.scm @@ -144,7 +144,7 @@ (define u-boot-beaglebone-black-bootloader (bootloader (inherit u-boot-bootloader) - (package u-boot-am335x-boneblack) + (package u-boot-am335x-evm-boneblack) (disk-image-installer install-beaglebone-black-u-boot))) (define u-boot-allwinner-bootloader diff --git a/gnu/packages/bootloaders.scm b/gnu/packages/bootloaders.scm index bd9f7bb577..c8b8adbc93 100644 --- a/gnu/packages/bootloaders.scm +++ b/gnu/packages/bootloaders.scm @@ -889,7 +889,7 @@ appended to the package description." (define-public u-boot-malta (make-u-boot-package "malta" "mips64el-linux-gnuabi64")) -(define-public u-boot-am335x-boneblack +(define-public u-boot-am335x-evm-boneblack (make-u-boot-package "am335x_evm" "arm-linux-gnueabihf" ;; Patch out other device trees to build an image small enough to fit From f86475d012e528285c62a143e679dacb2a3240e4 Mon Sep 17 00:00:00 2001 From: Danial Behzadi Date: Tue, 20 Dec 2022 15:21:38 +0330 Subject: [PATCH 562/790] gnu: tractor: Update to 4.0. --- gnu/packages/tor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/tor.scm b/gnu/packages/tor.scm index 5b0ea278ba..c21eab23dc 100644 --- a/gnu/packages/tor.scm +++ b/gnu/packages/tor.scm @@ -434,14 +434,14 @@ Potential client and exit connections are scrubbed of sensitive information.") (define-public tractor (package (name "tractor") - (version "3.14") + (version "4.0") (source (origin (method url-fetch) (uri (pypi-uri "traxtor" version)) (sha256 (base32 - "06jhsg179rfckagrpk9r8wqp44anf1bchm3ins2saf5806f0n5lw")))) + "107iwkhw9rxbp4samlcw24gdvgqh23rd7z60lrl1b4iljmhqjvcs")))) (build-system python-build-system) (native-inputs `(("glib:bin" ,glib "bin"))) ; for glib-compile-schemas. From 7c9cbc8d73cd7a385686db1ee8552e4760584a82 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 21 Dec 2022 10:00:45 +0100 Subject: [PATCH 563/790] gnu: tractor: Use gexp. * gnu/packages/tor.scm (tractor)[native-inputs]: Drop label. [arguments]: Use gexp; drop trailing #T from build phases. --- gnu/packages/tor.scm | 29 +++++++++++++---------------- 1 file changed, 13 insertions(+), 16 deletions(-) diff --git a/gnu/packages/tor.scm b/gnu/packages/tor.scm index c21eab23dc..d88a840906 100644 --- a/gnu/packages/tor.scm +++ b/gnu/packages/tor.scm @@ -6,7 +6,7 @@ ;;; Copyright © 2017–2021 Tobias Geerinckx-Rice ;;; Copyright © 2017, 2018, 2019, 2021 Eric Bavier ;;; Copyright © 2017 Rutger Helling -;;; Copyright © 2018 Ricardo Wurmus +;;; Copyright © 2018, 2022 Ricardo Wurmus ;;; Copyright © 2020 Vincent Legoll ;;; Copyright © 2020 Brice Waegeneire ;;; Copyright © 2020 André Batista @@ -444,7 +444,7 @@ Potential client and exit connections are scrubbed of sensitive information.") "107iwkhw9rxbp4samlcw24gdvgqh23rd7z60lrl1b4iljmhqjvcs")))) (build-system python-build-system) (native-inputs - `(("glib:bin" ,glib "bin"))) ; for glib-compile-schemas. + (list (list glib "bin"))) ; for glib-compile-schemas. (inputs (list python-fire python-psutil @@ -453,20 +453,17 @@ Potential client and exit connections are scrubbed of sensitive information.") python-stem python-termcolor)) (arguments - `(#:phases - (modify-phases %standard-phases - (add-after 'install 'install-man-page - (lambda* (#:key outputs #:allow-other-keys) - (let* ((out (assoc-ref outputs "out")) - (man1 (string-append out "/share/man/man1"))) - (install-file "tractor/man/tractor.1" man1) - #t))) - (add-after 'install 'install-gschema - (lambda* (#:key outputs #:allow-other-keys) - (let* ((out (assoc-ref outputs "out")) - (schemas (string-append out "/share/glib-2.0/schemas"))) - (install-file "tractor/tractor.gschema.xml" schemas) - #t)))))) + (list + #:phases + #~(modify-phases %standard-phases + (add-after 'install 'install-man-page + (lambda _ + (let ((man1 (string-append #$output "/share/man/man1"))) + (install-file "tractor/man/tractor.1" man1)))) + (add-after 'install 'install-gschema + (lambda _ + (let ((schemas (string-append #$output "/share/glib-2.0/schemas"))) + (install-file "tractor/tractor.gschema.xml" schemas))))))) (home-page "https://framagit.org/tractor") (synopsis "Setup an onion routing proxy") (description From 6ad3b7029762b5a73d9a4ac006f3efe5f083ff6e Mon Sep 17 00:00:00 2001 From: Nicolas Goaziou Date: Wed, 21 Dec 2022 10:37:46 +0100 Subject: [PATCH 564/790] gnu: emacs-graphql: Update to 0.1.2. * gnu/packages/emacs-xyz.scm (emacs-graphql): Update to 0.1.2. [source]: Remove snippet. The file it removed no longer exist in the code base. [propagated-inputs]: Add EMACS-GHUB. --- gnu/packages/emacs-xyz.scm | 44 +++++++++++++++++--------------------- 1 file changed, 20 insertions(+), 24 deletions(-) diff --git a/gnu/packages/emacs-xyz.scm b/gnu/packages/emacs-xyz.scm index 6e1d05dceb..ad18e9f856 100644 --- a/gnu/packages/emacs-xyz.scm +++ b/gnu/packages/emacs-xyz.scm @@ -1577,33 +1577,29 @@ you will die. The game builds the list of words from the active buffer.") (license license:gpl2+)))) (define-public emacs-graphql - (package - (name "emacs-graphql") - (version "0.1.1") - (source (origin - (modules '((guix build utils))) - ;; Remove examples file with references to external packages as - ;; they do not exist at compilation time. - (snippet - '(begin (delete-file "examples.el"))) - (method git-fetch) - (uri (git-reference - (url "https://github.com/vermiculus/graphql.el") - (commit version))) - (file-name (git-file-name name version)) - (sha256 - (base32 - "0sp0skc1rnhi39szfbq1i99pdgd3bhn4c15cff05iqhjy2d4hniw")))) - (build-system emacs-build-system) - (home-page - "https://github.com/vermiculus/graphql.el") - (synopsis "GraphQL utilities") - (description - "GraphQL.el provides a generally-applicable domain-specific language for + (let ((commit "b57b5ca5d2d0837e1fb4a4f30c051d5f3e643f0f")) ;version bump + (package + (name "emacs-graphql") + (version "0.1.2") + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/vermiculus/graphql.el") + (commit commit))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "18k2c2b7y5qgc7qpkqjmz1nv61w470ja3vwprmy5dlkzficzqsvf")))) + (build-system emacs-build-system) + (propagated-inputs (list emacs-ghub)) + (home-page "https://github.com/vermiculus/graphql.el") + (synopsis "GraphQL utilities") + (description + "GraphQL.el provides a generally-applicable domain-specific language for creating and executing GraphQL queries against your favorite web services. GraphQL is a data query language and runtime designed and used to request and deliver data to mobile and web apps.") - (license license:gpl3+))) + (license license:gpl3+)))) (define-public emacs-graphql-mode ;; No tagged commit. No "Version" keyword either. From 09b96f763df22e422bfbd5dc56ef362327a0e0f7 Mon Sep 17 00:00:00 2001 From: Nicolas Goaziou Date: Wed, 21 Dec 2022 10:53:41 +0100 Subject: [PATCH 565/790] gnu: emacs-graphql: Run tests. * gnu/packages/emacs-xyz.scm (emacs-graphql)[arguments]: Run tests. [native-inputs]: Add EMACS-ERT-RUNNER. --- gnu/packages/emacs-xyz.scm | 12 ++++++++++++ 1 file changed, 12 insertions(+) diff --git a/gnu/packages/emacs-xyz.scm b/gnu/packages/emacs-xyz.scm index ad18e9f856..69573c1fc2 100644 --- a/gnu/packages/emacs-xyz.scm +++ b/gnu/packages/emacs-xyz.scm @@ -1591,6 +1591,18 @@ you will die. The game builds the list of words from the active buffer.") (base32 "18k2c2b7y5qgc7qpkqjmz1nv61w470ja3vwprmy5dlkzficzqsvf")))) (build-system emacs-build-system) + (arguments + (list + #:tests? #true + #:test-command #~(list "ert-runner") + #:phases + #~(modify-phases %standard-phases + (add-after 'unpack 'skip-failing-test + (lambda _ + (substitute* "test/graphql-test.el" + (("\\(ert-deftest correct-tag .*" all) + (string-append all " (skip-unless nil)")))))))) + (native-inputs (list emacs-ert-runner)) (propagated-inputs (list emacs-ghub)) (home-page "https://github.com/vermiculus/graphql.el") (synopsis "GraphQL utilities") From b2684adc119fd4801704e5370d4d390ca8bc1b7c Mon Sep 17 00:00:00 2001 From: Nicolas Goaziou Date: Wed, 21 Dec 2022 10:57:06 +0100 Subject: [PATCH 566/790] gnu: emacs-fountain-mode: Update to 3.6.2. * gnu/packages/emacs-xyz.scm (emacs-fountain-mode): Update to 3.6.2. --- gnu/packages/emacs-xyz.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/emacs-xyz.scm b/gnu/packages/emacs-xyz.scm index 69573c1fc2..3790b7cd23 100644 --- a/gnu/packages/emacs-xyz.scm +++ b/gnu/packages/emacs-xyz.scm @@ -5115,7 +5115,7 @@ files and directories.") (define-public emacs-fountain-mode (package (name "emacs-fountain-mode") - (version "3.6.1") + (version "3.6.2") (source (origin (method git-fetch) @@ -5124,7 +5124,7 @@ files and directories.") (commit (string-append "v" version)))) (file-name (git-file-name name version)) (sha256 - (base32 "1b1yjgink8psyggzkvqzwfnnimmawsv83yl34ccg9921z8bx27mb")))) + (base32 "0mml0in6xxhfv4mdb7rl9k8m6xwmrjl5bb301p8d56sfng982pdl")))) (build-system emacs-build-system) (home-page "https://github.com/rnkn/fountain-mode") (synopsis "Major mode for screenwriting in Fountain markup") From f81a6f5be8923427eab23e17de1e006d60b06f79 Mon Sep 17 00:00:00 2001 From: Nicolas Goaziou Date: Wed, 21 Dec 2022 11:13:36 +0100 Subject: [PATCH 567/790] gnu: emacs-fountain-mode: Add contributed theme. * gnu/packages/emacs-xyz.scm (emacs-fountain-mode)[arguments]: Install Elisp file located in the "contrib" sub-directory. --- gnu/packages/emacs-xyz.scm | 6 ++++++ 1 file changed, 6 insertions(+) diff --git a/gnu/packages/emacs-xyz.scm b/gnu/packages/emacs-xyz.scm index 3790b7cd23..e4baa141f0 100644 --- a/gnu/packages/emacs-xyz.scm +++ b/gnu/packages/emacs-xyz.scm @@ -5125,6 +5125,12 @@ files and directories.") (file-name (git-file-name name version)) (sha256 (base32 "0mml0in6xxhfv4mdb7rl9k8m6xwmrjl5bb301p8d56sfng982pdl")))) + (arguments + (list + #:phases #~(modify-phases %standard-phases + (add-after 'unpack 'add-contrib + (lambda _ + (copy-recursively "contrib" ".")))))) (build-system emacs-build-system) (home-page "https://github.com/rnkn/fountain-mode") (synopsis "Major mode for screenwriting in Fountain markup") From 7833acab0da02335941974608510c02e2d1d8069 Mon Sep 17 00:00:00 2001 From: Nicolas Goaziou Date: Wed, 21 Dec 2022 11:17:44 +0100 Subject: [PATCH 568/790] gnu: pyzo: Update to 4.12.4. * gnu/packages/python-xyz.scm (pyzo): Update to 4.12.4. --- gnu/packages/python-xyz.scm | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index 3ea2763b49..ee25a2d655 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -27002,17 +27002,17 @@ accessor layer.") (define-public pyzo (package (name "pyzo") - (version "4.12.3") + (version "4.12.4") (source (origin (method git-fetch) (uri (git-reference - (url "https://github.com/pyzo/pyzo.git") + (url "https://github.com/pyzo/pyzo") (commit (string-append "v" version)))) (file-name (git-file-name name version)) (sha256 (base32 - "0v6rgp52bf9za2spxx9c1yc6wmskvlsj81iw0gipjy7y8vpypgn2")))) + "10qqilbh7n4z2656qbr9gllvgi7xq11xcm2bv64h02jmkb7m4m6n")))) (build-system python-build-system) (arguments `(#:phases From 228db28165dcde2a11d3f98c96935b65098eecc6 Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Wed, 21 Dec 2022 17:20:41 +0200 Subject: [PATCH 569/790] gnu: seabios: Enable for all architectures. * gnu/packages/firmware.scm (seabios)[native-inputs]: When not building from an i686-linux or x86_64-linux machine add cross-gcc and cross-binutils for i686-linux-gnu. [arguments]: When not building from an i686-linux or x86_64-linux machine adjust the Makefile to find the cross build tools needed. [supported-architectures]: Remove field. --- gnu/packages/firmware.scm | 23 +++++++++++++++++++---- 1 file changed, 19 insertions(+), 4 deletions(-) diff --git a/gnu/packages/firmware.scm b/gnu/packages/firmware.scm index 2e2b48162f..66e4b63d40 100644 --- a/gnu/packages/firmware.scm +++ b/gnu/packages/firmware.scm @@ -72,7 +72,8 @@ #:use-module (gnu packages tls) #:use-module (gnu packages version-control) #:use-module (gnu packages web) - #:use-module (gnu packages xml)) + #:use-module (gnu packages xml) + #:use-module (ice-9 match)) (define-public ath9k-htc-firmware (package @@ -418,7 +419,13 @@ executing in M-mode.") ;; Delete IASL-generated files. (for-each delete-file (find-files "." "\\.hex$")))))) (build-system gnu-build-system) - (native-inputs (list acpica python-wrapper)) + (native-inputs + (append + (list acpica python-wrapper) + (if (member (%current-system) '("i686-linux" "x86_64-linux")) + '() + (list (cross-gcc "i686-linux-gnu") + (cross-binutils "i686-linux-gnu"))))) (arguments (list #:tests? #f ;no tests @@ -440,7 +447,16 @@ executing in M-mode.") (call-with-output-file ".version" (lambda (port) (format port #$(package-version this-package)))) - (setenv "CC" "gcc"))) + ;; If we use (cc-for-target) then we have the system prefix + ;; twice or we might have the wrong prefix. + (setenv "CC" "gcc") + #$@(match (%current-system) + ((or "i686-linux" "x86_64-linux") + #~()) + (_ + #~((substitute* "Makefile" + (("CROSS_PREFIX=") + "CROSS_PREFIX=i686-linux-gnu-"))))))) (add-before 'build 'build-description-tables (lambda _ ;; Regenerate the ACPI description tables. @@ -522,7 +538,6 @@ executing in M-mode.") (description "SeaBIOS is an implementation of a 16bit x86 BIOS. SeaBIOS can run in an emulator or it can run natively on X86 hardware with the use of coreboot.") - (supported-systems '("i686-linux" "x86_64-linux")) ;; Dual licensed. (license (list license:gpl3+ license:lgpl3+ ;; src/fw/acpi-dsdt.dsl is lgpl2 From 70d9a3171792ce1c409ba86398fd23c84d5c95ac Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Sat, 17 Dec 2022 23:26:09 +0100 Subject: [PATCH 570/790] gnu: QEMU: Unbundle SeaBIOS. * gnu/packages/virtualization.scm (qemu)[source](snippet): Delete SeaBIOS ROMs and source code. [arguments]: Add replace-firmwares and delete-firmwares phases. [inputs]: Add SEABIOS. [native-inputs]: Add ACPICA. While here, sort inputs. --- gnu/packages/virtualization.scm | 69 +++++++++++++++++++++++++++++---- 1 file changed, 61 insertions(+), 8 deletions(-) diff --git a/gnu/packages/virtualization.scm b/gnu/packages/virtualization.scm index 6890f13233..d0f5fd5af4 100644 --- a/gnu/packages/virtualization.scm +++ b/gnu/packages/virtualization.scm @@ -175,10 +175,13 @@ (modules '((guix build utils))) (snippet '(begin + ;; TODO: Scrub all firmwares from this directory! + (with-directory-excursion "pc-bios" + ;; Delete firmwares provided by SeaBIOS. + (for-each delete-file (find-files "." "^(bios|vgabios).*\\.bin$"))) ;; Delete bundled code that we provide externally. - ;; TODO: Unbundle SeaBIOS! (for-each delete-file-recursively - '("dtc" "meson")))))) + '("dtc" "meson" "roms/seabios")))))) (outputs '("out" "static" "doc")) ;5.3 MiB of HTML docs (build-system gnu-build-system) (arguments @@ -189,15 +192,20 @@ (not (string=? "i686-linux" (%current-system)))) #:configure-flags #~(let ((gcc (search-input-file %build-inputs "/bin/gcc")) + (meson (search-input-file %build-inputs "bin/meson")) + (seabios (search-input-file %build-inputs + "share/firmware/bios.bin")) (out #$output)) (list (string-append "--cc=" gcc) ;; Some architectures insist on using HOST_CC. (string-append "--host-cc=" gcc) + (string-append "--meson=" meson) (string-append "--prefix=" out) + "--sysconfdir=/etc" - (string-append "--meson=" (search-input-file %build-inputs - "bin/meson")) "--enable-fdt=system" + (string-append "--firmwarepath=" out "/share/qemu:" + (dirname seabios)) (string-append "--smbd=" out "/libexec/samba-wrapper") "--disable-debug-info" ;for space considerations ;; The binaries need to be linked against -lrt. @@ -211,6 +219,33 @@ ,@%gnu-build-system-modules) #:phases #~(modify-phases %standard-phases + ;; Since we removed the bundled firmwares above, many tests + ;; can't work. Re-add them here. + (add-after 'unpack 'replace-firmwares + (lambda* (#:key inputs #:allow-other-keys) + (let* ((seabios (dirname (search-input-file + inputs "share/firmware/bios.bin"))) + (seabios-firmwares (find-files seabios "\\.bin$")) + (allowed-differences + ;; Ignore minor differences (addresses etc) in the firmware + ;; data tables compared to what the test suite expects. + '("tests/data/acpi/pc/SSDT.dimmpxm" + "tests/data/acpi/pc/DSDT.dimmpxm" + "tests/data/acpi/pc/ERST.acpierst" + "tests/data/acpi/q35/ERST.acpierst" + "tests/data/acpi/q35/DSDT.cxl")) + (allowed-differences-whitelist + (open-file "tests/qtest/bios-tables-test-allowed-diff.h" + "a"))) + (with-directory-excursion "pc-bios" + (for-each (lambda (file) + (symlink file (basename file))) + seabios-firmwares)) + (for-each (lambda (file) + (format allowed-differences-whitelist + "\"~a\",~%" file)) + allowed-differences) + (close-port allowed-differences-whitelist)))) (add-after 'unpack 'extend-test-time-outs (lambda _ ;; These tests can time out on heavily-loaded and/or slow storage. @@ -277,17 +312,22 @@ (mkdir-p "b/qemu") (chdir "b/qemu") (apply invoke "../../configure" configure-flags))) + ;; Configure, build and install QEMU user-emulation static binaries. (add-after 'configure 'configure-user-static (lambda* (#:key inputs outputs #:allow-other-keys) (let* ((static (assoc-ref outputs "static")) (gcc (search-input-file inputs "/bin/gcc")) + (seabios (search-input-file inputs "/share/firmware/bios.bin")) ;; This is the common set of configure flags; it is ;; duplicated here to isolate this phase from manipulations ;; to the #:configure-flags build argument, as done in ;; derived packages such as qemu-minimal. (configure-flags (list (string-append "--cc=" gcc) (string-append "--host-cc=" gcc) + (string-append "--firmwarepath=" + #$output "/share/qemu:" + (dirname seabios)) "--sysconfdir=/etc" "--disable-debug-info"))) (mkdir-p "../user-static") @@ -313,6 +353,15 @@ (scandir "." (cut string-suffix? "-linux-user" <>)))))))) + + (add-after 'install 'delete-firmwares + (lambda _ + ;; Delete firmares that are accessible on --firmwarepath. + ;; For some reason tests fail if we simply remove them from + ;; pc-bios/meson.build, hence this roundabout way. + (with-directory-excursion (string-append #$output "/share/qemu") + (for-each delete-file + (find-files "." "^(vga)?bios(-[a-z0-9-]+)?\\.bin$"))))) ;; Create a wrapper for Samba. This allows QEMU to use Samba without ;; pulling it in as an input. Note that you need to explicitly install ;; Samba in your Guix profile for Samba support. @@ -357,6 +406,7 @@ exec smbd $@"))) pixman pulseaudio sdl2 + seabios spice usbredir util-linux @@ -367,13 +417,16 @@ exec smbd $@"))) zlib `(,zstd "lib"))) (native-inputs - (list gettext-minimal - `(,glib "bin") ;gtester, etc. - perl - flex + ;; Note: acpica is here only to pretty-print firmware differences with IASL + ;; (see the replace-firmwares phase above). + (list acpica bison + flex + gettext-minimal + `(,glib "bin") ;gtester, etc. meson-0.63 ninja + perl pkg-config python-wrapper python-sphinx From 5b99829b5511479a2c157998df513ffddc1fe2ec Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Mon, 12 Dec 2022 11:23:05 +0200 Subject: [PATCH 571/790] gnu: julia-fillarrays: Update to 0.13.6. * gnu/packages/julia-xyz.scm (julia-fillarrays): Update to 0.13.6. [propagated-inputs]: Add julia-aqua. --- gnu/packages/julia-xyz.scm | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) diff --git a/gnu/packages/julia-xyz.scm b/gnu/packages/julia-xyz.scm index d2fae6a465..72bc595c7a 100644 --- a/gnu/packages/julia-xyz.scm +++ b/gnu/packages/julia-xyz.scm @@ -1915,7 +1915,7 @@ working with filesystem paths in Julia.") (define-public julia-fillarrays (package (name "julia-fillarrays") - (version "0.12.6") + (version "0.13.6") (source (origin (method git-fetch) @@ -1924,8 +1924,10 @@ working with filesystem paths in Julia.") (commit (string-append "v" version)))) (file-name (git-file-name name version)) (sha256 - (base32 "1sx96pzrgyh8k7x2w8vmyi6cazlmp7rg1n7wbl47qfzqjggka6kz")))) + (base32 "1c4i8awmw9qq8dqfhxwjh76mc1nlmzrl5j754fpnbajv8p49gdv5")))) (build-system julia-build-system) + (propagated-inputs + (list julia-aqua)) (inputs ;required by tests (list julia-staticarrays)) (home-page "https://github.com/JuliaArrays/FillArrays.jl") From a5bdf0a9e7ec5f04572a8b44ecb72b02e70ac368 Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Mon, 12 Dec 2022 11:46:50 +0200 Subject: [PATCH 572/790] gnu: julia-arraylayouts: Update to 0.8.16. * gnu/packages/julia-xyz.scm (julia-arraylayouts): Update to 0.8.16. [arguments]: Add a phase to mark a test broken. [native-inputs]: Add julia-stablerngs. --- gnu/packages/julia-xyz.scm | 14 ++++++++++++-- 1 file changed, 12 insertions(+), 2 deletions(-) diff --git a/gnu/packages/julia-xyz.scm b/gnu/packages/julia-xyz.scm index 72bc595c7a..441821e80a 100644 --- a/gnu/packages/julia-xyz.scm +++ b/gnu/packages/julia-xyz.scm @@ -192,7 +192,7 @@ no issues with the upgrade.") (define-public julia-arraylayouts (package (name "julia-arraylayouts") - (version "0.7.6") + (version "0.8.16") (source (origin (method git-fetch) @@ -201,10 +201,20 @@ no issues with the upgrade.") (commit (string-append "v" version)))) (file-name (git-file-name name version)) (sha256 - (base32 "05q62pks8j23pgbrfny072rrwzrz6q19l68srnjxxv39ncmdmrvg")))) + (base32 "1j11jid4scw9icrbr8g6myp17nabjzmf4f40cichb20lzf1agz8l")))) (build-system julia-build-system) + (arguments + (list + #:phases + #~(modify-phases %standard-phases + (add-after 'unpack 'adjust-tests + (lambda _ + (substitute* "test/test_layoutarray.jl" + (("@test all\\(B") "@test_broken all(B"))))))) (propagated-inputs (list julia-fillarrays)) + (native-inputs + (list julia-stablerngs)) (home-page "https://github.com/JuliaMatrices/ArrayLayouts.jl") (synopsis "Array layouts and general fast linear algebra") (description "This package implements a trait-based framework for describing From c8fed74a3a87eccd59a11f1154e65b7dcd94e1fe Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Mon, 12 Dec 2022 12:25:48 +0200 Subject: [PATCH 573/790] gnu: julia-coordinatetransformations: Update to 0.6.2-1.78f5a5c. * gnu/packages/julia-xyz.scm (julia-coordinatetransformations): Update to 0.6.2-1.78f5a5c. --- gnu/packages/julia-xyz.scm | 49 ++++++++++++++++++++------------------ 1 file changed, 26 insertions(+), 23 deletions(-) diff --git a/gnu/packages/julia-xyz.scm b/gnu/packages/julia-xyz.scm index 441821e80a..b31ef2faac 100644 --- a/gnu/packages/julia-xyz.scm +++ b/gnu/packages/julia-xyz.scm @@ -1099,28 +1099,31 @@ for construction of objects.") (license license:expat))) (define-public julia-coordinatetransformations - (package - (name "julia-coordinatetransformations") - (version "0.6.1") - (source - (origin - (method git-fetch) - (uri (git-reference - (url "https://github.com/JuliaGeometry/CoordinateTransformations.jl") - (commit (string-append "v" version)))) - (file-name (git-file-name name version)) - (sha256 - (base32 "15zbkn32v7xlz7559s0r5a0vkwmjwsswxaqpzijly4lky4jnp33d")))) - (build-system julia-build-system) - (propagated-inputs - (list julia-staticarrays)) - (native-inputs - (list julia-documenter - julia-forwarddiff - julia-unitful)) - (home-page "https://github.com/JuliaGeometry/CoordinateTransformations.jl") - (synopsis "Coordinate transformations in Julia") - (description "@code{CoordinateTransformations} is a Julia package to manage + ;; Test suite fixed after the last release. + (let ((commit "78f5a5cc8cf77f21407b4f175673fa4f6bf86633") + (revision "1")) + (package + (name "julia-coordinatetransformations") + (version (git-version "0.6.2" revision commit)) + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/JuliaGeometry/CoordinateTransformations.jl") + (commit commit))) + (file-name (git-file-name name version)) + (sha256 + (base32 "026g3b2m2z509jdlqvd46yhnhg8y6m00plr3k7cjlbzrfi2yjjn8")))) + (build-system julia-build-system) + (propagated-inputs + (list julia-staticarrays)) + (native-inputs + (list julia-documenter + julia-forwarddiff + julia-unitful)) + (home-page "https://github.com/JuliaGeometry/CoordinateTransformations.jl") + (synopsis "Coordinate transformations in Julia") + (description "@code{CoordinateTransformations} is a Julia package to manage simple or complex networks of coordinate system transformations. Transformations can be easily applied, inverted, composed, and differentiated (both with respect to the input coordinates and with respect to transformation @@ -1129,7 +1132,7 @@ light-weight and efficient enough for, e.g., real-time graphical applications, while support for both explicit and automatic differentiation makes it easy to perform optimization and therefore ideal for computer vision applications such as SLAM (simultaneous localization and mapping).") - (license license:expat))) + (license license:expat)))) (define-public julia-crayons (package From 2bd22272daeabd37b00c7fcfd63c2d50c97e2747 Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Mon, 12 Dec 2022 12:50:42 +0200 Subject: [PATCH 574/790] gnu: julia-mappedarrays: Update to 0.4.1. * gnu/packages/julia-xyz.scm (julia-mappedarrays): Update to 0.4.1. [source]: Add snippet to fix deprecation warning and to fix the testsuite. [arguments]: Add 'adjust-tests phase to skip a test and absorb the i686-linux specific phase 'fix-tests-int32-i686. [native-inputs]: Remove julia-colortypes. Add julia-colors. --- gnu/packages/julia-xyz.scm | 34 ++++++++++++++++++++++++---------- 1 file changed, 24 insertions(+), 10 deletions(-) diff --git a/gnu/packages/julia-xyz.scm b/gnu/packages/julia-xyz.scm index b31ef2faac..01a3569e8d 100644 --- a/gnu/packages/julia-xyz.scm +++ b/gnu/packages/julia-xyz.scm @@ -3438,7 +3438,7 @@ that let you do deep transformations of code.") (define-public julia-mappedarrays (package (name "julia-mappedarrays") - (version "0.4.0") + (version "0.4.1") (source (origin (method git-fetch) @@ -3447,22 +3447,36 @@ that let you do deep transformations of code.") (commit (string-append "v" version)))) (file-name (git-file-name name version)) (sha256 - (base32 "0l5adird8m1cmnsxwhzi5hcr7q9bm1rf7a6018zc7kcn2yxdshy3")))) + (base32 "08kb28dv1zzqbbxblhyllgs4sjxyp76dgjqhdizcq4zg4i1kls6p")) + (snippet + #~(begin + (use-modules (guix build utils)) + ;; Fix deprecation warning + ;; https://github.com/JuliaArrays/MappedArrays.jl/pull/51 + (substitute* "src/MappedArrays.jl" + (("Vararg\\{<:AbstractArray") "Vararg{AbstractArray")) + ;; Fix test failures + ;; https://github.com/JuliaArrays/MappedArrays.jl/pull/50 + (substitute* "test/runtests.jl" + (("_zero\\(x\\) = x > 0 \\? x : 0") + "_zero(x) = ismissing(x) ? x : (x > 0 ? x : 0)")))))) (build-system julia-build-system) (arguments (list #:phases - (if (target-64bit?) - #~%standard-phases - #~(modify-phases %standard-phases - (add-after 'unpack 'fix-tests-int32-i686 - (lambda _ - (substitute* "test/runtests.jl" - (("Int64") "Int32")))))))) + #~(modify-phases %standard-phases + (add-after 'unpack 'adjust-tests + (lambda _ + (substitute* "test/runtests.jl" + ((".*@test_throws ErrorException b.*") "")) + + (when #$(not (target-64bit?)) + (substitute* "test/runtests.jl" + (("Int64") "Int32")))))))) (propagated-inputs (list julia-fixedpointnumbers)) (native-inputs - (list julia-colortypes + (list julia-colors julia-fixedpointnumbers julia-offsetarrays)) (home-page "https://github.com/JuliaArrays/MappedArrays.jl") From 147a38520ec12c7926bf6f717b3fbfb4d60c523d Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Mon, 12 Dec 2022 13:00:31 +0200 Subject: [PATCH 575/790] gnu: julia-imagecore: Update to 0.9.4. * gnu/packages/julia-xyz.scm (julia-imagecore): Update to 0.9.4. --- gnu/packages/julia-xyz.scm | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/gnu/packages/julia-xyz.scm b/gnu/packages/julia-xyz.scm index 01a3569e8d..8ab401e4ba 100644 --- a/gnu/packages/julia-xyz.scm +++ b/gnu/packages/julia-xyz.scm @@ -2583,7 +2583,7 @@ dependencies.") (define-public julia-imagecore (package (name "julia-imagecore") - (version "0.9.1") + (version "0.9.4") (source (origin (method git-fetch) @@ -2592,7 +2592,7 @@ dependencies.") (commit (string-append "v" version)))) (file-name (git-file-name name version)) (sha256 - (base32 "0h9m3pl3wic1jrgaqkdifz24cya5vxd3m6qdmm37pxg2y2ii2vcq")))) + (base32 "0a6m3cszgh2bfsgs08i64f1h1pwh6by4267rvwyvdk470z0ayc8q")))) (build-system julia-build-system) (arguments (list #:tests? #f)) ; Cycle with ImageMagick.jl. @@ -2609,7 +2609,7 @@ dependencies.") julia-reexport)) ;(native-inputs ; `(("julia-aqua" ,julia-aqua) - ; ("julia-colorvectorspace" ,julia-colorvectorspace) + ; ("julia-blockarrays" ,julia-blockarrays) ; ("julia-documenter" ,julia-documenter) ; ("julia-fftw" ,julia-fftw) ; ("julia-imageinterminal" ,julia-imageinterminal) From c0dd27fd9839be129d284160b4f868172dec133c Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Mon, 12 Dec 2022 13:01:40 +0200 Subject: [PATCH 576/790] gnu: julia-imagebase: Update to 0.1.5. * gnu/packages/julia-xyz.scm (julia-imagebase): Update to 0.1.5. --- gnu/packages/julia-xyz.scm | 15 ++++++++++----- 1 file changed, 10 insertions(+), 5 deletions(-) diff --git a/gnu/packages/julia-xyz.scm b/gnu/packages/julia-xyz.scm index 8ab401e4ba..aeaf664897 100644 --- a/gnu/packages/julia-xyz.scm +++ b/gnu/packages/julia-xyz.scm @@ -2552,7 +2552,7 @@ such arrays easy via traits.") (define-public julia-imagebase (package (name "julia-imagebase") - (version "0.1.1") + (version "0.1.5") (source (origin (method git-fetch) @@ -2561,7 +2561,7 @@ such arrays easy via traits.") (commit (string-append "v" version)))) (file-name (git-file-name name version)) (sha256 - (base32 "1n63f2zs6ail9pcl7rzgv3l0z8v1idjsaza3zgvgy7iacxsdpcj2")))) + (base32 "00gi268jsyhlkadkkbyiffph6c8yb7zw34px76n6hs7dkfzp6jm3")))) (build-system julia-build-system) (arguments (list #:tests? #f)) ; Cycle with ImageMagick.jl. @@ -2569,9 +2569,14 @@ such arrays easy via traits.") (list julia-imagecore julia-reexport)) ;(native-inputs - ; `(("julia-imagemagick" ,julia-imagemagick) - ; ("julia-offsetarrays" ,julia-offsetarrays) - ; ("julia-testimages" ,julia-testimages))) + ; (list julia-aqua + ; julia-documenter + ; julia-imagefiltering + ; julia-imageio + ; julia-imagemagick + ; julia-offsetarrays + ; jula-statistics + ; julia-testimages)) (home-page "https://github.com/JuliaImages/ImageBase.jl") (synopsis "Wrapper package around ImageCore") (description "This is a twin package to @code{ImageCore} with functions that From a7762f14b74abedabd1c8b58dd096d9de8c98f10 Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Mon, 12 Dec 2022 13:02:58 +0200 Subject: [PATCH 577/790] gnu: julia-imagetransformations: Update to 0.9.5. * gnu/packages/julia-xyz.scm (julia-imagetransformations): Update to 0.9.5. [propagated-inputs]: Remove julia-identityranges. Add julia-imagebase. --- gnu/packages/julia-xyz.scm | 15 +++++++++------ 1 file changed, 9 insertions(+), 6 deletions(-) diff --git a/gnu/packages/julia-xyz.scm b/gnu/packages/julia-xyz.scm index aeaf664897..81722de859 100644 --- a/gnu/packages/julia-xyz.scm +++ b/gnu/packages/julia-xyz.scm @@ -2781,7 +2781,7 @@ inline presentation of greyscale or color images.") (define-public julia-imagetransformations (package (name "julia-imagetransformations") - (version "0.8.12") + (version "0.9.5") (source (origin (method git-fetch) @@ -2790,7 +2790,7 @@ inline presentation of greyscale or color images.") (commit (string-append "v" version)))) (file-name (git-file-name name version)) (sha256 - (base32 "0i8gw68hljshsy9wdl5mrpbb31irhmayqyglsxi7jwm88iy9pxhm")))) + (base32 "1wavfs5chq8s9ma0k8fxfaqam4560w4l2j3lhbd9aqsjlgvi3swc")))) (build-system julia-build-system) (arguments (list #:tests? #f)) ; Cycle with ImageMagick.jl. @@ -2798,16 +2798,19 @@ inline presentation of greyscale or color images.") (list julia-axisalgorithms julia-colorvectorspace julia-coordinatetransformations - julia-identityranges + julia-imagebase julia-imagecore julia-interpolations julia-offsetarrays julia-rotations julia-staticarrays)) ;(native-inputs - ; `(("julia-imagemagick" ,julia-imagemagick) - ; ("julia-referencetests" ,julia-referencetests) - ; ("julia-testimages" ,julia-testimages))) + ; (list julia-endpointranges + ; julia-imageio + ; julia-imagemagick + ; julia-referencetests + ; julia-tau + ; julia-testimages)) (home-page "https://github.com/JuliaImages/ImageTransformations.jl") (synopsis "Geometric transformations on images for Julia") (description "This package provides support for image resizing, image From c822cb7cb501da46afb478fd5a59cf68f4a8fbf5 Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Wed, 14 Dec 2022 12:51:45 +0200 Subject: [PATCH 578/790] gnu: Remove julia-identityranges. * gnu/packages/julia-xyz.scm (julia-identityranges): Delete variable. --- gnu/packages/julia-xyz.scm | 26 -------------------------- 1 file changed, 26 deletions(-) diff --git a/gnu/packages/julia-xyz.scm b/gnu/packages/julia-xyz.scm index 81722de859..e072a76e18 100644 --- a/gnu/packages/julia-xyz.scm +++ b/gnu/packages/julia-xyz.scm @@ -2475,32 +2475,6 @@ library for parsing HTML.") implementing both a client and a server.") (license license:expat))) -(define-public julia-identityranges - (package - (name "julia-identityranges") - (version "0.3.1") - (source - (origin - (method git-fetch) - (uri (git-reference - (url "https://github.com/JuliaArrays/IdentityRanges.jl") - (commit (string-append "v" version)))) - (file-name (git-file-name name version)) - (sha256 - (base32 "0jvl4xn8f8k70sn473li5q62wbiycl5qi25b5k456h3a0j1lbiml")))) - (build-system julia-build-system) - (propagated-inputs - (list julia-offsetarrays)) - (home-page "https://github.com/JuliaArrays/IdentityRanges.jl") - (synopsis "Ranges that preserve indices of views") - (description "@code{IdentityRanges} are Julia-language a helper type for -creating \"views\" of arrays. They are a custom type of AbstractUnitRange that -makes it easy to preserve the indices of array views. The key property of an -@code{IdentityRange r} is that @code{r[i] == i} (hence the name of the -type/package), and that they support arbitrary start/stop indices (i.e., not -just starting at 1).") - (license license:expat))) - (define-public julia-ifelse (package (name "julia-ifelse") From 4ec253bdf4dab1d079fb364fc85430f8734bc463 Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Mon, 12 Dec 2022 22:26:06 +0200 Subject: [PATCH 579/790] gnu: Add julia-irrationalconstants. * gnu/packages/julia-xyz.scm (julia-irrationalconstants): New variable. --- gnu/packages/julia-xyz.scm | 46 ++++++++++++++++++++++++++++++++++++++ 1 file changed, 46 insertions(+) diff --git a/gnu/packages/julia-xyz.scm b/gnu/packages/julia-xyz.scm index e072a76e18..3c854c729a 100644 --- a/gnu/packages/julia-xyz.scm +++ b/gnu/packages/julia-xyz.scm @@ -3104,6 +3104,52 @@ function, which captures the standard output and standard error, and returns it as a string together with the return value.") (license license:expat))) +(define-public julia-irrationalconstants + (package + (name "julia-irrationalconstants") + (version "0.1.1") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/JuliaMath/IrrationalConstants.jl") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 "1a007iyh26x67a1bj6fcz7pfxa43kn2v7jpmnz727jkk3xgppg2s")))) + (build-system julia-build-system) + (home-page "https://github.com/JuliaMath/IrrationalConstants.jl") + (synopsis "Additional irrationals for Julia") + (description "This package provides these irrational constants: +@itemize +@item +@item twoπ = 2π +@item fourπ = 4π +@item halfπ = π / 2 +@item quartπ = π / 4 +@item invπ = 1 / π +@item twoinvπ = 2 / π +@item fourinvπ = 4 / π +@item inv2π = 1 / (2π) +@item inv4π = 1 / (4π) +@item sqrt2 = √2 +@item sqrt3 = √3 +@item sqrtπ = √π +@item sqrt2π = √2π +@item sqrt4π = √4π +@item sqrthalfπ = √(π / 2) +@item invsqrt2 = 1 / √2 +@item invsqrtπ = 1 / √π +@item invsqrt2π = 1 / √2π +@item loghalf = log(1 / 2) +@item logtwo = log(2) +@item logten = log(10) +@item logπ = log(π) +@item log2π = log(2π) +@item log4π = log(4π) +@end itemize") + (license license:expat))) + (define-public julia-irtools (package (name "julia-irtools") From a1cfa757d75cf2b87a5298ce1ced9adf0c9e39b4 Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Wed, 14 Dec 2022 12:50:35 +0200 Subject: [PATCH 580/790] gnu: Add julia-inversefunctions. * gnu/packages/julia-xyz.scm (julia-inversefunctions): New variable. --- gnu/packages/julia-xyz.scm | 21 +++++++++++++++++++++ 1 file changed, 21 insertions(+) diff --git a/gnu/packages/julia-xyz.scm b/gnu/packages/julia-xyz.scm index 3c854c729a..068b4742cd 100644 --- a/gnu/packages/julia-xyz.scm +++ b/gnu/packages/julia-xyz.scm @@ -3060,6 +3060,27 @@ container mapping @code{(K,V)} pairs via the type @code{IntervalTree{K, V}}. The type @code{K} may be any ordered type.") (license license:expat)))) +(define-public julia-inversefunctions + (package + (name "julia-inversefunctions") + (version "0.1.8") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/JuliaMath/InverseFunctions.jl") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 "05g9f6i735x7syfr56l4yf4fy71kgdisjc6cfxi4jkf46iq86a69")))) + (build-system julia-build-system) + (native-inputs + (list julia-documenter)) + (home-page "https://github.com/JuliaMath/InverseFunctions.jl") + (synopsis "Interface for function inversion") + (description "This package provides an interface to invert functions.") + (license license:expat))) + (define-public julia-invertedindices (package (name "julia-invertedindices") From 615d8b08ee102c803d13d47c4d7c404ef2fa5160 Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Wed, 14 Dec 2022 12:50:39 +0200 Subject: [PATCH 581/790] gnu: Add julia-changesofvariables. * gnu/packages/julia-xyz.scm (julia-changesofvariables): New variable. --- gnu/packages/julia-xyz.scm | 27 +++++++++++++++++++++++++++ 1 file changed, 27 insertions(+) diff --git a/gnu/packages/julia-xyz.scm b/gnu/packages/julia-xyz.scm index 068b4742cd..405a631cc1 100644 --- a/gnu/packages/julia-xyz.scm +++ b/gnu/packages/julia-xyz.scm @@ -822,6 +822,33 @@ can be a test-only dependency, allowing it to have potentially heavy dependencies, while keeping @code{ChainRulesCore.jl} as light-weight as possible.") (license license:expat))) +(define-public julia-changesofvariables + (package + (name "julia-changesofvariables") + (version "0.1.4") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/JuliaMath/ChangesOfVariables.jl") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 "1migyhiqr1rq496302wlkb0s5l8zwqs97ajfkip0jzpvrk2s2xxy")))) + (build-system julia-build-system) + (arguments + ;; Pulls in ForwardDiff, would have a cyclical + ;; dependency with LogExpFunctions. + (list #:tests? #f)) + (propagated-inputs + (list julia-chainrulescore)) + (home-page "https://github.com/JuliaMath/ChangesOfVariables.jl") + (synopsis "Interface for transformation functions in Julia") + (description "This package defines functionality to calculate volume element +changes for functions that perform a change of variables (like coordinate +transformations).") + (license license:expat))) + (define-public julia-codeczlib (package (name "julia-codeczlib") From 8a2731ac94938d3f39b489cad64145adeed4f60c Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Mon, 12 Dec 2022 22:26:48 +0200 Subject: [PATCH 582/790] gnu: julia-logexpfunctions: Update to 0.3.17. * gnu/packages/julia-xyz.scm (julia-logexpfunctions): Update to 0.3.17. [propagated-inputs]: Add julia-chainrulescore, julia-changesofvariables, julia-inversefunctions and julia-irrationalcontants. [native-inputs]: Add julia-chainrulestestutils. --- gnu/packages/julia-xyz.scm | 13 +++++++++---- 1 file changed, 9 insertions(+), 4 deletions(-) diff --git a/gnu/packages/julia-xyz.scm b/gnu/packages/julia-xyz.scm index 405a631cc1..687ecc07db 100644 --- a/gnu/packages/julia-xyz.scm +++ b/gnu/packages/julia-xyz.scm @@ -3467,7 +3467,7 @@ implemented in Julia.") (define-public julia-logexpfunctions (package (name "julia-logexpfunctions") - (version "0.2.4") + (version "0.3.17") (source (origin (method git-fetch) @@ -3476,12 +3476,17 @@ implemented in Julia.") (commit (string-append "v" version)))) (file-name (git-file-name name version)) (sha256 - (base32 "0rvms3mmq8a1viqlyzdgs2ccddcy6j0c677dlb8m5nk6hkiwr16n")))) + (base32 "0272c1256r42y6g4wsjmgpwcl5s7z98b8sfmyycckqf0zp5dzxg4")))) (build-system julia-build-system) (propagated-inputs - (list julia-docstringextensions)) + (list julia-chainrulescore + julia-changesofvariables + julia-docstringextensions + julia-inversefunctions + julia-irrationalconstants)) (native-inputs - (list julia-offsetarrays)) + (list julia-chainrulestestutils + julia-offsetarrays)) (home-page "https://github.com/JuliaStats/LogExpFunctions.jl") (synopsis "Special functions based on @code{log} and @code{exp}") (description "Various special functions based on log and exp moved from From fe3a0fad9e2af77c91eba0269c4a47eb41ff2323 Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Mon, 12 Dec 2022 22:38:38 +0200 Subject: [PATCH 583/790] gnu: julia-nanmath: Update to 0.3.7. * gnu/packages/julia-xyz.scm (julia-nanmath): Update to 0.3.7. --- gnu/packages/julia-xyz.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/julia-xyz.scm b/gnu/packages/julia-xyz.scm index 687ecc07db..c59a575de6 100644 --- a/gnu/packages/julia-xyz.scm +++ b/gnu/packages/julia-xyz.scm @@ -3907,7 +3907,7 @@ still being completely generic (define-public julia-nanmath (package (name "julia-nanmath") - (version "0.3.5") + (version "0.3.7") (source (origin (method git-fetch) @@ -3916,7 +3916,7 @@ still being completely generic (commit (string-append "v" version)))) (file-name (git-file-name name version)) (sha256 - (base32 "1hczhz00qj99w63vp627kwk02l2sr2qmzc2rkwwkdwvzy670p25q")))) + (base32 "1fwqa2fzl84a86ppjb2xaqh93b5gg42zyrclbjfdm5l0044hwii6")))) (build-system julia-build-system) (home-page "https://github.com/mlubin/NaNMath.jl") (synopsis "Implementations of basic math functions") From cebacaa3515bcd05ea55da51922b9fb6c05e3bfa Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Mon, 12 Dec 2022 22:40:40 +0200 Subject: [PATCH 584/790] gnu: julia-diffrules: Update to 1.12.2. * gnu/packages/julia-xyz.scm (julia-diffrules): Update to 1.12.2. [propagated-inputs]: Add julia-irriationalconstants, julia-logexpfunctions. [native-inputs]: Add julia-finitedifferences. --- gnu/packages/julia-xyz.scm | 10 +++++++--- 1 file changed, 7 insertions(+), 3 deletions(-) diff --git a/gnu/packages/julia-xyz.scm b/gnu/packages/julia-xyz.scm index c59a575de6..16bd50c3a3 100644 --- a/gnu/packages/julia-xyz.scm +++ b/gnu/packages/julia-xyz.scm @@ -1670,7 +1670,7 @@ be passed to in-place differentiation methods instead of an output buffer.") (define-public julia-diffrules (package (name "julia-diffrules") - (version "1.0.2") + (version "1.12.2") (source (origin (method git-fetch) @@ -1679,11 +1679,15 @@ be passed to in-place differentiation methods instead of an output buffer.") (commit (string-append "v" version)))) (file-name (git-file-name name version)) (sha256 - (base32 "0cwjvj4gma7924fm3yas0nf0jlnwwx4v7fi79ii3s290lkdldzfl")))) + (base32 "0l983kzy01y7qqw42pi0ihpvx3yzfnwrhcmk38avw7y513qlm7vf")))) (build-system julia-build-system) (propagated-inputs - (list julia-nanmath + (list julia-irrationalconstants + julia-logexpfunctions + julia-nanmath julia-specialfunctions)) + (native-inputs + (list julia-finitedifferences)) (home-page "https://github.com/JuliaDiff/DiffRules.jl") (synopsis "Primitive differentiation rules") (description "This package provides primitive differentiation rules that From f4f590e735f9eb49c46cb818477868bbe21c0649 Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Mon, 12 Dec 2022 22:56:08 +0200 Subject: [PATCH 585/790] gnu: julia-forwarddiff: Update to 0.10.34. * gnu/packages/julia-xyz.scm (julia-forwarddiff): Update to 0.10.34. [propagated-inputs]: Add julia-calculus, julia-difftests. --- gnu/packages/julia-xyz.scm | 8 +++++--- 1 file changed, 5 insertions(+), 3 deletions(-) diff --git a/gnu/packages/julia-xyz.scm b/gnu/packages/julia-xyz.scm index 16bd50c3a3..50db34ac6e 100644 --- a/gnu/packages/julia-xyz.scm +++ b/gnu/packages/julia-xyz.scm @@ -2113,7 +2113,7 @@ c-style numerical formatting.") (define-public julia-forwarddiff (package (name "julia-forwarddiff") - (version "0.10.18") + (version "0.10.34") (source (origin (method git-fetch) @@ -2122,7 +2122,7 @@ c-style numerical formatting.") (commit (string-append "v" version)))) (file-name (git-file-name name version)) (sha256 - (base32 "1vb46x8mcn61g1l14qrk22c043khg2ml4q1ci7h4k2v34f2ak5fs")))) + (base32 "1lwjw2jzkffwk06hfc30vxhv36ng3gf12qjc43swmqiakkd3m5jx")))) (build-system julia-build-system) (arguments ;; XXXX: Unexpected and non-deterministic failures for i686, e.g., @@ -2135,9 +2135,11 @@ c-style numerical formatting.") (list julia-calculus julia-difftests)) (propagated-inputs - (list julia-commonsubexpressions + (list julia-calculus + julia-commonsubexpressions julia-diffresults julia-diffrules + julia-difftests julia-nanmath julia-specialfunctions julia-staticarrays)) From ff7d15ef7d4a7951e82c9cb9607aa5afa5c6efa7 Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Mon, 12 Dec 2022 23:35:41 +0200 Subject: [PATCH 586/790] gnu: julia-safetestsets: Fix build. * gnu/packages/julia-xyz.scm (julia-safetestsets)[arguments]: Add phase to fix the version string in the generated Project.toml. --- gnu/packages/julia-xyz.scm | 8 +++++++- 1 file changed, 7 insertions(+), 1 deletion(-) diff --git a/gnu/packages/julia-xyz.scm b/gnu/packages/julia-xyz.scm index 50db34ac6e..fae7736e54 100644 --- a/gnu/packages/julia-xyz.scm +++ b/gnu/packages/julia-xyz.scm @@ -4919,7 +4919,13 @@ through matrix-vector multiplication.") (arguments (list #:julia-package-name "SafeTestsets" - #:julia-package-uuid "1bc83da4-3b8d-516f-aca4-4fe02f6d838f")) + #:julia-package-uuid "1bc83da4-3b8d-516f-aca4-4fe02f6d838f" + #:phases + #~(modify-phases %standard-phases + (add-after 'link-depot 'fix-package-toml + (lambda _ + (substitute* "Project.toml" + (("version = .*") "version = \"0.0.1\"\n"))))))) (native-inputs (list julia-staticarrays)) (home-page "https://github.com/YingboMa/SafeTestsets.jl") From d50025ded8029c63cc68ba5048d4f850c746fedb Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Mon, 12 Dec 2022 23:43:39 +0200 Subject: [PATCH 587/790] gnu: Add julia-shiftedarrays. * gnu/packages/julia-xyz.scm (julia-shiftedarrays): New variable. --- gnu/packages/julia-xyz.scm | 20 ++++++++++++++++++++ 1 file changed, 20 insertions(+) diff --git a/gnu/packages/julia-xyz.scm b/gnu/packages/julia-xyz.scm index fae7736e54..f04203e44e 100644 --- a/gnu/packages/julia-xyz.scm +++ b/gnu/packages/julia-xyz.scm @@ -5028,6 +5028,26 @@ files that the user must interact with through a file browser.") argument.") (license license:expat))) +(define-public julia-shiftedarrays + (package + (name "julia-shiftedarrays") + (version "1.0.0") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/JuliaArrays/ShiftedArrays.jl") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 "0wy7k29qx2lvj587kiz31fzdc60808mjsgpp41h6b682ypz8rw0c")))) + (build-system julia-build-system) + (home-page "https://github.com/JuliaArrays/ShiftedArrays.jl") + (synopsis "Lazy shifted arrays for data analysis in Julia") + (description + "This package provides an implementation of shifted arrays for Julia.") + (license license:expat))) + (define-public julia-showoff (package (name "julia-showoff") From 3fb804967a589720b47bbe0d0e1d50ebae55eb84 Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Tue, 13 Dec 2022 09:06:13 +0200 Subject: [PATCH 588/790] gnu: julia-invertedindices: Update to 1.1.0. * gnu/packages/julia-xyz.scm (julia-invertedindices): Update to 1.1.0. --- gnu/packages/julia-xyz.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/julia-xyz.scm b/gnu/packages/julia-xyz.scm index f04203e44e..b38848cfe4 100644 --- a/gnu/packages/julia-xyz.scm +++ b/gnu/packages/julia-xyz.scm @@ -3117,7 +3117,7 @@ The type @code{K} may be any ordered type.") (define-public julia-invertedindices (package (name "julia-invertedindices") - (version "1.0.0") + (version "1.1.0") (source (origin (method git-fetch) @@ -3126,7 +3126,7 @@ The type @code{K} may be any ordered type.") (commit (string-append "v" version)))) (file-name (git-file-name name version)) (sha256 - (base32 "1179z20yxnkyziip7gn26wr1g3k3ssl1ci7pig3khc900f62di46")))) + (base32 "15ym4dzyi4fkz0dznni032w3c84zmfa6mrzj2ljqvlqx1i6agqis")))) (build-system julia-build-system) (native-inputs (list julia-offsetarrays)) From 6f4c87b493b333090d9717db7e8cc4a1a49af094 Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Tue, 13 Dec 2022 09:29:25 +0200 Subject: [PATCH 589/790] gnu: julia-categoricalarrays: Update to 0.10.7. * gnu/packages/julia-xyz.scm (julia-categoricalarrays): Update to 0.10.7. [arguments]: Add phase to skip tests depending on julia-plots. [native-inputs]: Add julia-json, julia-json3, julia-recipesbase, julia-sentinelarrays, julia-structtypes. [propagated-inputs]: Add julia-requires, julia-sentinelarrays. --- gnu/packages/julia-xyz.scm | 23 ++++++++++++++++++++--- 1 file changed, 20 insertions(+), 3 deletions(-) diff --git a/gnu/packages/julia-xyz.scm b/gnu/packages/julia-xyz.scm index b38848cfe4..e0cc40e6ca 100644 --- a/gnu/packages/julia-xyz.scm +++ b/gnu/packages/julia-xyz.scm @@ -679,7 +679,7 @@ methods.") (define-public julia-categoricalarrays (package (name "julia-categoricalarrays") - (version "0.9.7") + (version "0.10.7") (source (origin (method git-fetch) @@ -688,16 +688,33 @@ methods.") (commit (string-append "v" version)))) (file-name (git-file-name name version)) (sha256 - (base32 "1bcfylxdaizgasnmlkjjkf4dgfvy2y9ycnphw2d0z6mm9vx3n04x")))) + (base32 "17fix7wlwqbif5jbcrbi0a0ghdl3429km3l6lqa962p7jf1gjd2d")))) (build-system julia-build-system) + (arguments + (list + #:phases + #~(modify-phases %standard-phases + (add-after 'unpack 'adjust-tests + (lambda _ + ;; Plots.jl isn't packaged yet. + (substitute* "test/runtests.jl" + ((".*13_arraycommon\\.jl.*") ""))))))) (native-inputs - (list julia-pooledarrays)) + (list julia-json + julia-json3 + ;julia-plots + julia-pooledarrays + julia-recipesbase + julia-sentinelarrays + julia-structtypes)) (propagated-inputs (list julia-dataapi julia-json julia-json3 julia-missings julia-recipesbase + julia-requires + julia-sentinelarrays julia-structtypes)) (home-page "https://github.com/JuliaData/CategoricalArrays.jl") (synopsis "Arrays for working with categorical data") From b786dcb7934e8b33bf5f2a4c81bf79afb92fb94c Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Tue, 13 Dec 2022 09:48:49 +0200 Subject: [PATCH 590/790] gnu: julia-pooledarrays: Update to 1.4.2. * gnu/packages/julia-xyz.scm (julia-pooledarrays): Update to 1.4.2. [native-inputs]: Add julia-offsetarrays. --- gnu/packages/julia-xyz.scm | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) diff --git a/gnu/packages/julia-xyz.scm b/gnu/packages/julia-xyz.scm index e0cc40e6ca..1c3ae041e4 100644 --- a/gnu/packages/julia-xyz.scm +++ b/gnu/packages/julia-xyz.scm @@ -4285,7 +4285,7 @@ plotting components.") (define-public julia-pooledarrays (package (name "julia-pooledarrays") - (version "1.3.0") + (version "1.4.2") (source (origin (method git-fetch) @@ -4294,10 +4294,12 @@ plotting components.") (commit (string-append "v" version)))) (file-name (git-file-name name version)) (sha256 - (base32 "0qdwvf1p5z6z0q4s4hn85ysd8wq47zy6hlzddc5ijvhk86ccqlrr")))) + (base32 "0g30d46n8cc8vr9icjhfkqz2il2185ijh7xhfy9vhcnmllzpd0yg")))) (build-system julia-build-system) (propagated-inputs (list julia-dataapi)) + (native-inputs + (list julia-offsetarrays)) (home-page "https://github.com/JuliaData/PooledArrays.jl") (synopsis "Pooled representation of arrays in Julia") (description "This package provides a pooled representation of arrays for From 3ef53be9aca7aad7e8ab423d91417b94f483fba1 Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Tue, 13 Dec 2022 10:24:52 +0200 Subject: [PATCH 591/790] gnu: julia-dataapi: Update to 1.13.0. * gnu/packages/julia-xyz.scm (julia-dataapi): Update to 1.13.0. --- gnu/packages/julia-xyz.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/julia-xyz.scm b/gnu/packages/julia-xyz.scm index 1c3ae041e4..2c9b0a48e4 100644 --- a/gnu/packages/julia-xyz.scm +++ b/gnu/packages/julia-xyz.scm @@ -1246,7 +1246,7 @@ as comma-delimited (csv), tab-delimited (tsv), or otherwise.") (define-public julia-dataapi (package (name "julia-dataapi") - (version "1.7.0") + (version "1.13.0") (source (origin (method git-fetch) @@ -1255,7 +1255,7 @@ as comma-delimited (csv), tab-delimited (tsv), or otherwise.") (commit (string-append "v" version)))) (file-name (git-file-name name version)) (sha256 - (base32 "0swk31p83fycz5cdj4fg6b0wfqj473lnx94q2fl7ybxkkc6afba7")))) + (base32 "1x5pdpjlbk29766ark7rmzjbl0rhxmsb1cp04lc891aknh30rn3i")))) (build-system julia-build-system) (home-page "https://github.com/JuliaData/DataAPI.jl") (synopsis "Data-focused namespace for packages to share functions") From 8154f07422ba96c96970cf1d04de450ce563160d Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Tue, 13 Dec 2022 11:44:44 +0200 Subject: [PATCH 592/790] gnu: julia-offsetarrays: Update to 1.12.8. * gnu/packages/julia-xyz.scm (julia-offsetarrays): Update to 1.12.8. --- gnu/packages/julia-xyz.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/julia-xyz.scm b/gnu/packages/julia-xyz.scm index 2c9b0a48e4..64a3948806 100644 --- a/gnu/packages/julia-xyz.scm +++ b/gnu/packages/julia-xyz.scm @@ -4115,7 +4115,7 @@ which they were added to the collection.") (define-public julia-offsetarrays (package (name "julia-offsetarrays") - (version "1.10.3") + (version "1.12.8") (source (origin (method git-fetch) @@ -4124,7 +4124,7 @@ which they were added to the collection.") (commit (string-append "v" version)))) (file-name (git-file-name name version)) (sha256 - (base32 "0j5a8ar8yc0j9h87gwfyrcqm23wpyv5yv5gn8vzilpg4vr0fiasc")))) + (base32 "09cidr42q0xwp6wwyaw09hl580vqi85wb5f78pxrxcfm75yg3xki")))) (build-system julia-build-system) (propagated-inputs (list julia-adapt)) From 0147f38df6ddd81629c73d3a06d92a9d2fcca874 Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Tue, 13 Dec 2022 12:47:14 +0200 Subject: [PATCH 593/790] gnu: julia-dataframes: Update to 1.3.6. * gnu/packages/julia-xyz.scm (julia-dataframes): Update to 1.3.6. [arguments]: Adjust 'skip-failing-test phase to adjust a test to pass with julia-1.8. [propagated-inputs]: Add julia-categoricalarrays, julia-compat, julia-shiftedarrays, julia-unitful. [native-inputs]: Add julia-shiftedarrays. --- gnu/packages/julia-xyz.scm | 19 ++++++++++++++----- 1 file changed, 14 insertions(+), 5 deletions(-) diff --git a/gnu/packages/julia-xyz.scm b/gnu/packages/julia-xyz.scm index 64a3948806..3c6658baf6 100644 --- a/gnu/packages/julia-xyz.scm +++ b/gnu/packages/julia-xyz.scm @@ -1269,7 +1269,7 @@ dependency on it.") (define-public julia-dataframes (package (name "julia-dataframes") - (version "1.2.2") + (version "1.3.6") (source (origin (method git-fetch) @@ -1278,7 +1278,7 @@ dependency on it.") (commit (string-append "v" version)))) (file-name (git-file-name name version)) (sha256 - (base32 "1bk0amrghgjrkyn1mm4ac23swwbgszl1d0qyl9137qj5zvv9dasp")))) + (base32 "01ybc1ckn5wi7kwp29g5ms4m3g650856z4xv71racbdr8475pmg5")))) (build-system julia-build-system) (arguments (list @@ -1295,24 +1295,33 @@ dependency on it.") (string-append all "return\n"))) (substitute* "test/join.jl" (("test (levels\\(outerjoin\\(B)" _ test) - (string-append "test_nowarn " test)))))))) + (string-append "test_nowarn " test))) + ;; Compat with julia-1.8, remove with next package update. + (substitute* "test/indexing_offset.jl" + (("@test_throws ErrorException") + "@test_throws Base.CanonicalIndexError"))))))) (propagated-inputs - (list julia-dataapi + (list julia-categoricalarrays + julia-compat + julia-dataapi julia-invertedindices julia-iteratorinterfaceextensions julia-missings julia-pooledarrays julia-prettytables julia-reexport + julia-shiftedarrays julia-sortingalgorithms julia-tables - julia-tabletraits)) + julia-tabletraits + julia-unitful)) (native-inputs (list julia-categoricalarrays julia-combinatorics julia-datastructures julia-datavalues julia-offsetarrays + julia-shiftedarrays julia-unitful)) (home-page "https://dataframes.juliadata.org/stable/") (synopsis "In-memory tabular data") From 66dda9a799dee971b76e8bcfd648d4acfb761d5f Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Tue, 13 Dec 2022 13:23:39 +0200 Subject: [PATCH 594/790] gnu: julia-reversediff: Update to 1.14.4. * gnu/packages/julia-xyz.scm (julia-reversediff): Update to 1.14.4. [propagated-inputs]: Add julia-chainrulescore, julia-difftests, julia-logexpfunctions. --- gnu/packages/julia-xyz.scm | 9 ++++++--- 1 file changed, 6 insertions(+), 3 deletions(-) diff --git a/gnu/packages/julia-xyz.scm b/gnu/packages/julia-xyz.scm index 3c6658baf6..666be6093d 100644 --- a/gnu/packages/julia-xyz.scm +++ b/gnu/packages/julia-xyz.scm @@ -4830,7 +4830,7 @@ can be avoided.") (define-public julia-reversediff (package (name "julia-reversediff") - (version "1.9.0") + (version "1.14.4") (source (origin (method git-fetch) @@ -4839,7 +4839,7 @@ can be avoided.") (commit (string-append "v" version)))) (file-name (git-file-name name version)) (sha256 - (base32 "1wrr6sqj2xl9grkvdp88rw3manxy9vbx28zq2wssya5ns1xabsnl")))) + (base32 "0hwsjmr4wiscqa5kaj4mw0i4agyyzdcmq4r1gp2i563nc1ziaylg")))) (build-system julia-build-system) (arguments ;; XXXX: Test suite failing for i686, e.g., @@ -4849,10 +4849,13 @@ can be avoided.") (list #:tests? (not (or (%current-target-system) (target-x86-32?))))) (propagated-inputs - (list julia-diffresults + (list julia-chainrulescore + julia-diffresults julia-diffrules + julia-difftests julia-forwarddiff julia-functionwrappers + julia-logexpfunctions julia-macrotools julia-nanmath julia-specialfunctions From 288ffff36e28f47f147a24e7e068cc6e64c4e901 Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Tue, 13 Dec 2022 13:41:30 +0200 Subject: [PATCH 595/790] gnu: julia-functors: Update to 0.4.1. * gnu/packages/julia-xyz.scm (julia-functors): Update to 0.4.1. [propagated-inputs]: Add julia-documenter, julia-staticarrays, julia-zygote. --- gnu/packages/julia-xyz.scm | 8 ++++++-- 1 file changed, 6 insertions(+), 2 deletions(-) diff --git a/gnu/packages/julia-xyz.scm b/gnu/packages/julia-xyz.scm index 666be6093d..4f60cca957 100644 --- a/gnu/packages/julia-xyz.scm +++ b/gnu/packages/julia-xyz.scm @@ -2209,7 +2209,7 @@ arbitrary functions.") (define-public julia-functors (package (name "julia-functors") - (version "0.2.7") + (version "0.4.1") (source (origin (method git-fetch) @@ -2218,8 +2218,12 @@ arbitrary functions.") (commit (string-append "v" version)))) (file-name (git-file-name name version)) (sha256 - (base32 "03ry1wn1y2jssq65l29bi6q4ki041aa6gl1nd2w6cgl00k2mrxf3")))) + (base32 "00rzbj2rs2lq91wz8qyxq14bg7p9i49dq7y44fvxn6jaikha2ymw")))) (build-system julia-build-system) + (native-inputs + (list julia-documenter + julia-staticarrays + julia-zygote)) (home-page "https://fluxml.ai/Functors.jl/stable/") (synopsis "Design pattern for structures as in machine learning") (description "This package provides tools to express a design pattern for From df13c6988a21131f62a2f0c3abb75cda5d09c37a Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Tue, 13 Dec 2022 13:49:22 +0200 Subject: [PATCH 596/790] gnu: julia-zygoterules: Update to 0.2.2. * gnu/packages/julia-xyz.scm (julia-zygoterules): Update to 0.2.2. --- gnu/packages/julia-xyz.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/julia-xyz.scm b/gnu/packages/julia-xyz.scm index 4f60cca957..0ec5a695de 100644 --- a/gnu/packages/julia-xyz.scm +++ b/gnu/packages/julia-xyz.scm @@ -6032,7 +6032,7 @@ archives in Julia.") (define-public julia-zygoterules (package (name "julia-zygoterules") - (version "0.2.1") + (version "0.2.2") (source (origin (method git-fetch) @@ -6041,7 +6041,7 @@ archives in Julia.") (commit (string-append "v" version)))) (file-name (git-file-name name version)) (sha256 - (base32 "07i2mf6rr5b8i6l82qgwl5arsb5pwyyzyfasgnszhdqllk9501bs")))) + (base32 "0h9m9ibxfcw9cqa7p0aylpvibvlxsn5nlfzkz1pk68jy58vkzhca")))) (build-system julia-build-system) (propagated-inputs (list julia-macrotools)) From 8b84b47a52f696995c9e7233c4dd6a8551ca3775 Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Tue, 13 Dec 2022 13:50:05 +0200 Subject: [PATCH 597/790] gnu: julia-zygote: Update to 0.6.41. * gnu/packages/julia-xyz.scm (julia-zygote): Update to 0.6.41. [propagated-inputs]: Add julia-chainrulescore, julia-logexpfuntions. --- gnu/packages/julia-xyz.scm | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) diff --git a/gnu/packages/julia-xyz.scm b/gnu/packages/julia-xyz.scm index 0ec5a695de..54d98fdee2 100644 --- a/gnu/packages/julia-xyz.scm +++ b/gnu/packages/julia-xyz.scm @@ -6054,7 +6054,7 @@ Zygote, without depending on Zygote itself.") (define-public julia-zygote (package (name "julia-zygote") - (version "0.6.17") + (version "0.6.41") (source (origin (method git-fetch) @@ -6063,17 +6063,19 @@ Zygote, without depending on Zygote itself.") (commit (string-append "v" version)))) (file-name (git-file-name name version)) (sha256 - (base32 "1cx66sp30s34ln6p0fpqk1ggjxfxg2gp8791zz3cl85dmk4dl14b")))) + (base32 "02bgj6m1j25sm3pa5sgmds706qpxk1qsbm0s2j3rjlrz9xn7glgk")))) (build-system julia-build-system) (arguments (list #:tests? #f)) ;require CUDA, not packaged yet (propagated-inputs (list julia-abstractffts julia-chainrules + julia-chainrulescore julia-diffrules julia-fillarrays julia-forwarddiff julia-irtools + julia-logexpfunctions julia-macrotools julia-nanmath julia-requires From c42652d57815a88b724f392bd32dcb5f71196939 Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Tue, 13 Dec 2022 21:13:31 +0200 Subject: [PATCH 598/790] gnu: julia-nnlib: Update to 0.7.34. * gnu/packages/julia-xyz.scm (julia-nnlib): Update to 0.7.34. [arguments]: Rename 'skip-cuda-tests to 'skip-some-tests. Adjust to skip doctests. [propagated-inputs]: Add julia-compat. --- gnu/packages/julia-xyz.scm | 13 +++++++++---- 1 file changed, 9 insertions(+), 4 deletions(-) diff --git a/gnu/packages/julia-xyz.scm b/gnu/packages/julia-xyz.scm index 54d98fdee2..3a66bc1fa6 100644 --- a/gnu/packages/julia-xyz.scm +++ b/gnu/packages/julia-xyz.scm @@ -3992,7 +3992,7 @@ interface to interact with these types.") (define-public julia-nnlib (package (name "julia-nnlib") - (version "0.7.29") + (version "0.7.34") (source (origin (method git-fetch) @@ -4001,21 +4001,26 @@ interface to interact with these types.") (commit (string-append "v" version)))) (file-name (git-file-name name version)) (sha256 - (base32 "16vn5w5274kcywh1xp0zqjk5q10xrk125aznz5av6wifwrvghk8s")))) + (base32 "1xzlh7pj6aqmbkrskqgwvifprg9a6xkkdh00ls6f6xnzqfrnhwna")))) (build-system julia-build-system) (arguments (list #:phases #~(modify-phases %standard-phases - (add-after 'link-depot 'skip-cuda-tests + (add-after 'link-depot 'skip-some-tests (lambda _ (substitute* "test/runtests.jl" + ;; Skip the CUDA tests (("using CUDA") "") - (("&& CUDA\\.functional\\(\\)") "")) + (("&& CUDA\\.functional\\(\\)") "") + + ;; UnicodePlots is only used for the doctests + (("if VERSION <.*") "if true\n")) (setenv "NNLIB_TEST_CUDA" "false")))))) (propagated-inputs (list julia-adapt julia-chainrulescore + julia-compat julia-requires)) (native-inputs (list julia-chainrulestestutils From c3aef63223757650985647fe13dd70fe1b80b0d3 Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Tue, 13 Dec 2022 21:15:05 +0200 Subject: [PATCH 599/790] gnu: julia-chainrulescore: Update to 1.12.2. * gnu/packages/julia-xyz.scm (julia-chainrulescore): Update to 1.12.2. [arguments]: Adjust 'adjust-tests phase for changes in the source. --- gnu/packages/julia-xyz.scm | 8 +++++--- 1 file changed, 5 insertions(+), 3 deletions(-) diff --git a/gnu/packages/julia-xyz.scm b/gnu/packages/julia-xyz.scm index 3a66bc1fa6..d6e301c5e8 100644 --- a/gnu/packages/julia-xyz.scm +++ b/gnu/packages/julia-xyz.scm @@ -776,7 +776,7 @@ execute forward-, reverse-, and mixed-mode primitives.") (define-public julia-chainrulescore (package (name "julia-chainrulescore") - (version "1.0.2") + (version "1.12.2") (source (origin (method git-fetch) @@ -785,7 +785,7 @@ execute forward-, reverse-, and mixed-mode primitives.") (commit (string-append "v" version)))) (file-name (git-file-name name version)) (sha256 - (base32 "1866xv30h1bi7f2m993nljzf58wwmv8zlgn6ffn9j3wckch1nfpb")))) + (base32 "0lgfcsb7f6c7knhiz5dbqh8x47d370pn71y9ys2y6763g0b4pm61")))) (build-system julia-build-system) (arguments (list @@ -793,7 +793,9 @@ execute forward-, reverse-, and mixed-mode primitives.") #~(modify-phases %standard-phases (add-after 'unpack 'adjust-tests (lambda _ - (substitute* "test/differentials/composite.jl" + (substitute* "test/tangent_types/tangent.jl" + ;; This test is disabled after the release. + (("@test haskey.*Float.*") "") (("@test (.*construct)" _ test) (string-append "@test_broken " test)))))))) (inputs ;required for tests From 59eea190c6e0ec83babe8acfb7c8f527e8ff1772 Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Tue, 13 Dec 2022 21:15:56 +0200 Subject: [PATCH 600/790] gnu: julia-chainrulestestutils: Update to 1.5.1. * gnu/packages/julia-xyz.scm (julia-chainrulestestutils): Update to 1.5.1. --- gnu/packages/julia-xyz.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/julia-xyz.scm b/gnu/packages/julia-xyz.scm index d6e301c5e8..da18f01b47 100644 --- a/gnu/packages/julia-xyz.scm +++ b/gnu/packages/julia-xyz.scm @@ -812,7 +812,7 @@ sensitivities for functions without the need to depend on ChainRules itself.") (define-public julia-chainrulestestutils (package (name "julia-chainrulestestutils") - (version "1.2.3") + (version "1.5.1") (source (origin (method git-fetch) @@ -821,7 +821,7 @@ sensitivities for functions without the need to depend on ChainRules itself.") (commit (string-append "v" version)))) (file-name (git-file-name name version)) (sha256 - (base32 "1vlkyp72d514gyb4k3yhjl1g7f24ncmz61j56p4sdi9f76rk9fx9")))) + (base32 "0vk7cpp049pjj7g5zqxr7djp5v0swhvhq3wvkxyw8m8xvqlnfncc")))) (build-system julia-build-system) (propagated-inputs (list julia-chainrulescore From 907ae061700fed724fa8c7e1f3152ea64768e0e9 Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Tue, 13 Dec 2022 21:12:03 +0200 Subject: [PATCH 601/790] gnu: Add julia-realdot. * gnu/packages/julia-xyz.scm (julia-realdot): New variable. --- gnu/packages/julia-xyz.scm | 23 +++++++++++++++++++++++ 1 file changed, 23 insertions(+) diff --git a/gnu/packages/julia-xyz.scm b/gnu/packages/julia-xyz.scm index da18f01b47..5bffb4fa03 100644 --- a/gnu/packages/julia-xyz.scm +++ b/gnu/packages/julia-xyz.scm @@ -4663,6 +4663,29 @@ by Ranges.") type, which make some sacrifices but have better computational performance.") (license license:expat))) +(define-public julia-realdot + (package + (name "julia-realdot") + (version "0.1.0") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/JuliaMath/RealDot.jl") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 "1jr8dq110j8axjfz936b1lqqcnqg3979rfg11w76rq1iz7zgi691")))) + (build-system julia-build-system) + (home-page "https://github.com/JuliaMath/RealDot.jl") + (synopsis "Compute realdot efficiently") + (description "This package only contains and exports a single function +@code{realdot(x, y)}. It computes @code{real(LinearAlgebra.dot(x, y))} while +avoiding computing the imaginary part of @code{LinearAlgebra.dot(x, y)} if +possible. The real dot product is useful when one treats complex numbers as +embedded in a real vector space.") + (license license:expat))) + (define-public julia-recipesbase (package (name "julia-recipesbase") From d303b26aae071058cf61d4ffd670dba86ce0aeee Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Tue, 13 Dec 2022 21:16:48 +0200 Subject: [PATCH 602/790] gnu: julia-chainrules: Update to 1.35.0. * gnu/packages/julia-xyz.scm (julia-chainrules): Update to 1.35.0. [arguments]: Skip tests. [inputs]: Comment out inputs. [propagated-inputs]: Remove julia-reexport, julia-requires. Add julia-irrationalconstants, julia-realdot. --- gnu/packages/julia-xyz.scm | 19 ++++++++++--------- 1 file changed, 10 insertions(+), 9 deletions(-) diff --git a/gnu/packages/julia-xyz.scm b/gnu/packages/julia-xyz.scm index 5bffb4fa03..53612f5a1e 100644 --- a/gnu/packages/julia-xyz.scm +++ b/gnu/packages/julia-xyz.scm @@ -745,7 +745,7 @@ variables, both with unordered (nominal variables) and ordered categories (define-public julia-chainrules (package (name "julia-chainrules") - (version "1.1.0") + (version "1.35.0") (source (origin (method git-fetch) @@ -754,18 +754,19 @@ variables, both with unordered (nominal variables) and ordered categories (commit (string-append "v" version)))) (file-name (git-file-name name version)) (sha256 - (base32 "0if93pd3b3scg2x3gmk1cbwjk0ax1n792vy8c38y3xl7jpd5cb70")))) + (base32 "17irgz3gamyrmzsjhq4s1n1sblvhkj10yg5y5y53yr631cl2fr6a")))) (build-system julia-build-system) - (inputs ;required for test - (list julia-chainrulestestutils - julia-finitedifferences - julia-nanmath - julia-specialfunctions)) + (arguments + (list #:tests? #f)) ; JuliaInterpreter.jl not packaged yet. + ;(inputs ;required for test + ; (list julia-chainrulestestutils + ; julia-finitedifferences + ; julia-juliainterpreter)) (propagated-inputs (list julia-chainrulescore julia-compat - julia-reexport - julia-requires)) + julia-irrationalconstants + julia-realdot)) (home-page "https://github.com/JuliaDiff/ChainRules.jl") (synopsis "Common utilities for automatic differentiation") (description "The is package provides a variety of common utilities that From ca8be377a2415070b1a3a5e47ae0347347424f97 Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Tue, 13 Dec 2022 21:12:39 +0200 Subject: [PATCH 603/790] gnu: Add julia-optimisers. * gnu/packages/julia-xyz.scm (julia-optimisers): New variable. --- gnu/packages/julia-xyz.scm | 27 +++++++++++++++++++++++++++ 1 file changed, 27 insertions(+) diff --git a/gnu/packages/julia-xyz.scm b/gnu/packages/julia-xyz.scm index 53612f5a1e..39062f5971 100644 --- a/gnu/packages/julia-xyz.scm +++ b/gnu/packages/julia-xyz.scm @@ -4083,6 +4083,33 @@ doesn't provide any other \"high-level\" functionality like layers or AD.") optimization of functions.") (license license:expat))) +(define-public julia-optimisers + (package + (name "julia-optimisers") + (version "0.2.13") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/FluxML/Optimisers.jl") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 "1xs51r365l6r56rpm08kba00nfcl5jlglwy8494w06vbi22ysbq7")))) + (build-system julia-build-system) + (propagated-inputs + (list julia-chainrulescore + julia-functors + julia-zygote)) + (native-inputs + (list julia-staticarrays + julia-zygote)) + (home-page "https://github.com/FluxML/Optimisers.jl") + (synopsis "Optimisers and utilities for learning loops") + (description "@code{Optimisers.jl} defines many standard gradient-based +optimisation rules, and tools for applying them to deeply nested models.") + (license license:expat))) + (define-public julia-optimtestproblems (package (name "julia-optimtestproblems") From 8bc31f951b438d569756af6c432ee6100d0ffa05 Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Tue, 13 Dec 2022 21:18:31 +0200 Subject: [PATCH 604/790] gnu: julia-tracker: Update to 0.2.22. * gnu/packages/julia-xyz.scm (julia-tracker): Update to 0.2.22. [source]: Remove patch. [propagated-inputs]: Add julia-functors, julia-logexpfunctions, julia-optimisers. * gnu/packages/patches/julia-tracker-16-compat.patch: Remove file. * gnu/local.mk (dist_patch_DATA): Remove it. --- gnu/local.mk | 1 - gnu/packages/julia-xyz.scm | 8 ++-- .../patches/julia-tracker-16-compat.patch | 40 ------------------- 3 files changed, 5 insertions(+), 44 deletions(-) delete mode 100644 gnu/packages/patches/julia-tracker-16-compat.patch diff --git a/gnu/local.mk b/gnu/local.mk index faad95d902..45d05de02d 100644 --- a/gnu/local.mk +++ b/gnu/local.mk @@ -1378,7 +1378,6 @@ dist_patch_DATA = \ %D%/packages/patches/json-c-0.12-CVE-2020-12762.patch \ %D%/packages/patches/jsoncpp-pkg-config-version.patch \ %D%/packages/patches/julia-SOURCE_DATE_EPOCH-mtime.patch \ - %D%/packages/patches/julia-tracker-16-compat.patch \ %D%/packages/patches/libffi-3.3-powerpc-fixes.patch \ %D%/packages/patches/libffi-float128-powerpc64le.patch \ %D%/packages/patches/libgeotiff-fix-tests-with-proj-9.1.1.patch \ diff --git a/gnu/packages/julia-xyz.scm b/gnu/packages/julia-xyz.scm index 39062f5971..87424eea88 100644 --- a/gnu/packages/julia-xyz.scm +++ b/gnu/packages/julia-xyz.scm @@ -5784,7 +5784,7 @@ package.") (define-public julia-tracker (package (name "julia-tracker") - (version "0.2.12") + (version "0.2.22") (source (origin (method git-fetch) @@ -5793,16 +5793,18 @@ package.") (commit (string-append "v" version)))) (file-name (git-file-name name version)) (sha256 - (base32 "1s4mdywbp7nli7z985fqaj1rs4i6d92b1jx3lhg0qhk1s5wc0v8j")) - (patches (search-patches "julia-tracker-16-compat.patch")))) + (base32 "0sxncn999dc5j15y0h3cw28x41pv5qjaw64drhy1y4rn3na48504")))) (build-system julia-build-system) (propagated-inputs (list julia-adapt julia-diffrules julia-forwarddiff + julia-functors + julia-logexpfunctions julia-macrotools julia-nanmath julia-nnlib + julia-optimisers julia-requires julia-specialfunctions)) (native-inputs diff --git a/gnu/packages/patches/julia-tracker-16-compat.patch b/gnu/packages/patches/julia-tracker-16-compat.patch deleted file mode 100644 index 4fff423e44..0000000000 --- a/gnu/packages/patches/julia-tracker-16-compat.patch +++ /dev/null @@ -1,40 +0,0 @@ -https://github.com/FluxML/Tracker.jl/commit/f6550ba38a9ea5802e2de4fa9c939929ba711f0d.patch -from an upstream pull request -https://github.com/FluxML/Tracker.jl/pull/94 - - -From f6550ba38a9ea5802e2de4fa9c939929ba711f0d Mon Sep 17 00:00:00 2001 -From: Michael Abbott -Date: Wed, 3 Feb 2021 22:58:33 +0100 -Subject: [PATCH] two fixes for 1.6 - ---- - src/lib/array.jl | 2 +- - src/lib/real.jl | 1 + - 2 files changed, 2 insertions(+), 1 deletion(-) - -diff --git a/src/lib/array.jl b/src/lib/array.jl -index 92f2b39..f8cbbac 100644 ---- a/src/lib/array.jl -+++ b/src/lib/array.jl -@@ -298,7 +298,7 @@ Base.reverse(xs::TrackedArray; dims) = track(reverse, xs, dims = dims) - @grad reverse(xs; dims) = reverse(data(xs), dims = dims), Δ -> (reverse(Δ, dims = dims), nothing) - Base.reverse(xs::TrackedVector) = track(reverse, xs) - @grad reverse(xs::TrackedVector) = reverse(data(xs)), Δ -> (reverse(Δ),) --Base.reverse(xs::TrackedVector, start, stop) = track(reverse, xs, start, stop) -+Base.reverse(xs::TrackedVector, start::Integer, stop::Integer) = track(reverse, xs, start, stop) - @grad reverse(xs, start, stop) = reverse(data(xs), start, stop), Δ -> (reverse(Δ, start, stop), nothing, nothing) - - function _kron(mat1::AbstractMatrix,mat2::AbstractMatrix) -diff --git a/src/lib/real.jl b/src/lib/real.jl -index 737afd8..e1975ac 100644 ---- a/src/lib/real.jl -+++ b/src/lib/real.jl -@@ -55,6 +55,7 @@ for f in :[isinf, isnan, isfinite].args - end - - Printf.fix_dec(x::TrackedReal, n::Int, a...) = Printf.fix_dec(data(x), n, a...) -+Printf.tofloat(x::TrackedReal) = Printf.tofloat(data(x)) - - Base.float(x::TrackedReal) = x - From cb1f6878c190da135d718d47a6184e2efa992b4a Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Tue, 13 Dec 2022 21:54:43 +0200 Subject: [PATCH 605/790] gnu: julia-specialfunctions: Update to 1.8.7. * gnu/packages/julia-xyz.scm (julia-specialfunctions): Update to 1.8.7. [propagated-inputs]: Add julia-irrationalconstants. --- gnu/packages/julia-xyz.scm | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/gnu/packages/julia-xyz.scm b/gnu/packages/julia-xyz.scm index 87424eea88..c9a270c653 100644 --- a/gnu/packages/julia-xyz.scm +++ b/gnu/packages/julia-xyz.scm @@ -5265,7 +5265,7 @@ timsort and radixsort.") (define-public julia-specialfunctions (package (name "julia-specialfunctions") - (version "1.6.0") + (version "1.8.7") (source (origin (method git-fetch) @@ -5274,12 +5274,13 @@ timsort and radixsort.") (commit (string-append "v" version)))) (file-name (git-file-name name version)) (sha256 - (base32 "0nfpnglx7zl9g20w2mgfkg17hcw9ri0shaq2rwplj0ij5pwz8yf0")))) + (base32 "0shlgx9lkbjb1awdf5lrbkq06bmkyahc92qay2a049b4lvqrhj7a")))) (build-system julia-build-system) (inputs (list julia-chainrulestestutils)) (propagated-inputs (list julia-chainrulescore + julia-irrationalconstants julia-logexpfunctions julia-openspecfun-jll)) (home-page "https://github.com/JuliaMath/SpecialFunctions.jl") From 4c66bcdf4771e8e1fb032f3a2207d7d2b9b09fb3 Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Wed, 14 Dec 2022 11:24:45 +0200 Subject: [PATCH 606/790] gnu: julia-lazyarrays: Update to 0.22.16. * gnu/packages/julia-xyz.scm (julia-lazyarrays): Update to 0.22.16. [propagated-inputs]: Add julia-aqua. [native-inputs]: Add julia-aqua. --- gnu/packages/julia-xyz.scm | 10 ++++++---- 1 file changed, 6 insertions(+), 4 deletions(-) diff --git a/gnu/packages/julia-xyz.scm b/gnu/packages/julia-xyz.scm index c9a270c653..61e1d6f5fa 100644 --- a/gnu/packages/julia-xyz.scm +++ b/gnu/packages/julia-xyz.scm @@ -3423,7 +3423,7 @@ equations in string literals in the Julia language.") (define-public julia-lazyarrays (package (name "julia-lazyarrays") - (version "0.22.2") + (version "0.22.16") (source (origin (method git-fetch) @@ -3432,7 +3432,7 @@ equations in string literals in the Julia language.") (commit (string-append "v" version)))) (file-name (git-file-name name version)) (sha256 - (base32 "17rhlrmgfvdw8w62pg32ikr9j4xy2ylr7mx7ar0hnpzryv929rp5")))) + (base32 "127yld4f26lchw5jwp30g2jkjbm7narfsxwcbggy7dfp43s531c5")))) (build-system julia-build-system) (arguments (list @@ -3445,13 +3445,15 @@ equations in string literals in the Julia language.") (substitute* "test/multests.jl" (("Int64") "Int32")))))))) (propagated-inputs - (list julia-arraylayouts + (list julia-aqua + julia-arraylayouts julia-fillarrays julia-macrotools julia-matrixfactorizations julia-staticarrays)) (native-inputs - (list julia-tracker)) + (list julia-aqua + julia-tracker)) (home-page "https://github.com/JuliaArrays/LazyArrays.jl") (synopsis "Lazy arrays and linear algebra") (description "This package supports lazy analogues of array operations like From 2f63589b9b2c9349e2d25ce599d6e21e0cc5309a Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Wed, 14 Dec 2022 11:28:14 +0200 Subject: [PATCH 607/790] gnu: julia-bson: Update to 0.3.6. * gnu/packages/julia-xyz.scm (julia-bson): Update to 0.3.6. --- gnu/packages/julia-xyz.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/julia-xyz.scm b/gnu/packages/julia-xyz.scm index 61e1d6f5fa..a6934a6a54 100644 --- a/gnu/packages/julia-xyz.scm +++ b/gnu/packages/julia-xyz.scm @@ -601,7 +601,7 @@ A @code{BlockBandedMatrix} is a subtype of @code{BlockMatrix} of (define-public julia-bson (package (name "julia-bson") - (version "0.3.3") + (version "0.3.6") (source (origin (method git-fetch) @@ -610,7 +610,7 @@ A @code{BlockBandedMatrix} is a subtype of @code{BlockMatrix} of (commit (string-append "v" version)))) (file-name (git-file-name name version)) (sha256 - (base32 "1l5608ma2ys7v2gpcqbiv9mwfc6yrlqkihrfx1pf7fgv5llhd4fn")))) + (base32 "1accra3casg66fhn5r07hz3rgs7qf9ld9ajnz8f80aid85zyp891")))) (build-system julia-build-system) (native-inputs (list julia-dataframes)) From 3fe107790287f6e8fe2c8b570152e89c32532c6c Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Wed, 14 Dec 2022 11:46:39 +0200 Subject: [PATCH 608/790] gnu: julia-interpolations: Update to 0.13.6. * gnu/packages/julia-xyz.scm (julia-interpolations): Update to 0.13.6. [propagated-inputs]: Add julia-chainrulescore. [native-inputs]: Add julia-colorvectorspace. --- gnu/packages/julia-xyz.scm | 11 +++++++---- 1 file changed, 7 insertions(+), 4 deletions(-) diff --git a/gnu/packages/julia-xyz.scm b/gnu/packages/julia-xyz.scm index a6934a6a54..0f060aecdd 100644 --- a/gnu/packages/julia-xyz.scm +++ b/gnu/packages/julia-xyz.scm @@ -3021,7 +3021,7 @@ each one has a fixed size. Currently support inline strings from 1 byte up to (define-public julia-interpolations (package (name "julia-interpolations") - (version "0.13.3") + (version "0.13.6") (source (origin (method git-fetch) @@ -3030,7 +3030,7 @@ each one has a fixed size. Currently support inline strings from 1 byte up to (commit (string-append "v" version)))) (file-name (git-file-name name version)) (sha256 - (base32 "1236c20k388qlh7k74mhf7hkbn0vf7ss8b1rgh1a6aj0234ayfnc")))) + (base32 "1skzvgd63rhj1zpn45gi3974rbrir9p2y17zyfmkz6c6nird7bkj")))) (build-system julia-build-system) (arguments (list @@ -3043,16 +3043,19 @@ each one has a fixed size. Currently support inline strings from 1 byte up to (target-x86-32?))))) (propagated-inputs (list julia-axisalgorithms + julia-chainrulescore julia-offsetarrays julia-ratios julia-requires julia-staticarrays julia-woodburymatrices)) (native-inputs - (list julia-dualnumbers + (list julia-colorvectorspace + julia-dualnumbers julia-forwarddiff julia-offsetarrays - julia-unitful julia-zygote)) + julia-unitful + julia-zygote)) (home-page "https://github.com/JuliaMath/Interpolations.jl") (synopsis "Continuous interpolation of discrete datasets") (description "This package implements a variety of interpolation schemes for From b4e9e72ecf722fe7397b49e729f2346824769c04 Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Wed, 14 Dec 2022 11:55:04 +0200 Subject: [PATCH 609/790] gnu: julia-requires: Update to 1.3.0. * gnu/packages/julia-xyz.scm (julia-requires): Update to 1.3.0. [propagated-inputs, inputs]: Move packages ... [native-inputs]: ... to here. --- gnu/packages/julia-xyz.scm | 13 ++++++------- 1 file changed, 6 insertions(+), 7 deletions(-) diff --git a/gnu/packages/julia-xyz.scm b/gnu/packages/julia-xyz.scm index 0f060aecdd..9dfb7b0cd6 100644 --- a/gnu/packages/julia-xyz.scm +++ b/gnu/packages/julia-xyz.scm @@ -4869,7 +4869,7 @@ package can help create and update if need be.") (define-public julia-requires (package (name "julia-requires") - (version "1.1.3") + (version "1.3.0") (source (origin (method git-fetch) @@ -4878,14 +4878,13 @@ package can help create and update if need be.") (commit (string-append "v" version)))) (file-name (git-file-name name version)) (sha256 - (base32 "03hyfy7c0ma45b0y756j76awi3az2ii4bz4s8cxm3xw9yy1z7b01")))) + (base32 "0gmqs7f17aq500lbdff4ibws00f8m0pnzskvf4b3ig520xv3n3nm")))) (build-system julia-build-system) (arguments - (list #:parallel-tests? #f)) - (inputs ;required for test - (list julia-example)) - (propagated-inputs - (list julia-colors)) + (list #:parallel-tests? #f)) ; Test suite has race conditions. + (native-inputs + (list julia-colors + julia-example)) (home-page "https://github.com/JuliaPackaging/Requires.jl/") (synopsis "Faster package loader") (description "This package make loading packages faster, maybe. It From 24203f4c8bfb2e121d0cf9663cab7a010d969bb4 Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Wed, 14 Dec 2022 11:57:42 +0200 Subject: [PATCH 610/790] gnu: julia-colors: Update to 0.12.9. * gnu/packages/julia-xyz.scm (julia-colors): Update to 0.12.9. [arguments]: Add phase to skip ambiguities tests. [native-inputs]: Add julia-abstracttrees. --- gnu/packages/julia-xyz.scm | 14 ++++++++++++-- 1 file changed, 12 insertions(+), 2 deletions(-) diff --git a/gnu/packages/julia-xyz.scm b/gnu/packages/julia-xyz.scm index 9dfb7b0cd6..f642a6816e 100644 --- a/gnu/packages/julia-xyz.scm +++ b/gnu/packages/julia-xyz.scm @@ -895,7 +895,7 @@ transformations).") (define-public julia-colors (package (name "julia-colors") - (version "0.12.8") + (version "0.12.9") (source (origin (method git-fetch) @@ -904,12 +904,22 @@ transformations).") (commit (string-append "v" version)))) (file-name (git-file-name name version)) (sha256 - (base32 "0kx3hq7rf8p5zx6ly9k5j90zijmc7yrwmy96cgkl2ibdfbnhmya3")))) + (base32 "1g0fvvz09pfk6jxqrdplwkw1yywcqvwjd3ga24hblq71mah367n6")))) (build-system julia-build-system) + (arguments + (list + #:phases + #~(modify-phases %standard-phases + (add-after 'unpack 'adjust-tests + (lambda _ + (substitute* "test/runtests.jl" + ((".*detect_ambiguities.*") ""))))))) (propagated-inputs (list julia-colortypes julia-fixedpointnumbers julia-reexport)) + (native-inputs + (list julia-abstracttrees)) (home-page "https://github.com/JuliaGraphics/Colors.jl") (synopsis "Tools for dealing with color") (description "This package provides a wide array of functions for dealing From 0d8da17c29249eec535fd6ea311e22202229ddd7 Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Wed, 14 Dec 2022 11:58:45 +0200 Subject: [PATCH 611/790] gnu: julia-colorvectorspace: Update to 0.9.9. * gnu/packages/julia-xyz.scm (julia-colorvectorspace): Update to 0.9.9. [arguments]: Skip tests. [propagated-inputs]: Add julia-fixedpointnumbers. --- gnu/packages/julia-xyz.scm | 8 ++++++-- 1 file changed, 6 insertions(+), 2 deletions(-) diff --git a/gnu/packages/julia-xyz.scm b/gnu/packages/julia-xyz.scm index f642a6816e..2f29df20b8 100644 --- a/gnu/packages/julia-xyz.scm +++ b/gnu/packages/julia-xyz.scm @@ -990,7 +990,7 @@ with.") (define-public julia-colorvectorspace (package (name "julia-colorvectorspace") - (version "0.9.7") + (version "0.9.9") (source (origin (method git-fetch) @@ -999,10 +999,14 @@ with.") (commit (string-append "v" version)))) (file-name (git-file-name name version)) (sha256 - (base32 "02gk7f5g5wjxdasbjf8bvv1m7clksh7mw1xmygjdirjz1q0d6dwi")))) + (base32 "07scws2bn2z3f2crhnx1zxk3zk3vzfv9iz6lv3i9785nplmsgdx9")))) (build-system julia-build-system) + (arguments + (list + #:tests? #f)) ; TODO: Reenable the test suite. (propagated-inputs (list julia-colortypes + julia-fixedpointnumbers julia-specialfunctions julia-tensorcore)) (native-inputs From d0d99aa75cd7e2959b38d2c5220c672eee8f8f09 Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Wed, 14 Dec 2022 12:19:55 +0200 Subject: [PATCH 612/790] gnu: julia-plotutils: Update to 1.2.0. * gnu/packages/julia-xyz.scm (julia-plotutils): Update to 1.2.0. [arguments]: Add a phase to adjust the test suite. --- gnu/packages/julia-xyz.scm | 13 +++++++++++-- 1 file changed, 11 insertions(+), 2 deletions(-) diff --git a/gnu/packages/julia-xyz.scm b/gnu/packages/julia-xyz.scm index 2f29df20b8..d838c4677d 100644 --- a/gnu/packages/julia-xyz.scm +++ b/gnu/packages/julia-xyz.scm @@ -4326,7 +4326,7 @@ actual computation.") (define-public julia-plotutils (package (name "julia-plotutils") - (version "1.0.15") + (version "1.2.0") (source (origin (method git-fetch) @@ -4335,8 +4335,17 @@ actual computation.") (commit (string-append "v" version)))) (file-name (git-file-name name version)) (sha256 - (base32 "12aw5gkkcfhpczv2w510k65w1j0hjnh825ihimi223v8plsi5105")))) + (base32 "1yml9ayaniqnzx5r8sfjckifcm99ck7qhc19cd8fs0bwzkh7nza7")))) (build-system julia-build-system) + (arguments + (list + #:phases + #~(modify-phases %standard-phases + (add-after 'unpack 'adjust-test-suite + (lambda _ + (substitute* "test/runtests.jl" + (("(@test_throws) ErrorException (.*notacolor)" _ @test notacolor) + (string-append @test " ArgumentError " notacolor)))))))) (propagated-inputs (list julia-colors julia-colorschemes From 2c838a6fc75b0289714694ce0435b5811fb9e9ce Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Wed, 14 Dec 2022 14:55:55 +0200 Subject: [PATCH 613/790] gnu: julia-indexablebitvectors: Limit to 64-bit systems. * gnu/packages/julia-xyz.scm (julia-indexablebitvectors) [supported-systems]: New field. --- gnu/packages/julia-xyz.scm | 3 +++ 1 file changed, 3 insertions(+) diff --git a/gnu/packages/julia-xyz.scm b/gnu/packages/julia-xyz.scm index d838c4677d..cae6b9237c 100644 --- a/gnu/packages/julia-xyz.scm +++ b/gnu/packages/julia-xyz.scm @@ -2903,6 +2903,9 @@ number of occurrences of bit @code{b} in @code{bv[1:i]} index of i-th occurrence of @code{b} in @code{bv}. @end itemize and other shortcuts or types.") + ;; There are plenty of places in the code which rely on the + ;; length of an Integer in a 64-bit system. + (supported-systems %64bit-supported-systems) (license license:expat))) (define-public julia-indexing From 160974597edefb0f964237c903bb42460e461f8f Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Wed, 14 Dec 2022 15:05:09 +0200 Subject: [PATCH 614/790] gnu: julia-blockarrays: Update to 0.16.23. * gnu/packages/julia-xyz.scm (julia-blockarrays): Update to 0.16.23. [native-inputs]: Remove julia-lazyarrays; add julia-aqua. --- gnu/packages/julia-xyz.scm | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/gnu/packages/julia-xyz.scm b/gnu/packages/julia-xyz.scm index cae6b9237c..e55687eadc 100644 --- a/gnu/packages/julia-xyz.scm +++ b/gnu/packages/julia-xyz.scm @@ -527,7 +527,7 @@ and amino acids that are used ny otherBioJulia packages.") (define-public julia-blockarrays (package (name "julia-blockarrays") - (version "0.16.8") + (version "0.16.23") (source (origin (method git-fetch) @@ -536,7 +536,7 @@ and amino acids that are used ny otherBioJulia packages.") (commit (string-append "v" version)))) (file-name (git-file-name name version)) (sha256 - (base32 "1by26036fk9mawmcgqxpwizgbs398v9p6vrbsgg7h6llqn3q9iw1")))) + (base32 "14gby25ixbp9ha0y2aj4gnjkzha4c7v4y3sicicgbkysnq921qd0")))) (build-system julia-build-system) (arguments (list @@ -552,7 +552,7 @@ and amino acids that are used ny otherBioJulia packages.") (list julia-arraylayouts julia-fillarrays)) (native-inputs - (list julia-lazyarrays + (list julia-aqua julia-offsetarrays julia-staticarrays)) (home-page "https://github.com/JuliaArrays/BlockArrays.jl") From 826e6414a4f7229a7ba616109e105c61adc4d7c4 Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Wed, 14 Dec 2022 15:05:10 +0200 Subject: [PATCH 615/790] gnu: julia-scanbyte: Update to 0.3.2. * gnu/packages/julia-xyz.scm (julia-scanbyte): Update to 0.3.2. --- gnu/packages/julia-xyz.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/julia-xyz.scm b/gnu/packages/julia-xyz.scm index e55687eadc..d3d8bb5c4e 100644 --- a/gnu/packages/julia-xyz.scm +++ b/gnu/packages/julia-xyz.scm @@ -5082,7 +5082,7 @@ a loadable module.") (define-public julia-scanbyte (package (name "julia-scanbyte") - (version "0.3") + (version "0.3.2") (source (origin (method git-fetch) @@ -5091,7 +5091,7 @@ a loadable module.") (commit (string-append "v" version)))) (file-name (git-file-name name version)) (sha256 - (base32 "0dqqa3d7c87358144pji6ik8xlki2hj0hkvjs72j5aypfms8rwn3")))) + (base32 "1c18hkcb0h6l437v2s02kijjkyly91mqark84czvh8yzxm19hr7k")))) (build-system julia-build-system) (propagated-inputs (list julia-simd)) From 53436955c42430690457e89399984709894616c0 Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Wed, 14 Dec 2022 16:10:32 +0200 Subject: [PATCH 616/790] gnu: julia-scanbyte: Limit to x86_64-linux. * gnu/packages/julia-xyz.scm (julia-scanbyte)[supported-systems]: New field. --- gnu/packages/julia-xyz.scm | 2 ++ 1 file changed, 2 insertions(+) diff --git a/gnu/packages/julia-xyz.scm b/gnu/packages/julia-xyz.scm index d3d8bb5c4e..6a610a3268 100644 --- a/gnu/packages/julia-xyz.scm +++ b/gnu/packages/julia-xyz.scm @@ -5100,6 +5100,8 @@ a loadable module.") (description "This package finds the first occurrence of a byte or set of bytes in a chunk of memory. Think of it like a much faster version of @code{findfirst} that only iterates over bytes in memory.") + ;; https://github.com/jakobnissen/ScanByte.jl/issues/2 + (supported-systems '("x86_64-linux")) (license license:expat))) (define-public julia-scratch From bedb7311e10dc54c97c215266bbe12bb70b70ece Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Wed, 14 Dec 2022 17:17:13 +0200 Subject: [PATCH 617/790] gnu: julia-matrixfactorizations: Update to 0.9.3. * gnu/packages/julia-xyz.scm (julia-matrixfactorizations): Update to 0.9.3. [arguments]: Re-enable one of the skipped tests. --- gnu/packages/julia-xyz.scm | 8 +++----- 1 file changed, 3 insertions(+), 5 deletions(-) diff --git a/gnu/packages/julia-xyz.scm b/gnu/packages/julia-xyz.scm index 6a610a3268..f85be84ebf 100644 --- a/gnu/packages/julia-xyz.scm +++ b/gnu/packages/julia-xyz.scm @@ -3634,7 +3634,7 @@ comes from the fact that @code{M == map(f, A)}.") (define-public julia-matrixfactorizations (package (name "julia-matrixfactorizations") - (version "0.8.4") + (version "0.9.3") (source (origin (method git-fetch) @@ -3643,7 +3643,7 @@ comes from the fact that @code{M == map(f, A)}.") (commit (string-append "v" version)))) (file-name (git-file-name name version)) (sha256 - (base32 "15zvcv2l4iqmjpnqjyx2kry7a85p652nbjy9pj3wq0piksqcz4jb")))) + (base32 "0sqmig01irmvh617h2rsw44hl39qwv2913nlqjsdz9si5vli2hsl")))) (build-system julia-build-system) (arguments (list @@ -3651,10 +3651,8 @@ comes from the fact that @code{M == map(f, A)}.") #~(modify-phases %standard-phases (add-after 'link-depot 'skip-failing-test (lambda _ - ;; Tests with math functions are hard. (substitute* "test/test_ul.jl" - (("@test @inferred\\(logdet") "@test @test_nowarn(logdet") - ;; Also skip the REPL test. + ;; Don't warn on the REPL test. (("test String") "test_nowarn String"))))))) (propagated-inputs (list julia-arraylayouts)) From 3dc512f9a21dc14df4b52a124d1952a83d881169 Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Wed, 14 Dec 2022 19:32:12 +0200 Subject: [PATCH 618/790] gnu: Add julia-static-0.6. * gnu/packages/julia-xyz.scm (julia-static-0.6): New variable. --- gnu/packages/julia-xyz.scm | 15 +++++++++++++++ 1 file changed, 15 insertions(+) diff --git a/gnu/packages/julia-xyz.scm b/gnu/packages/julia-xyz.scm index f85be84ebf..76d5fe9ca3 100644 --- a/gnu/packages/julia-xyz.scm +++ b/gnu/packages/julia-xyz.scm @@ -5433,6 +5433,21 @@ There are multiple ways to understand @code{StackView}: types and a common interface that is shared between them.") (license license:expat))) +(define-public julia-static-0.6 + (package + (inherit julia-static) + (name "julia-static") + (version "0.6.6") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/SciML/Static.jl") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 "03ri8nl046cz7l433p0nlr84yywxvjykyymqparm8lxxwkv0rxqd")))))) + (define-public julia-staticarrays (package (name "julia-staticarrays") From 1529ba07deb82e1bea236a8c65a670a37f8b2197 Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Wed, 14 Dec 2022 19:32:20 +0200 Subject: [PATCH 619/790] gnu: julia-arrayinterface: Update to 5.0.8. * gnu/packages/julia-xyz.scm (julia-arrayinterface): Update to 5.0.8. [propagated-inputs]: Remove julia-static; add julia-compat and julia-static-0.6. [native-inputs]: Add julia-static-0.6. --- gnu/packages/julia-xyz.scm | 10 ++++++---- 1 file changed, 6 insertions(+), 4 deletions(-) diff --git a/gnu/packages/julia-xyz.scm b/gnu/packages/julia-xyz.scm index 76d5fe9ca3..99c42ce6f4 100644 --- a/gnu/packages/julia-xyz.scm +++ b/gnu/packages/julia-xyz.scm @@ -149,7 +149,7 @@ provides functions to run a few automatable checks for Julia packages.") (define-public julia-arrayinterface (package (name "julia-arrayinterface") - (version "3.1.19") + (version "5.0.8") (source (origin (method git-fetch) @@ -158,7 +158,7 @@ provides functions to run a few automatable checks for Julia packages.") (commit (string-append "v" version)))) (file-name (git-file-name name version)) (sha256 - (base32 "0cmldnzvdgmfnrnrzgj6v1mfr2rvk5096392rwmhd3iyx7v0pq33")))) + (base32 "0b0h4ihc8sykd96rn16vpk5kfk0p1si5iim61cixk9x12ma8ia3h")))) (build-system julia-build-system) (arguments ;; XXXX: Unexpected failures for i686, e.g., @@ -168,15 +168,17 @@ provides functions to run a few automatable checks for Julia packages.") (list #:tests? (not (or (%current-target-system) (target-x86-32?))))) (propagated-inputs - (list julia-ifelse + (list julia-compat + julia-ifelse julia-requires - julia-static)) + julia-static-0.6)) (native-inputs (list julia-aqua julia-bandedmatrices julia-blockbandedmatrices julia-ifelse julia-offsetarrays + julia-static-0.6 julia-staticarrays)) (home-page "https://github.com/JuliaArrays/ArrayInterface.jl") (synopsis "Base array interface primitives") From 1ebdd56b954e5136ed16e9b8581be5e05d485c2d Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Wed, 14 Dec 2022 19:32:20 +0200 Subject: [PATCH 620/790] gnu: julia-bandedmatrices: Update to 0.17.9. * gnu/packages/julia-xyz.scm (julia-bandedmatrices): Update to 0.17.9. [propagated-inputs]: Add julia-aqua. [native-inputs]: Add julia-aqua. --- gnu/packages/julia-xyz.scm | 10 ++++++---- 1 file changed, 6 insertions(+), 4 deletions(-) diff --git a/gnu/packages/julia-xyz.scm b/gnu/packages/julia-xyz.scm index 99c42ce6f4..ae2d6a1f9c 100644 --- a/gnu/packages/julia-xyz.scm +++ b/gnu/packages/julia-xyz.scm @@ -311,7 +311,7 @@ axes, allowing column names or interval selections.") (define-public julia-bandedmatrices (package (name "julia-bandedmatrices") - (version "0.16.10") + (version "0.17.9") (source (origin (method git-fetch) @@ -320,13 +320,15 @@ axes, allowing column names or interval selections.") (commit (string-append "v" version)))) (file-name (git-file-name name version)) (sha256 - (base32 "0rlfj9gr9ss621v5kw5b06206yaak21s2vq9vk7r8a7p2ylncism")))) + (base32 "0nrcasjdpwf15z7l2lzyhxjqxlnqk5if78s15sh4gdgxf9kzj3a6")))) (build-system julia-build-system) (propagated-inputs - (list julia-arraylayouts + (list julia-aqua + julia-arraylayouts julia-fillarrays)) (native-inputs - (list julia-genericlinearalgebra)) + (list julia-aqua + julia-genericlinearalgebra)) (home-page "https://github.com/JuliaMatrices/BandedMatrices.jl") (synopsis "Julia package for representing banded matrices") (description "This package supports representing banded matrices by only From 611d7427ebb471d636748026cd35bcfb5238881b Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Wed, 14 Dec 2022 19:32:21 +0200 Subject: [PATCH 621/790] gnu: julia-blockbandedmatrices: Update to 0.11.9. * gnu/packages/julia-xyz.scm (julia-blockbandedmatrices): Update to 0.11.9. --- gnu/packages/julia-xyz.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/julia-xyz.scm b/gnu/packages/julia-xyz.scm index ae2d6a1f9c..cdd29504cf 100644 --- a/gnu/packages/julia-xyz.scm +++ b/gnu/packages/julia-xyz.scm @@ -577,7 +577,7 @@ access to the full matrix to use in in for example a linear solver.") (define-public julia-blockbandedmatrices (package (name "julia-blockbandedmatrices") - (version "0.10.7") + (version "0.11.9") (source (origin (method git-fetch) @@ -586,7 +586,7 @@ access to the full matrix to use in in for example a linear solver.") (commit (string-append "v" version)))) (file-name (git-file-name name version)) (sha256 - (base32 "10n1r6kmmv2wa307jfg9y2m6p16j8hngjp3fjavpbdy1r5haasm9")))) + (base32 "1qag5awl8cmsyhpajv6llhpqbzxfii1bacppbjvmb1fqs9s0lifd")))) (build-system julia-build-system) (propagated-inputs (list julia-arraylayouts From 204ad23d796aa004461044f3504f825309a13ac6 Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Wed, 14 Dec 2022 19:39:16 +0200 Subject: [PATCH 622/790] gnu: julia-ellipsisnotation: Update to 1.6.0. * gnu/packages/julia-xyz.scm (julia-ellipsisnotation): Update to 1.6.0. [arguments]: Remove phase adjusting the test suite. --- gnu/packages/julia-xyz.scm | 13 ++----------- 1 file changed, 2 insertions(+), 11 deletions(-) diff --git a/gnu/packages/julia-xyz.scm b/gnu/packages/julia-xyz.scm index cdd29504cf..81d59ff620 100644 --- a/gnu/packages/julia-xyz.scm +++ b/gnu/packages/julia-xyz.scm @@ -1801,7 +1801,7 @@ combinations of dual numbers with predefined Julia numeric types.") (define-public julia-ellipsisnotation (package (name "julia-ellipsisnotation") - (version "1.1.0") + (version "1.6.0") (source (origin (method git-fetch) @@ -1810,17 +1810,8 @@ combinations of dual numbers with predefined Julia numeric types.") (commit (string-append "v" version)))) (file-name (git-file-name name version)) (sha256 - (base32 "0py46kxl702r8pw3v7x4cqllf7yc91b0dr7vb60xh2qi7d6y3jc7")))) + (base32 "0l4fc180chhxlq9d67122c0lgq2hfsxsmcgml2bfl2rnh13gya2b")))) (build-system julia-build-system) - (arguments - (list - #:phases - #~(modify-phases %standard-phases - (add-after 'link-depot 'adjust-test-suite - (lambda _ - (substitute* "test/runtests.jl" - ;; Seems to not play nicely with Julia-1.6. - ((".*basic.jl.*") ""))))))) (propagated-inputs (list julia-arrayinterface)) (home-page "https://github.com/ChrisRackauckas/EllipsisNotation.jl") From aae30d5420e944f6d318c34b90562d9d0fe7e181 Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Wed, 14 Dec 2022 20:47:37 +0200 Subject: [PATCH 623/790] gnu: julia-axisarrays: Update to 0.4.6. * gnu/packages/julia-xyz.scm (julia-axisarrays): Update to 0.4.6. --- gnu/packages/julia-xyz.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/julia-xyz.scm b/gnu/packages/julia-xyz.scm index 81d59ff620..f89ac7b585 100644 --- a/gnu/packages/julia-xyz.scm +++ b/gnu/packages/julia-xyz.scm @@ -280,7 +280,7 @@ axis (dimension).") (define-public julia-axisarrays (package (name "julia-axisarrays") - (version "0.4.4") + (version "0.4.6") (source (origin (method git-fetch) @@ -289,7 +289,7 @@ axis (dimension).") (commit (string-append "v" version)))) (file-name (git-file-name name version)) (sha256 - (base32 "03kzan1lm4fxfhzv1xjg3ysf6y7nagcc61vfz15kvdrp1dqxlynk")))) + (base32 "1bsd6y866ldfb4072hfm8fvc2k0vy72z2blcwfy2mpj8dlyskx3n")))) (build-system julia-build-system) (propagated-inputs (list julia-rangearrays From bc7f25239e4c67c05a7984b055bf7a84a14526d5 Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Wed, 14 Dec 2022 20:47:42 +0200 Subject: [PATCH 624/790] gnu: julia-graphics: Update to 1.1.2. * gnu/packages/julia-xyz.scm (julia-graphics): Update to 1.1.2. --- gnu/packages/julia-xyz.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/julia-xyz.scm b/gnu/packages/julia-xyz.scm index f89ac7b585..0ed7db6a7e 100644 --- a/gnu/packages/julia-xyz.scm +++ b/gnu/packages/julia-xyz.scm @@ -2446,7 +2446,7 @@ visualisation applications.") (define-public julia-graphics (package (name "julia-graphics") - (version "1.1.0") + (version "1.1.2") (source (origin (method git-fetch) @@ -2455,7 +2455,7 @@ visualisation applications.") (commit (string-append "v" version)))) (file-name (git-file-name name version)) (sha256 - (base32 "10h1s09v7qkvrjr6l678zamb1p248n8jv4rrwkf8g7d2bpfz9amn")))) + (base32 "083fppcbmchgnqp4xqdsd4asavq51jq31w8ak35ns701534hr82p")))) (build-system julia-build-system) (propagated-inputs (list julia-colors From b1f31d4e47730ba6acda1118d8816c97134c6076 Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Wed, 14 Dec 2022 20:47:42 +0200 Subject: [PATCH 625/790] gnu: julia-imageaxes: Update to 0.6.10. * gnu/packages/julia-xyz.scm (julia-imageaxes): Update to 0.6.10. [arguments]: Add a phase to skip a greyscale test. [propagated-inputs]: Add julia-imagebase. [native-inputs]: Add julia-aqua and julia-documenter. --- gnu/packages/julia-xyz.scm | 18 +++++++++++++++--- 1 file changed, 15 insertions(+), 3 deletions(-) diff --git a/gnu/packages/julia-xyz.scm b/gnu/packages/julia-xyz.scm index 0ed7db6a7e..a862a7d673 100644 --- a/gnu/packages/julia-xyz.scm +++ b/gnu/packages/julia-xyz.scm @@ -2573,7 +2573,7 @@ conditional ifelse. It is similar to @code{Core.ifelse} but it is extendable.") (define-public julia-imageaxes (package (name "julia-imageaxes") - (version "0.6.9") + (version "0.6.10") (source (origin (method git-fetch) @@ -2582,15 +2582,27 @@ conditional ifelse. It is similar to @code{Core.ifelse} but it is extendable.") (commit (string-append "v" version)))) (file-name (git-file-name name version)) (sha256 - (base32 "15zqxani1jjh8849s7rdps6b6prqdwv8yxx893y536vkpk7i07qd")))) + (base32 "15f3y46vcr88fplr7rlibrm3k852p8rzwid5dgmbhc03a8xqd50s")))) (build-system julia-build-system) + (arguments + (list + #:phases + #~(modify-phases %standard-phases + (add-after 'unpack 'adjust-tests + (lambda _ + (substitute* "test/runtests.jl" + ;; Skip the constantly failing grayscale test. + (("@test summary") "@test_broken summary"))))))) (propagated-inputs (list julia-axisarrays + julia-imagebase julia-imagecore julia-reexport julia-simpletraits)) (native-inputs - (list julia-unitful)) + (list julia-aqua + julia-documenter + julia-unitful)) (home-page "https://github.com/JuliaImages/ImageAxes.jl") (synopsis "Julia package for giving \"meaning\" to the axes of an image") (description "This small package supports the representation of images as From ff6d119829c86060ecfe8d99cf2996e7ceb0bd4b Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Wed, 14 Dec 2022 20:47:42 +0200 Subject: [PATCH 626/790] gnu: julia-paddedviews: Update to 0.5.11. * gnu/packages/julia-xyz.scm (julia-paddedviews): Update to 0.5.11. --- gnu/packages/julia-xyz.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/julia-xyz.scm b/gnu/packages/julia-xyz.scm index a862a7d673..dbe7f5d2b5 100644 --- a/gnu/packages/julia-xyz.scm +++ b/gnu/packages/julia-xyz.scm @@ -4215,7 +4215,7 @@ languages like Fortran.") (define-public julia-paddedviews (package (name "julia-paddedviews") - (version "0.5.8") + (version "0.5.11") (source (origin (method git-fetch) @@ -4224,7 +4224,7 @@ languages like Fortran.") (commit (string-append "v" version)))) (file-name (git-file-name name version)) (sha256 - (base32 "0ran2vj6ahlzib0g77y7g0jhavy3k9s2mqq23ybpgp9z677wf26h")))) + (base32 "1835q06g6ymqh1k7625ssahwm46j08370v2inb61y1lw8vd99f3x")))) (build-system julia-build-system) (propagated-inputs (list julia-offsetarrays)) From 5b19dffd98501b705e539497714d4894ed153192 Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Wed, 14 Dec 2022 22:24:42 +0200 Subject: [PATCH 627/790] gnu: julia-imagemetadata: Update to 0.9.8. * gnu/packages/julia-xyz.scm (julia-imagemetadata): Update to 0.9.8. [arguments]: Add phase to skip greyscale test. [propagated-inputs]: Remove julia-indirectarrays; add julia-imagebase. [native-inputs]: Add julia-indirectarrays. --- gnu/packages/julia-xyz.scm | 21 ++++++++++++++++----- 1 file changed, 16 insertions(+), 5 deletions(-) diff --git a/gnu/packages/julia-xyz.scm b/gnu/packages/julia-xyz.scm index dbe7f5d2b5..29e1cb0d90 100644 --- a/gnu/packages/julia-xyz.scm +++ b/gnu/packages/julia-xyz.scm @@ -2775,7 +2775,7 @@ It was split off from @code{Images.jl} to make image I/O more modular.") (define-public julia-imagemetadata (package (name "julia-imagemetadata") - (version "0.9.6") + (version "0.9.8") (source (origin (method git-fetch) @@ -2784,15 +2784,26 @@ It was split off from @code{Images.jl} to make image I/O more modular.") (commit (string-append "v" version)))) (file-name (git-file-name name version)) (sha256 - (base32 "0iv154ms370xgcr56bwsjl13iwmy671cbxjl9ld5yfj85pclcwi1")))) + (base32 "0rdzvya5szlkg5ds3fw7lpk47hn16655i6265czwf8fxs3hb1gvf")))) (build-system julia-build-system) + (arguments + (list + #:phases + #~(modify-phases %standard-phases + (add-after 'unpack 'adjust-tests + (lambda _ + (substitute* "test/operations.jl" + ;; Skip the constantly failing greyscale test. + (("\\@testset \\\"operations.*" all) + (string-append all " return\n")))))))) (propagated-inputs (list julia-axisarrays julia-imageaxes - julia-imagecore - julia-indirectarrays)) + julia-imagebase + julia-imagecore)) (native-inputs - (list julia-offsetarrays + (list julia-indirectarrays + julia-offsetarrays julia-simpletraits julia-unitful)) (home-page "https://github.com/JuliaImages/ImageMetadata.jl") From 30465558bd2ac1863013fd8382c0fc6b2233acc3 Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Thu, 8 Dec 2022 23:27:57 -0500 Subject: [PATCH 628/790] guix system: Skip initrd modules check when using --target. * guix/scripts/system.scm (perform-action): Do not call CHECK-INITRD-MODULES when the %current-target-system parameter is set. --- guix/scripts/system.scm | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/guix/scripts/system.scm b/guix/scripts/system.scm index 6482318168..6fd915cb5e 100644 --- a/guix/scripts/system.scm +++ b/guix/scripts/system.scm @@ -842,7 +842,10 @@ static checks." (check-mapped-devices os) (when (zero? (getuid)) (check-file-system-availability (operating-system-file-systems os)) - (check-initrd-modules os))) + (unless (%current-target-system) + ;; Skip the check if the user is making use of --target, as it cannot + ;; be checked against the running kernel. + (check-initrd-modules os)))) (mlet* %store-monad ((sys (system-derivation-for-action image action From e69259352a5a989b5cb5a572ad7e7af24c957def Mon Sep 17 00:00:00 2001 From: pukkamustard Date: Fri, 16 Dec 2022 13:25:00 +0000 Subject: [PATCH 629/790] gnu: Add ocaml-5.0. * gnu/packages/ocaml.scm (ocaml-5.0): New variable. Signed-off-by: Julien Lepiller --- gnu/packages/ocaml.scm | 61 ++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 61 insertions(+) diff --git a/gnu/packages/ocaml.scm b/gnu/packages/ocaml.scm index e0bedf74f9..376f06e02c 100644 --- a/gnu/packages/ocaml.scm +++ b/gnu/packages/ocaml.scm @@ -185,6 +185,67 @@ OCaml and can effectively bootstrap OCaml 4.07. This package produces a native @command{ocamlc} and a bytecode @command{ocamllex}.") (license license:expat)))) +(define-public ocaml-5.0 + (package + (name "ocaml") + (version "5.0.0") + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/ocaml/ocaml") + (commit version))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "1p0p8wldrnbr61wfy3x4122017g4k5gjvfwlg3mvlqn8r2fxn2m5")))) + (build-system gnu-build-system) + (native-search-paths + (list (search-path-specification + (variable "OCAMLPATH") + (files (list "lib/ocaml" "lib/ocaml/site-lib"))) + (search-path-specification + (variable "CAML_LD_LIBRARY_PATH") + (files (list "lib/ocaml/site-lib/stubslibs" + "lib/ocaml/site-lib/stublibs"))))) + (native-inputs + (list perl pkg-config)) + (inputs + (list libx11 libiberty ;needed for objdump support + zlib)) ;also needed for objdump support + (arguments + `(#:configure-flags '("--enable-ocamltest") + #:test-target "tests" + #:make-flags '("world.opt") + #:phases + (modify-phases %standard-phases + (add-after 'unpack 'patch-/bin/sh-references + (lambda* (#:key inputs #:allow-other-keys) + (let* ((sh (search-input-file inputs "/bin/sh")) + (quoted-sh (string-append "\"" sh "\""))) + (with-fluids ((%default-port-encoding #f)) + (for-each + (lambda (file) + (substitute* file + (("\"/bin/sh\"") + (begin + (format (current-error-port) "\ +patch-/bin/sh-references: ~a: changing `\"/bin/sh\"' to `~a'~%" + file quoted-sh) + quoted-sh)))) + (find-files "." "\\.ml$"))))))))) + (home-page "https://ocaml.org/") + (synopsis "The OCaml programming language") + (description + "OCaml is a general purpose industrial-strength programming language with +an emphasis on expressiveness and safety. Developed for more than 20 years at +Inria it benefits from one of the most advanced type systems and supports +functional, imperative and object-oriented styles of programming.") + ;; The compiler is distributed under qpl1.0 with a change to choice of + ;; law: the license is governed by the laws of France. The library is + ;; distributed under lgpl2.0. + (license (list license:qpl license:lgpl2.0)))) + + (define-public ocaml-4.14 (package (name "ocaml") From a58dfd3eed2b600bfda76b3ef8564cf46d4615cb Mon Sep 17 00:00:00 2001 From: pukkamustard Date: Fri, 16 Dec 2022 13:25:01 +0000 Subject: [PATCH 630/790] gnu: ocaml-findlib: Update to 1.9.5. * gnu/packages/ocaml.scm (ocaml-findlib): Update to 1.9.5. Signed-off-by: Julien Lepiller --- gnu/packages/ocaml.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/ocaml.scm b/gnu/packages/ocaml.scm index 376f06e02c..5772189648 100644 --- a/gnu/packages/ocaml.scm +++ b/gnu/packages/ocaml.scm @@ -1404,14 +1404,14 @@ to the other.") (define-public ocaml-findlib (package (name "ocaml-findlib") - (version "1.9.3") + (version "1.9.5") (source (origin (method url-fetch) (uri (string-append "http://download.camlcity.org/download/" "findlib" "-" version ".tar.gz")) (sha256 (base32 - "0hfcwamcvinmww59b5i4yxbf0kxyzkp5qv3d1c7ybn9q52vgq463")))) + "0w9578j1561f5gi51sn2jgxm3kh3sn88cpannhdkqcdg1kk08iqd")))) (build-system gnu-build-system) (native-inputs (list m4 ocaml)) From 616e81894692cc9364df3a1cd9e59260a0480c5b Mon Sep 17 00:00:00 2001 From: pukkamustard Date: Fri, 16 Dec 2022 13:25:02 +0000 Subject: [PATCH 631/790] gnu: Add ocaml5.0-findlib * gnu/packages/ocaml.scm (ocaml5.0-findlib): New variable. Signed-off-by: Julien Lepiller --- gnu/packages/ocaml.scm | 7 +++++++ 1 file changed, 7 insertions(+) diff --git a/gnu/packages/ocaml.scm b/gnu/packages/ocaml.scm index 5772189648..1ce4872674 100644 --- a/gnu/packages/ocaml.scm +++ b/gnu/packages/ocaml.scm @@ -1466,6 +1466,13 @@ compilers that can directly deal with packages.") (native-inputs (list m4 ocaml-4.09)))) +(define-public ocaml5.0-findlib + (package + (inherit ocaml-findlib) + (name "ocaml5.0-findlib") + (native-inputs + (list m4 ocaml-5.0)))) + (define-public ocaml-ounit2 (package (name "ocaml-ounit2") From 052ec8bcc73d1c37e20a8eba85b4431bcff5447c Mon Sep 17 00:00:00 2001 From: pukkamustard Date: Fri, 16 Dec 2022 13:25:03 +0000 Subject: [PATCH 632/790] guix: ocaml: Add package-with-ocaml5.0. * guix/build-system/ocaml.scm (package-with-ocaml5.0) (strip-ocaml5.0-variant): New variables. * gnu/packages/ocaml.scm (ocaml5.0-dune-bootstrap) (ocaml5.0-dune, ocaml5.0-dune-configurator) (ocaml5.0-csexp, ocaml5.0-result): New variables. Signed-off-by: Julien Lepiller --- gnu/packages/ocaml.scm | 54 ++++++++++++++++++++++++++++++++++--- guix/build-system/ocaml.scm | 27 +++++++++++++++++++ 2 files changed, 77 insertions(+), 4 deletions(-) diff --git a/gnu/packages/ocaml.scm b/gnu/packages/ocaml.scm index 1ce4872674..adbb76711e 100644 --- a/gnu/packages/ocaml.scm +++ b/gnu/packages/ocaml.scm @@ -1820,6 +1820,9 @@ following a very simple s-expression syntax.") (define ocaml4.09-dune-bootstrap (package-with-ocaml4.09 dune-bootstrap)) +(define ocaml5.0-dune-bootstrap + (package-with-ocaml5.0 dune-bootstrap)) + (define-public dune-configurator (package (inherit dune-bootstrap) @@ -1840,7 +1843,8 @@ following a very simple s-expression syntax.") (delete-file-recursively "vendor/pp")))))) (propagated-inputs (list ocaml-csexp)) - (properties `((ocaml4.09-variant . ,(delay ocaml4.09-dune-configurator)))) + (properties `((ocaml4.09-variant . ,(delay ocaml4.09-dune-configurator)) + (ocaml5.0-variant . ,(delay ocaml5.0-dune-configurator)))) (synopsis "Dune helper library for gathering system configuration") (description "Dune-configurator is a small library that helps writing OCaml scripts that test features available on the system, in order to generate @@ -1865,13 +1869,25 @@ config.h files for instance. Among other things, dune-configurator allows one t (propagated-inputs `(("ocaml-csexp" ,ocaml4.09-csexp))))) +(define-public ocaml5.0-dune-configurator + (package + (inherit dune-configurator) + (name "ocaml5.0-dune-configurator") + (arguments + `(,@(package-arguments dune-configurator) + #:dune ,ocaml5.0-dune-bootstrap + #:ocaml ,ocaml-5.0 + #:findlib ,ocaml5.0-findlib)) + (propagated-inputs (list ocaml5.0-csexp)))) + (define-public dune (package (inherit dune-bootstrap) (propagated-inputs (list dune-configurator)) (properties `((ocaml4.07-variant . ,(delay ocaml4.07-dune)) - (ocaml4.09-variant . ,(delay ocaml4.09-dune)))))) + (ocaml4.09-variant . ,(delay ocaml4.09-dune)) + (ocaml5.0-variant . ,(delay ocaml5.0-dune)))))) (define-public ocaml4.09-dune (package @@ -1893,6 +1909,12 @@ config.h files for instance. Among other things, dune-configurator allows one t (base32 "0l4x0x2fz135pljv88zj8y6w1ninsqw0gn1mdxzprd6wbxbyn8wr")))))) +(define-public ocaml5.0-dune + (package + (inherit ocaml5.0-dune-bootstrap) + (propagated-inputs + (list ocaml5.0-dune-configurator)))) + (define-public ocaml-csexp (package (name "ocaml-csexp") @@ -1918,7 +1940,8 @@ config.h files for instance. Among other things, dune-configurator allows one t #t))))) (propagated-inputs (list ocaml-result)) - (properties `((ocaml4.09-variant . ,(delay ocaml4.09-csexp)))) + (properties `((ocaml4.09-variant . ,(delay ocaml4.09-csexp)) + (ocaml5.0-variant . ,(delay ocaml5.0-csexp)))) (home-page "https://github.com/ocaml-dune/csexp") (synopsis "Parsing and printing of S-expressions in Canonical form") (description "This library provides minimal support for Canonical @@ -1947,6 +1970,18 @@ module of this library is parameterised by the type of S-expressions.") (propagated-inputs `(("ocaml-result" ,ocaml4.09-result))))) +(define-public ocaml5.0-csexp + (package + (inherit ocaml-csexp) + (name "ocaml5.0-csexp") + (arguments + `(#:ocaml ,ocaml-5.0 + #:findlib ,ocaml5.0-findlib + ,@(substitute-keyword-arguments (package-arguments ocaml-csexp) + ((#:dune _) ocaml5.0-dune-bootstrap)))) + (propagated-inputs + `(("ocaml-result" ,ocaml5.0-result))))) + (define-public ocaml-migrate-parsetree (package (name "ocaml-migrate-parsetree") @@ -2132,7 +2167,8 @@ bitsrings in Erlang style as primitives to the language."))) (arguments `(#:test-target "." #:dune ,dune-bootstrap)) - (properties `((ocaml4.09-variant . ,(delay ocaml4.09-result)))) + (properties `((ocaml4.09-variant . ,(delay ocaml4.09-result)) + (ocaml5.0-variant . ,(delay ocaml5.0-result)))) (home-page "https://github.com/janestreet/result") (synopsis "Compatibility Result module") (description "Uses the new result type defined in OCaml >= 4.03 while @@ -2149,6 +2185,16 @@ defined in this library.") #:dune ,ocaml4.09-dune-bootstrap #:ocaml ,ocaml-4.09 #:findlib ,ocaml4.09-findlib)))) + +(define-public ocaml5.0-result + (package + (inherit ocaml-result) + (name "ocaml5.0-result") + (arguments + `(#:test-target "." + #:dune ,ocaml5.0-dune-bootstrap + #:ocaml ,ocaml-5.0 + #:findlib ,ocaml5.0-findlib)))) (define-public ocaml-topkg (package diff --git a/guix/build-system/ocaml.scm b/guix/build-system/ocaml.scm index 5ced9d243b..b08985cd4d 100644 --- a/guix/build-system/ocaml.scm +++ b/guix/build-system/ocaml.scm @@ -32,6 +32,8 @@ strip-ocaml4.07-variant package-with-ocaml4.09 strip-ocaml4.09-variant + package-with-ocaml5.0 + strip-ocaml5.0-variant default-findlib default-ocaml lower @@ -111,6 +113,18 @@ (let ((module (resolve-interface '(gnu packages ocaml)))) (module-ref module 'ocaml4.09-dune))) +(define (default-ocaml5.0) + (let ((ocaml (resolve-interface '(gnu packages ocaml)))) + (module-ref ocaml 'ocaml-5.0))) + +(define (default-ocaml5.0-findlib) + (let ((module (resolve-interface '(gnu packages ocaml)))) + (module-ref module 'ocaml5.0-findlib))) + +(define (default-ocaml5.0-dune) + (let ((module (resolve-interface '(gnu packages ocaml)))) + (module-ref module 'ocaml5.0-dune))) + (define* (package-with-explicit-ocaml ocaml findlib dune old-prefix new-prefix #:key variant-property) "Return a procedure of one argument, P. The procedure creates a package @@ -199,6 +213,19 @@ pre-defined variants." (inherit p) (properties (alist-delete 'ocaml4.09-variant (package-properties p))))) +(define package-with-ocaml5.0 + (package-with-explicit-ocaml (delay (default-ocaml5.0)) + (delay (default-ocaml5.0-findlib)) + (delay (default-ocaml5.0-dune)) + "ocaml-" "ocaml5.0-" + #:variant-property 'ocaml5.0-variant)) + +(define (strip-ocaml5.0-variant p) + "Remove the 'ocaml5.0-variant' property from P." + (package + (inherit p) + (properties (alist-delete 'ocaml5.0-variant (package-properties p))))) + (define* (lower name #:key source inputs native-inputs outputs system target (ocaml (default-ocaml)) From 642cf11aa2715b939ed450ccddc00860b22b709e Mon Sep 17 00:00:00 2001 From: pukkamustard Date: Fri, 16 Dec 2022 13:25:04 +0000 Subject: [PATCH 633/790] gnu: opam: Use OCaml 4.14 compiled version when building OCaml 5.0 packages. * gnu/packages/ocaml.scm (opam)[properties]: Add ocaml5.0-variant. (opam)[propagated-inputs]: Move to inputs. Signed-off-by: Julien Lepiller --- gnu/packages/ocaml.scm | 10 ++++++---- 1 file changed, 6 insertions(+), 4 deletions(-) diff --git a/gnu/packages/ocaml.scm b/gnu/packages/ocaml.scm index adbb76711e..f32d7b4f22 100644 --- a/gnu/packages/ocaml.scm +++ b/gnu/packages/ocaml.scm @@ -962,10 +962,12 @@ name = Guix Builder") ("opam-repo-f372039d" ,(opam-repo "f372039db86a970ef3e662adbfe0d4f5cd980701" "0ld7fcry6ss6fmrpswvr6bikgx299w97h0gwrjjh7kd7rydsjdws"))))) (inputs - (list ocaml ncurses curl bubblewrap)) - (propagated-inputs - (list ocaml-cmdliner ocaml-dose3 ocaml-mccs ocaml-opam-file-format - ocaml-re)) + (list ocaml ncurses curl bubblewrap ocaml-cmdliner ocaml-dose3 + ocaml-mccs ocaml-opam-file-format ocaml-re)) + (properties + ;; OPAM is used as a tool and not as a library, we can use the OCaml 4.14 + ;; compiled opam until opam is compatible with OCaml 5.0. + `((ocaml5.0-variant . ,(delay opam)))) (home-page "http://opam.ocamlpro.com/") (synopsis "Package manager for OCaml") (description From a8e1dc8edffb51eb3acea8dc82642f498e6ec895 Mon Sep 17 00:00:00 2001 From: pukkamustard Date: Fri, 16 Dec 2022 13:25:05 +0000 Subject: [PATCH 634/790] gnu: Add ocaml-psq. * gnu/packages/ocaml.scm (ocaml-psq): New variable. Signed-off-by: Julien Lepiller --- gnu/packages/ocaml.scm | 22 ++++++++++++++++++++++ 1 file changed, 22 insertions(+) diff --git a/gnu/packages/ocaml.scm b/gnu/packages/ocaml.scm index f32d7b4f22..3c072672b7 100644 --- a/gnu/packages/ocaml.scm +++ b/gnu/packages/ocaml.scm @@ -2723,6 +2723,28 @@ for mapping files in memory. This function is the same as the @command{Unix.map_file} function added in OCaml >= 4.06.") (license (list license:qpl license:lgpl2.0)))) +(define-public ocaml-psq + (package + (name "ocaml-psq") + (version "0.2.1") + (home-page "https://github.com/pqwy/psq") + (source + (origin + (method git-fetch) + (uri (git-reference + (url home-page) + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 (base32 + "0ahxbzkbq5sw8sqv31c2lil2zny4076q8b0dc7h5slq7i2r23d79")))) + (build-system dune-build-system) + (native-inputs (list ocaml-qcheck ocaml-alcotest)) + (synopsis "Functional Priority Search Queues for OCaml") + (description + "This library provides Functional Priority Search Queues for OCaml. +Typical applications are searches, schedulers and caches.") + (license license:isc))) + (define-public ocaml-lwt (package (name "ocaml-lwt") From c60fae72d874203e2d3a21e51a6961358926be99 Mon Sep 17 00:00:00 2001 From: pukkamustard Date: Fri, 16 Dec 2022 13:25:06 +0000 Subject: [PATCH 635/790] gnu: Add ocaml-monolith. * gnu/packages/ocaml.scm (ocaml-monolith): New variable. Signed-off-by: Julien Lepiller --- gnu/packages/ocaml.scm | 25 +++++++++++++++++++++++++ 1 file changed, 25 insertions(+) diff --git a/gnu/packages/ocaml.scm b/gnu/packages/ocaml.scm index 3c072672b7..b9f6bb13df 100644 --- a/gnu/packages/ocaml.scm +++ b/gnu/packages/ocaml.scm @@ -8665,6 +8665,31 @@ Using this package, you can run afl-fuzz in ``persistent mode'', which avoids repeated forking and is much faster.") (license license:expat))) +(define-public ocaml-monolith + (package + (name "ocaml-monolith") + (version "20210525") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://gitlab.inria.fr/fpottier/monolith") + (commit version))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "1b6jj4ivl9ni8kba7wls4xsqdy8nm7q9mnx9347jvb99dmmlj5mc")))) + (build-system dune-build-system) + (arguments `(#:test-target ".")) + (propagated-inputs (list ocaml-afl-persistent ocaml-pprint ocaml-seq)) + (home-page "https://gitlab.inria.fr/fpottier/monolith") + (synopsis "Framework for testing an OCaml library using afl-fuzz") + (description "Monolith offers facilities for testing an OCaml library (for +instance, a data structure implementation) by comparing it against a reference +implementation. It can be used to perform either random testing or fuzz +testing by using the @code{afl-fuzz} tool.") + (license license:lgpl3+))) + (define-public ocaml-pprint (package (name "ocaml-pprint") From cdca7347756e4ae230bbe2d6795451e649bc634e Mon Sep 17 00:00:00 2001 From: pukkamustard Date: Fri, 16 Dec 2022 13:25:07 +0000 Subject: [PATCH 636/790] gnu: Add ocaml-optint. * gnu/packages/ocaml.scm (ocaml-optint): New variable. Signed-off-by: Julien Lepiller --- gnu/packages/ocaml.scm | 25 +++++++++++++++++++++++++ 1 file changed, 25 insertions(+) diff --git a/gnu/packages/ocaml.scm b/gnu/packages/ocaml.scm index b9f6bb13df..1d30eadd92 100644 --- a/gnu/packages/ocaml.scm +++ b/gnu/packages/ocaml.scm @@ -2745,6 +2745,31 @@ for mapping files in memory. This function is the same as the Typical applications are searches, schedulers and caches.") (license license:isc))) +(define-public ocaml-optint + (package + (name "ocaml-optint") + (version "0.3.0") + (home-page "https://github.com/mirage/optint") + (source + (origin + (method git-fetch) + (uri (git-reference + (url home-page) + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 (base32 + "1qj32bcw1in7s6raxdvbmjr3lvj99iwv98x1ar9cwxp4zf8ybfss")))) + (build-system dune-build-system) + (arguments `(#:test-target ".")) + (native-inputs (list ocaml-crowbar ocaml-monolith ocaml-fmt)) + (synopsis "Efficient integer types on 64-bit architectures for OCaml") + (description + "This OCaml library provides two new integer types, @code{Optint.t} and +@code{Int63.t}, which guarantee efficient representation on 64-bit +architectures and provide a best-effort boxed representation on 32-bit +architectures.") + (license license:isc))) + (define-public ocaml-lwt (package (name "ocaml-lwt") From be311533902900f16ff58cc18061ca4522441033 Mon Sep 17 00:00:00 2001 From: pukkamustard Date: Fri, 16 Dec 2022 13:25:08 +0000 Subject: [PATCH 637/790] gnu: Add ocaml-hmap. * gnu/packages/ocaml.scm (ocaml-hmap): New variable. Signed-off-by: Julien Lepiller --- gnu/packages/ocaml.scm | 26 ++++++++++++++++++++++++++ 1 file changed, 26 insertions(+) diff --git a/gnu/packages/ocaml.scm b/gnu/packages/ocaml.scm index 1d30eadd92..4a45f5f73b 100644 --- a/gnu/packages/ocaml.scm +++ b/gnu/packages/ocaml.scm @@ -2770,6 +2770,32 @@ architectures and provide a best-effort boxed representation on 32-bit architectures.") (license license:isc))) +(define-public ocaml-hmap + (package + (name "ocaml-hmap") + (version "0.8.1") + (source + (origin + (method url-fetch) + (uri "https://erratique.ch/software/hmap/releases/hmap-0.8.1.tbz") + (sha256 + (base32 "10xyjy4ab87z7jnghy0wnla9wrmazgyhdwhr4hdmxxdn28dxn03a")))) + (build-system ocaml-build-system) + (arguments + `(#:build-flags + (list "build" "--tests" "true") + #:phases + (modify-phases %standard-phases + (delete 'configure)))) + (native-inputs (list ocaml-topkg ocamlbuild opam)) + (home-page "https://erratique.ch/software/hmap") + (synopsis "Heterogeneous value maps for OCaml") + (description + "Hmap provides heterogeneous value maps for OCaml. These maps bind keys to +values with arbitrary types. Keys witness the type of the value they are bound +to which allows adding and looking up bindings in a type safe manner.") + (license license:isc))) + (define-public ocaml-lwt (package (name "ocaml-lwt") From 11c1621b536ee29daf8091f65f4f9d7c77a5f16d Mon Sep 17 00:00:00 2001 From: pukkamustard Date: Fri, 16 Dec 2022 13:25:09 +0000 Subject: [PATCH 638/790] gnu: Add ocaml5.0-base. * gnu/packages/ocaml.scm (ocaml5.0-base): New variable. Signed-off-by: Julien Lepiller --- gnu/packages/ocaml.scm | 25 ++++++++++++++++++++++++- 1 file changed, 24 insertions(+), 1 deletion(-) diff --git a/gnu/packages/ocaml.scm b/gnu/packages/ocaml.scm index 4a45f5f73b..430e6a341b 100644 --- a/gnu/packages/ocaml.scm +++ b/gnu/packages/ocaml.scm @@ -5487,7 +5487,8 @@ functionality for parsing and pretty-printing s-expressions.") (build-system dune-build-system) (propagated-inputs (list ocaml-sexplib0)) - (properties `((ocaml4.07-variant . ,(delay ocaml4.07-base)))) + (properties `((ocaml4.07-variant . ,(delay ocaml4.07-base)) + (ocaml5.0-variant . ,(delay ocaml5.0-base)))) (synopsis "Full standard library replacement for OCaml") (description @@ -5502,6 +5503,28 @@ provided by companion libraries such as @url{https://github.com/janestreet/stdio, ocaml-stdio}.") (license license:expat))) +(define-public ocaml5.0-base + ;; This version contains fixes for OCaml 5.0 + ;; (see https://github.com/ocaml/opam-repository/pull/21851) + (let ((commit "423dbad212f55506767d758b1ceb2d6e0ee8e7f5") + (revision "0")) + (package-with-ocaml5.0 + (package + (inherit ocaml-base) + (name "ocaml-base") + (version (git-version "0.15.0" revision commit)) + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/kit-ty-kate/base") + (commit commit))) + (file-name (git-file-name "ocaml5.0-base" version)) + (sha256 + (base32 + "15vsiv3q53l1bzrvqgspf3lp2104s9dzw62z3nl75f53jvjvsyf6")))) + (properties '()))))) + (define-public ocaml4.07-base (package-with-ocaml4.07 (package From 17f5a0da47ac5ad5f50a8f36a988670fea8d4d2a Mon Sep 17 00:00:00 2001 From: pukkamustard Date: Fri, 16 Dec 2022 13:25:10 +0000 Subject: [PATCH 639/790] gnu: Update ocaml-ppxlib to 0.25.1. * gnu/packages/ocaml.scm (ocaml-ppxlib): Update to 0.25.1. Signed-off-by: Julien Lepiller --- gnu/packages/ocaml.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/ocaml.scm b/gnu/packages/ocaml.scm index 430e6a341b..972da2fd96 100644 --- a/gnu/packages/ocaml.scm +++ b/gnu/packages/ocaml.scm @@ -5677,7 +5677,7 @@ as part of the same ocaml-migrate-parsetree driver.") (define-public ocaml-ppxlib (package (name "ocaml-ppxlib") - (version "0.25.0") + (version "0.25.1") (home-page "https://github.com/ocaml-ppx/ppxlib") (source (origin @@ -5688,7 +5688,7 @@ as part of the same ocaml-migrate-parsetree driver.") (file-name (git-file-name name version)) (sha256 (base32 - "0wlqvyqy9ccp7z981blv42aqwq7zfq93cakbahjyy48hiiir6vp2")))) + "1402fzv5mg5grf3hb82fqsdkzxk07yfp9hvjh33dzjwjsqfhx3wi")))) (build-system dune-build-system) (arguments `(#:phases From fdf2b2e459048c6e2e9d53fb97927c2912266fc8 Mon Sep 17 00:00:00 2001 From: pukkamustard Date: Fri, 16 Dec 2022 13:25:11 +0000 Subject: [PATCH 640/790] gnu: Update ocaml-qcheck to 0.20. * gnu/packages/ocaml.scm (ocaml-qcheck): Update to 0.20. Signed-off-by: Julien Lepiller --- gnu/packages/ocaml.scm | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/gnu/packages/ocaml.scm b/gnu/packages/ocaml.scm index 972da2fd96..8bed5e9cc0 100644 --- a/gnu/packages/ocaml.scm +++ b/gnu/packages/ocaml.scm @@ -1688,7 +1688,7 @@ archive(native) = \"frontc.cmxa\"")))) (define-public ocaml-qcheck (package (name "ocaml-qcheck") - (version "0.18.1") + (version "0.20") (source (origin (method git-fetch) @@ -1697,12 +1697,12 @@ archive(native) = \"frontc.cmxa\"")))) (commit (string-append "v" version)))) (file-name (git-file-name name version)) (sha256 - (base32 "0g3r8lrw6fsdphgpnp08saxyxk1vd3chpmb564ir2qnsp716vz6z")))) + (base32 "1r0m5p1dd06lbgfxqdpl1ya4vb8252z7hqkvdi9k444g4rx2ay3p")))) (build-system dune-build-system) (arguments `(#:test-target ".")) (propagated-inputs - (list ocaml-alcotest ocaml-ounit)) + (list ocaml-alcotest ocaml-ounit ocaml-ppxlib)) (native-inputs (list ocamlbuild)) (properties `((ocaml4.07-variant . ,(delay ocaml4.07-qcheck)))) From e3a2f0447bd9781f56926a30a63b30518a7548fc Mon Sep 17 00:00:00 2001 From: pukkamustard Date: Fri, 16 Dec 2022 13:25:12 +0000 Subject: [PATCH 641/790] gnu: Add ocaml5.0-ppx-expect. * gnu/packages/ocaml.scm (ocaml5.0-ppx-expect): New variable. Signed-off-by: Julien Lepiller --- gnu/packages/ocaml.scm | 25 ++++++++++++++++++++++++- 1 file changed, 24 insertions(+), 1 deletion(-) diff --git a/gnu/packages/ocaml.scm b/gnu/packages/ocaml.scm index 8bed5e9cc0..631f69d56d 100644 --- a/gnu/packages/ocaml.scm +++ b/gnu/packages/ocaml.scm @@ -6757,7 +6757,8 @@ useful errors on failure.") ocaml-migrate-parsetree ocaml-re)) (properties `((upstream-name . "ppx_expect") - (ocaml4.07-variant . ,(delay ocaml4.07-ppx-expect)))) + (ocaml4.07-variant . ,(delay ocaml4.07-ppx-expect)) + (ocaml5.0-variant . ,(delay ocaml5.0-ppx-expect)))) (home-page "https://github.com/janestreet/ppx_expect") (synopsis "Cram like framework for OCaml") (description "Expect-test is a framework for writing tests in OCaml, similar @@ -6767,6 +6768,28 @@ output-generating code, interleaved with @code{%expect} extension expressions to denote the expected output.") (license license:asl2.0))) +(define-public ocaml5.0-ppx-expect + ;; Contains fixes for OCaml 5.0 + ;; (https://github.com/janestreet/ppx_expect/pull/39/). + (let ((commit "83edfc1ee779e8dcdd975e26715c2e688326befa") + (revision "0")) + (package-with-ocaml5.0 + (package + (inherit ocaml-ppx-expect) + (name "ocaml-ppx-expect") + (version (git-version "0.15.0" revision commit)) + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/janestreet/ppx_expect") + (commit commit))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "05r7wlmrhb5biwyw6bjcpmr77srglijcbf7nm7h2hiil0d0i7bkz")))) + (properties '()))))) + (define-public ocaml4.07-ppx-expect (package-with-ocaml4.07 (package From 7a19cb115f0cc91b8542f86c398384b6bb594003 Mon Sep 17 00:00:00 2001 From: pukkamustard Date: Fri, 16 Dec 2022 13:25:13 +0000 Subject: [PATCH 642/790] gnu: Update ocaml-odoc to 2.2.0. * gnu/packages/ocaml.scm (ocaml-odoc): Update to 2.2.0. Signed-off-by: Julien Lepiller --- gnu/packages/ocaml.scm | 6 ++---- 1 file changed, 2 insertions(+), 4 deletions(-) diff --git a/gnu/packages/ocaml.scm b/gnu/packages/ocaml.scm index 631f69d56d..4095c9231c 100644 --- a/gnu/packages/ocaml.scm +++ b/gnu/packages/ocaml.scm @@ -7808,9 +7808,7 @@ then run the Bisect_ppx report tool on the generated visitation files.") (define-public ocaml-odoc (package (name "ocaml-odoc") - ;; 2.2.0-alpha contains fixes for Dune 3.0 compatibility - ;; (https://github.com/ocaml/odoc/commit/6ac97f3148f7791ec7451785ef4dbd9ca0daf2d1) - (version "2.2.0-alpha") + (version "2.2.0") (source (origin (method git-fetch) @@ -7819,7 +7817,7 @@ then run the Bisect_ppx report tool on the generated visitation files.") (commit version))) (file-name (git-file-name name version)) (sha256 - (base32 "07zjkk455l51i29lcayzrc1q8j5bvbv97sscv8yhcj7x6h6q2nag")))) + (base32 "19mww1lyrdi705aw3lwql6xc7p11fcq5gprmhyxpb4x80gnvlzrh")))) (build-system dune-build-system) (arguments `(#:tests? #f; not compatible with current version of ocaml-yojson From 048217e73c9ed6459ec8252163335c2982deefc6 Mon Sep 17 00:00:00 2001 From: pukkamustard Date: Fri, 16 Dec 2022 13:25:14 +0000 Subject: [PATCH 643/790] gnu: Add ocaml5.0-crowbar. * gnu/packages/ocaml.scm (ocaml5.0-crowbar): New variable. Signed-off-by: Julien Lepiller --- gnu/packages/ocaml.scm | 9 +++++++++ 1 file changed, 9 insertions(+) diff --git a/gnu/packages/ocaml.scm b/gnu/packages/ocaml.scm index 4095c9231c..1ca3c19842 100644 --- a/gnu/packages/ocaml.scm +++ b/gnu/packages/ocaml.scm @@ -8839,12 +8839,21 @@ document and by the text width.") ocaml-uunf ocaml-uutf ocaml-pprint)) + (properties `((ocaml5.0-variant . ,(delay ocaml5.0-crowbar)))) (synopsis "Ocaml library for tests, let a fuzzer find failing cases") (description "Crowbar is a library for testing code, combining QuickCheck-style property-based testing and the magical bug-finding powers of @uref{http://lcamtuf.coredump.cx/afl/, afl-fuzz}.") (license license:expat))) +(define-public ocaml5.0-crowbar + (package-with-ocaml5.0 + (package + (inherit ocaml-crowbar) + ;; Tests require ocaml-calendar which does not work with OCaml 5.0 + (arguments `(#:tests? #f)) + (properties '())))) + (define-public ocaml-eqaf (package (name "ocaml-eqaf") From 74f5ddef813b38e26ea0a6339fe732670b8ad8bc Mon Sep 17 00:00:00 2001 From: pukkamustard Date: Fri, 16 Dec 2022 13:25:15 +0000 Subject: [PATCH 644/790] gnu: Add ocaml-lwt-dllist. * gnu/packages/ocaml.scm (ocaml-lwt-dllist): New variable. Signed-off-by: Julien Lepiller --- gnu/packages/ocaml.scm | 21 +++++++++++++++++++++ 1 file changed, 21 insertions(+) diff --git a/gnu/packages/ocaml.scm b/gnu/packages/ocaml.scm index 1ca3c19842..cb845b7ead 100644 --- a/gnu/packages/ocaml.scm +++ b/gnu/packages/ocaml.scm @@ -2826,6 +2826,27 @@ process. Also, in many cases, Lwt threads can interact without the need for locks or other synchronization primitives.") (license license:lgpl2.1))) +(define-public ocaml-lwt-dllist + (package + (name "ocaml-lwt-dllist") + (version "1.0.1") + (home-page "https://github.com/mirage/lwt-dllist") + (source (origin + (method git-fetch) + (uri (git-reference + (url home-page) + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "18bi8fb4yly1pyf43pjvvdhlyzb3wkgxifffx9d1g9y2mwsng6jw")))) + (build-system dune-build-system) + (native-inputs (list ocaml-lwt)) + (synopsis "OCaml library providing mutable doubly-linked list with Lwt iterators") + (description "This OCaml library provides an implementation of a mutable +doubly-linked list with Lwt iterators.") + (license license:expat))) + (define-public ocaml-luv (package (name "ocaml-luv") From 8160d05e83d8b9284d3c6b18218cf639db90141b Mon Sep 17 00:00:00 2001 From: pukkamustard Date: Fri, 16 Dec 2022 13:25:16 +0000 Subject: [PATCH 645/790] gnu: Add ocaml5.0-ctypes * gnu/packages/ocaml.scm (ocaml5.0-ctypes): New variable. Signed-off-by: Julien Lepiller --- gnu/packages/ocaml.scm | 28 ++++++++++++++++++++++++++++ 1 file changed, 28 insertions(+) diff --git a/gnu/packages/ocaml.scm b/gnu/packages/ocaml.scm index cb845b7ead..9040748fce 100644 --- a/gnu/packages/ocaml.scm +++ b/gnu/packages/ocaml.scm @@ -4800,6 +4800,7 @@ long and size_t whose sizes depend on the host platform.") ("integers" ,ocaml-integers))) (inputs (list libffi)) + (properties `((ocaml5.0-variant . ,(delay ocaml5.0-ctypes)))) (synopsis "Library for binding to C libraries using pure OCaml") (description "Ctypes is a library for binding to C libraries using pure OCaml. The primary aim is to make writing C extensions as straightforward as @@ -4810,6 +4811,33 @@ functions that you want to call, then bind directly to those functions -- all without writing or generating any C!") (license license:expat))) +(define-public ocaml5.0-ctypes + ;; Contains fix to support OCaml 5.0 + ;; (https://github.com/ocamllabs/ocaml-ctypes/pull/709) + (let ((commit "52ff621f47dbc1ee5a90c30af0ae0474549946b4") + (revision "0")) + (package-with-ocaml5.0 + (package + (inherit ocaml-ctypes) + (name "ocaml-ctypes") + (version (git-version "0.20.1" revision commit)) + (home-page "https://github.com/ocamllabs/ocaml-ctypes") + (arguments + (append + ;; Some tests fail. Failure seems to be due to OCaml 5.0. + `(#:tests? #f) + (package-arguments ocaml-ctypes))) + (source (origin + (method git-fetch) + (uri (git-reference + (url home-page) + (commit commit))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "0vyiryqchz0mdfhal7bdivqsk5yhvzzckrqv495rlpbdxzklcp7g")))) + (properties '()))))) + (define-public ocaml-ocb-stubblr (package (name "ocaml-ocb-stubblr") From f883cb9ecd6ca14bf89aad4d2eb0e52809d8bd23 Mon Sep 17 00:00:00 2001 From: pukkamustard Date: Fri, 16 Dec 2022 13:25:17 +0000 Subject: [PATCH 646/790] gnu: Add ocaml-bechamel. * gnu/packages/ocaml.scm (ocaml-bechamel): New variable. Signed-off-by: Julien Lepiller --- gnu/packages/ocaml.scm | 24 ++++++++++++++++++++++++ 1 file changed, 24 insertions(+) diff --git a/gnu/packages/ocaml.scm b/gnu/packages/ocaml.scm index 9040748fce..7e54245865 100644 --- a/gnu/packages/ocaml.scm +++ b/gnu/packages/ocaml.scm @@ -3610,6 +3610,30 @@ your functions and to easily compare the results. A statistical test is used to determine whether the results truly differ.") (license license:lgpl3+))) +(define-public ocaml-bechamel + (package + (name "ocaml-bechamel") + (version "0.3.0") + (home-page "https://github.com/mirage/bechamel") + (source + (origin + (method git-fetch) + (uri (git-reference + (url home-page) + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 "1x7sf45iy5dzx7kknbkkvpna42rcwpj5p55y0nqsg2fb4srj0b1q")))) + (build-system dune-build-system) + (arguments `(#:package "bechamel")) + (propagated-inputs (list ocaml-fmt ocaml-stdlib-shims)) + (synopsis "Yet Another Benchmark in OCaml") + (description + "BEnchmark for a CHAMEL/camel/caml which is agnostic to the system. It's a +micro-benchmark tool for OCaml which lets the user to re-analyzes and prints +samples.") + (license license:expat))) + (define-public ocaml-batteries (package (name "ocaml-batteries") From 2cb15f8501233255c600d1c6ccdc1d6c3b881f35 Mon Sep 17 00:00:00 2001 From: pukkamustard Date: Fri, 16 Dec 2022 13:25:18 +0000 Subject: [PATCH 647/790] gnu: ocaml-mdx: Move inputs to propagated-inputs. * gnu/packages/ocaml.scm (ocaml-mdx): Move inputs to propagated-inputs. Signed-off-by: Julien Lepiller --- gnu/packages/ocaml.scm | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/gnu/packages/ocaml.scm b/gnu/packages/ocaml.scm index 7e54245865..cef9d16d6e 100644 --- a/gnu/packages/ocaml.scm +++ b/gnu/packages/ocaml.scm @@ -8142,7 +8142,7 @@ variants.") (("`") "'") (("COMMAND") "[COMMAND]") (("\\.\\.\\.") "…"))))))) - (inputs + (propagated-inputs (list ocaml-fmt ocaml-astring ocaml-logs From 14fae62df8dabffce711c4805c9fdd7a226f906a Mon Sep 17 00:00:00 2001 From: pukkamustard Date: Fri, 16 Dec 2022 13:25:19 +0000 Subject: [PATCH 648/790] gnu: Add ocaml5.0-eio. * gnu/packages/ocaml.scm (ocaml5.0-eio): New variable. Signed-off-by: Julien Lepiller --- gnu/packages/ocaml.scm | 37 +++++++++++++++++++++++++++++++++++++ 1 file changed, 37 insertions(+) diff --git a/gnu/packages/ocaml.scm b/gnu/packages/ocaml.scm index cef9d16d6e..769a628acc 100644 --- a/gnu/packages/ocaml.scm +++ b/gnu/packages/ocaml.scm @@ -2796,6 +2796,43 @@ values with arbitrary types. Keys witness the type of the value they are bound to which allows adding and looking up bindings in a type safe manner.") (license license:isc))) +(define ocaml-eio + (package + (name "ocaml-eio") + (version "0.7") + (home-page "https://github.com/ocaml-multicore/eio") + (source + (origin + (method git-fetch) + (uri (git-reference + (url home-page) + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 (base32 + "118raxdwv6pn5b152ffdhmwdi0l4wlwflcj2nmckfmm7v1z2fq4s")))) + (build-system dune-build-system) + (arguments `(#:package "eio" + #:test-target ".")) + (propagated-inputs (list ocaml-bigstringaf + ocaml-cstruct + ocaml-lwt + ocaml-lwt-dllist + ocaml-logs + ocaml-optint + ocaml-psq + ocaml-fmt + ocaml-hmap + ocaml-mtime + ocaml-odoc)) + (native-inputs (list ocaml-astring ocaml-crowbar ocaml-alcotest)) + (synopsis "Effect-based direct-style IO API for OCaml") + (description "This package provides an effect-based IO API for multicore +OCaml with fibers.") + (license license:isc))) + +(define-public ocaml5.0-eio + (package-with-ocaml5.0 ocaml-eio)) + (define-public ocaml-lwt (package (name "ocaml-lwt") From 2b335e87f7f25bfa5e51f3d840673a3bf8d6d014 Mon Sep 17 00:00:00 2001 From: pukkamustard Date: Fri, 16 Dec 2022 13:25:20 +0000 Subject: [PATCH 649/790] gnu: Add ocaml5.0-eio-luv. * gnu/packages/ocaml.scm (ocaml5.0-eio-luv): New variable. Signed-off-by: Julien Lepiller --- gnu/packages/ocaml.scm | 15 +++++++++++++++ 1 file changed, 15 insertions(+) diff --git a/gnu/packages/ocaml.scm b/gnu/packages/ocaml.scm index 769a628acc..c78d8a2b6d 100644 --- a/gnu/packages/ocaml.scm +++ b/gnu/packages/ocaml.scm @@ -2833,6 +2833,21 @@ OCaml with fibers.") (define-public ocaml5.0-eio (package-with-ocaml5.0 ocaml-eio)) +(define ocaml-eio-luv + (package + (inherit ocaml-eio) + (name "ocaml-eio-luv") + (arguments `(#:package "eio_luv" + #:test-target ".")) + (propagated-inputs (list ocaml-eio ocaml-luv)) + (native-inputs (list ocaml-mdx)) + (synopsis "Libuv-based backend for Ocaml Eio") + (description "@code{Eio_luv} provides a cross-platform backend for +@code{Ocaml Eio}'s APIs using luv (libuv)"))) + +(define-public ocaml5.0-eio-luv + (package-with-ocaml5.0 ocaml-eio-luv)) + (define-public ocaml-lwt (package (name "ocaml-lwt") From c9865228778941fcee95c501a414e270c6b31fa3 Mon Sep 17 00:00:00 2001 From: pukkamustard Date: Fri, 16 Dec 2022 13:25:21 +0000 Subject: [PATCH 650/790] gnu: Add ocaml-uring. * gnu/packages/ocaml.scm (ocaml-uring): New variable. Signed-off-by: Julien Lepiller --- gnu/packages/ocaml.scm | 32 ++++++++++++++++++++++++++++++++ 1 file changed, 32 insertions(+) diff --git a/gnu/packages/ocaml.scm b/gnu/packages/ocaml.scm index c78d8a2b6d..d69ffaa969 100644 --- a/gnu/packages/ocaml.scm +++ b/gnu/packages/ocaml.scm @@ -2848,6 +2848,38 @@ OCaml with fibers.") (define-public ocaml5.0-eio-luv (package-with-ocaml5.0 ocaml-eio-luv)) +(define-public ocaml-uring + (package + (name "ocaml-uring") + (version "0.4") + (home-page "https://github.com/ocaml-multicore/ocaml-uring") + (source + (origin + (method git-fetch) + (uri (git-reference + (url home-page) + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 (base32 + "0k70y7nb2wrk2yql0pwnrhsp1x7k9ld4gd8iihbv6r34kcm3a5m1")))) + (build-system dune-build-system) + (arguments `(#:test-target ".")) + (propagated-inputs + (list ocaml-cstruct + ocaml-fmt + ocaml-optint)) + (native-inputs + (list ocaml-lwt + ocaml-bechamel + ocaml-logs + ocaml-cmdliner + ocaml-mdx)) + (synopsis "OCaml bindings for Linux io_uring") + (description "This package provides OCaml bindings to the Linux +@code{io_uring} kernel IO interfaces.") + (license + (list license:isc license:expat)))) + (define-public ocaml-lwt (package (name "ocaml-lwt") From 417be516def1853d2ef9bf40a31d9eba759451e9 Mon Sep 17 00:00:00 2001 From: pukkamustard Date: Fri, 16 Dec 2022 13:25:22 +0000 Subject: [PATCH 651/790] gnu: Add ocaml5.0-eio-linux. * gnu/packages/ocaml.scm (ocaml5.0-eio-linux): New variable. Signed-off-by: Julien Lepiller --- gnu/packages/ocaml.scm | 23 +++++++++++++++++++++++ 1 file changed, 23 insertions(+) diff --git a/gnu/packages/ocaml.scm b/gnu/packages/ocaml.scm index d69ffaa969..30c3d93eaa 100644 --- a/gnu/packages/ocaml.scm +++ b/gnu/packages/ocaml.scm @@ -2880,6 +2880,29 @@ OCaml with fibers.") (license (list license:isc license:expat)))) +(define ocaml-eio-linux + (package + (inherit ocaml-eio) + (name "ocaml-eio-linux") + (arguments `(#:package "eio_linux" + #:test-target ".")) + (propagated-inputs + (list ocaml-eio + ocaml-uring + ocaml-logs + ocaml-fmt)) + (native-inputs + (list ocaml-mdx + ocaml-alcotest + ocaml-mdx)) + (synopsis "Linux backend for ocaml-eio") + (description "@code{Eio_linux} provides a Linux io-uring backend for +@code{Ocaml Eio} APIs, plus a low-level API that can be used directly +(in non-portable code)."))) + +(define-public ocaml5.0-eio-linux + (package-with-ocaml5.0 ocaml-eio-linux)) + (define-public ocaml-lwt (package (name "ocaml-lwt") From cb1fe1c6905a2e40ca767035809f6b35cd35fe22 Mon Sep 17 00:00:00 2001 From: pukkamustard Date: Fri, 16 Dec 2022 13:25:23 +0000 Subject: [PATCH 652/790] gnu: Add ocaml5.0-eio-main. * gnu/packages/ocaml.scm (ocaml5.0-eio-main): New variable. Signed-off-by: Julien Lepiller --- gnu/packages/ocaml.scm | 21 +++++++++++++++++++++ 1 file changed, 21 insertions(+) diff --git a/gnu/packages/ocaml.scm b/gnu/packages/ocaml.scm index 30c3d93eaa..3eb155b8a7 100644 --- a/gnu/packages/ocaml.scm +++ b/gnu/packages/ocaml.scm @@ -2903,6 +2903,27 @@ OCaml with fibers.") (define-public ocaml5.0-eio-linux (package-with-ocaml5.0 ocaml-eio-linux)) +(define ocaml-eio-main + (package + (inherit ocaml-eio) + (name "ocaml-eio-main") + (arguments `(#:package "eio_main" + #:test-target "." + ;; tests require network + #:tests? #f)) + (propagated-inputs + (list ocaml-eio + ocaml-eio-luv + ocaml-eio-linux)) + (native-inputs + (list ocaml-mdx)) + (synopsis "Eio backend selector") + (description "@code{Eio_main} selects an appropriate backend (e.g. +@samp{eio_linux} or @samp{eio_luv}), depending on your platform."))) + +(define-public ocaml5.0-eio-main + (package-with-ocaml5.0 ocaml-eio-main)) + (define-public ocaml-lwt (package (name "ocaml-lwt") From f127f0fbf3112e7c3ebeeeb0da8b7747ca3b0f20 Mon Sep 17 00:00:00 2001 From: pukkamustard Date: Fri, 16 Dec 2022 13:25:24 +0000 Subject: [PATCH 653/790] gnu: Update ocaml-merlin-lib to 4.7-414. * gnu/packages/ocaml.scm (ocaml-merlin-lib): Update to 4.7-414. Signed-off-by: Julien Lepiller --- gnu/packages/ocaml.scm | 8 +++++--- 1 file changed, 5 insertions(+), 3 deletions(-) diff --git a/gnu/packages/ocaml.scm b/gnu/packages/ocaml.scm index 3eb155b8a7..c31ad6c8f9 100644 --- a/gnu/packages/ocaml.scm +++ b/gnu/packages/ocaml.scm @@ -5369,7 +5369,7 @@ serializers and deserializers from type definitions.") (define-public ocaml-merlin-lib (package (name "ocaml-merlin-lib") - (version "4.6-414") + (version "4.7-414") (source (origin (method git-fetch) @@ -5379,7 +5379,7 @@ serializers and deserializers from type definitions.") (file-name (git-file-name name version)) (sha256 (base32 - "1cpa9x45w54l4mqqmc8z3s5gscggw37gb6z9i7wwss86fj1wgclh")))) + "1bd4j2zq0lyszbkibgky1z9swv4scb7ljww3fv1kqy0cya743b5l")))) (build-system dune-build-system) (arguments '(#:package "merlin-lib" #:tests? #f)) ; no tests @@ -5416,7 +5416,9 @@ interfaces and the standard higher-level merlin protocol.") (propagated-inputs (list ocaml-merlin-lib ocaml-yojson)) (native-inputs (list ocaml-dot-merlin-reader ; required for tests - ocaml-mdx jq)) + ocaml-ppxlib + ocaml-mdx + jq)) (synopsis "Context sensitive completion for OCaml in Vim and Emacs") (description "Merlin is an editor service that provides modern IDE features for OCaml. Emacs and Vim support is provided out-of-the-box. From 134480a381cbf38453c8cd4333b873ad2a51765e Mon Sep 17 00:00:00 2001 From: pukkamustard Date: Fri, 16 Dec 2022 13:25:25 +0000 Subject: [PATCH 654/790] gnu: Add ocaml5.0-merlin-lib. * gnu/packages/ocaml.scm (ocaml5.0-merlin-lib): New variable. Signed-off-by: Julien Lepiller --- gnu/packages/ocaml.scm | 22 ++++++++++++++++++++++ 1 file changed, 22 insertions(+) diff --git a/gnu/packages/ocaml.scm b/gnu/packages/ocaml.scm index c31ad6c8f9..30e895eee6 100644 --- a/gnu/packages/ocaml.scm +++ b/gnu/packages/ocaml.scm @@ -5384,12 +5384,34 @@ serializers and deserializers from type definitions.") (arguments '(#:package "merlin-lib" #:tests? #f)) ; no tests (propagated-inputs (list ocaml-csexp ocaml-menhir)) + (properties `((ocaml5.0-variant . ,(delay ocaml5.0-merlin-lib)))) (home-page "https://ocaml.github.io/merlin/") (synopsis "Merlin libraries") (description "These libraries provides access to low-level compiler interfaces and the standard higher-level merlin protocol.") (license license:expat))) +;; the 500 indicates that this version is for OCaml 5.0 +(define ocaml-merlin-lib-500 + (package + (inherit ocaml-merlin-lib) + (name "ocaml-merlin-lib") + (version "4.7.1-500") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/ocaml/merlin") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "05a87i2dkzv800nwb6y7b2j45avg8gs3gzb5a98wrj1i5zjqwh01")))) + (properties '()))) + +(define-public ocaml5.0-merlin-lib + (package-with-ocaml5.0 ocaml-merlin-lib-500)) + (define-public ocaml-dot-merlin-reader (package (inherit ocaml-merlin-lib) From 8ed74a17870839513539b884bf203a0b52bc5a9c Mon Sep 17 00:00:00 2001 From: pukkamustard Date: Fri, 16 Dec 2022 13:25:26 +0000 Subject: [PATCH 655/790] gnu: Add ocaml5.0-dot-merlin-reader. * gnu/packages/ocaml.scm (ocaml5.0-dot-merlin-reader): New variable. Signed-off-by: Julien Lepiller --- gnu/packages/ocaml.scm | 13 +++++++++++++ 1 file changed, 13 insertions(+) diff --git a/gnu/packages/ocaml.scm b/gnu/packages/ocaml.scm index 30e895eee6..c986a9f354 100644 --- a/gnu/packages/ocaml.scm +++ b/gnu/packages/ocaml.scm @@ -5419,10 +5419,23 @@ interfaces and the standard higher-level merlin protocol.") (arguments '(#:package "dot-merlin-reader" #:tests? #f)) ; no tests (propagated-inputs (list ocaml-merlin-lib)) + (properties `((ocaml5.0-variant . ,(delay ocaml5.0-dot-merlin-reader)))) (synopsis "Reads config files for @code{ocaml-merlin}") (description "@code{ocaml-dot-merlin-reader} is an external reader for @code{ocaml-merlin} configurations."))) +(define-public ocaml5.0-dot-merlin-reader + (package-with-ocaml5.0 + (package + (inherit ocaml-merlin-lib-500) + (name "ocaml-dot-merlin-reader") + (arguments '(#:package "dot-merlin-reader" + #:tests? #f)) ; no tests + (propagated-inputs (list ocaml5.0-merlin-lib)) + (synopsis "Reads config files for @code{ocaml-merlin}") + (description "@code{ocaml-dot-merlin-reader} is an external reader for +@code{ocaml-merlin} configurations.")))) + (define-public ocaml-merlin (package (inherit ocaml-dot-merlin-reader) From fe5836feaf61a7758c2291d9f665b227de3fa9b7 Mon Sep 17 00:00:00 2001 From: pukkamustard Date: Fri, 16 Dec 2022 13:25:27 +0000 Subject: [PATCH 656/790] gnu: Add ocaml5.0-merlin. * gnu/packages/ocaml.scm (ocaml5.0-merlin): New variable. Signed-off-by: Julien Lepiller --- gnu/packages/ocaml.scm | 27 +++++++++++++++++++++++++++ 1 file changed, 27 insertions(+) diff --git a/gnu/packages/ocaml.scm b/gnu/packages/ocaml.scm index c986a9f354..94b4fd514e 100644 --- a/gnu/packages/ocaml.scm +++ b/gnu/packages/ocaml.scm @@ -5449,6 +5449,7 @@ interfaces and the standard higher-level merlin protocol.") (when tests? (invoke "dune" "runtest" "-p" "merlin,dot-merlin-reader"))))))) (propagated-inputs (list ocaml-merlin-lib ocaml-yojson)) + (properties `((ocaml5.0-variant . ,(delay ocaml5.0-merlin)))) (native-inputs (list ocaml-dot-merlin-reader ; required for tests ocaml-ppxlib @@ -5461,6 +5462,32 @@ External contributors added support for Visual Studio Code, Sublime Text and Atom.") (license license:expat))) +(define-public ocaml5.0-merlin + (package-with-ocaml5.0 + (package + (inherit ocaml-merlin-lib-500) + (name "ocaml-merlin") + (arguments + '(#:package "merlin" + #:phases + (modify-phases %standard-phases + (replace 'check + (lambda* (#:key tests? #:allow-other-keys) + (when tests? + (invoke "dune" "runtest" "-p" "merlin,dot-merlin-reader"))))))) + (propagated-inputs (list ocaml-merlin-lib ocaml-yojson)) + (native-inputs + (list ocaml-dot-merlin-reader ; required for tests + ocaml-ppxlib + ocaml-mdx + jq)) + (synopsis "Context sensitive completion for OCaml in Vim and Emacs") + (description "Merlin is an editor service that provides modern IDE +features for OCaml. Emacs and Vim support is provided out-of-the-box. +External contributors added support for Visual Studio Code, Sublime Text and +Atom.") + (license license:expat)))) + (define-public ocaml-gsl (package (name "ocaml-gsl") From 5ccc017389cbb28bf93111225496cf726609b22b Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 21 Dec 2022 14:40:29 +0100 Subject: [PATCH 657/790] gnu: Add htslib-1.14. * gnu/packages/bioinformatics.scm (htslib-1.14): New variable. --- gnu/packages/bioinformatics.scm | 12 ++++++++++++ 1 file changed, 12 insertions(+) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index c41cdfbd86..08a7cbe118 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -4768,6 +4768,18 @@ data. It also provides the @command{bgzip}, @command{htsfile}, and ;; the rest is released under the Expat license (license (list license:expat license:bsd-3)))) +(define-public htslib-1.14 + (package/inherit htslib + (version "1.14") + (source (origin + (method url-fetch) + (uri (string-append + "https://github.com/samtools/htslib/releases/download/" + version "/htslib-" version ".tar.bz2")) + (sha256 + (base32 + "0pwk8yhhvb85mi1d2qhwsb4samc3rmbcrq7b1s0jz0glaa7in8pd")))))) + (define-public htslib-1.12 (package/inherit htslib (version "1.12") From e34639c2621326e82dc706defcb2054e9c69e3e7 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 21 Dec 2022 18:33:53 +0100 Subject: [PATCH 658/790] gnu: pbbam: Use htslib 1.14. * gnu/packages/bioinformatics.scm (pbbam)[propagated-inputs]: Replace htslib with htslib-1.14. --- gnu/packages/bioinformatics.scm | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 08a7cbe118..c23c86d4d2 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -607,7 +607,7 @@ for all types of microbial diversity analyses.") (string-append "'" (which "sh") "'")))))))) ;; These libraries are listed as "Required" in the pkg-config file. (propagated-inputs - (list htslib pbcopper zlib)) + (list htslib-1.14 pbcopper zlib)) (inputs (list boost samtools)) (native-inputs From 50948b8c3ddfe7912e9d1aa8fc69da5acb87c752 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 21 Dec 2022 14:40:41 +0100 Subject: [PATCH 659/790] gnu: htslib: Update to 1.16. * gnu/packages/bioinformatics.scm (htslib): Update to 1.16. --- gnu/packages/bioinformatics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index c23c86d4d2..779d7a5293 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -4734,7 +4734,7 @@ performance.") (define-public htslib (package (name "htslib") - (version "1.14") + (version "1.16") (source (origin (method url-fetch) (uri (string-append @@ -4742,7 +4742,7 @@ performance.") version "/htslib-" version ".tar.bz2")) (sha256 (base32 - "0pwk8yhhvb85mi1d2qhwsb4samc3rmbcrq7b1s0jz0glaa7in8pd")))) + "093r1n4s134k50m9a925yn95gyi90ps5dlgc6gq4qwvkzxx7qsv0")))) (build-system gnu-build-system) ;; Let htslib translate "gs://" and "s3://" to regular https links with ;; "--enable-gcs" and "--enable-s3". For these options to work, we also From bc4eac5d79488700eec52c9aae4b3cf296875b7e Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 21 Dec 2022 13:21:43 +0100 Subject: [PATCH 660/790] gnu: python-pysam: Update to 0.20.0. * gnu/packages/bioinformatics.scm (python-pysam): Update to 0.20.0. [build-system]: Use pyproject-build-system. --- gnu/packages/bioinformatics.scm | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 779d7a5293..dcaea8a6b2 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -2333,7 +2333,7 @@ has several key features: (define-public python-pysam (package (name "python-pysam") - (version "0.18.0") + (version "0.20.0") (source (origin (method git-fetch) ;; Test data is missing on PyPi. @@ -2343,12 +2343,12 @@ has several key features: (file-name (git-file-name name version)) (sha256 (base32 - "042ca27r6634xg2ixgvq1079cp714wmm6ml7bwc1snn0wxxzywfg")) + "1dq6jwwm98lm30ijdgqc5xz5ppda4nj999y6qs78mhw8x0kij8gg")) (modules '((guix build utils))) (snippet '(begin ;; FIXME: Unbundle samtools and bcftools. (delete-file-recursively "htslib"))))) - (build-system python-build-system) + (build-system pyproject-build-system) (arguments `(#:phases (modify-phases %standard-phases From 1194cb1c4030b5c07d05c98f429b73509e524177 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 21 Dec 2022 23:02:14 +0100 Subject: [PATCH 661/790] gnu: python-plastid: Update to 0.6.0. * gnu/packages/bioinformatics.scm (python-plastid): Update to 0.6.0. [source]: Fetch from git repository. [build-system]: Use pyproject-build-system. [arguments]: Enable tests; add build phases 'unpack-test-data and 'build-extensions. [inputs]: Add openssl. [native-inputs]: Add test data. --- gnu/packages/bioinformatics.scm | 40 ++++++++++++++++++++++++++------- 1 file changed, 32 insertions(+), 8 deletions(-) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index dcaea8a6b2..d8fd2ac3d6 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -2417,17 +2417,31 @@ UCSC genome browser.") (define-public python-plastid (package (name "python-plastid") - (version "0.5.1") + (version "0.6.0") (source (origin - (method url-fetch) - (uri (pypi-uri "plastid" version)) + (method git-fetch) + (uri (git-reference + (url "https://github.com/joshuagryphon/plastid") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) (sha256 (base32 - "1a7mdky2xw02y88l51f58pqk8039ahdp6sblj3zx58zarmy2pqyl")))) - (build-system python-build-system) + "1ka9j08j6i105l89w8b7sg0l8lm3lcrxzy4cjl5dp4cxdmycap62")))) + (build-system pyproject-build-system) (arguments - ;; Some test files are not included. - `(#:tests? #f)) + (list + #:phases + #~(modify-phases %standard-phases + (add-after 'unpack 'unpack-test-data + (lambda* (#:key inputs #:allow-other-keys) + (invoke "tar" "-C" "plastid/test" + "-xf" (assoc-ref inputs "test-data")) + ;; This one requires bowtie-build + (delete-file "plastid/test/functional/test_crossmap.py"))) + (add-before 'check 'build-extensions + (lambda _ + ;; Cython extensions have to be built before running the tests. + (invoke "python3" "setup.py" "build_ext" "--inplace")))))) (propagated-inputs (list python-numpy python-scipy @@ -2437,8 +2451,18 @@ UCSC genome browser.") python-biopython python-twobitreader python-termcolor)) + (inputs + (list openssl)) (native-inputs - (list python-cython python-nose)) + `(("python-cython" ,python-cython) + ("python-nose" ,python-nose) + ("test-data" + ,(origin + (method url-fetch) + (uri "https://www.dropbox.com/s/np3wlfvp6gx8tb8/2022-05-04.plastid-test-data.tar.bz2?dl=1") + (file-name "plastid-test-data-2022-05-04.tar.bz2") + (sha256 + (base32 "1szsji06m2r21flnvxg84jnj5zmlk6z10c9651v9ag71nxj9rbzn")))))) (home-page "https://github.com/joshuagryphon/plastid") (synopsis "Python library for genomic analysis") (description From 9e495087d24bcd57937cd79cf373a8bd13e1c240 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 21 Dec 2022 13:21:52 +0100 Subject: [PATCH 662/790] gnu: Add vembrane. * gnu/packages/bioinformatics.scm (vembrane): New variable. --- gnu/packages/bioinformatics.scm | 38 +++++++++++++++++++++++++++++++++ 1 file changed, 38 insertions(+) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index d8fd2ac3d6..d003822f30 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -14443,6 +14443,44 @@ contigs. It then uses paired read information, if available, to retrieve the repeated areas between contigs.") (license license:gpl2+))) +(define-public vembrane + (package + (name "vembrane") + (version "0.13.2") + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/vembrane/vembrane") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "1gdih56gpqd8ks3sd4ah844kac09hi3g073k9gvazb32ah50900w")))) + (build-system pyproject-build-system) + (arguments + (list + #:phases + '(modify-phases %standard-phases + (add-after 'unpack 'relax-requirements + (lambda _ + (substitute* "pyproject.toml" + (("pysam = \"\\^0.19\"") "pysam = \"^0.20\"") + (("numpy = \\{ version = \"\\^1.23\"") + "numpy = { version = \"^1\""))))))) + (inputs + (list python-asttokens python-intervaltree python-numpy + python-pysam python-pyyaml)) + (native-inputs + (list poetry python-pytest)) + (home-page "https://github.com/vembrane/vembrane") + (synopsis "Filter VCF/BCF files with Python expressions.") + (description "Vembrane allows to simultaneously filter variants based on +any INFO or FORMAT field, CHROM, POS, ID, REF, ALT, QUAL, FILTER, and the +annotation field ANN. When filtering based on ANN, annotation entries are +filtered first. If no annotation entry remains, the entire variant is +deleted.") + (license license:expat))) + (define-public python-velocyto (package (name "python-velocyto") From d07543b8862cecbbc6da69a1f3eda2eb605ccb2e Mon Sep 17 00:00:00 2001 From: Navid Afkhami Date: Thu, 22 Dec 2022 00:14:05 +0100 Subject: [PATCH 663/790] gnu: Add python-bamnostic. * gnu/packages/bioinformatics.scm (python-bamnostic): New variable. Signed-off-by: Ricardo Wurmus --- gnu/packages/bioinformatics.scm | 19 +++++++++++++++++++ 1 file changed, 19 insertions(+) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index d003822f30..f80f8b9842 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -3670,6 +3670,25 @@ software to answer ad hoc questions.") go-golang-org-x-image go-golang-org-x-text)))) +(define-public python-bamnostic + (package + (name "python-bamnostic") + (version "1.1.8") + (source (origin + (method url-fetch) + (uri (pypi-uri "bamnostic" version)) + (sha256 + (base32 + "0cjpzyqz6r4lmiwry2gcxdczwpkhl3lyyjg4s8addln17691ysxk")))) + (build-system pyproject-build-system) + (propagated-inputs (list python-pytest)) + (home-page "https://github.com/betteridiot/bamnostic/") + (synopsis "Tool for binary alignment map, random access and parsing") + (description + "Bamnostic is a pure Python @dfn{Binary Alignment Map} (BAM) file parser +and random access tool.") + (license license:bsd-3))) + (define-public exonerate (package (name "exonerate") From 87c3fab8543396d09be5513aff91c1245aca4229 Mon Sep 17 00:00:00 2001 From: Navid Afkhami Date: Thu, 22 Dec 2022 00:16:36 +0100 Subject: [PATCH 664/790] gnu: Add python-episcanpy. * gnu/packages/bioinformatics.scm (python-episcanpy): New variable. Signed-off-by: Ricardo Wurmus --- gnu/packages/bioinformatics.scm | 56 +++++++++++++++++++++++++++++++++ 1 file changed, 56 insertions(+) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index f80f8b9842..160c44df98 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -3689,6 +3689,62 @@ software to answer ad hoc questions.") and random access tool.") (license license:bsd-3))) +(define-public python-episcanpy + (package + (name "python-episcanpy") + (version "0.4.0") + (source (origin + (method url-fetch) + (uri (pypi-uri "episcanpy" version)) + (sha256 + (base32 + "1qqcyhyzy6idpjmidfdpzwk02hbxm25rymz42h51nlk0vd4r2wwm")))) + (build-system pyproject-build-system) + (arguments + (list + ;; The tests import episcanpy.api, but this is known to not work. + ;; See https://github.com/colomemaria/epiScanpy/issues/133 + #:tests? #false + #:phases + '(modify-phases %standard-phases + ;; Numba needs a writable dir to cache functions. + (add-before 'build 'set-numba-cache-dir + (lambda _ + (setenv "NUMBA_CACHE_DIR" "/tmp")))))) + (propagated-inputs + (list python-anndata + python-bamnostic + python-h5py + python-intervaltree + python-joblib + python-kneed + python-legacy-api-wrap + python-matplotlib + python-natsort + python-networkx + python-numba + python-numpy + python-packaging + python-pandas + python-scanpy + python-scikit-learn + python-scipy + python-seaborn + python-statsmodels + python-tqdm + python-pysam + python-tbb + python-umap-learn)) + (native-inputs (list python-pytest python-setuptools-scm)) + (home-page "https://github.com/colomemaria/epiScanpy") + (synopsis "Tool for epigenomics single cell analysis") + (description + "EpiScanpy is a toolkit to analyse single-cell open +chromatin (scATAC-seq) and single-cell DNA methylation (for example scBS-seq) +data. EpiScanpy is the epigenomic extension of the very popular scRNA-seq +analysis tool Scanpy (Genome Biology, 2018).") + (license license:bsd-3))) + (define-public exonerate (package (name "exonerate") From 30143cdad2a041545e270f19f2cbb5ef46093749 Mon Sep 17 00:00:00 2001 From: Andrew Tropin Date: Thu, 22 Dec 2022 09:59:12 +0400 Subject: [PATCH 665/790] gnu: fheroes2: Update to 1.0.0. * gnu/packages/games.scm (fheroes2): Update to 1.0.0. --- gnu/packages/games.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/games.scm b/gnu/packages/games.scm index 6064dabbaa..54cf17e963 100644 --- a/gnu/packages/games.scm +++ b/gnu/packages/games.scm @@ -11020,7 +11020,7 @@ disassembly of the DOS version, extended with new features.") (define-public fheroes2 (package (name "fheroes2") - (version "0.9.11") + (version "1.0.0") (source (origin (method git-fetch) @@ -11029,7 +11029,7 @@ disassembly of the DOS version, extended with new features.") (commit version))) (file-name (git-file-name name version)) (sha256 - (base32 "1m8649srzg3j2b1hs4x2y8fib6hn7v0afv4c7bjnfk4bhpi4cqd7")))) + (base32 "0bvp9xhzlh4d6q5jlvz4nciald75g9v0vahzax47q9xgajnbibzk")))) (build-system cmake-build-system) (arguments `(#:tests? #f ; no tests From 0744540d09ddef8dbf25cc5d65da9d029dab338c Mon Sep 17 00:00:00 2001 From: Vagrant Cascadian Date: Thu, 27 Oct 2022 13:13:28 -0700 Subject: [PATCH 666/790] gnu: guile-ssh: Update to 0.16.0. * gnu/packages/ssh.scm (guile-ssh): Update to 0.16.0. --- gnu/packages/ssh.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/ssh.scm b/gnu/packages/ssh.scm index babed807f9..65280bc4da 100644 --- a/gnu/packages/ssh.scm +++ b/gnu/packages/ssh.scm @@ -318,7 +318,7 @@ Additionally, various channel-specific options can be negotiated.") (define-public guile-ssh (package (name "guile-ssh") - (version "0.15.1") + (version "0.16.0") (home-page "https://github.com/artyom-poptsov/guile-ssh") (source (origin (method git-fetch) @@ -328,7 +328,7 @@ Additionally, various channel-specific options can be negotiated.") (file-name (git-file-name name version)) (sha256 (base32 - "0zzn5hsf97b35gixyg4z14sspl15qwnp52y4h89wra4y31l7467q")))) + "1ka5ayrg7kysx3bi5d8s0z6n12sdc06qp9gc4k9h2mlw3vz187ny")))) (build-system gnu-build-system) (outputs '("out" "debug")) (arguments From 7c2dab7dd459bd596e127630fc9603ff87cb7cfd Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Thu, 22 Dec 2022 11:00:56 +0200 Subject: [PATCH 667/790] gnu: xterm: Update to 377. * gnu/packages/xorg.scm (xterm): Update to 377. --- gnu/packages/xorg.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/xorg.scm b/gnu/packages/xorg.scm index 7767a35afe..16b211f7d2 100644 --- a/gnu/packages/xorg.scm +++ b/gnu/packages/xorg.scm @@ -5983,7 +5983,7 @@ to answer a question. Xmessage can also exit after a specified time.") (define-public xterm (package (name "xterm") - (version "374") + (version "377") (source (origin (method url-fetch) @@ -5993,7 +5993,7 @@ to answer a question. Xmessage can also exit after a specified time.") (string-append "ftp://ftp.invisible-island.net/xterm/" "xterm-" version ".tgz"))) (sha256 - (base32 "1xdxq65di3vncy8jyl12mpjif613xklnfx7vd5xnsk8dcwkddm0i")) + (base32 "1clhm4c8d7vmz0dn6qz2c6g68wxl8f2ba8a7c1zdk3jxlkkqy46v")) (patches (search-patches "xterm-370-explicit-xcursor.patch")))) (build-system gnu-build-system) From 2a4930a1e6d15a835bcd3db016ce09b197efe372 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 22 Dec 2022 10:25:09 +0100 Subject: [PATCH 668/790] gnu: Add wiggletools. * gnu/packages/bioinformatics.scm (wiggletools): New variable. --- gnu/packages/bioinformatics.scm | 41 +++++++++++++++++++++++++++++++++ 1 file changed, 41 insertions(+) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 160c44df98..b2c4f98531 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -17637,6 +17637,47 @@ module capable of computing base-level alignments for very large sequences.") (home-page "https://github.com/ekg/wfmash") (license license:expat))) +(define-public wiggletools + (package + (name "wiggletools") + (version "1.2.11") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/Ensembl/WiggleTools/") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "1g3qla4l1g583nzlgyww5jqxpq87ndpn9cmjls098bgqjyn5292q")))) + (build-system gnu-build-system) + (arguments + (list + ;; Tests require internet access + #:tests? #false + #:make-flags + #~(list "Wiggletools" + (string-append "CC=" #$(cc-for-target))) + #:phases + #~(modify-phases %standard-phases + (delete 'configure) + (replace 'install + (lambda _ + (install-file "bin/wiggletools" + (string-append #$output "/bin"))))))) + (inputs + (list curl ; XXX: needed by libbigwig + htslib libbigwig gsl xz zlib)) + (home-page "https://github.com/Ensembl/WiggleTools/") + (synopsis "Operations on the space of numerical functions defined on the genome") + (description "The WiggleTools package allows genomewide data files to be +manipulated as numerical functions, equipped with all the standard functional +analysis operators (sum, product, product by a scalar, comparators), and +derived statistics (mean, median, variance, stddev, t-test, Wilcoxon's rank +sum test, etc).") + (license license:asl2.0))) + (define-public flair (package (name "flair") From 6d2f312b23558c23e99ca7e025b8b07d190e086a Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 22 Dec 2022 11:17:52 +0100 Subject: [PATCH 669/790] gnu: Add r-rhtslib12. * gnu/packages/bioinformatics.scm (r-rhtslib12): New variable. --- gnu/packages/bioinformatics.scm | 27 +++++++++++++++++++++++++++ 1 file changed, 27 insertions(+) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index b2c4f98531..70abdae0f0 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -574,6 +574,33 @@ and utilities for PacBio C++ applications.") for all types of microbial diversity analyses.") (license license:expat)))) +(define-public r-rhtslib12 + (let ((commit "ee186daf04876969c7f31c16a0e0fda8e7c16a30") + (revision "1")) + (package + (name "r-rhtslib12") + (version (git-version "1.23.2" revision commit)) + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/haizi-zh/Rhtslib12") + (commit commit))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "0a3kkp0phi2fq6ip8p9vfj3axn7l15f2mb51a6v3ai4nlkhqqawj")))) + (properties `((upstream-name . "Rhtslib12"))) + (build-system r-build-system) + (propagated-inputs (list curl zlib r-zlibbioc)) + (native-inputs (list pkg-config r-knitr)) + (home-page "https://github.com/haizi-zh/Rhtslib12") + (synopsis "HTSlib high-throughput sequencing library as an R package") + (description + "This package provides version 1.12 of the HTSlib C library for +high-throughput sequence analysis. The package is primarily useful to +developers of other R packages who wish to make use of HTSlib.") + (license license:lgpl2.0+)))) + (define-public pbbam (package (name "pbbam") From d8a9d55b57f86b029ebce051d3411d288339eb84 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 22 Dec 2022 11:18:02 +0100 Subject: [PATCH 670/790] gnu: Add r-bedtorch. * gnu/packages/bioinformatics.scm (r-bedtorch): New variable. --- gnu/packages/bioinformatics.scm | 40 +++++++++++++++++++++++++++++++++ 1 file changed, 40 insertions(+) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 70abdae0f0..8cdce01e73 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -538,6 +538,46 @@ BED, GFF/GTF, VCF.") and utilities for PacBio C++ applications.") (license license:bsd-3))) +(define-public r-bedtorch + (let ((commit "f5ff4f83b94f59eac660333c64e4b2f296b35cea") + (revision "1")) + (package + (name "r-bedtorch") + (version (git-version "0.1.12.12" revision commit)) + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/haizi-zh/bedtorch/") + (commit commit))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "08l04iqf54b5995gc7rvqqd7w327fwqs7qjyhc9y5cqfj8yv4c48")))) + (properties `((upstream-name . "bedtorch"))) + (build-system r-build-system) + (propagated-inputs + (list r-assertthat + r-curl + r-data-table + r-dplyr + r-genomeinfodb + r-genomicranges + r-purrr + r-r-utils + r-rcpp + r-rcurl + r-readr + r-rhtslib12 + r-s4vectors + r-stringr + r-tidyr)) + (home-page "https://github.com/haizi-zh/bedtorch/") + (synopsis "R package for fast BED-file manipulation") + (description + "The goal of bedtorch is to provide a fast BED file manipulation tool +suite native in R.") + (license license:expat)))) + (define-public r-btools (let ((commit "fa21d4ca01d37ea4d98b45582453f3bf95cbc2b5") (revision "1")) From c1d543203e6de2ca31da82097f23b31a4250315e Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Thu, 22 Dec 2022 14:28:21 +0200 Subject: [PATCH 671/790] gnu: openvpn: Update to 2.5.8. * gnu/packages/vpn.scm (openvpn): Update to 2.5.8. --- gnu/packages/vpn.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/vpn.scm b/gnu/packages/vpn.scm index 608e63a0a5..f38fd28cea 100644 --- a/gnu/packages/vpn.scm +++ b/gnu/packages/vpn.scm @@ -796,7 +796,7 @@ this process. It is compatible with Fortinet VPNs.") (define-public openvpn (package (name "openvpn") - (version "2.5.7") + (version "2.5.8") (source (origin (method url-fetch) (uri (string-append @@ -804,7 +804,7 @@ this process. It is compatible with Fortinet VPNs.") version ".tar.gz")) (sha256 (base32 - "0s1yq530j4i4kicgvsxgl532vyn03gfhlxfdnsb43j05k4w0ld08")))) + "1cixqm4gn2d1v8qkbww75j30fzvxz13gc7whcmz54i0x4fvibwx6")))) (build-system gnu-build-system) (arguments '(#:configure-flags '("--enable-iproute2=yes"))) From aeabddcfc576961c8c6697b64408bdf034104b9e Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Thu, 22 Dec 2022 14:06:01 +0100 Subject: [PATCH 672/790] gnu: QEMU: Don't provide --firmwarepath for user-mode binaries. * gnu/packages/virtualization.scm (qemu)[arguments]: Remove --firmwarepath from the user-mode emulation configure invocation. --- gnu/packages/virtualization.scm | 4 ---- 1 file changed, 4 deletions(-) diff --git a/gnu/packages/virtualization.scm b/gnu/packages/virtualization.scm index d0f5fd5af4..4a048450a5 100644 --- a/gnu/packages/virtualization.scm +++ b/gnu/packages/virtualization.scm @@ -318,16 +318,12 @@ (lambda* (#:key inputs outputs #:allow-other-keys) (let* ((static (assoc-ref outputs "static")) (gcc (search-input-file inputs "/bin/gcc")) - (seabios (search-input-file inputs "/share/firmware/bios.bin")) ;; This is the common set of configure flags; it is ;; duplicated here to isolate this phase from manipulations ;; to the #:configure-flags build argument, as done in ;; derived packages such as qemu-minimal. (configure-flags (list (string-append "--cc=" gcc) (string-append "--host-cc=" gcc) - (string-append "--firmwarepath=" - #$output "/share/qemu:" - (dirname seabios)) "--sysconfdir=/etc" "--disable-debug-info"))) (mkdir-p "../user-static") From ffc0037458674d80267878ccec370300c45a0209 Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Tue, 20 Dec 2022 17:00:15 +0100 Subject: [PATCH 673/790] gnu: SeaBIOS: Split QEMU variants out to separate package. * gnu/packages/firmware.scm (seabios)[arguments]: Move custom build and install phases out to ... (seabios-qemu): ... this new variable. * gnu/packages/virtualization.scm (qemu)[inputs]: Change from SEABIOS to SEABIOS-QEMU. --- gnu/packages/firmware.scm | 193 ++++++++++++++++++-------------- gnu/packages/virtualization.scm | 2 +- 2 files changed, 109 insertions(+), 86 deletions(-) diff --git a/gnu/packages/firmware.scm b/gnu/packages/firmware.scm index 66e4b63d40..03c84fbe88 100644 --- a/gnu/packages/firmware.scm +++ b/gnu/packages/firmware.scm @@ -420,12 +420,7 @@ executing in M-mode.") (for-each delete-file (find-files "." "\\.hex$")))))) (build-system gnu-build-system) (native-inputs - (append - (list acpica python-wrapper) - (if (member (%current-system) '("i686-linux" "x86_64-linux")) - '() - (list (cross-gcc "i686-linux-gnu") - (cross-binutils "i686-linux-gnu"))))) + (list acpica python-wrapper)) (arguments (list #:tests? #f ;no tests @@ -435,9 +430,6 @@ executing in M-mode.") ;; by Build_overview.md. #~'("EXTRAVERSION=/GNU Guix" "V=1") ;build verbosely - #:modules `(,@%gnu-build-system-modules - (ice-9 threads) - (ice-9 match)) #:phases #~(modify-phases %standard-phases (replace 'configure @@ -449,95 +441,23 @@ executing in M-mode.") (format port #$(package-version this-package)))) ;; If we use (cc-for-target) then we have the system prefix ;; twice or we might have the wrong prefix. - (setenv "CC" "gcc") - #$@(match (%current-system) - ((or "i686-linux" "x86_64-linux") - #~()) - (_ - #~((substitute* "Makefile" - (("CROSS_PREFIX=") - "CROSS_PREFIX=i686-linux-gnu-"))))))) + (setenv "CC" "gcc"))) (add-before 'build 'build-description-tables (lambda _ ;; Regenerate the ACPI description tables. (invoke "make" "iasl") ;; Clear temporary files added by the iasl target. (invoke "make" "clean"))) - (replace 'build - (lambda* (#:key (make-flags #~'()) #:allow-other-keys) - ;; Note: These BIOS configurations are taken from QEMUs roms/ - ;; directory. - (let ((biosen - '(;; The standard BIOS using default options. - ("bios-256k" . ("QEMU=y" "ROM_SIZE=256" "ATA_DMA=n")) - ;; A minimal BIOS for old QEMU machine types. - ("bios-128k" - . ("QEMU=y" "ROM_SIZE=128" "ATA_DMA=n" "BOOTSPLASH=n" - "XEN=n" "USB_OHCI=n" "USB_XHCI=n" "USB_UAS=n" - "SDCARD=n" "TCGBIOS=n" "MPT_SCSI=n" "ESP_SCSI=n" - "MEGASAS=n" "PVSCSI=n" "NVME=n" "USE_SMM=n" - "VGAHOOKS=n" "HOST_BIOS_GEOMETRY=n" "ACPI_PARSE=n")) - ;; Minimal BIOS for the "microvm" machine type. - ("bios-microvm" - . ("QEMU=y" "ROM_SIZE=128" "XEN=n" "BOOTSPLASH=n" "ATA=n" - "AHCI=n" "SDCARD=n" "PVSCSI=n" "ESP_SCSI=n" "LSI_SCSI=n" - "MEGASAS=n" "MPT_SCSI=n" "FLOPPY=n" "FLASH_FLOPPY=n" - "NVME=n" "PS2PORT=n" "USB=n" "LPT=n" "RTC_TIMER=n" - "USE_SMM=n" "PMTIMER=n" "TCGBIOS=n" "HARDWARE_IRQ=n" - "ACPI_PARSE=y")))) - (vgabiosen - '(("ati" . ("VGA_ATI=y" "VGA_PCI=y")) - ("bochs-display" . ("DISPLAY_BOCHS=y" "VGA_PCI=y")) - ("cirrus" . ("VGA_CIRRUS=y" "VGA_PCI=y")) - ("stdvga" . ("VGA_BOCHS=y" "VGA_PCI=y")) - ("virtio" . ("VGA_BOCHS=y" "VGA_BOCHS_VIRTIO=y" "VGA_PCI=y")) - ("vmware" . ("VGA_BOCHS=y" "VGA_BOCHS_VMWARE=y" "VGA_PCI=y")) - ("qxl" . ("VGA_BOCHS=y" "VGA_BOCHS_QXL=y" "VGA_PCI=y")) - ("isavga" . ("VGA_BOCHS=y" "VGA_PCI=n")) - ("ramfb" . ("VGA_RAMFB=y" "VGA_PCI=n"))))) - (mkdir "out") - (n-par-for-each (parallel-job-count) - (match-lambda - ((target . config) - (let* ((dot-config (string-append (getcwd) "/" target - "/.config")) - (flags (append make-flags - (list (string-append "KCONFIG_CONFIG=" - dot-config) - (string-append "OUT=" target "/"))))) - (mkdir target) - (call-with-output-file dot-config - (lambda (port) - (for-each (lambda (entry) - (format port "CONFIG_~a~%" entry)) - config))) - (apply invoke "make" "oldnoconfig" flags) - (apply invoke "make" flags) - (link (string-append target "/" - (if (string-prefix? "vgabios" target) - "vgabios.bin" "bios.bin")) - (string-append "out/" target ".bin"))))) - (append biosen - (map (lambda (pair) - `(,(string-append "vgabios-" (car pair)) - . - ,(cons "BUILD_VGABIOS=y" (cdr pair)))) - vgabiosen)))))) (replace 'install (lambda _ - (let ((firmware (string-append #$output "/share/firmware"))) - (for-each (lambda (bios) - (install-file bios firmware)) - (find-files "out" "\\.bin$")) - (with-directory-excursion firmware - ;; Compatibility symlinks for QEMU. - (symlink "bios-128k.bin" "bios.bin") - (symlink "vgabios-isavga.bin" "vgabios.bin")))))))) + (install-file "out/bios.bin" + (string-append #$output "/share/firmware"))))))) (home-page "https://www.seabios.org/SeaBIOS") (synopsis "x86 BIOS implementation") (description "SeaBIOS is an implementation of a 16bit x86 BIOS. SeaBIOS can run in an emulator or it can run natively on X86 hardware with the use of coreboot.") + (supported-systems '("i686-linux" "x86_64-linux")) ;; Dual licensed. (license (list license:gpl3+ license:lgpl3+ ;; src/fw/acpi-dsdt.dsl is lgpl2 @@ -546,6 +466,109 @@ coreboot.") ;; cpl with a linking exception. license:cpl1.0)))) +(define-public seabios-qemu + (package/inherit seabios + (name "seabios-qemu") + (native-inputs + (if (member (%current-system) '("i686-linux" "x86_64-linux")) + (package-native-inputs seabios) + (modify-inputs (package-native-inputs seabios) + (prepend (cross-gcc "i686-linux-gnu") + (cross-binutils "i686-linux-gnu"))))) + (supported-systems %supported-systems) + (arguments + (substitute-keyword-arguments (package-arguments seabios) + ((#:modules modules %gnu-build-system-modules) + `((ice-9 match) + (ice-9 threads) + ,@modules)) + ((#:phases phases) + #~(modify-phases #$phases + #$@(match (%current-system) + ((or "i686-linux" "x86_64-linux") + #~()) + (_ + #~((add-after 'configure 'configure-cross + (lambda _ + (substitute* "Makefile" + (("CROSS_PREFIX=") + "CROSS_PREFIX=i686-linux-gnu-"))))))) + (replace 'build + (lambda* (#:key (make-flags #~'()) #:allow-other-keys) + ;; Note: These BIOS configurations are taken from QEMUs roms/ + ;; directory. + (let ((biosen + '( ;; The standard BIOS using default options. + ("bios-256k" . ("QEMU=y" "ROM_SIZE=256" "ATA_DMA=n")) + ;; A minimal BIOS for old QEMU machine types. + ("bios-128k" + . ("QEMU=y" "ROM_SIZE=128" "ATA_DMA=n" "BOOTSPLASH=n" + "XEN=n" "USB_OHCI=n" "USB_XHCI=n" "USB_UAS=n" + "SDCARD=n" "TCGBIOS=n" "MPT_SCSI=n" "ESP_SCSI=n" + "MEGASAS=n" "PVSCSI=n" "NVME=n" "USE_SMM=n" + "VGAHOOKS=n" "HOST_BIOS_GEOMETRY=n" "ACPI_PARSE=n")) + ;; Minimal BIOS for the "microvm" machine type. + ("bios-microvm" + . ("QEMU=y" "ROM_SIZE=128" "XEN=n" "BOOTSPLASH=n" + "ATA=n" "AHCI=n" "SDCARD=n" "PVSCSI=n" "ESP_SCSI=n" + "LSI_SCSI=n" "MEGASAS=n" "MPT_SCSI=n" "FLOPPY=n" + "FLASH_FLOPPY=n" "NVME=n" "PS2PORT=n" "USB=n" + "LPT=n" "RTC_TIMER=n" "USE_SMM=n" "PMTIMER=n" + "TCGBIOS=n" "HARDWARE_IRQ=n" "ACPI_PARSE=y")))) + (vgabiosen + '(("ati" . ("VGA_ATI=y" "VGA_PCI=y")) + ("bochs-display" . ("DISPLAY_BOCHS=y" "VGA_PCI=y")) + ("cirrus" . ("VGA_CIRRUS=y" "VGA_PCI=y")) + ("stdvga" . ("VGA_BOCHS=y" "VGA_PCI=y")) + ("virtio" . ("VGA_BOCHS=y" "VGA_BOCHS_VIRTIO=y" + "VGA_PCI=y")) + ("vmware" . ("VGA_BOCHS=y" "VGA_BOCHS_VMWARE=y" + "VGA_PCI=y")) + ("qxl" . ("VGA_BOCHS=y" "VGA_BOCHS_QXL=y" + "VGA_PCI=y")) + ("isavga" . ("VGA_BOCHS=y" "VGA_PCI=n")) + ("ramfb" . ("VGA_RAMFB=y" "VGA_PCI=n"))))) + (mkdir "out") + (n-par-for-each + (parallel-job-count) + (match-lambda + ((target . config) + (let* ((dot-config (string-append (getcwd) "/" target + "/.config")) + (flags (append + make-flags + (list (string-append "KCONFIG_CONFIG=" + dot-config) + (string-append "OUT=" target "/"))))) + (mkdir target) + (call-with-output-file dot-config + (lambda (port) + (for-each (lambda (entry) + (format port "CONFIG_~a~%" entry)) + config))) + (apply invoke "make" "oldnoconfig" flags) + (apply invoke "make" flags) + (link (string-append target "/" + (if (string-prefix? "vgabios" target) + "vgabios.bin" "bios.bin")) + (string-append "out/" target ".bin"))))) + (append biosen + (map (lambda (pair) + `(,(string-append "vgabios-" (car pair)) + . + ,(cons "BUILD_VGABIOS=y" (cdr pair)))) + vgabiosen)))))) + (replace 'install + (lambda _ + (let ((firmware (string-append #$output "/share/firmware"))) + (for-each (lambda (bios) + (install-file bios firmware)) + (find-files "out" "\\.bin$")) + (with-directory-excursion firmware + ;; Compatibility symlinks for QEMU. + (symlink "bios-128k.bin" "bios.bin") + (symlink "vgabios-isavga.bin" "vgabios.bin"))))))))))) + (define-public edk2-tools (package (name "edk2-tools") diff --git a/gnu/packages/virtualization.scm b/gnu/packages/virtualization.scm index 4a048450a5..18289dd963 100644 --- a/gnu/packages/virtualization.scm +++ b/gnu/packages/virtualization.scm @@ -402,7 +402,7 @@ exec smbd $@"))) pixman pulseaudio sdl2 - seabios + seabios-qemu spice usbredir util-linux From a5dbe84a619cd3b04c242ff7e76c452a74b79428 Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Tue, 20 Dec 2022 22:25:46 +0100 Subject: [PATCH 674/790] gnu: ipxe-qemu: Cross-compile on non x86_64. * gnu/packages/bootloaders.scm (ipxe-qemu)[native-inputs]: When not targeting x86_64, add CROSS-GCC and CROSS-BINUTILS. [arguments]: Set CROSS_COMPILE in that case. --- gnu/packages/bootloaders.scm | 19 ++++++++++++++----- 1 file changed, 14 insertions(+), 5 deletions(-) diff --git a/gnu/packages/bootloaders.scm b/gnu/packages/bootloaders.scm index c8b8adbc93..04d7eefae2 100644 --- a/gnu/packages/bootloaders.scm +++ b/gnu/packages/bootloaders.scm @@ -1535,8 +1535,14 @@ the features of iPXE without the hassle of reflashing.") (package/inherit ipxe (name "ipxe-qemu") (native-inputs - (modify-inputs (package-native-inputs ipxe) - (prepend edk2-tools))) + ;; QEMU uses a 64-bit UEFI firmware. + (if (target-x86-64?) + (modify-inputs (package-native-inputs ipxe) + (prepend edk2-tools)) + (modify-inputs (package-native-inputs ipxe) + (prepend edk2-tools + (cross-gcc "x86_64-linux-gnu") + (cross-binutils "x86_64-linux-gnu"))))) (arguments (let ((roms ;; Alist of ROM -> (VID . DID) entries. This list and below @@ -1554,14 +1560,17 @@ the features of iPXE without the hassle of reflashing.") `((ice-9 match) ,@modules)) ((#:make-flags flags) #~(append (delete "everything" #$flags) - '("CONFIG=qemu") + '("CONFIG=qemu" + #$@(if (target-x86-64?) + '() + '("CROSS_COMPILE=x86_64-linux-gnu-"))) (map (match-lambda ((_ . (vid . did)) (string-append "bin/" vid did ".rom"))) '#$roms) (map (match-lambda ((_ . (vid . did)) - (string-append "bin-efi/" + (string-append "bin-x86_64-efi/" vid did ".efidrv"))) '#$roms))) ((#:phases phases) @@ -1582,7 +1591,7 @@ the features of iPXE without the hassle of reflashing.") "-l" "0x02" "-f" (string-append "0x" vid) "-i" (string-append "0x" did) - "-ec" (string-append "bin-efi/" + "-ec" (string-append "bin-x86_64-efi/" vid did ".efidrv") "-o" (string-append firmware "/efi-" name ".rom"))))) From ba7f6f0bf3922968d16ad433da818928381e1578 Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Thu, 22 Dec 2022 13:25:50 +0100 Subject: [PATCH 675/790] gnu: QEMU: Unbundle iPXE. * gnu/packages/virtualization.scm (qemu)[source](snippet): Purge iPXE. [arguments]: Re-add firmware files from IPXE-QEMU. [inputs]: Add IPXE-QEMU. --- gnu/packages/virtualization.scm | 23 ++++++++++++++++++----- 1 file changed, 18 insertions(+), 5 deletions(-) diff --git a/gnu/packages/virtualization.scm b/gnu/packages/virtualization.scm index 18289dd963..5c832beb9f 100644 --- a/gnu/packages/virtualization.scm +++ b/gnu/packages/virtualization.scm @@ -178,10 +178,14 @@ ;; TODO: Scrub all firmwares from this directory! (with-directory-excursion "pc-bios" ;; Delete firmwares provided by SeaBIOS. - (for-each delete-file (find-files "." "^(bios|vgabios).*\\.bin$"))) + (for-each delete-file (find-files "." "^(bios|vgabios).*\\.bin$")) + ;; Delete iPXE firmwares. + (for-each delete-file (find-files "." "^(efi|pxe)-.*\\.rom$"))) ;; Delete bundled code that we provide externally. (for-each delete-file-recursively - '("dtc" "meson" "roms/seabios")))))) + '("dtc" "meson" + "roms/ipxe" + "roms/seabios")))))) (outputs '("out" "static" "doc")) ;5.3 MiB of HTML docs (build-system gnu-build-system) (arguments @@ -195,6 +199,8 @@ (meson (search-input-file %build-inputs "bin/meson")) (seabios (search-input-file %build-inputs "share/firmware/bios.bin")) + (ipxe (search-input-file %build-inputs + "share/firmware/pxe-virtio.rom")) (out #$output)) (list (string-append "--cc=" gcc) ;; Some architectures insist on using HOST_CC. @@ -205,7 +211,8 @@ "--sysconfdir=/etc" "--enable-fdt=system" (string-append "--firmwarepath=" out "/share/qemu:" - (dirname seabios)) + (dirname seabios) ":" + (dirname ipxe)) (string-append "--smbd=" out "/libexec/samba-wrapper") "--disable-debug-info" ;for space considerations ;; The binaries need to be linked against -lrt. @@ -226,6 +233,9 @@ (let* ((seabios (dirname (search-input-file inputs "share/firmware/bios.bin"))) (seabios-firmwares (find-files seabios "\\.bin$")) + (ipxe (dirname (search-input-file + inputs "share/firmware/pxe-virtio.rom"))) + (ipxe-firmwares (find-files ipxe "\\.rom$")) (allowed-differences ;; Ignore minor differences (addresses etc) in the firmware ;; data tables compared to what the test suite expects. @@ -240,7 +250,7 @@ (with-directory-excursion "pc-bios" (for-each (lambda (file) (symlink file (basename file))) - seabios-firmwares)) + (append seabios-firmwares ipxe-firmwares))) (for-each (lambda (file) (format allowed-differences-whitelist "\"~a\",~%" file)) @@ -357,7 +367,9 @@ ;; pc-bios/meson.build, hence this roundabout way. (with-directory-excursion (string-append #$output "/share/qemu") (for-each delete-file - (find-files "." "^(vga)?bios(-[a-z0-9-]+)?\\.bin$"))))) + (append + (find-files "." "^(vga)?bios(-[a-z0-9-]+)?\\.bin$") + (find-files "." "^(efi|pxe)-.*\\.rom$")))))) ;; Create a wrapper for Samba. This allows QEMU to use Samba without ;; pulling it in as an input. Note that you need to explicitly install ;; Samba in your Guix profile for Samba support. @@ -385,6 +397,7 @@ exec smbd $@"))) dtc glib gtk+ + ipxe-qemu libaio libcacard ;smartcard support attr libcap-ng ;VirtFS support From 209aed9511f41b2bfabe32d2e280192e64e3d54b Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Thu, 22 Dec 2022 13:50:30 +0100 Subject: [PATCH 676/790] gnu: Install QEMU firmare files to 'share/qemu'. This paves the way for using a native search path in the future. * gnu/packages/bootloaders.scm (ipxe-qemu)[arguments]: Install firmware files to 'share/qemu' instead of 'share/firmware'. * gnu/packages/firmware.scm (seabios-qemu)[arguments]: Likewise. * gnu/packages/virtualization.scm (qemu)[arguments]: Adjust accordingly. --- gnu/packages/bootloaders.scm | 2 +- gnu/packages/firmware.scm | 2 +- gnu/packages/virtualization.scm | 8 ++++---- 3 files changed, 6 insertions(+), 6 deletions(-) diff --git a/gnu/packages/bootloaders.scm b/gnu/packages/bootloaders.scm index 04d7eefae2..7c4c92ad9d 100644 --- a/gnu/packages/bootloaders.scm +++ b/gnu/packages/bootloaders.scm @@ -1577,7 +1577,7 @@ the features of iPXE without the hassle of reflashing.") #~(modify-phases #$phases (replace 'install (lambda _ - (let ((firmware (string-append #$output "/share/firmware"))) + (let ((firmware (string-append #$output "/share/qemu"))) (mkdir-p firmware) (for-each (match-lambda diff --git a/gnu/packages/firmware.scm b/gnu/packages/firmware.scm index 03c84fbe88..eac3176d72 100644 --- a/gnu/packages/firmware.scm +++ b/gnu/packages/firmware.scm @@ -560,7 +560,7 @@ coreboot.") vgabiosen)))))) (replace 'install (lambda _ - (let ((firmware (string-append #$output "/share/firmware"))) + (let ((firmware (string-append #$output "/share/qemu"))) (for-each (lambda (bios) (install-file bios firmware)) (find-files "out" "\\.bin$")) diff --git a/gnu/packages/virtualization.scm b/gnu/packages/virtualization.scm index 5c832beb9f..9f1db849a3 100644 --- a/gnu/packages/virtualization.scm +++ b/gnu/packages/virtualization.scm @@ -198,9 +198,9 @@ #~(let ((gcc (search-input-file %build-inputs "/bin/gcc")) (meson (search-input-file %build-inputs "bin/meson")) (seabios (search-input-file %build-inputs - "share/firmware/bios.bin")) + "share/qemu/bios.bin")) (ipxe (search-input-file %build-inputs - "share/firmware/pxe-virtio.rom")) + "share/qemu/pxe-virtio.rom")) (out #$output)) (list (string-append "--cc=" gcc) ;; Some architectures insist on using HOST_CC. @@ -231,10 +231,10 @@ (add-after 'unpack 'replace-firmwares (lambda* (#:key inputs #:allow-other-keys) (let* ((seabios (dirname (search-input-file - inputs "share/firmware/bios.bin"))) + inputs "share/qemu/bios.bin"))) (seabios-firmwares (find-files seabios "\\.bin$")) (ipxe (dirname (search-input-file - inputs "share/firmware/pxe-virtio.rom"))) + inputs "share/qemu/pxe-virtio.rom"))) (ipxe-firmwares (find-files ipxe "\\.rom$")) (allowed-differences ;; Ignore minor differences (addresses etc) in the firmware From 9279775d6904830b8ffa0bf7bf06e0904aeca323 Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Thu, 22 Dec 2022 14:24:30 +0100 Subject: [PATCH 677/790] gnu: iPXE: Embed the actual package version. * gnu/packages/bootloaders.scm (ipxe)[arguments]: Add phase to set the proper version. --- gnu/packages/bootloaders.scm | 10 +++++++++- 1 file changed, 9 insertions(+), 1 deletion(-) diff --git a/gnu/packages/bootloaders.scm b/gnu/packages/bootloaders.scm index 7c4c92ad9d..464a6f54c1 100644 --- a/gnu/packages/bootloaders.scm +++ b/gnu/packages/bootloaders.scm @@ -1419,7 +1419,7 @@ order to add a suitable bootloader menu entry.") ;; ;; TODO: Bump this timestamp at each modifications of the package (not only ;; for updates) by running: date +%s. - (let ((timestamp "1591706427")) + (let ((timestamp "1671715380")) (package (name "ipxe") (version "1.21.1") @@ -1481,6 +1481,14 @@ order to add a suitable bootloader menu entry.") (modify-phases %standard-phases (add-after 'unpack 'enter-source-directory (lambda _ (chdir "src") #t)) + (add-after 'enter-source-directory 'set-version + (lambda _ + ;; When not building from a git checkout, iPXE encodes the + ;; version as "1.0.0+". Use the package version instead. + (substitute* "Makefile" + (("^VERSION[[:blank:]]+=.*") + (string-append "VERSION = " ,(package-version this-package) + "-guix\n"))))) (add-after 'enter-source-directory 'set-options (lambda _ (substitute* "config/general.h" From 368e00cce0e843f483abb993e0b1cbc66ed97029 Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Thu, 22 Dec 2022 15:52:23 +0100 Subject: [PATCH 678/790] gnu: Add sgabios. * gnu/packages/firmware.scm (sgabios): New variable. --- gnu/packages/firmware.scm | 53 +++++++++++++++++++++++++++++++++++++++ 1 file changed, 53 insertions(+) diff --git a/gnu/packages/firmware.scm b/gnu/packages/firmware.scm index eac3176d72..54b19dd5fa 100644 --- a/gnu/packages/firmware.scm +++ b/gnu/packages/firmware.scm @@ -569,6 +569,59 @@ coreboot.") (symlink "bios-128k.bin" "bios.bin") (symlink "vgabios-isavga.bin" "vgabios.bin"))))))))))) +(define-public sgabios + ;; There are no tags in the repository. + (let ((commit "72f39d48bedf044e202fd51fecf3e2218fc2ae66") + (revision "0")) + (package + (name "sgabios") + (version (git-version "0.0" revision commit)) + (home-page "https://gitlab.com/qemu-project/sgabios") + (source (origin + (method git-fetch) + (uri (git-reference (url home-page) (commit commit))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "0ybl021i0xaz18wzq4q13ifypy5b3dj8m11c8m0qdiq00g06vm0i")))) + (build-system gnu-build-system) + (arguments + (list #:make-flags + #~'(#$@(if (member (%current-system) '("i686-linux" "x86_64-linux")) + #~("CC=gcc") + #~("CC=i686-linux-gnu-gcc" "LD=i686-linux-gnu-ld")) + "HOSTCC=gcc") + #:parallel-build? #f + #:tests? #f ;no tests + #:phases + #~(modify-phases %standard-phases + (add-after 'unpack 'build-reproducibly + (lambda _ + (substitute* "Makefile" + (("BUILD_DATE = .*") + "BUILD_DATE = \\\"Jan 1 1970\\\"\n") + (("BUILD_SHORT_DATE = .*") + "BUILD_SHORT_DATE = \\\"1/1/70\\\"\n")))) + (delete 'configure) + (replace 'install + (lambda _ + (install-file "sgabios.bin" + (string-append #$output "/share/qemu"))))))) + (native-inputs + (if (member (%current-system) '("i686-linux" "x86_64-linux")) + '() + (list (cross-gcc "i686-linux-gnu") + (cross-binutils "i686-linux-gnu")))) + (synopsis "Serial graphics adapter BIOS") + (description + "SGABIOS provides a means for legacy PC software to communicate with an +attached serial console as if a VGA card is attached. It is designed to be +inserted into a BIOS as an option ROM to provide over a serial port the display +and input capabilites normally handled by a VGA adapter and a keyboard, and +additionally provide hooks for logging displayed characters for later collection +after an operating system boots.") + (license license:asl2.0)))) + (define-public edk2-tools (package (name "edk2-tools") From c9392e6fc6d92f3df8642b6fa0197f62f7f4d7bd Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Thu, 22 Dec 2022 16:00:56 +0100 Subject: [PATCH 679/790] gnu: QEMU: Unbundle SGABIOS. * gnu/packages/virtualization.scm (qemu)[source]: Purge sgabios. [arguments]: Replace bundled variant with the one from INPUTS. [inputs]: Add SGABIOS. --- gnu/packages/virtualization.scm | 16 +++++++++++++--- 1 file changed, 13 insertions(+), 3 deletions(-) diff --git a/gnu/packages/virtualization.scm b/gnu/packages/virtualization.scm index 9f1db849a3..945584bd0a 100644 --- a/gnu/packages/virtualization.scm +++ b/gnu/packages/virtualization.scm @@ -179,13 +179,16 @@ (with-directory-excursion "pc-bios" ;; Delete firmwares provided by SeaBIOS. (for-each delete-file (find-files "." "^(bios|vgabios).*\\.bin$")) + ;; Delete SGABIOS. + (delete-file "sgabios.bin") ;; Delete iPXE firmwares. (for-each delete-file (find-files "." "^(efi|pxe)-.*\\.rom$"))) ;; Delete bundled code that we provide externally. (for-each delete-file-recursively '("dtc" "meson" "roms/ipxe" - "roms/seabios")))))) + "roms/seabios" + "roms/sgabios")))))) (outputs '("out" "static" "doc")) ;5.3 MiB of HTML docs (build-system gnu-build-system) (arguments @@ -199,6 +202,8 @@ (meson (search-input-file %build-inputs "bin/meson")) (seabios (search-input-file %build-inputs "share/qemu/bios.bin")) + (sgabios (search-input-file %build-inputs + "/share/qemu/sgabios.bin")) (ipxe (search-input-file %build-inputs "share/qemu/pxe-virtio.rom")) (out #$output)) @@ -212,7 +217,8 @@ "--enable-fdt=system" (string-append "--firmwarepath=" out "/share/qemu:" (dirname seabios) ":" - (dirname ipxe)) + (dirname ipxe) ":" + (dirname sgabios)) (string-append "--smbd=" out "/libexec/samba-wrapper") "--disable-debug-info" ;for space considerations ;; The binaries need to be linked against -lrt. @@ -233,6 +239,7 @@ (let* ((seabios (dirname (search-input-file inputs "share/qemu/bios.bin"))) (seabios-firmwares (find-files seabios "\\.bin$")) + (sgabios (search-input-file inputs "share/qemu/sgabios.bin")) (ipxe (dirname (search-input-file inputs "share/qemu/pxe-virtio.rom"))) (ipxe-firmwares (find-files ipxe "\\.rom$")) @@ -250,7 +257,8 @@ (with-directory-excursion "pc-bios" (for-each (lambda (file) (symlink file (basename file))) - (append seabios-firmwares ipxe-firmwares))) + (append seabios-firmwares ipxe-firmwares + (list sgabios)))) (for-each (lambda (file) (format allowed-differences-whitelist "\"~a\",~%" file)) @@ -368,6 +376,7 @@ (with-directory-excursion (string-append #$output "/share/qemu") (for-each delete-file (append + '("sgabios.bin") (find-files "." "^(vga)?bios(-[a-z0-9-]+)?\\.bin$") (find-files "." "^(efi|pxe)-.*\\.rom$")))))) ;; Create a wrapper for Samba. This allows QEMU to use Samba without @@ -416,6 +425,7 @@ exec smbd $@"))) pulseaudio sdl2 seabios-qemu + sgabios spice usbredir util-linux From dade92613bdd2bc2d9bc91dbd1574d2ec31da130 Mon Sep 17 00:00:00 2001 From: Guillaume Le Vaillant Date: Thu, 22 Dec 2022 16:31:46 +0100 Subject: [PATCH 680/790] gnu: Add dsd. * gnu/packages/radio.scm (dsd): New variable. --- gnu/packages/radio.scm | 35 +++++++++++++++++++++++++++++++++++ 1 file changed, 35 insertions(+) diff --git a/gnu/packages/radio.scm b/gnu/packages/radio.scm index 9642f0e068..a57174ff3a 100644 --- a/gnu/packages/radio.scm +++ b/gnu/packages/radio.scm @@ -2202,6 +2202,41 @@ Codec.") Audio Broadcasting}.") (license license:gpl2+)))) +(define-public dsd + (let ((commit "59423fa46be8b41ef0bd2f3d2b45590600be29f0") + (revision "1")) + (package + (name "dsd") + (version (git-version "1.7.0" revision commit)) + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/szechyjs/dsd") + (commit commit))) + (file-name (git-file-name name version)) + (sha256 + (base32 "128gvgkanvh4n5bjnzkfk419hf5fdbad94fb8d8lv67h94vfchyd")))) + (build-system cmake-build-system) + (native-inputs + (list pkg-config)) + (inputs + (list itpp libsndfile mbelib portaudio)) + (arguments + (list #:phases + #~(modify-phases %standard-phases + (add-after 'unpack 'fix-itpp-detection + (lambda _ + (substitute* "cmake/FindITPP.cmake" + (("libitpp\\.dll") + "itpp_debug"))))))) + (synopsis "Digital speech decoder") + (description + "DSD is able to decode several digital voice formats used in radio +transmissions.") + (home-page "https://github.com/szechyjs/dsd") + (license (list license:expat license:gpl2))))) + (define-public dsdcc (package (name "dsdcc") From d2cd3290ea4fed6417e6192676a55ee158256df0 Mon Sep 17 00:00:00 2001 From: Michael Rohleder Date: Tue, 20 Dec 2022 01:07:46 +0100 Subject: [PATCH 681/790] gnu: stockfish: Update to 15.1. * gnu/packages/games.scm (stockfish): Update to 15.1. [arguments]: Renamed phase remove-m-flag to remove-m-flag-and-net-target. Add removing of the net target in the Makefile, because it wants networking. Signed-off-by: Guillaume Le Vaillant --- gnu/packages/games.scm | 18 ++++++++++-------- 1 file changed, 10 insertions(+), 8 deletions(-) diff --git a/gnu/packages/games.scm b/gnu/packages/games.scm index 54cf17e963..7dd73dcb4a 100644 --- a/gnu/packages/games.scm +++ b/gnu/packages/games.scm @@ -52,7 +52,7 @@ ;;; Copyright © 2020 Vitaliy Shatrov ;;; Copyright © 2020 Jack Hill ;;; Copyright © 2020 Vincent Legoll -;;; Copyright © 2020, 2021 Michael Rohleder +;;; Copyright © 2020, 2021, 2022 Michael Rohleder ;;; Copyright © 2020 Trevor Hass ;;; Copyright © 2020, 2021 Liliana Marie Prikler ;;; Copyright © 2020 Lu hux @@ -10336,10 +10336,10 @@ etc. You can also play games on FICS or against an engine.") (license license:gpl2+))) (define-public stockfish - (let ((neural-network-revision "6877cd24400e")) ; also update hash below + (let ((neural-network-revision "ad9b42354671")) ; also update hash below (package (name "stockfish") - (version "15") + (version "15.1") (source (origin (method git-fetch) @@ -10348,7 +10348,7 @@ etc. You can also play games on FICS or against an engine.") (commit (string-append "sf_" version)))) (file-name (git-file-name name version)) (sha256 - (base32 "1v19v6qhwbf31wpc3qcih4dvqxwqkh0p426skgjin6ags31hkbmh")))) + (base32 "0zmnv8vbhhid73pjyxg56r4ckm887znv4d55br370plm3p5b56xa")))) (build-system gnu-build-system) (inputs `(("neural-network" @@ -10358,7 +10358,7 @@ etc. You can also play games on FICS or against an engine.") neural-network-revision ".nnue")) (sha256 (base32 - "1qyna598c0v7gdpycc6kpl12h5a2wa50dqray6gv208f80jcsxv8")))))) + "11mpdhnsfggldgvmzwmya64pp3fndyppi2fkdf8kfhbi8qsl56xd")))))) (arguments `(#:tests? #f #:make-flags (list "-C" "src" @@ -10388,11 +10388,13 @@ etc. You can also play games on FICS or against an engine.") (copy-file (assoc-ref inputs "neural-network") (format #f "src/nn-~a.nnue" ,neural-network-revision)))) - ;; Guix doesn't use a multiarch gcc. - (add-after 'unpack 'remove-m-flag + (add-after 'unpack 'remove-m-flag-and-net-target (lambda _ (substitute* "src/Makefile" - (("-m\\$\\(bits\\)") ""))))))) + ;; Guix doesn't use a multiarch gcc. + (("-m\\$\\(bits\\)") "") + ;; Dont depend on net target. + ((": net") ": "))))))) (synopsis "Strong chess engine") (description "Stockfish is a very strong chess engine. It is much stronger than the From 9922da2829028765a9385506aa36b16ef2cf5eac Mon Sep 17 00:00:00 2001 From: Leo Famulari Date: Wed, 21 Dec 2022 19:24:09 -0500 Subject: [PATCH 682/790] gnu: linux-libre: Update to 6.0.15. * gnu/packages/linux.scm (linux-libre-6.0-version): Update to 6.0.15. (linux-libre-6.0-pristine-source): Update hash. --- gnu/packages/linux.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/linux.scm b/gnu/packages/linux.scm index 4cb97d1b82..14e44e423b 100644 --- a/gnu/packages/linux.scm +++ b/gnu/packages/linux.scm @@ -480,7 +480,7 @@ corresponding UPSTREAM-SOURCE (an origin), using the given DEBLOB-SCRIPTS." ;; The current "stable" kernels. That is, the most recently released major ;; versions that are still supported upstream. -(define-public linux-libre-6.0-version "6.0.14") +(define-public linux-libre-6.0-version "6.0.15") (define-public linux-libre-6.0-gnu-revision "gnu") (define deblob-scripts-6.0 (linux-libre-deblob-scripts @@ -490,7 +490,7 @@ corresponding UPSTREAM-SOURCE (an origin), using the given DEBLOB-SCRIPTS." (base32 "16g2bin3xay30zfss1vlb7pwcss5giaxaksp4v1gk05wn51wjrqr"))) (define-public linux-libre-6.0-pristine-source (let ((version linux-libre-6.0-version) - (hash (base32 "0862g1djm2hlcw44ks08494pbsd44syb7k0z8dqjbynggxz8zway"))) + (hash (base32 "08389890gq4b9vkvrb22lzkr4blkn3a5ma074ns19gl89wyyp16l"))) (make-linux-libre-source version (%upstream-linux-source version hash) deblob-scripts-6.0))) From dd575627b301eaf09be16e5e3bf660b1abf277b1 Mon Sep 17 00:00:00 2001 From: Leo Famulari Date: Wed, 21 Dec 2022 19:24:31 -0500 Subject: [PATCH 683/790] gnu: linux-libre 5.15: Update to 5.15.85. * gnu/packages/linux.scm (linux-libre-5.15-version): Update to 5.15.85. (linux-libre-5.15-pristine-source): Update hash. --- gnu/packages/linux.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/linux.scm b/gnu/packages/linux.scm index 14e44e423b..8ed5503185 100644 --- a/gnu/packages/linux.scm +++ b/gnu/packages/linux.scm @@ -498,7 +498,7 @@ corresponding UPSTREAM-SOURCE (an origin), using the given DEBLOB-SCRIPTS." ;; The "longterm" kernels — the older releases with long-term upstream support. ;; Here are the support timelines: ;; -(define-public linux-libre-5.15-version "5.15.84") +(define-public linux-libre-5.15-version "5.15.85") (define-public linux-libre-5.15-gnu-revision "gnu") (define deblob-scripts-5.15 (linux-libre-deblob-scripts @@ -508,7 +508,7 @@ corresponding UPSTREAM-SOURCE (an origin), using the given DEBLOB-SCRIPTS." (base32 "1m73pgx8v047xb2gck2g7j7khniis8c9akn9vhzgsdfglrf8p6fj"))) (define-public linux-libre-5.15-pristine-source (let ((version linux-libre-5.15-version) - (hash (base32 "05w29fh1k40iwsm7h67i86lv6jw075micav5b5dy7hjrn06c739i"))) + (hash (base32 "024qhjh9mgfnanr1qd8002n6a4wpn98lajli12a0m3n9z8lsw2rc"))) (make-linux-libre-source version (%upstream-linux-source version hash) deblob-scripts-5.15))) From 1be1961a1c28c7e7231683199061ba87f6a088e1 Mon Sep 17 00:00:00 2001 From: Leo Famulari Date: Wed, 21 Dec 2022 19:24:46 -0500 Subject: [PATCH 684/790] gnu: linux-libre 5.10: Update to 5.10.161. * gnu/packages/linux.scm (linux-libre-5.10-version): Update to 5.10.161. (linux-libre-5.10-pristine-source): Update hash. --- gnu/packages/linux.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/linux.scm b/gnu/packages/linux.scm index 8ed5503185..ddf7025832 100644 --- a/gnu/packages/linux.scm +++ b/gnu/packages/linux.scm @@ -513,7 +513,7 @@ corresponding UPSTREAM-SOURCE (an origin), using the given DEBLOB-SCRIPTS." (%upstream-linux-source version hash) deblob-scripts-5.15))) -(define-public linux-libre-5.10-version "5.10.160") +(define-public linux-libre-5.10-version "5.10.161") (define-public linux-libre-5.10-gnu-revision "gnu1") (define deblob-scripts-5.10 (linux-libre-deblob-scripts @@ -523,7 +523,7 @@ corresponding UPSTREAM-SOURCE (an origin), using the given DEBLOB-SCRIPTS." (base32 "0a96g4pjdgwvxn2wpz6rfc8nwdlkw138r9pp66kvfrrn08i313ii"))) (define-public linux-libre-5.10-pristine-source (let ((version linux-libre-5.10-version) - (hash (base32 "02w4mapfhds26ahqy5ijm5a6mlh9a5f4q3488l898qz8r9m0gm9h"))) + (hash (base32 "0ya04njrxr4d37zkxvivmn5f0bdvcb504pyp9ahwz8nqpk8gdaks"))) (make-linux-libre-source version (%upstream-linux-source version hash) deblob-scripts-5.10))) From 6ce7904a85154fece2c159d26b39bfa54b36101a Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Thu, 22 Dec 2022 22:09:58 +0200 Subject: [PATCH 685/790] gnu: ipxe-qemu: Fix building on 32-bit systems. * gnu/packages/bootloaders.scm (ipxe-qemu)[native-inputs]: When building from a 32-bit system add a binutils variant capable of assembling 64-bit instructions and an ld-wrapper using it. --- gnu/packages/bootloaders.scm | 25 +++++++++++++++++++++---- 1 file changed, 21 insertions(+), 4 deletions(-) diff --git a/gnu/packages/bootloaders.scm b/gnu/packages/bootloaders.scm index 464a6f54c1..57705cf596 100644 --- a/gnu/packages/bootloaders.scm +++ b/gnu/packages/bootloaders.scm @@ -1547,10 +1547,27 @@ the features of iPXE without the hassle of reflashing.") (if (target-x86-64?) (modify-inputs (package-native-inputs ipxe) (prepend edk2-tools)) - (modify-inputs (package-native-inputs ipxe) - (prepend edk2-tools - (cross-gcc "x86_64-linux-gnu") - (cross-binutils "x86_64-linux-gnu"))))) + (if (target-64bit?) + (modify-inputs (package-native-inputs ipxe) + (prepend edk2-tools + (cross-gcc "x86_64-linux-gnu") + (cross-binutils "x86_64-linux-gnu"))) + ;; Our default 32-bit binutils is not 64-bit capable. + (let ((binutils-64-bit-bfd + (package/inherit + binutils + (name "binutils-64-bit-bfd") + (arguments + (substitute-keyword-arguments (package-arguments binutils) + ((#:configure-flags flags ''()) + `(cons "--enable-64-bit-bfd" ,flags))))))) + (modify-inputs (package-native-inputs ipxe) + (prepend edk2-tools + (make-ld-wrapper "ld-wrapper-64-bit-bfd" + #:binutils binutils) + binutils-64-bit-bfd + (cross-gcc "x86_64-linux-gnu") + (cross-binutils "x86_64-linux-gnu"))))))) (arguments (let ((roms ;; Alist of ROM -> (VID . DID) entries. This list and below From fc29138074f6b6bb804f3bcb7afaefe95b0e50d5 Mon Sep 17 00:00:00 2001 From: florhizome Date: Mon, 12 Dec 2022 10:39:46 +0000 Subject: [PATCH 686/790] gnu: emacs-dashboard: Update to 1.7.0-0.a69cc10. * gnu/packages/emacs-xyz.scm (emacs-dashboard): Update to 1.7.0-0.a69cc10. Signed-off-by: Nicolas Goaziou --- gnu/packages/emacs-xyz.scm | 65 ++++++++++++++++++++------------------ 1 file changed, 34 insertions(+), 31 deletions(-) diff --git a/gnu/packages/emacs-xyz.scm b/gnu/packages/emacs-xyz.scm index e4baa141f0..55eb279365 100644 --- a/gnu/packages/emacs-xyz.scm +++ b/gnu/packages/emacs-xyz.scm @@ -23176,38 +23176,41 @@ Emacs minor mode to escape sequences in code.") (license license:gpl3+)))) (define-public emacs-dashboard - (package - (name "emacs-dashboard") - (version "1.7.0") - (source - (origin - (method git-fetch) - (uri (git-reference - (url "https://github.com/rakanalh/emacs-dashboard") - (commit version))) - (file-name (git-file-name name version)) - (sha256 - (base32 "1qv4cqjy2s2d2bysbq10vq1axpbd8qc3jn1s1r81lxqkcja8zasa")))) - (build-system emacs-build-system) - (propagated-inputs - (list emacs-page-break-lines)) - (arguments - '(#:include '("\\.el$" "\\.txt$" "\\.png$") - #:phases - (modify-phases %standard-phases - (add-after 'unpack 'patch-dashboard-widgets - ;; This phase fixes compilation error. - (lambda _ - (chmod "dashboard-widgets.el" #o666) - (emacs-substitute-variables "dashboard-widgets.el" - ("dashboard-init-info" - '(format "Loaded in %s" (emacs-init-time)))) - #t))))) - (home-page "https://github.com/rakanalh/emacs-dashboard") - (synopsis "Startup screen extracted from Spacemacs") - (description "This package provides an extensible Emacs dashboard, with + (let ((version "1.7.0") + (commit "a69cc103aebd957f967e431399681b6d9d6b52fc") + (revision "0")) + (package + (name "emacs-dashboard") + (version (git-version version revision commit)) + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/rakanalh/emacs-dashboard") + (commit commit))) + (file-name (git-file-name name version)) + (sha256 + (base32 "1c6snnpc9rp6zhhdz411wyh2wn56yq2cdmxxqsp1ibvac8cbb1pq")))) + (build-system emacs-build-system) + (propagated-inputs + (list emacs-page-break-lines)) + (arguments + '(#:include '("\\.el$" "\\.txt$" "\\.png$") + #:phases + (modify-phases %standard-phases + (add-after 'unpack 'patch-dashboard-widgets + ;; This phase fixes compilation error. + (lambda _ + (chmod "dashboard-widgets.el" #o666) + (emacs-substitute-variables "dashboard-widgets.el" + ("dashboard-init-info" + '(format "Loaded in %s" (emacs-init-time)))) + #t))))) + (home-page "https://github.com/rakanalh/emacs-dashboard") + (synopsis "Startup screen extracted from Spacemacs") + (description "This package provides an extensible Emacs dashboard, with sections for bookmarks, projectil projects, org-agenda and more.") - (license license:gpl3+))) + (license license:gpl3+)))) (define-public emacs-slime-company (package From 82ab75b6a2d186afc2a4c98e7079a692076c138f Mon Sep 17 00:00:00 2001 From: Nicolas Goaziou Date: Thu, 22 Dec 2022 23:21:49 +0100 Subject: [PATCH 687/790] gnu: emacs-dashboard: Improve package style. * gnu/packages/emacs-xyz.scm (emacs-dashboard)[arguments]: Use G-expressions. <#:include>: Use %default-include. <#:phases>: Remove trailing #T, and unnecessary call to CHMOD. [description]: Properly capitalize it. --- gnu/packages/emacs-xyz.scm | 25 ++++++++++++------------- 1 file changed, 12 insertions(+), 13 deletions(-) diff --git a/gnu/packages/emacs-xyz.scm b/gnu/packages/emacs-xyz.scm index 55eb279365..e87500a65f 100644 --- a/gnu/packages/emacs-xyz.scm +++ b/gnu/packages/emacs-xyz.scm @@ -23192,24 +23192,23 @@ Emacs minor mode to escape sequences in code.") (sha256 (base32 "1c6snnpc9rp6zhhdz411wyh2wn56yq2cdmxxqsp1ibvac8cbb1pq")))) (build-system emacs-build-system) + (arguments + (list + #:include #~(cons* "\\.txt$" "\\.png$" %default-include) + #:phases + #~(modify-phases %standard-phases + (add-after 'unpack 'patch-dashboard-widgets + ;; This phase fixes compilation error. + (lambda _ + (emacs-substitute-variables "dashboard-widgets.el" + ("dashboard-init-info" + '(format "Loaded in %s" (emacs-init-time))))))))) (propagated-inputs (list emacs-page-break-lines)) - (arguments - '(#:include '("\\.el$" "\\.txt$" "\\.png$") - #:phases - (modify-phases %standard-phases - (add-after 'unpack 'patch-dashboard-widgets - ;; This phase fixes compilation error. - (lambda _ - (chmod "dashboard-widgets.el" #o666) - (emacs-substitute-variables "dashboard-widgets.el" - ("dashboard-init-info" - '(format "Loaded in %s" (emacs-init-time)))) - #t))))) (home-page "https://github.com/rakanalh/emacs-dashboard") (synopsis "Startup screen extracted from Spacemacs") (description "This package provides an extensible Emacs dashboard, with -sections for bookmarks, projectil projects, org-agenda and more.") +sections for bookmarks, Projectile projects, Org Agenda and more.") (license license:gpl3+)))) (define-public emacs-slime-company From 29e2d45b11017e44a52dd00b2f0d9f727347250d Mon Sep 17 00:00:00 2001 From: Hilton Chain Date: Thu, 22 Dec 2022 12:45:07 +0800 Subject: [PATCH 688/790] gnu: emacs-god-mode: Update to 2.18.0. * gnu/packages/emacs-xyz.scm (emacs-god-mode): Update to 2.18.0. [source,home-page]: Changed URL. Signed-off-by: Nicolas Goaziou --- gnu/packages/emacs-xyz.scm | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/gnu/packages/emacs-xyz.scm b/gnu/packages/emacs-xyz.scm index e87500a65f..33c6a0a1b4 100644 --- a/gnu/packages/emacs-xyz.scm +++ b/gnu/packages/emacs-xyz.scm @@ -9070,19 +9070,19 @@ just provides syntax highlighting.") (define-public emacs-god-mode (package (name "emacs-god-mode") - (version "2.17.3") + (version "2.18.0") (source (origin (method git-fetch) (uri (git-reference - (url "https://github.com/chrisdone/god-mode") + (url "https://github.com/emacsorphanage/god-mode") (commit version))) (file-name (git-file-name name version)) (sha256 (base32 - "1wsc04l5j5a9y5439qx85pcchxjnjgcgwbffw3l30q9zlblvc58b")))) + "1njln47w25ix9w0xjv02110ngr8d8ma3w7db0x4xcxhihbl65zly")))) (build-system emacs-build-system) - (home-page "https://github.com/chrisdone/god-mode") + (home-page "https://github.com/emacsorphanage/god-mode") (synopsis "Minor mode for entering commands without modifier keys") (description "This package provides a global minor mode for entering Emacs commands From f4672d97950d7b59fa31a8e5c8a885d08485a790 Mon Sep 17 00:00:00 2001 From: Nicolas Goaziou Date: Thu, 22 Dec 2022 23:27:24 +0100 Subject: [PATCH 689/790] gnu: emacs-god-mode: Run tests. * gnu/packages/emacs-xyz.scm (emacs-god-mode)[arguments]: Run tests. [native-inputs]: Add EMACS-ECUKES. --- gnu/packages/emacs-xyz.scm | 6 ++++++ 1 file changed, 6 insertions(+) diff --git a/gnu/packages/emacs-xyz.scm b/gnu/packages/emacs-xyz.scm index 33c6a0a1b4..497e16d17b 100644 --- a/gnu/packages/emacs-xyz.scm +++ b/gnu/packages/emacs-xyz.scm @@ -9082,6 +9082,12 @@ just provides syntax highlighting.") (base32 "1njln47w25ix9w0xjv02110ngr8d8ma3w7db0x4xcxhihbl65zly")))) (build-system emacs-build-system) + (arguments + (list #:tests? #true + #:test-command + #~(list "emacs" "--no-init-file" "--batch" + "--eval=(require 'ecukes)" "--eval=(ecukes)"))) + (native-inputs (list emacs-ecukes)) (home-page "https://github.com/emacsorphanage/god-mode") (synopsis "Minor mode for entering commands without modifier keys") (description From 75b0388a9093069c1eef141ae6849816d90a5c0b Mon Sep 17 00:00:00 2001 From: Morgan Willcock Date: Wed, 21 Dec 2022 21:38:18 +0000 Subject: [PATCH 690/790] gnu: emacs-org-msg: Update to 4.0. * gnu/packages/emacs-xyz.scm (emacs-org-msg): Update to 4.0. Signed-off-by: Nicolas Goaziou --- gnu/packages/emacs-xyz.scm | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/gnu/packages/emacs-xyz.scm b/gnu/packages/emacs-xyz.scm index 497e16d17b..e12444bb64 100644 --- a/gnu/packages/emacs-xyz.scm +++ b/gnu/packages/emacs-xyz.scm @@ -9337,11 +9337,11 @@ email.") (license license:gpl3+))) (define-public emacs-org-msg - ;; No git tags. The commit below corresponds to the release of version 3.3. - (let ((commit "89e746c0a864031eef940758230bc7263a6f2289")) + ;; No git tags. The commit below corresponds to the release of version 4.0. + (let ((commit "60e22e446325a9b3387396459d98be7c1c52579d")) (package (name "emacs-org-msg") - (version "3.3") + (version "4.0") (source (origin (method git-fetch) @@ -9350,7 +9350,7 @@ email.") (commit commit))) (file-name (git-file-name name version)) (sha256 - (base32 "15gd5zbxvdallyra9lmpb9i1r2mmwz0j0i0ra7j9imnbfiz3ln9r")))) + (base32 "077g7gvn1k6i2x4m2kd3dkrznc89f5a5pd916wsmpy703pv0aca5")))) (build-system emacs-build-system) (propagated-inputs (list emacs-htmlize)) From c8495bfc7909107cd6ad3bc98ccaed9a177c2a16 Mon Sep 17 00:00:00 2001 From: Nicolas Goaziou Date: Thu, 22 Dec 2022 23:38:13 +0100 Subject: [PATCH 691/790] gnu: emacs-marginalia: Update to 1.0. * gnu/packages/emacs-xyz.scm (emacs-marginalia): Update to 1.0. --- gnu/packages/emacs-xyz.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/emacs-xyz.scm b/gnu/packages/emacs-xyz.scm index e12444bb64..967a4648ba 100644 --- a/gnu/packages/emacs-xyz.scm +++ b/gnu/packages/emacs-xyz.scm @@ -10373,7 +10373,7 @@ expansion and overwriting the marked region with a new snippet completion.") (define-public emacs-marginalia (package (name "emacs-marginalia") - (version "0.15") + (version "1.0") (source (origin (method git-fetch) @@ -10382,7 +10382,7 @@ expansion and overwriting the marked region with a new snippet completion.") (commit version))) (file-name (git-file-name name version)) (sha256 - (base32 "0ncdyczalvl677nim0iha003xway7rwxw8y35vcvkgsdk4vzv848")))) + (base32 "1rf4xgb82j1g6ybrzz7ak9hlk86d4r0hcprbqz05hvjnb8nyfa4c")))) (build-system emacs-build-system) (home-page "https://github.com/minad/marginalia") (synopsis "Marginalia in the minibuffer completions") From 1b29fccff2334fb5d6e979a290233a452969e39b Mon Sep 17 00:00:00 2001 From: Nicolas Goaziou Date: Thu, 22 Dec 2022 23:39:30 +0100 Subject: [PATCH 692/790] gnu: emacs-mood-line: Update to 2.0.0. * gnu/packages/emacs-xyz.scm (emacs-mood-line): Update to 2.0.0. --- gnu/packages/emacs-xyz.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/emacs-xyz.scm b/gnu/packages/emacs-xyz.scm index 967a4648ba..0aa4525e8d 100644 --- a/gnu/packages/emacs-xyz.scm +++ b/gnu/packages/emacs-xyz.scm @@ -30782,7 +30782,7 @@ icon support, git integration, and several other utilities.") (define-public emacs-mood-line (package (name "emacs-mood-line") - (version "1.2.5") + (version "2.0.0") (source (origin (method git-fetch) @@ -30791,7 +30791,7 @@ icon support, git integration, and several other utilities.") (commit version))) (file-name (git-file-name name version)) (sha256 - (base32 "0z6s80j259xf8nxjxcsmp7wyvpcg5wyx58brlrbwg1aa9hl3fxga")))) + (base32 "0g29di2g8w8639z8d73kq9x2p8krzmjfn1bqd5jsv28v77j80k8h")))) (build-system emacs-build-system) (home-page "https://gitlab.com/jessieh/mood-line") (synopsis "Minimal mode-line for Emacs") From dd4eee55819a4c4eb68a8e0db0bf6cecfeac3136 Mon Sep 17 00:00:00 2001 From: Andrew Tropin Date: Thu, 22 Dec 2022 10:22:00 +0400 Subject: [PATCH 693/790] home: xdg: Add with-imported-modules to xdg activation script. Without it activation doesn't work when called in clean environment. * gnu/home/services/xdg.scm (ensure-xdg-base-dirs-on-activation): Add with-imported-modules to xdg activation script. --- gnu/home/services/xdg.scm | 35 +++++++++++++++++++---------------- 1 file changed, 19 insertions(+), 16 deletions(-) diff --git a/gnu/home/services/xdg.scm b/gnu/home/services/xdg.scm index fb2dbb393e..3007493f85 100644 --- a/gnu/home/services/xdg.scm +++ b/gnu/home/services/xdg.scm @@ -120,22 +120,25 @@ services more consistent.")) home-xdg-base-directories-configuration-fields)) (define (ensure-xdg-base-dirs-on-activation config) - #~(map (lambda (xdg-base-dir-variable) - ((@ (guix build utils) mkdir-p) - (getenv - xdg-base-dir-variable))) - '#$(filter-map - (lambda (field) - (let ((variable - (string-append - "XDG_" - (object->snake-case-string - (configuration-field-name field) 'upper)))) - ;; XDG_RUNTIME_DIR shouldn't be created during activation - ;; and will be provided by elogind or other service. - (and (not (string=? "XDG_RUNTIME_DIR" variable)) - variable))) - home-xdg-base-directories-configuration-fields))) + (with-imported-modules '((guix build utils)) + #~(begin + (use-modules (guix build utils)) + (map (lambda (xdg-base-dir-variable) + (mkdir-p + (getenv + xdg-base-dir-variable))) + '#$(filter-map + (lambda (field) + (let ((variable + (string-append + "XDG_" + (object->snake-case-string + (configuration-field-name field) 'upper)))) + ;; XDG_RUNTIME_DIR shouldn't be created during activation + ;; and will be provided by elogind or other service. + (and (not (string=? "XDG_RUNTIME_DIR" variable)) + variable))) + home-xdg-base-directories-configuration-fields))))) (define (last-extension-or-cfg config extensions) "Picks configuration value from last provided extension. If there From 66188398c446bdf9ce044fa539536e9b54c28c60 Mon Sep 17 00:00:00 2001 From: Roman Scherer Date: Thu, 22 Dec 2022 19:41:14 +0100 Subject: [PATCH 694/790] gnu: netcdf: Update to 4.9.0. * gnu/packages/maths.scm (netcdf): Update to 4.9.0. [source]: Use new URI. [inputs]: Add libxml2 and unzip. [arguments]: Update 'configure-flags'. Add 'fix-test-rcmerge' phase. Signed-off-by: Guillaume Le Vaillant --- gnu/packages/maths.scm | 34 +++++++++++++++++++++------------- 1 file changed, 21 insertions(+), 13 deletions(-) diff --git a/gnu/packages/maths.scm b/gnu/packages/maths.scm index 050450e12c..5ff7389a02 100644 --- a/gnu/packages/maths.scm +++ b/gnu/packages/maths.scm @@ -58,6 +58,7 @@ ;;; Copyright © 2022 Liliana Marie Prikler ;;; Copyright © 2022 Maximilian Heisinger ;;; Copyright © 2022 Akira Kyle +;;; Copyright © 2022 Roman Scherer ;;; ;;; This file is part of GNU Guix. ;;; @@ -1852,16 +1853,16 @@ similar to MATLAB, GNU Octave or SciPy.") (define-public netcdf (package (name "netcdf") - (version "4.7.4") + (version "4.9.0") (source (origin (method url-fetch) (uri (string-append - "https://www.unidata.ucar.edu/downloads/netcdf/ftp/" - "netcdf-c-" version ".tar.gz")) + "https://downloads.unidata.ucar.edu/netcdf-c/" version + "/netcdf-c-" version ".tar.gz")) (sha256 (base32 - "1a2fpp15a2rl1m50gcvvzd9y6bavl6vjf9zzf63sz5gdmq06yiqf")) + "0j8b814mjdqvqanzmrxpq8hn33n22cdzb3gf9vhya24wnwi615ac")) (modules '((guix build utils))) (snippet ;; Make sure this variable is defined only once. Failing to do so @@ -1874,13 +1875,18 @@ similar to MATLAB, GNU Octave or SciPy.") (native-inputs (list m4 doxygen graphviz)) (inputs - `(("hdf4" ,hdf4-alt) + `(("curl" ,curl) + ("hdf4" ,hdf4-alt) ("hdf5" ,hdf5) - ("curl" ,curl) - ("zlib" ,zlib) - ("libjpeg" ,libjpeg-turbo))) + ("libjpeg" ,libjpeg-turbo) + ("libxml2" ,libxml2) + ("unzip" ,unzip) + ("zlib" ,zlib))) (arguments - `(#:configure-flags '("--enable-doxygen" "--enable-dot" "--enable-hdf4") + `(#:configure-flags '("--enable-doxygen" + "--enable-dot" + "--enable-hdf4" + "--disable-dap-remote-tests") #:phases (modify-phases %standard-phases (add-before 'configure 'fix-source-date @@ -1891,8 +1897,7 @@ similar to MATLAB, GNU Octave or SciPy.") ;; package not reproducible. (substitute* "./configure" (("date -u -d \"\\$\\{SOURCE_DATE_EPOCH\\}\"") - "date --date='@0'")) - #t)) + "date --date='@0'")))) (add-after 'configure 'patch-settings (lambda _ ;; libnetcdf.settings contains the full filename of the compilers @@ -1901,8 +1906,11 @@ similar to MATLAB, GNU Octave or SciPy.") ;; store items. (substitute* "libnetcdf.settings" (("(/gnu/store/)([0-9A-Za-z]*)" all prefix hash) - (string-append prefix (string-take hash 10) "..."))) - #t))) + (string-append prefix (string-take hash 10) "..."))))) + (add-before 'check 'fix-test-rcmerge + (lambda _ + ;; Set HOME, to fix the test-rcmerge test. + (setenv "HOME" "/tmp")))) #:parallel-tests? #f)) ;various race conditions (home-page "https://www.unidata.ucar.edu/software/netcdf/") From 9923100a42ffa80f604c1c13a5e999e6a4c15146 Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Fri, 23 Dec 2022 09:42:27 +0200 Subject: [PATCH 695/790] gnu: sgabios: Fix build on cross-build architectures. * gnu/packages/firmware.scm (sgabios)[arguments]: When cross-building add a make-flag to use the correct objcopy. --- gnu/packages/firmware.scm | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/gnu/packages/firmware.scm b/gnu/packages/firmware.scm index 54b19dd5fa..1b4fd61241 100644 --- a/gnu/packages/firmware.scm +++ b/gnu/packages/firmware.scm @@ -589,7 +589,9 @@ coreboot.") (list #:make-flags #~'(#$@(if (member (%current-system) '("i686-linux" "x86_64-linux")) #~("CC=gcc") - #~("CC=i686-linux-gnu-gcc" "LD=i686-linux-gnu-ld")) + #~("CC=i686-linux-gnu-gcc" + "LD=i686-linux-gnu-ld" + "OBJCOPY=i686-linux-gnu-objcopy")) "HOSTCC=gcc") #:parallel-build? #f #:tests? #f ;no tests From e26d6a6de0925ed0d80e23f58ea4150cd0539f1e Mon Sep 17 00:00:00 2001 From: Nicolas Goaziou Date: Fri, 23 Dec 2022 15:09:46 +0100 Subject: [PATCH 696/790] gnu: emacs-subed: Update to 1.0.28. * gnu/packages/emacs-xyz.scm (emacs-subed): Update to 1.0.28. --- gnu/packages/emacs-xyz.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/emacs-xyz.scm b/gnu/packages/emacs-xyz.scm index 0aa4525e8d..652a5a4991 100644 --- a/gnu/packages/emacs-xyz.scm +++ b/gnu/packages/emacs-xyz.scm @@ -7389,14 +7389,14 @@ user.") (define-public emacs-subed (package (name "emacs-subed") - (version "1.0.27") + (version "1.0.28") (source (origin (method url-fetch) (uri (string-append "https://elpa.nongnu.org/nongnu/subed-" version ".tar")) (sha256 (base32 - "0nyhrlpvvglc3gd2wv20j34mws6f6s2j7q73b4lf3j0mw9yq1cgf")))) + "0z1bxg5sqvvm9zblbjyfp5llq0v1pkjq9c7ygais8ad68ck1b51f")))) (arguments (list #:tests? #t From 3a77238721e9f5b8c678634a96f1f675e02996c8 Mon Sep 17 00:00:00 2001 From: Nicolas Goaziou Date: Fri, 23 Dec 2022 15:10:56 +0100 Subject: [PATCH 697/790] gnu: emacs-vertico: Update to 1.0. * gnu/packages/emacs-xyz.scm (emacs-vertico): Update to 1.0. --- gnu/packages/emacs-xyz.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/emacs-xyz.scm b/gnu/packages/emacs-xyz.scm index 652a5a4991..66b52bdac8 100644 --- a/gnu/packages/emacs-xyz.scm +++ b/gnu/packages/emacs-xyz.scm @@ -33485,7 +33485,7 @@ and preferred services can easily be configured.") (define-public emacs-vertico (package (name "emacs-vertico") - (version "0.29") + (version "1.0") (source (origin (method git-fetch) @@ -33494,7 +33494,7 @@ and preferred services can easily be configured.") (commit version))) (file-name (git-file-name name version)) (sha256 - (base32 "0gqfq7yni470yys9blarmsinjgf1025azlr09g1842w20hwrs7hc")))) + (base32 "0g2zy70gks24g7i4qj1ijx57g016svbymb8l493j81c4bhc88mjl")))) (build-system emacs-build-system) (arguments `(#:phases From dd8a20355e6e2bc349b7af00f309629fb054ed09 Mon Sep 17 00:00:00 2001 From: Nicolas Goaziou Date: Fri, 23 Dec 2022 15:16:06 +0100 Subject: [PATCH 698/790] gnu: emacs-cider: Update to 1.6.0. * gnu/packages/emacs-xyz.scm (emacs-cider): Update to 1.6.0. --- gnu/packages/emacs-xyz.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/emacs-xyz.scm b/gnu/packages/emacs-xyz.scm index 66b52bdac8..758cc84dff 100644 --- a/gnu/packages/emacs-xyz.scm +++ b/gnu/packages/emacs-xyz.scm @@ -13388,7 +13388,7 @@ implementation.") (define-public emacs-cider (package (name "emacs-cider") - (version "1.5.0") + (version "1.6.0") (source (origin (method git-fetch) @@ -13397,7 +13397,7 @@ implementation.") (commit (string-append "v" version)))) (file-name (git-file-name name version)) (sha256 - (base32 "1ih902n8p3pl1apprprkyrlnrp2dxli86y5k09zahy9mglfz2z5n")))) + (base32 "1a3xbfn1id8dcy3178kmdnzcvh7lq2pdwwg4axhncw6jq9hqiqja")))) (build-system emacs-build-system) (arguments '(#:exclude ;don't exclude 'cider-test.el' From 558494674da1b4b4de24b966560fec716dabe378 Mon Sep 17 00:00:00 2001 From: Guillaume Le Vaillant Date: Fri, 23 Dec 2022 16:33:16 +0100 Subject: [PATCH 699/790] gnu: aptdec: Update to 1.7-3.4d4a0c9. * gnu/packages/radio.scm (aptdec): Update to 1.7-3.4d4a0c9. --- gnu/packages/radio.scm | 9 +++++---- 1 file changed, 5 insertions(+), 4 deletions(-) diff --git a/gnu/packages/radio.scm b/gnu/packages/radio.scm index a57174ff3a..6021e10c7f 100644 --- a/gnu/packages/radio.scm +++ b/gnu/packages/radio.scm @@ -559,8 +559,8 @@ It is a GUI for @code{soapy_power}, @code{hackrf_sweep}, @code{rtl_power}, (define-public aptdec ;; No release since 2013, use commit directly. - (let ((commit "51405971fd4e97714d1e987269e49c6edfe4e0da") - (revision "2")) + (let ((commit "4d4a0c9787a27d1eba26b9299c23ae9c66e56716") + (revision "3")) (package (name "aptdec") (version (git-version "1.7" revision commit)) @@ -569,10 +569,11 @@ It is a GUI for @code{soapy_power}, @code{hackrf_sweep}, @code{rtl_power}, (method git-fetch) (uri (git-reference (url "https://github.com/Xerbo/aptdec") - (commit commit))) + (commit commit) + (recursive? #t))) (file-name (git-file-name name version)) (sha256 - (base32 "0fzkhqnbkc2dd39jzb5m5mwcl31b0x3w0yykpx4s195llq4bdvis")))) + (base32 "09dvvwk4bs9d4bf9z74ixvhzghwzmlbqbx1dn20hbhpm0bgxwk8m")))) (build-system cmake-build-system) (inputs (list libpng libsndfile)) From 11aa1e6ad1eba8a6df33fbeb3b882fc23fbdba45 Mon Sep 17 00:00:00 2001 From: Guillaume Le Vaillant Date: Fri, 23 Dec 2022 16:38:32 +0100 Subject: [PATCH 700/790] gnu: sdrangel: Update to 7.8.5. * gnu/packages/radio.scm (sdrangel): Update to 7.8.5. [arguments]: Remove 'fix-boost-compatibility' phase. --- gnu/packages/radio.scm | 13 +++---------- 1 file changed, 3 insertions(+), 10 deletions(-) diff --git a/gnu/packages/radio.scm b/gnu/packages/radio.scm index 6021e10c7f..aae30b7911 100644 --- a/gnu/packages/radio.scm +++ b/gnu/packages/radio.scm @@ -2280,7 +2280,7 @@ voice formats.") (define-public sdrangel (package (name "sdrangel") - (version "7.6.2") + (version "7.8.5") (source (origin (method git-fetch) @@ -2289,7 +2289,7 @@ voice formats.") (commit (string-append "v" version)))) (file-name (git-file-name name version)) (sha256 - (base32 "193iwwb4mbr29mlgaqb67j8214k10k2q0ky9fcl1ja52vmdzz71b")))) + (base32 "0kfzmxbhfpvs8csfbhnl5nij6nlbr00s43392wfq35vnnkbgk5lv")))) (build-system qt-build-system) (native-inputs (list doxygen graphviz pkg-config)) @@ -2357,14 +2357,7 @@ voice formats.") ;; …but force extensions that are guaranteed to be available. (substitute* file ((".*cmake_pop_check_state" eof) - (string-append "force_ext_available(SSE2)\n" eof))))))) - (add-after 'unpack 'fix-boost-compatibility - (lambda _ - (substitute* - '("plugins/channelrx/noisefigure/noisefigure.cpp" - "plugins/channelrx/noisefigure/noisefigureenrdialog.cpp") - (("boost::math::barycentric_rational") - "boost::math::interpolators::barycentric_rational"))))))) + (string-append "force_ext_available(SSE2)\n" eof)))))))))) (home-page "https://github.com/f4exb/sdrangel/wiki") (synopsis "Software defined radio") (description From a3c26687885305a6a9fda3aef3c66a9fcc962e67 Mon Sep 17 00:00:00 2001 From: Nicolas Goaziou Date: Fri, 23 Dec 2022 15:23:26 +0100 Subject: [PATCH 701/790] gnu: fet: Update to 6.7.7. * gnu/packages/education.scm (fet): Update to 6.7.7. --- gnu/packages/education.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/education.scm b/gnu/packages/education.scm index 9a30abe8df..c6829738c4 100644 --- a/gnu/packages/education.scm +++ b/gnu/packages/education.scm @@ -582,7 +582,7 @@ a pen-tablet display and a beamer.") (define-public fet (package (name "fet") - (version "6.7.6") + (version "6.7.7") (source (origin (method url-fetch) @@ -591,7 +591,7 @@ a pen-tablet display and a beamer.") (list (string-append directory base) (string-append directory "old/" base)))) (sha256 - (base32 "0psvnplwp5n7v1j3ywxpq6vykjv1276n66f7ral7c70vjf4h7109")))) + (base32 "08rm3yka3swr6wf3lcmzh2jlq5ajxi8c6nd2likqzvbg6plrjx6b")))) (build-system gnu-build-system) (arguments (list From ef060487a21833f097485b583fd7f5813109444e Mon Sep 17 00:00:00 2001 From: Nicolas Goaziou Date: Fri, 23 Dec 2022 19:06:47 +0100 Subject: [PATCH 702/790] gnu: naev: Update to 0.10.0. * gnu/packages/games.scm (naev): Update to 0.10.0. [inputs]: Add ENET, PCRE2. --- gnu/packages/games.scm | 8 +++++--- 1 file changed, 5 insertions(+), 3 deletions(-) diff --git a/gnu/packages/games.scm b/gnu/packages/games.scm index 7dd73dcb4a..19c689dee1 100644 --- a/gnu/packages/games.scm +++ b/gnu/packages/games.scm @@ -7930,7 +7930,7 @@ ncurses for text display.") (define-public naev (package (name "naev") - (version "0.9.4") + (version "0.10.0") (source (origin (method git-fetch) @@ -7940,7 +7940,7 @@ ncurses for text display.") (recursive? #t))) ; for game data (file-name (git-file-name name version)) (sha256 - (base32 "0isswidhxhs2q5c4cxryjr8y8ibfxckpfyccly3b4lg1nxvm5gjv")))) + (base32 "183dbi4a91xggxm1rmn7vr8rq519yz7b3zhrd03azsg6fxylv9wn")))) (build-system meson-build-system) (arguments ;; XXX: Do not add debugging symbols, which cause the build to fail. @@ -7949,7 +7949,8 @@ ncurses for text display.") (native-inputs (list gettext-minimal pkg-config)) (inputs - (list freetype + (list enet + freetype glpk libpng libunibreak @@ -7959,6 +7960,7 @@ ncurses for text display.") luajit openal openblas + pcre2 physfs python python-pyyaml From f28d792719abb82cc920486e6d6f14eacc44370c Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Fri, 23 Dec 2022 16:44:58 +0100 Subject: [PATCH 703/790] etc: SELinux: Label guix-daemon executable in profile. * etc/guix-daemon.cil.in: Add file rule for "guix-daemon" in current-guix profile. --- etc/guix-daemon.cil.in | 2 ++ 1 file changed, 2 insertions(+) diff --git a/etc/guix-daemon.cil.in b/etc/guix-daemon.cil.in index f4767ff666..ba100a4535 100644 --- a/etc/guix-daemon.cil.in +++ b/etc/guix-daemon.cil.in @@ -447,6 +447,8 @@ any (unconfined_u object_r guix_store_content_t (low low))) (filecon "@prefix@/bin/guix-daemon" file (system_u object_r guix_daemon_exec_t (low low))) + (filecon "@guix_localstatedir@/guix/profiles/per-user/[^/]+/current-guix/bin/guix-daemon" + file (system_u object_r guix_daemon_exec_t (low low))) (filecon "@storedir@/.+-(guix-.+|profile)/bin/guix-daemon" file (system_u object_r guix_daemon_exec_t (low low))) (filecon "@storedir@/[a-z0-9]+-guix-daemon" From 4a134ed32e69ba888d988d2ed924a1531a54551b Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Fri, 23 Dec 2022 16:47:11 +0100 Subject: [PATCH 704/790] etc: SELinux: Allow daemon to search run state directories. * etc/guix-daemon.cil.in: Import types init_var_run_t and system_dbusd_var_run_t; add rules. --- etc/guix-daemon.cil.in | 20 +++++++++++++++----- 1 file changed, 15 insertions(+), 5 deletions(-) diff --git a/etc/guix-daemon.cil.in b/etc/guix-daemon.cil.in index ba100a4535..0245c36231 100644 --- a/etc/guix-daemon.cil.in +++ b/etc/guix-daemon.cil.in @@ -1,6 +1,6 @@ ; -*- lisp -*- ;;; GNU Guix --- Functional package management for GNU -;;; Copyright © 2018 Ricardo Wurmus +;;; Copyright © 2018, 2022 Ricardo Wurmus ;;; Copyright © 2020 Daniel Brooks ;;; Copyright © 2020 Marius Bakke ;;; @@ -37,11 +37,13 @@ (block guix_daemon ;; Require existing types - (typeattributeset cil_gen_require init_t) - (typeattributeset cil_gen_require tmp_t) - (typeattributeset cil_gen_require nscd_var_run_t) - (typeattributeset cil_gen_require var_log_t) (typeattributeset cil_gen_require domain) + (typeattributeset cil_gen_require init_t) + (typeattributeset cil_gen_require init_var_run_t) + (typeattributeset cil_gen_require nscd_var_run_t) + (typeattributeset cil_gen_require system_dbusd_var_run_t) + (typeattributeset cil_gen_require tmp_t) + (typeattributeset cil_gen_require var_log_t) ;; Declare own types (type guix_daemon_t) @@ -284,6 +286,14 @@ guix_store_content_t (sock_file (create getattr setattr unlink write))) + ;; Access to run state directories + (allow guix_daemon_t + system_dbusd_var_run_t + (dir (search))) + (allow guix_daemon_t + init_var_run_t + (dir (search))) + ;; Access to configuration files and directories (allow guix_daemon_t guix_daemon_conf_t From afaeb657b118e6998342110deab8c8110b824417 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Fri, 23 Dec 2022 16:48:20 +0100 Subject: [PATCH 705/790] etc: SELinux: Allow init process to setattr on profile directories. * etc/guix-daemon.cil.in: Add rule. --- etc/guix-daemon.cil.in | 3 +++ 1 file changed, 3 insertions(+) diff --git a/etc/guix-daemon.cil.in b/etc/guix-daemon.cil.in index 0245c36231..f55ef226c1 100644 --- a/etc/guix-daemon.cil.in +++ b/etc/guix-daemon.cil.in @@ -94,6 +94,9 @@ (allow init_t guix_store_content_t (file (open read execute))) + (allow init_t + guix_profiles_t + (dir (setattr))) ;; guix-daemon needs to know the names of users (allow guix_daemon_t From 672c48f15d86f7acd2e6e96c91256245b25e4bd5 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Fri, 23 Dec 2022 16:50:58 +0100 Subject: [PATCH 706/790] doc: Suggest remounting store before relabeling the file system. * doc/guix.texi (Installing the SELinux policy): Mention that the store may need to be remounted before writing to it. --- doc/guix.texi | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) diff --git a/doc/guix.texi b/doc/guix.texi index fd03da8c97..a515f13bf2 100644 --- a/doc/guix.texi +++ b/doc/guix.texi @@ -1522,8 +1522,10 @@ To install the policy run this command as root: semodule -i etc/guix-daemon.cil @end example -Then relabel the file system with @code{restorecon} or by a different -mechanism provided by your system. +Then relabel the file system with @code{restorecon -vR /} or by a +different mechanism provided by your system. You may need to remount +@file{/gnu/store} to make it writable first, e.g. with @code{mount -o +remount,rw /gnu/store}. Once the policy is installed, the file system has been relabeled, and the daemon has been restarted, it should be running in the From 0a45d4bad485b6f27833a1a57cffbaae63407f98 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Fri, 23 Dec 2022 16:52:02 +0100 Subject: [PATCH 707/790] doc: Wrap $localstatedir in Texinfo syntax. * doc/guix.texi (Limitations): Use @file syntax. --- doc/guix.texi | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/doc/guix.texi b/doc/guix.texi index a515f13bf2..e25692fd27 100644 --- a/doc/guix.texi +++ b/doc/guix.texi @@ -1558,7 +1558,7 @@ but it would be preferable to define socket rules for only this label. @code{guix gc} cannot access arbitrary links to profiles. By design, the file label of the destination of a symlink is independent of the file label of the link itself. Although all profiles under -$localstatedir are labelled, the links to these profiles inherit the +@file{$localstatedir} are labelled, the links to these profiles inherit the label of the directory they are in. For links in the user’s home directory this will be @code{user_home_t}. But for links from the root user’s home directory, or @file{/tmp}, or the HTTP server’s working From ad141242f8d2a1e9f69f59e53aa26b897c6cd3a6 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Fri, 23 Dec 2022 20:16:03 +0100 Subject: [PATCH 708/790] gnu: Add apache-arrow-for-ceph. * gnu/packages/databases.scm (apache-arrow-for-ceph): New variable. --- gnu/packages/databases.scm | 132 +++++++++++++++++++++++++++++++++++++ 1 file changed, 132 insertions(+) diff --git a/gnu/packages/databases.scm b/gnu/packages/databases.scm index 83515ad17e..2a24ba580d 100644 --- a/gnu/packages/databases.scm +++ b/gnu/packages/databases.scm @@ -4310,6 +4310,138 @@ language-bindings for structure manipulation. It also provides IPC and common algorithm implementations.") (license license:asl2.0))) +(define-public apache-arrow-for-ceph + (package + (name "apache-arrow") + (version "6.0.1") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/apache/arrow") + (commit (string-append "apache-arrow-" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "0mcw361akqw4sxnnpnr9c9v1zk4hphk6gcq763pcb19yzljh88ig")))) + (build-system cmake-build-system) + (arguments + `(#:tests? #f + #:phases + (modify-phases %standard-phases + (add-before 'configure 'enter-source-directory + (lambda _ (chdir "cpp"))) + (add-after 'unpack 'set-env + (lambda* (#:key inputs #:allow-other-keys) + (substitute* "cpp/src/parquet/parquet.pc.in" + (("includedir=\\$\\{prefix\\}/") + "includedir=")) + (substitute* "cpp/cmake_modules/ThirdpartyToolchain.cmake" + (("set\\(xsimd_SOURCE.*") "")) + (setenv "BOOST_ROOT" (assoc-ref inputs "boost")) + (setenv "BROTLI_HOME" (assoc-ref inputs "brotli")) + (setenv "FLATBUFFERS_HOME" (assoc-ref inputs "flatbuffers")) + (setenv "RAPIDJSON_HOME" (assoc-ref inputs "rapidjson"))))) + #:build-type "Release" + #:configure-flags + (list "-DARROW_PYTHON=ON" + "-DARROW_GLOG=ON" + ;; Parquet options + "-DARROW_PARQUET=ON" + "-DPARQUET_BUILD_EXECUTABLES=ON" + ;; The maintainers disallow using system versions of + ;; jemalloc: + ;; https://issues.apache.org/jira/browse/ARROW-3507. This + ;; is unfortunate because jemalloc increases performance: + ;; https://arrow.apache.org/blog/2018/07/20/jemalloc/. + "-DARROW_JEMALLOC=OFF" + + ;; The CMake option ARROW_DEPENDENCY_SOURCE is a global + ;; option that instructs the build system how to resolve + ;; each dependency. SYSTEM = Finding the dependency in + ;; system paths using CMake's built-in find_package + ;; function, or using pkg-config for packages that do not + ;; have this feature + "-DARROW_DEPENDENCY_SOURCE=SYSTEM" + "-Dxsimd_SOURCE=SYSTEM" + + "-DARROW_RUNTIME_SIMD_LEVEL=NONE" + "-DARROW_SIMD_LEVEL=NONE" + "-DARROW_PACKAGE_KIND=Guix" + + ;; Split output into its component packages. + (string-append "-DCMAKE_INSTALL_PREFIX=" + (assoc-ref %outputs "lib")) + (string-append "-DCMAKE_INSTALL_RPATH=" + (assoc-ref %outputs "lib") + "/lib") + (string-append "-DCMAKE_INSTALL_BINDIR=" + (assoc-ref %outputs "out") + "/bin") + (string-append "-DCMAKE_INSTALL_INCLUDEDIR=" + (assoc-ref %outputs "include") + "/share/include") + + "-DARROW_WITH_SNAPPY=ON" + "-DARROW_WITH_ZLIB=ON" + "-DARROW_WITH_ZSTD=ON" + "-DARROW_WITH_LZ4=ON" + "-DARROW_COMPUTE=ON" + "-DARROW_CSV=ON" + "-DARROW_DATASET=ON" + "-DARROW_FILESYSTEM=ON" + "-DARROW_HDFS=ON" + "-DARROW_JSON=ON" + ;; Arrow Python C++ integration library (required for + ;; building pyarrow). This library must be built against + ;; the same Python version for which you are building + ;; pyarrow. NumPy must also be installed. Enabling this + ;; option also enables ARROW_COMPUTE, ARROW_CSV, + ;; ARROW_DATASET, ARROW_FILESYSTEM, ARROW_HDFS, and + ;; ARROW_JSON. + "-DARROW_PYTHON=ON" + + ;; Building the tests forces on all the + ;; optional features and the use of static + ;; libraries. + "-DARROW_BUILD_TESTS=OFF" + "-DBENCHMARK_ENABLE_GTEST_TESTS=OFF" + ;;"-DBENCHMARK_ENABLE_TESTING=OFF" + "-DARROW_BUILD_STATIC=OFF"))) + (inputs + (list boost + brotli + bzip2 + double-conversion + gflags + glog + grpc + protobuf + python + python-numpy + rapidjson + re2 + snappy + xsimd)) + ;; These are all listed under Requires.private in arrow.pc + (propagated-inputs + (list (list apache-thrift "lib") + lz4 + utf8proc + zlib + (list zstd "lib"))) + (native-inputs + (list pkg-config)) + (outputs '("out" "lib" "include")) + (home-page "https://arrow.apache.org/") + (synopsis "Columnar in-memory analytics") + (description "Apache Arrow is a columnar in-memory analytics layer +designed to accelerate big data. It houses a set of canonical in-memory +representations of flat and hierarchical data along with multiple +language-bindings for structure manipulation. It also provides IPC and common +algorithm implementations.") + (license license:asl2.0))) + (define-public apache-arrow-0.16 (package (name "apache-arrow") From b6d9e266a740c9706524bdd5c978f70e088675f1 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Fri, 23 Dec 2022 20:17:15 +0100 Subject: [PATCH 709/790] gnu: ceph: Update to 17.2.5. * gnu/packages/storage.scm (ceph): Update to 17.2.5. [source]: Remove obsolete patches; remove bundled sources for arrow. [arguments]: Disable parallel build; use system arrow. [inputs]: Drop input labels; add apache-thrift, apache-arrow-for-ceph, and utf8proc. * gnu/packages/patches/ceph-boost-compat.patch: Delete file. * gnu/packages/patches/ceph-rocksdb-compat.patch: Delete file. * gnu/local.mk (dist_patch_DATA): Remove them. --- gnu/local.mk | 2 - gnu/packages/patches/ceph-boost-compat.patch | 18 -- .../patches/ceph-rocksdb-compat.patch | 303 ------------------ gnu/packages/storage.scm | 216 +++++++------ 4 files changed, 118 insertions(+), 421 deletions(-) delete mode 100644 gnu/packages/patches/ceph-boost-compat.patch delete mode 100644 gnu/packages/patches/ceph-rocksdb-compat.patch diff --git a/gnu/local.mk b/gnu/local.mk index 45d05de02d..a75a7252af 100644 --- a/gnu/local.mk +++ b/gnu/local.mk @@ -963,8 +963,6 @@ dist_patch_DATA = \ %D%/packages/patches/cdrkit-libre-cross-compile.patch \ %D%/packages/patches/cdrtools-3.01-mkisofs-isoinfo.patch \ %D%/packages/patches/ceph-disable-cpu-optimizations.patch \ - %D%/packages/patches/ceph-boost-compat.patch \ - %D%/packages/patches/ceph-rocksdb-compat.patch \ %D%/packages/patches/chmlib-inttypes.patch \ %D%/packages/patches/cl-asdf-config-directories.patch \ %D%/packages/patches/clamav-config-llvm-libs.patch \ diff --git a/gnu/packages/patches/ceph-boost-compat.patch b/gnu/packages/patches/ceph-boost-compat.patch deleted file mode 100644 index 1aecfbbed5..0000000000 --- a/gnu/packages/patches/ceph-boost-compat.patch +++ /dev/null @@ -1,18 +0,0 @@ -Add extra includes required for Boost 1.75 and later. - -Taken from upstram: - - https://github.com/ceph/ceph/commit/ebf3a0398f18eab67d2ba25e6a10b41ff140f6a4 - -diff --git a/src/rgw/rgw_string.h b/src/rgw/rgw_string.h -index 257daa9c1fe6e..90e64f98a2587 100644 ---- a/src/rgw/rgw_string.h -+++ b/src/rgw/rgw_string.h -@@ -8,5 +8,7 @@ - #include - #include - #include -+#include -+#include - - #include diff --git a/gnu/packages/patches/ceph-rocksdb-compat.patch b/gnu/packages/patches/ceph-rocksdb-compat.patch deleted file mode 100644 index 9fb9b0caeb..0000000000 --- a/gnu/packages/patches/ceph-rocksdb-compat.patch +++ /dev/null @@ -1,303 +0,0 @@ -Adjust for newer versions of RocksDB. - -Taken from upstream: - - https://github.com/ceph/ceph/pull/42815 - https://github.com/ceph/ceph/commit/ff7f192ea3cf88ca1098bcf9396ff4f8ed1e8792.diff - -diff --git a/src/kv/rocksdb_cache/BinnedLRUCache.cc b/src/kv/rocksdb_cache/BinnedLRUCache.cc -index 0d657883e92de..47c56e2ddd769 100644 ---- a/src/kv/rocksdb_cache/BinnedLRUCache.cc -+++ b/src/kv/rocksdb_cache/BinnedLRUCache.cc -@@ -151,13 +151,20 @@ void BinnedLRUCacheShard::EraseUnRefEntries() { - } - } - --void BinnedLRUCacheShard::ApplyToAllCacheEntries(void (*callback)(void*, size_t), -- bool thread_safe) { -+void BinnedLRUCacheShard::ApplyToAllCacheEntries( -+ const std::function& callback, -+ bool thread_safe) -+{ - if (thread_safe) { - mutex_.lock(); - } - table_.ApplyToAllCacheEntries( -- [callback](BinnedLRUHandle* h) { callback(h->value, h->charge); }); -+ [callback](BinnedLRUHandle* h) { -+ callback(h->key(), h->value, h->charge, h->deleter); -+ }); - if (thread_safe) { - mutex_.unlock(); - } -@@ -345,7 +352,7 @@ bool BinnedLRUCacheShard::Release(rocksdb::Cache::Handle* handle, bool force_era - - rocksdb::Status BinnedLRUCacheShard::Insert(const rocksdb::Slice& key, uint32_t hash, void* value, - size_t charge, -- void (*deleter)(const rocksdb::Slice& key, void* value), -+ DeleterFn deleter, - rocksdb::Cache::Handle** handle, rocksdb::Cache::Priority priority) { - auto e = new BinnedLRUHandle(); - rocksdb::Status s; -@@ -464,6 +471,12 @@ std::string BinnedLRUCacheShard::GetPrintableOptions() const { - return std::string(buffer); - } - -+DeleterFn BinnedLRUCacheShard::GetDeleter(rocksdb::Cache::Handle* h) const -+{ -+ auto* handle = reinterpret_cast(h); -+ return handle->deleter; -+} -+ - BinnedLRUCache::BinnedLRUCache(CephContext *c, - size_t capacity, - int num_shard_bits, -@@ -519,6 +532,13 @@ void BinnedLRUCache::DisownData() { - #endif // !__SANITIZE_ADDRESS__ - } - -+#if (ROCKSDB_MAJOR >= 6 && ROCKSDB_MINOR >= 22) -+DeleterFn BinnedLRUCache::GetDeleter(Handle* handle) const -+{ -+ return reinterpret_cast(handle)->deleter; -+} -+#endif -+ - size_t BinnedLRUCache::TEST_GetLRUSize() { - size_t lru_size_of_all_shards = 0; - for (int i = 0; i < num_shards_; i++) { -diff --git a/src/kv/rocksdb_cache/BinnedLRUCache.h b/src/kv/rocksdb_cache/BinnedLRUCache.h -index 85608be0e5734..88bf4502e8927 100644 ---- a/src/kv/rocksdb_cache/BinnedLRUCache.h -+++ b/src/kv/rocksdb_cache/BinnedLRUCache.h -@@ -56,7 +56,7 @@ std::shared_ptr NewBinnedLRUCache( - - struct BinnedLRUHandle { - void* value; -- void (*deleter)(const rocksdb::Slice&, void* value); -+ DeleterFn deleter; - BinnedLRUHandle* next_hash; - BinnedLRUHandle* next; - BinnedLRUHandle* prev; -@@ -189,7 +189,7 @@ class alignas(CACHE_LINE_SIZE) BinnedLRUCacheShard : public CacheShard { - // Like Cache methods, but with an extra "hash" parameter. - virtual rocksdb::Status Insert(const rocksdb::Slice& key, uint32_t hash, void* value, - size_t charge, -- void (*deleter)(const rocksdb::Slice& key, void* value), -+ DeleterFn deleter, - rocksdb::Cache::Handle** handle, - rocksdb::Cache::Priority priority) override; - virtual rocksdb::Cache::Handle* Lookup(const rocksdb::Slice& key, uint32_t hash) override; -@@ -205,13 +205,19 @@ class alignas(CACHE_LINE_SIZE) BinnedLRUCacheShard : public CacheShard { - virtual size_t GetUsage() const override; - virtual size_t GetPinnedUsage() const override; - -- virtual void ApplyToAllCacheEntries(void (*callback)(void*, size_t), -- bool thread_safe) override; -+ virtual void ApplyToAllCacheEntries( -+ const std::function& callback, -+ bool thread_safe) override; - - virtual void EraseUnRefEntries() override; - - virtual std::string GetPrintableOptions() const override; - -+ virtual DeleterFn GetDeleter(rocksdb::Cache::Handle* handle) const override; -+ - void TEST_GetLRUList(BinnedLRUHandle** lru, BinnedLRUHandle** lru_low_pri); - - // Retrieves number of elements in LRU, for unit test purpose only -@@ -304,7 +310,9 @@ class BinnedLRUCache : public ShardedCache { - virtual size_t GetCharge(Handle* handle) const override; - virtual uint32_t GetHash(Handle* handle) const override; - virtual void DisownData() override; -- -+#if (ROCKSDB_MAJOR >= 6 && ROCKSDB_MINOR >= 22) -+ virtual DeleterFn GetDeleter(Handle* handle) const override; -+#endif - // Retrieves number of elements in LRU, for unit test purpose only - size_t TEST_GetLRUSize(); - // Sets the high pri pool ratio -diff --git a/src/kv/rocksdb_cache/ShardedCache.cc b/src/kv/rocksdb_cache/ShardedCache.cc -index 367140a94d8be..6cbd89ad6472c 100644 ---- a/src/kv/rocksdb_cache/ShardedCache.cc -+++ b/src/kv/rocksdb_cache/ShardedCache.cc -@@ -44,7 +44,7 @@ void ShardedCache::SetStrictCapacityLimit(bool strict_capacity_limit) { - } - - rocksdb::Status ShardedCache::Insert(const rocksdb::Slice& key, void* value, size_t charge, -- void (*deleter)(const rocksdb::Slice& key, void* value), -+ DeleterFn deleter, - rocksdb::Cache::Handle** handle, Priority priority) { - uint32_t hash = HashSlice(key); - return GetShard(Shard(hash)) -@@ -109,13 +109,36 @@ size_t ShardedCache::GetPinnedUsage() const { - return usage; - } - -+#if (ROCKSDB_MAJOR >= 6 && ROCKSDB_MINOR >= 22) -+DeleterFn ShardedCache::GetDeleter(Handle* handle) const -+{ -+ uint32_t hash = GetHash(handle); -+ return GetShard(Shard(hash))->GetDeleter(handle); -+} -+ -+void ShardedCache::ApplyToAllEntries( -+ const std::function& callback, -+ const ApplyToAllEntriesOptions& opts) -+{ -+ int num_shards = 1 << num_shard_bits_; -+ for (int s = 0; s < num_shards; s++) { -+ GetShard(s)->ApplyToAllCacheEntries(callback, true /* thread_safe */); -+ } -+} -+#else - void ShardedCache::ApplyToAllCacheEntries(void (*callback)(void*, size_t), - bool thread_safe) { - int num_shards = 1 << num_shard_bits_; - for (int s = 0; s < num_shards; s++) { -- GetShard(s)->ApplyToAllCacheEntries(callback, thread_safe); -+ GetShard(s)->ApplyToAllCacheEntries( -+ [callback](const rocksdb::Slice&, void* value, size_t charge, DeleterFn) { -+ callback(value, charge); -+ }, -+ thread_safe); - } - } -+#endif - - void ShardedCache::EraseUnRefEntries() { - int num_shards = 1 << num_shard_bits_; -@@ -131,7 +154,7 @@ std::string ShardedCache::GetPrintableOptions() const { - char buffer[kBufferSize]; - { - std::lock_guard l(capacity_mutex_); -- snprintf(buffer, kBufferSize, " capacity : %" ROCKSDB_PRIszt "\n", -+ snprintf(buffer, kBufferSize, " capacity : %zu\n", - capacity_); - ret.append(buffer); - snprintf(buffer, kBufferSize, " num_shard_bits : %d\n", num_shard_bits_); -diff --git a/src/kv/rocksdb_cache/ShardedCache.h b/src/kv/rocksdb_cache/ShardedCache.h -index 4d64893ab1c7b..f98421a09a33a 100644 ---- a/src/kv/rocksdb_cache/ShardedCache.h -+++ b/src/kv/rocksdb_cache/ShardedCache.h -@@ -14,6 +14,7 @@ - #include - #include - -+#include "rocksdb/version.h" - #include "rocksdb/cache.h" - #include "include/ceph_hash.h" - #include "common/PriorityCache.h" -@@ -22,10 +23,11 @@ - #ifndef CACHE_LINE_SIZE - #define CACHE_LINE_SIZE 64 // XXX arch-specific define - #endif --#define ROCKSDB_PRIszt "zu" - - namespace rocksdb_cache { - -+using DeleterFn = void (*)(const rocksdb::Slice& key, void* value); -+ - // Single cache shard interface. - class CacheShard { - public: -@@ -34,7 +36,7 @@ class CacheShard { - - virtual rocksdb::Status Insert(const rocksdb::Slice& key, uint32_t hash, void* value, - size_t charge, -- void (*deleter)(const rocksdb::Slice& key, void* value), -+ DeleterFn deleter, - rocksdb::Cache::Handle** handle, rocksdb::Cache::Priority priority) = 0; - virtual rocksdb::Cache::Handle* Lookup(const rocksdb::Slice& key, uint32_t hash) = 0; - virtual bool Ref(rocksdb::Cache::Handle* handle) = 0; -@@ -44,10 +46,15 @@ class CacheShard { - virtual void SetStrictCapacityLimit(bool strict_capacity_limit) = 0; - virtual size_t GetUsage() const = 0; - virtual size_t GetPinnedUsage() const = 0; -- virtual void ApplyToAllCacheEntries(void (*callback)(void*, size_t), -- bool thread_safe) = 0; -+ virtual void ApplyToAllCacheEntries( -+ const std::function& callback, -+ bool thread_safe) = 0; - virtual void EraseUnRefEntries() = 0; - virtual std::string GetPrintableOptions() const { return ""; } -+ virtual DeleterFn GetDeleter(rocksdb::Cache::Handle* handle) const = 0; - }; - - // Generic cache interface which shards cache by hash of keys. 2^num_shard_bits -@@ -57,34 +64,43 @@ class ShardedCache : public rocksdb::Cache, public PriorityCache::PriCache { - public: - ShardedCache(size_t capacity, int num_shard_bits, bool strict_capacity_limit); - virtual ~ShardedCache() = default; -+ // rocksdb::Cache - virtual const char* Name() const override = 0; -- virtual CacheShard* GetShard(int shard) = 0; -- virtual const CacheShard* GetShard(int shard) const = 0; -- virtual void* Value(Handle* handle) override = 0; -- virtual size_t GetCharge(Handle* handle) const = 0; -- virtual uint32_t GetHash(Handle* handle) const = 0; -- virtual void DisownData() override = 0; -- -- virtual void SetCapacity(size_t capacity) override; -- virtual void SetStrictCapacityLimit(bool strict_capacity_limit) override; -- - virtual rocksdb::Status Insert(const rocksdb::Slice& key, void* value, size_t charge, -- void (*deleter)(const rocksdb::Slice& key, void* value), -+ DeleterFn, - rocksdb::Cache::Handle** handle, Priority priority) override; - virtual rocksdb::Cache::Handle* Lookup(const rocksdb::Slice& key, rocksdb::Statistics* stats) override; - virtual bool Ref(rocksdb::Cache::Handle* handle) override; - virtual bool Release(rocksdb::Cache::Handle* handle, bool force_erase = false) override; -+ virtual void* Value(Handle* handle) override = 0; - virtual void Erase(const rocksdb::Slice& key) override; - virtual uint64_t NewId() override; -- virtual size_t GetCapacity() const override; -+ virtual void SetCapacity(size_t capacity) override; -+ virtual void SetStrictCapacityLimit(bool strict_capacity_limit) override; - virtual bool HasStrictCapacityLimit() const override; -+ virtual size_t GetCapacity() const override; - virtual size_t GetUsage() const override; - virtual size_t GetUsage(rocksdb::Cache::Handle* handle) const override; - virtual size_t GetPinnedUsage() const override; -+ virtual size_t GetCharge(Handle* handle) const = 0; -+#if (ROCKSDB_MAJOR >= 6 && ROCKSDB_MINOR >= 22) -+ virtual DeleterFn GetDeleter(Handle* handle) const override; -+#endif -+ virtual void DisownData() override = 0; -+#if (ROCKSDB_MAJOR >= 6 && ROCKSDB_MINOR >= 22) -+ virtual void ApplyToAllEntries( -+ const std::function& callback, -+ const ApplyToAllEntriesOptions& opts) override; -+#else - virtual void ApplyToAllCacheEntries(void (*callback)(void*, size_t), - bool thread_safe) override; -+#endif - virtual void EraseUnRefEntries() override; - virtual std::string GetPrintableOptions() const override; -+ virtual CacheShard* GetShard(int shard) = 0; -+ virtual const CacheShard* GetShard(int shard) const = 0; -+ virtual uint32_t GetHash(Handle* handle) const = 0; - - int GetNumShardBits() const { return num_shard_bits_; } - -@@ -120,7 +136,7 @@ class ShardedCache : public rocksdb::Cache, public PriorityCache::PriCache { - // return Hash(s.data(), s.size(), 0); - } - -- uint32_t Shard(uint32_t hash) { -+ uint32_t Shard(uint32_t hash) const { - // Note, hash >> 32 yields hash in gcc, not the zero we expect! - return (num_shard_bits_ > 0) ? (hash >> (32 - num_shard_bits_)) : 0; - } diff --git a/gnu/packages/storage.scm b/gnu/packages/storage.scm index 9d360e8eb3..f9b76b1d38 100644 --- a/gnu/packages/storage.scm +++ b/gnu/packages/storage.scm @@ -3,6 +3,7 @@ ;;; Copyright © 2017 Rutger Helling ;;; Copyright © 2020, 2022 Tobias Geerinckx-Rice ;;; Copyright © 2021 Greg Hogan +;;; Copyright © 2022 Ricardo Wurmus ;;; ;;; This file is part of GNU Guix. ;;; @@ -50,8 +51,10 @@ #:use-module (gnu packages pretty-print) #:use-module (gnu packages python) #:use-module (gnu packages python-xyz) + #:use-module (gnu packages rpc) #:use-module (gnu packages sphinx) #:use-module (gnu packages sqlite) + #:use-module (gnu packages textutils) #:use-module (gnu packages tls) #:use-module (gnu packages web) #:use-module (gnu packages xml)) @@ -59,23 +62,22 @@ (define-public ceph (package (name "ceph") - (version "16.2.9") + (version "17.2.5") (source (origin (method url-fetch) (uri (string-append "https://download.ceph.com/tarballs/ceph-" version ".tar.gz")) (sha256 (base32 - "1yf62k9wlx9pmggwa5c05wfqzy28sdm4b465y4iqrgc9dkrgin08")) + "16mjj6cyrpdn49ig82mmrv984vqfdf24d6i4n9sghfli8z0nj8in")) (patches (search-patches - "ceph-disable-cpu-optimizations.patch" - "ceph-boost-compat.patch" - "ceph-rocksdb-compat.patch")) + "ceph-disable-cpu-optimizations.patch")) (modules '((guix build utils))) (snippet '(for-each delete-file-recursively '(;; TODO: Unbundle these: + "src/arrow" ;;"src/isa-l" ;;"src/lua" ;;"src/xxHash" @@ -87,11 +89,14 @@ "src/rapidjson" "src/spdk" "src/rocksdb" - "src/boost"))))) + "src/boost" + "src/utf8proc"))))) (build-system cmake-build-system) (arguments - `(#:configure-flags - (let* ((out (assoc-ref %outputs "out")) + (list + #:parallel-build? #f ;because mgr_legacy_options.h is not built in time + #:configure-flags + '(let* ((out (assoc-ref %outputs "out")) (lib (assoc-ref %outputs "lib")) (libdir (string-append lib "/lib"))) (list (string-append "-DCMAKE_INSTALL_PREFIX=" out) @@ -112,11 +117,13 @@ (assoc-ref %build-inputs "xfsprogs") "/include") "-DCMAKE_INSTALL_LOCALSTATEDIR=/var" "-DBUILD_SHARED_LIBS=ON" - "-DWITH_SYSTEM_ROCKSDB=ON" + "-DWITH_SYSTEM_ARROW=ON" "-DWITH_SYSTEM_BOOST=ON" + "-DWITH_SYSTEM_ROCKSDB=ON" + "-DWITH_SYSTEM_UTF8PROC=ON" ;; TODO: Enable these when available in Guix. - "-DWITH_MGR_DASHBOARD_FRONTEND=OFF" ;requires node + nodeenv + "-DWITH_MGR_DASHBOARD_FRONTEND=OFF" ;requires node + nodeenv "-DWITH_BABELTRACE=OFF" "-DWITH_LTTNG=OFF" "-DWITH_SPDK=OFF" @@ -136,102 +143,115 @@ ;; resolved. #:tests? #f #:phases - (modify-phases %standard-phases - (add-after 'unpack 'patch-source - (lambda* (#:key outputs #:allow-other-keys) - (let ((out (assoc-ref outputs "out")) - (lib (assoc-ref outputs "lib"))) + `(modify-phases %standard-phases + (add-after 'unpack 'patch-source + (lambda* (#:key outputs #:allow-other-keys) + (let ((out (assoc-ref outputs "out")) + (lib (assoc-ref outputs "lib"))) - (substitute* "cmake/modules/Distutils.cmake" - ;; Prevent creation of Python eggs. - (("setup.py install") - "setup.py install --single-version-externally-managed --root=/") - ;; Inject the -rpath linker argument when linking - ;; Python C libraries so RUNPATH gets set up correctly. - (("LDFLAGS=(.*)\n" _ flags) - (string-append "LDFLAGS=\\\"" flags - " -Wl,-rpath=" lib "/lib\\\"\n"))) + (substitute* "src/rgw/store/dbstore/sqlite/CMakeLists.txt" + (("add_library\\(sqlite_db \\$") + "add_library(sqlite_db STATIC $")) + (substitute* "src/rgw/store/dbstore/CMakeLists.txt" + (("add_library\\(dbstore \\$") + "add_library(dbstore STATIC $") + (("add_library\\(dbstore_lib \\$") + "add_library(dbstore_lib STATIC $")) - ;; Statically link libcrc32 because it does not get installed, - ;; yet several libraries end up referring to it. - (substitute* "src/common/CMakeLists.txt" - (("add_library\\(crc32") - "add_library(crc32 STATIC")) + (substitute* "cmake/modules/Distutils.cmake" + ;; Prevent creation of Python eggs. + (("setup.py install") + "setup.py install --single-version-externally-managed --root=/") + ;; Inject the -rpath linker argument when linking + ;; Python C libraries so RUNPATH gets set up correctly. + (("LDFLAGS=(.*)\n" _ flags) + (string-append "LDFLAGS=\\\"" flags + " -Wl,-rpath=" lib "/lib\\\"\n"))) - (substitute* "udev/50-rbd.rules" - (("/usr/bin/ceph-rbdnamer") - (string-append out "/bin/ceph-rbdnamer")))))) - (add-before 'install 'set-install-environment - (lambda* (#:key outputs #:allow-other-keys) - (let* ((out (assoc-ref outputs "out")) - (py3sitedir - (string-append out "/lib/python" - ,(version-major+minor - (package-version python)) - "/site-packages"))) - ;; The Python install scripts refuses to function if - ;; the install directory is not on PYTHONPATH. - (setenv "PYTHONPATH" py3sitedir)))) - (add-after 'install 'wrap-python-scripts - (lambda* (#:key inputs outputs #:allow-other-keys) - (let* ((out (assoc-ref outputs "out")) - (scripts '("bin/ceph" "bin/cephfs-top" "sbin/ceph-volume")) - (dependencies (map (lambda (input) - (assoc-ref inputs input)) - '("python-prettytable" "python-pyyaml"))) - (sitedir (lambda (package) - (string-append package - "/lib/python" - ,(version-major+minor - (package-version python)) - "/site-packages"))) - (PYTHONPATH (string-join (map sitedir (cons out dependencies)) - ":"))) - (for-each (lambda (executable) - (wrap-program (string-append out "/" executable) - `("GUIX_PYTHONPATH" ":" prefix (,PYTHONPATH)))) - scripts))))))) + ;; Statically link libcrc32 because it does not get installed, + ;; yet several libraries end up referring to it. + (substitute* "src/common/CMakeLists.txt" + (("add_library\\(crc32") + "add_library(crc32 STATIC")) + + (substitute* "udev/50-rbd.rules" + (("/usr/bin/ceph-rbdnamer") + (string-append out "/bin/ceph-rbdnamer")))))) + (add-before 'install 'set-install-environment + (lambda* (#:key outputs #:allow-other-keys) + (let* ((out (assoc-ref outputs "out")) + (py3sitedir + (string-append out "/lib/python" + ,(version-major+minor + (package-version python)) + "/site-packages"))) + ;; The Python install scripts refuses to function if + ;; the install directory is not on PYTHONPATH. + (setenv "PYTHONPATH" py3sitedir)))) + (add-after 'install 'wrap-python-scripts + (lambda* (#:key inputs outputs #:allow-other-keys) + (let* ((out (assoc-ref outputs "out")) + (scripts '("bin/ceph" "bin/cephfs-top" "sbin/ceph-volume")) + (dependencies (map (lambda (input) + (assoc-ref inputs input)) + '("python-prettytable" "python-pyyaml"))) + (sitedir (lambda (package) + (string-append package + "/lib/python" + ,(version-major+minor + (package-version python)) + "/site-packages"))) + (PYTHONPATH (string-join (map sitedir (cons out dependencies)) + ":"))) + (for-each (lambda (executable) + (wrap-program (string-append out "/" executable) + `("GUIX_PYTHONPATH" ":" prefix (,PYTHONPATH)))) + scripts))))))) (outputs '("out" "lib")) (native-inputs (list gperf pkg-config python-cython python-sphinx yasm)) (inputs - `(("boost" ,boost) - ("curl" ,curl) - ("cryptsetup" ,cryptsetup) - ("expat" ,expat) - ("fcgi" ,fcgi) - ("fmt" ,fmt-8) - ("fuse" ,fuse) - ("icu4c" ,icu4c) - ("jemalloc" ,jemalloc) - ("keyutils" ,keyutils) - ("leveldb" ,leveldb) - ("libaio" ,libaio) - ("libatomic-ops" ,libatomic-ops) - ("libcap-ng" ,libcap-ng) - ("libnl" ,libnl) - ("librdkafka" ,librdkafka) - ("lua" ,lua) - ("lz4" ,lz4) - ("oath-toolkit" ,oath-toolkit) - ("openldap" ,openldap) - ("openssl" ,openssl) - ("ncurses" ,ncurses) - ("nss" ,nss) - ("python-prettytable" ,python-prettytable) ;used by ceph_daemon.py - ("python-pyyaml" ,python-pyyaml) ;from python-common/setup.py - ("python" ,python) - ("rapidjson" ,rapidjson) - ("rdma-core" ,rdma-core) - ("rocksdb" ,rocksdb) - ("snappy" ,snappy) - ("sqlite" ,sqlite) - ("udev" ,eudev) - ("util-linux" ,util-linux) - ("util-linux:lib" ,util-linux "lib") - ("xfsprogs" ,xfsprogs) - ("zlib" ,zlib))) + (list `(,apache-thrift "lib") + `(,apache-thrift "include") + `(,apache-arrow-for-ceph "lib") + boost + curl + cryptsetup + eudev + expat + fcgi + fmt-8 + fuse + icu4c + jemalloc + keyutils + leveldb + libaio + libatomic-ops + libcap-ng + libnl + librdkafka + lua + lz4 + oath-toolkit + openldap + openssl + ncurses + nss + python-prettytable ;used by ceph_daemon.py + python-pyyaml ;from python-common/setup.py + python + rapidjson + rdma-core + rocksdb + snappy + sqlite + utf8proc + util-linux + `(,util-linux "lib") + xfsprogs + zlib)) (home-page "https://ceph.com/") (synopsis "Distributed object store and file system") (description From ddd6b70591dfa51d41aa14bab295b8508a07152d Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 24 Dec 2022 00:28:05 +0100 Subject: [PATCH 710/790] gnu: Add emacs-loccur. * gnu/packages/emacs-xyz.scm (emacs-loccur): New variable. --- gnu/packages/emacs-xyz.scm | 26 +++++++++++++++++++++++++- 1 file changed, 25 insertions(+), 1 deletion(-) diff --git a/gnu/packages/emacs-xyz.scm b/gnu/packages/emacs-xyz.scm index 758cc84dff..8fec7b058f 100644 --- a/gnu/packages/emacs-xyz.scm +++ b/gnu/packages/emacs-xyz.scm @@ -4,7 +4,7 @@ ;;; Copyright © 2014, 2015, 2016, 2017, 2018 Mark H Weaver ;;; Copyright © 2014, 2015, 2016, 2017, 2018, 2019 Alex Kost ;;; Copyright © 2015 Federico Beffa -;;; Copyright © 2015, 2016, 2017, 2018, 2019, 2020, 2021 Ricardo Wurmus +;;; Copyright © 2015, 2016, 2017, 2018, 2019, 2020, 2021, 2022 Ricardo Wurmus ;;; Copyright © 2016, 2017, 2018, 2019 Chris Marusich ;;; Copyright © 2015, 2016, 2018, 2020 Christine Lemmer-Webber ;;; Copyright © 2016 Adriano Peluso @@ -10681,6 +10681,30 @@ another (presumably currently running) Emacs Lisp file.") after buffer changes.") (license license:gpl3+))) +(define-public emacs-loccur + (let ((commit "01b7afa62589432a98171074abb8c5a1e089034a") + (revision "1")) + (package + (name "emacs-loccur") + (version (git-version "1.2.5" revision commit)) + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/fourier/loccur/") + (commit commit))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "1b1x1xsiwqzsiss1jc6w990v1vfvbn5d5w67yzmx59s9ldjmdqq2")))) + (build-system emacs-build-system) + (home-page "https://github.com/fourier/loccur") + (synopsis "Perform an occur-like folding in current buffer") + (description + "Loccur is a tool to quickly navigate a file. It is a minor mode for +Emacs acting like occur but w/o creating a new window. It just hides all the +text excepting lines containing matches.") + (license license:gpl3+)))) + (define-public emacs-realgud (package (name "emacs-realgud") From 83b1a2f68239993fbbe5035c5a7868dac8570b15 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ludovic=20Court=C3=A8s?= Date: Fri, 23 Dec 2022 22:35:21 +0100 Subject: [PATCH 711/790] gnu: julia-documenter: Depend on 'git-minimal/fixed'. That way the main 'git-minimal' package can be updated without causing a rebuild of all the dependents of 'julia-documenter'. * gnu/packages/julia-xyz.scm (julia-documenter)[native-inputs]: Replace 'git-minimal' by 'git-minimal/fixed'. --- gnu/packages/julia-xyz.scm | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/gnu/packages/julia-xyz.scm b/gnu/packages/julia-xyz.scm index 29e1cb0d90..414aba03f0 100644 --- a/gnu/packages/julia-xyz.scm +++ b/gnu/packages/julia-xyz.scm @@ -1614,7 +1614,7 @@ valuable enough at this time.") (inputs (list python-wrapper)) (native-inputs - (list git-minimal + (list git-minimal/fixed ;needed for the "Utilities" test julia-documentermarkdown julia-documentertools)) (home-page "https://juliadocs.github.io/Documenter.jl") From 9203de5250f0a5754f251ead40b0f1a75f985a72 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ludovic=20Court=C3=A8s?= Date: Fri, 23 Dec 2022 23:46:55 +0100 Subject: [PATCH 712/790] gnu: ocamlformat: Depend on 'git-minimal/fixed'. * gnu/packages/ocaml.scm (ocamlformat): Replace 'git-minimal' with 'git-minimal/fixed'. --- gnu/packages/ocaml.scm | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/gnu/packages/ocaml.scm b/gnu/packages/ocaml.scm index 94b4fd514e..1bdaa40901 100644 --- a/gnu/packages/ocaml.scm +++ b/gnu/packages/ocaml.scm @@ -8703,7 +8703,8 @@ defined in OCaml 4.12.0.") ocaml-uuseg ocaml-uutf)) (native-inputs - (list git-minimal ocaml-alcotest ocaml-ocp-indent ocaml-bisect-ppx)) + (list git-minimal/fixed ;for tests + ocaml-alcotest ocaml-ocp-indent ocaml-bisect-ppx)) (home-page "https://github.com/ocaml-ppx/ocamlformat") (synopsis "Auto-formatter for OCaml code") (description "OCamlFormat is a tool to automatically format OCaml code in From 0dcca97c9f1f937a7d6157d14a1dcdb92ce9fa20 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ludovic=20Court=C3=A8s?= Date: Fri, 23 Dec 2022 23:59:55 +0100 Subject: [PATCH 713/790] gnu: opam: Depend on 'git-minimal/fixed'. * gnu/packages/ocaml.scm (opam)[native-inputs]: Replace 'git-minimal' with 'git-minimal/fixed'. --- gnu/packages/ocaml.scm | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/gnu/packages/ocaml.scm b/gnu/packages/ocaml.scm index 1bdaa40901..5109cd052a 100644 --- a/gnu/packages/ocaml.scm +++ b/gnu/packages/ocaml.scm @@ -941,7 +941,7 @@ name = Guix Builder") ("ocaml-cppo" ,ocaml-cppo) ;; For tests. - ("git" ,git-minimal) + ("git" ,git-minimal/fixed) ("openssl" ,openssl) ("python" ,python-wrapper) ("rsync" ,rsync) From 8f31575ad13e01206c130e43495c6cc5c755de61 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ludovic=20Court=C3=A8s?= Date: Sat, 24 Dec 2022 00:33:14 +0100 Subject: [PATCH 714/790] gnu: gnome-photos: Depend on 'git-minimal/fixed'. * gnu/packages/gnome.scm (gnome-photos)[arguments]: Pass #:disallowed-references. [native-inputs]: Replace 'git-minimal' with 'git-minimal/fixed'. --- gnu/packages/gnome.scm | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/gnu/packages/gnome.scm b/gnu/packages/gnome.scm index b6ff8d4fe7..c0bb62ff84 100644 --- a/gnu/packages/gnome.scm +++ b/gnu/packages/gnome.scm @@ -889,6 +889,7 @@ tomorrow, the rest of the week and for special occasions.") (build-system meson-build-system) (arguments (list + #:disallowed-references (list (this-package-native-input "git-minimal")) #:glib-or-gtk? #t #:configure-flags #~(list "-Ddogtail=false" ; Not available @@ -909,7 +910,7 @@ tomorrow, the rest of the week and for special occasions.") (list dbus desktop-file-utils gettext-minimal - git-minimal + git-minimal/fixed `(,glib "bin") gobject-introspection gsettings-desktop-schemas From bae13578f7b03735c1cfcd1addb31a05fa413c44 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ludovic=20Court=C3=A8s?= Date: Sat, 24 Dec 2022 00:43:20 +0100 Subject: [PATCH 715/790] gnu: python-scikit-build: Depend on 'git-minimal/fixed'. * gnu/packages/python-xyz.scm (python-scikit-build)[native-inputs]: Replace 'git-minimal' with 'git-minimal/fixed'. --- gnu/packages/python-xyz.scm | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index ee25a2d655..6b71d6872e 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -28550,7 +28550,7 @@ and frame grabber interface.") (native-inputs (list cmake-minimal gfortran - git-minimal + git-minimal/fixed ;for tests ninja python-coverage python-cython From 69fc67b6bbd84bae2dfda1dcfc667946a368298a Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ludovic=20Court=C3=A8s?= Date: Sat, 24 Dec 2022 00:12:19 +0100 Subject: [PATCH 716/790] hurd-boot: Fix list of devices with translators. Fixes a regression introduced in 450f7740283ce160a7482d1c75e6e0ab17f2a6f0 and e3c6575ee93741a43003cd1aa4663151dd90b9f5, which introduced unquote-splicing without changing quote to quasiquote. * gnu/build/hurd-boot.scm (set-hurd-device-translators)[devices]: Use quasiquote, note quote. --- gnu/build/hurd-boot.scm | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/gnu/build/hurd-boot.scm b/gnu/build/hurd-boot.scm index e068ffc202..abcf0304c2 100644 --- a/gnu/build/hurd-boot.scm +++ b/gnu/build/hurd-boot.scm @@ -194,7 +194,7 @@ set." ("proc" ("/hurd/procfs" "--stat-mode=444")))) (define devices - '(("dev/full" ("/hurd/null" "--full") #o666) + `(("dev/full" ("/hurd/null" "--full") #o666) ("dev/null" ("/hurd/null") #o666) ("dev/random" ("/hurd/random" "--seed-file" "/var/lib/random-seed") #o644) From 3532fc6ba4d36ae055f11245a29fb6e8e54c545c Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ludovic=20Court=C3=A8s?= Date: Sat, 24 Dec 2022 00:35:32 +0100 Subject: [PATCH 717/790] gnu: libtirpc-hurd: Fix cross-compilation. Fixes a regression introduced in 517618b2401c2ab5861e63df60ae49918b94f727, whereby the "wrong" 'krb5-config' script would be picked. * gnu/packages/onc-rpc.scm (libtirpc/hurd)[arguments]: Turn #:configure-flags into a gexp to refer to the right "mit-krb5". --- gnu/packages/onc-rpc.scm | 9 +++++---- 1 file changed, 5 insertions(+), 4 deletions(-) diff --git a/gnu/packages/onc-rpc.scm b/gnu/packages/onc-rpc.scm index 4495622191..3928e80476 100644 --- a/gnu/packages/onc-rpc.scm +++ b/gnu/packages/onc-rpc.scm @@ -1,5 +1,5 @@ ;;; GNU Guix --- Functional package management for GNU -;;; Copyright © 2014, 2017, 2018 Ludovic Courtès +;;; Copyright © 2014, 2017, 2018, 2022 Ludovic Courtès ;;; Copyright © 2016 John Darrington ;;; Copyright © 2017, 2018 Leo Famulari ;;; Copyright © 2018, 2021 Tobias Geerinckx-Rice @@ -27,6 +27,7 @@ #:use-module (guix licenses) #:use-module (guix packages) #:use-module (guix download) + #:use-module (guix gexp) #:use-module (guix git-download) #:use-module (gnu packages) #:use-module (gnu packages autotools) @@ -84,9 +85,9 @@ IPv4 and IPv6. ONC RPC is notably used by the network file system (NFS).") (substitute-keyword-arguments (package-arguments libtirpc) ((#:configure-flags flags ''()) ;; When cross-building the target system's krb5-config should be used. - `(list (string-append "ac_cv_prog_KRB5_CONFIG=" - (assoc-ref %build-inputs "mit-krb5") - "/bin/krb5-config"))))))) + #~(list (string-append "ac_cv_prog_KRB5_CONFIG=" + #$(this-package-input "mit-krb5") + "/bin/krb5-config"))))))) (define libtirpc/fixed (package From 528c79e7ac3d9e05c92af6c9fed12fe357162b27 Mon Sep 17 00:00:00 2001 From: Sughosha Date: Sat, 17 Dec 2022 06:31:58 +0000 Subject: [PATCH 718/790] gnu: gnome-shell-extension-unite-shell: Update to 69. * gnu/packages/gnome-xyz.scm (gnome-shell-extension-unite-shell): Update to 69. Signed-off-by: Liliana Marie Prikler --- gnu/packages/gnome-xyz.scm | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/gnu/packages/gnome-xyz.scm b/gnu/packages/gnome-xyz.scm index 8be9c55000..f825d2055c 100644 --- a/gnu/packages/gnome-xyz.scm +++ b/gnu/packages/gnome-xyz.scm @@ -361,16 +361,16 @@ copy, move, delete, or edit your files.") (define-public gnome-shell-extension-unite-shell (package (name "gnome-shell-extension-unite-shell") - (version "65") + (version "69") (source (origin (method git-fetch) (uri (git-reference (url "https://github.com/hardpixel/unite-shell") - (commit "127edac6396b89cdedec003bdff38820e6a0f91f"))) + (commit (string-append "v" version)))) (file-name (git-file-name name version)) (sha256 (base32 - "1lzhf7hlvzg62nxjfpv265315qibcjz5dv08dzpfckf2dx68nab4")))) + "10yh6ylyp43ykcza180iak08wfypay3raqf3p0vrj9ngm98qzq70")))) (build-system copy-build-system) (native-inputs (list `(,glib "bin") gettext-minimal)) (inputs (list xprop)) From 8ebb5b64fda69d79b9acf9874782637da7bb67c6 Mon Sep 17 00:00:00 2001 From: Sughosha Date: Sat, 17 Dec 2022 06:43:13 +0000 Subject: [PATCH 719/790] gnu: gnome-shell-extension-vertical-overview: Update to 10. * gnu/packages/gnome-xyz.scm (gnome-shell-extension-vertical-overview): Update to 10. Signed-off-by: Liliana Marie Prikler --- gnu/packages/gnome-xyz.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/gnome-xyz.scm b/gnu/packages/gnome-xyz.scm index f825d2055c..04b9ea2fe1 100644 --- a/gnu/packages/gnome-xyz.scm +++ b/gnu/packages/gnome-xyz.scm @@ -934,7 +934,7 @@ copies you now want to paste.") (define-public gnome-shell-extension-vertical-overview (package (name "gnome-shell-extension-vertical-overview") - (version "9") + (version "10") (source (origin (method git-fetch) @@ -943,7 +943,7 @@ copies you now want to paste.") (commit (string-append "v" version)))) (sha256 (base32 - "0pkby00rjipj04z68d6i3rr7mzm01dckf2vl3iz6yvbl39602icl")) + "1sqkbg93qqrq47wyfnh2flg7dpsmv5c2pmkx8kgqhnbl7j2kgi0l")) (file-name (git-file-name name version)) (snippet '(begin (delete-file "schemas/gschemas.compiled"))))) From 1cb49932d7f43e68b6ef6e07c20b562682f7f279 Mon Sep 17 00:00:00 2001 From: Sughosha Date: Sat, 17 Dec 2022 06:53:46 +0000 Subject: [PATCH 720/790] gnu: gnome-shell-extension-burn-my-windows: Update to 22. * gnu/packages/gnome-xyz (gnome-shell-extension-burn-my-windows): Update to 22. Signed-off-by: Liliana Marie Prikler --- gnu/packages/gnome-xyz.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/gnome-xyz.scm b/gnu/packages/gnome-xyz.scm index 04b9ea2fe1..62ffddbb44 100644 --- a/gnu/packages/gnome-xyz.scm +++ b/gnu/packages/gnome-xyz.scm @@ -1015,7 +1015,7 @@ position when the mouse is moved rapidly.") (define-public gnome-shell-extension-burn-my-windows (package (name "gnome-shell-extension-burn-my-windows") - (version "21") + (version "22") (source (origin (method git-fetch) @@ -1024,7 +1024,7 @@ position when the mouse is moved rapidly.") (commit (string-append "v" version)))) (sha256 (base32 - "07ckfl47pq83nhb77v230zfxlz3imga3s8nn3sr9cq4zxvbkj2r4")) + "185xrf330d9bflmk0l61cnzlylnppb2v4yz6v6ygkk4zpwyil8np")) (file-name (git-file-name name version)))) (build-system copy-build-system) (arguments From 9cadac9787a03093550a1132bf7d20eb4eaf4df9 Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Sun, 18 Dec 2022 01:00:00 +0100 Subject: [PATCH 721/790] doc: Fix typo. * doc/contributing.texi (Sending a Patch Series): Fix e-mail address of . Reported by Denis 'GNUtoo' Carikli . --- doc/contributing.texi | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/doc/contributing.texi b/doc/contributing.texi index 6a8ffd6524..efc2a05cce 100644 --- a/doc/contributing.texi +++ b/doc/contributing.texi @@ -1514,7 +1514,7 @@ that we can send the rest of the patches to. @example $ git send-email outgoing/0000-cover-letter.patch -a \ - --to=guix-patches@@debbugs.gnu.org \ + --to=guix-patches@@gnu.org \ $(etc/teams.scm cc-members ...) $ rm outgoing/0000-cover-letter.patch # we don't want to resend it! @end example From f8841c086e892fbea92773bfb1bb35dbd28455cc Mon Sep 17 00:00:00 2001 From: Vinicius Monego Date: Thu, 8 Dec 2022 18:20:53 -0300 Subject: [PATCH 722/790] gnu: homebank: Update to 5.6. * gnu/packages/finance.scm (homebank): Update to 5.6. --- gnu/packages/finance.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/finance.scm b/gnu/packages/finance.scm index f9ee7acaa1..f5906ec738 100644 --- a/gnu/packages/finance.scm +++ b/gnu/packages/finance.scm @@ -271,14 +271,14 @@ Accounting.") (define-public homebank (package (name "homebank") - (version "5.5.8") + (version "5.6") (source (origin (method url-fetch) (uri (string-append "http://homebank.free.fr/public/homebank-" version ".tar.gz")) (sha256 (base32 - "11fgmdqsnxdqma1ffljbcl7w1ahx0s5p41hjy600f8zarsrmnyjh")))) + "1ig00d3wby6lisz3vbyb5qm7h4a6npfwqyphdl8fjgibzpapq5a1")))) (build-system glib-or-gtk-build-system) (native-inputs (list pkg-config intltool)) From 7e7659d34fb223ebd73e8c931d3b5c882d320869 Mon Sep 17 00:00:00 2001 From: Vinicius Monego Date: Sat, 24 Dec 2022 07:54:09 -0300 Subject: [PATCH 723/790] gnu: shotcut: Update to 22.12.21. * gnu/packages/video.scm (shotcut): Update to 22.12.21. --- gnu/packages/video.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/video.scm b/gnu/packages/video.scm index e32186f5ce..d1d50df304 100644 --- a/gnu/packages/video.scm +++ b/gnu/packages/video.scm @@ -4885,7 +4885,7 @@ transitions, and effects and then export your film to many common formats.") (define-public shotcut (package (name "shotcut") - (version "22.11.25") + (version "22.12.21") (source (origin (method git-fetch) @@ -4894,7 +4894,7 @@ transitions, and effects and then export your film to many common formats.") (commit (string-append "v" version)))) (file-name (git-file-name name version)) (sha256 - (base32 "01qv0lb57kgmi5shcnhjwf47vqvbyjndxx6v7ha3sh4x5r8x0mrn")))) + (base32 "1hchnywsrkvnz07r2i1cffg1a8zi59pcpswz8x93a0rdc42hlk3d")))) (build-system qt-build-system) (arguments `(#:tests? #f ;there are no tests From aae8371f72805cc35e31817e4120468eee4a4a80 Mon Sep 17 00:00:00 2001 From: Guillaume Le Vaillant Date: Sat, 24 Dec 2022 14:39:07 +0100 Subject: [PATCH 724/790] gnu: qdmr: Update to 0.10.4. * gnu/packages/radio.scm (qdmr): Update to 0.10.4. --- gnu/packages/radio.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/radio.scm b/gnu/packages/radio.scm index aae30b7911..5cc3bf077a 100644 --- a/gnu/packages/radio.scm +++ b/gnu/packages/radio.scm @@ -2738,7 +2738,7 @@ Navigation Satellite System.") (define-public qdmr (package (name "qdmr") - (version "0.10.3") + (version "0.10.4") (source (origin (method git-fetch) (uri (git-reference @@ -2747,7 +2747,7 @@ Navigation Satellite System.") (file-name (git-file-name name version)) (sha256 (base32 - "037vkwk974zrwacxafslkb3mbw9258v9sdpwdvb23msjzbc3snrn")))) + "1svxdfb5snxs2y1dwyb0j10ill9ribj4hw1rk023866yzn2zd0l9")))) (build-system cmake-build-system) (arguments (list #:tests? #f ;no tests From 8bf58c1b35c3f0195fdce76c73328c4e156412c3 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 24 Dec 2022 16:32:39 +0100 Subject: [PATCH 725/790] gnu: mumi: Update to 0.0.4-1.18acd2b. * gnu/packages/mail.scm (mumi): Update to 0.0.4-1.18acd2b. --- gnu/packages/mail.scm | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/gnu/packages/mail.scm b/gnu/packages/mail.scm index 6ce961e2c8..011bc88565 100644 --- a/gnu/packages/mail.scm +++ b/gnu/packages/mail.scm @@ -4026,11 +4026,11 @@ It is a replacement for the @command{urlview} program.") (license license:gpl2+))) (define-public mumi - (let ((commit "350b2dfbe22bea82ca2d5739d5aebbf9277fe7b7") + (let ((commit "18acd2b3ecdff309bc8788a82421531b3d332ac8") (revision "1")) (package (name "mumi") - (version (git-version "0.0.3" revision commit)) + (version (git-version "0.0.4" revision commit)) (source (origin (method git-fetch) (uri (git-reference @@ -4039,7 +4039,7 @@ It is a replacement for the @command{urlview} program.") (file-name (git-file-name name version)) (sha256 (base32 - "1i728cf5shsh0rcv38z244855s2jhifj91prq7c2zk99fsiadw50")))) + "0czzik71aa32zpn1wwg18f68zjhdssmc7ljrkq5ksfhqsn0hkgmz")))) (build-system gnu-build-system) (arguments (list From 36bc92a3ec2113e9aeff0c68737771f521de5b10 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sun, 25 Dec 2022 00:26:02 +0100 Subject: [PATCH 726/790] gnu: mumi: Update to 0.0.4-2.0a90eed. * gnu/packages/mail.scm (mumi): Update to 0.0.4-2.0a90eed. --- gnu/packages/mail.scm | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/gnu/packages/mail.scm b/gnu/packages/mail.scm index 011bc88565..c9916c2e93 100644 --- a/gnu/packages/mail.scm +++ b/gnu/packages/mail.scm @@ -4026,8 +4026,8 @@ It is a replacement for the @command{urlview} program.") (license license:gpl2+))) (define-public mumi - (let ((commit "18acd2b3ecdff309bc8788a82421531b3d332ac8") - (revision "1")) + (let ((commit "0a90eeda9b5e12a2f83e3917c46fa539f308d0c8") + (revision "2")) (package (name "mumi") (version (git-version "0.0.4" revision commit)) @@ -4039,7 +4039,7 @@ It is a replacement for the @command{urlview} program.") (file-name (git-file-name name version)) (sha256 (base32 - "0czzik71aa32zpn1wwg18f68zjhdssmc7ljrkq5ksfhqsn0hkgmz")))) + "1yxi1vvygrk8qd0mqh65qh1g99r5d4rlymj8amcn80ggi3z32byk")))) (build-system gnu-build-system) (arguments (list From 860e949896b1a9ae5427f4cf9fa690fdcaae48a0 Mon Sep 17 00:00:00 2001 From: "Artyom V. Poptsov" Date: Sun, 11 Dec 2022 08:19:29 +0300 Subject: [PATCH 727/790] gnu: freecad: Fix the package hash. * gnu/packages/engineering.scm (freecad): Fix the package hash. Signed-off-by: Andrew Tropin --- gnu/packages/engineering.scm | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/gnu/packages/engineering.scm b/gnu/packages/engineering.scm index 0426762dbd..b995366978 100644 --- a/gnu/packages/engineering.scm +++ b/gnu/packages/engineering.scm @@ -2437,7 +2437,7 @@ comments."))) (commit version))) (file-name (git-file-name name version)) (sha256 - (base32 "02976k91ypv41rqdl27jbmyhnhgx7k5bj520lcqs8qzgcdsynd03")))) + (base32 "0wsfz2jqfhmqshyr1n4qxcc3c6a96gyll4h34vn2zzvvcnncn9rb")))) (build-system qt-build-system) (native-inputs (list doxygen From c97de4a989f73addcc5eae23f90084575fe83357 Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Sun, 25 Dec 2022 12:02:05 +0100 Subject: [PATCH 728/790] services: ganeti: Label mcron jobs. * gnu/services/ganeti.scm (ganeti-watcher-jobs): Label job as "ganeti-watcher". (ganeti-cleaner-jobs): Labels jobs as "ganeti master cleaner" and "ganeti node cleaner". --- gnu/services/ganeti.scm | 9 ++++++--- 1 file changed, 6 insertions(+), 3 deletions(-) diff --git a/gnu/services/ganeti.scm b/gnu/services/ganeti.scm index f8127e8721..f4fec3833e 100644 --- a/gnu/services/ganeti.scm +++ b/gnu/services/ganeti.scm @@ -683,7 +683,8 @@ information to OS install scripts or instances."))) #~(#$schedule)) ((? list?) #~('#$schedule))) - #$(ganeti-watcher-command config)))))) + #$(ganeti-watcher-command config) + "ganeti-watcher"))))) (define ganeti-watcher-service-type (service-type (name 'ganeti-watcher) @@ -725,7 +726,8 @@ is declared offline by known master candidates."))) #~('#$master-schedule))) (lambda () (system* #$(file-append ganeti "/sbin/ganeti-cleaner") - "master"))) + "master")) + "ganeti master cleaner") #~(job #$@(match node-schedule ((? string?) #~(#$node-schedule)) @@ -733,7 +735,8 @@ is declared offline by known master candidates."))) #~('#$node-schedule))) (lambda () (system* #$(file-append ganeti "/sbin/ganeti-cleaner") - "node"))))))) + "node")) + "ganeti node cleaner"))))) (define ganeti-cleaner-service-type (service-type (name 'ganeti-cleaner) From 53a1fce25afdaf81c964c8867f3b9cce61b846ba Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Sun, 25 Dec 2022 12:33:57 +0100 Subject: [PATCH 729/790] gnu: Add openbios-qemu-ppc. * gnu/packages/firmware.scm (make-openbios-package): New procedure. (openbios-qemu-ppc): New variable. * gnu/packages/patches/openbios-gcc-warnings.patch: New file. * gnu/local.mk (dist_patch_DATA): Adjust accordingly. --- gnu/local.mk | 1 + gnu/packages/firmware.scm | 76 +++++++++++++++ .../patches/openbios-gcc-warnings.patch | 95 +++++++++++++++++++ 3 files changed, 172 insertions(+) create mode 100644 gnu/packages/patches/openbios-gcc-warnings.patch diff --git a/gnu/local.mk b/gnu/local.mk index a75a7252af..034131b5f8 100644 --- a/gnu/local.mk +++ b/gnu/local.mk @@ -1605,6 +1605,7 @@ dist_patch_DATA = \ %D%/packages/patches/onnx-use-system-googletest.patch \ %D%/packages/patches/onnx-shared-libraries.patch \ %D%/packages/patches/onnx-skip-model-downloads.patch \ + %D%/packages/patches/openbios-gcc-warnings.patch \ %D%/packages/patches/openboardview-use-system-imgui.patch \ %D%/packages/patches/openboardview-use-system-utf8.patch \ %D%/packages/patches/openbox-python3.patch \ diff --git a/gnu/packages/firmware.scm b/gnu/packages/firmware.scm index 1b4fd61241..226a0e8029 100644 --- a/gnu/packages/firmware.scm +++ b/gnu/packages/firmware.scm @@ -343,6 +343,82 @@ broadband modem as found, for example, on PinePhone.") (home-page "https://gitlab.com/mobian1/devices/eg25-manager") (license license:gpl3+))) +(define* (make-openbios-package name arch) + (let ((target (cond + ((string-suffix? "ppc" arch) + "powerpc-linux-gnu") + ((string-suffix? "amd64" arch) + "x86_64-linux-gnu") + ((string-suffix? "x86" arch) + "i686-linux-gnu") + (else (string-append arch "-linux-gnu"))))) + (package + (name name) + (version "1.1") + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/openbios/openbios") + (commit (string-append "v" version)))) + (file-name (git-file-name "openbios" version)) + (patches (search-patches "openbios-gcc-warnings.patch")) + (sha256 + (base32 + "11cr0097aiw4hc07v5hfl95753ikyra5ig4nv899ci7l42ilrrbr")))) + (build-system gnu-build-system) + (arguments + (list #:tests? #f ;no tests + #:phases + #~(modify-phases %standard-phases + (add-after 'unpack 'build-reproducibly + (lambda _ + (substitute* "Makefile.target" + (("TZ=UTC date \\+") + "TZ=UTC date --date=@1 +")))) + (replace 'configure + (lambda _ + (invoke "./config/scripts/switch-arch" #$arch))) + (replace 'install + (lambda _ + (let ((build-target + (if (string-contains #$arch "-") + (car (reverse (string-split #$arch #\-))) + #$arch))) + (for-each (lambda (elf) + (install-file elf + (string-append #$output + "/share/firmware"))) + (find-files (string-append "obj-" build-target) + "\\.elf$")))))))) + (native-inputs + (append (if (string-prefix? (%current-system) target) + '() + (list (cross-gcc target) (cross-binutils target))) + (list libxslt which))) + (home-page "https://openfirmware.info/Welcome_to_OpenBIOS") + (synopsis "Open Firmware implementation") + (description + "OpenBIOS is an implementation of the IEEE 1275-1994 \"Open Firmware\" +specification. It can be used as a system firmware, as a boot loader, or +provide OpenFirmware functionality on top of an already running system.") + ;; Some files are GPLv2 only. + (license license:gpl2)))) + +(define-public openbios-qemu-ppc + (let ((base (make-openbios-package "openbios-qemu-ppc" "qemu-ppc"))) + (package + (inherit base) + (arguments + (substitute-keyword-arguments (package-arguments base) + ((#:phases phases) + #~(modify-phases #$phases + (add-after 'install 'rename-executable + (lambda _ + (with-directory-excursion #$output + (rename-file "share/firmware" "share/qemu") + (rename-file "share/qemu/openbios-qemu.elf" + "share/qemu/openbios-ppc"))))))))))) + (define* (make-opensbi-package platform name #:optional (arch "riscv64")) (package (name name) diff --git a/gnu/packages/patches/openbios-gcc-warnings.patch b/gnu/packages/patches/openbios-gcc-warnings.patch new file mode 100644 index 0000000000..b96cecc31e --- /dev/null +++ b/gnu/packages/patches/openbios-gcc-warnings.patch @@ -0,0 +1,95 @@ +Fix warnings with recent versions of GCC. + +This is a combination of these commits: + + https://github.com/openbios/openbios/commit/14be7d187a327a89c068c4e2551d5012a3c25703 + https://github.com/openbios/openbios/commit/0e6b8b3cb4a25a4680f238bae76de5e370e706c8 + https://github.com/openbios/openbios/commit/51067854a7606cceb8b1e0a3d2108da69ff46973 + +...with minor adaptations to apply on 1.1. + + +diff --git a/arch/sparc32/context.c b/arch/sparc32/context.c +--- a/arch/sparc32/context.c ++++ b/arch/sparc32/context.c +@@ -86,7 +86,7 @@ struct context *switch_to(struct context *ctx) + __context = ctx; + asm __volatile__ ("\n\tcall __switch_context" + "\n\tnop" ::: "g1", "g2", "g3", "g4", "g5", "g6", "g7", +- "o0", "o1", "o2", "o3", "o4", "o5", "sp", "o7", ++ "o0", "o1", "o2", "o3", "o4", "o5", "o7", + "l0", "l1", "l2", "l3", "l4", "l5", "l6", "l7", + "i0", "i1", "i2", "i3", "i4", "i5", "i7", + "f0", "f1", "f2", "f3", "f4", "f5", "f6", "f7", "f8", "f9", +diff --git a/drivers/cuda.c b/drivers/cuda.c +--- a/drivers/cuda.c ++++ b/drivers/cuda.c +@@ -355,7 +355,7 @@ static void + rtc_init(char *path) + { + phandle_t ph, aliases; +- char buf[64]; ++ char buf[128]; + + snprintf(buf, sizeof(buf), "%s/rtc", path); + REGISTER_NAMED_NODE(rtc, buf); +diff --git a/drivers/ide.c b/drivers/ide.c +--- a/drivers/ide.c ++++ b/drivers/ide.c +@@ -987,7 +987,7 @@ ob_ide_identify_drive(struct ide_drive *drive) + drive->sect = id.sectors; + } + +- strncpy(drive->model, (char*)id.model, sizeof(id.model)); ++ strncpy(drive->model, (char*)id.model, sizeof(drive->model)); + drive->model[40] = '\0'; + return 0; + } +diff --git a/fs/hfs/hfs_fs.c b/fs/hfs/hfs_fs.c +--- a/fs/hfs/hfs_fs.c ++++ b/fs/hfs/hfs_fs.c +@@ -86,7 +86,7 @@ _search( hfsvol *vol, const char *path, const char *sname, hfsfile **ret_fd ) + + strncpy( buf, path, sizeof(buf) ); + if( buf[strlen(buf)-1] != ':' ) +- strncat( buf, ":", sizeof(buf) ); ++ strncat( buf, ":", sizeof(buf) - 1 ); + buf[sizeof(buf)-1] = 0; + p = buf + strlen( buf ); + +@@ -101,7 +101,7 @@ _search( hfsvol *vol, const char *path, const char *sname, hfsfile **ret_fd ) + *p = 0; + topdir = 0; + +- strncat( buf, ent.name, sizeof(buf) ); ++ strncat( buf, ent.name, sizeof(buf) - 1); + if( (status=_search(vol, buf, sname, ret_fd)) != 2 ) + continue; + topdir = 1; +diff --git a/libc/string.c b/libc/string.c +--- a/libc/string.c ++++ b/libc/string.c +@@ -349,10 +349,7 @@ int memcmp(const void * cs,const void * ct,size_t count) + char * + strdup( const char *str ) + { +- char *p; +- if( !str ) +- return NULL; +- p = malloc( strlen(str) + 1 ); ++ char *p = malloc( strlen(str) + 1 ); + strcpy( p, str ); + return p; + } +diff --git a/packages/nvram.c b/packages/nvram.c +--- a/packages/nvram.c ++++ b/packages/nvram.c +@@ -105,7 +105,7 @@ create_free_part( char *ptr, int size ) + nvpart_t *nvp = (nvpart_t*)ptr; + memset( nvp, 0, size ); + +- strncpy( nvp->name, "777777777777", sizeof(nvp->name) ); ++ strncpy( nvp->name, "77777777777", sizeof(nvp->name) ); + nvp->signature = NV_SIG_FREE; + nvp->len_hi = (size /16) >> 8; + nvp->len_lo = size /16; From 71b8707100e2fbc00f123566717ba3958c6afabb Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Sun, 25 Dec 2022 12:34:31 +0100 Subject: [PATCH 730/790] gnu: QEMU: Unbundle OpenBIOS. * gnu/packages/virtualization.scm (qemu)[source](snippet): Remove precompiled PPC OpenBIOS firmware, and its source code. [arguments]: Replace with the one from Guix. [inputs]: Add OPENBIOS-QEMU-PPC. --- gnu/packages/virtualization.scm | 14 ++++++++++++-- 1 file changed, 12 insertions(+), 2 deletions(-) diff --git a/gnu/packages/virtualization.scm b/gnu/packages/virtualization.scm index 945584bd0a..ec453c1f38 100644 --- a/gnu/packages/virtualization.scm +++ b/gnu/packages/virtualization.scm @@ -181,12 +181,16 @@ (for-each delete-file (find-files "." "^(bios|vgabios).*\\.bin$")) ;; Delete SGABIOS. (delete-file "sgabios.bin") + ;; Delete ppc64 OpenBIOS. TODO: Remove sparc32 and sparc64 too + ;; once they are supported in Guix. + (delete-file "openbios-ppc") ;; Delete iPXE firmwares. (for-each delete-file (find-files "." "^(efi|pxe)-.*\\.rom$"))) ;; Delete bundled code that we provide externally. (for-each delete-file-recursively '("dtc" "meson" "roms/ipxe" + "roms/openbios" "roms/seabios" "roms/sgabios")))))) (outputs '("out" "static" "doc")) ;5.3 MiB of HTML docs @@ -200,6 +204,8 @@ #:configure-flags #~(let ((gcc (search-input-file %build-inputs "/bin/gcc")) (meson (search-input-file %build-inputs "bin/meson")) + (openbios (search-input-file %build-inputs + "share/qemu/openbios-ppc")) (seabios (search-input-file %build-inputs "share/qemu/bios.bin")) (sgabios (search-input-file %build-inputs @@ -218,6 +224,7 @@ (string-append "--firmwarepath=" out "/share/qemu:" (dirname seabios) ":" (dirname ipxe) ":" + (dirname openbios) ":" (dirname sgabios)) (string-append "--smbd=" out "/libexec/samba-wrapper") "--disable-debug-info" ;for space considerations @@ -243,6 +250,8 @@ (ipxe (dirname (search-input-file inputs "share/qemu/pxe-virtio.rom"))) (ipxe-firmwares (find-files ipxe "\\.rom$")) + (openbios (search-input-file + inputs "share/qemu/openbios-ppc")) (allowed-differences ;; Ignore minor differences (addresses etc) in the firmware ;; data tables compared to what the test suite expects. @@ -258,7 +267,7 @@ (for-each (lambda (file) (symlink file (basename file))) (append seabios-firmwares ipxe-firmwares - (list sgabios)))) + (list openbios sgabios)))) (for-each (lambda (file) (format allowed-differences-whitelist "\"~a\",~%" file)) @@ -376,7 +385,7 @@ (with-directory-excursion (string-append #$output "/share/qemu") (for-each delete-file (append - '("sgabios.bin") + '("openbios-ppc" "sgabios.bin") (find-files "." "^(vga)?bios(-[a-z0-9-]+)?\\.bin$") (find-files "." "^(efi|pxe)-.*\\.rom$")))))) ;; Create a wrapper for Samba. This allows QEMU to use Samba without @@ -420,6 +429,7 @@ exec smbd $@"))) libusb ;USB pass-through support mesa ncurses + openbios-qemu-ppc ;; ("pciutils" ,pciutils) pixman pulseaudio From 699aef4bc6500cf2fff75be803c44dc9e34edc3e Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Sun, 25 Dec 2022 12:44:49 +0100 Subject: [PATCH 731/790] gnu: opensbi: Use the same source file name regardless of variant. * gnu/packages/firmware.scm (make-opensbi-package)[source](file-name): Don't use the NAME variable which changes depending on the variant. --- gnu/packages/firmware.scm | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/gnu/packages/firmware.scm b/gnu/packages/firmware.scm index 226a0e8029..b231fd7659 100644 --- a/gnu/packages/firmware.scm +++ b/gnu/packages/firmware.scm @@ -429,7 +429,7 @@ provide OpenFirmware functionality on top of an already running system.") (uri (git-reference (url "https://github.com/riscv-software-src/opensbi") (commit (string-append "v" version)))) - (file-name (git-file-name name version)) + (file-name (git-file-name "opensbi" version)) (sha256 (base32 "0xlnhl965286kvizyjm571qbhj3l5n71a02dmbmgxzcqapzgi9wk")))) (build-system gnu-build-system) From c8e836991df304f59ab713ce12a38490e33e169b Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Sun, 25 Dec 2022 13:41:13 +0100 Subject: [PATCH 732/790] gnu: Add opensbi-qemu. * gnu/packages/firmware.scm (opensbi-qemu): New variable. --- gnu/packages/firmware.scm | 24 ++++++++++++++++++++++++ 1 file changed, 24 insertions(+) diff --git a/gnu/packages/firmware.scm b/gnu/packages/firmware.scm index b231fd7659..4d4fc8fe23 100644 --- a/gnu/packages/firmware.scm +++ b/gnu/packages/firmware.scm @@ -34,6 +34,7 @@ #:use-module (guix git-download) #:use-module (guix build-system gnu) #:use-module (guix build-system meson) + #:use-module (guix build-system trivial) #:use-module (gnu packages) #:use-module (gnu packages admin) #:use-module (gnu packages autotools) @@ -476,6 +477,29 @@ executing in M-mode.") (define-public opensbi-generic (make-opensbi-package "generic" "opensbi-generic")) +(define-public opensbi-qemu + (package + (inherit opensbi-generic) + (name "opensbi-qemu") + (native-inputs '()) + (inputs (list opensbi-generic)) + (build-system trivial-build-system) + (arguments + (list #:modules '((guix build utils)) + #:builder + #~(begin + (use-modules ((guix build utils))) + (let ((opensbi-riscv64 (search-input-file %build-inputs + "fw_dynamic.bin")) + (out (string-append #$output "/share/qemu"))) + (mkdir-p out) + (symlink opensbi-riscv64 + (string-append + out "/opensbi-riscv64-generic-fw_dynamic.bin")))))) + (synopsis "OpenSBI firmware files for QEMU") + (description + "This package contains OpenSBI firmware files for use with QEMU."))) + (define-public seabios (package (name "seabios") From f81c05d89bf9a91cb46524cb777f65d0295e6981 Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Sun, 25 Dec 2022 13:44:17 +0100 Subject: [PATCH 733/790] gnu: QEMU: Unbundle OpenSBI. * gnu/packages/virtualization.scm (qemu)[source](snippet): Delete precompiled riscv64 firmware, and its source code. [arguments]: Provide OpenSBI. [inputs]: Add OPENSBI-QEMU. --- gnu/packages/virtualization.scm | 19 +++++++++++++++++-- 1 file changed, 17 insertions(+), 2 deletions(-) diff --git a/gnu/packages/virtualization.scm b/gnu/packages/virtualization.scm index ec453c1f38..64a26edb02 100644 --- a/gnu/packages/virtualization.scm +++ b/gnu/packages/virtualization.scm @@ -184,6 +184,9 @@ ;; Delete ppc64 OpenBIOS. TODO: Remove sparc32 and sparc64 too ;; once they are supported in Guix. (delete-file "openbios-ppc") + ;; Delete riscv64 OpenSBI. TODO: Remove riscv32 when supported + ;; in Guix. + (delete-file "opensbi-riscv64-generic-fw_dynamic.bin") ;; Delete iPXE firmwares. (for-each delete-file (find-files "." "^(efi|pxe)-.*\\.rom$"))) ;; Delete bundled code that we provide externally. @@ -191,6 +194,7 @@ '("dtc" "meson" "roms/ipxe" "roms/openbios" + "roms/opensbi" "roms/seabios" "roms/sgabios")))))) (outputs '("out" "static" "doc")) ;5.3 MiB of HTML docs @@ -206,6 +210,9 @@ (meson (search-input-file %build-inputs "bin/meson")) (openbios (search-input-file %build-inputs "share/qemu/openbios-ppc")) + (opensbi (search-input-file + %build-inputs + "share/qemu/opensbi-riscv64-generic-fw_dynamic.bin")) (seabios (search-input-file %build-inputs "share/qemu/bios.bin")) (sgabios (search-input-file %build-inputs @@ -225,6 +232,7 @@ (dirname seabios) ":" (dirname ipxe) ":" (dirname openbios) ":" + (dirname opensbi) ":" (dirname sgabios)) (string-append "--smbd=" out "/libexec/samba-wrapper") "--disable-debug-info" ;for space considerations @@ -252,6 +260,10 @@ (ipxe-firmwares (find-files ipxe "\\.rom$")) (openbios (search-input-file inputs "share/qemu/openbios-ppc")) + (opensbi-riscv64 + (search-input-file + inputs + "share/qemu/opensbi-riscv64-generic-fw_dynamic.bin")) (allowed-differences ;; Ignore minor differences (addresses etc) in the firmware ;; data tables compared to what the test suite expects. @@ -267,7 +279,7 @@ (for-each (lambda (file) (symlink file (basename file))) (append seabios-firmwares ipxe-firmwares - (list openbios sgabios)))) + (list openbios opensbi-riscv64 sgabios)))) (for-each (lambda (file) (format allowed-differences-whitelist "\"~a\",~%" file)) @@ -385,7 +397,9 @@ (with-directory-excursion (string-append #$output "/share/qemu") (for-each delete-file (append - '("openbios-ppc" "sgabios.bin") + '("openbios-ppc" + "opensbi-riscv64-generic-fw_dynamic.bin" + "sgabios.bin") (find-files "." "^(vga)?bios(-[a-z0-9-]+)?\\.bin$") (find-files "." "^(efi|pxe)-.*\\.rom$")))))) ;; Create a wrapper for Samba. This allows QEMU to use Samba without @@ -430,6 +444,7 @@ exec smbd $@"))) mesa ncurses openbios-qemu-ppc + opensbi-qemu ;; ("pciutils" ,pciutils) pixman pulseaudio From 2967abf1a2ae6787842c04752949f3c214da9338 Mon Sep 17 00:00:00 2001 From: Timo Wilken Date: Sun, 18 Dec 2022 18:19:47 +0100 Subject: [PATCH 734/790] services: wireguard: Allow specifying pre-shared keys. * gnu/services/vpn.scm ()[preshared-key]: New field. * doc/guix.texi (VPN Services): Document it. Signed-off-by: Mathieu Othacehe --- doc/guix.texi | 4 ++++ gnu/services/vpn.scm | 15 ++++++++++++++- 2 files changed, 18 insertions(+), 1 deletion(-) diff --git a/doc/guix.texi b/doc/guix.texi index e25692fd27..c5ae350a47 100644 --- a/doc/guix.texi +++ b/doc/guix.texi @@ -31770,6 +31770,10 @@ The optional endpoint for the peer, such as @item @code{public-key} The peer public-key represented as a base64 string. +@item @code{preshared-key} (default: @code{#f}) +An optional pre-shared key file for this peer. The given file will not +be autogenerated. + @item @code{allowed-ips} A list of IP addresses from which incoming traffic for this peer is allowed and to which incoming traffic for this peer is directed. diff --git a/gnu/services/vpn.scm b/gnu/services/vpn.scm index 7b3bb8903c..4103f89ecf 100644 --- a/gnu/services/vpn.scm +++ b/gnu/services/vpn.scm @@ -10,6 +10,7 @@ ;;; Copyright © 2021 jgart ;;; Copyright © 2021 Nathan Dehnel ;;; Copyright © 2022 Cameron V Chaparro +;;; Copyright © 2022 Timo Wilken ;;; ;;; This file is part of GNU Guix. ;;; @@ -61,6 +62,7 @@ wireguard-peer-endpoint wireguard-peer-allowed-ips wireguard-peer-public-key + wireguard-peer-preshared-key wireguard-peer-keep-alive wireguard-configuration @@ -709,6 +711,8 @@ strongSwan."))) (endpoint wireguard-peer-endpoint (default #f)) ;string (public-key wireguard-peer-public-key) ;string + (preshared-key wireguard-peer-preshared-key + (default #f)) ;string (allowed-ips wireguard-peer-allowed-ips) ;list of strings (keep-alive wireguard-peer-keep-alive (default #f))) ;integer @@ -762,10 +766,18 @@ AllowedIPs = ~a (format #f "PersistentKeepalive = ~a\n" keep-alive) "\n")))) + (define (peers->preshared-keys peer keys) + (let ((public-key (wireguard-peer-public-key peer)) + (preshared-key (wireguard-peer-preshared-key peer))) + (if preshared-key + (cons* public-key preshared-key keys) + keys))) + (match-record config (wireguard interface addresses port private-key peers dns pre-up post-up pre-down post-down table) (let* ((config-file (string-append interface ".conf")) + (peer-keys (fold peers->preshared-keys (list) peers)) (peers (map peer->config peers)) (config (computed-file @@ -780,7 +792,7 @@ AllowedIPs = ~a Address = ~a ~a ~a -PostUp = ~a set %i private-key ~a +PostUp = ~a set %i private-key ~a~{ peer ~a preshared-key ~a~} ~a ~a ~a @@ -800,6 +812,7 @@ PostUp = ~a set %i private-key ~a "\n")) #$(file-append wireguard "/bin/wg") #$private-key + '#$peer-keys #$(if (null? post-up) "" (string-join From 34feda1defbfbc23999489d3b9e1fa6bffbedd3b Mon Sep 17 00:00:00 2001 From: "Artyom V. Poptsov" Date: Sun, 18 Dec 2022 21:54:22 +0300 Subject: [PATCH 735/790] gnu: guile-png: Update to 0.3.0. * gnu/packages/guile-xyz.scm (guile-png): Update to 0.3.0. [arguments]: Patch tests to silence Guile-SMC logs. Signed-off-by: Mathieu Othacehe --- gnu/packages/guile-xyz.scm | 17 ++++++++++++++--- 1 file changed, 14 insertions(+), 3 deletions(-) diff --git a/gnu/packages/guile-xyz.scm b/gnu/packages/guile-xyz.scm index 3fa75b26d1..50872b3f36 100644 --- a/gnu/packages/guile-xyz.scm +++ b/gnu/packages/guile-xyz.scm @@ -3726,7 +3726,7 @@ debugging code.") (define-public guile-png (package (name "guile-png") - (version "0.2.0") + (version "0.3.0") (source (origin (method git-fetch) (uri (git-reference @@ -3735,10 +3735,21 @@ debugging code.") (file-name (string-append name "-" version "-checkout")) (sha256 (base32 - "1nk81z2cf9fsyppq5ly0yjw7yvdk5qraf71in7ayzdkngphhfgfx")))) + "1lv2cjzgrr0yshqng96l6bnn8pjmljv8qcn4w3wldh97ns7qigds")))) (build-system gnu-build-system) (arguments - `(#:make-flags '("GUILE_AUTO_COMPILE=0"))) ;to prevent guild warnings + `(#:make-flags '("GUILE_AUTO_COMPILE=0") ;to prevent guild warnings + #:phases + (modify-phases %standard-phases + ;; Guile-PNG tries to log parser messages to the syslog which is not + ;; available during the build. + (add-after 'unpack 'fix-tests + (lambda* (#:key inputs outputs #:allow-other-keys) + (substitute* "tests/graphics.scm" + ((" \\(png graphics\\)\\)") + (string-append " (png graphics)\n" + " (png fsm context))\n" + "(log-clear-handlers!)")))))))) (native-inputs (list autoconf automake pkg-config texinfo)) (inputs (list bash-minimal guile-3.0 guile-lib guile-zlib)) (propagated-inputs (list guile-smc)) From 40cdf888925a2285a33f2e0bb39f2ccc1323a130 Mon Sep 17 00:00:00 2001 From: Michael Rohleder Date: Fri, 16 Dec 2022 12:05:04 +0100 Subject: [PATCH 736/790] gnu: vcsh: Update to 2.0.5. * gnu/packages/version-control.scm (vcsh): Update to 2.0.5. [native-inputs]: Remove which. Add autoconf, automake, ronn-ng, perl, perl-test-harness, perl-shell-command, perl-test-most, pkg-config. [inputs]: Remove perl, perl-test-harness, perl-shell-command, perl-test-most. [arguments]: Remove phase install-bash-completion. Add phase fix-version-gen. Remove deletion of configure and build phases. Signed-off-by: Mathieu Othacehe --- gnu/packages/version-control.scm | 33 ++++++++++++++++++-------------- 1 file changed, 19 insertions(+), 14 deletions(-) diff --git a/gnu/packages/version-control.scm b/gnu/packages/version-control.scm index 5da93fa0ce..5a5e4eb7a4 100644 --- a/gnu/packages/version-control.scm +++ b/gnu/packages/version-control.scm @@ -1408,7 +1408,7 @@ manipulate them in various ways.") (define-public vcsh (package (name "vcsh") - (version "1.20190621-4") + (version "2.0.5") (source (origin (method git-fetch) @@ -1417,25 +1417,30 @@ manipulate them in various ways.") (commit (string-append "v" version)))) (file-name (git-file-name name version)) (sha256 - (base32 "1gx5nbqyprgy6picns5hxky3lyzkqfq3xhm614f0wcdi58xrsdh0")))) + (base32 "15lb09c2q261p1pp5r7j9k8389ybrd2q19xhnp1nnha6gs78i4wq")))) (build-system gnu-build-system) (native-inputs - (list which)) + (list autoconf + automake + ;; for man page + ronn-ng + ;; for tests + perl + perl-test-harness + perl-shell-command + perl-test-most + ;; for bash-completion + pkg-config)) (inputs - (list git perl perl-test-harness perl-shell-command perl-test-most)) + (list git)) (arguments '(#:phases (modify-phases %standard-phases - (delete 'configure) - (delete 'build) - (add-after 'install 'install-bash-completion - ;; As of 1.20190621, zsh completion is installed by default but bash - ;; completion is not. Do so manually. - (lambda* (#:key outputs #:allow-other-keys) - (let* ((out (assoc-ref outputs "out")) - (completions (string-append out "/etc/bash_completion.d"))) - (mkdir-p completions) - (copy-file "_vcsh_bash" (string-append completions "/vcsh")))))) + (add-before 'bootstrap 'fix-version-gen + (lambda _ + (call-with-output-file ".tarball-version" + (lambda (port) + (display version port)))))) #:make-flags (list (string-append "PREFIX=" (assoc-ref %outputs "out"))) #:test-target "test")) From cb823181d34119971ef76c2f517bfb28ddcc5ea0 Mon Sep 17 00:00:00 2001 From: Michael Rohleder Date: Fri, 16 Dec 2022 12:40:30 +0100 Subject: [PATCH 737/790] gnu: xfce4-taskmanager: Update to 1.5.5. * gnu/packages/xfce.scm (xfce4-taskmanager): Update to 1.5.5. [inputs]: Add libxfce4ui. Signed-off-by: Mathieu Othacehe --- gnu/packages/xfce.scm | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/gnu/packages/xfce.scm b/gnu/packages/xfce.scm index 720a36e3b9..418d13acb1 100644 --- a/gnu/packages/xfce.scm +++ b/gnu/packages/xfce.scm @@ -1174,7 +1174,7 @@ the desktop wallpaper.") (define-public xfce4-taskmanager (package (name "xfce4-taskmanager") - (version "1.4.2") + (version "1.5.5") (source (origin (method url-fetch) (uri (string-append "https://archive.xfce.org/src/apps/" @@ -1182,7 +1182,7 @@ the desktop wallpaper.") "xfce4-taskmanager-" version ".tar.bz2")) (sha256 (base32 - "1ya81si7xhqqbbc9lfcjg2i1pi1qdfw1pnjry7kf95f1w50244nd")))) + "1rcaalqv6sdsnc6ick8fifgkqcf2xiflw9yk5szqn2qs4jx02kzn")))) (build-system gnu-build-system) (native-inputs (list intltool pkg-config)) @@ -1190,6 +1190,7 @@ the desktop wallpaper.") (list libwnck libxmu gtk+ + libxfce4ui ;; FIXME: Remove libxext and libxt when libxmu propagates them. libxext libxt)) From d93ab41288423403583d0f01cd106992a1ebed19 Mon Sep 17 00:00:00 2001 From: Michael Rohleder Date: Fri, 16 Dec 2022 12:44:02 +0100 Subject: [PATCH 738/790] gnu: xfce4-notifyd: Update to 0.6.5. * gnu/packages/xfce.scm (xfce4-notifyd): Update to 0.6.5. Signed-off-by: Mathieu Othacehe --- gnu/packages/xfce.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/xfce.scm b/gnu/packages/xfce.scm index 418d13acb1..c91355b953 100644 --- a/gnu/packages/xfce.scm +++ b/gnu/packages/xfce.scm @@ -1234,7 +1234,7 @@ several different time zones.") (define-public xfce4-notifyd (package (name "xfce4-notifyd") - (version "0.6.4") + (version "0.6.5") (source (origin (method url-fetch) (uri (string-append "https://archive.xfce.org/src/apps/" @@ -1242,7 +1242,7 @@ several different time zones.") name "-" version ".tar.bz2")) (sha256 (base32 - "1xi0j4qk8hhcd3xj4wvzs170n2010z0bv8w1mm53g5gqj7q7ikhf")))) + "0425pfp0y17daw77q39vi48lkw3j5yj4724i3hin1rq5k7j30wav")))) (build-system glib-or-gtk-build-system) (native-inputs (list intltool pkg-config)) From 333f359f7a3e5abf633d61629d266cd90309fe87 Mon Sep 17 00:00:00 2001 From: Michael Rohleder Date: Fri, 16 Dec 2022 12:48:35 +0100 Subject: [PATCH 739/790] gnu: ristretto: Update to 0.12.4. * gnu/packages/xfce.scm (ristretto): Update to 0.12.4. Signed-off-by: Mathieu Othacehe --- gnu/packages/xfce.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/xfce.scm b/gnu/packages/xfce.scm index c91355b953..a00f701ab0 100644 --- a/gnu/packages/xfce.scm +++ b/gnu/packages/xfce.scm @@ -1146,7 +1146,7 @@ inhibit interface which allows applications to prevent automatic sleep.") (define-public ristretto (package (name "ristretto") - (version "0.12.3") + (version "0.12.4") (source (origin (method url-fetch) (uri (string-append "https://archive.xfce.org/src/apps/ristretto/" @@ -1154,7 +1154,7 @@ inhibit interface which allows applications to prevent automatic sleep.") "ristretto-" version ".tar.bz2")) (sha256 (base32 - "0gizrn49ayamb1sqfxi3mdxas9dz4dw1sv3iyji718az48hp13w6")))) + "0c3rx02bk74fip7ishdxnbn0l9f48qbiglckzclz7v758fbmq074")))) (build-system gnu-build-system) (native-inputs (list intltool desktop-file-utils From 91bcc26b1c97d440c203ea9e258ca56a89377bc8 Mon Sep 17 00:00:00 2001 From: Michael Rohleder Date: Fri, 16 Dec 2022 10:42:04 +0100 Subject: [PATCH 740/790] gnu: hstr: Update to 2.6. * gnu/packages/shellutils.scm (hstr): Update to 2.6. Signed-off-by: Mathieu Othacehe --- gnu/packages/shellutils.scm | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/gnu/packages/shellutils.scm b/gnu/packages/shellutils.scm index b1c1373376..a192bd16f7 100644 --- a/gnu/packages/shellutils.scm +++ b/gnu/packages/shellutils.scm @@ -6,7 +6,7 @@ ;;; Copyright © 2018, 2020 Tobias Geerinckx-Rice ;;; Copyright © 2018 Benjamin Slade ;;; Copyright © 2019 Collin J. Doering -;;; Copyright © 2020 Michael Rohleder +;;; Copyright © 2020, 2022 Michael Rohleder ;;; Copyright © 2020 aecepoglu ;;; Copyright © 2020 Dion Mendel ;;; Copyright © 2021 Brice Waegeneire @@ -519,7 +519,7 @@ below the current cursor position, scrolling the screen if necessary.") (define-public hstr (package (name "hstr") - (version "2.5") + (version "2.6") (source (origin (method git-fetch) (uri (git-reference @@ -528,7 +528,7 @@ below the current cursor position, scrolling the screen if necessary.") (file-name (git-file-name name version)) (sha256 (base32 - "0xg10jyiq12bcygi6aa9qq9pki7bipdsvsza037p2iqix19jg0x8")))) + "1iqvqm4mirx7imwwmz4blxbsr215lcgbw3h31ssbs3fk54hq7xn9")))) (build-system gnu-build-system) (arguments `(#:phases From 10a661c8c86d17b72669a71099bad101273d3e4d Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Sun, 25 Dec 2022 09:54:42 +0200 Subject: [PATCH 741/790] gnu: syslinux: Honor #:tests? flag. * gnu/packages/bootloaders.scm (syslinux)[arguments]: Adjust custom 'check phase to honor the #:tests? flag. --- gnu/packages/bootloaders.scm | 13 +++++++------ 1 file changed, 7 insertions(+), 6 deletions(-) diff --git a/gnu/packages/bootloaders.scm b/gnu/packages/bootloaders.scm index 57705cf596..89f051f337 100644 --- a/gnu/packages/bootloaders.scm +++ b/gnu/packages/bootloaders.scm @@ -537,12 +537,13 @@ The SUBDIR argument defaults to \"efi/Guix\", as it is also the case for (lambda _ (invoke "chmod" "a+w" "utils/isohybrid.in"))) (replace 'check - (lambda _ - (setenv "CC" "gcc") - (substitute* "tests/unittest/include/unittest/unittest.h" - ;; Don't look up headers under /usr. - (("/usr/include/") "")) - (invoke "make" "unittest")))))) + (lambda* (#:key tests? #:allow-other-keys) + (when tests? + (setenv "CC" "gcc") + (substitute* "tests/unittest/include/unittest/unittest.h" + ;; Don't look up headers under /usr. + (("/usr/include/") "")) + (invoke "make" "unittest"))))))) (home-page "https://www.syslinux.org") (synopsis "Lightweight Linux bootloader") (description "Syslinux is a lightweight Linux bootloader.") From c408b9042f52ab327fede0b58da7ad0ec58b9aa4 Mon Sep 17 00:00:00 2001 From: jgart Date: Sun, 25 Dec 2022 10:11:47 -0600 Subject: [PATCH 742/790] gnu: Add emacs-snow. * gnu/packages/emacs-xyz.scm (emacs-snow): New variable. Signed-off-by: Nicolas Goaziou --- gnu/packages/emacs-xyz.scm | 23 +++++++++++++++++++++++ 1 file changed, 23 insertions(+) diff --git a/gnu/packages/emacs-xyz.scm b/gnu/packages/emacs-xyz.scm index 8fec7b058f..c8b27d6608 100644 --- a/gnu/packages/emacs-xyz.scm +++ b/gnu/packages/emacs-xyz.scm @@ -901,6 +901,29 @@ of the segments available in that package using icons from information in the mode line.") (license license:expat))) +(define-public emacs-snow + (let ((commit "35ea06f19047ac99eaff9663cb035491c4a13e07") + (revision "0")) + (package + (name "emacs-snow") + (version (git-version "0" revision commit)) + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/alphapapa/snow.el") + (commit commit))) + (file-name (git-file-name name version)) + (sha256 + (base32 "1pcqvg70r1k73k3jxgz5qzwqsvwjnwvpfrbjf4b54smglz2nvz19")))) + (build-system emacs-build-system) + (home-page "https://github.com/alphapapa/snow.el/") + (synopsis "Let it snow in Emacs") + (description "This package adds a command @code{snow} that displays +a buffer in which it snows. The storm varies in intensity, a gentle breeze +blows at times, and snow accumulates on the terrain in the scene.") + (license license:gpl3+)))) + (define-public emacs-spongebob (let ((commit "ae8ae6ba0dc57b7357ba87ff0609d27c4a0a5f51") (revision "0")) From 3fe33baed6d2620c122899d355b8eac9d8f99f8e Mon Sep 17 00:00:00 2001 From: Nicolas Goaziou Date: Sun, 25 Dec 2022 22:49:49 +0100 Subject: [PATCH 743/790] gnu: emacs-ement: Update to 0.5.2. * gnu/packages/emacs-xyz.scm (emacs-ement): Update to 0.5.2. --- gnu/packages/emacs-xyz.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/emacs-xyz.scm b/gnu/packages/emacs-xyz.scm index c8b27d6608..548695bedf 100644 --- a/gnu/packages/emacs-xyz.scm +++ b/gnu/packages/emacs-xyz.scm @@ -17946,7 +17946,7 @@ which avoids some of the issues with using Emacs’s built-in Url library.") (define-public emacs-ement (package (name "emacs-ement") - (version "0.5.1") + (version "0.5.2") (source (origin (method git-fetch) @@ -17955,7 +17955,7 @@ which avoids some of the issues with using Emacs’s built-in Url library.") (commit (string-append "v" version)))) (file-name (git-file-name name version)) (sha256 - (base32 "17spz9z7anzgqgcddsv5rqr6qa6yada3yrvz81z0knbpls5qqp6a")))) + (base32 "1gc5b0mzh4a4xxbzfgjx5m830rymnf93qn2k5jvj7kmwnh15w89h")))) (build-system emacs-build-system) (arguments `(#:emacs ,emacs)) ;need libxml support From 2b101bf9e70adc9fff81d13e441bcc0bb12c90a3 Mon Sep 17 00:00:00 2001 From: Nicolas Goaziou Date: Sun, 25 Dec 2022 22:56:16 +0100 Subject: [PATCH 744/790] gnu: emacs-circadian: Update to 0.3.3. * gnu/packages/emacs-xyz.scm (emacs-circadian): Update to 0.3.3. [arguments]<#:test-command>: Update test procedure. [native-inputs]: Remove EMACS-ERT-RUNNER. --- gnu/packages/emacs-xyz.scm | 11 +++++++---- 1 file changed, 7 insertions(+), 4 deletions(-) diff --git a/gnu/packages/emacs-xyz.scm b/gnu/packages/emacs-xyz.scm index 548695bedf..fb4c9b70f9 100644 --- a/gnu/packages/emacs-xyz.scm +++ b/gnu/packages/emacs-xyz.scm @@ -20466,7 +20466,7 @@ timestamps by providing a @code{ts} struct.") (define-public emacs-circadian (package (name "emacs-circadian") - (version "0.3.2") + (version "0.3.3") (source (origin (method git-fetch) @@ -20475,14 +20475,17 @@ timestamps by providing a @code{ts} struct.") (commit version))) (file-name (git-file-name name version)) (sha256 - (base32 "0wpsykmai3idz0bgfl07hwl9nr4x9sgprvqgw8jln4dz2wf5gdic")))) + (base32 "1hydxhmcchaprfmp08xr6nlksz6y97jbf4mswj69bgdfjfbf22km")))) (arguments (list #:tests? #t - #:test-command #~(list "ert-runner"))) + #:test-command + #~(list "emacs" "--batch" + "-l" "test.el" + "--eval" "(ert-run-tests-batch-and-exit test-order)"))) (build-system emacs-build-system) (native-inputs - (list emacs-el-mock emacs-ert-runner)) + (list emacs-el-mock)) (home-page "https://github.com/guidoschmidt/circadian.el") (synopsis "Theme-switching for Emacs based on daytime") (description "Circadian may reduce eye strain by automatically switching From badad2653f832db2212ce4c159dfd305971fddb3 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ludovic=20Court=C3=A8s?= Date: Mon, 26 Dec 2022 00:06:26 +0100 Subject: [PATCH 745/790] gnu: pipe-viewer: Update to 0.4.4. * gnu/packages/video.scm (pipe-viewer): Update to 0.4.4. --- gnu/packages/video.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/video.scm b/gnu/packages/video.scm index d1d50df304..456376d597 100644 --- a/gnu/packages/video.scm +++ b/gnu/packages/video.scm @@ -1125,7 +1125,7 @@ H.264 (MPEG-4 AVC) video streams.") (define-public pipe-viewer (package (name "pipe-viewer") - (version "0.2.3") + (version "0.4.4") (source (origin (method git-fetch) @@ -1135,7 +1135,7 @@ H.264 (MPEG-4 AVC) video streams.") (commit version))) (file-name (git-file-name name version)) (sha256 - (base32 "0c2v4pj86442sp71ndjmvd2bl1grp6g9ya2ywdaihq1f2djk6jxl")))) + (base32 "0ka5az3aq2khql9nlxnrbkbs7afmp07r2fkx5pvmh6mqnriaimq3")))) (build-system perl-build-system) (arguments `(#:imported-modules From 800b3234fb375276dc023d4ffe24a9150115ddbc Mon Sep 17 00:00:00 2001 From: Yarl Baudig Date: Mon, 5 Dec 2022 21:41:01 +0100 Subject: [PATCH 746/790] shell: Make --help show --system and --list-systems. MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit These options are callable and documented in the manual but not shown by --help. * guix/scripts/shell.scm: Make --help show --system and --list-systems. Signed-off-by: Ludovic Courtès --- guix/scripts/shell.scm | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/guix/scripts/shell.scm b/guix/scripts/shell.scm index 2fc1dc942a..64b5c2e8e9 100644 --- a/guix/scripts/shell.scm +++ b/guix/scripts/shell.scm @@ -20,7 +20,8 @@ #:use-module (guix ui) #:use-module ((guix diagnostics) #:select (location)) #:use-module (guix scripts environment) - #:autoload (guix scripts build) (show-build-options-help) + #:autoload (guix scripts build) (show-build-options-help + show-native-build-options-help) #:autoload (guix transformations) (options->transformation transformation-option-key? show-transformation-options-help) @@ -76,6 +77,8 @@ interactive shell in that environment.\n")) (newline) (show-build-options-help) (newline) + (show-native-build-options-help) + (newline) (show-transformation-options-help) (newline) (display (G_ " From 58d129c460fec60642b46f3fd32956d4bf7d9296 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?=E5=AE=8B=E6=96=87=E6=AD=A6?= Date: Fri, 9 Dec 2022 14:51:44 +0800 Subject: [PATCH 747/790] teams: Add localization. MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * etc/teams.scm.in (localization): New team. Signed-off-by: Ludovic Courtès --- etc/teams.scm.in | 11 +++++++++++ 1 file changed, 11 insertions(+) diff --git a/etc/teams.scm.in b/etc/teams.scm.in index aa38a3b798..b784821a98 100644 --- a/etc/teams.scm.in +++ b/etc/teams.scm.in @@ -360,6 +360,17 @@ asdf-build-system." "gnu/packages/motti.scm" "guix/build/minetest-build-system.scm"))) +(define-team localization + (team 'localization + #:name "Localization (l10n) team" + #:description + "Localization of your system to specific languages." + #:scope (list "gnu/packages/anthy.scm" + "gnu/packages/fcitx5.scm" + "gnu/packages/fcitx.scm" + "gnu/packages/fonts.scm" + "gnu/packages/ibus.scm"))) + (define-team translations (team 'translations #:name "Translations" From 5f6bd3f92dee29e3463cba24287618214e3d454e Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?=E5=AE=8B=E6=96=87=E6=AD=A6?= Date: Fri, 9 Dec 2022 14:51:45 +0800 Subject: [PATCH 748/790] =?UTF-8?q?teams:=20Add=20=E5=AE=8B=E6=96=87?= =?UTF-8?q?=E6=AD=A6.?= MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * etc/team.scm.in: Add 宋文武. Signed-off-by: Ludovic Courtès --- etc/teams.scm.in | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/etc/teams.scm.in b/etc/teams.scm.in index b784821a98..f42a7f6f28 100644 --- a/etc/teams.scm.in +++ b/etc/teams.scm.in @@ -515,6 +515,10 @@ importer." "rg@raghavgururajan.name") mentors) +(define-member (person "宋文武" + "iyzsong@envs.net") + games localization) + (define (find-team name) (or (hash-ref %teams (string->symbol name)) From bc157ca62b75b7e7563ca9d1c4de89489d79deb8 Mon Sep 17 00:00:00 2001 From: Tobias Kortkamp Date: Fri, 9 Dec 2022 14:13:50 +0100 Subject: [PATCH 749/790] gnu: Add wvkbd. MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * gnu/packages/xdisorg.scm (wvkbd): New variable. Co-authored-by: Ludovic Courtès --- gnu/packages/xdisorg.scm | 51 ++++++++++++++++++++++++++++++++++++++++ 1 file changed, 51 insertions(+) diff --git a/gnu/packages/xdisorg.scm b/gnu/packages/xdisorg.scm index 5c4fd79091..10edfc7379 100644 --- a/gnu/packages/xdisorg.scm +++ b/gnu/packages/xdisorg.scm @@ -56,6 +56,7 @@ ;;; Copyright © 2022 Jai Vetrivelan ;;; Copyright © 2022 Derek Chuank ;;; Copyright © 2022 Wamm K. D. +;;; Copyright © 2022 Tobias Kortkamp ;;; ;;; This file is part of GNU Guix. ;;; @@ -3268,3 +3269,53 @@ light filter or night light.") (description "@code{ydotool} is a Linux command-line tool that simulates keyboard input, mouse actions, etc. programmatically or manually.") (license license:agpl3+))) + +(define-public wvkbd + (package + (name "wvkbd") + (version "0.12") + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://git.sr.ht/~proycon/wvkbd") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "05zl6jhw7pj7w2cd02m3i0zzn1z99kzwh2mlg9h96j5aw1x1lvp6")))) + (build-system gnu-build-system) + (arguments + (list #:tests? #f ;no tests + #:make-flags #~(list (string-append "CC=" + #$(cc-for-target)) + (string-append "PREFIX=" + #$output)) + #:phases #~(modify-phases %standard-phases + (add-after 'unpack 'fix-cross-compile + (lambda _ + (substitute* "Makefile" + (("pkg-config") + #$(pkg-config-for-target))))) + (delete 'configure)))) + (native-inputs (list wayland ;for wayland-scanner + pkg-config)) + (inputs (list libxkbcommon cairo pango harfbuzz wayland)) + (home-page "https://git.sr.ht/~proycon/wvkbd") + (synopsis "On-screen keyboard for wlroots compositors") + (description + "This package provides on-screen keyboard for wlroots compositors with +the following features: + +@itemize +@item Typing, modifier locking, layout switching +@item Positive visual feedback on key presses +@item On-the-fly layout and keymap switching +@item Custom color schemes +@item International layouts (cyrillic, arabic) +@item Emoji support +@item Compose key for character variants (e.g. diacritics) +@item Show/hide keyboard on signals (SIGUSR1 = hide, SIGUSR2 = show, SIGRTMIN = toggle) +@item Automatic portrait/landscape detection and subsequent layout switching +@end itemize") + (license (list license:expat ;3 files under Expat license (see 'LICENSE') + license:gpl3+)))) ;the rest is GPLv3+ From 9369c1ccf47d9bf6f2e28a9454c1c329a2044f19 Mon Sep 17 00:00:00 2001 From: Ivan Vilata i Balaguer Date: Mon, 12 Dec 2022 20:27:37 +0100 Subject: [PATCH 750/790] gnu: services: Fix bluetooth-service docstring. MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * gnu/services/desktop.scm (bluetooth-service): Sync docstring with info, remove mention to group not really needed to access D-Bus service. * doc/guix.texi (Desktop Services): Also remove mention to group here. Signed-off-by: Ludovic Courtès --- doc/guix.texi | 2 -- gnu/services/desktop.scm | 4 +--- 2 files changed, 1 insertion(+), 5 deletions(-) diff --git a/doc/guix.texi b/doc/guix.texi index c5ae350a47..efd281d9b0 100644 --- a/doc/guix.texi +++ b/doc/guix.texi @@ -23238,8 +23238,6 @@ manages all the Bluetooth devices and provides a number of D-Bus interfaces. When AUTO-ENABLE? is true, the bluetooth controller is powered automatically at boot, which can be useful when using a bluetooth keyboard or mouse. - -Users need to be in the @code{lp} group to access the D-Bus service. @end deffn @deffn {Scheme Variable} bluetooth-service-type diff --git a/gnu/services/desktop.scm b/gnu/services/desktop.scm index ac29e8d38a..9fd77642a1 100644 --- a/gnu/services/desktop.scm +++ b/gnu/services/desktop.scm @@ -838,9 +838,7 @@ Bluetooth devices and provides a number of D-Bus interfaces."))) "Return a service that runs the @command{bluetoothd} daemon, which manages all the Bluetooth devices and provides a number of D-Bus interfaces. When AUTO-ENABLE? is true, the bluetooth controller is powered automatically at -boot. - -Users need to be in the @code{lp} group to access the D-Bus service. +boot, which can be useful when using a bluetooth keyboard or mouse. " (service bluetooth-service-type (bluetooth-configuration From c50cd1bbece27097456242f246f89c053e7cc1a2 Mon Sep 17 00:00:00 2001 From: dan Date: Wed, 9 Nov 2022 04:05:53 +0800 Subject: [PATCH 751/790] images: wsl2: Create XDG_RUNTIME_DIR on first login. * gnu/system/images/wsl2.scm (wsl-boot-program): Create XDG_RUNTIME_DIR on first login and set it. Signed-off-by: Mathieu Othacehe --- gnu/system/images/wsl2.scm | 15 +++++++++++++-- 1 file changed, 13 insertions(+), 2 deletions(-) diff --git a/gnu/system/images/wsl2.scm b/gnu/system/images/wsl2.scm index 80c2e775b4..d9aaa1a271 100644 --- a/gnu/system/images/wsl2.scm +++ b/gnu/system/images/wsl2.scm @@ -1,6 +1,7 @@ ;;; GNU Guix --- Functional package management for GNU ;;; Copyright © 2022 Alex Griffin ;;; Copyright © 2022 Mathieu Othacehe +;;; Copyright © 2022 dan ;;; ;;; This file is part of GNU Guix. ;;; @@ -75,7 +76,11 @@ USER." (let* ((pw (getpw #$user)) (shell (passwd:shell pw)) (sudo #+(file-append sudo "/bin/sudo")) - (args (cdr (command-line)))) + (args (cdr (command-line))) + (uid (passwd:uid pw)) + (gid (passwd:gid pw)) + (runtime-dir (string-append "/run/user/" + (number->string uid)))) ;; Save the value of $PATH set by WSL. Useful for finding ;; Windows binaries to run with WSL's binfmt interop. (setenv "WSLPATH" (getenv "PATH")) @@ -88,9 +93,15 @@ USER." MS_REMOUNT #:update-mtab? #f) + ;; Create XDG_RUNTIME_DIR for the login user. + (unless (file-exists? runtime-dir) + (mkdir runtime-dir) + (chown runtime-dir uid gid)) + (setenv "XDG_RUNTIME_DIR" runtime-dir) + ;; Start login shell as user. (apply execl sudo "sudo" - "--preserve-env=WSLPATH" + "--preserve-env=WSLPATH,XDG_RUNTIME_DIR" "-u" #$user "--" shell "-l" args)))))) From a274a6a1acb99738f02de7b226e6a0d3883ec353 Mon Sep 17 00:00:00 2001 From: Hartmut Goebel Date: Sat, 27 Aug 2022 13:05:33 +0200 Subject: [PATCH 752/790] upstream-updater: Rename record field. MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit The next commits will make the functions, which are currently importing the latest version of a package, change into importing the latest or a given version of the package (for those updaters supporting specifying a version). Thus the name ‘latest‘ is no longer appropriate. * guix/upstream.scm (upstream-updater) Rename field [latest] to [import]. (lookup-updater, package-latest-release) Adjust fieldname accordingly. * guix/gnu-maintenance.scm (%gnu-updater, %gnu-ftp-updater, %savannah-updater, %sourceforge-updater, %xorg-updater, %kernel.org-updater, %generic-html-updater), guix/import/cpan.scm (%cpan-updater), guix/import/cran.scm (%cran-updater, %bioconductor-updater), guix/import/crate.scm (%crate-updater), guix/import/egg.scm (%egg-updater), guix/import/elpa.scm (%elpa-updater), guix/import/gem.scm (%gem-updater), guix/import/git.scm (%generic-git-updater), guix/import/github.scm (%github-updater), guix/import/gnome.scm (%gnome-updater), guix/import/hackage.scm (%hackage-updater), guix/import/hexpm.scm (%hexpm-updater), guix/import/kde.scm (%kde-updater), guix/import/launchpad.scm (%launchpad-updater), guix/import/minetest.scm (%minetest-updater), guix/import/opam.scm (%opam-updater), guix/import/pypi.scm (%pypi-updater), guix/import/stackage.scm (%stackage-updater), tests/import-github.scm (found-sexp) tests/transformations.scm ("options->transformation, with-latest"): Adjust fieldname accordingly. --- guix/gnu-maintenance.scm | 14 +++++++------- guix/import/cpan.scm | 2 +- guix/import/cran.scm | 4 ++-- guix/import/crate.scm | 2 +- guix/import/egg.scm | 2 +- guix/import/elpa.scm | 2 +- guix/import/gem.scm | 2 +- guix/import/git.scm | 2 +- guix/import/github.scm | 2 +- guix/import/gnome.scm | 2 +- guix/import/hackage.scm | 2 +- guix/import/hexpm.scm | 2 +- guix/import/kde.scm | 2 +- guix/import/launchpad.scm | 2 +- guix/import/minetest.scm | 2 +- guix/import/opam.scm | 2 +- guix/import/pypi.scm | 2 +- guix/import/stackage.scm | 2 +- guix/upstream.scm | 10 +++++----- tests/import-github.scm | 2 +- tests/transformations.scm | 8 ++++---- 21 files changed, 35 insertions(+), 35 deletions(-) diff --git a/guix/gnu-maintenance.scm b/guix/gnu-maintenance.scm index 2881a6be43..3067ee18b3 100644 --- a/guix/gnu-maintenance.scm +++ b/guix/gnu-maintenance.scm @@ -848,7 +848,7 @@ the directory containing its source tarball." (name 'gnu) (description "Updater for GNU packages") (pred gnu-hosted?) - (latest latest-gnu-release))) + (import latest-gnu-release))) (define %gnu-ftp-updater ;; This is for GNU packages taken from alternate locations, such as @@ -859,41 +859,41 @@ the directory containing its source tarball." (pred (lambda (package) (and (not (gnu-hosted? package)) (pure-gnu-package? package)))) - (latest latest-release*))) + (import latest-release*))) (define %savannah-updater (upstream-updater (name 'savannah) (description "Updater for packages hosted on savannah.gnu.org") (pred (url-prefix-predicate "mirror://savannah/")) - (latest latest-savannah-release))) + (import latest-savannah-release))) (define %sourceforge-updater (upstream-updater (name 'sourceforge) (description "Updater for packages hosted on sourceforge.net") (pred (url-prefix-predicate "mirror://sourceforge/")) - (latest latest-sourceforge-release))) + (import latest-sourceforge-release))) (define %xorg-updater (upstream-updater (name 'xorg) (description "Updater for X.org packages") (pred (url-prefix-predicate "mirror://xorg/")) - (latest latest-xorg-release))) + (import latest-xorg-release))) (define %kernel.org-updater (upstream-updater (name 'kernel.org) (description "Updater for packages hosted on kernel.org") (pred (url-prefix-predicate "mirror://kernel.org/")) - (latest latest-kernel.org-release))) + (import latest-kernel.org-release))) (define %generic-html-updater (upstream-updater (name 'generic-html) (description "Updater that crawls HTML pages.") (pred html-updatable-package?) - (latest latest-html-updatable-release))) + (import latest-html-updatable-release))) ;;; gnu-maintenance.scm ends here diff --git a/guix/import/cpan.scm b/guix/import/cpan.scm index 87abe9c2f1..cb2d3dd410 100644 --- a/guix/import/cpan.scm +++ b/guix/import/cpan.scm @@ -358,4 +358,4 @@ in RELEASE, a record." (name 'cpan) (description "Updater for CPAN packages") (pred cpan-package?) - (latest latest-release))) + (import latest-release))) diff --git a/guix/import/cran.scm b/guix/import/cran.scm index 48fbc1dccb..473d8c4f5b 100644 --- a/guix/import/cran.scm +++ b/guix/import/cran.scm @@ -776,13 +776,13 @@ s-expression corresponding to that package, or #f on failure." (name 'cran) (description "Updater for CRAN packages") (pred cran-package?) - (latest latest-cran-release))) + (import latest-cran-release))) (define %bioconductor-updater (upstream-updater (name 'bioconductor) (description "Updater for Bioconductor packages") (pred bioconductor-package?) - (latest latest-bioconductor-release))) + (import latest-bioconductor-release))) ;;; cran.scm ends here diff --git a/guix/import/crate.scm b/guix/import/crate.scm index c76d7e9c1a..51bfcd7bed 100644 --- a/guix/import/crate.scm +++ b/guix/import/crate.scm @@ -370,5 +370,5 @@ look up the development dependencs for the given crate." (name 'crate) (description "Updater for crates.io packages") (pred crate-package?) - (latest latest-release))) + (import latest-release))) diff --git a/guix/import/egg.scm b/guix/import/egg.scm index 0d6d72c465..2ad48c3399 100644 --- a/guix/import/egg.scm +++ b/guix/import/egg.scm @@ -348,6 +348,6 @@ not work." (name 'egg) (description "Updater for CHICKEN egg packages") (pred egg-package?) - (latest latest-release))) + (import latest-release))) ;;; egg.scm ends here diff --git a/guix/import/elpa.scm b/guix/import/elpa.scm index 9399f45ebc..1dbdff9391 100644 --- a/guix/import/elpa.scm +++ b/guix/import/elpa.scm @@ -444,7 +444,7 @@ type ''." (name 'elpa) (description "Updater for ELPA packages") (pred package-from-elpa-repository?) - (latest latest-release))) + (import latest-release))) (define elpa-guix-name (cut guix-name "emacs-" <>)) diff --git a/guix/import/gem.scm b/guix/import/gem.scm index ad1343bff4..1c6c55baa6 100644 --- a/guix/import/gem.scm +++ b/guix/import/gem.scm @@ -189,7 +189,7 @@ package on RubyGems." (name 'gem) (description "Updater for RubyGem packages") (pred gem-package?) - (latest latest-release))) + (import latest-release))) (define* (gem-recursive-import package-name #:optional version) (recursive-import package-name diff --git a/guix/import/git.scm b/guix/import/git.scm index 4cf404677c..bb5ba4d97e 100644 --- a/guix/import/git.scm +++ b/guix/import/git.scm @@ -226,4 +226,4 @@ tag, or #false and #false if the latest version could not be determined." (name 'generic-git) (description "Updater for packages hosted on Git repositories") (pred git-package?) - (latest latest-git-release))) + (import latest-git-release))) diff --git a/guix/import/github.scm b/guix/import/github.scm index e1a1af7133..ac6ef06eda 100644 --- a/guix/import/github.scm +++ b/guix/import/github.scm @@ -330,6 +330,6 @@ releases." (name 'github) (description "Updater for GitHub packages") (pred github-package?) - (latest latest-release))) + (import latest-release))) diff --git a/guix/import/gnome.scm b/guix/import/gnome.scm index 9d8cd8ec76..09c6dbbd0d 100644 --- a/guix/import/gnome.scm +++ b/guix/import/gnome.scm @@ -130,4 +130,4 @@ https://discourse.gnome.org/t/new-gnome-versioning-scheme/4235" (name 'gnome) (description "Updater for GNOME packages") (pred (url-prefix-predicate "mirror://gnome/")) - (latest latest-gnome-release))) + (import latest-gnome-release))) diff --git a/guix/import/hackage.scm b/guix/import/hackage.scm index 878a7d2f9c..d56f52a221 100644 --- a/guix/import/hackage.scm +++ b/guix/import/hackage.scm @@ -381,6 +381,6 @@ respectively." (name 'hackage) (description "Updater for Hackage packages") (pred hackage-package?) - (latest latest-release))) + (import latest-release))) ;;; cabal.scm ends here diff --git a/guix/import/hexpm.scm b/guix/import/hexpm.scm index 2a7a9f3d82..3b63837393 100644 --- a/guix/import/hexpm.scm +++ b/guix/import/hexpm.scm @@ -344,4 +344,4 @@ latest version of PACKAGE-NAME." (name 'hexpm) (description "Updater for hex.pm packages") (pred (url-prefix-predicate hexpm-package-url)) - (latest latest-release))) + (import latest-release))) diff --git a/guix/import/kde.scm b/guix/import/kde.scm index 6873418d62..510d823a4f 100644 --- a/guix/import/kde.scm +++ b/guix/import/kde.scm @@ -187,4 +187,4 @@ not be determined." (name 'kde) (description "Updater for KDE packages") (pred (url-prefix-predicate "mirror://kde/")) - (latest latest-kde-release))) + (import latest-kde-release))) diff --git a/guix/import/launchpad.scm b/guix/import/launchpad.scm index aeb447b0a5..b7e0295c4e 100644 --- a/guix/import/launchpad.scm +++ b/guix/import/launchpad.scm @@ -145,4 +145,4 @@ for example, 'linuxdcpp'. Return #f if there is no releases." (name 'launchpad) (description "Updater for Launchpad packages") (pred launchpad-package?) - (latest latest-release))) + (import latest-release))) diff --git a/guix/import/minetest.scm b/guix/import/minetest.scm index 43cfb533e2..6581013215 100644 --- a/guix/import/minetest.scm +++ b/guix/import/minetest.scm @@ -513,4 +513,4 @@ or #false if the latest release couldn't be determined." (name 'minetest) (description "Updater for Minetest packages on ContentDB") (pred minetest-package?) - (latest latest-minetest-release))) + (import latest-minetest-release))) diff --git a/guix/import/opam.scm b/guix/import/opam.scm index b4b5a6eaad..8a5aa4d8c6 100644 --- a/guix/import/opam.scm +++ b/guix/import/opam.scm @@ -435,4 +435,4 @@ package in OPAM." (name 'opam) (description "Updater for OPAM packages") (pred opam-package?) - (latest latest-release))) + (import latest-release))) diff --git a/guix/import/pypi.scm b/guix/import/pypi.scm index 4760fc3dae..3e3e949283 100644 --- a/guix/import/pypi.scm +++ b/guix/import/pypi.scm @@ -583,4 +583,4 @@ source. To build it from source, refer to the upstream repository at (name 'pypi) (description "Updater for PyPI packages") (pred pypi-package?) - (latest latest-release))) + (import latest-release))) diff --git a/guix/import/stackage.scm b/guix/import/stackage.scm index 49be982a7f..af9809304f 100644 --- a/guix/import/stackage.scm +++ b/guix/import/stackage.scm @@ -175,6 +175,6 @@ PACKAGE or #f if the package is not included in the Stackage LTS release." (name 'stackage) (description "Updater for Stackage LTS packages") (pred stackage-lts-package?) - (latest latest-lts-release))) + (import latest-lts-release))) ;;; stackage.scm ends here diff --git a/guix/upstream.scm b/guix/upstream.scm index 32736940aa..3b576898ec 100644 --- a/guix/upstream.scm +++ b/guix/upstream.scm @@ -66,7 +66,7 @@ upstream-updater-name upstream-updater-description upstream-updater-predicate - upstream-updater-latest + upstream-updater-import upstream-input-change? upstream-input-change-name @@ -241,7 +241,7 @@ correspond to the same version." (name upstream-updater-name) (description upstream-updater-description) (pred upstream-updater-predicate) - (latest upstream-updater-latest)) + (import upstream-updater-import)) (define (importer-modules) "Return the list of importer modules." @@ -272,7 +272,7 @@ correspond to the same version." "Return an updater among UPDATERS that matches PACKAGE, or #f if none of them matches." (find (match-lambda - (($ name description pred latest) + (($ name description pred import) (pred package))) updaters)) @@ -285,9 +285,9 @@ them until one of them returns an upstream source. It is the caller's responsibility to ensure that the returned source is newer than the current one." (any (match-lambda - (($ name description pred latest) + (($ name description pred import) (and (pred package) - (latest package)))) + (import package)))) updaters)) (define* (package-latest-release* package diff --git a/tests/import-github.scm b/tests/import-github.scm index 4d3f8cfc7e..5100296540 100644 --- a/tests/import-github.scm +++ b/tests/import-github.scm @@ -92,7 +92,7 @@ (define* (found-sexp old-version old-commit tags releases) (and=> (call-with-releases (lambda () - ((upstream-updater-latest %github-updater) + ((upstream-updater-import %github-updater) (example-package old-version old-commit))) tags releases) upstream-source->sexp)) diff --git a/tests/transformations.scm b/tests/transformations.scm index 47b1fc650d..5c136e1d48 100644 --- a/tests/transformations.scm +++ b/tests/transformations.scm @@ -488,10 +488,10 @@ (name 'dummy) (pred (const #t)) (description "") - (latest (const (upstream-source - (package "foo") - (version "42.0") - (urls '("http://example.org"))))))))) + (import (const (upstream-source + (package "foo") + (version "42.0") + (urls '("http://example.org"))))))))) (let* ((p (dummy-package "foo" (version "1.0"))) (t (options->transformation `((with-latest . "foo"))))) From 9500c11c8bf4e75894bfe67f839ffdbbf219ae2b Mon Sep 17 00:00:00 2001 From: Hartmut Goebel Date: Fri, 24 Jun 2022 21:27:40 +0200 Subject: [PATCH 753/790] import: cpan: Remove unused exports. * guix/import/cpan.scm (#:export): Remove unused exports. --- guix/import/cpan.scm | 21 +-------------------- 1 file changed, 1 insertion(+), 20 deletions(-) diff --git a/guix/import/cpan.scm b/guix/import/cpan.scm index cb2d3dd410..a929dc62e3 100644 --- a/guix/import/cpan.scm +++ b/guix/import/cpan.scm @@ -39,26 +39,7 @@ #:use-module (guix packages) #:use-module (guix upstream) #:use-module (guix derivations) - #:export (cpan-dependency? - cpan-dependency-relationship - cpan-dependency-phase - cpan-dependency-module - cpan-dependency-version - - cpan-release? - cpan-release-license - cpan-release-author - cpan-release-version - cpan-release-module - cpan-release-distribution - cpan-release-download-url - cpan-release-abstract - cpan-release-home-page - cpan-release-dependencies - json->cpan-release - - cpan-fetch - cpan->guix-package + #:export (cpan->guix-package metacpan-url->mirror-url %cpan-updater From 21703b5120a1e1c141bcf6114de21944edd944db Mon Sep 17 00:00:00 2001 From: Hartmut Goebel Date: Fri, 24 Jun 2022 22:01:35 +0200 Subject: [PATCH 754/790] import: Issue error-message if version is given. These importer don't support importing a specific version, thus the updater does neither. Issue an error message in case version is given. * guix/import/cpan.scm (latest-release), guix/import/elpa.scm (latest-release), guix/import/hackage.scm (latest-release), guix/import/minetest.scm (latest-minetest-release), guix/import/opam.scm (latest-release): Add #:version argument, issue error if version is given. * guix/import/cran.scm (latest-cran-release): Same. (latest-bioconductor-release) Same. : rename to . * guix/import/stackage.scm (latest-lts-release): For each generated updater, add #:version argument and issue error if version is given. --- guix/import/cpan.scm | 9 ++++++++- guix/import/cran.scm | 19 +++++++++++++++---- guix/import/elpa.scm | 9 ++++++++- guix/import/hackage.scm | 10 +++++++++- guix/import/minetest.scm | 10 +++++++++- guix/import/opam.scm | 9 ++++++++- guix/import/stackage.scm | 8 +++++++- 7 files changed, 64 insertions(+), 10 deletions(-) diff --git a/guix/import/cpan.scm b/guix/import/cpan.scm index a929dc62e3..8972b87080 100644 --- a/guix/import/cpan.scm +++ b/guix/import/cpan.scm @@ -4,6 +4,7 @@ ;;; Copyright © 2016 Alex Sassmannshausen ;;; Copyright © 2017, 2018 Tobias Geerinckx-Rice ;;; Copyright © 2020, 2021 Ludovic Courtès +;;; Copyright © 2022 Hartmut Goebel ;;; ;;; This file is part of GNU Guix. ;;; @@ -29,6 +30,7 @@ #:use-module (srfi srfi-26) #:use-module (json) #:use-module (gcrypt hash) + #:use-module (guix diagnostics) #:use-module (guix store) #:use-module (guix utils) #:use-module (guix base32) @@ -305,8 +307,13 @@ in RELEASE, a record." ")")))) (url-predicate (cut regexp-exec cpan-rx <>)))) -(define (latest-release package) +(define* (latest-release package #:key (version #f)) "Return an for the latest release of PACKAGE." + (when version + (error + (formatted-message + (G_ "~a updater doesn't support updating to a specific version, sorry.") + "cpan"))) (match (cpan-fetch (package->upstream-name package)) (#f #f) (release diff --git a/guix/import/cran.scm b/guix/import/cran.scm index 473d8c4f5b..1ed3580315 100644 --- a/guix/import/cran.scm +++ b/guix/import/cran.scm @@ -5,6 +5,7 @@ ;;; Copyright © 2020 Martin Becze ;;; Copyright © 2021 Sarah Morgensen ;;; Copyright © 2021 Simon Tournier +;;; Copyright © 2022 Hartmut Goebel ;;; ;;; This file is part of GNU Guix. ;;; @@ -693,8 +694,13 @@ s-expression corresponding to that package, or #f on failure." (_ #f))) (_ #f))))) -(define (latest-cran-release pkg) +(define* (latest-cran-release pkg #:key (version #f)) "Return an for the latest release of the package PKG." + (when version + (error + (formatted-message + (G_ "~a provides only the latest version of each package, sorry.") + "CRAN"))) (define upstream-name (package->upstream-name pkg)) @@ -713,20 +719,25 @@ s-expression corresponding to that package, or #f on failure." (changed-inputs pkg (description->package 'cran meta))))))) -(define (latest-bioconductor-release pkg) +(define* (latest-bioconductor-release pkg #:key (version #f)) "Return an for the latest release of the package PKG." + (when version + (error + (formatted-message + (G_ "~a provides only the latest version of each package, sorry.") + "bioconductor.org"))) (define upstream-name (package->upstream-name pkg)) - (define version + (define latest-version (latest-bioconductor-package-version upstream-name)) (and version ;; Bioconductor does not provide signatures. (upstream-source (package (package-name pkg)) - (version version) + (version latest-version) (urls (bioconductor-uri upstream-name version)) (input-changes (changed-inputs diff --git a/guix/import/elpa.scm b/guix/import/elpa.scm index 1dbdff9391..f9e9f2de53 100644 --- a/guix/import/elpa.scm +++ b/guix/import/elpa.scm @@ -7,6 +7,7 @@ ;;; Copyright © 2021 Xinglu Chen ;;; Copyright © 2021 Sarah Morgensen ;;; Copyright © 2021 Simon Tournier +;;; Copyright © 2022 Hartmut Goebel ;;; ;;; This file is part of GNU Guix. ;;; @@ -35,6 +36,7 @@ #:use-module (srfi srfi-26) #:use-module (srfi srfi-34) #:use-module (srfi srfi-35) + #:use-module (guix diagnostics) #:use-module ((guix download) #:select (download-to-store)) #:use-module (guix import utils) #:use-module (guix http-client) @@ -400,11 +402,16 @@ type ''." (string-drop (package-name package) 6) (package-name package)))) -(define (latest-release package) +(define* (latest-release package #:key (version #f)) "Return an for the latest release of PACKAGE." (define name (guix-package->elpa-name package)) (define repo (elpa-repository package)) + (when version + (error + (formatted-message + (G_ "~a updater doesn't support updating to a specific version, sorry.") + "elpa"))) (match (elpa-package-info name repo) (#f ;; No info, perhaps because PACKAGE is not truly an ELPA package. diff --git a/guix/import/hackage.scm b/guix/import/hackage.scm index d56f52a221..3c2cd75db4 100644 --- a/guix/import/hackage.scm +++ b/guix/import/hackage.scm @@ -7,6 +7,7 @@ ;;; Copyright © 2021 Xinglu Chen ;;; Copyright © 2021 Sarah Morgensen ;;; Copyright © 2019 Simon Tournier +;;; Copyright © 2022 Hartmut Goebel ;;; ;;; This file is part of GNU Guix. ;;; @@ -30,10 +31,12 @@ #:use-module (srfi srfi-34) #:use-module (srfi srfi-26) #:use-module (srfi srfi-1) + #:use-module (guix diagnostics) #:use-module ((guix download) #:select (download-to-store url-fetch)) #:use-module ((guix utils) #:select (package-name->name+version canonical-newline-port)) #:use-module (guix http-client) + #:use-module (guix i18n) #:use-module (guix import utils) #:use-module (guix import cabal) #:use-module (guix store) @@ -359,8 +362,13 @@ respectively." (let ((hackage-rx (make-regexp "(https?://hackage.haskell.org|mirror://hackage/)"))) (url-predicate (cut regexp-exec hackage-rx <>)))) -(define (latest-release package) +(define* (latest-release package #:key (version #f)) "Return an for the latest release of PACKAGE." + (when version + (error + (formatted-message + (G_ "~a updater doesn't support updating to a specific version, sorry.") + "hackage"))) (let* ((hackage-name (guix-package->hackage-name package)) (cabal-meta (hackage-fetch hackage-name))) (match cabal-meta diff --git a/guix/import/minetest.scm b/guix/import/minetest.scm index 6581013215..1f1cfc834d 100644 --- a/guix/import/minetest.scm +++ b/guix/import/minetest.scm @@ -1,5 +1,6 @@ ;;; GNU Guix --- Functional package management for GNU ;;; Copyright © 2021, 2022 Maxime Devos +;;; Copyright © 2022 Hartmut Goebel ;;; ;;; This file is part of GNU Guix. ;;; @@ -25,6 +26,7 @@ #:use-module (srfi srfi-2) #:use-module (srfi srfi-11) #:use-module (srfi srfi-26) + #:use-module (guix diagnostics) #:use-module ((guix packages) #:prefix package:) #:use-module (guix upstream) #:use-module (guix utils) @@ -486,7 +488,7 @@ list of AUTHOR/NAME strings." (and (string-prefix? "minetest-" (package:package-name pkg)) (assq-ref (package:package-properties pkg) 'upstream-name))) -(define (latest-minetest-release pkg) +(define* (latest-minetest-release pkg #:key (version #f)) "Return an for the latest release of the package PKG, or #false if the latest release couldn't be determined." (define author/name @@ -494,6 +496,12 @@ or #false if the latest release couldn't be determined." (define contentdb-package (contentdb-fetch author/name)) ; TODO warn if #f? (define release (latest-release author/name)) (define source (package:package-source pkg)) + + (when version + (error + (formatted-message + (G_ "~a updater doesn't support updating to a specific version, sorry.") + "minetest"))) (and contentdb-package release (release-commit release) ; not always set ;; Only continue if both the old and new version number are both diff --git a/guix/import/opam.scm b/guix/import/opam.scm index 8a5aa4d8c6..59dbb7cb8b 100644 --- a/guix/import/opam.scm +++ b/guix/import/opam.scm @@ -4,6 +4,7 @@ ;;; Copyright © 2021 Xinglu Chen ;;; Copyright © 2021 Sarah Morgensen ;;; Copyright © 2021, 2022 Alice Brenon +;;; Copyright © 2022 Hartmut Goebel ;;; ;;; This file is part of GNU Guix. ;;; @@ -35,6 +36,7 @@ #:use-module ((guix build utils) #:select (dump-port find-files mkdir-p)) #:use-module (guix build-system) #:use-module (guix build-system ocaml) + #:use-module (guix diagnostics) #:use-module (guix http-client) #:use-module (guix ui) #:use-module (guix packages) @@ -417,8 +419,13 @@ package in OPAM." (member (build-system-name (package-build-system package)) '(dune ocaml)) (not (string-prefix? "ocaml4" (package-name package))))) -(define (latest-release package) +(define* (latest-release package #:key (version #f)) "Return an for the latest release of PACKAGE." + (when version + (error + (formatted-message + (G_ "~a updater doesn't support updating to a specific version, sorry.") + "opam"))) (and-let* ((opam-name (guix-package->opam-name package)) (opam-file (opam-fetch opam-name)) (version (assoc-ref opam-file "version")) diff --git a/guix/import/stackage.scm b/guix/import/stackage.scm index af9809304f..e54df95985 100644 --- a/guix/import/stackage.scm +++ b/guix/import/stackage.scm @@ -4,6 +4,7 @@ ;;; Copyright © 2020 Martin Becze ;;; Copyright © 2021 Xinglu Chem ;;; Copyright © 2021 Ludovic Courtès +;;; Copyright © 2022 Hartmut Goebel ;;; ;;; This file is part of GNU Guix. ;;; @@ -139,9 +140,14 @@ included in the Stackage LTS release." (mlambda () (stackage-lts-packages (stackage-lts-info-fetch %default-lts-version))))) - (lambda* (pkg) + (lambda* (pkg #:key (version #f)) "Return an for the latest Stackage LTS release of PACKAGE or #f if the package is not included in the Stackage LTS release." + (when version + (error + (formatted-message + (G_ "~a updater doesn't support updating to a specific version, sorry.") + "stackage"))) (let* ((hackage-name (guix-package->hackage-name pkg)) (version (lts-package-version (packages) hackage-name)) (name-version (hackage-name-version hackage-name version))) From abc72eeac0e2763a5662564813a19211869a6796 Mon Sep 17 00:00:00 2001 From: Hartmut Goebel Date: Wed, 29 Jun 2022 15:02:07 +0200 Subject: [PATCH 755/790] import: sourceforge: Issue error-message if version is given. Due to the complicated directory structure at sourceforce, enabling the sourceforge importer to update to a specific version is very complicated to implement. Since only 2.0% of the packages in guix are covered by this updater I dedided to not implement this. * guix/gnu-maintenance.scm (latest-sourceforge-release): Add #:version argument. Issue error-message if version is given. --- guix/gnu-maintenance.scm | 10 +++++++++- 1 file changed, 9 insertions(+), 1 deletion(-) diff --git a/guix/gnu-maintenance.scm b/guix/gnu-maintenance.scm index 3067ee18b3..e414de8e28 100644 --- a/guix/gnu-maintenance.scm +++ b/guix/gnu-maintenance.scm @@ -37,6 +37,8 @@ #:autoload (guix download) (%mirrors) #:use-module (guix ftp-client) #:use-module (guix utils) + #:use-module (guix diagnostics) + #:use-module (guix i18n) #:use-module (guix memoization) #:use-module (guix records) #:use-module (guix upstream) @@ -705,7 +707,7 @@ GNOME packages; EMMS is included though, because its releases are on gnu.org." #:base-url %savannah-base #:directory directory))) -(define (latest-sourceforge-release package) +(define* (latest-sourceforge-release package #:key (version #f)) "Return the latest release of PACKAGE." (define (uri-append uri extension) ;; Return URI with EXTENSION appended. @@ -720,6 +722,12 @@ GNOME packages; EMMS is included though, because its releases are on gnu.org." ((200 302) #t) (else #f)))) + (when version + (error + (formatted-message + (G_ "Updating to a specific version is not yet implemented for ~a, sorry.") + "sourceforge"))) + (let* ((name (package-upstream-name package)) (base (string-append "https://sourceforge.net/projects/" name "/files")) From 53af5605438aa2dbf84cd3539d5524a02a4675da Mon Sep 17 00:00:00 2001 From: Hartmut Goebel Date: Fri, 24 Jun 2022 22:53:24 +0200 Subject: [PATCH 756/790] gnu-maintenance: Allow updating to a specific version. MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * guix/gnu-maintenance.scm (latest-ftp-release): Rename to … (import-ftp-release) … this, add #:version argument. If version is given, try to find the respective version. (latest-html-release): Rename to … (import-html-release) … this, add #:version argument. If version is given, try to find the respective version. (latest-gnu-release): Rename to … (import-gnu-release) … this, add #:version argument. Refactor to first select archives for respective package, the find the requested or latest version, then create the upstream-source. (latest-release): Rename to … (import-release) … this, add #:version argument, pass on to … (import-ftp-release) … this. (import-release*): Rename to … (import-release*) … this, add #:version argument, pass on to … (latest-release) … this. (latest-savannah-release): Rename to … (import-savannah-release) … this, add keword-argument version, pass on to … (import-html-release) … this. (latest-xorg-release): Rename to … (import-xorg-release) … this, add keword-argument version, pass on to … (import-ftp-release) … this. (latest-kernel.org-release): Rename to … (import-kernel.org-release) … this, add #:version argument, pass on to … (import-html-release) … this. (latest-html-updatable-release): Rename to … (import-html-updatable-release) … this, add #:version argument, pass on to … (import-html-release) … this. * guix/import/gnu.scm(gnu->guix-package): Adjust function call. --- guix/gnu-maintenance.scm | 173 ++++++++++++++++++++++++--------------- guix/import/gnu.scm | 2 +- 2 files changed, 106 insertions(+), 69 deletions(-) diff --git a/guix/gnu-maintenance.scm b/guix/gnu-maintenance.scm index e414de8e28..8e60e52ea0 100644 --- a/guix/gnu-maintenance.scm +++ b/guix/gnu-maintenance.scm @@ -66,7 +66,7 @@ release-file? releases - latest-release + import-release gnu-release-archive-types gnu-package-name->name+version @@ -333,14 +333,17 @@ name/directory pairs." files) result))))))) -(define* (latest-ftp-release project +(define* (import-ftp-release project #:key + (version #f) (server "ftp.gnu.org") (directory (string-append "/gnu/" project)) (file->signature (cut string-append <> ".sig"))) "Return an for the latest release of PROJECT on SERVER -under DIRECTORY, or #f. Use FTP-OPEN and FTP-CLOSE to open (resp. close) FTP -connections; this can be useful to reuse connections. +under DIRECTORY, or #f. Optionally include a VERSION string to fetch a specific version. + +Use FTP-OPEN and FTP-CLOSE to open (resp. close) FTP connections; this can be +useful to reuse connections. FILE->SIGNATURE must be a procedure; it is passed a source file URL and must return the corresponding signature URL, or #f it signatures are unavailable." @@ -407,8 +410,12 @@ return the corresponding signature URL, or #f it signatures are unavailable." ;; Assume that SUBDIRS correspond to versions, and jump into the ;; one with the highest version number. - (let* ((release (reduce latest-release #f - (coalesce-sources releases))) + (let* ((release (if version + (find (lambda (upstream) + (string=? (upstream-source-version upstream) version)) + (coalesce-sources releases)) + (reduce latest-release #f + (coalesce-sources releases)))) (result (if (and result release) (latest-release release result) (or release result))) @@ -420,13 +427,16 @@ return the corresponding signature URL, or #f it signatures are unavailable." (ftp-close conn) result)))))) -(define* (latest-release package +(define* (import-release package #:key + (version #f) (server "ftp.gnu.org") (directory (string-append "/gnu/" package))) "Return the for the latest version of PACKAGE or #f. -PACKAGE must be the canonical name of a GNU package." - (latest-ftp-release package +PACKAGE must be the canonical name of a GNU package. Optionally include a +VERSION string to fetch a specific version." + (import-ftp-release package + #:version version #:server server #:directory directory)) @@ -442,14 +452,15 @@ of EXP otherwise." (close-port port)) #f))) -(define (latest-release* package) - "Like 'latest-release', but (1) take a object, and (2) ignore FTP +(define* (import-release* package #:key (version #f)) + "Like 'import-release', but (1) take a object, and (2) ignore FTP errors that might occur when PACKAGE is not actually a GNU package, or not hosted on ftp.gnu.org, or not under that name (this is the case for \"emacs-auctex\", for instance.)" (let-values (((server directory) (ftp-server/directory package))) - (false-if-ftp-error (latest-release (package-upstream-name package) + (false-if-ftp-error (import-release (package-upstream-name package) + #:version version #:server server #:directory directory)))) @@ -474,14 +485,18 @@ hosted on ftp.gnu.org, or not under that name (this is the case for (_ links)))) -(define* (latest-html-release package +(define* (import-html-release package #:key + (version #f) (base-url "https://kernel.org/pub") (directory (string-append "/" package)) file->signature) "Return an for the latest release of PACKAGE (a string) on -SERVER under DIRECTORY, or #f. BASE-URL should be the URL of an HTML page, -typically a directory listing as found on 'https://kernel.org/pub'. +SERVER under DIRECTORY, or #f. Optionally include a VERSION string to fetch a +specific version. + +BASE-URL should be the URL of an HTML page, typically a directory listing as +found on 'https://kernel.org/pub'. When FILE->SIGNATURE is omitted or #f, guess the detached signature file name, if any. Otherwise, FILE->SIGNATURE must be a procedure; it is passed a source @@ -554,13 +569,18 @@ are unavailable." (match candidates (() #f) ((first . _) - ;; Select the most recent release and return it. - (reduce (lambda (r1 r2) - (if (version>? (upstream-source-version r1) - (upstream-source-version r2)) - r1 r2)) - first - (coalesce-sources candidates)))))) + (if version + ;; find matching release version and return it + (find (lambda (upstream) + (string=? (upstream-source-version upstream) version)) + (coalesce-sources candidates)) + ;; Select the most recent release and return it. + (reduce (lambda (r1 r2) + (if (version>? (upstream-source-version r1) + (upstream-source-version r2)) + r1 r2)) + first + (coalesce-sources candidates))))))) ;;; @@ -592,9 +612,9 @@ are unavailable." (call-with-gzip-input-port port (compose string->lines get-string-all)))))) -(define (latest-gnu-release package) +(define* (import-gnu-release package #:key (version #f)) "Return the latest release of PACKAGE, a GNU package available via -ftp.gnu.org. +ftp.gnu.org. Optionally include a VERSION string to fetch a specific version. This method does not rely on FTP access at all; instead, it browses the file list available from %GNU-FILE-LIST-URI over HTTP(S)." @@ -604,42 +624,50 @@ list available from %GNU-FILE-LIST-URI over HTTP(S)." (define (better-tarball? tarball1 tarball2) (string=? (file-extension tarball1) archive-type)) + (define (find-latest-tarball-version tarballs) + (fold (lambda (file1 file2) + (if (and file2 + (version>? (tarball-sans-extension (basename file2)) + (tarball-sans-extension (basename file1)))) + file2 + file1)) + #f + tarballs)) + (let-values (((server directory) (ftp-server/directory package)) ((name) (package-upstream-name package))) (let* ((files (ftp.gnu.org-files)) + ;; select tarballs for this package (relevant (filter (lambda (file) (and (string-prefix? "/gnu" file) (string-contains file directory) (release-file? name (basename file)))) - files))) - (match (sort relevant (lambda (file1 file2) - (version>? (tarball-sans-extension - (basename file1)) - (tarball-sans-extension - (basename file2))))) - ((and tarballs (reference _ ...)) - (let* ((version (tarball->version reference)) - (tarballs (filter (lambda (file) - (string=? (tarball-sans-extension - (basename file)) - (tarball-sans-extension - (basename reference)))) - tarballs))) - (upstream-source - (package name) - (version version) - (urls (map (lambda (file) - (string-append "mirror://gnu/" - (string-drop file - (string-length "/gnu/")))) + files)) + ;; find latest version + (version (or version + (and (not (null? relevant)) + (tarball->version + (find-latest-tarball-version relevant))))) + ;; find tarballs matching this version + (tarballs (filter (lambda (file) + (string=? version (tarball->version file))) + relevant))) + (match tarballs + (() #f) + (_ + (upstream-source + (package name) + (version version) + (urls (map (lambda (file) + (string-append "mirror://gnu/" + (string-drop file + (string-length "/gnu/")))) ;; Sort so that the tarball with the same compression ;; format as currently used in PACKAGE comes first. (sort tarballs better-tarball?))) - (signature-urls (map (cut string-append <> ".sig") urls))))) - (() - #f))))) + (signature-urls (map (cut string-append <> ".sig") urls)))))))) (define %package-name-rx ;; Regexp for a package name, e.g., "foo-X.Y". Since TeXmacs uses @@ -693,8 +721,9 @@ GNOME packages; EMMS is included though, because its releases are on gnu.org." ;; HTML (unlike .) "https://de.freedif.org/savannah/") -(define (latest-savannah-release package) - "Return the latest release of PACKAGE." +(define* (import-savannah-release package #:key (version #f)) + "Return the latest release of PACKAGE. Optionally include a VERSION string +to fetch a specific version." (let* ((uri (string->uri (match (origin-uri (package-source package)) ((? string? uri) uri) @@ -703,12 +732,14 @@ GNOME packages; EMMS is included though, because its releases are on gnu.org." (directory (dirname (uri-path uri)))) ;; Note: We use the default 'file->signature', which adds ".sig", ".asc", ;; or whichever detached signature naming scheme PACKAGE uses. - (latest-html-release package + (import-html-release package + #:version version #:base-url %savannah-base #:directory directory))) (define* (latest-sourceforge-release package #:key (version #f)) - "Return the latest release of PACKAGE." + "Return the latest release of PACKAGE. Optionally include a VERSION string +to fetch a specific version." (define (uri-append uri extension) ;; Return URI with EXTENSION appended. (build-uri (uri-scheme uri) @@ -766,21 +797,24 @@ GNOME packages; EMMS is included though, because its releases are on gnu.org." (when port (close-port port)))))) -(define (latest-xorg-release package) - "Return the latest release of PACKAGE." +(define* (import-xorg-release package #:key (version #f)) + "Return the latest release of PACKAGE. Optionally include a VERSION string +to fetch a specific version." (let ((uri (string->uri (origin-uri (package-source package))))) (false-if-ftp-error - (latest-ftp-release + (import-ftp-release (package-name package) + #:version version #:server "ftp.freedesktop.org" #:directory (string-append "/pub/xorg/" (dirname (uri-path uri))))))) -(define (latest-kernel.org-release package) - "Return the latest release of PACKAGE, the name of a kernel.org package." +(define* (import-kernel.org-release package #:key (version #f)) + "Return the latest release of PACKAGE, the name of a kernel.org package. +Optionally include a VERSION string to fetch a specific version." (define %kernel.org-base ;; This URL and sub-directories thereof are nginx-generated directory - ;; listings suitable for 'latest-html-release'. + ;; listings suitable for 'import-html-release'. "https://mirrors.edge.kernel.org/pub") (define (file->signature file) @@ -792,7 +826,8 @@ GNOME packages; EMMS is included though, because its releases are on gnu.org." ((uri mirrors ...) uri)))) (package (package-upstream-name package)) (directory (dirname (uri-path uri)))) - (latest-html-release package + (import-html-release package + #:version version #:base-url %kernel.org-base #:directory directory #:file->signature file->signature))) @@ -819,9 +854,10 @@ GNOME packages; EMMS is included though, because its releases are on gnu.org." (or (assoc-ref (package-properties package) 'release-monitoring-url) (http-url? package))))) -(define (latest-html-updatable-release package) +(define* (import-html-updatable-release package #:key (version #f)) "Return the latest release of PACKAGE. Do that by crawling the HTML page of -the directory containing its source tarball." +the directory containing its source tarball. Optionally include a VERSION +string to fetch a specific version." (let* ((uri (string->uri (match (origin-uri (package-source package)) ((? string? url) url) @@ -838,7 +874,8 @@ the directory containing its source tarball." (catch #t (lambda () (guard (c ((http-get-error? c) #f)) - (latest-html-release package + (import-html-release package + #:version version #:base-url base #:directory directory))) (lambda (key . args) @@ -856,7 +893,7 @@ the directory containing its source tarball." (name 'gnu) (description "Updater for GNU packages") (pred gnu-hosted?) - (import latest-gnu-release))) + (import import-gnu-release))) (define %gnu-ftp-updater ;; This is for GNU packages taken from alternate locations, such as @@ -867,14 +904,14 @@ the directory containing its source tarball." (pred (lambda (package) (and (not (gnu-hosted? package)) (pure-gnu-package? package)))) - (import latest-release*))) + (import import-release*))) (define %savannah-updater (upstream-updater (name 'savannah) (description "Updater for packages hosted on savannah.gnu.org") (pred (url-prefix-predicate "mirror://savannah/")) - (import latest-savannah-release))) + (import import-savannah-release))) (define %sourceforge-updater (upstream-updater @@ -888,20 +925,20 @@ the directory containing its source tarball." (name 'xorg) (description "Updater for X.org packages") (pred (url-prefix-predicate "mirror://xorg/")) - (import latest-xorg-release))) + (import import-xorg-release))) (define %kernel.org-updater (upstream-updater (name 'kernel.org) (description "Updater for packages hosted on kernel.org") (pred (url-prefix-predicate "mirror://kernel.org/")) - (import latest-kernel.org-release))) + (import import-kernel.org-release))) (define %generic-html-updater (upstream-updater (name 'generic-html) (description "Updater that crawls HTML pages.") (pred html-updatable-package?) - (import latest-html-updatable-release))) + (import import-html-updatable-release))) ;;; gnu-maintenance.scm ends here diff --git a/guix/import/gnu.scm b/guix/import/gnu.scm index 2b9b71feb0..139c32a545 100644 --- a/guix/import/gnu.scm +++ b/guix/import/gnu.scm @@ -117,7 +117,7 @@ details.)" (unless package (raise (formatted-message (G_ "no GNU package found for ~a") name))) - (match (latest-release name) + (match (import-release name) ((? upstream-source? release) (let ((version (upstream-source-version release))) (gnu-package->sexp package release #:key-download key-download))) From 7c4aab1f7ddfff5959d45e9b6d45abb6d5013e0e Mon Sep 17 00:00:00 2001 From: Hartmut Goebel Date: Tue, 28 Jun 2022 19:15:04 +0200 Subject: [PATCH 757/790] import: crate: Allow updating to a specific version. * guix/import/crate.scm (latest-release): Rename to 'import-release', add #:version argument. If version is given, return an upstream-source for this version. --- guix/import/crate.scm | 10 ++++++---- 1 file changed, 6 insertions(+), 4 deletions(-) diff --git a/guix/import/crate.scm b/guix/import/crate.scm index 51bfcd7bed..339dbcd74c 100644 --- a/guix/import/crate.scm +++ b/guix/import/crate.scm @@ -3,6 +3,7 @@ ;;; Copyright © 2019, 2020, 2021 Ludovic Courtès ;;; Copyright © 2019, 2020 Martin Becze ;;; Copyright © 2021 Nicolas Goaziou +;;; Copyright © 2022 Hartmut Goebel ;;; ;;; This file is part of GNU Guix. ;;; @@ -354,11 +355,12 @@ look up the development dependencs for the given crate." (define crate-package? (url-predicate crate-url?)) -(define (latest-release package) - "Return an for the latest release of PACKAGE." +(define* (import-release package #:key (version #f)) + "Return an for the latest release of PACKAGE. Optionally +include a VERSION string to fetch a specific version." (let* ((crate-name (guix-package->crate-name package)) (crate (lookup-crate crate-name)) - (version (crate-latest-version crate)) + (version (or version (crate-latest-version crate))) (url (crate-uri crate-name version))) (upstream-source (package (package-name package)) @@ -370,5 +372,5 @@ look up the development dependencs for the given crate." (name 'crate) (description "Updater for crates.io packages") (pred crate-package?) - (import latest-release))) + (import import-release))) From af44a8550c1cc2624cf956839c35280b1e152ac5 Mon Sep 17 00:00:00 2001 From: Hartmut Goebel Date: Tue, 28 Jun 2022 21:07:05 +0200 Subject: [PATCH 758/790] import: egg: Allow updating to a specific version. * guix/import/egg.scm (latest-release): Rename to 'import-release', add #:version argument. If version is given, return an upstream-source for this version. --- guix/import/egg.scm | 10 ++++++---- 1 file changed, 6 insertions(+), 4 deletions(-) diff --git a/guix/import/egg.scm b/guix/import/egg.scm index 2ad48c3399..10a40fe4f8 100644 --- a/guix/import/egg.scm +++ b/guix/import/egg.scm @@ -2,6 +2,7 @@ ;;; Copyright © 2021 Xinglu Chen ;;; Copyright © 2021 Tobias Geerinckx-Rice ;;; Copyright © 2021 Sarah Morgensen +;;; Copyright © 2022 Hartmut Goebel ;;; ;;; This file is part of GNU Guix. ;;; @@ -333,10 +334,11 @@ not work." ;;; Updater. ;;; -(define (latest-release package) - "Return an @code{} for the latest release of PACKAGE." +(define* (import-release package #:key (version #f)) + "Return an @code{} for the latest release of PACKAGE. +Optionally include a VERSION string to fetch a specific version." (let* ((egg-name (guix-package->egg-name package)) - (version (find-latest-version egg-name)) + (version (or version (find-latest-version egg-name))) (source-url (egg-uri egg-name version))) (upstream-source (package (package-name package)) @@ -348,6 +350,6 @@ not work." (name 'egg) (description "Updater for CHICKEN egg packages") (pred egg-package?) - (import latest-release))) + (import import-release))) ;;; egg.scm ends here From 1e39f475a2695490bb9a229981e91fc23a899e6d Mon Sep 17 00:00:00 2001 From: Hartmut Goebel Date: Tue, 1 Nov 2022 11:37:28 +0100 Subject: [PATCH 759/790] import: gem: Allow updating to a specific version. * guix/import/gem.scm (latest-release): Rename to 'import-release', add #:version argument. If version is given, return an upstream-source for this version. --- guix/import/gem.scm | 7 ++++--- 1 file changed, 4 insertions(+), 3 deletions(-) diff --git a/guix/import/gem.scm b/guix/import/gem.scm index 1c6c55baa6..8ad0662628 100644 --- a/guix/import/gem.scm +++ b/guix/import/gem.scm @@ -6,6 +6,7 @@ ;;; Copyright © 2020 Martin Becze ;;; Copyright © 2021 Sarah Morgensen ;;; Copyright © 2022 Taiju HIGASHI +;;; Copyright © 2022 Hartmut Goebel ;;; ;;; This file is part of GNU Guix. ;;; @@ -173,11 +174,11 @@ package on RubyGems." (define gem-package? (url-prefix-predicate "https://rubygems.org/downloads/")) -(define (latest-release package) +(define* (import-release package #:key (version #f)) "Return an for the latest release of PACKAGE." (let* ((gem-name (guix-package->gem-name package)) (gem (rubygems-fetch gem-name)) - (version (gem-version gem)) + (version (or version (gem-version gem))) (url (rubygems-uri gem-name version))) (upstream-source (package (package-name package)) @@ -189,7 +190,7 @@ package on RubyGems." (name 'gem) (description "Updater for RubyGem packages") (pred gem-package?) - (import latest-release))) + (import import-release))) (define* (gem-recursive-import package-name #:optional version) (recursive-import package-name From 6da60453e25f3941202ab51f74821c9ed7299bca Mon Sep 17 00:00:00 2001 From: Hartmut Goebel Date: Thu, 30 Jun 2022 11:05:13 +0200 Subject: [PATCH 760/790] import: git: Allow updating to a specific version. * guix/import/git.scm (latest-tag): Add #:version argument. If version is given, try to find the respective version tag. (latest-git-tag-version): Add #:version argument and pass it on to called functions. (latest-releease) Rename to 'import-release', add #:version argument and pass it on to called functions. --- guix/import/git.scm | 37 ++++++++++++++++++++++++++----------- 1 file changed, 26 insertions(+), 11 deletions(-) diff --git a/guix/import/git.scm b/guix/import/git.scm index bb5ba4d97e..c15943bd7c 100644 --- a/guix/import/git.scm +++ b/guix/import/git.scm @@ -2,6 +2,7 @@ ;;; Copyright © 2021 Xinglu Chen ;;; Copyright © 2021 Sarah Morgensen ;;; Copyright © 2022 Maxime Devos +;;; Copyright © 2022 Hartmut Goebel ;;; ;;; This file is part of GNU Guix. ;;; @@ -146,9 +147,11 @@ version corresponding to the tag, and the cdr is the name of the tag." tags) entry tag) %pre-release-rx)) @@ -169,13 +172,22 @@ repository at URL." ((null? versions->tags) (git-no-valid-tags-error)) (else - (match (last versions->tags) - ((version . tag) - (values version tag))))))) + (let ((versions (if version + (filter (match-lambda + ((candidate-version . tag) + (string=? version candidate-version))) + versions->tags) + versions->tags))) + (if (null? versions) + (values #f #f) + (match (last versions) + ((version . tag) + (values version tag))))))))) -(define (latest-git-tag-version package) +(define* (latest-git-tag-version package #:key (version #f)) "Given a PACKAGE, return the latest version of it and the corresponding git -tag, or #false and #false if the latest version could not be determined." +tag, or #false and #false if the latest version could not be determined. +Optionally include a VERSION string to fetch a specific version." (guard (c ((or (git-no-tags-error? c) (git-no-valid-tags-error? c)) (warning (or (package-field-location package 'source) (package-location package)) @@ -193,6 +205,7 @@ tag, or #false and #false if the latest version could not be determined." (url (git-reference-url (origin-uri source))) (property (cute assq-ref (package-properties package) <>))) (latest-tag url + #:version version #:prefix (property 'release-tag-prefix) #:suffix (property 'release-tag-suffix) #:delim (property 'release-tag-version-delimiter) @@ -206,12 +219,14 @@ tag, or #false and #false if the latest version could not be determined." (git-reference? (origin-uri origin)))) (_ #f))) -(define (latest-git-release package) - "Return an for the latest release of PACKAGE." +(define* (import-git-release package #:key (version #f)) + "Return an for the latest release of PACKAGE. +Optionally include a VERSION string to fetch a specific version." (let* ((name (package-name package)) (old-version (package-version package)) (old-reference (origin-uri (package-source package))) - (new-version new-version-tag (latest-git-tag-version package))) + (new-version new-version-tag + (latest-git-tag-version package #:version version))) (and new-version new-version-tag (upstream-source (package name) @@ -226,4 +241,4 @@ tag, or #false and #false if the latest version could not be determined." (name 'generic-git) (description "Updater for packages hosted on Git repositories") (pred git-package?) - (import latest-git-release))) + (import import-git-release))) From be3f48bff0a1331e099c5c53305b11a78e3001fc Mon Sep 17 00:00:00 2001 From: Hartmut Goebel Date: Wed, 29 Jun 2022 14:13:55 +0200 Subject: [PATCH 761/790] import: github: Allow updating to a specific version. * guix/import/github.scm (latest-released-version): Add #:version argument. If version is given, try to find the respective release. (latest-releease) Rename to 'import-release', add #:version argument and pass it on to 'latest-released-version'. --- guix/import/github.scm | 36 ++++++++++++++++++++++++------------ 1 file changed, 24 insertions(+), 12 deletions(-) diff --git a/guix/import/github.scm b/guix/import/github.scm index ac6ef06eda..a1bda5ec43 100644 --- a/guix/import/github.scm +++ b/guix/import/github.scm @@ -249,11 +249,13 @@ Alternatively, you can wait until your rate limit is reset, or use the #:headers headers))) (x x))))))))) -(define (latest-released-version url package-name) +(define* (latest-released-version url package-name #:key (version #f)) "Return the newest released version and its tag given a string URL like 'https://github.com/arq5x/bedtools2/archive/v2.24.0.tar.gz' and the name of the package e.g. 'bedtools2'. Return #f (two values) if there are no -releases." +releases. + +Optionally include a VERSION string to fetch a specific version." (define (pre-release? x) (assoc-ref x "prerelease")) @@ -290,16 +292,25 @@ releases." (match (and=> (fetch-releases-or-tags url) vector->list) (#f (values #f #f)) (json - (match (sort (filter-map release->version - (match (remove pre-release? json) - (() json) ; keep everything - (releases releases))) - (lambda (x y) (version>? (car x) (car y)))) + (let ((releases (filter-map release->version + (match (remove pre-release? json) + (() json) ; keep everything + (releases releases))))) + (match (if version + ;; Find matching release version. + (filter (match-lambda + ((candidate-version . tag) + (string=? version candidate-version))) + releases) + ;; Sort releases descending. + (sort releases + (lambda (x y) (version>? (car x) (car y))))) (((latest-version . tag) . _) (values latest-version tag)) - (() (values #f #f)))))) + (() (values #f #f))))))) -(define (latest-release pkg) - "Return an for the latest release of PKG." +(define* (import-release pkg #:key (version #f)) + "Return an for the latest release of PKG. +Optionally include a VERSION string to fetch a specific version." (define (github-uri uri) (match uri ((? string? url) @@ -313,7 +324,8 @@ releases." (source-uri (github-uri original-uri)) (name (package-name pkg)) (newest-version version-tag - (latest-released-version source-uri name))) + (latest-released-version source-uri name + #:version version))) (if newest-version (upstream-source (package name) @@ -330,6 +342,6 @@ releases." (name 'github) (description "Updater for GitHub packages") (pred github-package?) - (import latest-release))) + (import import-release))) From c7faeae2b1d313a6a04ecb6d3cac2dfd35320e29 Mon Sep 17 00:00:00 2001 From: Hartmut Goebel Date: Wed, 29 Jun 2022 10:51:12 +0200 Subject: [PATCH 762/790] import: gnome: Allow updating to a specific version. * guix/import/gnome.scm (latest-gnome-release): Rename to 'import-gnome-release', add #:version argument. If version is given, try to find the respective version [find-latest-release]: New function, based on former code. [find-version-release]: New function. --- guix/import/gnome.scm | 47 +++++++++++++++++++++++++++---------------- 1 file changed, 30 insertions(+), 17 deletions(-) diff --git a/guix/import/gnome.scm b/guix/import/gnome.scm index 09c6dbbd0d..3c5a96fdde 100644 --- a/guix/import/gnome.scm +++ b/guix/import/gnome.scm @@ -1,6 +1,7 @@ ;;; GNU Guix --- Functional package management for GNU ;;; Copyright © 2017, 2019, 2021 Ludovic Courtès ;;; Copyright © 2022 Maxim Cournoyer +;;; Copyright © 2022 Hartmut Goebel ;;; ;;; This file is part of GNU Guix. ;;; @@ -57,9 +58,10 @@ source for metadata." name "/" relative-url)))) '("tar.lz" "tar.xz" "tar.bz2" "tar.gz"))))))) -(define (latest-gnome-release package) +(define* (import-gnome-release package #:key (version #f)) "Return the latest release of PACKAGE, a GNOME package, or #f if it could -not be determined." +not be determined. Optionally include a VERSION string to fetch a specific +version." (define %not-dot (char-set-complement (char-set #\.))) @@ -88,6 +90,28 @@ https://discourse.gnome.org/t/new-gnome-versioning-scheme/4235" ;; Some packages like "NetworkManager" have camel-case names. (package-upstream-name package)) + (define (find-latest-release releases) + (fold (match-lambda* + (((key . value) result) + (cond ((release-version? key) + (match result + (#f + (cons key value)) + ((newest . _) + (if (version>? key newest) + (cons key value) + result)))) + (else + result)))) + #f + releases)) + + (define (find-version-release releases version) + (find (match-lambda + ((key . value) + (string=? key version))) + releases)) + (guard (c ((http-get-error? c) (if (= 404 (http-get-error-code c)) #f @@ -108,20 +132,9 @@ https://discourse.gnome.org/t/new-gnome-versioning-scheme/4235" (match json (#(4 releases _ ...) (let* ((releases (assoc-ref releases upstream-name)) - (latest (fold (match-lambda* - (((key . value) result) - (cond ((release-version? key) - (match result - (#f - (cons key value)) - ((newest . _) - (if (version>? key newest) - (cons key value) - result)))) - (else - result)))) - #f - releases))) + (latest (if version + (find-version-release releases version) + (find-latest-release releases)))) (and latest (jsonish->upstream-source upstream-name latest)))))))) @@ -130,4 +143,4 @@ https://discourse.gnome.org/t/new-gnome-versioning-scheme/4235" (name 'gnome) (description "Updater for GNOME packages") (pred (url-prefix-predicate "mirror://gnome/")) - (import latest-gnome-release))) + (import import-gnome-release))) From e689f970335a67bc0aea611f1502cfeb6f4b6650 Mon Sep 17 00:00:00 2001 From: Hartmut Goebel Date: Wed, 29 Jun 2022 09:39:51 +0200 Subject: [PATCH 763/790] import: hexpm: Allow updating to a specific version. * guix/import/hexpm.scm (latest-release): Rename to 'import-release', add #:version argument. If version is given, return an upstream-source for this version. --- guix/import/hexpm.scm | 9 +++++---- 1 file changed, 5 insertions(+), 4 deletions(-) diff --git a/guix/import/hexpm.scm b/guix/import/hexpm.scm index 3b63837393..8a009fd245 100644 --- a/guix/import/hexpm.scm +++ b/guix/import/hexpm.scm @@ -328,11 +328,12 @@ latest version of PACKAGE-NAME." ;;; Updater ;;; -(define (latest-release package) - "Return an for the latest release of PACKAGE." +(define* (import-release package #:key (version #f)) + "Return an for the latest release of PACKAGE. Optionally +include a VERSION string to fetch a specific version." (let* ((hexpm-name (guix-package->hexpm-name package)) (hexpm (lookup-hexpm hexpm-name)) - (version (hexpm-latest-release hexpm)) + (version (or version (hexpm-latest-release hexpm))) (url (hexpm-uri hexpm-name version))) (upstream-source (package (package-name package)) @@ -344,4 +345,4 @@ latest version of PACKAGE-NAME." (name 'hexpm) (description "Updater for hex.pm packages") (pred (url-prefix-predicate hexpm-package-url)) - (import latest-release))) + (import import-release))) From 424a871f1f3517db2718c76550619b2fa1e0309b Mon Sep 17 00:00:00 2001 From: Hartmut Goebel Date: Wed, 29 Jun 2022 12:29:08 +0200 Subject: [PATCH 764/790] import: kde: Allow updating to a specific version. * guix/import/kde.scm (latest-kde-release): Rename to 'import-kde-release', add #:version argument. Rework the code to not sort the relevant files, but just find the requested or latest version. [find-latest-archive-version]: New function. --- guix/import/kde.scm | 61 ++++++++++++++++++++++++++------------------- 1 file changed, 36 insertions(+), 25 deletions(-) diff --git a/guix/import/kde.scm b/guix/import/kde.scm index 510d823a4f..3566312eca 100644 --- a/guix/import/kde.scm +++ b/guix/import/kde.scm @@ -28,6 +28,7 @@ #:use-module (ice-9 match) #:use-module (ice-9 rdelim) #:use-module (ice-9 regex) + #:use-module (srfi srfi-1) #:use-module (srfi srfi-11) #:use-module (web uri) @@ -149,42 +150,52 @@ Output: (string-join (map version->pattern directory-parts) "/") "/")))) -(define (latest-kde-release package) +(define* (import-kde-release package #:key (version #f)) "Return the latest release of PACKAGE, a KDE package, or #f if it could -not be determined." +not be determined. Optionally include a VERSION string to fetch a specific +version." + + (define (find-latest-archive-version archives) + (fold (lambda (file1 file2) + (if (and file2 + (version>? (tarball-sans-extension (basename file2)) + (tarball-sans-extension (basename file1)))) + file2 + file1)) + #f + archives)) + (let* ((uri (string->uri (origin-uri (package-source package)))) (path-rx (uri->kde-path-pattern uri)) (name (package-upstream-name package)) (files (download.kde.org-files)) + ;; select archives for this package (relevant (filter (lambda (file) (and (regexp-exec path-rx file) (release-file? name (basename file)))) - files))) - (match (sort relevant (lambda (file1 file2) - (version>? (tarball-sans-extension - (basename file1)) - (tarball-sans-extension - (basename file2))))) - ((and tarballs (reference _ ...)) - (let* ((version (tarball->version reference)) - (tarballs (filter (lambda (file) - (string=? (tarball-sans-extension - (basename file)) - (tarball-sans-extension - (basename reference)))) - tarballs))) - (upstream-source - (package name) - (version version) - (urls (map (lambda (file) - (string-append "mirror://kde/" file)) - tarballs))))) - (() - #f)))) + files)) + ;; Find latest version. + (version (or version + (and (not (null? relevant)) + (tarball->version (find-latest-archive-version relevant))))) + ;; Find archives matching this version. + (tarballs (filter (lambda (file) + (string=? version (tarball->version file))) + relevant))) + (match tarballs + (() #f) + (_ + (upstream-source + (package name) + (version version) + (urls (map (lambda (file) + (string-append "mirror://kde/" file)) + tarballs))))))) + (define %kde-updater (upstream-updater (name 'kde) (description "Updater for KDE packages") (pred (url-prefix-predicate "mirror://kde/")) - (import latest-kde-release))) + (import import-kde-release))) From 3986caacae773c7f2f69a013b44d3d64dffe9f50 Mon Sep 17 00:00:00 2001 From: Hartmut Goebel Date: Wed, 29 Jun 2022 10:15:47 +0200 Subject: [PATCH 765/790] import: launchpad: Allow updating to a specific version. * guix/import/launchpad.scm (latest-release): Rename to 'import-release', add #:version argument. If version is given, return an upstream-source for this version. --- guix/import/launchpad.scm | 10 ++++++---- 1 file changed, 6 insertions(+), 4 deletions(-) diff --git a/guix/import/launchpad.scm b/guix/import/launchpad.scm index b7e0295c4e..01953ea69c 100644 --- a/guix/import/launchpad.scm +++ b/guix/import/launchpad.scm @@ -2,6 +2,7 @@ ;;; Copyright © 2019, 2020 Arun Isaac ;;; Copyright © 2021 Matthew James Kraai ;;; Copyright © 2020 Brice Waegeneire +;;; Copyright © 2022 Hartmut Goebel ;;; ;;; This file is part of GNU Guix. ;;; @@ -121,8 +122,9 @@ for example, 'linuxdcpp'. Return #f if there is no releases." (last (remove pre-release? (vector->list (assoc-ref json "entries")))) "version")))) -(define (latest-release pkg) - "Return an for the latest release of PKG." +(define* (import-release pkg #:key (version #f)) + "Return an for the latest release of PKG. Optionally +include a VERSION string to fetch a specific version." (define (origin-launchpad-uri origin) (match (origin-uri origin) ((? string? url) url) ; surely a Launchpad URL @@ -132,7 +134,7 @@ for example, 'linuxdcpp'. Return #f if there is no releases." (let* ((source-uri (origin-launchpad-uri (package-source pkg))) (name (package-name pkg)) (repository (launchpad-repository source-uri)) - (newest-version (latest-released-version repository))) + (newest-version (or version (latest-released-version repository)))) (if newest-version (upstream-source (package name) @@ -145,4 +147,4 @@ for example, 'linuxdcpp'. Return #f if there is no releases." (name 'launchpad) (description "Updater for Launchpad packages") (pred launchpad-package?) - (import latest-release))) + (import import-release))) From b82eb8d67add518c39af39227397b78285f89a50 Mon Sep 17 00:00:00 2001 From: Hartmut Goebel Date: Fri, 24 Jun 2022 22:31:10 +0200 Subject: [PATCH 766/790] import: pypi: Allow updating to a specific version. * guix/import/pypi.scm (latest-release): Rename to 'import-release', add #:version argument and pass it on to called functions. --- guix/import/pypi.scm | 14 ++++++++------ 1 file changed, 8 insertions(+), 6 deletions(-) diff --git a/guix/import/pypi.scm b/guix/import/pypi.scm index 3e3e949283..0e5998b36e 100644 --- a/guix/import/pypi.scm +++ b/guix/import/pypi.scm @@ -13,6 +13,7 @@ ;;; Copyright © 2021 Marius Bakke ;;; Copyright © 2022 Vivien Kraus ;;; Copyright © 2021 Simon Tournier +;;; Copyright © 2022 Hartmut Goebel ;;; ;;; This file is part of GNU Guix. ;;; @@ -556,15 +557,16 @@ source. To build it from source, refer to the upstream repository at (string-prefix? "https://pypi.org/packages" url) (string-prefix? "https://files.pythonhosted.org/packages" url))))) -(define (latest-release package) - "Return an for the latest release of PACKAGE." +(define* (import-release package #:key (version #f)) + "Return an for the latest release of PACKAGE. Optionally +include a VERSION string to fetch a specific version." (let* ((pypi-name (guix-package->pypi-name package)) (pypi-package (pypi-fetch pypi-name))) (and pypi-package (guard (c ((missing-source-error? c) #f)) (let* ((info (pypi-project-info pypi-package)) - (version (project-info-version info)) - (dist (source-release pypi-package)) + (version (or version (project-info-version info))) + (dist (source-release pypi-package version)) (url (distribution-url dist))) (upstream-source (urls (list url)) @@ -574,7 +576,7 @@ source. To build it from source, refer to the upstream repository at #f)) (input-changes (changed-inputs package - (pypi->guix-package pypi-name))) + (pypi->guix-package pypi-name #:version version))) (package (package-name package)) (version version))))))) @@ -583,4 +585,4 @@ source. To build it from source, refer to the upstream repository at (name 'pypi) (description "Updater for PyPI packages") (pred pypi-package?) - (import latest-release))) + (import import-release))) From 8aeccc6240ec45f0bc7bed655e0c8149ae4253eb Mon Sep 17 00:00:00 2001 From: Hartmut Goebel Date: Fri, 24 Jun 2022 20:40:57 +0200 Subject: [PATCH 767/790] refresh: Allow updating to a specific version. * guix/scripts/refresh.scm (options->packages)[args-packages]: Handle version specification in package name arguments. (update-package): Add #:version argument and pass it on to called functions. (guix-refresh): When updating, pass the specified version (if any) to update-package. [package-list-without-versions, package-list-with-versions]: New functions. --- guix/scripts/refresh.scm | 49 ++++++++++++++++++++++++++++++---------- 1 file changed, 37 insertions(+), 12 deletions(-) diff --git a/guix/scripts/refresh.scm b/guix/scripts/refresh.scm index 14329751f8..e0b94ce48d 100644 --- a/guix/scripts/refresh.scm +++ b/guix/scripts/refresh.scm @@ -9,6 +9,7 @@ ;;; Copyright © 2019 Ricardo Wurmus ;;; Copyright © 2020 Simon Tournier ;;; Copyright © 2021 Sarah Morgensen +;;; Copyright © 2022 Hartmut Goebel ;;; ;;; This file is part of GNU Guix. ;;; @@ -46,6 +47,7 @@ #:use-module (ice-9 vlist) #:use-module (ice-9 format) #:use-module (srfi srfi-1) + #:use-module (srfi srfi-9) #:use-module (srfi srfi-26) #:use-module (srfi srfi-37) #:use-module (srfi srfi-71) @@ -181,7 +183,7 @@ specified with `--select'.\n")) (newline) (show-bug-report-information)) -(define (options->packages opts) +(define (options->update-specs opts) "Return the list of packages requested by OPTS, honoring options like '--recursive'." (define core-package? @@ -224,7 +226,7 @@ update would trigger a complete rebuild." (('argument . spec) ;; Take either the specified version or the ;; latest one. - (specification->package spec)) + (update-specification->update-spec spec)) (('expression . exp) (read/eval-package-expression exp)) (_ #f)) @@ -254,6 +256,25 @@ update would trigger a complete rebuild." (with-monad %store-monad (return packages)))) + +;;; +;;; Utilities. +;;; + +(define-record-type + (update-spec package version) + update? + (package update-spec-package) + (version update-spec-version)) + +(define (update-specification->update-spec spec) + "Given SPEC, a package name like \"guile@2.0=2.0.8\", return a +record with two fields: the package to upgrade, and the target version." + (match (string-rindex spec #\=) + (#f (update-spec (specification->package spec) #f)) + (idx (update-spec (specification->package (substring spec 0 idx)) + (substring spec (1+ idx)))))) + ;;; ;;; Updates. @@ -298,7 +319,7 @@ update would trigger a complete rebuild." (G_ "no updater for ~a~%") (package-name package))) -(define* (update-package store package updaters +(define* (update-package store package version updaters #:key (key-download 'interactive) warn?) "Update the source file that defines PACKAGE with the new version. KEY-DOWNLOAD specifies a download policy for missing OpenPGP keys; allowed @@ -307,7 +328,7 @@ warn about packages that have no matching updater." (if (lookup-updater package updaters) (let ((version output source (package-update store package updaters - #:key-download key-download)) + #:key-download key-download #:version version)) (loc (or (package-field-location package 'version) (package-location package)))) (when version @@ -540,12 +561,12 @@ all are dependent packages: ~{~a~^ ~}~%") (with-error-handling (with-store store (run-with-store store - (mlet %store-monad ((packages (options->packages opts))) + (mlet %store-monad ((update-specs (options->update-specs opts))) (cond (list-dependent? - (list-dependents packages)) + (list-dependents (map update-spec-package update-specs))) (list-transitive? - (list-transitive packages)) + (list-transitive (map update-spec-package update-specs))) (update? (parameterize ((%openpgp-key-server (or (assoc-ref opts 'key-server) @@ -558,13 +579,17 @@ all are dependent packages: ~{~a~^ ~}~%") (string-append (config-directory) "/upstream/trustedkeys.kbx")))) (for-each - (cut update-package store <> updaters - #:key-download key-download - #:warn? warn?) - packages) + (lambda (update) + (update-package store + (update-spec-package update) + (update-spec-version update) + updaters + #:key-download key-download + #:warn? warn?)) + update-specs) (return #t))) (else (for-each (cut check-for-package-update <> updaters #:warn? warn?) - packages) + (map update-spec-package update-specs)) (return #t))))))))) From f7eaed685842769ffa3f77b62d4d604f110e62a3 Mon Sep 17 00:00:00 2001 From: Hartmut Goebel Date: Fri, 24 Jun 2022 22:36:38 +0200 Subject: [PATCH 768/790] upstream: Allow updating to a specific version. * guix/upstream.scm(package-latest-release): Add keyword-argument 'version' and pass it on to the updater's 'import' function. (package-update): add keyword-argument 'version' and pass it on to package-latest-release. Differentiate the error message issued when no package was found, depending on whether version was given or not. --- guix/upstream.scm | 17 +++++++++++------ 1 file changed, 11 insertions(+), 6 deletions(-) diff --git a/guix/upstream.scm b/guix/upstream.scm index 3b576898ec..f3ab9ab78b 100644 --- a/guix/upstream.scm +++ b/guix/upstream.scm @@ -4,6 +4,7 @@ ;;; Copyright © 2019, 2022 Ricardo Wurmus ;;; Copyright © 2021 Sarah Morgensen ;;; Copyright © 2021, 2022 Maxime Devos +;;; Copyright © 2022 Hartmut Goebel ;;; ;;; This file is part of GNU Guix. ;;; @@ -278,7 +279,8 @@ them matches." (define* (package-latest-release package #:optional - (updaters (force %updaters))) + (updaters (force %updaters)) + #:key (version #f)) "Return an upstream source to update PACKAGE, a object, or #f if none of UPDATERS matches PACKAGE. When several updaters match PACKAGE, try them until one of them returns an upstream source. It is the caller's @@ -287,7 +289,7 @@ one." (any (match-lambda (($ name description pred import) (and (pred package) - (import package)))) + (import package #:version version)))) updaters)) (define* (package-latest-release* package @@ -494,13 +496,13 @@ SOURCE, an ." (define* (package-update store package #:optional (updaters (force %updaters)) - #:key (key-download 'interactive)) + #:key (key-download 'interactive) (version #f)) "Return the new version, the file name of the new version tarball, and input changes for PACKAGE; return #f (three values) when PACKAGE is up-to-date; raise an error when the updater could not determine available releases. KEY-DOWNLOAD specifies a download policy for missing OpenPGP keys; allowed values: 'always', 'never', and 'interactive' (default)." - (match (package-latest-release package updaters) + (match (package-latest-release package updaters #:version version) ((? upstream-source? source) (if (version>? (upstream-source-version source) (package-version package)) @@ -524,8 +526,11 @@ this method: ~s") (values #f #f #f))) (#f ;; Warn rather than abort so that other updates can still take place. - (warning (G_ "updater failed to determine available releases for ~a~%") - (package-name package)) + (if version + (warning (G_ "updater failed to find release ~a@~a~%") + (package-name package) version) + (warning (G_ "updater failed to determine available releases for ~a~%") + (package-name package))) (values #f #f #f)))) (define* (update-package-source package source hash) From 7c476873e0300711bf92668cf01abd28f7295ead Mon Sep 17 00:00:00 2001 From: Hartmut Goebel Date: Sun, 28 Aug 2022 15:00:52 +0200 Subject: [PATCH 769/790] doc: Describe how to update to a specific version. * doc/guix.texi (Invoking guix refresh): Describe how to update to a specific version. --- doc/guix.texi | 19 +++++++++++++++++++ 1 file changed, 19 insertions(+) diff --git a/doc/guix.texi b/doc/guix.texi index efd281d9b0..e94f1c24ed 100644 --- a/doc/guix.texi +++ b/doc/guix.texi @@ -13934,6 +13934,25 @@ gnu/packages/multiprecision.scm:40:12: 6.1.2 is already the latest version of gm @end table +If for some reason you don't want to update to the latest version, you +can update to a specific version by appending an equal sign and the +desired version number to the package specification. Note that not all +updaters support this; an error is reported when an updater cannot +refresh to the specified version. + +@example +$ guix refresh trytond-party +gnu/packages/guile.scm:392:2: guile would be upgraded from 3.0.3 to 3.0.5 +$ guix refresh -u guile=3.0.4 +@dots{} +gnu/packages/guile.scm:392:2: guile: updating from version 3.0.3 to version 3.0.4... +@dots{} +$ guix refresh -u guile@@2.0=2.0.12 +@dots{} +gnu/packages/guile.scm:147:2: guile: updating from version 2.0.10 to version 2.0.12... +@dots{} +@end example + Sometimes the upstream name differs from the package name used in Guix, and @command{guix refresh} needs a little help. Most updaters honor the @code{upstream-name} property in package definitions, which can be used From 60d4652c5d33dd81ed05afd708e6a127584d59cd Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Fri, 9 Dec 2022 00:27:39 -0500 Subject: [PATCH 770/790] image: Enhance compatibility of the root ext4 partition. Generating a raw-with-offset image would previously not be bootable with U-Boot. * gnu/system/image.scm (root-partition) [file-system-options]: New field. --- gnu/system/image.scm | 3 +++ 1 file changed, 3 insertions(+) diff --git a/gnu/system/image.scm b/gnu/system/image.scm index d518a05a51..afef79185f 100644 --- a/gnu/system/image.scm +++ b/gnu/system/image.scm @@ -138,6 +138,9 @@ parent image record." (size 'guess) (label root-label) (file-system "ext4") + ;; Disable the metadata_csum and 64bit features of ext4, for compatibility + ;; with U-Boot. + (file-system-options (list "-O" "^metadata_csum,^64bit")) (flags '(boot)) (initializer (gexp initialize-root-partition)))) From 8f93a1e01a879ae026678dd92c18e2a2a49be540 Mon Sep 17 00:00:00 2001 From: Andrew Tropin Date: Tue, 27 Dec 2022 12:35:41 +0400 Subject: [PATCH 771/790] snippets: Remove unwanted git-commit-mode invocation. We only need to check if git-commit-mode is t, not enable it in all text-mode buffers. * etc/snippets/tempel/text-mode: Remove unwanted git-commit-mode invocation. --- etc/snippets/tempel/text-mode | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/etc/snippets/tempel/text-mode b/etc/snippets/tempel/text-mode index fd0e95eaa6..1cda91cba0 100644 --- a/etc/snippets/tempel/text-mode +++ b/etc/snippets/tempel/text-mode @@ -1,6 +1,6 @@ -*- mode: lisp-data -*- -text-mode :when (and (fboundp 'git-commit-mode) (git-commit-mode)) +text-mode :when (and (fboundp 'git-commit-mode) git-commit-mode) (add\ "gnu: Add " (p (with-temp-buffer From 86e4c50e25396e7a115948556b90930938487528 Mon Sep 17 00:00:00 2001 From: Leo Famulari Date: Tue, 27 Dec 2022 12:48:14 -0500 Subject: [PATCH 772/790] gnu: linux-libre-documentation: Organize. This package was miscategorized as a "Generic kernel package". * gnu/packages/linux.scm (linux-libre-documentation): Move variable into its own section. --- gnu/packages/linux.scm | 78 ++++++++++++++++++++++-------------------- 1 file changed, 41 insertions(+), 37 deletions(-) diff --git a/gnu/packages/linux.scm b/gnu/packages/linux.scm index ddf7025832..568c2b6b92 100644 --- a/gnu/packages/linux.scm +++ b/gnu/packages/linux.scm @@ -1085,43 +1085,6 @@ Linux kernel. It has been modified to remove all non-free binary blobs.") (define-public linux-libre-source linux-libre-6.0-source) (define-public linux-libre linux-libre-6.0) -(define-public linux-libre-documentation - (package - (inherit linux-libre) - (name "linux-libre-documentation") - (arguments - (list - #:tests? #f - #:phases #~(modify-phases %standard-phases - (delete 'configure) - (replace 'build - (lambda _ - (substitute* "Documentation/Makefile" - ;; Remove problematic environment check script. - ((".*scripts/sphinx-pre-install.*") "")) - (invoke "make" "infodocs"))) - (replace 'install - (lambda _ - (let* ((info-dir (string-append #$output "/share/info")) - (info (string-append info-dir - "/TheLinuxKernel.info.gz"))) - (with-directory-excursion "Documentation/output" - (invoke "make" "-C" "texinfo" "install-info" - (string-append "infodir=" info-dir))) - ;; Create a symlink, for convenience. - (symlink info (string-append info-dir - "/linux.info.gz")))))))) - (native-inputs - (list graphviz - perl - python - python-sphinx - texinfo - which)) - (synopsis "Documentation for the kernel Linux-Libre") - (description "This package provides the documentation for the kernel -Linux-Libre, as an Info manual. To consult it, run @samp{info linux}."))) - (define-public linux-libre-5.15 (make-linux-libre* linux-libre-5.15-version linux-libre-5.15-gnu-revision @@ -1903,6 +1866,47 @@ login password to @code{gpg-agent}. This can be useful if you are using a GnuPG-based password manager like @code{pass}.") (license license:gpl3+))) + +;;; +;;; Kernel documentation +;;; + +(define-public linux-libre-documentation + (package + (inherit linux-libre) + (name "linux-libre-documentation") + (arguments + (list + #:tests? #f + #:phases #~(modify-phases %standard-phases + (delete 'configure) + (replace 'build + (lambda _ + (substitute* "Documentation/Makefile" + ;; Remove problematic environment check script. + ((".*scripts/sphinx-pre-install.*") "")) + (invoke "make" "infodocs"))) + (replace 'install + (lambda _ + (let* ((info-dir (string-append #$output "/share/info")) + (info (string-append info-dir + "/TheLinuxKernel.info.gz"))) + (with-directory-excursion "Documentation/output" + (invoke "make" "-C" "texinfo" "install-info" + (string-append "infodir=" info-dir))) + ;; Create a symlink, for convenience. + (symlink info (string-append info-dir + "/linux.info.gz")))))))) + (native-inputs + (list graphviz + perl + python + python-sphinx + texinfo + which)) + (synopsis "Documentation for the kernel Linux-Libre") + (description "This package provides the documentation for the kernel +Linux-Libre, as an Info manual. To consult it, run @samp{info linux}."))) ;;; ;;; Miscellaneous. From aeb42167fd869275151294f045f6924d5c6cda57 Mon Sep 17 00:00:00 2001 From: Leo Famulari Date: Sun, 25 Dec 2022 12:59:17 -0500 Subject: [PATCH 773/790] gnu: Borg: Update to 1.2.3. * gnu/packages/backup.scm (borg): Update to 1.2.3. --- gnu/packages/backup.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/backup.scm b/gnu/packages/backup.scm index 00d95e7b3d..8e629c2592 100644 --- a/gnu/packages/backup.scm +++ b/gnu/packages/backup.scm @@ -633,13 +633,13 @@ detection, and lossless compression.") (define-public borg (package (name "borg") - (version "1.2.2") + (version "1.2.3") (source (origin (method url-fetch) (uri (pypi-uri "borgbackup" version)) (sha256 - (base32 "0q3jwmwwa3jlb02cbkcgh5a9cvwg64vawaypn41bdgpi8ds6hc6p")) + (base32 "11b7jqv9sw22a9512b270d12k3mrcgmmcaimh6bgm5iwcgw1h973")) (modules '((guix build utils))) (snippet #~(begin From fd0e69984f25bdf2405cf33b15a8bbb2010a7b85 Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Tue, 27 Dec 2022 12:15:55 -0500 Subject: [PATCH 774/790] gnu: jami: Update to 20221220.0956.79e1207. * gnu/packages/jami.scm (%jami-version): Update to 20221220.0956.79e1207. (%jami-sources): Remove all but the 'jami-disable-integration-tests.patch' and 'jami-libjami-headers-search.patch' patches. * gnu/packages/patches/jami-fix-qml-imports.patch: Delete file. * gnu/packages/patches/jami-fix-unit-tests-build.patch: Likewise. * gnu/packages/patches/jami-no-webengine.patch: Likewise. * gnu/packages/patches/jami-sip-contacts.patch: Likewise. * gnu/packages/patches/jami-sip-unregister.patch: Likewise. * gnu/packages/patches/jami-sipaccount-segfault.patch: Likewise. * gnu/packages/patches/jami-xcb-link.patch: Likewise. * gnu/local.mk (dist_patch_DATA): De-register them. --- gnu/local.mk | 7 - gnu/packages/jami.scm | 13 +- .../patches/jami-fix-qml-imports.patch | 78 ------ .../patches/jami-fix-unit-tests-build.patch | 139 ---------- gnu/packages/patches/jami-no-webengine.patch | 243 ------------------ gnu/packages/patches/jami-sip-contacts.patch | 38 --- .../patches/jami-sip-unregister.patch | 48 ---- .../patches/jami-sipaccount-segfault.patch | 30 --- gnu/packages/patches/jami-xcb-link.patch | 72 ------ 9 files changed, 3 insertions(+), 665 deletions(-) delete mode 100644 gnu/packages/patches/jami-fix-qml-imports.patch delete mode 100644 gnu/packages/patches/jami-fix-unit-tests-build.patch delete mode 100644 gnu/packages/patches/jami-no-webengine.patch delete mode 100644 gnu/packages/patches/jami-sip-contacts.patch delete mode 100644 gnu/packages/patches/jami-sip-unregister.patch delete mode 100644 gnu/packages/patches/jami-sipaccount-segfault.patch delete mode 100644 gnu/packages/patches/jami-xcb-link.patch diff --git a/gnu/local.mk b/gnu/local.mk index 034131b5f8..0d4028a161 100644 --- a/gnu/local.mk +++ b/gnu/local.mk @@ -1343,14 +1343,7 @@ dist_patch_DATA = \ %D%/packages/patches/isl-0.11.1-aarch64-support.patch \ %D%/packages/patches/itk-snap-alt-glibc-compat.patch \ %D%/packages/patches/jami-disable-integration-tests.patch \ - %D%/packages/patches/jami-fix-qml-imports.patch \ - %D%/packages/patches/jami-fix-unit-tests-build.patch \ %D%/packages/patches/jami-libjami-headers-search.patch \ - %D%/packages/patches/jami-no-webengine.patch \ - %D%/packages/patches/jami-sipaccount-segfault.patch \ - %D%/packages/patches/jami-sip-contacts.patch \ - %D%/packages/patches/jami-sip-unregister.patch \ - %D%/packages/patches/jami-xcb-link.patch \ %D%/packages/patches/jamvm-1.5.1-aarch64-support.patch \ %D%/packages/patches/jamvm-1.5.1-armv7-support.patch \ %D%/packages/patches/jamvm-2.0.0-aarch64-support.patch \ diff --git a/gnu/packages/jami.scm b/gnu/packages/jami.scm index 3bdcabdc17..a50d0cd309 100644 --- a/gnu/packages/jami.scm +++ b/gnu/packages/jami.scm @@ -69,7 +69,7 @@ #:use-module (guix packages) #:use-module (guix utils)) -(define %jami-version "20221031.1308.130cc26") +(define %jami-version "20221220.0956.79e1207") (define %jami-sources ;; Return an origin object of the tarball release sources archive of the @@ -93,16 +93,9 @@ "plugins")))) (sha256 (base32 - "0hbsjjs61n7268lyjnjb9lzfpkkd65fmz76l1bg4awlz1f3cyywm")) + "0g5709rmb9944s0ij9g4pm1b871f5z0s5nawvm10z14wx3y1np8m")) (patches (search-patches "jami-disable-integration-tests.patch" - "jami-libjami-headers-search.patch" - "jami-fix-unit-tests-build.patch" - "jami-fix-qml-imports.patch" - "jami-no-webengine.patch" - "jami-sipaccount-segfault.patch" - "jami-sip-contacts.patch" - "jami-sip-unregister.patch" - "jami-xcb-link.patch")))) + "jami-libjami-headers-search.patch")))) ;; Jami maintains a set of patches for some key dependencies (currently ;; pjproject and ffmpeg) of Jami that haven't yet been integrated upstream. diff --git a/gnu/packages/patches/jami-fix-qml-imports.patch b/gnu/packages/patches/jami-fix-qml-imports.patch deleted file mode 100644 index e24171785d..0000000000 --- a/gnu/packages/patches/jami-fix-qml-imports.patch +++ /dev/null @@ -1,78 +0,0 @@ -From 9c4d065093d18b5495d3193028457b7393daea4b Mon Sep 17 00:00:00 2001 -From: Maxim Cournoyer -Date: Mon, 7 Nov 2022 16:26:50 -0500 -Subject: [PATCH] tests: Fix broken QML import directives. - -Fixes -. - -Automated via: - $ find tests -name '*.qml' | xargs sed -i 's,qrc:/src,../../../src,' - -Change-Id: Ic1a2f419e3e328e8bf861e7fdf370f15da66675f ---- -Upstream status: https://review.jami.net/c/jami-client-qt/+/22990 - - tests/qml/src/tst_ChatViewFooter.qml | 2 +- - tests/qml/src/tst_FilesToSendContainer.qml | 2 +- - tests/qml/src/tst_PresenceIndicator.qml | 2 +- - tests/qml/src/tst_WizardView.qml | 4 ++-- - 4 files changed, 5 insertions(+), 5 deletions(-) - -diff --git a/client-qt/tests/qml/src/tst_ChatViewFooter.qml b/client-qt/tests/qml/src/tst_ChatViewFooter.qml -index 84316d78..b0cffe1a 100644 ---- a/client-qt/tests/qml/src/tst_ChatViewFooter.qml -+++ b/client-qt/tests/qml/src/tst_ChatViewFooter.qml -@@ -25,7 +25,7 @@ import QtTest - import net.jami.Models 1.1 - import net.jami.Constants 1.1 - --import "qrc:/src/app/mainview/components" -+import "../../../src/app/mainview/components" - - ColumnLayout { - id: root -diff --git a/client-qt/tests/qml/src/tst_FilesToSendContainer.qml b/client-qt/tests/qml/src/tst_FilesToSendContainer.qml -index b7f4810a..9432a44d 100644 ---- a/client-qt/tests/qml/src/tst_FilesToSendContainer.qml -+++ b/client-qt/tests/qml/src/tst_FilesToSendContainer.qml -@@ -25,7 +25,7 @@ import QtTest - import net.jami.Models 1.1 - import net.jami.Constants 1.1 - --import "qrc:/src/app/mainview/components" -+import "../../../src/app/mainview/components" - - ColumnLayout { - id: root -diff --git a/client-qt/tests/qml/src/tst_PresenceIndicator.qml b/client-qt/tests/qml/src/tst_PresenceIndicator.qml -index 0eda9169..46c048e8 100644 ---- a/client-qt/tests/qml/src/tst_PresenceIndicator.qml -+++ b/client-qt/tests/qml/src/tst_PresenceIndicator.qml -@@ -22,7 +22,7 @@ import QtTest - import net.jami.Models 1.1 - import net.jami.Constants 1.1 - --import "qrc:/src/app/commoncomponents" -+import "../../../src/app/commoncomponents" - - PresenceIndicator { - id: uut -diff --git a/client-qt/tests/qml/src/tst_WizardView.qml b/client-qt/tests/qml/src/tst_WizardView.qml -index 08698b7a..6a4f971d 100644 ---- a/client-qt/tests/qml/src/tst_WizardView.qml -+++ b/client-qt/tests/qml/src/tst_WizardView.qml -@@ -24,8 +24,8 @@ import net.jami.Models 1.1 - import net.jami.Constants 1.1 - import net.jami.Enums 1.1 - --import "qrc:/src/app/wizardview" --import "qrc:/src/app/commoncomponents" -+import "../../../src/app/wizardview" -+import "../../../src/app/commoncomponents" - - WizardView { - id: uut --- -2.37.3 - diff --git a/gnu/packages/patches/jami-fix-unit-tests-build.patch b/gnu/packages/patches/jami-fix-unit-tests-build.patch deleted file mode 100644 index 0216a4bd67..0000000000 --- a/gnu/packages/patches/jami-fix-unit-tests-build.patch +++ /dev/null @@ -1,139 +0,0 @@ -From 82ecd786a29344d57e6dd95ef0800bef9dd44542 Mon Sep 17 00:00:00 2001 -From: Maxim Cournoyer -Date: Sun, 6 Nov 2022 00:16:34 -0400 -Subject: [PATCH 3/3] tests: Fix various compilation failures. - -Fixes . - -* tests/CMakeLists.txt: Add "Widgets" Qt module to find_package call. -(QML_TEST_LIBS): Add Qt::Widgets. -* tests/CMakeLists.txt: Rename QML_LIBS to QT_LIBS, a regression -introduced in d82e3820706214d15d7cb7462978b7a43b798355. Remove the -dependency on on the Widgets module, now provided via QT_LIBS. -* tests/qml/main.cpp [WITH_WEBENGINE]: Include QtWebEngine modules -conditionally. -(main) [WITH_WEBENGINE]: Initialize webengine conditionally. -* tests/CMakeLists.txt: Link test objects with ${LIBCLIENT_NAME}. -* src/app/qmlregister.h (registerTypes): Change parent type from -MainApplication* to QObject* -* src/app/qmlregister.cpp (registerTypes): Likewise. -* tests/unittests/account_unittest.cpp (globalEnv): Remove variable. -* tests/unittests/contact_unittest.cpp: Likewise. ---- -Upstream status: https://review.jami.net/c/jami-client-qt/+/22984/1 - - src/app/qmlregister.cpp | 2 +- - src/app/qmlregister.h | 2 +- - tests/CMakeLists.txt | 6 +++--- - tests/qml/main.cpp | 7 ++++--- - tests/unittests/account_unittest.cpp | 2 -- - tests/unittests/contact_unittest.cpp | 2 -- - 6 files changed, 9 insertions(+), 12 deletions(-) - -diff --git a/client-qt/client-qt/src/app/qmlregister.cpp b/client-qt/src/app/qmlregister.cpp -index 285f7814..67222eb5 100644 ---- a/client-qt/client-qt/src/app/qmlregister.cpp -+++ b/client-qt/src/app/qmlregister.cpp -@@ -105,7 +105,7 @@ registerTypes(QQmlEngine* engine, - AppSettingsManager* settingsManager, - PreviewEngine* previewEngine, - ScreenInfo* screenInfo, -- MainApplication* parent) -+ QObject* parent) - { - // setup the adapters (their lifetimes are that of MainApplication) - auto callAdapter = new CallAdapter(systemTray, lrcInstance, parent); -diff --git a/client-qt/client-qt/src/app/qmlregister.h b/client-qt/src/app/qmlregister.h -index 38bfd091..aac0a887 100644 ---- a/client-qt/client-qt/src/app/qmlregister.h -+++ b/client-qt/src/app/qmlregister.h -@@ -67,5 +67,5 @@ void registerTypes(QQmlEngine* engine, - AppSettingsManager* appSettingsManager, - PreviewEngine* previewEngine, - ScreenInfo* screenInfo, -- MainApplication* parent); -+ QObject* parent); - } -diff --git a/client-qt/client-qt/tests/CMakeLists.txt b/client-qt/tests/CMakeLists.txt -index 8904d5ec..4e42b307 100644 ---- a/client-qt/client-qt/tests/CMakeLists.txt -+++ b/client-qt/tests/CMakeLists.txt -@@ -1,4 +1,4 @@ --find_package(Qt${QT_VERSION_MAJOR} CONFIG REQUIRED QuickTest Test) -+find_package(Qt${QT_VERSION_MAJOR} CONFIG REQUIRED QuickTest Test Widgets) - - if(MSVC) - # Download and unpack googletest for windows -@@ -15,7 +15,7 @@ else() - endif() - - enable_testing(true) --set(QML_TEST_LIBS ${QML_LIBS} Qt::QuickTest Qt::Test) -+set(QML_TEST_LIBS ${QT_LIBS} ${LIBCLIENT_NAME} Qt::QuickTest Qt::Test Qt::Widgets) - set(TESTS_INCLUDES - ${CMAKE_SOURCE_DIR}/src - ${CMAKE_SOURCE_DIR}/tests/qml -@@ -192,4 +192,4 @@ else() - ${LRC}/include) - - add_test(NAME UnitTests COMMAND unittests) --endif() -\ No newline at end of file -+endif() -diff --git a/client-qt/client-qt/tests/qml/main.cpp b/client-qt/tests/qml/main.cpp -index 09c02f3e..4c42027c 100644 ---- a/client-qt/client-qt/tests/qml/main.cpp -+++ b/client-qt/tests/qml/main.cpp -@@ -31,9 +31,10 @@ - #include - #include - #include -+#ifdef WITH_WEBENGINE - #include - #include -- -+#endif - #ifdef Q_OS_WIN - #include - #endif -@@ -155,9 +156,9 @@ main(int argc, char** argv) - // Adjust the argument count. - argc = std::distance(argv, end); - } -- -+#ifdef WITH_WEBENGINE - QtWebEngineQuick::initialize(); -- -+#endif - QTEST_SET_MAIN_SOURCE_PATH - Setup setup(muteDring); - return quick_test_main_with_setup(argc, argv, "qml_test", nullptr, &setup); -diff --git a/client-qt/client-qt/tests/unittests/account_unittest.cpp b/client-qt/tests/unittests/account_unittest.cpp -index aa98453e..5af2ad6e 100644 ---- a/client-qt/client-qt/tests/unittests/account_unittest.cpp -+++ b/client-qt/tests/unittests/account_unittest.cpp -@@ -19,8 +19,6 @@ - - #include "globaltestenvironment.h" - --TestEnvironment globalEnv; -- - /*! - * Test fixture for AccountAdapter testing - */ -diff --git a/client-qt/client-qt/tests/unittests/contact_unittest.cpp b/client-qt/tests/unittests/contact_unittest.cpp -index af8a9a22..b05cc856 100644 ---- a/client-qt/client-qt/tests/unittests/contact_unittest.cpp -+++ b/client-qt/tests/unittests/contact_unittest.cpp -@@ -18,8 +18,6 @@ - - #include "globaltestenvironment.h" - --TestEnvironment globalEnv; -- - /*! - * Test fixture for AccountAdapter testing - */ --- -2.37.3 - diff --git a/gnu/packages/patches/jami-no-webengine.patch b/gnu/packages/patches/jami-no-webengine.patch deleted file mode 100644 index f26cd8e3f5..0000000000 --- a/gnu/packages/patches/jami-no-webengine.patch +++ /dev/null @@ -1,243 +0,0 @@ -From 1f73d3c88e94f2d932c59cab8a02c72a325ccc20 Mon Sep 17 00:00:00 2001 -From: =?UTF-8?q?S=C3=A9bastien=20Blin?= - -Date: Fri, 11 Nov 2022 16:19:11 -0500 -Subject: [PATCH] misc: fix build without webengine - -Change-Id: I2511cd89e1ce7f60424f69ab6576d7fb992dd58c -GitLab: #881 ---- - .../components/DocumentsScrollview.qml | 1 - - src/app/mainview/components/FilePreview.qml | 1 - - src/app/mainview/components/MediaPreview.qml | 57 ++-------------- - .../mainview/components/SwarmDetailsPanel.qml | 1 - - src/app/nowebengine/VideoPreview.qml | 24 +++++++ - src/app/webengine/VideoPreview.qml | 68 +++++++++++++++++++ - 6 files changed, 99 insertions(+), 53 deletions(-) - create mode 100644 src/app/nowebengine/VideoPreview.qml - create mode 100644 src/app/webengine/VideoPreview.qml - -diff --git a/client-qt/src/app/mainview/components/DocumentsScrollview.qml b/client-qt/src/app/mainview/components/DocumentsScrollview.qml -index df516961..3338536a 100644 ---- a/client-qt/src/app/mainview/components/DocumentsScrollview.qml -+++ b/client-qt/src/app/mainview/components/DocumentsScrollview.qml -@@ -20,7 +20,6 @@ import QtQuick.Controls - import QtQuick.Layouts - import Qt.labs.platform - import Qt5Compat.GraphicalEffects --import QtWebEngine - - import net.jami.Models 1.1 - import net.jami.Adapters 1.1 -diff --git a/client-qt/src/app/mainview/components/FilePreview.qml b/client-qt/src/app/mainview/components/FilePreview.qml -index 57b1ec8b..fe8f3fd9 100644 ---- a/client-qt/src/app/mainview/components/FilePreview.qml -+++ b/client-qt/src/app/mainview/components/FilePreview.qml -@@ -19,7 +19,6 @@ import QtQuick.Controls - import QtQuick.Layouts - import Qt.labs.platform - import Qt5Compat.GraphicalEffects --import QtWebEngine - - import net.jami.Models 1.1 - import net.jami.Adapters 1.1 -diff --git a/client-qt/src/app/mainview/components/MediaPreview.qml b/client-qt/src/app/mainview/components/MediaPreview.qml -index 0c33bf3e..965f9343 100644 ---- a/client-qt/src/app/mainview/components/MediaPreview.qml -+++ b/client-qt/src/app/mainview/components/MediaPreview.qml -@@ -19,7 +19,6 @@ import QtQuick.Controls - import QtQuick.Layouts - import Qt.labs.platform - import Qt5Compat.GraphicalEffects --import QtWebEngine - - import net.jami.Models 1.1 - import net.jami.Adapters 1.1 -@@ -92,59 +91,17 @@ Component { - } - Component { - id: avMediaComp -- - Loader { -- property real msgRadius: 20 -- -- Rectangle { -- id: videoAudioRect -- color: JamiTheme.secondaryBackgroundColor -- anchors.fill: parent -- -- WebEngineView { -- id: wev -- -- property bool isVideo: mediaInfo.isVideo -- property string html: mediaInfo.html -- -- anchors.fill: parent -- anchors.verticalCenter: videoAudioRect.verticalCenter -- backgroundColor: JamiTheme.secondaryBackgroundColor -- anchors.topMargin: isVideo? 0 : wev.implicitHeight / 2 -- settings.fullScreenSupportEnabled: isVideo -- settings.javascriptCanOpenWindows: false -- Component.onCompleted: loadHtml(html, 'file://') -- onFullScreenRequested: function(request) { -- if (request.toggleOn) { -- layoutManager.pushFullScreenItem( -- this, -- videoAudioRect, -- null, -- function() { wev.fullScreenCancelled() }) -- } else if (!request.toggleOn) { -- layoutManager.removeFullScreenItem(this) -- } -- request.accept() -- } -- } -- -- layer.enabled: true -- layer.effect: OpacityMask { -- maskSource: Item { -- width: videoAudioRect.width -- height: videoAudioRect.height -- Rectangle { -- anchors.centerIn: parent -- width: videoAudioRect.width -- height: videoAudioRect.height -- radius: JamiTheme.swarmDetailsPageDocumentsMediaRadius -- } -- } -- } -+ Component.onCompleted: { -+ var qml = WITH_WEBENGINE ? -+ "qrc:/webengine/VideoPreview.qml" : -+ "qrc:/nowebengine/VideoPreview.qml" -+ setSource( qml, { isVideo: mediaInfo.isVideo, html:mediaInfo.html } ) - } -+ -+ property real msgRadius: 20 - } - } -- - Component { - id: imageMediaComp - -diff --git a/client-qt/src/app/mainview/components/SwarmDetailsPanel.qml b/client-qt/src/app/mainview/components/SwarmDetailsPanel.qml -index 0dd93bc2..7625a76e 100644 ---- a/client-qt/src/app/mainview/components/SwarmDetailsPanel.qml -+++ b/client-qt/src/app/mainview/components/SwarmDetailsPanel.qml -@@ -21,7 +21,6 @@ import QtQuick.Controls - import QtQuick.Layouts - import Qt.labs.platform - import Qt5Compat.GraphicalEffects --import QtWebEngine - - import net.jami.Models 1.1 - import net.jami.Adapters 1.1 -diff --git a/client-qt/src/app/nowebengine/VideoPreview.qml b/client-qt/src/app/nowebengine/VideoPreview.qml -new file mode 100644 -index 00000000..8c2e8a4f ---- /dev/null -+++ b/client-qt/src/app/nowebengine/VideoPreview.qml -@@ -0,0 +1,24 @@ -+/* -+ * Copyright (C) 2022 Savoir-faire Linux Inc. -+ * -+ * This program is free software; you can redistribute it and/or modify -+ * it under the terms of the GNU General Public License as published by -+ * the Free Software Foundation; either version 3 of the License, or -+ * (at your option) any later version. -+ * -+ * This program is distributed in the hope that it will be useful, -+ * but WITHOUT ANY WARRANTY; without even the implied warranty of -+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the -+ * GNU General Public License for more details. -+ * -+ * You should have received a copy of the GNU General Public License -+ * along with this program. If not, see . -+ */ -+ -+import QtQuick -+import QtQuick.Controls -+import QtQuick.Layouts -+ -+Rectangle { -+ property var mediaInfo: undefined -+} -\ No newline at end of file -diff --git a/client-qt/src/app/webengine/VideoPreview.qml b/client-qt/src/app/webengine/VideoPreview.qml -new file mode 100644 -index 00000000..edc03599 ---- /dev/null -+++ b/client-qt/src/app/webengine/VideoPreview.qml -@@ -0,0 +1,68 @@ -+/* -+ * Copyright (C) 2022 Savoir-faire Linux Inc. -+ * -+ * This program is free software; you can redistribute it and/or modify -+ * it under the terms of the GNU General Public License as published by -+ * the Free Software Foundation; either version 3 of the License, or -+ * (at your option) any later version. -+ * -+ * This program is distributed in the hope that it will be useful, -+ * but WITHOUT ANY WARRANTY; without even the implied warranty of -+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the -+ * GNU General Public License for more details. -+ * -+ * You should have received a copy of the GNU General Public License -+ * along with this program. If not, see . -+ */ -+ -+import QtQuick -+import QtWebEngine -+import Qt5Compat.GraphicalEffects -+ -+import net.jami.Constants 1.1 -+ -+Rectangle { -+ id: root -+ color: JamiTheme.secondaryBackgroundColor -+ anchors.fill: parent -+ property bool isVideo: false -+ property string html: "" -+ -+ WebEngineView { -+ id: wev -+ -+ anchors.fill: parent -+ anchors.verticalCenter: root.verticalCenter -+ backgroundColor: JamiTheme.secondaryBackgroundColor -+ anchors.topMargin: root.isVideo? 0 : wev.implicitHeight / 2 -+ settings.fullScreenSupportEnabled: root.isVideo -+ settings.javascriptCanOpenWindows: false -+ Component.onCompleted: loadHtml(root.html, 'file://') -+ onFullScreenRequested: function(request) { -+ if (request.toggleOn) { -+ layoutManager.pushFullScreenItem( -+ this, -+ root, -+ null, -+ function() { wev.fullScreenCancelled() }) -+ } else if (!request.toggleOn) { -+ layoutManager.removeFullScreenItem(this) -+ } -+ request.accept() -+ } -+ } -+ -+ layer.enabled: true -+ layer.effect: OpacityMask { -+ maskSource: Item { -+ width: root.width -+ height: root.height -+ Rectangle { -+ anchors.centerIn: parent -+ width: root.width -+ height: root.height -+ radius: JamiTheme.swarmDetailsPageDocumentsMediaRadius -+ } -+ } -+ } -+} -\ No newline at end of file --- -2.37.3 - diff --git a/gnu/packages/patches/jami-sip-contacts.patch b/gnu/packages/patches/jami-sip-contacts.patch deleted file mode 100644 index dce8f6b98d..0000000000 --- a/gnu/packages/patches/jami-sip-contacts.patch +++ /dev/null @@ -1,38 +0,0 @@ -From 3ba007d02bc19e499c8f3c2345302453028831a8 Mon Sep 17 00:00:00 2001 -From: =?UTF-8?q?S=C3=A9bastien=20Blin?= - -Date: Tue, 29 Nov 2022 09:26:20 -0500 -Subject: [PATCH] misc: fix incoming message sip - -We do not need to check contacts for SIP as it will be considered -automatically as a contact - -Change-Id: If78113e9d79dcd695c39c2d12c0441e2cb282737 ---- - src/libclient/conversationmodel.cpp | 8 ++++++-- - 1 file changed, 6 insertions(+), 2 deletions(-) - -diff --git a/client-qt/src/libclient/conversationmodel.cpp b/client-qt/src/libclient/conversationmodel.cpp -index dba206bd..5604a17c 100644 ---- a/client-qt/src/libclient/conversationmodel.cpp -+++ b/client-qt/src/libclient/conversationmodel.cpp -@@ -3611,8 +3611,12 @@ ConversationModelPimpl::addIncomingMessage(const QString& peerId, - try { - auto contact = linked.owner.contactModel->getContact(peerId); - isRequest = contact.profileInfo.type == profile::Type::PENDING; -- if (isRequest && !contact.isBanned && peerId != linked.owner.profileInfo.uri) { -- addContactRequest(peerId); -+ // if isSip, it will be a contact! -+ auto isSip = linked.owner.profileInfo.type == profile::Type::SIP; -+ if (isSip -+ || (isRequest && !contact.isBanned && peerId != linked.owner.profileInfo.uri)) { -+ if (!isSip) -+ addContactRequest(peerId); - convIds.push_back(storage::beginConversationWithPeer(db, contact.profileInfo.uri)); - auto& conv = getConversationForPeerUri(contact.profileInfo.uri).get(); - conv.uid = convIds[0]; - -base-commit: 6f30acf0043d07dcbe63ee8636509885a9b6fd76 --- -2.38.1 - diff --git a/gnu/packages/patches/jami-sip-unregister.patch b/gnu/packages/patches/jami-sip-unregister.patch deleted file mode 100644 index 1f0302bb12..0000000000 --- a/gnu/packages/patches/jami-sip-unregister.patch +++ /dev/null @@ -1,48 +0,0 @@ -From c1e6d664601b35a466f4e02e86a2c8181fdcca12 Mon Sep 17 00:00:00 2001 -From: Antoine Noreau -Date: Thu, 3 Nov 2022 15:35:40 -0400 -Subject: [PATCH] sip: ensure correct unregister upon closure - -Ensure SIP connections are gracefully terminated: -Removed duplicated register calls to SIP server - -Change-Id: I330e67cf9534504f92517996eb7b693b43d359d3 -Gitlab: #786 ---- - src/upnp/upnp_context.cpp | 11 ++++++++--- - 1 file changed, 8 insertions(+), 3 deletions(-) - -diff --git a/daemon/src/upnp/upnp_context.cpp b/daemon/src/upnp/upnp_context.cpp -index a447e2d75..c68fe502c 100644 ---- a/daemon/src/upnp/upnp_context.cpp -+++ b/daemon/src/upnp/upnp_context.cpp -@@ -143,7 +143,7 @@ void - UPnPContext::stopUpnp(bool forceRelease) - { - if (not isValidThread()) { -- runOnUpnpContextQueue([this] { stopUpnp(); }); -+ runOnUpnpContextQueue([this, forceRelease] { stopUpnp(forceRelease); }); - return; - } - -@@ -168,10 +168,15 @@ UPnPContext::stopUpnp(bool forceRelease) - preferredIgd_.reset(); - validIgdList_.clear(); - } -- - for (auto const& map : toRemoveList) { - requestRemoveMapping(map); -- updateMappingState(map, MappingState::FAILED); -+ -+ /* Notify is not needed in updateMappingState when -+ shutting down (hence set it to false). NotifyCallback -+ would trigger a new SIP registration and create a -+ false registered state upon program close. */ -+ -+ updateMappingState(map, MappingState::FAILED, false); - // We dont remove mappings with auto-update enabled, - // unless forceRelease is true. - if (not map->getAutoUpdate() or forceRelease) { --- -2.37.3 - diff --git a/gnu/packages/patches/jami-sipaccount-segfault.patch b/gnu/packages/patches/jami-sipaccount-segfault.patch deleted file mode 100644 index 1cef512124..0000000000 --- a/gnu/packages/patches/jami-sipaccount-segfault.patch +++ /dev/null @@ -1,30 +0,0 @@ -From e5a449d60abc667d85dacd75ad6e31d4ddca5853 Mon Sep 17 00:00:00 2001 -From: =?UTF-8?q?S=C3=A9bastien=20Blin?= - -Date: Thu, 17 Nov 2022 12:02:20 -0500 -Subject: [PATCH] sipaccount: fix potential null dereference - -Detected by sonarqube - -Change-Id: I606f9cf2458dda07471d0a67af8915c7ca13d410 ---- - src/sip/sipaccount.cpp | 3 ++- - 1 file changed, 2 insertions(+), 1 deletion(-) - -diff --git a/daemon/src/sip/sipaccount.cpp b/daemon/src/sip/sipaccount.cpp -index 695b71839..e544ac31a 100644 ---- a/daemon/src/sip/sipaccount.cpp -+++ b/daemon/src/sip/sipaccount.cpp -@@ -789,7 +789,8 @@ SIPAccount::sendRegister() - if (pjsip_regc_set_transport(regc, &tp_sel) != PJ_SUCCESS) - throw VoipLinkException("Unable to set transport"); - -- setUpTransmissionData(tdata, tp_sel.u.transport->key.type); -+ if (tp_sel.u.transport) -+ setUpTransmissionData(tdata, tp_sel.u.transport->key.type); - - // pjsip_regc_send increment the transport ref count by one, - if ((status = pjsip_regc_send(regc, tdata)) != PJ_SUCCESS) { --- -GitLab - diff --git a/gnu/packages/patches/jami-xcb-link.patch b/gnu/packages/patches/jami-xcb-link.patch deleted file mode 100644 index 6879493123..0000000000 --- a/gnu/packages/patches/jami-xcb-link.patch +++ /dev/null @@ -1,72 +0,0 @@ -From 3db2a7802422e69f50030db854abfb72fbc9caa4 Mon Sep 17 00:00:00 2001 -From: Maxim Cournoyer -Date: Fri, 11 Nov 2022 22:38:32 -0500 -Subject: [PATCH] Move xcb include/link directives from jami to libclient. - -Relates to . - -This problem was discovered when attempting to build the test suite: - - ld: ../src/libclient/liblibjamiclient.a(avmodel.cpp.o): undefined - reference to symbol 'xcb_get_setup' - -* CMakeLists.txt: [!(APPLE or MSVC] Move xcb includes and link directives to... -* src/libclient/CMakeLists.txt [!(APPLE or MSVC]: ... here. - -Change-Id: If9b6653e157081300caad8f13cafe4979a49630b ---- - CMakeLists.txt | 6 +----- - src/libclient/CMakeLists.txt | 6 ++++++ - 2 files changed, 7 insertions(+), 5 deletions(-) - -diff --git a/client-qt/CMakeLists.txt b/client-qt/CMakeLists.txt -index d0a8fd70..2a09fd6c 100644 ---- a/client-qt/CMakeLists.txt -+++ b/client-qt/CMakeLists.txt -@@ -384,8 +384,6 @@ elseif (NOT APPLE) - add_definitions(${LIBGDKPIXBUF_CFLAGS}) - endif() - -- pkg_check_modules(XCB xcb) -- - list(PREPEND CMAKE_PREFIX_PATH - ${LIBJAMI_CONTRIB_DIR}/native/ffmpeg/libavutil) - pkg_check_modules(LIBAVUTIL libavutil>=55.75.100) -@@ -398,7 +396,6 @@ elseif (NOT APPLE) - ${LIBNOTIFY_INCLUDE_DIRS} - ${LIBGDKPIXBUF_INCLUDE_DIRS} - ${GLIB_INCLUDE_DIRS} -- ${XCB_INCLUDE_DIRS} - ${LIBAVUTIL_INCLUDE_DIRS}) - - set(JAMI_DATA_PREFIX "${CMAKE_INSTALL_PREFIX}/share") -@@ -586,8 +583,7 @@ elseif (NOT APPLE) - ${LIBNOTIFY_LIBRARIES} - ${LIBGDKPIXBUF_LIBRARIES} - ${GLIB_LIBRARIES} -- ${GIO_LIBRARIES} -- ${XCB_LIBRARIES}) -+ ${GIO_LIBRARIES}) - - # Installation rules - install( -diff --git a/client-qt/src/libclient/CMakeLists.txt b/client-qt/src/libclient/CMakeLists.txt -index 99780f5f..1dd32677 100644 ---- a/client-qt/src/libclient/CMakeLists.txt -+++ b/client-qt/src/libclient/CMakeLists.txt -@@ -475,6 +475,12 @@ add_library(${LIBCLIENT_NAME} STATIC - foreach(QT_LIB ${QT_LIBS}) - target_link_libraries(${LIBCLIENT_NAME} ${QT_LIB}) - endforeach() -+ -+if(NOT(APPLE OR MSVC)) -+ pkg_check_modules(XCB xcb IMPORTED_TARGET) -+ target_link_libraries(${LIBCLIENT_NAME} PkgConfig::XCB) -+endif() -+ - if(ENABLE_LIBWRAP) - target_link_libraries(${LIBCLIENT_NAME} qtwrapper ${LIBJAMI_LIB}) - if (NOT (CMAKE_CXX_COMPILER_ID MATCHES "MSVC")) --- -2.37.3 - From 5e27c9a0d248fd930f74867fafd8c25874f41f41 Mon Sep 17 00:00:00 2001 From: kiasoc5 Date: Mon, 26 Dec 2022 15:33:55 -0500 Subject: [PATCH 775/790] gnu: fossil: Update to 2.20. * gnu/packages/version-control.scm (fossil): Update to 2.20. --- gnu/packages/version-control.scm | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/gnu/packages/version-control.scm b/gnu/packages/version-control.scm index 5a5e4eb7a4..9c8e031a90 100644 --- a/gnu/packages/version-control.scm +++ b/gnu/packages/version-control.scm @@ -2732,17 +2732,17 @@ by rclone usable with git-annex.") (define-public fossil (package (name "fossil") - (version "2.18") + (version "2.20") (source (origin (method url-fetch) (uri (string-append "https://www.fossil-scm.org/home/tarball/" - "84f25d7eb10c0714109d69bb2809abfa8b4b5c3d73b151a5b10df724dacd46d8" + "210e89a0597f225f49722b096cf5563bf193e920e02a9bd38503a906deacd416" "/fossil-src-" version ".tar.gz")) ;; XXX: Currently the above hash must be manually updated. (sha256 - (base32 "0cq7677p84nnbfvk2dsh3c3y900gslw3zaw8iipfq932vmf1s31h")) + (base32 "08g7img88n2nwcdkpzmg4aqbp2iy40nllgas53502dspm97ym4h8")) (modules '((guix build utils))) (snippet '(begin From a70a1d8edfb24b76bb42824e59a8e0358f4e0f2f Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Tue, 27 Dec 2022 19:47:23 +0100 Subject: [PATCH 776/790] gnu: fossil: Remove obsolete snippet. * gnu/packages/version-control.scm (fossil)[source]: Remove obsolete substitution. --- gnu/packages/version-control.scm | 7 +------ 1 file changed, 1 insertion(+), 6 deletions(-) diff --git a/gnu/packages/version-control.scm b/gnu/packages/version-control.scm index 9c8e031a90..2c1494a4dd 100644 --- a/gnu/packages/version-control.scm +++ b/gnu/packages/version-control.scm @@ -2745,12 +2745,7 @@ by rclone usable with git-annex.") (base32 "08g7img88n2nwcdkpzmg4aqbp2iy40nllgas53502dspm97ym4h8")) (modules '((guix build utils))) (snippet - '(begin - (delete-file-recursively "compat") - ;; Disable obsolete SQLite feature check; remove for 2.19. - (substitute* "tools/sqlcompattest.c" - ((".*\"ENABLE_JSON1\".*") - "")))))) + '(delete-file-recursively "compat")))) (build-system gnu-build-system) (native-inputs (list tcl ;for configuration only From a4461df9b2bd4695f0987efe27b62926924e89f1 Mon Sep 17 00:00:00 2001 From: Simon Josefsson Date: Sat, 24 Dec 2022 19:21:53 +0100 Subject: [PATCH 777/790] gnu: libksba: Update replacement to 1.6.3 [fixes CVE-2022-47629]. MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * gnu/packages/gnupg.scm (libksba/fixed): Update to 1.6.3. Signed-off-by: Ludovic Courtès --- gnu/packages/gnupg.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/gnupg.scm b/gnu/packages/gnupg.scm index 13b603b64a..ffd5d62a71 100644 --- a/gnu/packages/gnupg.scm +++ b/gnu/packages/gnupg.scm @@ -257,14 +257,14 @@ specifications are building blocks of S/MIME and TLS.") (define libksba/fixed (package (inherit libksba) - (version "1.6.2") + (version "1.6.3") (source (origin (method url-fetch) (uri (string-append "mirror://gnupg/libksba/libksba-" version ".tar.bz2")) (sha256 - (base32 "0wf9j9hlzvgn0vz6zg3fvcmpdr62v8bz1kzsvzdbs4lqqp51rq7w")))))) + (base32 "0p6y82j9y6n0l7scjgqhz3as9w13jiqjfx9n2jzynw89nf6wcwiz")))))) (define-public npth (package From e4f39ace86412f0c7cad999778b796abc13b1689 Mon Sep 17 00:00:00 2001 From: Remco van 't Veer Date: Sun, 25 Dec 2022 13:33:22 +0100 Subject: [PATCH 778/790] gnu: ruby: Add ruby-3.2. MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * gnu/packages/ruby.scm (ruby-3.2): New variable. Signed-off-by: Ludovic Courtès --- gnu/packages/ruby.scm | 18 ++++++++++++++++++ 1 file changed, 18 insertions(+) diff --git a/gnu/packages/ruby.scm b/gnu/packages/ruby.scm index c0eae1d57a..c0fd53ac14 100644 --- a/gnu/packages/ruby.scm +++ b/gnu/packages/ruby.scm @@ -81,6 +81,7 @@ #:use-module (gnu packages sqlite) #:use-module (gnu packages tls) #:use-module (gnu packages version-control) + #:use-module (gnu packages serialization) #:use-module (guix packages) #:use-module (guix download) #:use-module (guix git-download) @@ -236,6 +237,23 @@ a focus on simplicity and productivity.") (base32 "06ipqz45qcs0y1273gk2gwslxwd7jgighz3mzbddzg16k29n3qaf")))))) +(define-public ruby-3.2 + (package + (inherit ruby-3.1) + (version "3.2.0") + (source + (origin + (method url-fetch) + (uri (string-append "http://cache.ruby-lang.org/pub/ruby/" + (version-major+minor version) + "/ruby-" version ".tar.xz")) + (sha256 + (base32 + "1d18ifvdbf21cncpany948vc2gjw3qa36ck9b4i97pg60rrmgx6j")))) + (inputs + (modify-inputs (package-inputs ruby-3.1) + (prepend libyaml))))) + (define-public ruby ruby-2.7) (define-public mruby From c10238966ef936c294cdfe513c2d9fef7bb0671f Mon Sep 17 00:00:00 2001 From: Simon South Date: Thu, 22 Dec 2022 12:09:52 -0500 Subject: [PATCH 779/790] gnu: abc: Convey license information. MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * gnu/packages/fpga.scm (abc)[arguments]: Add #:license-file-regexp so license information is included in package output. [license]: Specify URI of actual package license. Signed-off-by: Ludovic Courtès --- gnu/packages/fpga.scm | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) diff --git a/gnu/packages/fpga.scm b/gnu/packages/fpga.scm index b2b3b63672..8784ba9c12 100644 --- a/gnu/packages/fpga.scm +++ b/gnu/packages/fpga.scm @@ -84,7 +84,8 @@ (inputs (list readline)) (arguments - `(#:tests? #f ; no check target + `(#:license-file-regexp "copyright.txt" + #:tests? #f ; no check target #:phases (modify-phases %standard-phases (delete 'configure) @@ -98,7 +99,8 @@ (description "ABC is a program for sequential logic synthesis and formal verification.") (license - (license:non-copyleft "https://fedoraproject.org/wiki/Licensing:MIT#Modern_Variants"))))) + (license:non-copyleft + "https://people.eecs.berkeley.edu/~alanmi/abc/copyright.htm"))))) (define-public iverilog (package From 79240b4b4eb3a3f62130d310660aef87ff43ced4 Mon Sep 17 00:00:00 2001 From: Simon South Date: Thu, 22 Dec 2022 12:09:53 -0500 Subject: [PATCH 780/790] gnu: abc: Use gexps. MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * gnu/packages/fpga.scm (abc)[arguments]: Use gexps; simplify "install" phase. Signed-off-by: Ludovic Courtès --- gnu/packages/fpga.scm | 18 ++++++++---------- 1 file changed, 8 insertions(+), 10 deletions(-) diff --git a/gnu/packages/fpga.scm b/gnu/packages/fpga.scm index 8784ba9c12..9bc387c762 100644 --- a/gnu/packages/fpga.scm +++ b/gnu/packages/fpga.scm @@ -84,16 +84,14 @@ (inputs (list readline)) (arguments - `(#:license-file-regexp "copyright.txt" - #:tests? #f ; no check target - #:phases - (modify-phases %standard-phases - (delete 'configure) - (replace 'install - (lambda* (#:key outputs #:allow-other-keys) - (let* ((out (assoc-ref outputs "out")) - (out-bin (string-append out "/bin"))) - (install-file "abc" out-bin))))))) + (list #:license-file-regexp "copyright.txt" + #:tests? #f ; no check target + #:phases + #~(modify-phases %standard-phases + (delete 'configure) + (replace 'install + (lambda _ + (install-file "abc" (string-append #$output "/bin"))))))) (home-page "https://people.eecs.berkeley.edu/~alanmi/abc/") (synopsis "Sequential logic synthesis and formal verification") (description "ABC is a program for sequential logic synthesis and From 94cab6a703cb21604cc56c481b418643f8454fc1 Mon Sep 17 00:00:00 2001 From: Simon South Date: Thu, 22 Dec 2022 12:09:54 -0500 Subject: [PATCH 781/790] gnu: abc: Update to 0.0-2.70cb339. MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * gnu/packages/fpga.scm (abc): Update to 0.0-2.70cb339. [source]: Fetch from current source-code repository. [native-inputs]: Remove as obsolete. [arguments]<#:tests?>: Update comment. Signed-off-by: Ludovic Courtès --- gnu/packages/fpga.scm | 19 +++++++++---------- 1 file changed, 9 insertions(+), 10 deletions(-) diff --git a/gnu/packages/fpga.scm b/gnu/packages/fpga.scm index 9bc387c762..acce5f8f82 100644 --- a/gnu/packages/fpga.scm +++ b/gnu/packages/fpga.scm @@ -65,27 +65,26 @@ #:use-module (gnu packages libusb)) (define-public abc - (let ((commit "5ae4b975c49c") - (revision "1")) + (let ((commit "70cb339f869e") + (revision "2")) (package (name "abc") (version (git-version "0.0" revision commit)) (source (origin - (method url-fetch) - (uri - (string-append "https://bitbucket.org/alanmi/abc/get/" commit ".zip")) - (file-name (string-append name "-" version "-checkout.zip")) + (method git-fetch) + (uri (git-reference + (url "https://github.com/berkeley-abc/abc") + (commit commit))) + (file-name (git-file-name name version)) (sha256 (base32 - "1syygi1x40rdryih3galr4q8yg1w5bvdzl75hd27v1xq0l5bz3d0")))) + "1ngxg4jvz8vwm74sbidysgz3v5lrzjcabkqj4nhcksi6hnhyc9m8")))) (build-system gnu-build-system) - (native-inputs - (list unzip)) (inputs (list readline)) (arguments (list #:license-file-regexp "copyright.txt" - #:tests? #f ; no check target + #:tests? #f ; no tests #:phases #~(modify-phases %standard-phases (delete 'configure) From 45c5710267212ea6c33eca770f8e223a7f3ecaec Mon Sep 17 00:00:00 2001 From: Simon South Date: Sun, 18 Dec 2022 13:46:54 -0500 Subject: [PATCH 782/790] gnu: ola: Update to 0.10.8. MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * gnu/packages/lighting.scm (ola): Update to 0.10.8. Signed-off-by: Ludovic Courtès --- gnu/packages/lighting.scm | 82 +++++++++++++++++++-------------------- 1 file changed, 39 insertions(+), 43 deletions(-) diff --git a/gnu/packages/lighting.scm b/gnu/packages/lighting.scm index 5850da84d8..5af49eea86 100644 --- a/gnu/packages/lighting.scm +++ b/gnu/packages/lighting.scm @@ -36,52 +36,48 @@ #:use-module (gnu packages protobuf)) (define-public ola - ;; Use a commit that allows building with libmicrohttpd 0.9.71. - ;; https://github.com/OpenLightingProject/ola/pull/1651 - (let ((commit "5d882936436240b312b3836afd199587beaca840") - (revision "0")) - (package - (name "ola") - (version (git-version "0.10.7" revision commit)) - (source - (origin - (method git-fetch) - (uri (git-reference - (url "https://github.com/OpenLightingProject/ola") - (commit commit))) - (sha256 - (base32 "1bhl3gvmvmnyrygfj13cibf2xirm285m8abjkaxq22hrqbsvab2m")) - (file-name (git-file-name name version)))) - (build-system gnu-build-system) - (native-inputs - (list bison - cppunit - flex - pkg-config - ;; For git repository bootstrapping. - autoconf - automake - libtool)) - (inputs - `(("libftdi" ,libftdi) - ("libmicrohttpd" ,libmicrohttpd) - ("libusb" ,libusb) - ("libuuid" ,util-linux "lib") - ("zlib" ,zlib))) - (propagated-inputs - (list protobuf)) ; for pkg-config --libs libola - (arguments - `( ;; G++ >= 4.8 macro expansion tracking requires lots of memory, causing - ;; build to fail on low memory systems. We disable that with the - ;; following configure flags. - #:configure-flags (list "CXXFLAGS=-ftrack-macro-expansion=0"))) - (synopsis "Framework for controlling entertainment lighting equipment") - (description "The Open Lighting Architecture is a framework for lighting + (package + (name "ola") + (version "0.10.8") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/OpenLightingProject/ola") + (commit version))) + (sha256 + (base32 "17dwmjdw87hv314gv5b1rmh5jglz8a0rzw7wj26xn74xw2jvxa6l")) + (file-name (git-file-name name version)))) + (build-system gnu-build-system) + (native-inputs + (list bison + cppunit + flex + pkg-config + ;; For git repository bootstrapping. + autoconf + automake + libtool)) + (inputs + `(("libftdi" ,libftdi) + ("libmicrohttpd" ,libmicrohttpd) + ("libusb" ,libusb) + ("libuuid" ,util-linux "lib") + ("zlib" ,zlib))) + (propagated-inputs + (list protobuf)) ; for pkg-config --libs libola + (arguments + `( ;; G++ >= 4.8 macro expansion tracking requires lots of memory, causing + ;; build to fail on low memory systems. We disable that with the + ;; following configure flags. + #:configure-flags (list "CXXFLAGS=-ftrack-macro-expansion=0"))) + (synopsis "Framework for controlling entertainment lighting equipment") + (description "The Open Lighting Architecture is a framework for lighting control information. It supports a range of protocols and over a dozen USB devices. It can run as a standalone service, which is useful for converting signals between protocols, or alternatively using the OLA API, it can be used as the backend for lighting control software. OLA runs on many different platforms including ARM, which makes it a perfect fit for low cost Ethernet to DMX gateways.") - (home-page "https://www.openlighting.org/ola") - (license license:lgpl2.1+)))) + (home-page "https://www.openlighting.org/ola") + (license license:lgpl2.1+))) From 5f8a51993e95775f5b2b753f709c8047d05c963e Mon Sep 17 00:00:00 2001 From: Simon South Date: Sun, 18 Dec 2022 13:46:55 -0500 Subject: [PATCH 783/790] gnu: ola: Remove input labels. MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * gnu/packages/lighting.scm (ola)[inputs]: Remove input labels. Signed-off-by: Ludovic Courtès --- gnu/packages/lighting.scm | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) diff --git a/gnu/packages/lighting.scm b/gnu/packages/lighting.scm index 5af49eea86..d0ad825d10 100644 --- a/gnu/packages/lighting.scm +++ b/gnu/packages/lighting.scm @@ -59,11 +59,11 @@ automake libtool)) (inputs - `(("libftdi" ,libftdi) - ("libmicrohttpd" ,libmicrohttpd) - ("libusb" ,libusb) - ("libuuid" ,util-linux "lib") - ("zlib" ,zlib))) + (list libftdi + libmicrohttpd + libusb + `(,util-linux "lib") + zlib)) (propagated-inputs (list protobuf)) ; for pkg-config --libs libola (arguments From 361aad5ce33afeefa269533c33141fc77f74837c Mon Sep 17 00:00:00 2001 From: Simon South Date: Sun, 18 Dec 2022 13:46:56 -0500 Subject: [PATCH 784/790] gnu: ola: Use gexps. MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * gnu/packages/lighting.scm (ola)[arguments]: Use gexps. Signed-off-by: Ludovic Courtès --- gnu/packages/lighting.scm | 10 ++++++---- 1 file changed, 6 insertions(+), 4 deletions(-) diff --git a/gnu/packages/lighting.scm b/gnu/packages/lighting.scm index d0ad825d10..6230963a4b 100644 --- a/gnu/packages/lighting.scm +++ b/gnu/packages/lighting.scm @@ -19,6 +19,7 @@ (define-module (gnu packages lighting) #:use-module (guix build-system gnu) + #:use-module (guix gexp) #:use-module (guix git-download) #:use-module ((guix licenses) #:prefix license:) #:use-module (guix packages) @@ -67,10 +68,11 @@ (propagated-inputs (list protobuf)) ; for pkg-config --libs libola (arguments - `( ;; G++ >= 4.8 macro expansion tracking requires lots of memory, causing - ;; build to fail on low memory systems. We disable that with the - ;; following configure flags. - #:configure-flags (list "CXXFLAGS=-ftrack-macro-expansion=0"))) + (list + ;; G++ >= 4.8 macro expansion tracking requires lots of memory, causing + ;; build to fail on low memory systems. We disable that with the + ;; following configure flags. + #:configure-flags #~(list "CXXFLAGS=-ftrack-macro-expansion=0"))) (synopsis "Framework for controlling entertainment lighting equipment") (description "The Open Lighting Architecture is a framework for lighting control information. It supports a range of protocols and over a dozen USB From 363b20b68584d71556c2d8912dd07cbdacabdb25 Mon Sep 17 00:00:00 2001 From: Attila Lendvai Date: Wed, 21 Dec 2022 23:14:55 -0300 Subject: [PATCH 785/790] records: match-record supports specifying a different variable name. MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit An example: (match-record obj (field1 (field2 custom-var-name) field3) ...) * guix/records.scm (match-record-inner): Add support for the new syntax. * tests/records.scm ("match-record, simple"): Add a simple test case for the new syntax. Signed-off-by: Ludovic Courtès --- guix/records.scm | 9 ++++++--- tests/records.scm | 4 ++-- 2 files changed, 8 insertions(+), 5 deletions(-) diff --git a/guix/records.scm b/guix/records.scm index 13463647c8..1f097c7108 100644 --- a/guix/records.scm +++ b/guix/records.scm @@ -592,13 +592,16 @@ found." (define-syntax match-record-inner (lambda (s) (syntax-case s () - ((_ record type (field rest ...) body ...) - #`(let-syntax ((field-offset (syntax-rules () + ((_ record type ((field variable) rest ...) body ...) + #'(let-syntax ((field-offset (syntax-rules () ((_ f) (lookup-field field 0 f))))) (let* ((offset (type map-fields field-offset)) - (field (struct-ref record offset))) + (variable (struct-ref record offset))) (match-record-inner record type (rest ...) body ...)))) + ((_ record type (field rest ...) body ...) + ;; Redirect to the canonical form above. + #'(match-record-inner record type ((field field) rest ...) body ...)) ((_ record type () body ...) #'(begin body ...))))) diff --git a/tests/records.scm b/tests/records.scm index 8504c8d5a5..b1203dfeb7 100644 --- a/tests/records.scm +++ b/tests/records.scm @@ -540,8 +540,8 @@ Description: 1st line, (first second) (list first second)) (match-record (foo (first 'a) (second 'b)) - (second first) - (list first second))))) + (second (first first/new-var)) + (list first/new-var second))))) (test-equal "match-record, unknown field" 'syntax-error From 5f222e7b7a088d741027b8ab9908ecb4cc79751a Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Mon, 26 Dec 2022 18:20:43 +0100 Subject: [PATCH 786/790] gnu: zeitgeist: Remove input labels. * gnu/packages/gnome.scm (zeitgeist)[arguments]: Use SEARCH-INPUT-DIRECTORY instead of label. [native-inputs, inputs]: Remove labels. --- gnu/packages/gnome.scm | 39 +++++++++++++++++++-------------------- 1 file changed, 19 insertions(+), 20 deletions(-) diff --git a/gnu/packages/gnome.scm b/gnu/packages/gnome.scm index c0bb62ff84..2078e91c23 100644 --- a/gnu/packages/gnome.scm +++ b/gnu/packages/gnome.scm @@ -766,8 +766,7 @@ of known objects without needing a central registrar.") (with-directory-excursion "doc/libzeitgeist" (substitute* "zeitgeist-gtkdoc-index.sgml" (("http://www.oasis-open.org/docbook/xml/4.3/") - (string-append (assoc-ref inputs "docbook-xml") - "/xml/dtd/docbook/")))))) + (search-input-directory inputs "/xml/dtd/docbook/")))))) (add-after 'patch-docbook-xml 'disable-failing-tests (lambda _ (substitute* "test/direct/Makefile.am" @@ -781,25 +780,25 @@ of known objects without needing a central registrar.") ;; To honor `autoreconf -vif` by build-system. (delete-file "autogen.sh")))))) (native-inputs - `(("autoconf" ,autoconf) - ("automake" ,automake) - ("docbook-xml" ,docbook-xml-4.3) - ("gettext" ,gettext-minimal) - ("gobject-introspection" ,gobject-introspection) - ("gtk-doc" ,gtk-doc/stable) - ("libtool" ,libtool) - ("pkg-config" ,pkg-config) - ("vala" ,vala) - ("xorg-server-for-tests" ,xorg-server-for-tests))) + (list autoconf + automake + docbook-xml-4.3 + gettext-minimal + gobject-introspection + gtk-doc/stable + libtool + pkg-config + vala + xorg-server-for-tests)) (inputs - `(("dee-icu" ,dee) - ("gtk+" ,gtk+) - ("json-glib" ,json-glib) - ("sqlite" ,sqlite) - ("telepathy-glib" ,telepathy-glib) - ("python" ,python-wrapper) - ("python-rdflib" ,python-rdflib) - ("xapian-config" ,xapian))) + (list dee + gtk+ + json-glib + sqlite + telepathy-glib + python-wrapper + python-rdflib + xapian)) (propagated-inputs (list glib)) (synopsis "Desktop Activity Logging") From fe14f88d56e349c24ed29efafd1c894a83615a9a Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Tue, 27 Dec 2022 21:10:19 +0100 Subject: [PATCH 787/790] doc: Update expired URL. * doc/guix.texi (DNS Services): Update knot-resolver documentation link. --- doc/guix.texi | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/doc/guix.texi b/doc/guix.texi index e94f1c24ed..053cd1ad41 100644 --- a/doc/guix.texi +++ b/doc/guix.texi @@ -31028,7 +31028,7 @@ cache.size = 100 * MB ")))) @end lisp -For more information, refer its @url{https://knot-resolver.readthedocs.org/en/stable/daemon.html#configuration, manual}. +For more information, refer its @url{https://knot-resolver.readthedocs.io/en/stable/config-overview.html, manual}. @end deffn @deftp {Data Type} knot-resolver-configuration From f17081333494c949060d614649fc96d9a3f4ab4f Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Tue, 27 Dec 2022 21:24:39 +0100 Subject: [PATCH 788/790] gnu: Open vSwitch: Update to 3.0.3. * gnu/packages/networking.scm (openvswitch): Update to 3.0.3. --- gnu/packages/networking.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/networking.scm b/gnu/packages/networking.scm index 8a2a7322ca..a7b51ed1ff 100644 --- a/gnu/packages/networking.scm +++ b/gnu/packages/networking.scm @@ -2760,7 +2760,7 @@ procedure calls (RPCs).") (define-public openvswitch (package (name "openvswitch") - (version "3.0.1") + (version "3.0.3") (source (origin (method url-fetch) (uri (string-append @@ -2768,7 +2768,7 @@ procedure calls (RPCs).") version ".tar.gz")) (sha256 (base32 - "0s5xbcchnfqlgrabjs76bwd5d6qhvjx352r274r5p7wis0b1g8g4")))) + "0qwlpnwjcyb7fpw6yp65mdqg20i1851z70xmvzxwxwpifq56a1pm")))) (build-system gnu-build-system) (arguments '(#:configure-flags From 7e6901618f7a4b9539d0e18ab24876126803b0e0 Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Tue, 27 Dec 2022 21:46:27 +0100 Subject: [PATCH 789/790] gnu: python-pycurl: Update to 7.45.2. * gnu/packages/python-web.scm (python-pycurl): Update to 7.45.2. --- gnu/packages/python-web.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/python-web.scm b/gnu/packages/python-web.scm index 18c0b47b67..25136c8448 100644 --- a/gnu/packages/python-web.scm +++ b/gnu/packages/python-web.scm @@ -1590,13 +1590,13 @@ Amazon S3 compatible object storage server.") (define-public python-pycurl (package (name "python-pycurl") - (version "7.43.0.5") + (version "7.45.2") (source (origin (method url-fetch) (uri (pypi-uri "pycurl" version)) (sha256 - (base32 "1cwlb76vddqp2mxqvjbhf367caddzy82rhangddjjhjqaj8x4zgc")))) + (base32 "1ji46b924caa4saxvjxs9h673yy0kif297nxpnjn84r7w05mjc2p")))) (build-system python-build-system) (arguments ;; The tests attempt to access external web servers, so we cannot run From 0cb8f7125b19264b01962c1249c3df4c5ce85aa9 Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Tue, 27 Dec 2022 21:46:46 +0100 Subject: [PATCH 790/790] gnu: python-bitarray: Update to 2.6.1. * gnu/packages/python-xyz.scm (python-bitarray): Update to 2.6.1. [arguments]: Override check phase. --- gnu/packages/python-xyz.scm | 14 ++++++++++++-- 1 file changed, 12 insertions(+), 2 deletions(-) diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index 6b71d6872e..d0cedf696a 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -1675,14 +1675,24 @@ and a list of words that are easier to remember for humans (the (define-public python-bitarray (package (name "python-bitarray") - (version "1.4.0") + (version "2.6.1") (source (origin (method url-fetch) (uri (pypi-uri "bitarray" version)) (sha256 (base32 - "177fj6wbw5jln54wpp6plcqy2329wjkwqwvgz7022rrg3xfrq49g")))) + "0c4jli872nzix81n1xirnrghlq2fdsxb570d9rnfvxi1694sah44")))) (build-system python-build-system) + (arguments + (list #:phases + #~(modify-phases %standard-phases + (replace 'check + (lambda* (#:key tests? #:allow-other-keys) + (when tests? + ;; Step out of the source directory to avoid interference. + (with-directory-excursion "/tmp" + (invoke "python" "-c" + "import bitarray; bitarray.test()")))))))) (home-page "https://github.com/ilanschnell/bitarray") (synopsis "Efficient arrays of booleans") (description "This package provides an object type which efficiently