From 4b5a0c0540fb1008daa6834f05aa94c85803e620 Mon Sep 17 00:00:00 2001 From: Leo Famulari Date: Wed, 11 Mar 2020 21:24:50 -0400 Subject: [PATCH 001/116] gnu: xxHash: Update to 0.7.3. * gnu/packages/digest.scm (xxhash): Update to 0.7.3. --- gnu/packages/digest.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/digest.scm b/gnu/packages/digest.scm index f76cbabcf8..1a9d58c0d3 100644 --- a/gnu/packages/digest.scm +++ b/gnu/packages/digest.scm @@ -25,7 +25,7 @@ (define-public xxhash (package (name "xxhash") - (version "0.7.2") + (version "0.7.3") (source (origin (method git-fetch) @@ -34,7 +34,7 @@ (commit (string-append "v" version)))) (file-name (git-file-name name version)) (sha256 - (base32 "1f9gl0cymmi92ihsfan0p4zmyf2hxwx4arjimpbmbp719nbcvdsx")))) + (base32 "0bin0jch6lbzl4f8y052a7azfgq2n7iwqihzgqmcccv5vq4vcx5a")))) (build-system gnu-build-system) (arguments `(#:make-flags From d7af0202a4db74b4c466fc96e12114df76b21706 Mon Sep 17 00:00:00 2001 From: Leo Famulari Date: Wed, 11 Mar 2020 21:27:36 -0400 Subject: [PATCH 002/116] gnu: Borg: Update to 1.1.11. * gnu/packages/backup.scm (borg): Update to 1.1.11. --- gnu/packages/backup.scm | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/gnu/packages/backup.scm b/gnu/packages/backup.scm index 9d8d984cb2..b18dbf30f0 100644 --- a/gnu/packages/backup.scm +++ b/gnu/packages/backup.scm @@ -520,13 +520,14 @@ detection, and lossless compression.") (define-public borg (package (name "borg") - (version "1.1.10") + (version "1.1.11") (source (origin (method url-fetch) (uri (pypi-uri "borgbackup" version)) (sha256 - (base32 "1pp70p4n5kamvcbl4d8021ggrxhyykmg9isjg4yd3wags8b19d7g")) + (base32 + "190gjzx83b6p64nqj840x382dgz9gfv0gm7wj585lnkrpa90j29n")) (modules '((guix build utils))) (snippet '(begin From ca0fe294d65aff8bd1b11d0c81e968870c0f1084 Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Thu, 12 Mar 2020 03:58:46 +0100 Subject: [PATCH 003/116] gnu: java-snappy: Update to 1.1.7.3. * gnu/packages/java-compression.scm (java-snappy): Update to 1.1.7.3. --- gnu/packages/java-compression.scm | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/gnu/packages/java-compression.scm b/gnu/packages/java-compression.scm index 3102c70d88..1c246f6a72 100644 --- a/gnu/packages/java-compression.scm +++ b/gnu/packages/java-compression.scm @@ -3,7 +3,7 @@ ;;; Copyright © 2017, 2018 Julien Lepiller ;;; Copyright © 2018 Marius Bakke ;;; Copyright © 2018 Mark H Weaver -;;; Copyright © 2018 Tobias Geerinckx-Rice +;;; Copyright © 2018, 2020 Tobias Geerinckx-Rice ;;; ;;; This file is part of GNU Guix. ;;; @@ -35,7 +35,7 @@ (define-public java-snappy (package (name "java-snappy") - (version "1.1.7.2") + (version "1.1.7.3") (source (origin (method url-fetch) (uri (string-append "https://github.com/xerial/snappy-java/archive/" @@ -43,7 +43,7 @@ (file-name (string-append name "-" version ".tar.gz")) (sha256 (base32 - "1p557vdv006ysgxbpp83krmq0066k46108vyiyka69w8i4i8rbbm")))) + "0v7mrc62v2wyr5l3c5xx11rn0k5bcl1l05cwr79xyw7zqr8k71qh")))) (build-system ant-build-system) (arguments `(#:jar-name "snappy.jar" From 0308944ab06a103791c853743c88280a2abc114f Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Thu, 12 Mar 2020 04:54:32 +0100 Subject: [PATCH 004/116] gnu: java-snappy: Don't use unstable tarball. MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * gnu/packages/java-compression.scm (java-snappy)[source]: Use GIT-FETCH and GIT-FILE-NAME. [arguments]: Add ‘make-git-checkout-writable’ phase. --- gnu/packages/java-compression.scm | 22 ++++++++++++++-------- 1 file changed, 14 insertions(+), 8 deletions(-) diff --git a/gnu/packages/java-compression.scm b/gnu/packages/java-compression.scm index 1c246f6a72..3a9082641c 100644 --- a/gnu/packages/java-compression.scm +++ b/gnu/packages/java-compression.scm @@ -25,6 +25,7 @@ #:use-module (guix utils) #:use-module (guix packages) #:use-module (guix download) + #:use-module (guix git-download) #:use-module (guix build-system ant) #:use-module (gnu packages) #:use-module (gnu packages compression) @@ -36,20 +37,25 @@ (package (name "java-snappy") (version "1.1.7.3") - (source (origin - (method url-fetch) - (uri (string-append "https://github.com/xerial/snappy-java/archive/" - version ".tar.gz")) - (file-name (string-append name "-" version ".tar.gz")) - (sha256 - (base32 - "0v7mrc62v2wyr5l3c5xx11rn0k5bcl1l05cwr79xyw7zqr8k71qh")))) + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/xerial/snappy-java") + (commit version))) + (sha256 + (base32 "07c145w1kv8g7dbwpy5xss142il7zr0qq78p2ih76azgl97n5cba")) + (file-name (git-file-name name version)))) (build-system ant-build-system) (arguments `(#:jar-name "snappy.jar" #:source-dir "src/main/java" #:phases (modify-phases %standard-phases + (add-after 'unpack 'make-git-checkout-writable + (lambda _ + (for-each make-file-writable (find-files ".")) + #t)) (add-before 'build 'remove-binaries (lambda _ (delete-file "lib/org/xerial/snappy/OSInfo.class") From dd8cf0097e899d0285756429cc29706ebf4211e7 Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Sun, 19 Jan 2020 01:28:54 +0100 Subject: [PATCH 005/116] gnu: picprog: Use HTTPS home page. * gnu/packages/embedded.scm (picprog)[home-page]: Use HTTPS. --- gnu/packages/embedded.scm | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/gnu/packages/embedded.scm b/gnu/packages/embedded.scm index 136add4e82..46c7a03104 100644 --- a/gnu/packages/embedded.scm +++ b/gnu/packages/embedded.scm @@ -1125,7 +1125,7 @@ SPI, I2C, JTAG.") (delete 'configure)))) (synopsis "Programs Microchip's PIC microcontrollers") (description "This program programs Microchip's PIC microcontrollers.") - (home-page "http://hyvatti.iki.fi/~jaakko/pic/picprog.html") + (home-page "https://hyvatti.iki.fi/~jaakko/pic/picprog.html") (license license:gpl3+))) (define-public fc-host-tools From fe6cfa99439b2cb13adbbe0370442c0bb655ceb9 Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Thu, 12 Mar 2020 03:38:34 +0100 Subject: [PATCH 006/116] gnu: simple-scan: Update to 3.36.0. * gnu/packages/gnome.scm (simple-scan): Update to 3.36.0. --- gnu/packages/gnome.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/gnome.scm b/gnu/packages/gnome.scm index 86d0b8881c..a08cd00d72 100644 --- a/gnu/packages/gnome.scm +++ b/gnu/packages/gnome.scm @@ -5384,7 +5384,7 @@ USB transfers with your high-level application or system daemon.") (define-public simple-scan (package (name "simple-scan") - (version "3.34.4") + (version "3.36.0") (source (origin (method url-fetch) @@ -5392,7 +5392,7 @@ USB transfers with your high-level application or system daemon.") (version-major+minor version) "/" "simple-scan-" version ".tar.xz")) (sha256 - (base32 "0xvy672zyl6jsdlnxma8nc2aqsx9k92jhp6wfxs0msj9ppp1nd3z")))) + (base32 "198l3yhqhb2wzfdcgi8fzbwycr0njn44583dazz6wy1gqbiqnzgm")))) (build-system meson-build-system) ;; TODO: Fix icons in home screen, About dialogue, and scan menu. (arguments From 32df41beef12af9a64f079788ac77a167fb3e5ab Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Thu, 12 Mar 2020 03:45:37 +0100 Subject: [PATCH 007/116] gnu: s6: Update to 2.9.1.0. * gnu/packages/skarnet.scm (s6): Update to 2.9.1.0. --- 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 6323169ee6..31768c814e 100644 --- a/gnu/packages/skarnet.scm +++ b/gnu/packages/skarnet.scm @@ -104,14 +104,14 @@ complexity."))) (define-public s6 (package (name "s6") - (version "2.9.0.1") + (version "2.9.1.0") (source (origin (method url-fetch) (uri (string-append "https://skarnet.org/software/s6/s6-" version ".tar.gz")) (sha256 - (base32 "0mvcjrz8nlj9p2zclmcv22b4y6bqzd2iz38arhgc989vdvrbmkg0")))) + (base32 "1xqzl2wnvcmcyhppk7mc10h1ac7fkik3i6gpyliwpf3d5i9mkqh5")))) (build-system gnu-build-system) (inputs `(("skalibs" ,skalibs) ("execline" ,execline))) From 7247b841954f941df47d482a8c39f2c9851a6c2d Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Sun, 19 Jan 2020 01:02:03 +0100 Subject: [PATCH 008/116] gnu: ephoto: Update source and home page URIs. * gnu/packages/enlightenment.scm (ephoto)[source]: Remove dead URI. [home-page]: Follow (HTTPS) redirection. --- gnu/packages/enlightenment.scm | 17 +++++++---------- 1 file changed, 7 insertions(+), 10 deletions(-) diff --git a/gnu/packages/enlightenment.scm b/gnu/packages/enlightenment.scm index d79ca949f2..4a65c55af9 100644 --- a/gnu/packages/enlightenment.scm +++ b/gnu/packages/enlightenment.scm @@ -515,15 +515,12 @@ and in creating applications based on the Enlightenment Foundation Library suite (name "ephoto") (version "1.5") (source - (origin - (method url-fetch) - (uri (list (string-append "http://www.smhouston.us/stuff/ephoto-" - version ".tar.xz") - (string-append "https://download.enlightenment.org/rel/" - "apps/ephoto/ephoto-" version ".tar.xz"))) - (sha256 - (base32 - "1q7v9abjp9jrs08xc7pqaac64yzax24dk1snjb9rciarzzh3mlzy")))) + (origin + (method url-fetch) + (uri (string-append "https://download.enlightenment.org/rel/" + "apps/ephoto/ephoto-" version ".tar.xz")) + (sha256 + (base32 "1q7v9abjp9jrs08xc7pqaac64yzax24dk1snjb9rciarzzh3mlzy")))) (build-system gnu-build-system) (arguments '(#:phases @@ -536,7 +533,7 @@ and in creating applications based on the Enlightenment Foundation Library suite ("pkg-config" ,pkg-config))) (inputs `(("efl" ,efl))) - (home-page "http://smhouston.us/ephoto/") + (home-page "https://smhouston.us/projects/ephoto/") (synopsis "EFL image viewer/editor/manipulator/slideshow creator") (description "Ephoto is an image viewer and editor written using the @dfn{Enlightenment Foundation Libraries} (EFL). It focuses on simplicity and From 094afc97c6e2315410427abd78e599768f2d6a40 Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Sat, 18 Jan 2020 23:51:27 +0100 Subject: [PATCH 009/116] gnu: gptfdisk: Use HTTPS home page. * gnu/packages/disk.scm (gptfdisk)[home-page]: Use HTTPS. --- gnu/packages/disk.scm | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/gnu/packages/disk.scm b/gnu/packages/disk.scm index 534b64ef95..f42f2900ec 100644 --- a/gnu/packages/disk.scm +++ b/gnu/packages/disk.scm @@ -199,7 +199,7 @@ tables, and it understands a variety of different formats.") (install-file "fixparts.8" man) (install-file "gdisk.8" man) (install-file "sgdisk.8" man))))))) - (home-page "http://www.rodsbooks.com/gdisk/") + (home-page "https://www.rodsbooks.com/gdisk/") (synopsis "Low-level GPT disk partitioning and formatting") (description "GPT fdisk (aka gdisk) is a text-mode partitioning tool that works on Globally Unique Identifier (@dfn{GUID}) Partition Table (@dfn{GPT}) From b5d32fb9dd9eeb9240507e7c7fa5da5a871a6644 Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Thu, 12 Mar 2020 03:52:24 +0100 Subject: [PATCH 010/116] gnu: xmobar: Update to 0.33. * gnu/packages/wm.scm (xmobar): Update to 0.33. --- gnu/packages/wm.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/wm.scm b/gnu/packages/wm.scm index f9b6ef9880..f5b9e62afe 100644 --- a/gnu/packages/wm.scm +++ b/gnu/packages/wm.scm @@ -691,14 +691,14 @@ tiled on several screens.") (define-public xmobar (package (name "xmobar") - (version "0.32") + (version "0.33") (source (origin (method url-fetch) (uri (string-append "mirror://hackage/package/xmobar/" "xmobar-" version ".tar.gz")) (sha256 (base32 - "0x2ki3v0pmhl4bva3qi1xx21axayc4sx1nkzhmk2ap4l0cj52jrd")))) + "1hr3qqykc5givcpcwrr9f2y920jmiinmxm5mcy6qgpgymgwqb618")))) (build-system haskell-build-system) (native-inputs `(("ghc-hspec" ,ghc-hspec) From dd42a2f3912d1aabf65b27d3f62c74a4039c9d62 Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Thu, 12 Mar 2020 03:54:50 +0100 Subject: [PATCH 011/116] gnu: libgme: Update to 0.6.3. * gnu/packages/music.scm (libgme): Update to 0.6.3. --- gnu/packages/music.scm | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/gnu/packages/music.scm b/gnu/packages/music.scm index 3690af83d7..f6585f60d4 100644 --- a/gnu/packages/music.scm +++ b/gnu/packages/music.scm @@ -864,7 +864,7 @@ interface. It is implemented as a frontend to @code{klick}.") (define-public libgme (package (name "libgme") - (version "0.6.2") + (version "0.6.3") (source (origin (method url-fetch) (uri (string-append "https://bitbucket.org/mpyne/game-music-emu/" @@ -872,10 +872,10 @@ interface. It is implemented as a frontend to @code{klick}.") ".tar.xz")) (sha256 (base32 - "0hkkmxbaas2sirlb5i4r10mgbbiaapjx8pazifabwba23m3wnijh")))) + "07857vdkak306d9s5g6fhmjyxk7vijzjhkmqb15s7ihfxx9lx8xb")))) (build-system cmake-build-system) (arguments - '(#:tests? #f)) ; no check target + '(#:tests? #f)) ; no check target (home-page "https://bitbucket.org/mpyne/game-music-emu") (synopsis "Video game music file playback library") (description From 286ab9d3f54da3f9c5196f4071686aa08059e0a0 Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Sun, 19 Jan 2020 01:31:22 +0100 Subject: [PATCH 012/116] gnu: rsound: Use HTTPS home page. * gnu/packages/audio.scm (rsound)[home-page]: Use HTTPS. --- gnu/packages/audio.scm | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/gnu/packages/audio.scm b/gnu/packages/audio.scm index 63227b89ea..ea65b4efb1 100644 --- a/gnu/packages/audio.scm +++ b/gnu/packages/audio.scm @@ -2992,7 +2992,7 @@ synthesizer written in C++.") (string-append "--prefix=" (assoc-ref outputs "out")))))) ;; No 'check' target. #:tests? #f)) - (home-page "http://themaister.net/rsound.html") + (home-page "https://themaister.net/rsound.html") (synopsis "Networked audio system") (description "RSound allows you to send audio from an application and transfer it From 62f6f9d99fdef05086251e8e10554990092c9844 Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Sun, 19 Jan 2020 01:01:50 +0100 Subject: [PATCH 013/116] gnu: faust: Use HTTPS home page. * gnu/packages/audio.scm (faust)[home-page]: Use HTTPS. --- gnu/packages/audio.scm | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/gnu/packages/audio.scm b/gnu/packages/audio.scm index ea65b4efb1..b6e0a436c3 100644 --- a/gnu/packages/audio.scm +++ b/gnu/packages/audio.scm @@ -1306,7 +1306,7 @@ PS, and DAB+.") #t))))) (native-inputs `(("unzip" ,unzip))) - (home-page "http://faust.grame.fr/") + (home-page "https://faust.grame.fr/") (synopsis "Signal processing language") (description "Faust is a programming language for realtime audio signal processing.") From f930814afae8e20125dab58b060a691ea8398e26 Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Thu, 12 Mar 2020 01:53:57 +0100 Subject: [PATCH 014/116] gnu: Add gitless. * gnu/packages/version-control.scm (gitless): New public variable. Co-authored-by: Tobias Geerinckx-Rice --- gnu/packages/version-control.scm | 70 ++++++++++++++++++++++++++++++++ 1 file changed, 70 insertions(+) diff --git a/gnu/packages/version-control.scm b/gnu/packages/version-control.scm index 52626f8076..5d0fa267a9 100644 --- a/gnu/packages/version-control.scm +++ b/gnu/packages/version-control.scm @@ -27,6 +27,7 @@ ;;; Copyright © 2019 Alex Griffin ;;; Copyright © 2020 Roel Janssen ;;; Copyright © 2020 Brice Waegeneire +;;; Copyright © 2020 John D. Boy ;;; ;;; This file is part of GNU Guix. ;;; @@ -531,6 +532,75 @@ everything from small to very large projects with speed and efficiency.") ("zlib" ,zlib) ("bash-for-tests" ,bash))))) +(define-public gitless + (package + (name "gitless") + (version "0.8.8") + (source + (origin + ;; The PyPI package lacks a test suite. Build directly from git. + (method git-fetch) + (uri (git-reference + (url "https://github.com/gitless-vcs/gitless") + (commit (string-append "v" version)))) + (sha256 + (base32 "048kl27zjr68hgs70g3l98ci9765wxva6azzrhcdys7nsdd493n6")) + (file-name (git-file-name name version)))) + (build-system python-build-system) + (arguments + `(#:phases + (modify-phases %standard-phases + (add-before 'build 'loosen-requirements + (lambda _ + (substitute* "setup.py" + ;; Using Guix's python-pygit2 1.1.0 appears to work fine… + (("pygit2==") "pygit2>=")) + #t)) + (add-before 'check 'prepare-for-tests + (lambda _ + ;; Find the 'gl' command. + (rename-file "gl.py" "gl") + (setenv "PATH" (string-append (getcwd) ":" (getenv "PATH"))) + + ;; The tests try to run git as if it were already set up. + (setenv "HOME" (getcwd)) + (invoke "git" "config" "--global" "user.email" "git@example.com") + (invoke "git" "config" "--global" "user.name" "Guix"))) + (replace 'wrap + (lambda* (#:key inputs outputs #:allow-other-keys) + (let ((out (assoc-ref outputs "out")) + (git (assoc-ref inputs "git"))) + (wrap-program (string-append out "/bin/gl") + `("PATH" ":" prefix (,(string-append git "/bin"))) + `("PYTHONPATH" ":" = + (,(string-append out "/lib/python" + ,(version-major+minor + (package-version python)) + "/site-packages:") + ,(getenv "PYTHONPATH")))) + #t)))))) + (native-inputs + `(("git-for-tests" ,git-minimal))) + (inputs + `(("git" ,git-minimal) + ("python-clint" ,python-clint) + ("python-pygit2" ,python-pygit2) + ("python-sh" ,python-sh))) + (home-page "https://gitless.com") + (synopsis "Simple version control system built on top of Git") + (description + "Gitless is a Git-compatible version control system that aims to be easy to +learn and use. It simplifies the common workflow by committing changes to +tracked files by default and saving any uncommitted changes as part of a branch. + +The friendly @command{gl} command-line interface gives feedback and helps you +figure out what to do next. + +Gitless is implemented on top of Git and its commits and repositories are +indistinguishable from Git's. You (or other contributors) can always fall back +on @command{git}, and use any regular Git hosting service.") + (license license:expat))) + (define-public libgit2 (package (name "libgit2") From a30f20d49cd1503841182d9da3ea148aaa329df6 Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Sun, 19 Jan 2020 00:28:57 +0100 Subject: [PATCH 015/116] gnu: dosbox: Use HTTPS home page. * gnu/packages/emulators.scm (dosbox)[home-page]: Use HTTPS. --- gnu/packages/emulators.scm | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/gnu/packages/emulators.scm b/gnu/packages/emulators.scm index 7e4c98fbc7..a46ae910cd 100644 --- a/gnu/packages/emulators.scm +++ b/gnu/packages/emulators.scm @@ -266,7 +266,7 @@ turbo speed, networked multiplayer, and graphical enhancements.") ("alsa-lib" ,alsa-lib) ("glu" ,glu) ("mesa" ,mesa))) - (home-page "http://www.dosbox.com") + (home-page "https://www.dosbox.com") (synopsis "X86 emulator with CGA/EGA/VGA/etc. graphics and sound") (description "DOSBox is a DOS-emulator that uses the SDL library. DOSBox also emulates CPU:286/386 realmode/protected mode, Directory From cf580e5ebf0ad7734bf9c1efabff994d5d69f6e9 Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Sun, 19 Jan 2020 00:08:56 +0100 Subject: [PATCH 016/116] gnu: mame: Use HTTPS home page. * gnu/packages/emulators.scm (mame)[home-page]: Use HTTPS. --- gnu/packages/emulators.scm | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/gnu/packages/emulators.scm b/gnu/packages/emulators.scm index a46ae910cd..3591b1740c 100644 --- a/gnu/packages/emulators.scm +++ b/gnu/packages/emulators.scm @@ -1453,7 +1453,7 @@ play them on systems for which they were never designed!") ("sqlite" ,sqlite) ("utf8proc" ,utf8proc) ("zlib" ,zlib))) - (home-page "http://mamedev.org/") + (home-page "https://www.mamedev.org") (synopsis "Multi-purpose emulation framework") (description "MAME's purpose is to preserve decades of software history. As electronic technology continues to rush forward, MAME From 81166ee48872bd0b705a505e0c9cd6ff256aae0e Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Sat, 18 Jan 2020 23:15:16 +0100 Subject: [PATCH 017/116] gnu: xlockmore: Use HTTPS home page. * gnu/packages/xdisorg.scm (xlockmore)[home-page]: Use HTTPS. --- gnu/packages/xdisorg.scm | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/gnu/packages/xdisorg.scm b/gnu/packages/xdisorg.scm index bc36de565e..f8f410a415 100644 --- a/gnu/packages/xdisorg.scm +++ b/gnu/packages/xdisorg.scm @@ -840,7 +840,7 @@ shows it again when the mouse cursor moves or a mouse button is pressed.") ("libXext" ,libxext) ("libXt" ,libxt) ("linux-pam" ,linux-pam))) - (home-page "http://sillycycle.com/xlockmore.html") + (home-page "https://sillycycle.com/xlockmore.html") (synopsis "Screen locker for the X Window System") (description "XLockMore is a classic screen locker and screen saver for the From bf8ee1c5046c7011d641e10277984c9bb7dc7c2f Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Thu, 12 Mar 2020 05:09:44 +0100 Subject: [PATCH 018/116] gnu: xlockmore: Update to 5.62. * gnu/packages/xdisorg.scm (xlockmore): Update to 5.62. --- gnu/packages/xdisorg.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/xdisorg.scm b/gnu/packages/xdisorg.scm index f8f410a415..92c958b963 100644 --- a/gnu/packages/xdisorg.scm +++ b/gnu/packages/xdisorg.scm @@ -817,7 +817,7 @@ shows it again when the mouse cursor moves or a mouse button is pressed.") (define-public xlockmore (package (name "xlockmore") - (version "5.59") + (version "5.62") (source (origin (method url-fetch) (uri (list (string-append "http://sillycycle.com/xlock/" @@ -828,7 +828,7 @@ shows it again when the mouse cursor moves or a mouse button is pressed.") "xlockmore-" version ".tar.xz"))) (sha256 (base32 - "0lajc5a4lki33b9mzfsi74q4hbivbmhwysp7mib4ivnyxianhaid")))) + "0b05wgj4mpssy4hd7km5c48i454dfg45p11mfmsr7xjd2gnz5gqi")))) (build-system gnu-build-system) (arguments '(#:configure-flags (list (string-append "--enable-appdefaultdir=" From d8ba1135eb3cc0a01f84675bec4979d58301f8f5 Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Thu, 12 Mar 2020 10:25:42 +0200 Subject: [PATCH 019/116] gnu: python2-ipython: Fix build. * gnu/packages/python-xyz.scm (python2-ipython)[arguments]: Adjust skipped tests. --- 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 8e8790b29a..8c3c0d2d69 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -5743,9 +5743,9 @@ computing.") (add-before 'check 'delete-broken-tests (lambda* (#:key inputs #:allow-other-keys) ;; These tests throw errors for unknown reasons. + (delete-file "IPython/core/tests/test_displayhook.py") + (delete-file "IPython/core/tests/test_magic_terminal.py") (delete-file "IPython/core/tests/test_profile.py") - (delete-file "IPython/core/tests/test_interactiveshell.py") - (delete-file "IPython/core/tests/test_magic.py") #t))))) (home-page "https://ipython.org") (synopsis "IPython is a tool for interactive computing in Python") From 04b4c43232d114d7bc4a415e3c6138c52d33a800 Mon Sep 17 00:00:00 2001 From: Danny Milosavljevic Date: Thu, 12 Mar 2020 09:54:11 +0100 Subject: [PATCH 020/116] doc: Fix description for "guix package -A". * doc/guix.texi (Invoking guix package): Fix description for "guix package -A". --- doc/guix.texi | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/doc/guix.texi b/doc/guix.texi index eb6eb99361..dd32b65fe0 100644 --- a/doc/guix.texi +++ b/doc/guix.texi @@ -3122,7 +3122,7 @@ the store. @itemx -A [@var{regexp}] List packages currently available in the distribution for this system (@pxref{GNU Distribution}). When @var{regexp} is specified, list only -installed packages whose name matches @var{regexp}. +available packages whose name matches @var{regexp}. For each package, print the following items separated by tabs: its name, its version string, the parts of the package (@pxref{Packages with From 0aedcf4bc3e36071609d5b1f8a52fd449ec05118 Mon Sep 17 00:00:00 2001 From: Guillaume Le Vaillant Date: Thu, 12 Mar 2020 09:33:47 +0100 Subject: [PATCH 021/116] gnu: txr: Update to 233. * gnu/packages/lisp.scm (txr): Update to 233. --- gnu/packages/lisp.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/lisp.scm b/gnu/packages/lisp.scm index b5d8fd30f3..2af0d78da3 100644 --- a/gnu/packages/lisp.scm +++ b/gnu/packages/lisp.scm @@ -797,7 +797,7 @@ enough to play the original mainframe Zork all the way through.") (define-public txr (package (name "txr") - (version "232") + (version "233") (source (origin (method git-fetch) @@ -808,7 +808,7 @@ enough to play the original mainframe Zork all the way through.") (patches (search-patches "txr-shell.patch")) (sha256 (base32 - "1vcnask4a1rxrljp4rcbkfihrndkv25l256l125vv39gjhf315xp")))) + "14dwjgx9lbfajk3q539m3v3b9j047q83ldnqb4cagbs8ampvhfbv")))) (build-system gnu-build-system) (arguments '(#:configure-flags '("cc=gcc") From 034d9544e276600dc2d8434b47a240e38a178852 Mon Sep 17 00:00:00 2001 From: Guillaume Le Vaillant Date: Thu, 12 Mar 2020 09:38:00 +0100 Subject: [PATCH 022/116] gnu: udiskie: Update to 2.1.0. * gnu/packages/freedesktop.scm (udiskie): Update to 2.1.0. --- gnu/packages/freedesktop.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/freedesktop.scm b/gnu/packages/freedesktop.scm index 02adf8eedd..5dbbcbd1fa 100644 --- a/gnu/packages/freedesktop.scm +++ b/gnu/packages/freedesktop.scm @@ -1593,14 +1593,14 @@ encoding names are iconv-compatible.") (define-public udiskie (package (name "udiskie") - (version "2.0.4") + (version "2.1.0") (source (origin (method url-fetch) (uri (pypi-uri "udiskie" version)) (sha256 (base32 - "0gjjzz0k8dlsk03fl2882lbl88hbv031ww72qj02gr65yph0jqgc")) + "0smib8vbs9q37n7ynhzyw97q16fgdkcdw7fw69lci0xvyq00v1dz")) ;; Remove support for the libappindicator library of the ;; Unity desktop environment which is not in Guix. (patches (search-patches "udiskie-no-appindicator.patch")))) From 69b03ecd954a251a4ef7ef33dd95656114360272 Mon Sep 17 00:00:00 2001 From: Guillaume Le Vaillant Date: Thu, 12 Mar 2020 09:43:26 +0100 Subject: [PATCH 023/116] gnu: jgmenu: Update to 4.1.0. * gnu/packages/xdisorg.scm (jgmenu): Update to 4.1.0. --- gnu/packages/xdisorg.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/xdisorg.scm b/gnu/packages/xdisorg.scm index 92c958b963..0a58755815 100644 --- a/gnu/packages/xdisorg.scm +++ b/gnu/packages/xdisorg.scm @@ -1971,7 +1971,7 @@ The cutbuffer and clipboard selection are always synchronized.") (define-public jgmenu (package (name "jgmenu") - (version "4.0.1") + (version "4.1.0") (source (origin (method git-fetch) @@ -1981,7 +1981,7 @@ The cutbuffer and clipboard selection are always synchronized.") (file-name (git-file-name name version)) (sha256 (base32 - "1q0rpg2d96sn3rrdi8m7bngnxxqyxilpjxi7skiw4gvpiv1akxjp")))) + "1wsh37rapb1bszlq36hvwxqvfds39hbvbl152m8as4zlh93wfvvk")))) (build-system gnu-build-system) (native-inputs `(("cppcheck" ,cppcheck) From ec73c90ee35a404b04b030b260c386011c0cbe94 Mon Sep 17 00:00:00 2001 From: Guillaume Le Vaillant Date: Thu, 12 Mar 2020 10:05:28 +0100 Subject: [PATCH 024/116] gnu: Add virtualpg. * gnu/packages/geo.scm (virtualpg): New variable. --- gnu/packages/geo.scm | 26 ++++++++++++++++++++++++++ 1 file changed, 26 insertions(+) diff --git a/gnu/packages/geo.scm b/gnu/packages/geo.scm index 05d177c3b1..7fd04f25c3 100644 --- a/gnu/packages/geo.scm +++ b/gnu/packages/geo.scm @@ -1523,3 +1523,29 @@ input file (in @code{.osm} or @code{.osm.pbf} format).") tools supporting SpatiaLite.") (home-page "https://www.gaia-gis.it/fossil/spatialite-tools/index") (license license:gpl3+))) + +(define-public virtualpg + (package + (name "virtualpg") + (version "1.0.2") + (source + (origin + (method url-fetch) + (uri (string-append "https://www.gaia-gis.it/gaia-sins/" + "virtualpg-" version ".tar.gz")) + (sha256 + (base32 "0kjipcd08vvn188xmwbs7sw41xcs06x47n2hbqshpjcr51mxbarp")))) + (build-system gnu-build-system) + (inputs + `(("postgresql" ,postgresql) + ("sqlite" ,sqlite))) + (synopsis "Allow SQLite/SpatiaLite to access PostgreSQL/PostGIS tables") + (description + "VirtualPG is a dynamic extension for the SQLite DBMS. It implements +the VirtualPostgres driver, allowing to directly exchange data between SQLite +and PostgreSQL; if SpatiaLite is available even PostGIS geometries can be +exchanged form one Spatial DBMS and the other.") + (home-page "https://www.gaia-gis.it/fossil/virtualpg/index") + (license (list license:gpl2+ + license:lgpl2.1+ + license:mpl1.1)))) From a20cfe71e9cd9450e9cfbe9e4bc478a0c726a2af Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ludovic=20Court=C3=A8s?= Date: Wed, 11 Mar 2020 23:53:19 +0100 Subject: [PATCH 025/116] gnu: guile-next: Enable JIT on ARMv7. JIT support on ARMv7 is fixed by "guile-3.0-crash.patch". * gnu/packages/guile.scm (guile-3.0)[arguments]: Remove. --- gnu/packages/guile.scm | 9 --------- 1 file changed, 9 deletions(-) diff --git a/gnu/packages/guile.scm b/gnu/packages/guile.scm index 1d9d93d774..80ac9ea706 100644 --- a/gnu/packages/guile.scm +++ b/gnu/packages/guile.scm @@ -303,15 +303,6 @@ without requiring the source code to be rewritten.") (patches (append (search-patches "guile-3.0-crash.patch") (origin-patches (package-source guile-2.2)))))) - - (arguments - (substitute-keyword-arguments (package-arguments guile-2.2) - ;; XXX: On ARMv7, work around by disabling - ;; JIT. - ((#:configure-flags flags '()) - (if (target-arm32?) - `(cons "--disable-jit" ,flags) - flags)))) (native-search-paths (list (search-path-specification (variable "GUILE_LOAD_PATH") From 7657e61d6b33fe758fd69355ed53efbd5310743c Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ludovic=20Court=C3=A8s?= Date: Thu, 12 Mar 2020 11:04:00 +0100 Subject: [PATCH 026/116] import: pypi: Rewrite to use 'define-json-mapping'. * guix/import/pypi.scm (non-empty-string-or-false): New procedure. (, , ): New record types. (pypi-fetch): Call 'json->pypi-project'. (latest-source-release, latest-wheel-release): Use the new record accessors instead of 'assoc-ref*'. (pypi->guix-package, latest-release): Likewise. * tests/pypi.scm (test-json): Add mandatory fields. --- guix/import/pypi.scm | 121 ++++++++++++++++++++++++++++++++----------- tests/pypi.scm | 3 ++ 2 files changed, 95 insertions(+), 29 deletions(-) diff --git a/guix/import/pypi.scm b/guix/import/pypi.scm index 10450155a0..f93fa8831f 100644 --- a/guix/import/pypi.scm +++ b/guix/import/pypi.scm @@ -1,7 +1,7 @@ ;;; GNU Guix --- Functional package management for GNU ;;; Copyright © 2014 David Thompson ;;; Copyright © 2015 Cyril Roelandt -;;; Copyright © 2015, 2016, 2017, 2019 Ludovic Courtès +;;; Copyright © 2015, 2016, 2017, 2019, 2020 Ludovic Courtès ;;; Copyright © 2017 Mathieu Othacehe ;;; Copyright © 2018 Ricardo Wurmus ;;; Copyright © 2019 Maxim Cournoyer @@ -43,6 +43,7 @@ #:use-module (guix import utils) #:use-module ((guix download) #:prefix download:) #:use-module (guix import json) + #:use-module (guix json) #:use-module (guix packages) #:use-module (guix upstream) #:use-module ((guix licenses) #:prefix license:) @@ -55,10 +56,67 @@ pypi->guix-package %pypi-updater)) +;; The PyPI API (notice the rhyme) is "documented" at: +;; . + +(define non-empty-string-or-false + (match-lambda + ("" #f) + ((? string? str) str) + ((or #nil #f) #f))) + +;; PyPI project. +(define-json-mapping make-pypi-project pypi-project? + json->pypi-project + (info pypi-project-info "info" json->project-info) ; + (last-serial pypi-project-last-serial "last_serial") ;integer + (releases pypi-project-releases "releases" ;string/* pairs + (match-lambda + (((versions . dictionaries) ...) + (map (lambda (version vector) + (cons version + (map json->distribution + (vector->list vector)))) + versions dictionaries)))) + (distributions pypi-project-distributions "urls" ;* + (lambda (vector) + (map json->distribution (vector->list vector))))) + +;; Project metadata. +(define-json-mapping make-project-info project-info? + json->project-info + (name project-info-name) ;string + (author project-info-author) ;string + (maintainer project-info-maintainer) ;string + (classifiers project-info-classifiers ;list of strings + "classifiers" vector->list) + (description project-info-description) ;string + (summary project-info-summary) ;string + (keywords project-info-keywords) ;string + (license project-info-license) ;string + (download-url project-info-download-url ;string | #f + "download_url" non-empty-string-or-false) + (home-page project-info-home-page ;string + "home_page") + (url project-info-url "project_url") ;string + (release-url project-info-release-url "release_url") ;string + (version project-info-version)) ;string + +;; Distribution: a URL along with cryptographic hashes and metadata. +(define-json-mapping make-distribution distribution? + json->distribution + (url distribution-url) ;string + (digests distribution-digests) ;list of string pairs + (file-name distribution-file-name "filename") ;string + (has-signature? distribution-has-signature? "hash_sig") ;Boolean + (package-type distribution-package-type "packagetype") ;"bdist_wheel" | ... + (python-version distribution-package-python-version + "python_version")) + (define (pypi-fetch name) - "Return an alist representation of the PyPI metadata for the package NAME, -or #f on failure." - (json-fetch (string-append "https://pypi.org/pypi/" name "/json"))) + "Return a record for package NAME, or #f on failure." + (and=> (json-fetch (string-append "https://pypi.org/pypi/" name "/json")) + json->pypi-project)) ;; For packages found on PyPI that lack a source distribution. (define-condition-type &missing-source-error &error @@ -67,22 +125,24 @@ or #f on failure." (define (latest-source-release pypi-package) "Return the latest source release for PYPI-PACKAGE." - (let ((releases (assoc-ref* pypi-package "releases" - (assoc-ref* pypi-package "info" "version")))) + (let ((releases (assoc-ref (pypi-project-releases pypi-package) + (project-info-version + (pypi-project-info pypi-package))))) (or (find (lambda (release) - (string=? "sdist" (assoc-ref release "packagetype"))) - (vector->list releases)) + (string=? "sdist" (distribution-package-type release))) + releases) (raise (condition (&missing-source-error (package pypi-package))))))) (define (latest-wheel-release pypi-package) "Return the url of the wheel for the latest release of pypi-package, or #f if there isn't any." - (let ((releases (assoc-ref* pypi-package "releases" - (assoc-ref* pypi-package "info" "version")))) + (let ((releases (assoc-ref (pypi-project-releases pypi-package) + (project-info-version + (pypi-project-info pypi-package))))) (or (find (lambda (release) - (string=? "bdist_wheel" (assoc-ref release "packagetype"))) - (vector->list releases)) + (string=? "bdist_wheel" (distribution-package-type release))) + releases) #f))) (define (python->package-name name) @@ -411,23 +471,25 @@ VERSION, SOURCE-URL, HOME-PAGE, SYNOPSIS, DESCRIPTION, and LICENSE." (lambda* (package-name) "Fetch the metadata for PACKAGE-NAME from pypi.org, and return the `package' s-expression corresponding to that package, or #f on failure." - (let ((package (pypi-fetch package-name))) - (and package + (let* ((project (pypi-fetch package-name)) + (info (and project (pypi-project-info project)))) + (and project (guard (c ((missing-source-error? c) (let ((package (missing-source-error-package c))) (leave (G_ "no source release for pypi package ~a ~a~%") - (assoc-ref* package "info" "name") - (assoc-ref* package "info" "version"))))) - (let ((name (assoc-ref* package "info" "name")) - (version (assoc-ref* package "info" "version")) - (release (assoc-ref (latest-source-release package) "url")) - (wheel (assoc-ref (latest-wheel-release package) "url")) - (synopsis (assoc-ref* package "info" "summary")) - (description (assoc-ref* package "info" "summary")) - (home-page (assoc-ref* package "info" "home_page")) - (license (string->license (assoc-ref* package "info" "license")))) - (make-pypi-sexp name version release wheel home-page synopsis - description license)))))))) + (project-info-name info) + (project-info-version info))))) + (make-pypi-sexp (project-info-name info) + (project-info-version info) + (and=> (latest-source-release project) + distribution-url) + (and=> (latest-wheel-release project) + distribution-url) + (project-info-home-page info) + (project-info-summary info) + (project-info-summary info) + (string->license + (project-info-license info))))))))) (define (pypi-recursive-import package-name) (recursive-import package-name #f @@ -472,9 +534,10 @@ VERSION, SOURCE-URL, HOME-PAGE, SYNOPSIS, DESCRIPTION, and LICENSE." (pypi-package (pypi-fetch pypi-name))) (and pypi-package (guard (c ((missing-source-error? c) #f)) - (let* ((metadata pypi-package) - (version (assoc-ref* metadata "info" "version")) - (url (assoc-ref (latest-source-release metadata) "url"))) + (let* ((info (pypi-project-info pypi-package)) + (version (project-info-version info)) + (url (distribution-url + (latest-source-release pypi-package)))) (upstream-source (package (package-name package)) (version version) diff --git a/tests/pypi.scm b/tests/pypi.scm index 43d45f1dd8..19af6e61fb 100644 --- a/tests/pypi.scm +++ b/tests/pypi.scm @@ -38,7 +38,10 @@ \"license\": \"GNU LGPL\", \"summary\": \"summary\", \"home_page\": \"http://example.com\", + \"classifiers\": [], + \"download_url\": \"\" }, + \"urls\": [], \"releases\": { \"1.0.0\": [ { From 2d0409a4a2cedb76ab7a96173e19304bb54b8701 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ludovic=20Court=C3=A8s?= Date: Thu, 12 Mar 2020 11:13:33 +0100 Subject: [PATCH 027/116] import: utils: Remove 'assoc-ref*'. * guix/import/utils.scm (assoc-ref*): Remove. --- guix/import/utils.scm | 10 +--------- 1 file changed, 1 insertion(+), 9 deletions(-) diff --git a/guix/import/utils.scm b/guix/import/utils.scm index d17d400ddf..94c8cb040b 100644 --- a/guix/import/utils.scm +++ b/guix/import/utils.scm @@ -1,5 +1,5 @@ ;;; GNU Guix --- Functional package management for GNU -;;; Copyright © 2012, 2013, 2018, 2019 Ludovic Courtès +;;; Copyright © 2012, 2013, 2018, 2019, 2020 Ludovic Courtès ;;; Copyright © 2016 Jelle Licht ;;; Copyright © 2016 David Craven ;;; Copyright © 2017, 2019 Ricardo Wurmus @@ -47,7 +47,6 @@ #:export (factorize-uri flatten - assoc-ref* url-fetch guix-hash-url @@ -110,13 +109,6 @@ of the string VERSION is replaced by the symbol 'version." (cons elem memo))) '() lst)) -(define (assoc-ref* alist key . rest) - "Return the value for KEY from ALIST. For each additional key specified, -recursively apply the procedure to the sub-list." - (if (null? rest) - (assoc-ref alist key) - (apply assoc-ref* (assoc-ref alist key) rest))) - (define (url-fetch url file-name) "Save the contents of URL to FILE-NAME. Return #f on failure." (parameterize ((current-output-port (current-error-port))) From c00ae79cca7f4b1c95669c5857c0e55e1b253f4f Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ludovic=20Court=C3=A8s?= Date: Thu, 12 Mar 2020 11:18:40 +0100 Subject: [PATCH 028/116] import: cpan: Gracefully handle missing projects. * guix/import/cpan.scm (cpan-fetch): Check whether 'json-fetch' returns #f. --- guix/import/cpan.scm | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/guix/import/cpan.scm b/guix/import/cpan.scm index 7a97c7f8e8..6bcd2ce9eb 100644 --- a/guix/import/cpan.scm +++ b/guix/import/cpan.scm @@ -181,9 +181,9 @@ return \"Test-Simple\"" or #f on failure. MODULE should be the distribution name, such as \"Test-Script\" for the \"Test::Script\" module." ;; This API always returns the latest release of the module. - (json->cpan-release - (json-fetch (string-append (%metacpan-base-url) "/release/" - name)))) + (and=> (json-fetch (string-append (%metacpan-base-url) "/release/" + name)) + json->cpan-release)) (define (cpan-home name) (string-append "https://metacpan.org/release/" name)) From f7537e30b892cef09d91902547c00e5fa9b66f3b Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ludovic=20Court=C3=A8s?= Date: Tue, 10 Mar 2020 16:45:57 +0100 Subject: [PATCH 029/116] inferior: Distinguish inferior exceptions. This avoids ambiguities when looking at a backtrace where the exception was actually thrown by an inferior in a very different context. * guix/inferior.scm (&inferior-exception): New condition type. (read-repl-response): Add optional 'inferior' parameter. Raise '&inferior-exception' instead of rethrowing to KEY when receiving an 'exception' message. (read-inferior-response): Pass INFERIOR to 'read-repl-response'. * tests/inferior.scm ("&inferior-exception"): New test. --- guix/inferior.scm | 21 +++++++++++++++++---- tests/inferior.scm | 13 ++++++++++++- 2 files changed, 29 insertions(+), 5 deletions(-) diff --git a/guix/inferior.scm b/guix/inferior.scm index 0236fb61ad..6b685ece30 100644 --- a/guix/inferior.scm +++ b/guix/inferior.scm @@ -63,6 +63,9 @@ inferior-eval inferior-eval-with-store inferior-object? + inferior-exception? + inferior-exception-arguments + inferior-exception-inferior read-repl-response inferior-packages @@ -195,8 +198,15 @@ equivalent. Return #f if the inferior could not be launched." (set-record-type-printer! write-inferior-object) -(define (read-repl-response port) - "Read a (guix repl) response from PORT and return it as a Scheme object." +;; Reified exception thrown by an inferior. +(define-condition-type &inferior-exception &error + inferior-exception? + (arguments inferior-exception-arguments) ;key + arguments + (inferior inferior-exception-inferior)) ; | #f + +(define* (read-repl-response port #:optional inferior) + "Read a (guix repl) response from PORT and return it as a Scheme object. +Raise '&inferior-exception' when an exception is read from PORT." (define sexp->object (match-lambda (('value value) @@ -208,10 +218,13 @@ equivalent. Return #f if the inferior could not be launched." (('values objects ...) (apply values (map sexp->object objects))) (('exception key objects ...) - (apply throw key (map sexp->object objects))))) + (raise (condition (&inferior-exception + (arguments (cons key (map sexp->object objects))) + (inferior inferior))))))) (define (read-inferior-response inferior) - (read-repl-response (inferior-socket inferior))) + (read-repl-response (inferior-socket inferior) + inferior)) (define (send-inferior-request exp inferior) (write exp (inferior-socket inferior)) diff --git a/tests/inferior.scm b/tests/inferior.scm index f54b6d6037..b4417d8629 100644 --- a/tests/inferior.scm +++ b/tests/inferior.scm @@ -1,5 +1,5 @@ ;;; GNU Guix --- Functional package management for GNU -;;; Copyright © 2018, 2019 Ludovic Courtès +;;; Copyright © 2018, 2019, 2020 Ludovic Courtès ;;; ;;; This file is part of GNU Guix. ;;; @@ -61,6 +61,17 @@ (close-inferior inferior) (list a (inferior-object? b)))))) +(test-equal "&inferior-exception" + '(a b c d) + (let ((inferior (open-inferior %top-builddir + #:command "scripts/guix"))) + (guard (c ((inferior-exception? c) + (close-inferior inferior) + (and (eq? inferior (inferior-exception-inferior c)) + (inferior-exception-arguments c)))) + (inferior-eval '(throw 'a 'b 'c 'd) inferior) + 'badness))) + (test-equal "inferior-packages" (take (sort (fold-packages (lambda (package lst) (cons (list (package-name package) From a669f6e27b5c078fdd7f4592cd5dc688a979a864 Mon Sep 17 00:00:00 2001 From: Felix Gruber Date: Tue, 10 Mar 2020 20:29:05 +0100 Subject: [PATCH 030/116] gnu: dune-*: set up MPI for tests MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * gnu/packages/maths.scm (dune-common, dune-grid, dune-istl, dune-alugrid): [arguments]: correctly set up MPI instead of disabling tests that require MPI. Signed-off-by: Ludovic Courtès --- gnu/packages/maths.scm | 110 ++++------------------------------------- 1 file changed, 10 insertions(+), 100 deletions(-) diff --git a/gnu/packages/maths.scm b/gnu/packages/maths.scm index 263f80f246..4235d5a0ad 100644 --- a/gnu/packages/maths.scm +++ b/gnu/packages/maths.scm @@ -4593,36 +4593,8 @@ linear algebra primitives specifically targeting graph analytics.") (add-after 'build 'build-tests (lambda* (#:key make-flags #:allow-other-keys) (apply invoke "make" "build_tests" make-flags))) - ;; These tests fail because they require a fully functional MPI - ;; environment. - (add-after 'unpack 'disable-failing-tests - (lambda _ - (setenv "ARGS" - (string-append "--exclude-regex '(" - (string-join - (list - "remoteindicestest" - "remoteindicestest-mpi-2" - "syncertest" - "syncertest-mpi-2" - "variablesizecommunicatortest" - "variablesizecommunicatortest-mpi-2" - "arithmetictestsuitetest" - "assertandreturntest" - "assertandreturntest_ndebug" - "concept" - "debugaligntest" - "mpicollectivecommunication" - "mpicollectivecommunication-mpi-2" - "mpiguardtest" - "mpiguardtest-mpi-2" - "mpihelpertest" - "mpihelpertest-mpi-2" - "mpihelpertest2" - "mpihelpertest2-mpi-2") - "|") - ")'")) - #t))))) + (add-before 'check 'mpi-setup + ,%openmpi-setup)))) (inputs `(("gmp" ,gmp) ("metis" ,metis) @@ -4703,54 +4675,8 @@ This package contains the basic DUNE geometry classes.") (add-after 'build 'build-tests (lambda* (#:key make-flags #:allow-other-keys) (apply invoke "make" "build_tests" make-flags))) - ;; These tests fail because they require a fully functional MPI - ;; environment. - (add-after 'unpack 'disable-failing-tests - (lambda _ - (setenv "ARGS" - (string-append "--exclude-regex '(" - (string-join - (list - "scsgmappertest" - "conformvolumevtktest" - "gnuplottest" - "nonconformboundaryvtktest" - "subsamplingvtktest" - "vtktest" - "vtktest-mpi-2" - "vtksequencetest" - "gmshtest-onedgrid" - "test-dgf-yasp" - "test-dgf-yasp-offset" - "test-dgf-oned" - "test-geogrid-yaspgrid" - "test-gridinfo" - "test-identitygrid" - "testiteratorranges" - "test-hierarchicsearch" - "test-parallel-ug-mpi-2" - "test-yaspgrid-backuprestore-equidistant" - "test-yaspgrid-backuprestore-equidistant-mpi-2" - "test-yaspgrid-backuprestore-equidistantoffset" - "test-yaspgrid-backuprestore-equidistantoffset-mpi-2" - "test-yaspgrid-backuprestore-tensor" - "test-yaspgrid-backuprestore-tensor-mpi-2" - "test-yaspgrid-tensorgridfactory" - "test-yaspgrid-tensorgridfactory-mpi-2" - "test-yaspgrid-yaspfactory-1d" - "test-yaspgrid-yaspfactory-1d-mpi-2" - "test-yaspgrid-yaspfactory-2d" - "test-yaspgrid-yaspfactory-2d-mpi-2" - "test-yaspgrid-yaspfactory-3d" - "test-yaspgrid-yaspfactory-3d-mpi-2" - "globalindexsettest" - "persistentcontainertest" - "structuredgridfactorytest" - "tensorgridfactorytest" - "vertexordertest") - "|") - ")'")) - #t))))) + (add-before 'check 'mpi-setup + ,%openmpi-setup)))) (inputs `(("dune-common" ,dune-common) ("dune-geometry" ,dune-geometry) @@ -4793,24 +4719,8 @@ This package contains the basic DUNE grid classes.") (add-after 'build 'build-tests (lambda* (#:key make-flags #:allow-other-keys) (apply invoke "make" "build_tests" make-flags))) - ;; These tests fail because they require a fully functional MPI - ;; environment. - (add-after 'unpack 'disable-failing-tests - (lambda _ - (setenv "ARGS" - (string-append "--exclude-regex '(" - (string-join - (list - "galerkintest" - "hierarchytest" - "pamgtest" - "pamg_comm_repart_test" - "matrixredisttest" - "vectorcommtest" - "matrixmarkettest") - "|") - ")'")) - #t))))) + (add-before 'check 'mpi-setup + ,%openmpi-setup)))) (inputs `(("dune-common" ,dune-common) ("openmpi" ,openmpi) @@ -4896,9 +4806,7 @@ assemble global function spaces on finite-element grids.") "1l9adgyjpra8mvwm445s0lpjshnb63jag85fb2hisbjn6bm320yj")))) (build-system cmake-build-system) (arguments - `(#:tests? #f ; 7 of 8 tests fail because they need a full MPI - ; environment - #:phases + `(#:phases (modify-phases %standard-phases (add-after 'unpack 'patch-include (lambda _ @@ -4910,7 +4818,9 @@ assemble global function spaces on finite-element grids.") (lambda* (#:key inputs make-flags #:allow-other-keys) (setenv "CPLUS_INCLUDE_PATH" (string-append (assoc-ref inputs "dune-grid") "/share")) - (apply invoke "make" "build_tests" make-flags)))))) + (apply invoke "make" "build_tests" make-flags))) + (add-before 'check 'mpi-setup + ,%openmpi-setup)))) (inputs `(("dune-common" ,dune-common) ("dune-geometry" ,dune-geometry) From 07ebb75d175e0285dc3a5f525f111e3a7c544ba0 Mon Sep 17 00:00:00 2001 From: Felix Gruber Date: Tue, 10 Mar 2020 20:29:06 +0100 Subject: [PATCH 031/116] gnu: Add dune-uggrid. MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * gnu/packages/maths.scm (dune-uggrid): New variable. (dune-grid)[propagated-inputs]: Add dune-uggrid dependency, so that the UGGrid class in dune-grid can be used by packages that have dune-grid as input. (dune-functions)[arguments]: Enable tests that previously weren't built as they require dune-uggrid. Signed-off-by: Ludovic Courtès --- gnu/packages/maths.scm | 53 +++++++++++++++++++++++++++++++++++++++++- 1 file changed, 52 insertions(+), 1 deletion(-) diff --git a/gnu/packages/maths.scm b/gnu/packages/maths.scm index 4235d5a0ad..ab1532cd05 100644 --- a/gnu/packages/maths.scm +++ b/gnu/packages/maths.scm @@ -4656,6 +4656,42 @@ This package contains the basic DUNE geometry classes.") ;; GPL version 2 with "runtime exception" (license license:gpl2))) +(define-public dune-uggrid + (package + (name "dune-uggrid") + (version "2.6.0") + (source + (origin + (method url-fetch) + (uri (string-append "https://dune-project.org/download/" + version "/dune-uggrid-" version ".tar.gz")) + (sha256 + (base32 + "05l7a1gb78mny49anyxk6rjvn66rhgm30y72v5cjg0m5kfgr1a1f")))) + (build-system cmake-build-system) + (arguments + `(#:phases + (modify-phases %standard-phases + (add-after 'build 'build-tests + (lambda* (#:key make-flags #:allow-other-keys) + (apply invoke "make" "build_tests" make-flags)))))) + (inputs + `(("dune-common" ,dune-common) + ("openmpi" ,openmpi))) + (native-inputs + `(("gfortran" ,gfortran) + ("pkg-config" ,pkg-config))) + (home-page "https://dune-project.org/") + (synopsis "Distributed and Unified Numerics Environment") + (description "DUNE, the Distributed and Unified Numerics Environment is a +modular toolbox for solving @dfn{partial differential equations} (PDEs) with +grid-based methods. It supports the easy implementation of methods like +@dfn{Finite Elements} (FE), @dfn{Finite Volumes} (FV), and also @dfn{Finite +Differences} (FD). + +This package contains the DUNE UG grid classes.") + (license license:lgpl2.1))) + (define-public dune-grid (package (name "dune-grid") @@ -4685,6 +4721,8 @@ This package contains the basic DUNE geometry classes.") ("openblas" ,openblas) ("openmpi" ,openmpi) ("python" ,python))) + (propagated-inputs + `(("dune-uggrid" ,dune-uggrid))) (native-inputs `(("gfortran" ,gfortran) ("pkg-config" ,pkg-config))) @@ -4898,7 +4936,20 @@ operating on statically typed trees of objects.") (base32 "1an8gb477n8j0kzpbrv7nr1snh8pxip0gsxq6w63jc83gg3dj200")))) (build-system cmake-build-system) - (arguments `(#:tests? #f)) ; FIXME: tests require dune-uugrid + (arguments + `(#:phases + (modify-phases %standard-phases + (add-after 'unpack 'disable-failing-tests + (lambda _ + (setenv "ARGS" + ;; unable to load GMSH file in this test + "--exclude-regex gridviewfunctionspacebasistest") + #t)) + (add-after 'build 'build-tests + (lambda* (#:key make-flags #:allow-other-keys) + (apply invoke "make" "build_tests" make-flags))) + (add-before 'check 'mpi-setup + ,%openmpi-setup)))) (inputs `(("dune-common" ,dune-common) ("dune-istl" ,dune-istl) From f1f9466e3326d2df8e6e266a7cdced09116b2492 Mon Sep 17 00:00:00 2001 From: Felix Gruber Date: Tue, 10 Mar 2020 20:29:07 +0100 Subject: [PATCH 032/116] gnu: Add dune-subgrid MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * gnu/packages/maths.scm (dune-subgrid): New variable. Signed-off-by: Ludovic Courtès --- gnu/packages/maths.scm | 43 ++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 43 insertions(+) diff --git a/gnu/packages/maths.scm b/gnu/packages/maths.scm index ab1532cd05..808fe3084f 100644 --- a/gnu/packages/maths.scm +++ b/gnu/packages/maths.scm @@ -4881,6 +4881,49 @@ implementation of the DUNE grid interface supporting either simplices or cubes.") (license license:gpl2+))) +(define-public dune-subgrid + (package + (name "dune-subgrid") + (version "2.6.0") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://git.imp.fu-berlin.de/agnumpde/dune-subgrid") + (commit "releases/2.6-1"))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "1gcv35rx3knqd54r4pp9rzd639db4j8w2r2ibq43w1mgwdcqhs64")))) + (build-system cmake-build-system) + (arguments + `(#:phases + (modify-phases %standard-phases + (add-after 'build 'build-tests + (lambda* (#:key make-flags #:allow-other-keys) + (apply invoke "make" "build_tests" make-flags))) + (add-before 'check 'mpi-setup + ,%openmpi-setup)))) + (inputs + `(("dune-common" ,dune-common) + ("dune-geometry" ,dune-geometry) + ("dune-grid" ,dune-grid) + ("openmpi" ,openmpi) + ;; Optional + ("metis" ,metis) + ("openblas" ,openblas) + ("gmp" ,gmp))) + (native-inputs + `(("gfortran" ,gfortran) + ("pkg-config" ,pkg-config))) + (home-page "http://numerik.mi.fu-berlin.de/dune-subgrid/index.php") + (synopsis "Distributed and Unified Numerics Environment") + (description "The dune-subgrid module allows to mark elements of +another hierarchical dune grid. The set of marked elements can then be +accessed as a hierarchical dune grid in its own right. Dune-Subgrid +provides the full grid interface including adaptive mesh refinement.") + (license license:gpl2+))) + (define-public dune-typetree (package (name "dune-typetree") From 0a703c04866c38ad5f9e0537013837a32b6d188a Mon Sep 17 00:00:00 2001 From: Felix Gruber Date: Tue, 10 Mar 2020 20:29:08 +0100 Subject: [PATCH 033/116] gnu: dune-istl: Build with suitesparse MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * gnu/packages/maths.scm (dune-istl)[inputs]: Add suitesparse to build additional solvers in dune-istl. Signed-off-by: Ludovic Courtès --- gnu/packages/maths.scm | 1 + 1 file changed, 1 insertion(+) diff --git a/gnu/packages/maths.scm b/gnu/packages/maths.scm index 808fe3084f..e694a5b187 100644 --- a/gnu/packages/maths.scm +++ b/gnu/packages/maths.scm @@ -4764,6 +4764,7 @@ This package contains the basic DUNE grid classes.") ("openmpi" ,openmpi) ;; Optional ("metis" ,metis) + ("suitesparse" ,suitesparse) ("superlu" ,superlu) ("openblas" ,openblas) ("gmp" ,gmp) From e4cdadc18d284f77b02d92d19205998596168a23 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 11 Mar 2020 21:25:29 +0100 Subject: [PATCH 034/116] gnu: r-cairo: Update to 1.5-11. * gnu/packages/statistics.scm (r-cairo): Update to 1.5-11. --- 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 547450c78b..5354f39b0c 100644 --- a/gnu/packages/statistics.scm +++ b/gnu/packages/statistics.scm @@ -5392,14 +5392,14 @@ genome-wide association studies can be analyzed efficiently.") (define-public r-cairo (package (name "r-cairo") - (version "1.5-10") + (version "1.5-11") (source (origin (method url-fetch) (uri (cran-uri "Cairo" version)) (sha256 (base32 - "1mdmd5zmjkh1b0x928zizgzh42x8swbajffb88rvnjfdhk1z0dvq")))) + "1k9kpxcg5n4g6x2gydv344f4w0snqbhww14fnbbj1bny0mmv28xg")))) (properties `((upstream-name . "Cairo"))) (build-system r-build-system) (inputs From c107e50a0eec0e805c7578e45998376fea39cff2 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 12 Mar 2020 12:18:36 +0100 Subject: [PATCH 035/116] gnu: mumi: Update to 0.0.0-7.6653e2d. * gnu/packages/mail.scm (mumi): Update to 0.0.0-7.6653e2d. [inputs]: Add guile-sqlite3. --- gnu/packages/mail.scm | 9 +++++---- 1 file changed, 5 insertions(+), 4 deletions(-) diff --git a/gnu/packages/mail.scm b/gnu/packages/mail.scm index 0573e70d07..fb5446107c 100644 --- a/gnu/packages/mail.scm +++ b/gnu/packages/mail.scm @@ -27,7 +27,7 @@ ;;; Copyright © 2018, 2019 Pierre Langlois ;;; Copyright © 2018 Alex Vong ;;; Copyright © 2018 Gábor Boskovits -;;; Copyright © 2018, 2019 Ricardo Wurmus +;;; Copyright © 2018, 2019, 2020 Ricardo Wurmus ;;; Copyright © 2019 Tanguy Le Carrour ;;; ;;; This file is part of GNU Guix. @@ -2960,8 +2960,8 @@ replacement for the @code{urlview} program.") (license gpl2+))) (define-public mumi - (let ((commit "a933a62a4b8528b416319759b9985db80f3fce14") - (revision "6")) + (let ((commit "6653e2d525b945fcd671dbfbf7b42cc588a1cf4b") + (revision "7")) (package (name "mumi") (version (git-version "0.0.0" revision commit)) @@ -2973,7 +2973,7 @@ replacement for the @code{urlview} program.") (file-name (git-file-name name version)) (sha256 (base32 - "0vlda7vjzpd942iz5vb471hj7ypml5gwl9s1am92klv6nk2vnvcx")))) + "0h1q61yl01hm7wygv1bv47ncg7l7gcw7aq8ny61g3hr1acsqysjf")))) (build-system gnu-build-system) (arguments `(#:modules ((guix build gnu-build-system) @@ -3005,6 +3005,7 @@ replacement for the @code{urlview} program.") `(("guile-debbugs" ,guile-debbugs) ("guile-email" ,guile-email) ("guile-json" ,guile-json-3) + ("guile-sqlite3" ,guile-sqlite3) ("guile-syntax-highlight" ,guile-syntax-highlight) ("gnutls" ,gnutls) ;needed to talk to https://debbugs.gnu.org ("guile" ,guile-2.2) From a595399230a7b1acb0b096b3d5a7474100014299 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 12 Mar 2020 12:19:42 +0100 Subject: [PATCH 036/116] services: mumi-service-type: Update to latest version of mumi. * gnu/services/web.scm (%mumi-activation): Create /var/mumi/db. (mumi-shepherd-services): Add service for mumi worker. --- gnu/services/web.scm | 14 +++++++++++++- 1 file changed, 13 insertions(+), 1 deletion(-) diff --git a/gnu/services/web.scm b/gnu/services/web.scm index 075140816a..d093f60c8d 100644 --- a/gnu/services/web.scm +++ b/gnu/services/web.scm @@ -10,6 +10,7 @@ ;;; Copyright © 2017, 2018, 2019 Christopher Baines ;;; Copyright © 2018 Marius Bakke ;;; Copyright © 2019 Florian Pelz +;;; Copyright © 2020 Ricardo Wurmus ;;; ;;; This file is part of GNU Guix. ;;; @@ -1670,12 +1671,14 @@ WSGIPassAuthorization On #~(begin (use-modules (guix build utils)) + (mkdir-p "/var/mumi/db") (mkdir-p "/var/mumi/mails") (let* ((pw (getpwnam "mumi")) (uid (passwd:uid pw)) (gid (passwd:gid pw))) (chown "/var/mumi" uid gid) - (chown "/var/mumi/mails" uid gid))))) + (chown "/var/mumi/mails" uid gid) + (chown "/var/mumi/db" uid gid))))) (define %mumi-accounts (list (user-group (name "mumi") (system? #t)) @@ -1696,6 +1699,15 @@ WSGIPassAuthorization On '(#$(file-append mumi "/bin/mumi")) #:user "mumi" #:group "mumi" #:log-file "/var/log/mumi.log")) + (stop #~(make-kill-destructor))) + (shepherd-service + (provision '(mumi-worker)) + (documentation "Mumi bug-tracking web interface.") + (requirement '(networking)) + (start #~(make-forkexec-constructor + '(#$(file-append mumi "/bin/mumi") "--worker") + #:user "mumi" #:group "mumi" + #:log-file "/var/log/mumi.worker.log")) (stop #~(make-kill-destructor))))) (define mumi-service-type From e8588a7847a4669a4e3a4ffca8865d8f1b9a227e Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Thu, 12 Mar 2020 10:59:39 +0200 Subject: [PATCH 037/116] gnu: python-jupyter-console: Specify python2 variant. * gnu/packages/python-xyz.scm (python-jupyter-console)[properties]: New field. Specify python2-jupyter-console as python2 variant. --- gnu/packages/python-xyz.scm | 1 + 1 file changed, 1 insertion(+) diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index 8c3c0d2d69..2466368512 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -8172,6 +8172,7 @@ in the data.") (description "This package provides a terminal-based console frontend for Jupyter kernels. It also allows for console-based interaction with non-Python Jupyter kernels such as IJulia and IRKernel.") + (properties `((python2-variant . ,(delay python2-jupyter-console)))) (license license:bsd-3))) (define-public python2-jupyter-console From b0aa58d8f1d63db2d4444db378e6dd4ee4b9313b Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Thu, 12 Mar 2020 11:00:41 +0200 Subject: [PATCH 038/116] gnu: python2-jupyter-console: Build with python2. * gnu/packages/python-xyz.scm (python2-jupyter-console)[arguments]: Add python keyword, set to python-2. --- gnu/packages/python-xyz.scm | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index 2466368512..61b4a8aa98 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -8187,8 +8187,9 @@ Jupyter kernels such as IJulia and IRKernel.") (base32 "1kam1qzgwr7srhm5r6aj90di5sws4bq0jmiw15452ddamb9yspal")))) (build-system python-build-system) - ;; Tests only run in an TTY. - (arguments `(#:tests? #f)) + (arguments + `(#:python ,python-2 + #:tests? #f)) ; Tests only run in a TTY. (propagated-inputs `(("python2-ipykernel" ,python2-ipykernel) ("python2-jupyter-client" ,python2-jupyter-client) From d56d3ae704a74e592368a7afc69e1d109ea967f4 Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Mon, 9 Mar 2020 17:30:31 +0200 Subject: [PATCH 039/116] gnu: grpc: Build shared libraries. * gnu/packages/machine-learning.scm (grpc)[outputs]: Add static. [arguments]: Copy configure-flags from cmake-build-system. Add custom phases 'configure-shared, 'install-shared-libraries and 'move-static-libs to build shared libs and move static libs to their own output. (tensorflow)[native-inputs]: Add grpc:static. --- gnu/packages/machine-learning.scm | 43 ++++++++++++++++++++++++++++--- 1 file changed, 40 insertions(+), 3 deletions(-) diff --git a/gnu/packages/machine-learning.scm b/gnu/packages/machine-learning.scm index 50c41dc113..52e639723b 100644 --- a/gnu/packages/machine-learning.scm +++ b/gnu/packages/machine-learning.scm @@ -1,6 +1,6 @@ ;;; GNU Guix --- Functional package management for GNU ;;; Copyright © 2015, 2016, 2017, 2018, 2019 Ricardo Wurmus -;;; Copyright © 2016 Efraim Flashner +;;; Copyright © 2016, 2020 Efraim Flashner ;;; Copyright © 2016, 2017 Marius Bakke ;;; Copyright © 2016 Hartmut Goebel ;;; Copyright © 2018, 2019 Tobias Geerinckx-Rice @@ -1285,6 +1285,7 @@ Python.") (package (name "grpc") (version "1.16.1") + (outputs '("out" "static")) (source (origin (method git-fetch) (uri (git-reference @@ -1301,7 +1302,42 @@ Python.") (list "-DgRPC_ZLIB_PROVIDER=package" "-DgRPC_CARES_PROVIDER=package" "-DgRPC_SSL_PROVIDER=package" - "-DgRPC_PROTOBUF_PROVIDER=package"))) + "-DgRPC_PROTOBUF_PROVIDER=package" + (string-append "-DCMAKE_INSTALL_PREFIX=" + (assoc-ref %outputs "out")) + "-DCMAKE_INSTALL_LIBDIR=lib" + (string-append "-DCMAKE_INSTALL_RPATH=" + (assoc-ref %outputs "out") "/lib") + "-DCMAKE_VERBOSE_MAKEFILE=ON") + #:phases + (modify-phases %standard-phases + (add-before 'configure 'configure-shared + (lambda* (#:key (configure-flags '()) #:allow-other-keys) + (mkdir "../build-shared") + (with-directory-excursion "../build-shared" + (apply invoke + "cmake" "../source" + "-DBUILD_SHARED_LIBS=ON" + configure-flags) + (apply invoke "make" + `("-j" ,(number->string (parallel-job-count))))))) + (add-after 'install 'install-shared-libraries + (lambda _ + (with-directory-excursion "../build-shared" + (invoke "make" "install")))) + (add-before 'strip 'move-static-libs + (lambda* (#:key outputs #:allow-other-keys) + (let ((out (assoc-ref outputs "out")) + (static (assoc-ref outputs "static"))) + (mkdir-p (string-append static "/lib")) + (with-directory-excursion + (string-append out "/lib") + (for-each + (lambda (file) + (rename-file file + (string-append static "/lib/" file))) + (find-files "." "\\.a$")))) + #t))))) (inputs `(("c-ares" ,c-ares/cmake) ("openssl" ,openssl) @@ -1731,6 +1767,7 @@ INSTALL_RPATH " (assoc-ref outputs "out") "/lib)\n"))) (sha256 (base32 "161g9841rjfsy5pn52fcis0s9hdr7rxvb06pad38j5rppfihvign"))))) + ("grpc" ,grpc "static") ("googletest" ,googletest) ("swig" ,swig) ("unzip" ,unzip))) @@ -1752,7 +1789,7 @@ INSTALL_RPATH " (assoc-ref outputs "out") "/lib)\n"))) ("libjpeg" ,libjpeg) ("libpng" ,libpng) ("giflib" ,giflib) - ("grpc" ,grpc) + ("grpc:bin" ,grpc) ("jsoncpp" ,jsoncpp-for-tensorflow) ("snappy" ,snappy) ("sqlite" ,sqlite) From 37109658a589285c3d70197adfdca20f1c48c355 Mon Sep 17 00:00:00 2001 From: Pierre Neidhardt Date: Mon, 9 Mar 2020 17:31:25 +0200 Subject: [PATCH 040/116] gnu: Add hyperledger-iroha-ed25519. * gnu/packages/hyperledger.scm (hyperledger-iroha-ed25519): New variable. --- gnu/packages/hyperledger.scm | 45 +++++++++++++++++++++++++++++++++++- 1 file changed, 44 insertions(+), 1 deletion(-) diff --git a/gnu/packages/hyperledger.scm b/gnu/packages/hyperledger.scm index 158a66e898..71194fba38 100644 --- a/gnu/packages/hyperledger.scm +++ b/gnu/packages/hyperledger.scm @@ -1,5 +1,5 @@ ;;; GNU Guix --- Functional package management for GNU -;;; Copyright © 2019 Pierre Neidhardt +;;; Copyright © 2019, 2020 Pierre Neidhardt ;;; Copyright © 2019 Tobias Geerinckx-Rice ;;; ;;; This file is part of GNU Guix. @@ -93,3 +93,46 @@ solutions, underpinned by a modular architecture focusing on confidentiality and resiliency. It is designed to support pluggable implementations of different components.") (license asl2.0))) + +(define-public hyperledger-iroha-ed25519 + (package + (name "hyperledger-iroha-ed25519") + (version "2.0.2") + (home-page "https://github.com/hyperledger/iroha-ed25519") + (source (origin + (method git-fetch) + (uri (git-reference + (url home-page) + (commit version))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "0kr1zwah8mhnpfrpk3h6hdafyqdl3ixhs7czdfscqv6vxqfiabc4")))) + (build-system cmake-build-system) + (native-inputs + `(("googletest" ,googletest))) + (arguments + `(#:tests? #f ; Tests don't build because CMake cannot find GTest main. + #:configure-flags '("-DHUNTER_ENABLED=OFF" + "-DBUILD=SHARED" + ;; TODO: x86_64 should use amd64-64-24k-pic but it + ;; fails to link when built as a shared library. + "-DEDIMPL=ref10" + "-DHASH=sha3_brainhub"))) + (synopsis "Ed25519 digital signature algorithm") + (description "This repository aims to provide modularized implementation +of the Ed25519 digital signature algorithm which is is described in +RFC8032 (@url{https://tools.ietf.org/html/rfc8032}). + +Originally Ed25519 consists of three modules: + +@itemize +@item digital signature algorithm itself +@item SHA512 hash function +@item random number generator, to generate keypairs +@end itemize + +This project offers at least two different C implementations for every +module. Every implementation can be replaced with another one at +link-time. New implementations can be added as well.") + (license asl2.0))) From f204d155e3d41e95dbd5e0eda42c74592c7b4262 Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Tue, 10 Mar 2020 09:47:29 +0200 Subject: [PATCH 041/116] gnu: Add boost-1.69. * gnu/packages/boost.scm (boost-1.69): New hidden package. --- gnu/packages/boost.scm | 25 ++++++++++++++++++++++++- 1 file changed, 24 insertions(+), 1 deletion(-) diff --git a/gnu/packages/boost.scm b/gnu/packages/boost.scm index 11fb8e1201..8bf2002adb 100644 --- a/gnu/packages/boost.scm +++ b/gnu/packages/boost.scm @@ -9,7 +9,7 @@ ;;; Copyright © 2018 Arun Isaac ;;; Copyright © 2018, 2019 Ricardo Wurmus ;;; Copyright © 2018 Maxim Cournoyer -;;; Copyright © 2018 Efraim Flashner +;;; Copyright © 2018, 2020 Efraim Flashner ;;; Copyright © 2019 Giacomo Leidi ;;; ;;; This file is part of GNU Guix. @@ -195,6 +195,29 @@ across a broad spectrum of applications.") (symlink "libboost_python27.a" "libboost_python.a")) #t))))))))) +(define-public boost-1.69 + (package + (inherit boost) + (name "boost") + (version "1.69.0") + (source (origin + (method url-fetch) + (uri (let ((version-with-underscores + (string-map (lambda (x) (if (eq? x #\.) #\_ x)) version))) + (list (string-append "mirror://sourceforge/boost/boost/" version + "/boost_" version-with-underscores ".tar.bz2") + (string-append "https://dl.bintray.com/boostorg/release/" + version "/source/boost_" + version-with-underscores ".tar.bz2")))) + (sha256 + (base32 + "01j4n142dz20lcgqji8d8hspp04p1nv7m8i6dz8w5lchfdhx8clg")))) + (arguments + (substitute-keyword-arguments (package-arguments boost) + ((#:make-flags flags) + `(cons* "cxxflags=-std=c++14" ,flags)))) + (properties '((hidden? . #t))))) + (define-public boost-for-mysql ;; Older version for MySQL 5.7.23. (package From 04ff192ec4c815cf9a2e71fc0c796a6c6ce19429 Mon Sep 17 00:00:00 2001 From: Pierre Neidhardt Date: Tue, 10 Mar 2020 09:57:00 +0200 Subject: [PATCH 042/116] gnu: Add hyperledger-iroha. This package was co-authored with Efraim Flashner * gnu/packages/hyperledger.scm (hyperledger-iroha): New variable. --- gnu/packages/hyperledger.scm | 81 +++++++++++++++++++++++++++++++++++- 1 file changed, 79 insertions(+), 2 deletions(-) diff --git a/gnu/packages/hyperledger.scm b/gnu/packages/hyperledger.scm index 71194fba38..f0b33e0deb 100644 --- a/gnu/packages/hyperledger.scm +++ b/gnu/packages/hyperledger.scm @@ -1,6 +1,7 @@ ;;; GNU Guix --- Functional package management for GNU ;;; Copyright © 2019, 2020 Pierre Neidhardt ;;; Copyright © 2019 Tobias Geerinckx-Rice +;;; Copyright © 2020 Efraim Flashner ;;; ;;; This file is part of GNU Guix. ;;; @@ -19,18 +20,28 @@ (define-module (gnu packages hyperledger) #:use-module (ice-9 match) + #:use-module (guix build-system cmake) #:use-module (guix build-system go) - #:use-module (guix build-system trivial) #:use-module (guix packages) #:use-module (guix download) #:use-module (guix git-download) #:use-module (guix licenses) #:use-module (gnu packages) #:use-module (gnu packages base) + #:use-module (gnu packages boost) + #:use-module (gnu packages check) #:use-module (gnu packages curl) + #:use-module (gnu packages databases) #:use-module (gnu packages docker) #:use-module (gnu packages golang) - #:use-module (gnu packages version-control)) + #:use-module (gnu packages logging) + #:use-module (gnu packages machine-learning) + #:use-module (gnu packages popt) + #:use-module (gnu packages pretty-print) + #:use-module (gnu packages protobuf) + #:use-module (gnu packages tbb) + #:use-module (gnu packages version-control) + #:use-module (gnu packages web)) (define-public hyperledger-fabric (package @@ -136,3 +147,69 @@ This project offers at least two different C implementations for every module. Every implementation can be replaced with another one at link-time. New implementations can be added as well.") (license asl2.0))) + +(define-public hyperledger-iroha + (package + (name "hyperledger-iroha") + (version "1.1.1") + (home-page "https://github.com/hyperledger/iroha") + (source (origin + (method git-fetch) + (uri (git-reference + (url home-page) + (commit version))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "014mbwq059yxwihw0mq8zgns53fsw8ckczi1lw8q9pz3pk86pa9b")) + (modules '((guix build utils))) + (snippet + '(begin + ;; https://github.com/hyperledger/iroha/commit/4dc710d2e9a067af866771318f673c7392797e48 + ;; Backport unversioned fmt dependency, remove next update: + (substitute* "libs/logger/logger.hpp" + (("fmt::v5") "fmt")) + #t)))) + (build-system cmake-build-system) + (arguments + `(#:configure-flags + '("-DTESTING=OFF" ; The tests fail to link correctly to googletest. + ;; Don't install the shared libraries of the dependencies: + "-DENABLE_LIBS_PACKAGING=OFF") + #:tests? #f + ;; https://iroha.readthedocs.io/en/latest/build/index.html#running-tests-optional + #:test-target ".")) + ;; https://github.com/hyperledger/iroha/blob/master/vcpkg/VCPKG_DEPS_LIST + (native-inputs + `(("fmt" ,fmt) + ("googletest" ,googletest) + ("rapidjson" ,rapidjson) + ("rxcpp" ,rxcpp) + ("spdlog" ,spdlog))) + (inputs + `(("boost" ,boost-1.69) + ("gflags" ,gflags) + ("grpc" ,grpc) + ("hyperledger-iroha-ed25519" ,hyperledger-iroha-ed25519) + ("postgresql" ,postgresql) + ("protobuf" ,protobuf) + ("soci" ,soci) + ("tbb" ,tbb))) + (synopsis "Simple, decentralized ledger") + (description "Iroha is a distributed ledger technology (DLT). Iroha has +essential functionality for your asset, information and identity management +needs, at the same time being a crash fault-tolerant tool. + +Iroha has the following features: + +@itemize +@item Creation and management of custom fungible assets, such as currencies, +kilos of gold, etc. +@item Management of user accounts +@item Taxonomy of accounts based on domains in the system +@item The system of rights and verification of user permissions for the +execution of transactions and queries in the system +@item Validation of business rules for transactions and queries in the system +@item Multisignature transactions +@end itemize\n") + (license asl2.0))) From 0b692ef2c6a1a1c6b8877ad9599b1ba506c1ec4a Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 12 Mar 2020 14:22:42 +0100 Subject: [PATCH 043/116] gnu: r-qtl: Update to 1.46-2. * gnu/packages/bioinformatics.scm (r-qtl): Update to 1.46-2. --- 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 d95b58b0bb..bd9f2b566e 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -8288,7 +8288,7 @@ throughput genetic sequencing data sets using regression methods.") (define-public r-qtl (package (name "r-qtl") - (version "1.45-11") + (version "1.46-2") (source (origin (method url-fetch) @@ -8296,7 +8296,7 @@ throughput genetic sequencing data sets using regression methods.") version ".tar.gz")) (sha256 (base32 - "1d6qgj602fm6zia3djl4hmca0ri4v57ffp3g93p2yc3cabx2hq90")))) + "0rbwcnvyy96gq1dsgpxx03pv423qya26h6ws5y0blj3blfdmj83a")))) (build-system r-build-system) (home-page "https://rqtl.org/") (synopsis "R package for analyzing QTL experiments in genetics") From e0061f512554f3c7058f7ad528441a22bd72f52e Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 12 Mar 2020 14:22:54 +0100 Subject: [PATCH 044/116] gnu: r-mlinterfaces: Update to 1.66.5. * gnu/packages/bioconductor.scm (r-mlinterfaces): Update to 1.66.5. --- 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 167cb00ece..c7892f83f1 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -3605,14 +3605,14 @@ profiles (GO and KEGG) of gene and gene clusters.") (define-public r-mlinterfaces (package (name "r-mlinterfaces") - (version "1.66.4") + (version "1.66.5") (source (origin (method url-fetch) (uri (bioconductor-uri "MLInterfaces" version)) (sha256 (base32 - "19hlicdndy2p45y7w91gnwi3wgq5s465a646z3qqk8gmn5sn614q")))) + "05bg7qcrv485m03rkyq3qg5hrr1m3y7zx49bipwaivzqm3s1mbw5")))) (properties `((upstream-name . "MLInterfaces"))) (build-system r-build-system) (propagated-inputs From 0754fefb7505feca3311df129a8f5f5f25c28712 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 12 Mar 2020 14:23:03 +0100 Subject: [PATCH 045/116] gnu: r-ggcyto: Update to 1.14.1. * gnu/packages/bioconductor.scm (r-ggcyto): Update to 1.14.1. [native-inputs]: Add r-knitr. --- gnu/packages/bioconductor.scm | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index c7892f83f1..0ddae43481 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -5570,14 +5570,14 @@ manipulation of flow cytometry data.") (define-public r-ggcyto (package (name "r-ggcyto") - (version "1.14.0") + (version "1.14.1") (source (origin (method url-fetch) (uri (bioconductor-uri "ggcyto" version)) (sha256 (base32 - "165qszvy5z176h1l3dnjb5dcm279b6bjl5n5gzz8wfn4xpn8anc8")))) + "16jwdslhmj1nsa28wmaircy15cq7qn8nsyiawinjv711qiqhgw50")))) (properties `((upstream-name . "ggcyto"))) (build-system r-build-system) (propagated-inputs @@ -5591,6 +5591,8 @@ manipulation of flow cytometry data.") ("r-rcolorbrewer" ,r-rcolorbrewer) ("r-rlang" ,r-rlang) ("r-scales" ,r-scales))) + (native-inputs + `(("r-knitr" ,r-knitr))) (home-page "https://github.com/RGLab/ggcyto/issues") (synopsis "Visualize Cytometry data with ggplot") (description From 6bd6097ed58b06544b3ac1ae571b7a175ec729c4 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 12 Mar 2020 14:23:19 +0100 Subject: [PATCH 046/116] gnu: r-cicero: Update to 1.4.4. * gnu/packages/bioconductor.scm (r-cicero): Update to 1.4.4. [native-inputs]: Add r-knitr. --- gnu/packages/bioconductor.scm | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 0ddae43481..4320bc0bb5 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -6027,14 +6027,14 @@ genes in the gene-set that are ranked above the leading edge).") (define-public r-cicero (package (name "r-cicero") - (version "1.4.2") + (version "1.4.4") (source (origin (method url-fetch) (uri (bioconductor-uri "cicero" version)) (sha256 (base32 - "154djqd32w87814ycfmfz27ikp17bnampvmvw5hzi5p2x9l3h82r")))) + "1ay1g2r0la4grcp1y8vcp211lfwzjf7j819ajzdirsh5dab8whld")))) (build-system r-build-system) (propagated-inputs `(("r-assertthat" ,r-assertthat) @@ -6058,6 +6058,8 @@ genes in the gene-set that are ranked above the leading edge).") ("r-tibble" ,r-tibble) ("r-tidyr" ,r-tidyr) ("r-vgam" ,r-vgam))) + (native-inputs + `(("r-knitr" ,r-knitr))) (home-page "https://bioconductor.org/packages/cicero/") (synopsis "Predict cis-co-accessibility from single-cell data") (description From 117270fb51fc7fda73f5b99c1f92195a1f863a59 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 12 Mar 2020 14:23:32 +0100 Subject: [PATCH 047/116] gnu: r-vctrs: Update to 0.2.4. * gnu/packages/cran.scm (r-vctrs): Update to 0.2.4. [native-inputs]: Add r-knitr. --- gnu/packages/cran.scm | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 4ef2f922ec..df4664b371 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -4066,20 +4066,22 @@ to variables on the left-hand side of the assignment.") (define-public r-vctrs (package (name "r-vctrs") - (version "0.2.3") + (version "0.2.4") (source (origin (method url-fetch) (uri (cran-uri "vctrs" version)) (sha256 (base32 - "1pnjnxp1pwsr083qa6xp5akls6q0pnjz8pq2m9d7z3kc1886sw8w")))) + "15sgzs6afvmhssk6jcg41rn3bvmzmbm4sgca6f6x8lfrsazvdj6w")))) (build-system r-build-system) (propagated-inputs `(("r-digest" ,r-digest) ("r-ellipsis" ,r-ellipsis) ("r-glue" ,r-glue) ("r-rlang" ,r-rlang))) + (native-inputs + `(("r-knitr" ,r-knitr))) (home-page "https://github.com/r-lib/vctrs") (synopsis "Vector helpers") (description From f7306e465e98726085b5ce65aecba16646306d77 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 12 Mar 2020 14:23:43 +0100 Subject: [PATCH 048/116] gnu: r-vim: Update to 5.1.1. * gnu/packages/cran.scm (r-vim): Update to 5.1.1. --- 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 df4664b371..8f829352a3 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -5170,14 +5170,14 @@ specific S3-method.") (define-public r-vim (package (name "r-vim") - (version "5.1.0") + (version "5.1.1") (source (origin (method url-fetch) (uri (cran-uri "VIM" version)) (sha256 (base32 - "09600piny3qrxrmh8844iwrvgrhwan1c3nlh6irqy1vjha2w4gb3")))) + "0w22ir0gvym7gqd6nw2j7w5ivlb3az1dkfxv33imimkb7c83056a")))) (properties `((upstream-name . "VIM"))) (build-system r-build-system) (propagated-inputs From cd26e5dee85cfb2fc8c1b9115d78ce03c0fbb441 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 12 Mar 2020 14:23:48 +0100 Subject: [PATCH 049/116] gnu: r-catdap: Update to 1.3.5. * gnu/packages/cran.scm (r-catdap): Update to 1.3.5. --- 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 8f829352a3..ce6a82e640 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -5305,14 +5305,14 @@ contain lags, diffs and missing values.") (define-public r-catdap (package (name "r-catdap") - (version "1.3.4") + (version "1.3.5") (source (origin (method url-fetch) (uri (cran-uri "catdap" version)) (sha256 (base32 - "0i877l61f6c75pczi235rzci67w29zv1d7z5zn5p5ymndclvlpl2")))) + "0fyhl69z2lznymvpzxra9qvcg85ggzkfjy68c6mzdmf1ja44d2k5")))) (build-system r-build-system) (native-inputs `(("gfortran" ,gfortran))) From 69a3c4ce514c38ec9e31ac78fe58870dc93a7e17 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 12 Mar 2020 14:23:58 +0100 Subject: [PATCH 050/116] gnu: r-sjplot: Update to 2.8.3. * gnu/packages/cran.scm (r-sjplot): Update to 2.8.3. [propagated-inputs]: Remove r-forcats. [native-inputs]: Remove r-knitr. --- 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 ce6a82e640..3ea40713cd 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -8587,20 +8587,19 @@ conversion of indices such as Cohen's d, r, odds, etc.") (define-public r-sjplot (package (name "r-sjplot") - (version "2.8.2") + (version "2.8.3") (source (origin (method url-fetch) (uri (cran-uri "sjPlot" version)) (sha256 - (base32 "16721a5006q0gv45zjcwnkykxhjkzpq5n35vhik0g0ixgm3a2vci")))) + (base32 "0ip1rkjlhyf3axlc8qqss1qq1f0xrda890c1jmcbhm98wwjw264f")))) (properties `((upstream-name . "sjPlot"))) (build-system r-build-system) (propagated-inputs `(("r-bayestestr" ,r-bayestestr) ("r-dplyr" ,r-dplyr) ("r-effectsize" ,r-effectsize) - ("r-forcats" ,r-forcats) ("r-ggeffects" ,r-ggeffects) ("r-ggplot2" ,r-ggplot2) ("r-insight" ,r-insight) @@ -8615,6 +8614,8 @@ conversion of indices such as Cohen's d, r, odds, etc.") ("r-sjmisc" ,r-sjmisc) ("r-sjstats" ,r-sjstats) ("r-tidyr" ,r-tidyr))) + (native-inputs + `(("r-knitr" ,r-knitr))) (home-page "https://strengejacke.github.io/sjPlot/") (synopsis "Data visualization for statistics in social science") (description From d520e4c94220a821c179f7e16f90018c368c8e48 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 12 Mar 2020 14:24:16 +0100 Subject: [PATCH 051/116] gnu: r-rcppparallel: Update to 5.0.0. * gnu/packages/cran.scm (r-rcppparallel): Update to 5.0.0. --- 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 3ea40713cd..04820020dc 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -9243,14 +9243,14 @@ package provides a minimal R interface by relying on the Rcpp package.") (define-public r-rcppparallel (package (name "r-rcppparallel") - (version "4.4.4") + (version "5.0.0") (source (origin (method url-fetch) (uri (cran-uri "RcppParallel" version)) (sha256 (base32 - "0p13f2mywjr7gmskf8ri4y8p5yr1bvr4xrpw2w11vdvafwz1vcia")))) + "1mhd6vp47xmfw533h0pkvydv96m57fspvd85g8m7iqb5rcxvhhdb")))) (properties `((upstream-name . "RcppParallel"))) (build-system r-build-system) (home-page "http://rcppcore.github.io/RcppParallel") From dca5a8143f885a35ba2407c19093f893caa81787 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 12 Mar 2020 14:24:24 +0100 Subject: [PATCH 052/116] gnu: r-tidytree: Update to 0.3.2. * gnu/packages/cran.scm (r-tidytree): Update to 0.3.2. [native-inputs]: Add r-knitr. --- gnu/packages/cran.scm | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 04820020dc..84b9529cf7 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -9826,13 +9826,13 @@ maps.") (define-public r-tidytree (package (name "r-tidytree") - (version "0.3.1") + (version "0.3.2") (source (origin (method url-fetch) (uri (cran-uri "tidytree" version)) (sha256 - (base32 "1bnzs62z2l8ck2h9gabmxvayizv4nfn8dmyzry83fv0cspjbyiv7")))) + (base32 "0dx9jn19mfykn20camsmq1amlgg0w6z5hn5rdqygs1fk1l5aazad")))) (build-system r-build-system) (propagated-inputs `(("r-ape" ,r-ape) @@ -9841,6 +9841,8 @@ maps.") ("r-magrittr" ,r-magrittr) ("r-rlang" ,r-rlang) ("r-tibble" ,r-tibble))) + (native-inputs + `(("r-knitr" ,r-knitr))) (home-page "https://github.com/GuangchuangYu/tidytree") (synopsis "Tidy tool for phylogenetic tree data manipulation") (description From a85aef2d75b681e4f7c9c8539eac9045d1e7b40e Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 12 Mar 2020 14:24:35 +0100 Subject: [PATCH 053/116] gnu: r-spatialextremes: Update to 2.0-8. * gnu/packages/cran.scm (r-spatialextremes): Update to 2.0-8. --- 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 84b9529cf7..7b346f2f51 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -11205,14 +11205,14 @@ covariance functions for large data sets.") (define-public r-spatialextremes (package (name "r-spatialextremes") - (version "2.0-7.2") + (version "2.0-8") (source (origin (method url-fetch) (uri (cran-uri "SpatialExtremes" version)) (sha256 (base32 - "0aqq9ryxi4xsdqjhc1lhb7ai8szs7m2vys6nn0ygps1w3pm4xwj8")))) + "0r2byz5xxc46zqnigdax28q7446ibmzmsmi10lmm2hdks3ml6sl3")))) (properties `((upstream-name . "SpatialExtremes"))) (build-system r-build-system) From f718c28cc6f8f4b338bf9483fd00522bccbf613c Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 12 Mar 2020 14:24:41 +0100 Subject: [PATCH 054/116] gnu: r-pegas: Update to 0.13. * gnu/packages/cran.scm (r-pegas): Update to 0.13. --- 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 7b346f2f51..2229ba06e5 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -13250,13 +13250,13 @@ also provided to illustrate various methods.") (define-public r-pegas (package (name "r-pegas") - (version "0.12") + (version "0.13") (source (origin (method url-fetch) (uri (cran-uri "pegas" version)) (sha256 - (base32 "0sb8cmz4d238mcb56hv9fa0cagm00k82r7aj4cj4lxa1flxlpy8p")))) + (base32 "002i7s4g0nhnq0v05gs0yssqiyhpq2f7rw2rhn31hsbgxc86frvy")))) (build-system r-build-system) (propagated-inputs `(("r-adegenet" ,r-adegenet) From 0cc0e7e3701be2bd455829d33a613dc62c99a138 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 12 Mar 2020 14:24:47 +0100 Subject: [PATCH 055/116] gnu: r-ggplotify: Update to 0.0.5. * gnu/packages/cran.scm (r-ggplotify): Update to 0.0.5. [native-inputs]: Add r-knitr. --- gnu/packages/cran.scm | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 2229ba06e5..e9af6440da 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -14082,19 +14082,21 @@ package.") (define-public r-ggplotify (package (name "r-ggplotify") - (version "0.0.4") + (version "0.0.5") (source (origin (method url-fetch) (uri (cran-uri "ggplotify" version)) (sha256 (base32 - "0nv3wdmxnc5ww9m3xlgnb0jp30j45dg33nqc6gg3y36svg8anjcg")))) + "0pfnp4lrissf21z7867kdm6slr979kchyva8iaf83i1302kscph3")))) (build-system r-build-system) (propagated-inputs `(("r-ggplot2" ,r-ggplot2) ("r-gridgraphics" ,r-gridgraphics) ("r-rvcheck" ,r-rvcheck))) + (native-inputs + `(("r-knitr" ,r-knitr))) (home-page "https://github.com/GuangchuangYu/ggplotify") (synopsis "Convert plots to @code{grob} or @code{ggplot} object") (description From 9d3d3d1bd55f34f02643df557ca3875ebf3e68b6 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 12 Mar 2020 14:25:03 +0100 Subject: [PATCH 056/116] gnu: r-ggfortify: Update to 0.4.9. * gnu/packages/cran.scm (r-ggfortify): Update to 0.4.9. [native-inputs]: Add r-knitr. --- gnu/packages/cran.scm | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index e9af6440da..0f9053bcfb 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -15219,14 +15219,14 @@ includes data sets from oceanography.") (define-public r-ggfortify (package (name "r-ggfortify") - (version "0.4.8") + (version "0.4.9") (source (origin (method url-fetch) (uri (cran-uri "ggfortify" version)) (sha256 (base32 - "191q2z7w0l4v7swjlxs2hjgbjngw2838688s7ygnj0kigsm310f3")))) + "1p6knrbyaynaqwd939w09hpf1zz1gn95cb46sfgppl8l98krb2h5")))) (build-system r-build-system) (propagated-inputs `(("r-dplyr" ,r-dplyr) @@ -15236,6 +15236,8 @@ includes data sets from oceanography.") ("r-stringr" ,r-stringr) ("r-tibble" ,r-tibble) ("r-tidyr" ,r-tidyr))) + (native-inputs + `(("r-knitr" ,r-knitr))) (home-page "https://github.com/sinhrks/ggfortify") (synopsis "Data visualization tools for statistical analysis results") (description From 40ac3dc3949d08210c9b1e6f0e509e488202fa69 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 12 Mar 2020 14:25:20 +0100 Subject: [PATCH 057/116] gnu: r-graphlayouts: Update to 0.6.0. * gnu/packages/cran.scm (r-graphlayouts): Update to 0.6.0. --- 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 0f9053bcfb..c57fadc6d7 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -15763,14 +15763,14 @@ be used further by e.g. graphic devices.") (define-public r-graphlayouts (package (name "r-graphlayouts") - (version "0.5.0") + (version "0.6.0") (source (origin (method url-fetch) (uri (cran-uri "graphlayouts" version)) (sha256 (base32 - "03dizbhhdhnzbj2i5zvqgs617kwcv4h2pha4f16adic0fph1rxl3")))) + "1la016m37kp79zk8p1yx9kaha8y6d4w52w39h0mzv1mfsi6d75w0")))) (properties `((upstream-name . "graphlayouts"))) (build-system r-build-system) (propagated-inputs From ca29e40dac82705bcc87bad7dfa324f7369f7f3d Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 12 Mar 2020 14:25:28 +0100 Subject: [PATCH 058/116] gnu: r-parameters: Update to 0.6.0. * gnu/packages/cran.scm (r-parameters): Update to 0.6.0. [native-inputs]: Add r-knitr. --- gnu/packages/cran.scm | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index c57fadc6d7..f4b72f1102 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -15880,19 +15880,21 @@ in pipelines.") (define-public r-parameters (package (name "r-parameters") - (version "0.5.0") + (version "0.6.0") (source (origin (method url-fetch) (uri (cran-uri "parameters" version)) (sha256 (base32 - "19cblrq079svp5j3wgikw5fsdbsp1w0f2llm7kcf1rg5w1aagjr7")))) + "0zin3ikc013hc713n5zs0dbhc3m4nfw1vhc3924z0mrww8r241xn")))) (properties `((upstream-name . "parameters"))) (build-system r-build-system) (propagated-inputs `(("r-bayestestr" ,r-bayestestr) ("r-insight" ,r-insight))) + (native-inputs + `(("r-knitr" ,r-knitr))) (home-page "https://cran.r-project.org/web/packages/parameters") (synopsis "Processing of model parameters") (description From 4dab179de2f7201a8bbb89a3095880f333cd609b Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 12 Mar 2020 14:25:40 +0100 Subject: [PATCH 059/116] gnu: r-cdm: Update to 7.5-15. * gnu/packages/cran.scm (r-cdm): Update to 7.5-15. --- 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 f4b72f1102..b2b4bab199 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -20097,14 +20097,14 @@ translated to input syntax for the R packages @code{sem} and @code{lavaan}.") (define-public r-cdm (package (name "r-cdm") - (version "7.4-19") + (version "7.5-15") (source (origin (method url-fetch) (uri (cran-uri "CDM" version)) (sha256 (base32 - "1ln1r3rk004fmk55iy08bjh3vv4wnkb8zg2wj3r9rq7pi8jn8fv4")))) + "159ny2dz0rf1r3k1mqlfwambffc8rx425sggf5bn51nybpzanq3l")))) (properties `((upstream-name . "CDM"))) (build-system r-build-system) (propagated-inputs From defbaab3f8ad3bd241d329e68a1ba563d65ec111 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 12 Mar 2020 14:25:47 +0100 Subject: [PATCH 060/116] gnu: r-tam: Update to 3.4-26. * gnu/packages/cran.scm (r-tam): Update to 3.4-26. --- 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 b2b4bab199..406ccc644b 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -20131,14 +20131,14 @@ well as Ravand and Robitzsch (2015).") (define-public r-tam (package (name "r-tam") - (version "3.3-10") + (version "3.4-26") (source (origin (method url-fetch) (uri (cran-uri "TAM" version)) (sha256 (base32 - "1rkjp5x6wrk1dfspp1imvfals0wvy4w1wb8a5mhfbnilc7vgnlbq")))) + "111d7qkxhwh1lfvldyh9d61pdb5vb6x8lr8n9h95ssvw07vjqvk9")))) (properties `((upstream-name . "TAM"))) (build-system r-build-system) (propagated-inputs From 09583a0f790a9f45985de260a7ffa405f774a6ab Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 12 Mar 2020 14:26:22 +0100 Subject: [PATCH 061/116] gnu: r-xml2: Update to 1.2.5. * gnu/packages/statistics.scm (r-xml2): Update to 1.2.5. [native-inputs]: Add r-knitr. --- gnu/packages/statistics.scm | 7 ++++--- 1 file changed, 4 insertions(+), 3 deletions(-) diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm index 5354f39b0c..64156408ac 100644 --- a/gnu/packages/statistics.scm +++ b/gnu/packages/statistics.scm @@ -1983,20 +1983,21 @@ and environmental data in the framework of Euclidean exploratory methods.") (define-public r-xml2 (package (name "r-xml2") - (version "1.2.2") + (version "1.2.5") (source (origin (method url-fetch) (uri (cran-uri "xml2" version)) (sha256 (base32 - "1x3q3a0xv8j0nx3hs4d3pfjm5g9nvaxmfrapba9f4nrkqi3z2l1h")))) + "0mp61gg8s3zfq10g10vjk0mrcx6d5gm81n4ji8an2my11g61yq94")))) (build-system r-build-system) (inputs `(("libxml2" ,libxml2) ("zlib" ,zlib))) (native-inputs - `(("pkg-config" ,pkg-config))) + `(("pkg-config" ,pkg-config) + ("r-knitr" ,r-knitr))) (propagated-inputs `(("r-rcpp" ,r-rcpp))) (home-page "https://github.com/hadley/xml2") From 66f1fead636d22c6a3d72126b5b809d6da165afe Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 12 Mar 2020 14:26:39 +0100 Subject: [PATCH 062/116] gnu: r-roxygen2: Update to 7.1.0. * gnu/packages/statistics.scm (r-roxygen2): Update to 7.1.0. [native-inputs]: Move r-knitr from here... [propagated-inputs]: ...to here. --- gnu/packages/statistics.scm | 7 +++---- 1 file changed, 3 insertions(+), 4 deletions(-) diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm index 64156408ac..e4d6723d86 100644 --- a/gnu/packages/statistics.scm +++ b/gnu/packages/statistics.scm @@ -2264,19 +2264,20 @@ tables, autolinks and strikethrough text.") (define-public r-roxygen2 (package (name "r-roxygen2") - (version "7.0.2") + (version "7.1.0") (source (origin (method url-fetch) (uri (cran-uri "roxygen2" version)) (sha256 (base32 - "162xag27hwwyadfwm5zpyy15nxwhw2vbhwapx3jmi9cfyryr68sq")))) + "00s1wzx5960k8pzgpz4kikjf4k061hyhnd278y65q6n0wzv3d6vy")))) (build-system r-build-system) (propagated-inputs `(("r-brew" ,r-brew) ("r-commonmark" ,r-commonmark) ("r-desc" ,r-desc) ("r-digest" ,r-digest) + ("r-knitr" ,r-knitr) ("r-pkgload" ,r-pkgload) ("r-purrr" ,r-purrr) ("r-r6" ,r-r6) @@ -2285,8 +2286,6 @@ tables, autolinks and strikethrough text.") ("r-stringi" ,r-stringi) ("r-stringr" ,r-stringr) ("r-xml2" ,r-xml2))) - (native-inputs - `(("r-knitr" ,r-knitr))) ; for vignettes (home-page "https://github.com/klutometis/roxygen") (synopsis "In-source documentation system for R") (description From 92d6c94a1687d9b56c59a2afd5172ab6a4d63bbe Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 12 Mar 2020 14:27:02 +0100 Subject: [PATCH 063/116] gnu: r-nloptr: Update to 1.2.2.1. * gnu/packages/statistics.scm (r-nloptr): Update to 1.2.2.1. --- 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 e4d6723d86..cee6dd477a 100644 --- a/gnu/packages/statistics.scm +++ b/gnu/packages/statistics.scm @@ -5101,14 +5101,14 @@ expected shortfall risk are also included.") (define-public r-nloptr (package (name "r-nloptr") - (version "1.2.2") + (version "1.2.2.1") (source (origin (method url-fetch) (uri (cran-uri "nloptr" version)) (sha256 (base32 - "19k7nd3a7cg35k5i1cwj1lhgfs02jb7bc2gwlammpq6j41rh4vr7")))) + "1bhh2v14phzndjhiq7yw9vych6vzn5yy3vk9q35zcp3jhjjbwdyh")))) (build-system r-build-system) (native-inputs `(("r-knitr" ,r-knitr) ; for building vignettes From 72e76113f7731190881267856d3f91775450f147 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 12 Mar 2020 14:27:12 +0100 Subject: [PATCH 064/116] gnu: r-car: Update to 3.0-7. * gnu/packages/statistics.scm (r-car): Update to 3.0-7. [native-inputs]: Add r-knitr. --- gnu/packages/statistics.scm | 8 +++++--- 1 file changed, 5 insertions(+), 3 deletions(-) diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm index cee6dd477a..6616780081 100644 --- a/gnu/packages/statistics.scm +++ b/gnu/packages/statistics.scm @@ -1,5 +1,5 @@ ;;; GNU Guix --- Functional package management for GNU -;;; Copyright © 2015, 2016, 2017, 2018, 2019 Ricardo Wurmus +;;; Copyright © 2015, 2016, 2017, 2018, 2019, 2020 Ricardo Wurmus ;;; Copyright © 2015 Vicente Vera Parra ;;; Copyright © 2016 Andreas Enge ;;; Copyright © 2016, 2017, 2019 Efraim Flashner @@ -5204,13 +5204,13 @@ Companion to Applied Regression, Third Edition, Sage.") (define-public r-car (package (name "r-car") - (version "3.0-6") + (version "3.0-7") (source (origin (method url-fetch) (uri (cran-uri "car" version)) (sha256 - (base32 "0yv5mwaa0ymrbis9590mx0zcj3w6j4drhs6ab13zhx4zc3x1b7b6")))) + (base32 "11sfk1l41j27mrfy16g7b02c570n3gy9icvpcrfjh1biykqa565d")))) (build-system r-build-system) (propagated-inputs `(("r-abind" ,r-abind) @@ -5224,6 +5224,8 @@ Companion to Applied Regression, Third Edition, Sage.") ("r-pbkrtest" ,r-pbkrtest) ("r-quantreg" ,r-quantreg) ("r-rio" ,r-rio))) + (native-inputs + `(("r-knitr" ,r-knitr))) (home-page "https://r-forge.r-project.org/projects/car/") (synopsis "Companion to applied regression") (description From 0c08e4bfa1cb760a8f103b5223f0220617a93025 Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Thu, 12 Mar 2020 16:39:56 +0200 Subject: [PATCH 065/116] gnu: edirect: Update to 13.3.20200128. * gnu/packages/bioinformatics.scm (edirect): Update to 13.3.20200128. [source]: Remove bundled certificate authority tarball. --- gnu/packages/bioinformatics.scm | 7 +++++-- 1 file changed, 5 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index bd9f2b566e..4dedee6223 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -2755,7 +2755,7 @@ quantitative phenotypes.") (define-public edirect (package (name "edirect") - (version "12.1.20190829") + (version "13.3.20200128") (source (origin (method url-fetch) (uri (string-append "ftp://ftp.ncbi.nlm.nih.gov/entrez/entrezdirect" @@ -2763,7 +2763,10 @@ quantitative phenotypes.") "/edirect-" version ".tar.gz")) (sha256 (base32 - "1xb330z28dgp7slrvp8r7rgncsasv9lpcpqim571yg728dq7xdik")))) + "093zp7klv81ph0y8mm8d78a9hnpfxbv2kdym70gzdf3vz176rw33")) + (modules '((guix build utils))) + (snippet + '(begin (delete-file "Mozilla-CA.tar.gz") #t)))) (build-system perl-build-system) (arguments `(#:phases From be78906592c761aa2a67e979074561e459efdcac Mon Sep 17 00:00:00 2001 From: Amar Singh Date: Thu, 12 Mar 2020 16:25:33 +0530 Subject: [PATCH 066/116] gnu: Add guile-torrent. * gnu/packages/guile-xyz.scm (guile-torrent): New variable. Signed-off-by: Mathieu Othacehe --- gnu/packages/guile-xyz.scm | 32 +++++++++++++++++++++++++++++++- 1 file changed, 31 insertions(+), 1 deletion(-) diff --git a/gnu/packages/guile-xyz.scm b/gnu/packages/guile-xyz.scm index b71b0178d6..9f8173657e 100644 --- a/gnu/packages/guile-xyz.scm +++ b/gnu/packages/guile-xyz.scm @@ -21,7 +21,7 @@ ;;; Copyright © 2018 Pierre-Antoine Rouby ;;; Copyright © 2018 Eric Bavier ;;; Copyright © 2019 swedebugia -;;; Copyright © 2019 Amar Singh +;;; Copyright © 2019, 2020 Amar Singh ;;; Copyright © 2019 Timothy Sample ;;; ;;; This file is part of GNU Guix. @@ -3144,3 +3144,33 @@ models and also supports a rich set of boolean query operators.") (inputs `(("guile" ,guile-next) ,@(alist-delete "guile" (package-inputs guile-xapian)))))) + +(define-public guile-torrent + (package + (name "guile-torrent") + (version "0.1.3") + (source (origin (method git-fetch) + (uri (git-reference + (url + "https://github.com/o-nly/torrent.git") + (commit version))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "1yiagi55ncq1x7s9n7salzywjm4l96y3n7y3s47a9anvz87mrmim")))) + (build-system gnu-build-system) + (native-inputs + `(("autoconf" ,autoconf) + ("automake" ,automake) + ("guile" ,guile-2.2) + ("texinfo" ,texinfo) + ("perl" ,perl) + ("pkg-config" ,pkg-config))) + (propagated-inputs + `(("guile-gcrypt" ,guile-gcrypt))) + (home-page "https://github.com/o-nly/torrent") + (synopsis "Torrent library for GNU Guile") + (description "This package provides facilities for working with +@code{.torrent} or metainfo files. Implements a bencode reader and writer +according to Bitorrent BEP003.") + (license license:gpl3+))) From cf2ac04f13d9266c7c8a2ebd2e85ef593231ac9d Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ludovic=20Court=C3=A8s?= Date: Fri, 6 Mar 2020 11:25:43 +0100 Subject: [PATCH 067/116] gexp: Add 'with-parameters'. * guix/gexp.scm (): New record type. (with-parameters): New macro. (compile-parameterized): New gexp compiler. * tests/gexp.scm ("with-parameters for %current-system") ("with-parameters for %current-target-system") ("with-parameters + file-append"): New tests. * doc/guix.texi (G-Expressions): Document it. --- .dir-locals.el | 1 + doc/guix.texi | 19 ++++++++++++++++ guix/gexp.scm | 59 ++++++++++++++++++++++++++++++++++++++++++++++++++ tests/gexp.scm | 38 ++++++++++++++++++++++++++++++++ 4 files changed, 117 insertions(+) diff --git a/.dir-locals.el b/.dir-locals.el index 5ce3fbc9a5..1976f7e60d 100644 --- a/.dir-locals.el +++ b/.dir-locals.el @@ -83,6 +83,7 @@ (eval . (put 'wrap-program 'scheme-indent-function 1)) (eval . (put 'with-imported-modules 'scheme-indent-function 1)) (eval . (put 'with-extensions 'scheme-indent-function 1)) + (eval . (put 'with-parameters 'scheme-indent-function 1)) (eval . (put 'with-database 'scheme-indent-function 2)) (eval . (put 'call-with-transaction 'scheme-indent-function 2)) diff --git a/doc/guix.texi b/doc/guix.texi index dd32b65fe0..4f8f7cfb2a 100644 --- a/doc/guix.texi +++ b/doc/guix.texi @@ -8022,6 +8022,25 @@ the second case, the resulting script contains a @code{(string-append @dots{})} expression to construct the file name @emph{at run time}. @end deffn +@deffn {Scheme Syntax} with-parameters ((@var{parameter} @var{value}) @dots{}) @var{exp} +This macro is similar to the @code{parameterize} form for +dynamically-bound @dfn{parameters} (@pxref{Parameters,,, guile, GNU +Guile Reference Manual}). The key difference is that it takes effect +when the file-like object returned by @var{exp} is lowered to a +derivation or store item. + +A typical use of @code{with-parameters} is to force the system in effect +for a given object: + +@lisp +(with-parameters ((%current-system "i686-linux")) + coreutils) +@end lisp + +The example above returns an object that corresponds to the i686 build +of Coreutils, regardless of the current value of @code{%current-system}. +@end deffn + Of course, in addition to gexps embedded in ``host'' code, there are also modules containing build tools. To make it clear that they are diff --git a/guix/gexp.scm b/guix/gexp.scm index a657921741..133e0f5679 100644 --- a/guix/gexp.scm +++ b/guix/gexp.scm @@ -82,6 +82,9 @@ raw-derivation-file raw-derivation-file? + with-parameters + parameterized? + load-path-expression gexp-modules @@ -523,6 +526,62 @@ SUFFIX." (base (expand base lowered output))) (string-append base (string-concatenate suffix))))))) +;; Representation of SRFI-39 parameter settings in the dynamic scope of an +;; object lowering. +(define-record-type + (parameterized bindings thunk) + parameterized? + (bindings parameterized-bindings) ;list of parameter/value pairs + (thunk parameterized-thunk)) ;thunk + +(define-syntax-rule (with-parameters ((param value) ...) body ...) + "Bind each PARAM to the corresponding VALUE for the extent during which BODY +is lowered. Consider this example: + + (with-parameters ((%current-system \"x86_64-linux\")) + coreutils) + +It returns a object that ensures %CURRENT-SYSTEM is set to +x86_64-linux when COREUTILS is lowered." + (parameterized (list (list param (lambda () value)) ...) + (lambda () + body ...))) + +(define-gexp-compiler compile-parameterized + compiler => + (lambda (parameterized system target) + (match (parameterized-bindings parameterized) + (((parameters values) ...) + (let ((fluids (map parameter-fluid parameters)) + (thunk (parameterized-thunk parameterized))) + ;; Install the PARAMETERS for the dynamic extent of THUNK. + (with-fluids* fluids + (map (lambda (thunk) (thunk)) values) + (lambda () + ;; Special-case '%current-system' and '%current-target-system' to + ;; make sure we get the desired effect. + (let ((system (if (memq %current-system parameters) + (%current-system) + system)) + (target (if (memq %current-target-system parameters) + (%current-target-system) + target))) + (lower-object (thunk) system #:target target)))))))) + + expander => (lambda (parameterized lowered output) + (match (parameterized-bindings parameterized) + (((parameters values) ...) + (let ((fluids (map parameter-fluid parameters)) + (thunk (parameterized-thunk parameterized))) + ;; Install the PARAMETERS for the dynamic extent of THUNK. + (with-fluids* fluids + (map (lambda (thunk) (thunk)) values) + (lambda () + ;; Delegate to the expander of the wrapped object. + (let* ((base (thunk)) + (expand (lookup-expander base))) + (expand base lowered output))))))))) + ;;; ;;; Inputs & outputs. diff --git a/tests/gexp.scm b/tests/gexp.scm index 9e38816c3d..6a42d3eb57 100644 --- a/tests/gexp.scm +++ b/tests/gexp.scm @@ -284,6 +284,44 @@ (((thing "out")) (eq? thing file)))))) +(test-assertm "with-parameters for %current-system" + (mlet* %store-monad ((system -> (match (%current-system) + ("aarch64-linux" "x86_64-linux") + (_ "aarch64-linux"))) + (drv (package->derivation coreutils system)) + (obj -> (with-parameters ((%current-system system)) + coreutils)) + (result (lower-object obj))) + (return (string=? (derivation-file-name drv) + (derivation-file-name result))))) + +(test-assertm "with-parameters for %current-target-system" + (mlet* %store-monad ((target -> "riscv64-linux-gnu") + (drv (package->cross-derivation coreutils target)) + (obj -> (with-parameters + ((%current-target-system target)) + coreutils)) + (result (lower-object obj))) + (return (string=? (derivation-file-name drv) + (derivation-file-name result))))) + +(test-assert "with-parameters + file-append" + (let* ((system (match (%current-system) + ("aarch64-linux" "x86_64-linux") + (_ "aarch64-linux"))) + (drv (package-derivation %store coreutils system)) + (param (make-parameter 7)) + (exp #~(here we go #$(with-parameters ((%current-system system) + (param 42)) + (if (= (param) 42) + (file-append coreutils "/bin/touch") + %bootstrap-guile))))) + (match (gexp->sexp* exp) + (('here 'we 'go (? string? result)) + (string=? result + (string-append (derivation->output-path drv) + "/bin/touch")))))) + (test-assert "ungexp + ungexp-native" (let* ((exp (gexp (list (ungexp-native %bootstrap-guile) (ungexp coreutils) From 22464cf32abcd38311eb29001a23b26f8c4c54dc Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ludovic=20Court=C3=A8s?= Date: Thu, 12 Mar 2020 15:44:26 +0100 Subject: [PATCH 068/116] gnu: singularity: Wrap programs so they find Coreutils. * gnu/packages/linux.scm (singularity)[arguments]: Add 'set-PATH' phase. --- gnu/packages/linux.scm | 14 +++++++++++++- 1 file changed, 13 insertions(+), 1 deletion(-) diff --git a/gnu/packages/linux.scm b/gnu/packages/linux.scm index b6048a8cfb..e864e17800 100644 --- a/gnu/packages/linux.scm +++ b/gnu/packages/linux.scm @@ -3494,7 +3494,19 @@ thanks to the use of namespaces.") (("if ! singularity_which mksquashfs") "if 0") (("if ! mksquashfs") (string-append "if ! " (which "mksquashfs")))) - #t))))) + #t)) + (add-after 'install 'set-PATH + (lambda* (#:key inputs outputs #:allow-other-keys) + ;; Have the 'singularity' and 'run-singularity' self-sufficient. + (let ((out (assoc-ref outputs "out")) + (coreutils (assoc-ref inputs "coreutils"))) + (wrap-program (string-append out "/bin/singularity") + `("PATH" ":" = (,(string-append coreutils "/bin")))) + (substitute* (string-append out "/bin/run-singularity") + (("/usr/bin/env singularity") + (string-append (which "env") " " + out "/bin/singularity"))) + #t)))))) (inputs `(("libarchive" ,libarchive) ("python" ,python-wrapper) From e0dbed64c530916ab600f193f5f6f6ad6177f7b3 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ludovic=20Court=C3=A8s?= Date: Thu, 12 Mar 2020 16:38:44 +0100 Subject: [PATCH 069/116] gnu: singularity: Do not use the "errors=remount-ro" squashfs option. This mount option stopped being supported with Linux-libre 5.4.5: http://ci.guix.gnu.org/build/2056359/details * gnu/packages/linux.scm (singularity)[source]: Remove "errors=remount-ro" mount option from source code. --- gnu/packages/linux.scm | 6 ++++++ 1 file changed, 6 insertions(+) diff --git a/gnu/packages/linux.scm b/gnu/packages/linux.scm index e864e17800..01986222e8 100644 --- a/gnu/packages/linux.scm +++ b/gnu/packages/linux.scm @@ -3482,6 +3482,12 @@ thanks to the use of namespaces.") _ program) (string-append "/run/setuid-programs/singularity-" program "-helper"))) + + ;; These squashfs mount options are apparently no longer + ;; supported since Linux-libre 5.4.5. + (substitute* "src/lib/image/squashfs/mount.c" + (("\"errors=remount-ro\"") + "NULL")) #t)))) (build-system gnu-build-system) (arguments From 71bb485541328cdce214ada44be998570571bf36 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ludovic=20Court=C3=A8s?= Date: Thu, 12 Mar 2020 18:10:26 +0100 Subject: [PATCH 070/116] weather: Add '--display-missing'. * guix/scripts/weather.scm (report-server-coverage): Add #:display-missing? and honor it. (show-help, %options): Add "--display-missing". (guix-weather): Pass #:display-missing? to 'report-server-coverage'. * doc/guix.texi (Invoking guix weather): Document it. --- doc/guix.texi | 3 +++ guix/scripts/weather.scm | 22 ++++++++++++++++++---- 2 files changed, 21 insertions(+), 4 deletions(-) diff --git a/doc/guix.texi b/doc/guix.texi index 4f8f7cfb2a..ca21857a31 100644 --- a/doc/guix.texi +++ b/doc/guix.texi @@ -10860,6 +10860,9 @@ likewise for @code{qgpgme} and the 46 packages that depend on it. If you are a Guix developer, or if you are taking care of this build farm, you'll probably want to have a closer look at these packages: they may simply fail to build. + +@item --display-missing +Display the list of store items for which substitutes are missing. @end table @node Invoking guix processes diff --git a/guix/scripts/weather.scm b/guix/scripts/weather.scm index 629844768a..60915d3451 100644 --- a/guix/scripts/weather.scm +++ b/guix/scripts/weather.scm @@ -175,8 +175,10 @@ about the derivations queued, as is the case with Hydra." #f ;no derivation information (lset-intersection string=? queued items))) -(define (report-server-coverage server items) - "Report the subset of ITEMS available as substitutes on SERVER." +(define* (report-server-coverage server items + #:key display-missing?) + "Report the subset of ITEMS available as substitutes on SERVER. +When DISPLAY-MISSING? is true, display the list of missing substitutes." (define MiB (* (expt 2 20) 1.)) (format #t (G_ "looking for ~h store items on ~a...~%") @@ -260,7 +262,12 @@ are queued~%") system (* (throughput builds build-timestamp) 3600.)))) - (histogram build-system cons '() latest))))))) + (histogram build-system cons '() latest)))) + + (when (and display-missing? (not (null? missing))) + (newline) + (format #t (G_ "Substitutes are missing for the following items:~%")) + (format #t "~{ ~a~%~}" missing))))) ;;; @@ -280,6 +287,8 @@ Report the availability of substitutes.\n")) -c, --coverage[=COUNT] show substitute coverage for packages with at least COUNT dependents")) + (display (G_ " + --display-missing display the list of missing substitutes")) (display (G_ " -s, --system=SYSTEM consider substitutes for SYSTEM--e.g., \"i686-linux\"")) (newline) @@ -318,6 +327,9 @@ Report the availability of substitutes.\n")) (alist-cons 'coverage (if arg (string->number* arg) 0) result))) + (option '("display-missing") #f #f + (lambda (opt name arg result) + (alist-cons 'display-missing? #t result))) (option '(#\s "system") #t #f (lambda (opt name arg result) (alist-cons 'system arg result))))) @@ -525,7 +537,9 @@ SERVER. Display information for packages with at least THRESHOLD dependents." (package-outputs packages system)) systems)))))) (for-each (lambda (server) - (report-server-coverage server items) + (report-server-coverage server items + #:display-missing? + (assoc-ref opts 'display-missing?)) (match (assoc-ref opts 'coverage) (#f #f) (threshold From 2843fed0e973145f01fb2004c99aca8e8837b332 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ludovic=20Court=C3=A8s?= Date: Thu, 12 Mar 2020 18:30:05 +0100 Subject: [PATCH 071/116] weather: Allow for multiple '--manifest' options. * guix/scripts/weather.scm (guix-weather)[package-list]: Account for all the 'manifest entries in OPTS. * doc/guix.texi (Invoking guix weather): Document it. --- doc/guix.texi | 3 +++ guix/scripts/weather.scm | 22 ++++++++++++---------- 2 files changed, 15 insertions(+), 10 deletions(-) diff --git a/doc/guix.texi b/doc/guix.texi index ca21857a31..9a5b5f7fbe 100644 --- a/doc/guix.texi +++ b/doc/guix.texi @@ -10830,6 +10830,9 @@ specified in @var{file}. @var{file} must contain a @dfn{manifest}, as with the @code{-m} option of @command{guix package} (@pxref{Invoking guix package}). +This option can be repeated several times, in which case the manifests +are concatenated. + @item --coverage[=@var{count}] @itemx -c [@var{count}] Report on substitute coverage for packages: list packages with at least diff --git a/guix/scripts/weather.scm b/guix/scripts/weather.scm index 60915d3451..733986be0c 100644 --- a/guix/scripts/weather.scm +++ b/guix/scripts/weather.scm @@ -499,17 +499,19 @@ SERVER. Display information for packages with at least THRESHOLD dependents." (define (guix-weather . args) (define (package-list opts) ;; Return the package list specified by OPTS. - (let ((file (assoc-ref opts 'manifest)) - (base (filter-map (match-lambda - (('argument . spec) - (specification->package spec)) - (_ - #f)) - opts))) - (if (and (not file) (null? base)) + (let ((files (filter-map (match-lambda + (('manifest . file) file) + (_ #f)) + opts)) + (base (filter-map (match-lambda + (('argument . spec) + (specification->package spec)) + (_ + #f)) + opts))) + (if (and (null? files) (null? base)) (all-packages) - (append base - (if file (load-manifest file) '()))))) + (append base (append-map load-manifest files))))) (with-error-handling (parameterize ((current-terminal-columns (terminal-columns)) From b431f6c9ccfa104811dc0697d6fec84bf8b08035 Mon Sep 17 00:00:00 2001 From: Alexandru-Sergiu Marton Date: Thu, 12 Mar 2020 17:14:15 +0200 Subject: [PATCH 072/116] gnu: ghc-extra: Update to 1.7.1. * gnu/packages/haskell-xyz.scm (ghc-extra): Update to 1.7.1. Signed-off-by: Leo Famulari --- gnu/packages/haskell-xyz.scm | 7 ++++--- 1 file changed, 4 insertions(+), 3 deletions(-) diff --git a/gnu/packages/haskell-xyz.scm b/gnu/packages/haskell-xyz.scm index e368082c03..418eb7cc46 100644 --- a/gnu/packages/haskell-xyz.scm +++ b/gnu/packages/haskell-xyz.scm @@ -3774,7 +3774,7 @@ versions of GHC (i.e., < 6.10).") (define-public ghc-extra (package (name "ghc-extra") - (version "1.6.18") + (version "1.7.1") (source (origin (method url-fetch) @@ -3784,12 +3784,13 @@ versions of GHC (i.e., < 6.10).") ".tar.gz")) (sha256 (base32 - "0jvd4l0hi8pf5899pxc32yc638y0mrc357w0rph99k3hm277i0cy")))) + "0zshxv9dnd8vksncmb8dj4wvq2wdybzwxyhmy2zp6a81icm4azx4")))) (build-system haskell-build-system) (inputs `(("ghc-clock" ,ghc-clock) ("ghc-semigroups" ,ghc-semigroups) - ("ghc-quickcheck" ,ghc-quickcheck))) + ("ghc-quickcheck" ,ghc-quickcheck) + ("ghc-quickcheck-instances" ,ghc-quickcheck-instances))) (home-page "https://github.com/ndmitchell/extra") (synopsis "Extra Haskell functions") (description "This library provides extra functions for the standard From 0f864175dcfa23562744630cb3313de583856a66 Mon Sep 17 00:00:00 2001 From: Carl Dong Date: Thu, 12 Mar 2020 00:01:20 -0400 Subject: [PATCH 073/116] gnu: mingw-w64-*: Update to 7.0.0. * gnu/packages/mingw.scm (make-mingw-w64): Update to 7.0.0. --- gnu/packages/mingw.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/mingw.scm b/gnu/packages/mingw.scm index 88c8d41ef8..d0785c5067 100644 --- a/gnu/packages/mingw.scm +++ b/gnu/packages/mingw.scm @@ -45,14 +45,14 @@ specified, recurse and return a mingw-w64 with support for winpthreads." (package (name (string-append "mingw-w64" "-" machine (if with-winpthreads? "-winpthreads" ""))) - (version "6.0.0") + (version "7.0.0") (source (origin (method url-fetch) (uri (string-append "https://sourceforge.net/projects/mingw-w64/files/mingw-w64/" "mingw-w64-release/mingw-w64-v" version ".tar.bz2")) (sha256 - (base32 "1w28mynv500y03h92nh87rgw3fnp82qwnjbxrrzqkmr63q812pl0")) + (base32 "0a5njsa2zw2ssdz10jkb10mhrf3cb8qp9avs89zqmw4n6pzxy85a")) (patches (search-patches "mingw-w64-6.0.0-gcc.patch")))) (native-inputs `(("xgcc-core" ,(if xgcc xgcc (cross-gcc triplet))) ("xbinutils" ,(if xbinutils xbinutils (cross-binutils triplet))) From dcd7a97b8c5a68cd82ca91988e371442c6002b20 Mon Sep 17 00:00:00 2001 From: Mark H Weaver Date: Thu, 12 Mar 2020 20:49:19 -0400 Subject: [PATCH 074/116] gnu: linux-libre@4.4: Update to 4.4.216. * gnu/packages/linux.scm (linux-libre-4.4-version): Update to 4.4.216. (linux-libre-4.4-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 01986222e8..0f4bc88ceb 100644 --- a/gnu/packages/linux.scm +++ b/gnu/packages/linux.scm @@ -394,10 +394,10 @@ corresponding UPSTREAM-SOURCE (an origin), using the given DEBLOB-SCRIPTS." (%upstream-linux-source version hash) deblob-scripts-4.9))) -(define-public linux-libre-4.4-version "4.4.215") +(define-public linux-libre-4.4-version "4.4.216") (define-public linux-libre-4.4-pristine-source (let ((version linux-libre-4.4-version) - (hash (base32 "00zy6cxwb16pqziiqs25pz5llryx2v2nbk9vvzpzxa8x43ad7g18"))) + (hash (base32 "1hjgh9brvxzi6ypgfnk07l3j28xsxgz88sdshnz19vj96bn1w70q"))) (make-linux-libre-source version (%upstream-linux-source version hash) deblob-scripts-4.4))) From e0d5a43e516a858a97f046a3f0241a753232fda9 Mon Sep 17 00:00:00 2001 From: Mark H Weaver Date: Thu, 12 Mar 2020 20:50:24 -0400 Subject: [PATCH 075/116] gnu: linux-libre@4.9: Update to 4.9.216. * gnu/packages/linux.scm (linux-libre-4.9-version): Update to 4.9.216. (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 0f4bc88ceb..ffb66b3644 100644 --- a/gnu/packages/linux.scm +++ b/gnu/packages/linux.scm @@ -386,10 +386,10 @@ 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 "4.9.215") +(define-public linux-libre-4.9-version "4.9.216") (define-public linux-libre-4.9-pristine-source (let ((version linux-libre-4.9-version) - (hash (base32 "0j4z2al318654z40w4f8zhh73zwpgn8igjr5k4mz401phm3jyvr3"))) + (hash (base32 "0lgv5k8v5xz9z2z4k42566bh0akyk1gr0dx6s1m1rjrzsf9k86l6"))) (make-linux-libre-source version (%upstream-linux-source version hash) deblob-scripts-4.9))) From 230a59d418f3835b586594b9b8dd9b6939fd4497 Mon Sep 17 00:00:00 2001 From: Mark H Weaver Date: Thu, 12 Mar 2020 20:50:52 -0400 Subject: [PATCH 076/116] gnu: linux-libre@4.14: Update to 4.14.173. * gnu/packages/linux.scm (linux-libre-4.14-version): Update to 4.14.173. (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 ffb66b3644..4f09440ec6 100644 --- a/gnu/packages/linux.scm +++ b/gnu/packages/linux.scm @@ -378,10 +378,10 @@ 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 "4.14.172") +(define-public linux-libre-4.14-version "4.14.173") (define-public linux-libre-4.14-pristine-source (let ((version linux-libre-4.14-version) - (hash (base32 "0yi13cky6jdswca7nrjgcrdxk8rnqdbhblhy6mws103mjfms2613"))) + (hash (base32 "0kxp3mgiags8hdax15masab9zr89xraqvl9ri7zwgksx8ixav0m2"))) (make-linux-libre-source version (%upstream-linux-source version hash) deblob-scripts-4.14))) From 2a2bef35b80ea8507be1c6faf873dd6bfa3e42b9 Mon Sep 17 00:00:00 2001 From: Mark H Weaver Date: Thu, 12 Mar 2020 20:51:25 -0400 Subject: [PATCH 077/116] gnu: linux-libre@4.19: Update to 4.19.109. * gnu/packages/linux.scm (linux-libre-4.19-version): Update to 4.19.109. (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 4f09440ec6..e4dc378466 100644 --- a/gnu/packages/linux.scm +++ b/gnu/packages/linux.scm @@ -370,10 +370,10 @@ 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 "4.19.108") +(define-public linux-libre-4.19-version "4.19.109") (define-public linux-libre-4.19-pristine-source (let ((version linux-libre-4.19-version) - (hash (base32 "18shyy1z2s8r26qb4rcz7gwl43dnmycjjywp9gss5zlfn2jyrbh9"))) + (hash (base32 "0kwnlv5336vqdf38dzn077ic17zkb4rl5khxmc47syzd9zm4fhnh"))) (make-linux-libre-source version (%upstream-linux-source version hash) deblob-scripts-4.19))) From ebbe8adc3faf2420a709177a5eda8e36cf8784dc Mon Sep 17 00:00:00 2001 From: Mark H Weaver Date: Thu, 12 Mar 2020 20:51:59 -0400 Subject: [PATCH 078/116] gnu: linux-libre: Update to 5.4.25. * gnu/packages/linux.scm (linux-libre-5.4-version): Update to 5.4.25. (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 e4dc378466..7f293a9071 100644 --- a/gnu/packages/linux.scm +++ b/gnu/packages/linux.scm @@ -362,10 +362,10 @@ corresponding UPSTREAM-SOURCE (an origin), using the given DEBLOB-SCRIPTS." "linux-" version ".tar.xz")) (sha256 hash))) -(define-public linux-libre-5.4-version "5.4.24") +(define-public linux-libre-5.4-version "5.4.25") (define-public linux-libre-5.4-pristine-source (let ((version linux-libre-5.4-version) - (hash (base32 "1cvy3mxwzll4f9j8i3hfmi0i0zq75aiafq1jskp9n4kq9iwar83z"))) + (hash (base32 "09ay0adc3s3m7qk0nj5lkmrp5i0q76a9kax0xix8914d115rgvf0"))) (make-linux-libre-source version (%upstream-linux-source version hash) deblob-scripts-5.4))) From 8320c72587255ab6649c32ef838762058ae95c5b Mon Sep 17 00:00:00 2001 From: Alex Griffin Date: Fri, 10 Jan 2020 13:25:19 -0600 Subject: [PATCH 079/116] gnu: go-github-com-sirupsen-logrus: Propagate inputs. * gnu/packages/golang.scm (go-github-com-sirupsen-logrus): Propagate inputs. --- gnu/packages/golang.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/golang.scm b/gnu/packages/golang.scm index 871b1fed2f..3b4e5192e5 100644 --- a/gnu/packages/golang.scm +++ b/gnu/packages/golang.scm @@ -14,7 +14,7 @@ ;;; Copyright © 2018 Pierre Neidhardt ;;; Copyright @ 2018, 2019 Katherine Cox-Buday ;;; Copyright @ 2019 Giovanni Biscuolo -;;; Copyright @ 2019 Alex Griffin +;;; Copyright @ 2019, 2020 Alex Griffin ;;; Copyright © 2019 Arun Isaac ;;; Copyright © 2020 Jack Hill ;;; @@ -1166,7 +1166,7 @@ GNU extensions} to the POSIX recommendations for command-line options.") (base32 "0g5z7al7kky11ai2dhac6gkp3b5pxsvx72yj3xg4wg3265gbn7yz")))) (build-system go-build-system) - (native-inputs + (propagated-inputs `(("go-golang-org-x-crypto" ,go-golang-org-x-crypto) ("go-github-com-stretchr-testify" From aff95768117381547a60f81f4a58d1d5582afc1a Mon Sep 17 00:00:00 2001 From: Alex Griffin Date: Fri, 10 Jan 2020 13:32:32 -0600 Subject: [PATCH 080/116] gnu: Add go-github-com-rifflock-lfshook. * gnu/packages/golang.scm (go-github-com-rifflock-lfshook): New variable. --- gnu/packages/golang.scm | 25 +++++++++++++++++++++++++ 1 file changed, 25 insertions(+) diff --git a/gnu/packages/golang.scm b/gnu/packages/golang.scm index 3b4e5192e5..470013b052 100644 --- a/gnu/packages/golang.scm +++ b/gnu/packages/golang.scm @@ -1181,6 +1181,31 @@ GNU extensions} to the POSIX recommendations for command-line options.") compatible with the standard library logger.") (license license:expat))) +(define-public go-github-com-rifflock-lfshook + (package + (name "go-github-com-rifflock-lfshook") + (version "2.4") + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/rifflock/lfshook.git") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "0wxqjcjfg8c0klmdgmbw3ckagby3wg9rkga9ihd4fsf05x5scxrc")))) + (build-system go-build-system) + (arguments + `(#:import-path "github.com/rifflock/lfshook")) + (propagated-inputs + `(("go-github-com-sirupsen-logrus" ,go-github-com-sirupsen-logrus))) + (home-page "https://github.com/rifflock/lfshook") + (synopsis "Local File System hook for Logrus logger") + (description "This package provides a hook for Logrus to write directly to +a file on the filesystem. The log levels are dynamic at instantiation of the +hook, so it is capable of logging at some or all levels.") + (license license:expat))) + (define-public go-github-com-kardianos-osext (let ((commit "ae77be60afb1dcacde03767a8c37337fad28ac14") (revision "1")) From 42c6503d3777cf1b1c3749efe847dc8025a34b94 Mon Sep 17 00:00:00 2001 From: Alex Griffin Date: Fri, 10 Jan 2020 13:36:57 -0600 Subject: [PATCH 081/116] gnu: Add go-github-com-mattn-go-zglob. * gnu/packages/golang.scm (go-github-com-mattn-go-zglob): New variable. --- gnu/packages/golang.scm | 22 ++++++++++++++++++++++ 1 file changed, 22 insertions(+) diff --git a/gnu/packages/golang.scm b/gnu/packages/golang.scm index 470013b052..0d92139311 100644 --- a/gnu/packages/golang.scm +++ b/gnu/packages/golang.scm @@ -3374,3 +3374,25 @@ test results.") data serialization format.") (home-page "https://github.com/golang/protobuf") (license license:bsd-3))) + +(define-public go-github-com-mattn-go-zglob + (package + (name "go-github-com-mattn-go-zglob") + (version "0.0.1") + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/mattn/go-zglob.git") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "1sncdyq5fbd42al4amyy91h7vlzm3wm6c9vl8za2pjgfgsd581fz")))) + (build-system go-build-system) + (arguments + `(#:import-path "github.com/mattn/go-zglob")) + (home-page "https://github.com/mattn/go-zglob") + (synopsis "Glob library that descends into other directories") + (description " A glob library that implements descending into other +directories. It is optimized for filewalking. ") + (license license:expat))) From 63299f2840edcd5d942b3433ffb205fcc1fb6eb4 Mon Sep 17 00:00:00 2001 From: Alex Griffin Date: Fri, 10 Jan 2020 13:37:30 -0600 Subject: [PATCH 082/116] gnu: Add browserpass-native. * gnu/packages/password-utils.scm (browserpass-native): New variable. --- gnu/packages/password-utils.scm | 80 ++++++++++++++++++++++++++++++++- 1 file changed, 79 insertions(+), 1 deletion(-) diff --git a/gnu/packages/password-utils.scm b/gnu/packages/password-utils.scm index 06214297f7..333fbfa026 100644 --- a/gnu/packages/password-utils.scm +++ b/gnu/packages/password-utils.scm @@ -6,7 +6,7 @@ ;;; Copyright © 2016 Jessica Tallon ;;; Copyright © 2016 Andreas Enge ;;; Copyright © 2016 Lukas Gradl -;;; Copyright © 2016, 2019 Alex Griffin +;;; Copyright © 2016, 2019, 2020 Alex Griffin ;;; Copyright © 2017 Leo Famulari ;;; Copyright © 2017, 2018 Clément Lassieur ;;; Copyright © 2017, 2018, 2019 Tobias Geerinckx-Rice @@ -46,6 +46,7 @@ #:use-module ((guix licenses) #:prefix license:) #:use-module (guix build-system cmake) #:use-module (guix build-system gnu) + #:use-module (guix build-system go) #:use-module (guix build-system trivial) #:use-module (guix download) #:use-module (guix git-download) @@ -65,6 +66,7 @@ #:use-module (gnu packages gettext) #:use-module (gnu packages glib) #:use-module (gnu packages gnupg) + #:use-module (gnu packages golang) #:use-module (gnu packages gtk) #:use-module (gnu packages guile) #:use-module (gnu packages kerberos) @@ -697,6 +699,82 @@ using password-store through rofi interface: @end enumerate") (license license:gpl3))) +(define-public browserpass-native + (package + (name "browserpass-native") + (version "3.0.6") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/browserpass/browserpass-native.git") + (commit version))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "0q3bsla07zjl6i69nj1axbkg2ia89pvh0jg6nlqgbm2kpzzbn0pz")))) + (build-system go-build-system) + (arguments + `(#:import-path "github.com/browserpass/browserpass-native" + #:install-source? #f + #:phases + (modify-phases %standard-phases + (add-before 'build 'patch-makefile + (lambda* (#:key outputs #:allow-other-keys) + (let ((out (assoc-ref outputs "out"))) + ;; This doesn't go in #:make-flags because the Makefile itself + ;; gets installed. + (substitute* + "src/github.com/browserpass/browserpass-native/Makefile" + (("PREFIX \\?= /usr") + (string-append "PREFIX ?= " out))) + #t))) + (add-before 'build 'configure + (lambda _ + (with-directory-excursion + "src/github.com/browserpass/browserpass-native" + (invoke "make" "configure")) + #t)) + (replace 'build + (lambda _ + (with-directory-excursion + "src/github.com/browserpass/browserpass-native" + (invoke "make")) + #t)) + (replace 'install + (lambda _ + (with-directory-excursion + "src/github.com/browserpass/browserpass-native" + (invoke "make" "install")) + #t)) + (add-after 'install 'wrap-executable + (lambda* (#:key inputs outputs #:allow-other-keys) + (let ((out (assoc-ref outputs "out")) + (gnupg (assoc-ref inputs "gnupg"))) + (wrap-program (string-append out "/bin/browserpass") + `("PATH" ":" prefix + (,(string-append gnupg "/bin")))) + #t)))))) + (native-inputs + `(("which" ,which))) + (inputs + `(("gnupg" ,gnupg) + ("go-github-com-mattn-go-zglob" ,go-github-com-mattn-go-zglob) + ("go-github-com-rifflock-lfshook" ,go-github-com-rifflock-lfshook) + ("go-github-com-sirupsen-logrus" ,go-github-com-sirupsen-logrus) + ("go-golang-org-x-sys" ,go-golang-org-x-sys))) + (home-page "https://github.com/browserpass/browserpass-native") + (synopsis "Browserpass native messaging host") + (description "Browserpass is a browser extension for pass, a +UNIX-based password store manager. It allows you to auto-fill or copy to +clipboard credentials for the current domain, protecting you from phishing +attacks. + +This package only contains the Browserpass native messaging host. You must +also install the browser extension for GNU IceCat or ungoogled-chromium +separately.") + (license license:isc))) + (define-public argon2 (package (name "argon2") From 136070022b0c488a304c7813d3a05b00f8998202 Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Sat, 18 Jan 2020 23:13:39 +0100 Subject: [PATCH 083/116] gnu: catdoc: Use HTTPS home page. * gnu/packages/textutils.scm (catdoc)[home-page]: Use HTTPS. --- gnu/packages/textutils.scm | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/gnu/packages/textutils.scm b/gnu/packages/textutils.scm index 1be7c69154..8510c6d1d0 100644 --- a/gnu/packages/textutils.scm +++ b/gnu/packages/textutils.scm @@ -561,7 +561,7 @@ runs Word\".") (lambda* (#:key outputs #:allow-other-keys) (let ((out (assoc-ref outputs "out"))) (mkdir-p (string-append out "/share/man/man1")))))))) - (home-page "http://www.wagner.pp.ru/~vitus/software/catdoc/") + (home-page "https://www.wagner.pp.ru/~vitus/software/catdoc/") (synopsis "MS-Word to TeX or plain text converter") (description "@command{catdoc} extracts text from MS-Word files, trying to preserve as many special printable characters as possible. It supports From 1bc64532b7a74f337a8dc56e9b7a9b0ff3b79ae9 Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Sat, 18 Jan 2020 22:57:19 +0100 Subject: [PATCH 084/116] gnu: libwebsockets: Use HTTPS home page. * gnu/packages/web.scm (libwebsockets)[home-page]: Use HTTPS. --- gnu/packages/web.scm | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/gnu/packages/web.scm b/gnu/packages/web.scm index 236dd1a506..d766d31785 100644 --- a/gnu/packages/web.scm +++ b/gnu/packages/web.scm @@ -1129,7 +1129,7 @@ parser written in ANSI C and a small validating JSON generator.") "Libwebsockets is a library that allows C programs to establish client and server WebSockets connections---a protocol layered above HTTP that allows for efficient socket-like bidirectional reliable communication channels.") - (home-page "http://libwebsockets.org/") + (home-page "https://libwebsockets.org") ;; This is LGPLv2.1-only with extra exceptions specified in 'LICENSE'. (license license:lgpl2.1))) From 2eed6813b6a447524fad8c29412a1efc8c135456 Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Sat, 18 Jan 2020 23:14:45 +0100 Subject: [PATCH 085/116] gnu: autobuild: Use HTTPS home page. * gnu/packages/autotools.scm (autobuild)[home-page]: Use HTTPS. --- gnu/packages/autotools.scm | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/gnu/packages/autotools.scm b/gnu/packages/autotools.scm index 2ba9950981..62e0b9291f 100644 --- a/gnu/packages/autotools.scm +++ b/gnu/packages/autotools.scm @@ -243,7 +243,7 @@ Autobuild generates an HTML summary file, containing links to each build log. The summary includes project name, version, build hostname, host type (cross compile aware), date of build, and indication of success or failure. The output is indexed in many ways to simplify browsing.") - (home-page "http://josefsson.org/autobuild/") + (home-page "https://josefsson.org/autobuild/") (license gpl3+))) (define-public automake From e2528a3cc1819d3fe24880c5cfec74f075d5f820 Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Fri, 13 Mar 2020 02:45:00 +0100 Subject: [PATCH 086/116] gnu: java-snappy@1.0: Don't use unstable tarball. * gnu/packages/java-compression.scm (java-snappy-1)[name]: Restate. [source]: Use GIT-FETCH and GIT-FILE-NAME. --- gnu/packages/java-compression.scm | 17 ++++++++++------- 1 file changed, 10 insertions(+), 7 deletions(-) diff --git a/gnu/packages/java-compression.scm b/gnu/packages/java-compression.scm index 3a9082641c..2dd65da305 100644 --- a/gnu/packages/java-compression.scm +++ b/gnu/packages/java-compression.scm @@ -131,14 +131,17 @@ compressor/decompressor.") (define-public java-snappy-1 (package (inherit java-snappy) + (name "java-snappy") (version "1.0.3-rc3") - (source (origin - (method url-fetch) - (uri (string-append "https://github.com/xerial/snappy-java/archive/" - "snappy-java-" version ".tar.gz")) - (sha256 - (base32 - "08hsxlqidiqck0q57fshwyv3ynyxy18vmhrai9fyc8mz17m7gsa3")))) + (source + (origin + (method git-fetch) + (uri (git-reference + (url (string-append "https://github.com/xerial/snappy-java")) + (commit (string-append "snappy-java-" version)))) + (sha256 + (base32 "0gbg3xmhniyh5p6w5zqj16fr15fa8j4raswd8pj00l4ixf5qa6m4")) + (file-name (git-file-name name version)))) (arguments `(#:jar-name "snappy.jar" #:source-dir "src/main/java" From 287e3d312440a103e8ca1e14b5b09a0ce0124e5e Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Fri, 13 Mar 2020 03:18:23 +0100 Subject: [PATCH 087/116] gnu: java-iq80-snappy: Don't use unstable tarball. * gnu/packages/java-compression.scm (java-iq80-snappy)[source]: Use GIT-FETCH and GIT-FILE-NAME. --- gnu/packages/java-compression.scm | 16 +++++++++------- 1 file changed, 9 insertions(+), 7 deletions(-) diff --git a/gnu/packages/java-compression.scm b/gnu/packages/java-compression.scm index 2dd65da305..536e1e6530 100644 --- a/gnu/packages/java-compression.scm +++ b/gnu/packages/java-compression.scm @@ -193,13 +193,15 @@ compressor/decompressor.") (package (name "java-iq80-snappy") (version "0.4") - (source (origin - (method url-fetch) - (uri (string-append "https://github.com/dain/snappy/archive/snappy-" - version ".tar.gz")) - (sha256 - (base32 - "0rb3zhci7w9wzd65lfnk7p3ip0n6gb58a9qpx8n7r0231gahyamf")))) + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/dain/snappy") + (commit (string-append "snappy-" version)))) + (sha256 + (base32 "1mswh207065rdzbxk6rxaqlxhbg1ngxa0vjc20knsn31kqbq1bcz")) + (file-name (git-file-name name version)))) (build-system ant-build-system) (arguments `(#:jar-name "iq80-snappy.jar" From 16b84f54bd870b938a1c1ede6fefcfff84a504f5 Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Sat, 18 Jan 2020 23:08:09 +0100 Subject: [PATCH 088/116] gnu: bastet: Use HTTPS home page. * gnu/packages/games.scm (bastet)[home-page]: Use HTTPS. --- gnu/packages/games.scm | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/gnu/packages/games.scm b/gnu/packages/games.scm index 9b4ff4df9a..f9c846d307 100644 --- a/gnu/packages/games.scm +++ b/gnu/packages/games.scm @@ -383,7 +383,7 @@ physics settings to tweak as well.") (inputs `(("boost" ,boost) ("ncurses" ,ncurses))) - (home-page "http://fph.altervista.org/prog/bastet.html") + (home-page "https://fph.altervista.org/prog/bastet.html") (synopsis "Antagonistic Tetris-style falling brick game for text terminals") (description "Bastet (short for Bastard Tetris) is a simple ncurses-based falling brick From b7afc63f0f664adfdfd79aa3cbb11eb270e7a8f6 Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Fri, 13 Mar 2020 05:28:39 +0100 Subject: [PATCH 089/116] gnu: sdparm: Update to 1.11. * gnu/packages/disk.scm (sdparm): Update to 1.11. [source]: Hard-code name. --- gnu/packages/disk.scm | 7 +++---- 1 file changed, 3 insertions(+), 4 deletions(-) diff --git a/gnu/packages/disk.scm b/gnu/packages/disk.scm index f42f2900ec..4373d52974 100644 --- a/gnu/packages/disk.scm +++ b/gnu/packages/disk.scm @@ -293,15 +293,14 @@ and a @command{fsck.vfat} compatibility symlink for use in an initrd.") (define-public sdparm (package (name "sdparm") - (version "1.10") + (version "1.11") (source (origin (method url-fetch) (uri (string-append "http://sg.danny.cz/sg/p/" - name "-" version ".tar.xz")) + "sdparm-" version ".tar.xz")) (sha256 - (base32 - "1jjq3lzgfy4r76rc26q02lv4wm5cb4dx5nh913h489zjrr4f3jbx")))) + (base32 "1nqjc4w2w47zavcbf5xmm53x1zbwgljaw1lpajcdi537cgy32fa8")))) (build-system gnu-build-system) (home-page "http://sg.danny.cz/sg/sdparm.html") (synopsis "Provide access to SCSI device parameters") From f50ef3493e6bdc0519fac57ffd32a5590fcca05d Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Sat, 18 Jan 2020 22:56:13 +0100 Subject: [PATCH 090/116] gnu: unqlite: Use HTTPS home page. * gnu/packages/databases.scm (unqlite)[home-page]: Use HTTPS. --- gnu/packages/databases.scm | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/gnu/packages/databases.scm b/gnu/packages/databases.scm index 9d42ba75fa..26b6a55a14 100644 --- a/gnu/packages/databases.scm +++ b/gnu/packages/databases.scm @@ -1852,7 +1852,7 @@ Driver.") "1sbpvhg15gadq0mpcy16q7k3rkg4b4dicpnn5xifpkpn02sqik3s")))) (build-system gnu-build-system) (arguments `(#:tests? #f)) ;No check target - (home-page "http://www.unqlite.org") + (home-page "https://www.unqlite.org") (synopsis "In-memory key/value and document store") (description "UnQLite is an in-process software library which implements a From d1548cb09f9294d0c68e2eb54f2f27a594b84fe2 Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Sat, 18 Jan 2020 23:20:26 +0100 Subject: [PATCH 091/116] gnu: fltk: Use HTTPS home page. * gnu/packages/fltk.scm (fltk)[home-page]: Use HTTPS. --- gnu/packages/fltk.scm | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/gnu/packages/fltk.scm b/gnu/packages/fltk.scm index f09b383ef1..573c0541bb 100644 --- a/gnu/packages/fltk.scm +++ b/gnu/packages/fltk.scm @@ -88,7 +88,7 @@ (("-lpng") (string-append "-L" png "/lib -lpng")) (("-lz") (string-append "-L" zlib "/lib -lz")))) #t))))) - (home-page "http://www.fltk.org") + (home-page "https://www.fltk.org") (synopsis "3D C++ GUI library") (description "FLTK is a C++ GUI toolkit providing modern GUI functionality without the bloat. It supports 3D graphics via OpenGL and its built-in GLUT From acf6168b5dd1d5f03ad22966b27540d4457d2863 Mon Sep 17 00:00:00 2001 From: Arun Isaac Date: Sat, 22 Feb 2020 13:18:17 +0530 Subject: [PATCH 092/116] gnu: uim: Do not install elisp files in guix.d. * gnu/packages/xorg.scm (uim)[arguments]: Pass %output/share/emacs to the --with-lispdir configure flag. Add fix-install-path phase after install phase. --- gnu/packages/xorg.scm | 16 ++++++++++++---- 1 file changed, 12 insertions(+), 4 deletions(-) diff --git a/gnu/packages/xorg.scm b/gnu/packages/xorg.scm index f951e565ff..a7ba6fe9eb 100644 --- a/gnu/packages/xorg.scm +++ b/gnu/packages/xorg.scm @@ -13,7 +13,7 @@ ;;; Copyright © 2016, 2017 John Darrington ;;; Copyright © 2017, 2018, 2019 Marius Bakke ;;; Copyright © 2017, 2018, 2019 Rutger Helling -;;; Copyright © 2017 Arun Isaac +;;; Copyright © 2017, 2020 Arun Isaac ;;; Copyright © 2018, 2019 Tobias Geerinckx-Rice ;;; Copyright © 2018 Kei Kebreau ;;; Copyright © 2018 Oleg Pykhalov @@ -6137,8 +6137,7 @@ X11 servers, Windows, or macOS.") (guix build emacs-utils)) #:configure-flags (list "--with-anthy-utf8" - (string-append "--with-lispdir=" %output - "/share/emacs/site-lisp/guix.d") + (string-append "--with-lispdir=" %output "/share/emacs") ;; Set proper runpath (string-append "LDFLAGS=-Wl,-rpath=" %output "/lib")) #:phases @@ -6151,8 +6150,17 @@ X11 servers, Windows, or macOS.") (string-append "\"" (assoc-ref outputs "out") "/bin/" executable "\""))) #t)) + ;; Fix installation path by renaming share/emacs/uim-el to + ;; share/emacs/site-lisp + (add-after 'install 'fix-install-path + (lambda* (#:key outputs #:allow-other-keys) + (let ((share-emacs (string-append (assoc-ref outputs "out") + "/share/emacs"))) + (rename-file (string-append share-emacs "/uim-el") + (string-append share-emacs "/site-lisp"))) + #t)) ;; Generate emacs autoloads for uim.el - (add-after 'install 'make-autoloads + (add-after 'fix-install-path 'make-autoloads (lambda* (#:key outputs #:allow-other-keys) (emacs-generate-autoloads ,name (string-append (assoc-ref outputs "out") From d5b0aa99f8d339b13dbea504bdb9a230e59915a0 Mon Sep 17 00:00:00 2001 From: Arun Isaac Date: Sat, 22 Feb 2020 22:06:06 +0530 Subject: [PATCH 093/116] gnu: uim: Use emacs-substitute-variables instead of substitute*. * gnu/packages/xorg.scm (uim)[arguments]: In the configure-uim-el phase, use emacs-substitute-variables instead of substitute*. --- gnu/packages/xorg.scm | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/gnu/packages/xorg.scm b/gnu/packages/xorg.scm index a7ba6fe9eb..2bf920b20d 100644 --- a/gnu/packages/xorg.scm +++ b/gnu/packages/xorg.scm @@ -6145,10 +6145,10 @@ X11 servers, Windows, or macOS.") ;; Set path of uim-el-agent and uim-el-helper-agent executables (add-after 'configure 'configure-uim-el (lambda* (#:key outputs #:allow-other-keys) - (substitute* "emacs/uim-var.el" - (("\"(uim-el-agent|uim-el-helper-agent)\"" _ executable) - (string-append "\"" (assoc-ref outputs "out") - "/bin/" executable "\""))) + (let ((out (assoc-ref outputs "out"))) + (emacs-substitute-variables "emacs/uim-var.el" + ("uim-el-agent" (string-append out "/bin/uim-el-agent")) + ("uim-el-helper-agent" (string-append out "/bin/uim-el-helper-agent")))) #t)) ;; Fix installation path by renaming share/emacs/uim-el to ;; share/emacs/site-lisp From e80d1c1992fb60c492520d61f3a3d1fef65cfdf2 Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Fri, 13 Mar 2020 14:19:44 +0200 Subject: [PATCH 094/116] gnu: httrack: Use texi markup in description. * gnu/packages/web.scm (httrack)[description]: Use texi markup. --- gnu/packages/web.scm | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/gnu/packages/web.scm b/gnu/packages/web.scm index d766d31785..8867a48849 100644 --- a/gnu/packages/web.scm +++ b/gnu/packages/web.scm @@ -7205,7 +7205,7 @@ the Internet to a local directory, building recursively all directories, getting HTML, images, and other files from the server to your computer. HTTrack arranges the original site's relative link-structure. Simply open -a page of the ``mirrored'' website in your browser, and you can browse the +a page of the @code{mirrored} website in your browser, and you can browse the site from link to link, as if you were viewing it online. HTTrack can also update an existing mirrored site, and resume interrupted downloads. From 10b99ddf4596a033eaf348dddf519639e029f9d1 Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Fri, 13 Mar 2020 14:26:22 +0200 Subject: [PATCH 095/116] gnu: cadaver: Satisfy 'guix lint'. * gnu/packages/web.scm (cadaver)[home-page]: Follow redirect. [description]: Always use two spaces. --- gnu/packages/web.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/web.scm b/gnu/packages/web.scm index 8867a48849..3d6f2d5dcf 100644 --- a/gnu/packages/web.scm +++ b/gnu/packages/web.scm @@ -6087,10 +6087,10 @@ file links.") (inputs `(("expat" ,expat) ("openssl" ,openssl))) - (home-page "http://www.webdav.org/cadaver") + (home-page "http://www.webdav.org/cadaver/") (synopsis "Command-line WebDAV client") (description - "Cadaver is a command-line WebDAV client for Unix. It supports + "Cadaver is a command-line WebDAV client for Unix. It supports file upload, download, on-screen display, namespace operations (move/copy), collection creation and deletion, and locking operations.") (license license:gpl2))) From be764b47ad1079df531f016c1946cbf98ff48c41 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ludovic=20Court=C3=A8s?= Date: Fri, 13 Mar 2020 10:53:49 +0100 Subject: [PATCH 096/116] weather: Exit with non-zero when coverage is below 100%. * guix/scripts/weather.scm (report-server-coverage): Return the coverage ratio. (guix-weather): Exit if and only if each server's coverage is 1. --- doc/guix.texi | 7 +++++-- guix/scripts/weather.scm | 29 +++++++++++++++++++---------- 2 files changed, 24 insertions(+), 12 deletions(-) diff --git a/doc/guix.texi b/doc/guix.texi index 9a5b5f7fbe..8acae26b9a 100644 --- a/doc/guix.texi +++ b/doc/guix.texi @@ -10809,8 +10809,11 @@ guix weather @var{options}@dots{} [@var{packages}@dots{}] When @var{packages} is omitted, @command{guix weather} checks the availability of substitutes for @emph{all} the packages, or for those specified with @option{--manifest}; otherwise it only considers the specified packages. It -is also possible to query specific system types with @option{--system}. The -available options are listed below. +is also possible to query specific system types with @option{--system}. +@command{guix weather} exits with a non-zero code when the fraction of +available substitutes is below 100%. + +The available options are listed below. @table @code @item --substitute-urls=@var{urls} diff --git a/guix/scripts/weather.scm b/guix/scripts/weather.scm index 733986be0c..913c84955e 100644 --- a/guix/scripts/weather.scm +++ b/guix/scripts/weather.scm @@ -178,7 +178,8 @@ about the derivations queued, as is the case with Hydra." (define* (report-server-coverage server items #:key display-missing?) "Report the subset of ITEMS available as substitutes on SERVER. -When DISPLAY-MISSING? is true, display the list of missing substitutes." +When DISPLAY-MISSING? is true, display the list of missing substitutes. +Return the coverage ratio, an exact number between 0 and 1." (define MiB (* (expt 2 20) 1.)) (format #t (G_ "looking for ~h store items on ~a...~%") @@ -267,7 +268,11 @@ are queued~%") (when (and display-missing? (not (null? missing))) (newline) (format #t (G_ "Substitutes are missing for the following items:~%")) - (format #t "~{ ~a~%~}" missing))))) + (format #t "~{ ~a~%~}" missing)) + + ;; Return the coverage ratio. + (let ((total (length items))) + (/ (- total (length missing)) total))))) ;;; @@ -538,16 +543,20 @@ SERVER. Display information for packages with at least THRESHOLD dependents." (lambda (system) (package-outputs packages system)) systems)))))) - (for-each (lambda (server) + (exit + (every (lambda (server) + (define coverage (report-server-coverage server items #:display-missing? - (assoc-ref opts 'display-missing?)) - (match (assoc-ref opts 'coverage) - (#f #f) - (threshold - (report-package-coverage server packages systems - #:threshold threshold)))) - urls))))) + (assoc-ref opts 'display-missing?))) + (match (assoc-ref opts 'coverage) + (#f #f) + (threshold + (report-package-coverage server packages systems + #:threshold threshold))) + + (= 1 coverage)) + urls)))))) ;;; Local Variables: ;;; eval: (put 'let/time 'scheme-indent-function 1) From a0feabdfdb5b0949ac16fc8280bbabe157cbd084 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ludovic=20Court=C3=A8s?= Date: Fri, 13 Mar 2020 11:32:35 +0100 Subject: [PATCH 097/116] weather: '--coverage' filters out non-package objects. This is a followup to d37b5a1b58824dafbe6f32b1c183661c147c660c. * guix/scripts/weather.scm (guix-weather): Filter PACKAGES passed to 'report-package-coverage'. --- guix/scripts/weather.scm | 6 +++++- 1 file changed, 5 insertions(+), 1 deletion(-) diff --git a/guix/scripts/weather.scm b/guix/scripts/weather.scm index 913c84955e..a9e0cba92a 100644 --- a/guix/scripts/weather.scm +++ b/guix/scripts/weather.scm @@ -552,7 +552,11 @@ SERVER. Display information for packages with at least THRESHOLD dependents." (match (assoc-ref opts 'coverage) (#f #f) (threshold - (report-package-coverage server packages systems + ;; PACKAGES may include non-package objects coming from a + ;; manifest. Filter them out. + (report-package-coverage server + (filter package? packages) + systems #:threshold threshold))) (= 1 coverage)) From b24ec854519c0e0815b19eeb246c47444aa687c5 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ludovic=20Court=C3=A8s?= Date: Fri, 13 Mar 2020 12:55:05 +0100 Subject: [PATCH 098/116] pack: Factorize 'mksquashfs' invocations. * guix/scripts/pack.scm (squashfs-image)[build](mksquashfs): New procedure. Replace instances of (invoke "mksquashfs" ...) with (mksquashfs ...). --- guix/scripts/pack.scm | 135 +++++++++++++++++++++--------------------- 1 file changed, 68 insertions(+), 67 deletions(-) diff --git a/guix/scripts/pack.scm b/guix/scripts/pack.scm index c8d8546e29..70239b64de 100644 --- a/guix/scripts/pack.scm +++ b/guix/scripts/pack.scm @@ -365,6 +365,9 @@ added to the pack." (define database #+database) (define entry-point #$entry-point) + (define (mksquashfs args) + (apply invoke "mksquashfs" args)) + (setenv "PATH" (string-append #$archiver "/bin")) ;; We need an empty file in order to have a valid file argument when @@ -376,92 +379,90 @@ added to the pack." ;; Add all store items. Unfortunately mksquashfs throws away all ;; ancestor directories and only keeps the basename. We fix this ;; in the following invocations of mksquashfs. - (apply invoke "mksquashfs" - `(,@(map store-info-item - (call-with-input-file "profile" - read-reference-graph)) - #$environment - ,#$output + (mksquashfs `(,@(map store-info-item + (call-with-input-file "profile" + read-reference-graph)) + #$environment + ,#$output - ;; Do not perform duplicate checking because we - ;; don't have any dupes. - "-no-duplicates" - "-comp" - ,#+(compressor-name compressor))) + ;; Do not perform duplicate checking because we + ;; don't have any dupes. + "-no-duplicates" + "-comp" + ,#+(compressor-name compressor))) ;; Here we reparent the store items. For each sub-directory of ;; the store prefix we need one invocation of "mksquashfs". (for-each (lambda (dir) - (apply invoke "mksquashfs" - `(".empty" - ,#$output - "-root-becomes" ,dir))) + (mksquashfs `(".empty" + ,#$output + "-root-becomes" ,dir))) (reverse (string-tokenize (%store-directory) (char-set-complement (char-set #\/))))) ;; Add symlinks and mount points. - (apply invoke "mksquashfs" - `(".empty" - ,#$output - ;; Create SYMLINKS via pseudo file definitions. - ,@(append-map - (match-lambda - ((source '-> target) - ;; Create relative symlinks to work around a bug in - ;; Singularity 2.x: - ;; https://bugs.gnu.org/34913 - ;; https://github.com/sylabs/singularity/issues/1487 - (let ((target (string-append #$profile "/" target))) - (list "-p" - (string-join - ;; name s mode uid gid symlink - (list source - "s" "777" "0" "0" - (relative-file-name (dirname source) - target))))))) - '#$symlinks*) + (mksquashfs + `(".empty" + ,#$output + ;; Create SYMLINKS via pseudo file definitions. + ,@(append-map + (match-lambda + ((source '-> target) + ;; Create relative symlinks to work around a bug in + ;; Singularity 2.x: + ;; https://bugs.gnu.org/34913 + ;; https://github.com/sylabs/singularity/issues/1487 + (let ((target (string-append #$profile "/" target))) + (list "-p" + (string-join + ;; name s mode uid gid symlink + (list source + "s" "777" "0" "0" + (relative-file-name (dirname source) + target))))))) + '#$symlinks*) - "-p" "/.singularity.d d 555 0 0" + "-p" "/.singularity.d d 555 0 0" - ;; Create the environment file. - "-p" "/.singularity.d/env d 555 0 0" - "-p" ,(string-append - "/.singularity.d/env/90-environment.sh s 777 0 0 " - (relative-file-name "/.singularity.d/env" - #$environment)) + ;; Create the environment file. + "-p" "/.singularity.d/env d 555 0 0" + "-p" ,(string-append + "/.singularity.d/env/90-environment.sh s 777 0 0 " + (relative-file-name "/.singularity.d/env" + #$environment)) - ;; Create /.singularity.d/actions, and optionally the 'run' - ;; script, used by 'singularity run'. - "-p" "/.singularity.d/actions d 555 0 0" + ;; Create /.singularity.d/actions, and optionally the 'run' + ;; script, used by 'singularity run'. + "-p" "/.singularity.d/actions d 555 0 0" - ,@(if entry-point - `(;; This one if for Singularity 2.x. - "-p" - ,(string-append - "/.singularity.d/actions/run s 777 0 0 " - (relative-file-name "/.singularity.d/actions" - (string-append #$profile "/" - entry-point))) + ,@(if entry-point + `(;; This one if for Singularity 2.x. + "-p" + ,(string-append + "/.singularity.d/actions/run s 777 0 0 " + (relative-file-name "/.singularity.d/actions" + (string-append #$profile "/" + entry-point))) - ;; This one is for Singularity 3.x. - "-p" - ,(string-append - "/.singularity.d/runscript s 777 0 0 " - (relative-file-name "/.singularity.d" - (string-append #$profile "/" - entry-point)))) - '()) + ;; This one is for Singularity 3.x. + "-p" + ,(string-append + "/.singularity.d/runscript s 777 0 0 " + (relative-file-name "/.singularity.d" + (string-append #$profile "/" + entry-point)))) + '()) - ;; Create empty mount points. - "-p" "/proc d 555 0 0" - "-p" "/sys d 555 0 0" - "-p" "/dev d 555 0 0" - "-p" "/home d 555 0 0")) + ;; Create empty mount points. + "-p" "/proc d 555 0 0" + "-p" "/sys d 555 0 0" + "-p" "/dev d 555 0 0" + "-p" "/home d 555 0 0")) (when database ;; Initialize /var/guix. (install-database-and-gc-roots "var-etc" database #$profile) - (invoke "mksquashfs" "var-etc" #$output))))) + (mksquashfs `("var-etc" ,#$output)))))) (gexp->derivation (string-append name (compressor-extension compressor) From b829864d747b3b24ef37cafe36e889527b060d4d Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ludovic=20Court=C3=A8s?= Date: Fri, 13 Mar 2020 13:02:01 +0100 Subject: [PATCH 099/116] pack: Make bit-reproducible squashfs images. Reported by Josh Marshall . * guix/scripts/pack.scm (squashfs-image)[build](mksquashfs): Always pass "-all-time", "-mkfs-time", "-force-uid", and "-force-gid" to 'mksquashfs'. --- guix/scripts/pack.scm | 10 +++++++++- 1 file changed, 9 insertions(+), 1 deletion(-) diff --git a/guix/scripts/pack.scm b/guix/scripts/pack.scm index 70239b64de..414e2d45f3 100644 --- a/guix/scripts/pack.scm +++ b/guix/scripts/pack.scm @@ -366,7 +366,15 @@ added to the pack." (define entry-point #$entry-point) (define (mksquashfs args) - (apply invoke "mksquashfs" args)) + (apply invoke "mksquashfs" + `(,@args + + ;; Set file times and the file system creation time to + ;; one second after the Epoch. + "-all-time" "1" "-mkfs-time" "1" + + ;; Reset all UIDs and GIDs. + "-force-uid" "0" "-force-gid" "0"))) (setenv "PATH" (string-append #$archiver "/bin")) From 24fb0dc0ab34ebb49509a3d5b4d84d8488670807 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ludovic=20Court=C3=A8s?= Date: Fri, 13 Mar 2020 13:06:59 +0100 Subject: [PATCH 100/116] pack: Do not create a squashfs "recovery file". Reported by Josh Marshall . * guix/scripts/pack.scm (squashfs-image)[build](mksquashfs): Always pass "-no-recovery". --- guix/scripts/pack.scm | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/guix/scripts/pack.scm b/guix/scripts/pack.scm index 414e2d45f3..652b4c63c4 100644 --- a/guix/scripts/pack.scm +++ b/guix/scripts/pack.scm @@ -369,6 +369,10 @@ added to the pack." (apply invoke "mksquashfs" `(,@args + ;; Do not create a "recovery file" when appending to the + ;; file system since it's useless in this case. + "-no-recovery" + ;; Set file times and the file system creation time to ;; one second after the Epoch. "-all-time" "1" "-mkfs-time" "1" From f292c5019111f92b6850afdca4b59f4146b9be3b Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ludovic=20Court=C3=A8s?= Date: Fri, 13 Mar 2020 17:30:15 +0100 Subject: [PATCH 101/116] maint: Add 'etc/release-manifest.scm'. * etc/release-manifest.scm: New file. * gnu/ci.scm (%cross-targets): Export. * build-aux/check-available-binaries.scm: Remove. * Makefile.am (EXTRA_DIST): Add 'etc/release-manifest.scm' and remove 'build-aux/check-available-binaries.scm'. (assert-binaries-available): Rewrite using 'guix weather -m'. --- Makefile.am | 7 +- build-aux/check-available-binaries.scm | 78 ------------------ etc/release-manifest.scm | 108 +++++++++++++++++++++++++ gnu/ci.scm | 3 +- 4 files changed, 114 insertions(+), 82 deletions(-) delete mode 100644 build-aux/check-available-binaries.scm create mode 100644 etc/release-manifest.scm diff --git a/Makefile.am b/Makefile.am index 3b951be7f5..d5829f3633 100644 --- a/Makefile.am +++ b/Makefile.am @@ -541,6 +541,7 @@ EXTRA_DIST += \ scripts/guix.in \ etc/guix-install.sh \ etc/news.scm \ + etc/release-manifest.scm \ etc/system-tests.scm \ build-aux/build-self.scm \ build-aux/compile-all.scm \ @@ -551,7 +552,6 @@ EXTRA_DIST += \ build-aux/cuirass/gnu-system.scm \ build-aux/cuirass/guix-modular.scm \ build-aux/cuirass/hydra-to-cuirass.scm \ - build-aux/check-available-binaries.scm \ build-aux/check-final-inputs-self-contained.scm \ build-aux/compile-as-derivation.scm \ build-aux/generate-authors.scm \ @@ -851,8 +851,9 @@ assert-no-store-file-names: # Make sure important substitutes are available. assert-binaries-available: $(GOBJECTS) - $(AM_V_at)$(top_builddir)/pre-inst-env "$(GUILE)" \ - "$(top_srcdir)/build-aux/check-available-binaries.scm" + $(AM_V_at)$(top_builddir)/pre-inst-env \ + guix weather -m "$(top_srcdir)/etc/release-manifest.scm" \ + --display-missing # Make sure the final inputs don't refer to bootstrap tools. assert-final-inputs-self-contained: $(GOBJECTS) diff --git a/build-aux/check-available-binaries.scm b/build-aux/check-available-binaries.scm deleted file mode 100644 index f39874ab71..0000000000 --- a/build-aux/check-available-binaries.scm +++ /dev/null @@ -1,78 +0,0 @@ -;;; GNU Guix --- Functional package management for GNU -;;; Copyright © 2013, 2014, 2015, 2016, 2017, 2018, 2019 Ludovic Courtès -;;; -;;; 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 the GNU General Public License -;;; along with GNU Guix. If not, see . - -;;; -;;; Check whether important binaries are available. -;;; - -(use-modules (guix store) - (guix grafts) - (guix packages) - (guix derivations) - (gnu packages) - (gnu packages certs) - (gnu packages emacs) - (gnu packages make-bootstrap) - (gnu packages ssh) - (srfi srfi-1) - (srfi srfi-26) - (ice-9 format)) - -(define (packages-for-system system) - "Return the list of packages to check for SYSTEM." - (let ((base (list %bootstrap-tarballs emacs nss-certs openssh))) - ;; On Intel systems, make sure key packages proposed by the installer are - ;; available. - (if (member system '("x86_64-linux" "i686-linux")) - (append (map specification->package - '("xfce" "gnome" "mate" "enlightenment" - "openbox" "awesome" "i3-wm" "ratpoison" - "network-manager-applet" "xlockmore" - "linux-libre" "grub-hybrid" "xorg-server" - "libreoffice" - ;; FIXME: Add IceCat when Rust is available on i686. - #;"icecat")) - base) - base))) - -(with-store store - (parameterize ((%graft? #f)) - (let* ((native (append-map (lambda (system) - (map (cut package-derivation store <> system) - (packages-for-system system))) - %hydra-supported-systems)) - (cross (map (cut package-cross-derivation store - %bootstrap-tarballs <>) - '("mips64el-linux-gnu" - "arm-linux-gnueabihf"))) - (total (append native cross))) - - (set-build-options store - #:use-substitutes? #t - #:substitute-urls %default-substitute-urls) - (let* ((total (map derivation->output-path total)) - (available (substitutable-paths store total)) - (missing (lset-difference string=? total available))) - (if (null? missing) - (format (current-error-port) - "~a packages found substitutable on~{ ~a~}~%" - (length total) %hydra-supported-systems) - (format (current-error-port) - "~a packages are not substitutable:~%~{ ~a~%~}~%" - (length missing) missing)) - (exit (null? missing)))))) diff --git a/etc/release-manifest.scm b/etc/release-manifest.scm new file mode 100644 index 0000000000..67b92c3921 --- /dev/null +++ b/etc/release-manifest.scm @@ -0,0 +1,108 @@ +;;; GNU Guix --- Functional package management for GNU +;;; Copyright © 2020 Ludovic Courtès +;;; +;;; 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 the GNU General Public License +;;; along with GNU Guix. If not, see . + +;;; This file returns a manifest containing release-critical bit, for all the +;;; supported architectures and cross-compilation targets. + +(use-modules (gnu packages) + (guix packages) + (guix profiles) + ((gnu ci) #:select (%cross-targets)) + (srfi srfi-1) + (srfi srfi-26)) + +(define* (package->manifest-entry* package system + #:key target) + "Return a manifest entry for PACKAGE on SYSTEM, optionally cross-compiled to +TARGET." + (manifest-entry + (inherit (package->manifest-entry package)) + (name (string-append (package-name package) "." system + (if target + (string-append "." target) + "'"))) + (item (with-parameters ((%current-system system) + (%current-target-system target)) + package)))) + +(define %base-packages + ;; Packages that must be substitutable on all the platforms Guix supports. + (map specification->package + '("bootstrap-tarballs" "gcc-toolchain" "nss-certs" + "openssh" "emacs" "vim" "python" "guile" "guix"))) + +(define %system-packages + ;; Key packages proposed by the Guix System installer. + (map specification->package + '("xorg-server" "xfce" "gnome" "mate" "enlightenment" + "openbox" "awesome" "i3-wm" "ratpoison" + "xlockmore" "slock" "libreoffice" + "connman" "network-manager" "network-manager-applet" + "openssh" "ntp" "tor" + "linux-libre" "grub-hybrid" + ;; FIXME: Add IceCat when Rust is available on i686. + ;;"icecat" + ))) + +(define %packages-to-cross-build + ;; Packages that must be cross-buildable from x86_64-linux. + (cons (@ (gnu packages gcc) gcc) + (map specification->package + '("coreutils" "grep" "sed" "findutils" "diffutils" "patch" + "gawk" "gettext" "gzip" "xz" + "hello" "guile@2.2" "zlib")))) + +(define %cross-bootstrap-targets + ;; Cross-compilation triplets for which 'bootstrap-tarballs' must be + ;; buildable. + '("i586-pc-gnu" + "arm-linux-gnueabihf" + "aarch64-linux-gnu")) + + +;;; +;;; Manifests. +;;; + +(define %base-manifest + (manifest + (append-map (lambda (system) + (map (cut package->manifest-entry* <> system) + %base-packages)) + %hydra-supported-systems))) + +(define %cross-manifest + (manifest + (append-map (lambda (target) + (map (cut package->manifest-entry* <> "x86_64-linux" + #:target target) + %packages-to-cross-build)) + %cross-targets))) + +(define %cross-bootstrap-manifest + (manifest + (map (lambda (target) + (package->manifest-entry* + (specification->package "bootstrap-tarballs") + "x86_64-linux" #:target target)) + %cross-bootstrap-targets))) + +;; Return the union of all three manifests. +(concatenate-manifests (list %base-manifest + %cross-manifest + %cross-bootstrap-manifest)) diff --git a/gnu/ci.scm b/gnu/ci.scm index e024c09ebc..44a6a87e1a 100644 --- a/gnu/ci.scm +++ b/gnu/ci.scm @@ -55,7 +55,8 @@ #:use-module (srfi srfi-1) #:use-module (srfi srfi-26) #:use-module (ice-9 match) - #:export (channel-source->package + #:export (%cross-targets + channel-source->package hydra-jobs)) ;;; Commentary: From 79a48038579361689982a279564e0d4130918de7 Mon Sep 17 00:00:00 2001 From: Alberto Eleuterio Flores Guerrero Date: Fri, 13 Mar 2020 21:31:40 +0100 Subject: [PATCH 102/116] gnu: Add barrage. * gnu/packages/games.scm (barrage): New variable. --- gnu/packages/games.scm | 33 +++++++++++++++++++++++++++++++++ 1 file changed, 33 insertions(+) diff --git a/gnu/packages/games.scm b/gnu/packages/games.scm index f9c846d307..2791b18dca 100644 --- a/gnu/packages/games.scm +++ b/gnu/packages/games.scm @@ -46,6 +46,7 @@ ;;; Copyright © 2019, 2020 Timotej Lazar ;;; Copyright © 2019 Josh Holland ;;; Copyright © 2017, 2019 Hartmut Goebel +;;; Copyright © 2020 Alberto Eleuterio Flores Guerrero ;;; ;;; This file is part of GNU Guix. ;;; @@ -10157,3 +10158,35 @@ best human chess grandmasters. It can be used with UCI-compatible GUIs like ChessX.") (home-page "https://stockfishchess.org/") (license license:gpl3+))) + +(define-public barrage + (package + (name "barrage") + (version "1.0.5") + (source + (origin + (method url-fetch) + (uri (string-append "mirror://sourceforge/lgames/barrage/" + "barrage-" version ".tar.gz")) + (sha256 + (base32 "0139wxyrir10cbkvkjn548xgmp84wax8mfwk80yxbxlcdamrg257")))) + (build-system gnu-build-system) + (inputs + `(("hicolor-icon-theme" ,hicolor-icon-theme) + ("sdl" ,sdl) + ("sdl-mixer" ,sdl-mixer))) + (arguments + `(#:configure-flags + (list + (string-append "CFLAGS=" + "-I" (assoc-ref %build-inputs "sdl-mixer") + "/include/SDL")))) + (home-page "http://lgames.sourceforge.net/Barrage/") + (synopsis "Violent point-and-click shooting game with nice effects") + (description + "Barrage is a rather destructive action game that puts you on a shooting +range with the objective to hit as many dummy targets as possible within +3 minutes. You control a gun that may either fire small or large grenades at +soldiers, jeeps and tanks. The gameplay is simple but it is not that easy to +get high scores.") + (license license:gpl2+))) From f08d654af697d3f52060ed505aa78e38cd8fe9da Mon Sep 17 00:00:00 2001 From: Vagrant Cascadian Date: Fri, 13 Mar 2020 20:34:14 +0000 Subject: [PATCH 103/116] gnu: Add python-capablerobot-usbhub. * gnu/packages/libusb (python-capablerobot-usbhub): New variable. --- gnu/packages/libusb.scm | 41 +++++++++++++++++++++++++++++++++++++++++ 1 file changed, 41 insertions(+) diff --git a/gnu/packages/libusb.scm b/gnu/packages/libusb.scm index f41ed6b9bc..01c138cb4e 100644 --- a/gnu/packages/libusb.scm +++ b/gnu/packages/libusb.scm @@ -302,6 +302,47 @@ wrapper for accessing libusb-1.0.") (define-public python2-pyusb (package-with-python2 python-pyusb)) +(define-public python-capablerobot-usbhub + (package + (name "python-capablerobot-usbhub") + (version "0.2.7") + (source + (origin + (method url-fetch) + (uri (pypi-uri "capablerobot_usbhub" version)) + (sha256 + (base32 + "1priic4iq2vn1rc711kzxwhxrwa508rkxrr193qdz2lw26kdhvix")))) + (build-system python-build-system) + (arguments + `(#:phases + (modify-phases %standard-phases + (add-after 'install 'install-udev-rules + (lambda* (#:key outputs #:allow-other-keys) + (let ((out (assoc-ref outputs "out"))) + (mkdir-p (string-append out "/lib/udev/rules.d")) + (copy-file "50-capablerobot-usbhub.rules" + (string-append out + "/lib/udev/rules.d/" + "50-capablerobot-usbhub.rules")) + #t)))))) + (propagated-inputs + `(("python-click" ,python-click) + ("python-construct" ,python-construct) + ("python-pyusb" ,python-pyusb) + ("python-pyyaml" ,python-pyyaml))) + (home-page + "https://github.com/CapableRobot/CapableRobot_USBHub_Driver") + (synopsis + "Host side driver for the Capable Robot Programmable USB Hub") + (description + "This package provides access to the internal state of the Capable Robot +USB Hub, allowing you to monitor and control the Hub from an upstream +computer. It also creates a transparent CircuitPython Bridge, allowing +unmodified CircuitPython code to run on the host computer and interact with +I2C and SPI devices attached to the USB Hub.") + (license license:expat))) + (define-public libplist (package (name "libplist") From 3c9d89b5e2da2731ccc56a4cb745e1868175db79 Mon Sep 17 00:00:00 2001 From: Leo Famulari Date: Fri, 13 Mar 2020 12:33:00 -0400 Subject: [PATCH 104/116] gnu: WebKitGTK: Update to 2.28.0 [fixes CVE-2020-10018]. * gnu/packages/webkit.scm (webkitgtk): Update to 2.28.0. --- gnu/packages/webkit.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/webkit.scm b/gnu/packages/webkit.scm index 1474b6623d..16e2b009fc 100644 --- a/gnu/packages/webkit.scm +++ b/gnu/packages/webkit.scm @@ -121,14 +121,14 @@ engine that uses Wayland for graphics output.") (define-public webkitgtk (package (name "webkitgtk") - (version "2.26.4") + (version "2.28.0") (source (origin (method url-fetch) (uri (string-append "https://www.webkitgtk.org/releases/" "webkitgtk-" version ".tar.xz")) (sha256 (base32 - "0gqi9f9njrdn8vad1zvr59b25arwc8r0n8bp25sgkbfz2c3r11j3")))) + "12qfs9w93c5kiyi14ynm4rf4ad3c213dvzmdrc9c3ab2iwbks7rn")))) (build-system cmake-build-system) (outputs '("out" "doc")) (arguments From 84f19b1d05fcbf68883d72eb7d25fc8aefe26d62 Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Sun, 19 Jan 2020 01:17:00 +0100 Subject: [PATCH 105/116] gnu: libsmpeg: Use HTTPS home page. * gnu/packages/video.scm (libsmpeg)[home-page]: Use HTTPS. --- gnu/packages/video.scm | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/gnu/packages/video.scm b/gnu/packages/video.scm index 41e6835baf..0e428f345d 100644 --- a/gnu/packages/video.scm +++ b/gnu/packages/video.scm @@ -2580,7 +2580,7 @@ Other features include a live preview and live streaming.") ("automake" ,automake))) (inputs `(("sdl" ,sdl2))) - (home-page "http://icculus.org/smpeg/") + (home-page "https://icculus.org/smpeg/") (synopsis "SDL MPEG decoding library") (description "SMPEG (SDL MPEG Player Library) is a free MPEG1 video player library From bbaaee631970a03bc8a929fb900fad57894d731d Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Fri, 13 Mar 2020 20:32:34 +0100 Subject: [PATCH 106/116] gnu: libpipeline: Update to 1.5.2. * gnu/packages/man.scm (libpipeline): Update to 1.5.2. --- 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 3f31ec96b3..4719777303 100644 --- a/gnu/packages/man.scm +++ b/gnu/packages/man.scm @@ -40,7 +40,7 @@ (define-public libpipeline (package (name "libpipeline") - (version "1.5.1") + (version "1.5.2") (source (origin (method url-fetch) (uri (string-append @@ -48,7 +48,7 @@ version ".tar.gz")) (sha256 (base32 - "0bwh5xz5f2czwb7f564jz1mp4znm8pldnvf65fs0hpw4gmmp0cyn")))) + "1ysrn22ixd4nmggy6f7qcsm7waadmlbg2i0n9mh6g7dfq54wcngx")))) (build-system gnu-build-system) (home-page "http://libpipeline.nongnu.org/") (synopsis "C library for manipulating pipelines of subprocesses") From 0d49a4bbe1df4b12abf1ca2710170b568e33c140 Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Sun, 19 Jan 2020 01:06:10 +0100 Subject: [PATCH 107/116] gnu: tegola: Use HTTPS home page. * gnu/packages/geo.scm (tegola)[home-page]: Use HTTPS. --- gnu/packages/geo.scm | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/gnu/packages/geo.scm b/gnu/packages/geo.scm index 7fd04f25c3..0e5afdae30 100644 --- a/gnu/packages/geo.scm +++ b/gnu/packages/geo.scm @@ -776,7 +776,7 @@ extension.") "cmd/tegola_lambda/main.go") (("version not set") ,version))) #t))))) - (home-page "http://tegola.io") + (home-page "https://tegola.io") (synopsis "Vector tile server for maps") (description "Tegola is a free vector tile server written in Go. Tegola takes geospatial data and slices it into vector tiles that can be efficiently From 78b2034b5bd879a86a1ab24db3f0da1bc2998055 Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Fri, 13 Mar 2020 22:14:18 +0100 Subject: [PATCH 108/116] gnu: perl-test2-suite: Correct name. MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * gnu/packages/perl-check.scm (perl-test2-bundle-extended): Rename to… (perl-test2-suite): …this. [name]: Adjust accordingly. (perl-test2-plugin-nowarnings)[propagated-inputs]: Use new name. * gnu/packages/perl.scm (perl-params-validationcompiler)[native-inputs]: Likewise. --- gnu/packages/perl-check.scm | 8 ++++---- gnu/packages/perl.scm | 2 +- 2 files changed, 5 insertions(+), 5 deletions(-) diff --git a/gnu/packages/perl-check.scm b/gnu/packages/perl-check.scm index 9944c31305..2f6976e70f 100644 --- a/gnu/packages/perl-check.scm +++ b/gnu/packages/perl-check.scm @@ -66,9 +66,9 @@ implementation as used in cperl. It does not store the mocked overrides lexically, just dynamically.") (license artistic2.0))) -(define-public perl-test2-bundle-extended +(define-public perl-test2-suite (package - (name "perl-test2-bundle-extended") + (name "perl-test2-suite") (version "0.000072") (source (origin @@ -88,7 +88,7 @@ lexically, just dynamically.") `(("perl-importer" ,perl-importer) ("perl-term-table" ,perl-term-table) ("perl-sub-info" ,perl-sub-info))) - (home-page "https://metacpan.org/pod/Test2::Bundle::Extended") + (home-page "https://metacpan.org/pod/Test2-Suite") (synopsis "Full set of tools for Test2::Suite") (description "This package provides a rich set of tools, plugins, bundles, etc built upon the Test2 testing library.") @@ -108,7 +108,7 @@ etc built upon the Test2 testing library.") "002qk6qsm0l6r2kaxywvc38w0yf0mlavgywq8li076pn6kcw3242")))) (build-system perl-build-system) (propagated-inputs - `(("perl-test2-bundle-extended" ,perl-test2-bundle-extended))) + `(("perl-test2-suite" ,perl-test2-suite))) (home-page "https://metacpan.org/release/Test2-Plugin-NoWarnings") (synopsis "Fail if tests warn") (description "Loading this plugin causes your tests to fail if there any diff --git a/gnu/packages/perl.scm b/gnu/packages/perl.scm index 26989330d4..ca06098c87 100644 --- a/gnu/packages/perl.scm +++ b/gnu/packages/perl.scm @@ -7201,8 +7201,8 @@ function call parameters to an arbitrary level of specificity.") (native-inputs ;; For tests. `(("perl-test-without-module" ,perl-test-without-module) - ("perl-test2-bundle-extended" ,perl-test2-bundle-extended) ("perl-test2-plugin-nowarnings" ,perl-test2-plugin-nowarnings) + ("perl-test2-suite" ,perl-test2-suite) ("perl-type-tiny" ,perl-type-tiny))) (propagated-inputs `(("perl-eval-closure" ,perl-eval-closure) From 9afbfc7a9a54dba6a64783f79f5bf8240604e62e Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Fri, 13 Mar 2020 22:18:27 +0100 Subject: [PATCH 109/116] gnu: perl-test2-plugin-nowarnings: Run all tests. * gnu/packages/perl-check.scm (perl-test2-plugin-nowarnings) [native-inputs]: Add perl-ipc-run3. --- gnu/packages/perl-check.scm | 2 ++ 1 file changed, 2 insertions(+) diff --git a/gnu/packages/perl-check.scm b/gnu/packages/perl-check.scm index 2f6976e70f..8bbe57ddfe 100644 --- a/gnu/packages/perl-check.scm +++ b/gnu/packages/perl-check.scm @@ -107,6 +107,8 @@ etc built upon the Test2 testing library.") (base32 "002qk6qsm0l6r2kaxywvc38w0yf0mlavgywq8li076pn6kcw3242")))) (build-system perl-build-system) + (native-inputs + `(("perl-ipc-run3" ,perl-ipc-run3))) (propagated-inputs `(("perl-test2-suite" ,perl-test2-suite))) (home-page "https://metacpan.org/release/Test2-Plugin-NoWarnings") From 788425c2a8df0545fd31cb8ed4578ecb635739c3 Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Sun, 19 Jan 2020 00:58:28 +0100 Subject: [PATCH 110/116] gnu: taglib: Use HTTPS home page. * gnu/packages/mp3.scm (taglib)[home-page]: Use HTTPS. --- gnu/packages/mp3.scm | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/gnu/packages/mp3.scm b/gnu/packages/mp3.scm index af3cc2540f..ae234afa29 100644 --- a/gnu/packages/mp3.scm +++ b/gnu/packages/mp3.scm @@ -172,7 +172,7 @@ a highly stable and efficient implementation.") '(#:tests? #f ; Tests are not ran with BUILD_SHARED_LIBS on. #:configure-flags (list "-DBUILD_SHARED_LIBS=ON"))) (inputs `(("zlib" ,zlib))) - (home-page "http://taglib.org") + (home-page "https://taglib.org") (synopsis "Library to access audio file meta-data") (description "TagLib is a C++ library for reading and editing the meta-data of several From d7d2b1dcfd17b2d964063aa6ef2ac03439afa54e Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Sun, 19 Jan 2020 00:57:45 +0100 Subject: [PATCH 111/116] gnu: miredo: Use HTTPS home page. * gnu/packages/networking.scm (miredo)[home-page]: Use HTTPS. --- gnu/packages/networking.scm | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/gnu/packages/networking.scm b/gnu/packages/networking.scm index 7f4009df9b..b7e79ce596 100644 --- a/gnu/packages/networking.scm +++ b/gnu/packages/networking.scm @@ -167,7 +167,7 @@ or, more generally, MAC addresses of the same category of hardware.") (substitute* "src/Makefile" (("^TESTS = .*") "TESTS = \n")) #t))))) - (home-page "http://www.remlab.net/miredo/") + (home-page "https://www.remlab.net/miredo/") (synopsis "Teredo IPv6 tunneling software") (description "Miredo is an implementation (client, relay, server) of the Teredo From 9dc6e542b57c45ea41418f36d6b1a09148b14f56 Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Fri, 13 Mar 2020 22:47:31 +0100 Subject: [PATCH 112/116] gnu: nginx: Update to 1.17.9. * gnu/packages/web.scm (nginx): Update to 1.17.9. --- gnu/packages/web.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/web.scm b/gnu/packages/web.scm index 3d6f2d5dcf..e8c505df97 100644 --- a/gnu/packages/web.scm +++ b/gnu/packages/web.scm @@ -221,14 +221,14 @@ Interface} specification.") ;; ’stable’ and recommends that “in general you deploy the NGINX mainline ;; branch at all times” (https://www.nginx.com/blog/nginx-1-6-1-7-released/) ;; Consider updating the nginx-documentation package together with this one. - (version "1.17.8") + (version "1.17.9") (source (origin (method url-fetch) (uri (string-append "https://nginx.org/download/nginx-" version ".tar.gz")) (sha256 (base32 - "0nwn4md8sxhks2j77qq1nvk5pfz3yykfhh2b507b6l2idp7kxllp")))) + "12dnrdxwnlid0wr797vdxj9z1fmxnk7ib55bznvl2g3mbi05vmkx")))) (build-system gnu-build-system) (inputs `(("openssl" ,openssl) ("pcre" ,pcre) From e819fc0285aff217960fe0ef7cd1240959decba1 Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Sun, 19 Jan 2020 00:55:03 +0100 Subject: [PATCH 113/116] gnu: trio: Use HTTPS home page. * gnu/packages/code.scm (trio)[home-page]: Use HTTPS. --- gnu/packages/code.scm | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/gnu/packages/code.scm b/gnu/packages/code.scm index 6af1d413b8..c1eaaf1aab 100644 --- a/gnu/packages/code.scm +++ b/gnu/packages/code.scm @@ -306,7 +306,7 @@ tools such as @command{grep}.") (base32 "02pwd5m5vq7hbrffgm2na1dfc249z50yyr5jv73vdw15bd7ygl44")))) (build-system gnu-build-system) - (home-page "http://daniel.haxx.se/projects/trio/") + (home-page "https://daniel.haxx.se/projects/trio/") (synopsis "Portable and extendable printf and string functions") (description "Trio is a set of @code{printf} and string functions designed be used by From 364a1374ad5e04a91cdc29203f0c8073eede72d4 Mon Sep 17 00:00:00 2001 From: Leo Famulari Date: Thu, 12 Mar 2020 15:16:58 -0400 Subject: [PATCH 114/116] gnu: BlueZ: Fix CVE-2020-0556. * gnu/packages/patches/bluez-CVE-2020-0556.patch: New file. * gnu/local.mk (dist_patch_DATA): Add it. * gnu/packages/linux.scm (bluez)[replacement]: New field. (bluez/fixed): New variable. --- gnu/local.mk | 1 + gnu/packages/linux.scm | 9 + .../patches/bluez-CVE-2020-0556.patch | 180 ++++++++++++++++++ 3 files changed, 190 insertions(+) create mode 100644 gnu/packages/patches/bluez-CVE-2020-0556.patch diff --git a/gnu/local.mk b/gnu/local.mk index 99baddea92..8e312e24e7 100644 --- a/gnu/local.mk +++ b/gnu/local.mk @@ -763,6 +763,7 @@ dist_patch_DATA = \ %D%/packages/patches/binutils-loongson-workaround.patch \ %D%/packages/patches/blender-2.79-newer-ffmpeg.patch \ %D%/packages/patches/blender-2.79-python-3.7-fix.patch \ + %D%/packages/patches/bluez-CVE-2020-0556.patch \ %D%/packages/patches/byobu-writable-status.patch \ %D%/packages/patches/calibre-no-updates-dialog.patch \ %D%/packages/patches/calibre-remove-test-bs4.patch \ diff --git a/gnu/packages/linux.scm b/gnu/packages/linux.scm index 7f293a9071..b9787f2ec5 100644 --- a/gnu/packages/linux.scm +++ b/gnu/packages/linux.scm @@ -3994,6 +3994,7 @@ Bluetooth audio output devices like headphones or loudspeakers.") (define-public bluez (package (name "bluez") + (replacement bluez/fixed) (version "5.52") (source (origin (method url-fetch) @@ -4059,6 +4060,14 @@ Bluetooth audio output devices like headphones or loudspeakers.") is flexible, efficient and uses a modular implementation.") (license license:gpl2+))) +(define bluez/fixed + (package + (inherit bluez) + (source (origin + (inherit (package-source bluez)) + (patches (append (origin-patches (package-source bluez)) + (search-patches "bluez-CVE-2020-0556.patch"))))))) + (define-public fuse-exfat (package (name "fuse-exfat") diff --git a/gnu/packages/patches/bluez-CVE-2020-0556.patch b/gnu/packages/patches/bluez-CVE-2020-0556.patch new file mode 100644 index 0000000000..7c34459a3a --- /dev/null +++ b/gnu/packages/patches/bluez-CVE-2020-0556.patch @@ -0,0 +1,180 @@ +Fix CVE-2020-0556: + +https://lore.kernel.org/linux-bluetooth/20200310023516.209146-1-alainm@chromium.org/ +https://www.intel.com/content/www/us/en/security-center/advisory/intel-sa-00352.html +http://cve.mitre.org/cgi-bin/cvename.cgi?name=CVE-2020-0556 + +Patches copied from upstream source repository: + +https://git.kernel.org/pub/scm/bluetooth/bluez.git/commit/?id=3cccdbab2324086588df4ccf5f892fb3ce1f1787 +https://git.kernel.org/pub/scm/bluetooth/bluez.git/commit/?id=8cdbd3b09f29da29374e2f83369df24228da0ad1 + +From 3cccdbab2324086588df4ccf5f892fb3ce1f1787 Mon Sep 17 00:00:00 2001 +From: Alain Michaud +Date: Tue, 10 Mar 2020 02:35:18 +0000 +Subject: [PATCH] HID accepts bonded device connections only. + +This change adds a configuration for platforms to choose a more secure +posture for the HID profile. While some older mice are known to not +support pairing or encryption, some platform may choose a more secure +posture by requiring the device to be bonded and require the +connection to be encrypted when bonding is required. + +Reference: +https://www.intel.com/content/www/us/en/security-center/advisory/intel-sa-00352.html +--- + profiles/input/device.c | 23 ++++++++++++++++++++++- + profiles/input/device.h | 1 + + profiles/input/input.conf | 8 ++++++++ + profiles/input/manager.c | 13 ++++++++++++- + 4 files changed, 43 insertions(+), 2 deletions(-) + +diff --git a/profiles/input/device.c b/profiles/input/device.c +index 2cb3811c8..d89da2d7c 100644 +--- a/profiles/input/device.c ++++ b/profiles/input/device.c +@@ -92,6 +92,7 @@ struct input_device { + + static int idle_timeout = 0; + static bool uhid_enabled = false; ++static bool classic_bonded_only = false; + + void input_set_idle_timeout(int timeout) + { +@@ -103,6 +104,11 @@ void input_enable_userspace_hid(bool state) + uhid_enabled = state; + } + ++void input_set_classic_bonded_only(bool state) ++{ ++ classic_bonded_only = state; ++} ++ + static void input_device_enter_reconnect_mode(struct input_device *idev); + static int connection_disconnect(struct input_device *idev, uint32_t flags); + +@@ -970,8 +976,18 @@ static int hidp_add_connection(struct input_device *idev) + if (device_name_known(idev->device)) + device_get_name(idev->device, req->name, sizeof(req->name)); + ++ /* Make sure the device is bonded if required */ ++ if (classic_bonded_only && !device_is_bonded(idev->device, ++ btd_device_get_bdaddr_type(idev->device))) { ++ error("Rejected connection from !bonded device %s", dst_addr); ++ goto cleanup; ++ } ++ + /* Encryption is mandatory for keyboards */ +- if (req->subclass & 0x40) { ++ /* Some platforms may choose to require encryption for all devices */ ++ /* Note that this only matters for pre 2.1 devices as otherwise the */ ++ /* device is encrypted by default by the lower layers */ ++ if (classic_bonded_only || req->subclass & 0x40) { + if (!bt_io_set(idev->intr_io, &gerr, + BT_IO_OPT_SEC_LEVEL, BT_IO_SEC_MEDIUM, + BT_IO_OPT_INVALID)) { +@@ -1203,6 +1219,11 @@ static void input_device_enter_reconnect_mode(struct input_device *idev) + DBG("path=%s reconnect_mode=%s", idev->path, + reconnect_mode_to_string(idev->reconnect_mode)); + ++ /* Make sure the device is bonded if required */ ++ if (classic_bonded_only && !device_is_bonded(idev->device, ++ btd_device_get_bdaddr_type(idev->device))) ++ return; ++ + /* Only attempt an auto-reconnect when the device is required to + * accept reconnections from the host. + */ +diff --git a/profiles/input/device.h b/profiles/input/device.h +index 51a9aee18..3044db673 100644 +--- a/profiles/input/device.h ++++ b/profiles/input/device.h +@@ -29,6 +29,7 @@ struct input_conn; + + void input_set_idle_timeout(int timeout); + void input_enable_userspace_hid(bool state); ++void input_set_classic_bonded_only(bool state); + + int input_device_register(struct btd_service *service); + void input_device_unregister(struct btd_service *service); +diff --git a/profiles/input/input.conf b/profiles/input/input.conf +index 3e1d65aae..166aff4a4 100644 +--- a/profiles/input/input.conf ++++ b/profiles/input/input.conf +@@ -11,3 +11,11 @@ + # Enable HID protocol handling in userspace input profile + # Defaults to false (HIDP handled in HIDP kernel module) + #UserspaceHID=true ++ ++# Limit HID connections to bonded devices ++# The HID Profile does not specify that devices must be bonded, however some ++# platforms may want to make sure that input connections only come from bonded ++# device connections. Several older mice have been known for not supporting ++# pairing/encryption. ++# Defaults to false to maximize device compatibility. ++#ClassicBondedOnly=true +diff --git a/profiles/input/manager.c b/profiles/input/manager.c +index 1d31b0652..5cd27b839 100644 +--- a/profiles/input/manager.c ++++ b/profiles/input/manager.c +@@ -96,7 +96,7 @@ static int input_init(void) + config = load_config_file(CONFIGDIR "/input.conf"); + if (config) { + int idle_timeout; +- gboolean uhid_enabled; ++ gboolean uhid_enabled, classic_bonded_only; + + idle_timeout = g_key_file_get_integer(config, "General", + "IdleTimeout", &err); +@@ -114,6 +114,17 @@ static int input_init(void) + input_enable_userspace_hid(uhid_enabled); + } else + g_clear_error(&err); ++ ++ classic_bonded_only = g_key_file_get_boolean(config, "General", ++ "ClassicBondedOnly", &err); ++ ++ if (!err) { ++ DBG("input.conf: ClassicBondedOnly=%s", ++ classic_bonded_only ? "true" : "false"); ++ input_set_classic_bonded_only(classic_bonded_only); ++ } else ++ g_clear_error(&err); ++ + } + + btd_profile_register(&input_profile); +-- +2.25.1 + +From 8cdbd3b09f29da29374e2f83369df24228da0ad1 Mon Sep 17 00:00:00 2001 +From: Alain Michaud +Date: Tue, 10 Mar 2020 02:35:16 +0000 +Subject: [PATCH] HOGP must only accept data from bonded devices. + +HOGP 1.0 Section 6.1 establishes that the HOGP must require bonding. + +Reference: +https://www.intel.com/content/www/us/en/security-center/advisory/intel-sa-00352.htm +--- + profiles/input/hog.c | 4 ++++ + 1 file changed, 4 insertions(+) + +diff --git a/profiles/input/hog.c b/profiles/input/hog.c +index 83c017dcb..dfac68921 100644 +--- a/profiles/input/hog.c ++++ b/profiles/input/hog.c +@@ -186,6 +186,10 @@ static int hog_accept(struct btd_service *service) + return -EINVAL; + } + ++ /* HOGP 1.0 Section 6.1 requires bonding */ ++ if (!device_is_bonded(device, btd_device_get_bdaddr_type(device))) ++ return -ECONNREFUSED; ++ + /* TODO: Replace GAttrib with bt_gatt_client */ + bt_hog_attach(dev->hog, attrib); + +-- +2.25.1 + From 39356057bce20f74120b6d227567a943556717cc Mon Sep 17 00:00:00 2001 From: Leo Famulari Date: Wed, 11 Mar 2020 15:31:59 -0400 Subject: [PATCH 115/116] doc: Update guidance about Python 2 package variants. * doc/contributing.texi (Python Modules): Don't recommend adding Python-2 package variants by default. --- doc/contributing.texi | 11 ++++++----- doc/guix.texi | 2 +- 2 files changed, 7 insertions(+), 6 deletions(-) diff --git a/doc/contributing.texi b/doc/contributing.texi index afcc030b4f..31b875f817 100644 --- a/doc/contributing.texi +++ b/doc/contributing.texi @@ -612,11 +612,12 @@ To avoid confusion and naming clashes with other programming languages, it seems desirable that the name of a package for a Python module contains the word @code{python}. -Some modules are compatible with only one version of Python, others with both. -If the package Foo compiles only with Python 3, we name it -@code{python-foo}; if it compiles only with Python 2, we name it -@code{python2-foo}. If it is compatible with both versions, we create two -packages with the corresponding names. +Some modules are compatible with only one version of Python, others with +both. If the package Foo is compiled with Python 3, we name it +@code{python-foo}. If it is compiled with Python 2, we name it +@code{python2-foo}. Packages should be added when they are necessary; +we don't add Python 2 variants of the package unless we are going to use +them. If a project already contains the word @code{python}, we drop this; for instance, the module python-dateutil is packaged under the names diff --git a/doc/guix.texi b/doc/guix.texi index 8acae26b9a..4658c6f5eb 100644 --- a/doc/guix.texi +++ b/doc/guix.texi @@ -28,7 +28,7 @@ Copyright @copyright{} 2014, 2015, 2016 Alex Kost@* Copyright @copyright{} 2015, 2016 Mathieu Lirzin@* Copyright @copyright{} 2014 Pierre-Antoine Rault@* Copyright @copyright{} 2015 Taylan Ulrich Bayırlı/Kammer@* -Copyright @copyright{} 2015, 2016, 2017, 2019 Leo Famulari@* +Copyright @copyright{} 2015, 2016, 2017, 2019, 2020 Leo Famulari@* Copyright @copyright{} 2015, 2016, 2017, 2018, 2019, 2020 Ricardo Wurmus@* Copyright @copyright{} 2016 Ben Woodcroft@* Copyright @copyright{} 2016, 2017, 2018 Chris Marusich@* From 989d564f4434c6e43df7ccb0d1701e89e243e404 Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Fri, 13 Mar 2020 20:18:53 +0100 Subject: [PATCH 116/116] gnu: launchmon: Fix build with GCC 7. * gnu/packages/admin.scm (launchmon)[source](modules, snippet): New fields. --- gnu/packages/admin.scm | 11 ++++++++++- 1 file changed, 10 insertions(+), 1 deletion(-) diff --git a/gnu/packages/admin.scm b/gnu/packages/admin.scm index 0f27e6370b..5ec34864e2 100644 --- a/gnu/packages/admin.scm +++ b/gnu/packages/admin.scm @@ -3170,7 +3170,16 @@ late.") version "/launchmon-v" version ".tar.gz")) (sha256 (base32 - "0fm3nd9mydm9v2bf7bh01dbgrfnpwkapxa3dsvy3x1z0rz61qc0x")))) + "0fm3nd9mydm9v2bf7bh01dbgrfnpwkapxa3dsvy3x1z0rz61qc0x")) + (modules '((guix build utils))) + (snippet + '(begin + ;; Fix build failure with GCC 7 due to a conversion error. + ;; Remove for versions > 1.0.2. + (substitute* "launchmon/src/linux/lmon_api/lmon_coloc_spawner.cxx" + ((" lmonpl = '\\\\0'") + " *lmonpl = '\\0'")) + #t)))) (build-system gnu-build-system) (inputs `(("mpi" ,openmpi)