From 6d60d7ccba5a8e06c17d55a1772fa7f4529b5eff Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 7 Sep 2023 21:39:41 +0200 Subject: [PATCH 001/268] gnu: Add fasttext. * gnu/packages/machine-learning.scm (fasttext): New variable. --- gnu/packages/machine-learning.scm | 22 ++++++++++++++++++++++ 1 file changed, 22 insertions(+) diff --git a/gnu/packages/machine-learning.scm b/gnu/packages/machine-learning.scm index 712abe9aff..598c97be5f 100644 --- a/gnu/packages/machine-learning.scm +++ b/gnu/packages/machine-learning.scm @@ -115,6 +115,28 @@ #:use-module (gnu packages xorg) #:use-module (ice-9 match)) +(define-public fasttext + (package + (name "fasttext") + (version "0.9.2") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/facebookresearch/fastText") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 "07cz2ghfq6amcljaxpdr5chbd64ph513y8zqmibfx2xwfp74xkhn")))) + (build-system cmake-build-system) + ;; Tests require downloading of test data. + (arguments (list #:tests? #false)) + (home-page "https://github.com/facebookresearch/fastText") + (synopsis "Library for fast text representation and classification") + (description "fastText is a library for efficient learning of word +representations and sentence classification.") + (license license:expat))) + (define-public fann ;; The last release is >100 commits behind, so we package from git. (let ((commit "d71d54788bee56ba4cf7522801270152da5209d7")) From 72745172d155e489936f694d6b9013cb76272370 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 7 Sep 2023 21:39:48 +0200 Subject: [PATCH 002/268] gnu: Add python-fasttext. * gnu/packages/machine-learning.scm (python-fasttext): New variable. --- gnu/packages/machine-learning.scm | 9 +++++++++ 1 file changed, 9 insertions(+) diff --git a/gnu/packages/machine-learning.scm b/gnu/packages/machine-learning.scm index 598c97be5f..f169d8895e 100644 --- a/gnu/packages/machine-learning.scm +++ b/gnu/packages/machine-learning.scm @@ -137,6 +137,15 @@ representations and sentence classification.") (license license:expat))) +(define-public python-fasttext + (package + (inherit fasttext) + (name "python-fasttext") + (build-system pyproject-build-system) + (propagated-inputs (list python-numpy python-scipy)) + (inputs (list fasttext)) + (native-inputs (list pybind11)))) + (define-public fann ;; The last release is >100 commits behind, so we package from git. (let ((commit "d71d54788bee56ba4cf7522801270152da5209d7")) From 0a69961953307040f4c3994ae09286768ce67c9c Mon Sep 17 00:00:00 2001 From: Philip McGrath Date: Wed, 23 Aug 2023 20:08:04 -0400 Subject: [PATCH 003/268] gnu: racket: Update to 8.10. * gnu/packages/patches/racket-rktboot-riscv64-support.patch: Move to ... * gnu/packages/patches/racket-backport-8.10-rktboot.patch: ... this file, together with a related upstreamed patch. * gnu/local.mk (dist_patch_DATA): Update accordingly. * gnu/packages/racket/scm (%racket-origin)[patches]: Likewise. (%racket-version): Update to 8.10. (racket)[inputs] : Update hashes. * gnu/packages/chez.scm (chez-scheme-for-racket): Update to 9.9.9-pre-release.17. Signed-off-by: Efraim Flashner --- gnu/local.mk | 2 +- gnu/packages/chez.scm | 2 +- .../racket-backport-8.10-rktboot.patch | 130 ++++++++++++++++++ .../racket-rktboot-riscv64-support.patch | 15 -- gnu/packages/racket.scm | 42 +++--- 5 files changed, 153 insertions(+), 38 deletions(-) create mode 100644 gnu/packages/patches/racket-backport-8.10-rktboot.patch delete mode 100644 gnu/packages/patches/racket-rktboot-riscv64-support.patch diff --git a/gnu/local.mk b/gnu/local.mk index 54aec9316a..f58d04cf91 100644 --- a/gnu/local.mk +++ b/gnu/local.mk @@ -1897,7 +1897,7 @@ dist_patch_DATA = \ %D%/packages/patches/rpcbind-CVE-2017-8779.patch \ %D%/packages/patches/rtags-separate-rct.patch \ %D%/packages/patches/racket-chez-scheme-bin-sh.patch \ - %D%/packages/patches/racket-rktboot-riscv64-support.patch \ + %D%/packages/patches/racket-backport-8.10-rktboot.patch \ %D%/packages/patches/racket-rktio-bin-sh.patch \ %D%/packages/patches/racket-zuo-bin-sh.patch \ %D%/packages/patches/remake-impure-dirs.patch \ diff --git a/gnu/packages/chez.scm b/gnu/packages/chez.scm index a5cb5a2e06..e5694ec1cf 100644 --- a/gnu/packages/chez.scm +++ b/gnu/packages/chez.scm @@ -466,7 +466,7 @@ and 32-bit PowerPC architectures.") (package (inherit chez-scheme) (name "chez-scheme-for-racket") - (version "9.9.9-pre-release.16") + (version "9.9.9-pre-release.17") ;; The version should match `scheme-version`. ;; See racket/src/ChezScheme/s/cmacros.ss c. line 360. ;; It will always be different than the upstream version! diff --git a/gnu/packages/patches/racket-backport-8.10-rktboot.patch b/gnu/packages/patches/racket-backport-8.10-rktboot.patch new file mode 100644 index 0000000000..834001bd83 --- /dev/null +++ b/gnu/packages/patches/racket-backport-8.10-rktboot.patch @@ -0,0 +1,130 @@ +From 5446e36e0685ec5c7b4f812dec5bf7959db4f906 Mon Sep 17 00:00:00 2001 +From: Efraim Flashner +Date: Thu, 20 Jul 2023 15:56:21 +0300 +Subject: [PATCH 1/2] rktboot: Add support for riscv64. + +(cherry picked from commit f80c5d001d5235556ae9cde617b1e3a1322d0505) +--- + racket/src/rktboot/machine-def.rkt | 1 + + 1 file changed, 1 insertion(+) + +diff --git a/racket/src/rktboot/machine-def.rkt b/racket/src/rktboot/machine-def.rkt +index 8ff0688652..59ebfc88d8 100644 +--- a/racket/src/rktboot/machine-def.rkt ++++ b/racket/src/rktboot/machine-def.rkt +@@ -25,6 +25,7 @@ + [(regexp-match? #rx"^t?arm32" target-machine) "arm32"] + [(regexp-match? #rx"^t?arm64" target-machine) "arm64"] + [(regexp-match? #rx"^t?ppc32" target-machine) "ppc32"] ++ [(regexp-match? #rx"^t?rv64" target-machine) "rv64"] + [(regexp-match? #rx"^t?pb" target-machine) "pb"] + [else (error "machine.def: cannot infer architecture")]))] + [s (regexp-replace* #rx"[$][(]Mend[)]" s + +base-commit: b10ecfb8311fca2d42636eea2ca12aff0b76b208 +-- +2.41.0 + + +From 6261c3582c386e770d654ca6a36f112834f35aef Mon Sep 17 00:00:00 2001 +From: Philip McGrath +Date: Sun, 16 Jul 2023 15:47:14 -0400 +Subject: [PATCH 2/2] rktboot: improve machene type inference + +Related to https://issues.guix.gnu.org/62231 +Related to https://github.com/racket/racket/issues/3948 + +(cherry picked from commit 005488491cee89e7db38109de4c9dcf2d8d5aef0) +--- + racket/src/rktboot/config.rkt | 73 +++++++++++++++++++++++++++++------ + 1 file changed, 61 insertions(+), 12 deletions(-) + +diff --git a/racket/src/rktboot/config.rkt b/racket/src/rktboot/config.rkt +index 7a969017ed..2b411e002c 100644 +--- a/racket/src/rktboot/config.rkt ++++ b/racket/src/rktboot/config.rkt +@@ -15,20 +15,69 @@ + (path->complete-path scheme-dir)))))) + (hash-set! ht 'make-boot-scheme-dir scheme-dir) + ++(define (infer-target-machine) ++ ;; Compute a native or pbarch machine string for the current platform. ++ ;; Some caveats: ++ ;; 1. A pbarch Racket will always infer a pbarch machine, ++ ;; even if a native machine exists. Hopefully this is an ++ ;; unlikely scenario: if you're running Racket CS, you've ++ ;; bootstrapped Chez somehow, so you could use `re.boot`. ++ ;; 2. A `tpb` or `pb` Racket on a 32-bit platform would still return ++ ;; 64 from `(system-type 'word)`, but, in addition to the above, ++ ;; it is not currently possible or desired to build Racket as ++ ;; `tpb` or `pb` (as opposed to pbarch variants): ++ ;; see . ++ ;; 3. On a hypothetical platform where Chez supported both the ++ ;; architecture and the OS, but not the combination of the two, ++ ;; (e.g. riscv64 Windows) this code would currently return a ++ ;; non-existent native machine (e.g. trv64nt) instead of a ++ ;; working pbarch machine. Presumably this could be fixed if ++ ;; such a platform came into existence. ++ (define s (path->string (system-library-subpath #f))) ++ (define arch+os ++ (cond ++ [(regexp-match #rx"^([^\\]+)\\\\([^\\]+)$" s) ++ => (λ (m) ++ (reverse (cdr m)))] ++ [(regexp-match #rx"^([^-]+)-(.+)$" s) ++ => cdr] ++ [else ++ (error 'infer-target-machine "unknown format for system library subpath" ++ "produced" (system-library-subpath #f))])) ++ (define arch ++ (case (car arch+os) ++ [("x86_64" "amd64") "a6"] ; https://github.com/racket/racket/issues/4691 ++ [("i386") "i3"] ++ [("aarch64") "arm64"] ++ [("arm") "arm32"] ++ [("ppc") "ppc32"] ++ [("riscv64") "rv64"] ++ [("unknown") #f] ; pb machine types ++ [else #f])) ++ (define os ++ (case (cadr arch+os) ++ [("macosx" "darwin" "ios") "osx"] ++ [("win32" "cygwin") "nt"] ++ [("linux" "android") "le"] ++ [("gnu-hurd") "gnu"] ++ [("freebsd") "fb"] ++ [("openbsd") "ob"] ++ [("netbsd") "nb"] ++ [("solaris") "s2"] ; NOT "sunos4" (I think) ++ [("qnx") "qnx"] ++ [("unknown") #f] ; pb machine types ++ [else #f])) ++ (if (and arch os) ++ (string-append "t" arch os) ++ (format "tpb~a~a" ++ (system-type 'word) ++ (if (system-big-endian?) ++ "b" ++ "l")))) ++ + (define target-machine (or (hash-ref ht 'make-boot-targate-machine #f) + (getenv "MACH") +- (case (system-type) +- [(macosx) (if (eqv? 64 (system-type 'word)) +- "ta6osx" +- "ti3osx")] +- [(windows) (if (eqv? 64 (system-type 'word)) +- "ta6nt" +- "ti3nt")] +- [else +- (case (path->string (system-library-subpath #f)) +- [("x86_64-linux") "ta6le"] +- [("i386-linux") "ti3le"] +- [else #f])]))) ++ (infer-target-machine))) + (hash-set! ht 'make-boot-targate-machine target-machine) + + (define optimize-level-init 3) +-- +2.41.0 + diff --git a/gnu/packages/patches/racket-rktboot-riscv64-support.patch b/gnu/packages/patches/racket-rktboot-riscv64-support.patch deleted file mode 100644 index f268b1e7f8..0000000000 --- a/gnu/packages/patches/racket-rktboot-riscv64-support.patch +++ /dev/null @@ -1,15 +0,0 @@ -Submitted upstream: -https://github.com/racket/racket/pull/4703 - -diff --git a/racket/src/rktboot/machine-def.rkt b/racket/src/rktboot/machine-def.rkt -index 8ff0688..59ebfc8 100644 ---- a/racket/src/rktboot/machine-def.rkt -+++ b/racket/src/rktboot/machine-def.rkt -@@ -25,6 +25,7 @@ - [(regexp-match? #rx"^t?arm32" target-machine) "arm32"] - [(regexp-match? #rx"^t?arm64" target-machine) "arm64"] - [(regexp-match? #rx"^t?ppc32" target-machine) "ppc32"] -+ [(regexp-match? #rx"^t?rv64" target-machine) "rv64"] - [(regexp-match? #rx"^t?pb" target-machine) "pb"] - [else (error "machine.def: cannot infer architecture")]))] - [s (regexp-replace* #rx"[$][(]Mend[)]" s diff --git a/gnu/packages/racket.scm b/gnu/packages/racket.scm index 03abd7cc41..b6ab687a21 100644 --- a/gnu/packages/racket.scm +++ b/gnu/packages/racket.scm @@ -190,7 +190,7 @@ ;; ;; CODE: -(define %racket-version "8.9") ; Remember to update chez-scheme-for-racket! +(define %racket-version "8.10") ; Remember to update chez-scheme-for-racket! (define %zuo-version "1.6") ; defined in racket/src/zuo/zuo.c (define %racket-commit (string-append "v" %racket-version)) @@ -201,10 +201,10 @@ (url "https://github.com/racket/racket") (commit %racket-commit))) (sha256 - (base32 "120djvscm2x1nv46is0kzwahd22rcc8gc0ssf12jnj7w290dpmra")) + (base32 "0xhra47lnz5aq2shvsil4vcravai4n86r4v1lza7r07n6s1pb9s5")) (file-name (git-file-name "racket" %racket-version)) (patches (search-patches "racket-chez-scheme-bin-sh.patch" - "racket-rktboot-riscv64-support.patch" + "racket-backport-8.10-rktboot.patch" "racket-rktio-bin-sh.patch" "racket-zuo-bin-sh.patch")) (modules '((guix build utils))) @@ -699,7 +699,7 @@ DrRacket IDE, are not included.") "contract-profile" (base32 "1xm2z8g0dpv5d9h2sg680vx1a8ix9gbsdpxxb8qv1w7akp73paj3") '(("contract-profile" "."))) (simple-racket-origin - "data" (base32 "08sj4m0g0cp7gwb0nq90m770f0c21b7ydif7nljc8rxmcdprfisc") + "data" (base32 "1pml8g3zgvnaiqb659psh99m70v96m6nh9zash2vfgir46j4rjnh") '("data" "data-doc" "data-enumerate-lib" "data-lib")) (simple-racket-origin "datalog" (base32 "0nf6cy4djpyhfvgpa6yn72apbz9s83gp0qg95pzjd0az4v6qwq1s") @@ -708,7 +708,7 @@ DrRacket IDE, are not included.") "db" (base32 "0xx0k8yw2vb9b4vk2dwjfbpixnmriqsv7kpv3fvfxbwyg42y0db5") '("db" "db-doc" "db-lib")) (simple-racket-origin - "deinprogramm" (base32 "0iv14kig8w6kwxxmcfsxskk6x7a4kgzppzgyznzgy1mk6p5rxbjg") + "deinprogramm" (base32 "0889154ssw56aq6iqxnzgjram9x6c64sscjzrhr4077vnv4h1c93") '("deinprogramm" "deinprogramm-signature")) (simple-racket-origin "distributed-places" (base32 "1dajpkj9balqcpv6cdk9hwjz592h1vq8rrx5vncariiac4vbdpa0") @@ -717,7 +717,7 @@ DrRacket IDE, are not included.") "draw" (base32 "0vf40hp6h14zgs0gx40jzdzxm4ai1vxwpmg65y00lwmdxc97b2ji") '("draw" "draw-doc" "draw-lib")) (simple-racket-origin - "drracket" (base32 "1b2fammrkb01kglf0n1rzdq2ngay4adnjh3gdmnza7mxz09y35m2") + "drracket" (base32 "0haban4fysr8i2w071nra9s97zkrrx5f5c874r9pr2k9bhqcp4jq") '("drracket" "drracket-plugin-lib" "drracket-tool" @@ -751,13 +751,13 @@ DrRacket IDE, are not included.") "games" (base32 "0kpn3izlx1ccd0pj0dnvmnrhny51b85xy418a7psj70lz8j8415d") '(("games" "."))) (simple-racket-origin - "gui" (base32 "01ydlr10gkdm66x1gx3im5lwiap0ssiph8nmaisv0xrnrirbnp51") + "gui" (base32 "1s2a8qgm7dqpxyi9plshdbaxzd8klc80i8ppjpc5i5xyhcfmzyvf") '("gui" "gui-doc" "gui-lib" "tex-table")) (simple-racket-origin "gui-pkg-manager" (base32 "1ji9448d723nklqvycwdswj0ni28sabrncag14f9mx47did5myb5") '("gui-pkg-manager-lib")) (simple-racket-origin - "htdp" (base32 "1qnnnh9d9kjzlaasql7gi0h8z893bzb9kffay00mwg2j0bfzsf2s") + "htdp" (base32 "0kd92rg8m8my11pq1dxvv6dyban77j6kvs368xsl6fr52jd7zbkl") '("htdp" "htdp-doc" "htdp-lib")) (simple-racket-origin "html" (base32 "18n1jnjgzfknc8nv8dppi85nb8q08gqdwkg6hfjk08x0p00anx2x") @@ -781,7 +781,7 @@ DrRacket IDE, are not included.") "make" (base32 "10852fj30bz5r46c3d99s37fkgy5yh44gb01j29sf3kxnhi0g2sa") '(("make" "."))) (simple-racket-origin - "math" (base32 "1qz4k6iwbrf9l7dhivrznghrpbqhxx14yczkgqpkz6yqawi642x9") + "math" (base32 "1l0r4xpbbjz0b2s6v3kn490zgs2q1dnj3ga95y1505jmcwgb2hl9") '("math" "math-doc" "math-lib")) (simple-racket-origin "mysterx" (base32 "11p9jzrafw0hizhl0cs4sxx7rv281185q8hryic2rpk0kzjdyr48") @@ -799,7 +799,7 @@ DrRacket IDE, are not included.") (url "https://github.com/RenaissanceBug/racket-cookies") (commit %racket-commit))) (sha256 (base32 - "0k0hifxhywl5c3hjcaiizc098dpyk001d981p572gly116yvjxc1")) + "05lnml9nszcq72k8bi4iwdyplp2iv23ywb2gmrs2hr8837fqi65y")) (file-name (git-file-name "RenaissanceBug-racket-cookies" %racket-version))) '("net-cookies" "net-cookies-doc" "net-cookies-lib")) @@ -825,7 +825,7 @@ DrRacket IDE, are not included.") "pconvert" (base32 "00czi0p399mmyrvxyrs5kniizpkqfxyz2ncxqi2jy79a7wk79pb1") '("pconvert-lib")) (simple-racket-origin - "pict" (base32 "0j6m95pq523pz526d7my8b3cg8a3jssag2mafxcq531prlnzq9sq") + "pict" (base32 "1vsn91r167wssaflzz080nsrcf0jfhl2a48zcj9hvdb77arbj8kc") '("pict" "pict-doc" "pict-lib")) (simple-racket-origin "pict-snip" (base32 "081nwiy4a0n4f7xws16hqbhf0j3kz5alizndi3nnyr3chm4kng6x") @@ -840,7 +840,7 @@ DrRacket IDE, are not included.") "planet" (base32 "0r2yqrzrmdjjyr14k6hhlzc5kzrcx3583m1s02mhrcmpfw0s85w9") '("planet" "planet-doc" "planet-lib")) (simple-racket-origin - "plot" (base32 "13i6cwkscb4j6zmdc122iidmykwpxfk8xjmq09c6gv77slfynivl") + "plot" (base32 "1p0jxrwdwkb7z6ppp2ccpdzmizjimfpkdgilvbgv8x6mmqf0bf6q") '("plot" "plot-compat" "plot-doc" "plot-gui-lib" "plot-lib")) (simple-racket-origin "preprocessor" (base32 "1p5aid58ifnjy4xl0ysh85cq39k25661v975jrpk182z3k5621mg") @@ -876,7 +876,7 @@ DrRacket IDE, are not included.") (git-file-name "jeapostrophe-racket-cheat" %racket-version))) '(("racket-cheat" "."))) (simple-racket-origin - "racklog" (base32 "0fbq0fpfb3l6h7h772dvkmlzlk2dnq5f8296xx1qxhhwypibqzr9") + "racklog" (base32 "0fr8xij0sssfnmwn6dfdi4jj3l62f2yj3jrjljv13kaycrfls032") '(("racklog" "."))) (simple-racket-origin "rackunit" (base32 "03v1yvqgk3f65caqiwnadq00sjbg813ic949hys29f4c8mxz6gic") @@ -895,7 +895,7 @@ DrRacket IDE, are not included.") "realm" (base32 "0rlvwyd6rpyl0zda4a5p8dp346fvqzc8555dgfnrhliymkxb6x4g") '(("realm" "."))) (simple-racket-origin - "redex" (base32 "16kyi4nxxi4a05gjarb9dayysg032vsad5mmwn1j6d6yxxhbw9jr") + "redex" (base32 "00pm0pj3h19a9dar4pzdn8q5l7bvl92q9gkh04k1ddlcx4af1m10") '("redex" "redex-benchmark" "redex-doc" @@ -910,7 +910,7 @@ DrRacket IDE, are not included.") "scheme-lib" (base32 "0pcf0y8rp4qyjhaz5ww5sr5diq0wpcdfrrnask7zapyklzx1jx8x") '(("scheme-lib" "."))) (simple-racket-origin - "scribble" (base32 "06q5jhfblps47ly9fv5pkcz3nk8akfgad9ank32dh1svagq9plzf") + "scribble" (base32 "1jnbvl98yn8dhblcx411jybd879g4aj6d136xi23i4zwwrbsiy6m") '("scribble" "scribble-doc" "scribble-html-lib" @@ -936,13 +936,13 @@ DrRacket IDE, are not included.") "slatex" (base32 "0pkm2isbbdk63slrbsxcql7rr0wdrw5kapw1xq4ps5k8dhlzv8x0") '(("slatex" "."))) (simple-racket-origin - "slideshow" (base32 "0phq0mvy0dh8hhbhxhmsini286dyggy6cgxq7mcwj4n2sbw38sas") + "slideshow" (base32 "0hmg5184cpxjb0ni6v2zkf4l29j8yyzm9pzv1gvmw2fm1rlrry4f") '("slideshow" "slideshow-doc" "slideshow-exe" "slideshow-lib" "slideshow-plugin")) (simple-racket-origin - "snip" (base32 "1j7sk364w2cggr4i5my1p2ibyvslrnj45xwxhihx6zypkbk59c3m") + "snip" (base32 "1b90ccqilnyszbphms3svm3c7dbk7870ifybjjipss5srb32mj2d") '("snip" "snip-lib")) (simple-racket-origin - "typed-racket" (base32 "0iz62xy2grkwyi4krz0chi3fswg74zd5s5jpdqyhxhdqq3gcscp0") + "typed-racket" (base32 "1721qgk1fplzwcgidg342anvykr88prvl1jag4vg8qxz8m28wi08") '("source-syntax" "typed-racket" "typed-racket-compatibility" @@ -953,13 +953,13 @@ DrRacket IDE, are not included.") "srfi" (base32 "0rvx49ni1v8ikbx1a6qg97pprpkxmy7cgl918f52hq7jlx91b71x") '("srfi" "srfi-doc" "srfi-lib" "srfi-lite-lib")) (simple-racket-origin - "string-constants" (base32 "1lxab9323xmxqs4mxbgr504xgcgsf9dvx2xsb4p92fjzsif0d64y") + "string-constants" (base32 "1jxbh91x1r65lahjlix61rmkjikcam2k5w97xj8r7p7z05240dih") '("string-constants" "string-constants-doc" "string-constants-lib")) (simple-racket-origin "swindle" (base32 "1q8vdxpzczzwdw2mys2caab45yvadmqkixsr29k8pl03n8dsg8j9") '(("swindle" "."))) (simple-racket-origin - "syntax-color" (base32 "03fjmpww2958sryicrrcrpqwq6ibslfxd86ckl1mgafm3kr02qhp") + "syntax-color" (base32 "0lcv6glhsx27lkz7wwalzgfr0nb0hdqjic54z3rcfxhag4p6sg8i") '("syntax-color" "syntax-color-doc" "syntax-color-lib")) (simple-racket-origin "trace" (base32 "070ihla5j796hdarn5wxdwn4xj0xnkm50shgh49jy994mribvhia") @@ -968,7 +968,7 @@ DrRacket IDE, are not included.") "unix-socket" (base32 "02dfwas5ynbpyz74w9kwb4wgb37y5wys7svrlmir8k0n9ph9vq0y") '("unix-socket" "unix-socket-doc" "unix-socket-lib")) (simple-racket-origin - "web-server" (base32 "0xfg0n0rg1g5rbqq4mm0qjgqkkrgm3ilzkffga2bjx253jrrrcai") + "web-server" (base32 "0sizb50rbnqmdx8igpqshj0hzsqyg30faf7wb9fs08sjs0lqkgsf") '("web-server" "web-server-doc" "web-server-lib")) (simple-racket-origin "wxme" (base32 "1qp5gr9gqsakiq3alw6m4yyv5vw4i3hp4y4nhq8vl2nkjmirvn0b") From bce0fe8293a15331ed8b4e9a76354988f10e1ef5 Mon Sep 17 00:00:00 2001 From: Philip McGrath Date: Wed, 23 Aug 2023 20:08:05 -0400 Subject: [PATCH 004/268] gnu: racket: Declare OpenSSL search paths. Otherwise, OpenSSL used via Racket fails to find certificates, e.g. when attempting to run 'raco pkg install'. Fixes . * gnu/packages/racket.scm (racket-minimal)[native-search-paths]: Add $SSL_CERT_DIR and $SSL_CERT_FILE. Signed-off-by: Efraim Flashner --- gnu/packages/racket.scm | 2 ++ 1 file changed, 2 insertions(+) diff --git a/gnu/packages/racket.scm b/gnu/packages/racket.scm index b6ab687a21..1e97f19dbb 100644 --- a/gnu/packages/racket.scm +++ b/gnu/packages/racket.scm @@ -29,6 +29,7 @@ #:use-module (guix build-system gnu) #:use-module (guix diagnostics) #:use-module (guix i18n) + #:use-module ((guix search-paths) #:select ($SSL_CERT_DIR $SSL_CERT_FILE)) #:use-module (srfi srfi-1) #:use-module (srfi srfi-26) #:use-module (srfi srfi-34) @@ -553,6 +554,7 @@ used to build the name of the resulting store item." "base" %racket-origin '(("base" "pkgs/base") ("racket-lib" "pkgs/racket-lib"))))) + (native-search-paths (list $SSL_CERT_DIR $SSL_CERT_FILE)) (build-system gnu-build-system) (arguments ;; Here and for the `racket` package, we're using #:configure-flags From bb20ab942e03cd9309e3ecbef22ea2f2946810db Mon Sep 17 00:00:00 2001 From: Philip McGrath Date: Wed, 23 Aug 2023 20:08:06 -0400 Subject: [PATCH 005/268] gnu: chez-scheme-for-racket-bootstrap-bootfiles: Remove workaround. Architecture autodetection in rktboot was fixed upstream, and the fix is included in racket-backport-8.10-rktboot.patch for Guix. This commit goes beyond reverting b4fbeae3d90a5d0f8146441772436df2eb471491: the upstream fix also supports 'pbarch' machine types, so we never need to supply a '--machine' argument to rktboot. * gnu/packages/chez.scm (chez-scheme-for-racket-bootstrap-bootfiles) [arguments]: Change 'build' phase to never use '--machine' for rktboot. Signed-off-by: Efraim Flashner --- gnu/packages/chez.scm | 8 +------- 1 file changed, 1 insertion(+), 7 deletions(-) diff --git a/gnu/packages/chez.scm b/gnu/packages/chez.scm index e5694ec1cf..3f53beac1a 100644 --- a/gnu/packages/chez.scm +++ b/gnu/packages/chez.scm @@ -691,13 +691,7 @@ source."))) #~(invoke (search-input-file (or native-inputs inputs) "/opt/racket-vm/bin/racket") - "../rktboot/main.rkt" - ;; Temporary handling of builds on non-x86 architectures, - ;; see https://github.com/racket/racket/issues/3948 - ;; Autodetect in rktboot only addresses x86 archs, so far. - #$@(let ((m (or (racket-cs-native-supported-system?) - (nix-system->pbarch-machine-type)))) - #~("--machine" #$m)))))))))))) + "../rktboot/main.rkt")))))))))) (supported-systems (package-supported-systems chez-scheme-for-racket)) (home-page "https://github.com/racket/ChezScheme") From 75ee7ec470683aca5fa062ee714491d575c19359 Mon Sep 17 00:00:00 2001 From: c4droid Date: Tue, 11 Apr 2023 18:03:07 +0800 Subject: [PATCH 006/268] gnu: python-pyspnego: Update to 0.8.0. * gnu/packages/python-xyz.scm (python-pyspnego): Update to 0.8.0. [source]: Download from pypi. [arguments]: Remove custom 'check phase. [build-system]: Switch to pyproject-build-system. Signed-off-by: Efraim Flashner --- gnu/packages/python-xyz.scm | 27 +++++++++------------------ 1 file changed, 9 insertions(+), 18 deletions(-) diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index c0e4b62418..aeaaeb4059 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -141,6 +141,7 @@ ;;; Copyright © 2023 Ontje Lünsdorf ;;; Copyright © 2023 Parnikkapore ;;; Copyright © 2023 Foundation Devices, Inc. +;;; Copyright © c4droid ;;; ;;; This file is part of GNU Guix. ;;; @@ -7474,24 +7475,14 @@ color scales, and color space conversion easy. It has support for: (define-public python-pyspnego (package (name "python-pyspnego") - (version "0.1.6") - (source - (origin - (method git-fetch) ;no tests in PyPI release - (uri (git-reference - (url "https://github.com/jborean93/pyspnego") - (commit (string-append "v" version)))) - (file-name (git-file-name name version)) - (sha256 - (base32 - "0pfh2x0539f0k2qi2pbjm64b2fqp64c63xxpinvg1yfaw915kgpb")))) - (build-system python-build-system) - (arguments - `(#:phases (modify-phases %standard-phases - (replace 'check - (lambda* (#:key tests? #:allow-other-keys) - (when tests? - (invoke "pytest"))))))) + (version "0.8.0") + (source (origin + (method url-fetch) + (uri (pypi-uri "pyspnego" version)) + (sha256 + (base32 + "1ps34laa0kvvp33az173hp5l0hnk8cr0bfqmlgw64ry5cv09qjg0")))) + (build-system pyproject-build-system) (native-inputs (list python-pytest python-pytest-mock)) (propagated-inputs From c6ac52e8e6aa6e77ac0824b378904b8269adc789 Mon Sep 17 00:00:00 2001 From: Charles Jackson Date: Tue, 5 Sep 2023 18:42:05 -0500 Subject: [PATCH 007/268] gnu: Add vim-vlime. * gnu/packages/vim.scm (vim-vlime): New variable. Signed-off-by: jgart --- gnu/packages/vim.scm | 56 +++++++++++++++++++++++++++++++++++++++++++- 1 file changed, 55 insertions(+), 1 deletion(-) diff --git a/gnu/packages/vim.scm b/gnu/packages/vim.scm index d58b022123..122f0f8ee7 100644 --- a/gnu/packages/vim.scm +++ b/gnu/packages/vim.scm @@ -13,6 +13,7 @@ ;;; Copyright © 2021 Tissevert ;;; Copyright © 2021 Foo Chuan Wei ;;; Copyright © 2022, 2023 Luis Henrique Gomes Higino +;;; Copyright © 2023 Charles Jackson ;;; ;;; This file is part of GNU Guix. ;;; @@ -30,7 +31,7 @@ ;;; along with GNU Guix. If not, see . (define-module (gnu packages vim) - #:use-module ((guix licenses) #:prefix license:) + #:use-module ((guix licenses) #:prefix license:) #:use-module (guix packages) #:use-module (guix gexp) #:use-module (guix utils) @@ -60,6 +61,7 @@ #:use-module (gnu packages jemalloc) #:use-module (gnu packages libevent) #:use-module (gnu packages linux) + #:use-module (gnu packages lisp-xyz) #:use-module (gnu packages lua) #:use-module (gnu packages ncurses) #:use-module (gnu packages perl) @@ -1113,6 +1115,58 @@ getting some of these features into Vim. It works with any REPL and isn't tied to Lisp.") (license license:expat)))) +(define-public vim-vlime + ;; The last tag is very outdated. + (let ((commit "c1ac16c1a50bec4c30da87cd4ce2af12e26fb022") + (revision "1")) + (package + (name "vim-vlime") + (version (git-version "0.4.0" revision commit)) + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/vlime/vlime") + (commit commit))) + (sha256 + (base32 "1dfc1wyjsgkckrklkzvk4whaz3ahaka59rvm7rc724mabmk83pmp")) + (file-name (git-file-name name version)))) + (build-system copy-build-system) + (arguments + '(#:install-plan + '(("vim/autoload" "share/vim/vimfiles/") + ("vim/doc" "share/vim/vimfiles/") + ("vim/ftplugin" "share/vim/vimfiles/") + ("vim/syntax" "share/vim/vimfiles/") + ("vim/test" "share/vim/vimfiles/") + ;; This is so the Vimscript part of Vlime can find the lisp files. + ("lisp" "share/vim/") + ;; This is so lisp can load Vlime without the Vim part. + ("lisp" "share/common-lisp/source/vlime")) + #:phases + (modify-phases %standard-phases + ;; Create a symbolic link to the .asd file so that + ;; (asdf:load-system "vlime") finds the system. + (add-after 'install 'link-asd + (lambda* (#:key outputs #:allow-other-keys) + (let ((out (assoc-ref outputs "out"))) + (mkdir-p (string-append out "/share/common-lisp/systems/")) + (symlink (string-append out "/share/common-lisp/source/vlime/vlime.asd") + (string-append out "/share/common-lisp/systems/vlime.asd")))))))) + (propagated-inputs + (list cl-alexandria + cl-slime-swank + cl-usocket + cl-vom + cl-yason)) + (home-page "https://github.com/vlime/vlime") + (synopsis "Common Lisp dev environment for Vim (and Neovim)") + (description "Vlime is similar to SLIME for Emacs and SLIMV for Vim. It +provides REPL integration, as well as omni-completions, cross reference +utilities, a nice inspector, debugger support, and many other great facilities +to aid you in your glorious Common Lisp hacking quest.") + (license license:expat)))) + (define-public vim-paredit ;; The last tagged version is from August 2013. (let ((commit "97d51d099523b37bb35cbcf3564cbfb46e66e4ec") From 7879ab4229d87a597713b96a779fc00bc0e34f3f Mon Sep 17 00:00:00 2001 From: Andy Tai Date: Thu, 27 Jul 2023 21:54:22 -0700 Subject: [PATCH 008/268] gnu: Add nsync. * gnu/packages/c.scm (nsync): New variable. Signed-off-by: Ricardo Wurmus --- gnu/packages/c.scm | 29 +++++++++++++++++++++++++++++ 1 file changed, 29 insertions(+) diff --git a/gnu/packages/c.scm b/gnu/packages/c.scm index 9e5b511b98..ea58c68262 100644 --- a/gnu/packages/c.scm +++ b/gnu/packages/c.scm @@ -17,6 +17,7 @@ ;;; Copyright © 2022 Artyom V. Poptsov ;;; Copyright © 2022 Ekaitz Zarraga ;;; Copyright © 2022 ( +;;; Copyright © 2022 Antero Mejr ;;; Copyright © 2023 zamfofex ;;; Copyright © 2023 Foundation Devices, Inc. ;;; @@ -1495,6 +1496,34 @@ string.h, but with a utf8* prefix instead of the str* prefix.") "This package provides a header-only unit testing library for C/C++.") (license license:unlicense)))) +(define-public nsync + (package + (name "nsync") + (version "1.26.0") + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/google/nsync") + (commit version))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "0qg58kkcbm4zqkql8j5yvrb7fpx09qsf7j93dwqb9s1y69l70kx4")))) + (build-system cmake-build-system) + (home-page "https://github.com/google/nsync") + (synopsis "C library for synchronization primitives") + (description + "nsync is a C library that exports various synchronization primitives: +@enumerate +@item locks, +@item condition variables, +@item run-once initialization, +@item waitable counter (useful for barriers), +@item waitable bit (useful for cancellation, or other conditions). +@end enumerate +") + (license license:asl2.0))) + (define-public ispc (package (name "ispc") From 2d366e309be381acc33c463b6bc55e3744e5c114 Mon Sep 17 00:00:00 2001 From: Andy Tai Date: Mon, 5 Jun 2023 23:45:11 -0700 Subject: [PATCH 009/268] gnu: Add ruy. * gnu/packages/maths.scm (ruy): New variable. Signed-off-by: Ricardo Wurmus --- gnu/packages/maths.scm | 36 ++++++++++++++++++++++++++++++++++++ 1 file changed, 36 insertions(+) diff --git a/gnu/packages/maths.scm b/gnu/packages/maths.scm index f413403207..38e71e18f8 100644 --- a/gnu/packages/maths.scm +++ b/gnu/packages/maths.scm @@ -8543,3 +8543,39 @@ statistical analysis, image enhancement, fluid dynamics simulations, numerical optimization, and modeling, simulation of explicit and implicit dynamical systems and symbolic manipulations.") (license license:cecill))) ;CeCILL v2.1 + +(define-public ruy + (let ((commit "caa244343de289f913c505100e6a463d46c174de") + (version "0") + (revision "1")) + (package + (name "ruy") + (version (git-version version revision commit)) + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/google/ruy") + (commit commit))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "0j2g90nzam4h52zwx2vpanj8m17068cfb1zi4hcy0pyk52kb11dy")))) + (build-system cmake-build-system) + (arguments + (list + #:configure-flags + #~(list "-DRUY_FIND_CPUINFO=ON" + ;; Needed to make sure code is relocatable for use in + ;; tensorflow. + "-DCMAKE_CXX_FLAGS=-fPIC "))) + (inputs (list cpuinfo)) + (native-inputs (list googletest)) + (home-page "https://github.com/google/ruy") + (synopsis "Matrix multiplication library") + (description + "Ruy is a matrix multiplication library. Its focus is to cover the +matrix multiplication needs of neural network inference engines. Its initial +user has been TensorFlow Lite, where it is used by default on the ARM CPU +architecture.") + (license license:asl2.0)))) + From 3eb77954f969df41c000e7018a6b598b9f562d8d Mon Sep 17 00:00:00 2001 From: Andy Tai Date: Sat, 2 Sep 2023 21:55:18 -0700 Subject: [PATCH 010/268] gnu: tensorflow-lite: Update to 2.12.1. * gnu/packages/algebra.scm (eigen-for-tensorflow-lite): Remove variable. * gnu/packages/machine-learning.scm (tensorflow-lite): Update to 2.12.1 [arguments]: Turn on GPU and RUY use; Use cmake to find packages already in Guix as dependencies for absl-cpp, eigen, flatbuffer, neon2ssl, cpuinfo, ruy. [arguments]: Remove operations setting up absl-cpp, eigen, ruy, and neon2ssl as native inouts as now we use Guix's packages of these as dependencies. Do default build phase. Add steps to install C shared library and benchmark_model tool. [inputs]: Add cpuinfo, eigen, fp16, mesa-header, opencl, pthreadpool, ruy, vulkan and xnnpack as explicit inputs. [native-inputs]: Remove local setup of neon2ssl and ruy as we now use Guix's packages of these as explicit dependencies. * gnu/packages/serialization.scm (flatbuffers-next-shared): New variable, flatbuffers-next built with -fPIC as needed by tensorflow-lite. Signed-off-by: Ricardo Wurmus --- gnu/packages/algebra.scm | 32 ----- gnu/packages/machine-learning.scm | 232 +++++++++++++++++------------- gnu/packages/serialization.scm | 11 ++ 3 files changed, 140 insertions(+), 135 deletions(-) diff --git a/gnu/packages/algebra.scm b/gnu/packages/algebra.scm index a717750c7b..b1ab755144 100644 --- a/gnu/packages/algebra.scm +++ b/gnu/packages/algebra.scm @@ -1154,38 +1154,6 @@ features, and more.") (substitute* "test/CMakeLists.txt" (("ei_add_test\\(stddeque") "#"))))))))))) -(define-public eigen-for-tensorflow-lite - ;; This commit was taken from - ;; tensorflow/lite/tools/cmake/modules/eigen.cmake - (let ((commit "d10b27fe37736d2944630ecd7557cefa95cf87c9") - (revision "1")) - (package (inherit eigen) - (name "eigen-for-tensorflow-lite") - (version (git-version "3.3.7" revision commit)) - (source (origin - (method git-fetch) - (uri (git-reference - (url "https://gitlab.com/libeigen/eigen") - (commit commit))) - (sha256 - (base32 - "0v8a20cwvwmp3hw4275b37frw33v92z0mr8f4dn6y8k0rz92hrrf")) - (file-name (git-file-name name version)) - (modules '((guix build utils))) - (snippet - ;; Ther are test failures in the "unsupported" directory, but - ;; maintainers say it's unsupported anyway, so just skip - ;; them. - '(begin - (substitute* "unsupported/CMakeLists.txt" - (("add_subdirectory\\(test.*") - "# Do not build the tests for unsupported features.\n")))))) - (arguments - (substitute-keyword-arguments (package-arguments eigen) - ((#:phases phases) - `(modify-phases ,phases - (delete 'disable-some-tests)))))))) - (define-public xtensor (package (name "xtensor") diff --git a/gnu/packages/machine-learning.scm b/gnu/packages/machine-learning.scm index f169d8895e..fd0be8d500 100644 --- a/gnu/packages/machine-learning.scm +++ b/gnu/packages/machine-learning.scm @@ -55,12 +55,14 @@ #:use-module (gnu packages) #:use-module (gnu packages adns) #:use-module (gnu packages algebra) + #:use-module (gnu packages assembly) #:use-module (gnu packages audio) #:use-module (gnu packages autotools) #:use-module (gnu packages base) #:use-module (gnu packages bash) #:use-module (gnu packages boost) #:use-module (gnu packages bdw-gc) + #:use-module (gnu packages c) #:use-module (gnu packages check) #:use-module (gnu packages compression) #:use-module (gnu packages cmake) @@ -89,6 +91,7 @@ #:use-module (gnu packages ninja) #:use-module (gnu packages ocaml) #:use-module (gnu packages onc-rpc) + #:use-module (gnu packages opencl) #:use-module (gnu packages parallel) #:use-module (gnu packages perl) #:use-module (gnu packages pkg-config) @@ -100,6 +103,7 @@ #:use-module (gnu packages python-science) #:use-module (gnu packages python-web) #:use-module (gnu packages python-xyz) + #:use-module (gnu packages regex) #:use-module (gnu packages rpc) #:use-module (gnu packages serialization) #:use-module (gnu packages sphinx) @@ -108,6 +112,7 @@ #:use-module (gnu packages swig) #:use-module (gnu packages time) #:use-module (gnu packages tls) + #:use-module (gnu packages vulkan) #:use-module (gnu packages video) #:use-module (gnu packages web) #:use-module (gnu packages xml) @@ -2967,7 +2972,7 @@ advanced research.") (define-public tensorflow-lite (package (name "tensorflow-lite") - (version "2.5.0") + (version "2.12.1") (source (origin (method git-fetch) @@ -2977,97 +2982,141 @@ advanced research.") (file-name (git-file-name name version)) (sha256 (base32 - "1jdw2i1rq06zqd6aabh7bbm0avsg4pygnfmd7gviv0blhih9054l")))) + "0jkgljdagdqllnxygl35r5bh3f9qmbczymfj357gm9krh59g2kmd")))) (build-system cmake-build-system) (arguments - `(#:tests? #false ; no "check" target - #:build-type "Release" - #:configure-flags - (list - "-DTFLITE_ENABLE_GPU=OFF" - "-DTFLITE_ENABLE_RUY=OFF" + (list + #:tests? #false ;tests are not building now + #:build-type "Release" + #:modules '((ice-9 match) + (guix build utils) + (guix build cmake-build-system)) + #:configure-flags + #~(list + ;; "-DTFLITE_KERNEL_TEST=ON" ; TODO: build tests + ;; so cmake can be used to find this from other packages + "-DTFLITE_ENABLE_INSTALL=ON" - ;; TODO: The build system attempts to build xnnpack from source. We - ;; would like to use our xnnpack package here, but this requires more - ;; work. - "-DTFLITE_ENABLE_XNNPACK=OFF" + ;; Use Guix's own packages as dependencies. + "-DCMAKE_FIND_PACKAGE_PREFER_CONFIG=ON" - ;; Pretend we've already fetched abseil. We won't actually build it - ;; but use the existing package. - "-Dabseil-cpp_POPULATED=TRUE" + "-DTFLITE_ENABLE_GPU=ON" + "-DTFLITE_ENABLE_RUY=ON" - ;; Don't fetch the sources. We have already built flatbuffers. - "-Dflatbuffers_POPULATED=TRUE" + ;; TODO: turn on Farmhash + ;;"-DSYSTEM_FARMHASH=ON" + (string-append "-Dabsl_DIR=" #$(this-package-input "abseil-cpp") + "/lib/cmake/absl") + (string-append "-DEigen3_DIR=" #$(this-package-input "eigen") + "/share/eigen3/cmake") + (string-append "-DFlatBuffers_DIR=" + #$(this-package-input "flatbuffers-shared") + "/lib/cmake/flatbuffers") + (string-append "-DNEON_2_SSE_DIR=" #$(this-package-input "neon2sse") + "/lib/cmake/NEON_2_SSE") + (string-append "-Dcpuinfo_DIR=" #$(this-package-input "cpuinfo") + "/share/cpuinfo") + (string-append "-Druy_DIR=" #$(this-package-input "ruy") + "/lib/cmake/ruy") - "-DFFT2D_SOURCE_DIR=/tmp/fft2d" - "-Dneon2sse_SOURCE_DIR=/tmp/neon2sse" - "-Dneon2sse_BINARY_DIR=/tmp/neon2sse-bin" - "-DFARMHASH_SOURCE_DIR=/tmp/farmhash" - "-Dgemmlowp_SOURCE_DIR=/tmp/gemmlowp" - (string-append "-DRUY_SOURCE_DIR=" - (assoc-ref %build-inputs "ruy-src"))) - #:phases - (modify-phases %standard-phases - (add-after 'unpack 'chdir - (lambda _ (chdir "tensorflow/lite"))) - (add-after 'chdir 'copy-sources - (lambda* (#:key inputs #:allow-other-keys) - ;; Use external cmake finders instead of these stubs that won't - ;; find anything but the bundled sources. - (delete-file "tools/cmake/modules/Findabsl.cmake") - (delete-file "tools/cmake/modules/Findeigen.cmake") + ;; TODO: The build system attempts to build xnnpack from source. We + ;; would like to use our xnnpack package here, but this requires more + ;; work. + "-DTFLITE_ENABLE_XNNPACK=OFF" - (substitute* "CMakeLists.txt" - (("find_package\\(eigen REQUIRED") - "find_package(eigen REQUIRED NAMES Eigen3")) - (substitute* "tools/cmake/modules/Findflatbuffers.cmake" - (("get_target_property.*") - (format #false "set(FLATBUFFERS_INCLUDE_DIRS ~a/include)\n" - (assoc-ref inputs "flatbuffers")))) + ;; Don't fetch the sources. We have these already + "-Degl_headers_POPULATED=TRUE" + "-Dfp16_headers_POPULATED=TRUE" + "-Dopencl_headers_POPULATED=TRUE" + "-Dopengl_headers_POPULATED=TRUE" + "-Dvulkan_headers_POPULATED=TRUE" + "-Dgoogletest_POPULATED=TRUE" + "-Dgoogle_benchmark_POPULATED=TRUE" + "-Dnsync_POPULATED=TRUE" + "-Dre2_POPULATED=TRUE" - ;; Don't fetch source code; we already have everything we need. - (substitute* '("tools/cmake/modules/fft2d.cmake" - "tools/cmake/modules/ruy.cmake" - "tools/cmake/modules/farmhash.cmake" - "tools/cmake/modules/neon2sse.cmake" - "tools/cmake/modules/gemmlowp.cmake") - (("OverridableFetchContent_Populate.*") "")) + "-DFFT2D_SOURCE_DIR=/tmp/fft2d" + "-DFARMHASH_SOURCE_DIR=/tmp/farmhash" + "-Dgemmlowp_SOURCE_DIR=/tmp/gemmlowp") + #:phases + #~(modify-phases %standard-phases + (add-after 'unpack 'chdir + (lambda _ (chdir "tensorflow/lite"))) + (add-after 'chdir 'copy-sources + (lambda* (#:key inputs #:allow-other-keys) + ;; TODO: properly use Guix's pthreaqdpool. We are not using + ;; pthreadpool because we are not enabling xnnpack + (substitute* "CMakeLists.txt" + (("if\\(NOT DEFINED PTHREADPOOL_SOURCE_DIR\\)") + "if(false)")) + (substitute* "CMakeLists.txt" + (("if\\(NOT TARGET pthreadpool\\)") + "if(false)")) - (mkdir-p "/tmp/farmhash") - (with-directory-excursion "/tmp/farmhash" - (invoke "tar" "--strip-components=1" - "-xf" (assoc-ref inputs "farmhash-src"))) + ;; Don't fetch source code; we already have everything we need. + (substitute* '("tools/cmake/modules/fft2d.cmake" + "tools/cmake/modules/farmhash.cmake" + "tools/cmake/modules/gemmlowp.cmake") + (("OverridableFetchContent_Populate.*") "")) - (mkdir-p "/tmp/fft2d") - (with-directory-excursion "/tmp/fft2d" - (invoke "tar" "--strip-components=1" - "-xf" (assoc-ref inputs "fft2d-src"))) + (mkdir-p "/tmp/farmhash") + (with-directory-excursion "/tmp/farmhash" + (invoke "tar" "--strip-components=1" + "-xf" (assoc-ref inputs "farmhash-src"))) - (copy-recursively (assoc-ref inputs "neon2sse-src") - "/tmp/neon2sse/") - (copy-recursively (assoc-ref inputs "gemmlowp-src") - "/tmp/gemmlowp/"))) - (add-after 'copy-sources 'prepare-shared-library-build - (lambda _ (chdir "c"))) - (replace 'install - (lambda* (#:key outputs #:allow-other-keys) - (let* ((out (assoc-ref outputs "out")) - (lib (string-append out "/lib")) - (headers (string-append out "/include/tensorflow/lite"))) - (install-file "../build/libtensorflowlite_c.so" lib) - (with-directory-excursion ".." - (for-each - (lambda (file) - (let ((target-dir (string-append headers "/" (dirname file)))) - (install-file file target-dir))) - (find-files "." "\\.h$"))))))))) + (mkdir-p "/tmp/fft2d") + (with-directory-excursion "/tmp/fft2d" + (invoke "tar" "--strip-components=1" + "-xf" (assoc-ref inputs "fft2d-src"))) + + (copy-recursively (assoc-ref inputs "gemmlowp-src") + "/tmp/gemmlowp/"))) + + (add-after 'build 'build-shared-library + (lambda* (#:key configure-flags #:allow-other-keys) + (mkdir-p "c") + (with-directory-excursion "c" + (apply invoke "cmake" (append configure-flags (list "../../lite/c"))) + (invoke "cmake" "--build" "." "-j" (number->string + (parallel-job-count)))))) + (add-after 'build-shared-library 'build-benchmark-model + (lambda _ + (invoke "cmake" "--build" "." "--target" "benchmark_model" + "-j" (number->string (parallel-job-count))))) + + (add-after 'install 'install-extra + (lambda* (#:key outputs #:allow-other-keys) + (let* ((out (assoc-ref outputs "out")) + (lib (string-append out "/lib")) + (bin (string-append out "/bin"))) + (install-file "../build/c/libtensorflowlite_c.so" lib) + (install-file "../build/tools/benchmark/benchmark_model" bin)))) + (replace 'check + (lambda* (#:key tests? #:allow-other-keys) + (when tests? + (invoke "ctest" "-L" "plain"))))))) (inputs `(("abseil-cpp" ,abseil-cpp-20200923.3) - ("eigen" ,eigen-for-tensorflow-lite) - ("flatbuffers" ,flatbuffers) - ("python" ,python))) + ("cpuinfo" ,cpuinfo) + ("eigen" ,eigen) + ("fp16" ,fp16) + ("flatbuffers-shared" ,flatbuffers-next-shared) + ;;("gemmlowp" ,gemmlowp) ; TODO + ("mesa-headers" ,mesa-headers) + ("neon2sse" ,neon2sse) + ("nsync" ,nsync) + ("opencl-clhpp" ,opencl-clhpp) + ("opencl-headers" ,opencl-headers) + ("opencl-icd-loader" ,opencl-icd-loader) + ("pthreadpool" ,pthreadpool) + ("python" ,python) + ("ruy" ,ruy) + ("re2" ,re2) + ;;("xnnpack" ,xnnpack) ; TODO: use Guix's copy of xnnpack + ("vulkan-headers" ,vulkan-headers))) (native-inputs `(("pkg-config" ,pkg-config) + ("googletest" ,googletest) ("gemmlowp-src" ;; The commit hash is taken from ;; "tensorflow/lite/tools/cmake/modules/gemmlowp.cmake". @@ -3081,17 +3130,6 @@ advanced research.") (sha256 (base32 "1sbp8kmr2azwlvfbzryy1frxi99jhsh1nc93bdbxdf8zdgpv0kxl"))))) - ("neon2sse-src" - ,(let ((commit "a1652fd5253afbf3e39357b012974f93511f6108")) - (origin - (method git-fetch) - (uri (git-reference - (url "https://github.com/intel/ARM_NEON_2_x86_SSE") - (commit commit))) - (file-name (git-file-name "neon2sse" (string-take commit 8))) - (sha256 - (base32 - "1q8gkxag9wlnwdwad2pclsrkwzrdjy94hyrkayrsvxyj7szb5y8i"))))) ("farmhash-src" ,(let ((commit "816a4ae622e964763ca0862d9dbd19324a1eaf45")) (origin @@ -3107,24 +3145,12 @@ advanced research.") ,(origin (method url-fetch) (uri (string-append "https://storage.googleapis.com/" - "mirror.tensorflow.org/" - "www.kurims.kyoto-u.ac.jp/~ooura/fft2d.tgz")) + "mirror.tensorflow.org/github.com/petewarden/" + "OouraFFT/archive/v1.0.tar.gz")) (file-name "fft2d.tar.gz") (sha256 (base32 - "1jfflzi74fag9z4qmgwvp90aif4dpbr1657izmxlgvf4hy8fk9xd")))) - ("ruy-src" - ,(let ((commit "9c56af3fce210a8a103eda19bd6f47c08a9e3d90")) - (origin - (method git-fetch) - (uri (git-reference - (url "https://github.com/google/ruy") - (commit commit) - (recursive? #true))) - (file-name (git-file-name "ruy" (string-take commit 8))) - (sha256 - (base32 - "1cfd5gk6kaj8kbl3h98gx1ap8czd59y6p8qq8nr28fklpyzf5cis"))))))) + "1jfflzi74fag9z4qmgwvp90aif4dpbr1657izmxlgvf4hy8fk9xd")))))) (home-page "https://tensorflow.org") (synopsis "Machine learning framework") (description diff --git a/gnu/packages/serialization.scm b/gnu/packages/serialization.scm index 9c114aaf39..c17d417d5e 100644 --- a/gnu/packages/serialization.scm +++ b/gnu/packages/serialization.scm @@ -811,6 +811,17 @@ game development and other performance-critical applications.") (base32 "1z3a6l8g2y53i5xzraswfs2i0i3kk52zv7nzc2q3fgisbyiri3pz")))))) +(define-public flatbuffers-next-shared + (package + (inherit flatbuffers-next) + (name "flatbuffers-shared") + (version "23.1.21") + (arguments + (substitute-keyword-arguments (package-arguments flatbuffers-next) + ((#:configure-flags flags) + ;; Compile with -fPIC, needed for shared lib. + #~(cons "-DFLATBUFFERS_CXX_FLAGS=-fPIC" #$flags)))))) + (define-public python-feather-format (package (name "python-feather-format") From 9144a7809a697ce57079f6f488648976d5e9c788 Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Fri, 8 Sep 2023 09:38:07 +0300 Subject: [PATCH 011/268] gnu: python-eventlet: Update to 0.33.3. * gnu/packages/python-xyz.scm (python-eventlet): Update to 0.33.3. [propagated-inputs]: Remove python-monotonic. [arguments]: Skip another test. --- gnu/packages/python-xyz.scm | 10 ++++++---- 1 file changed, 6 insertions(+), 4 deletions(-) diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index aeaaeb4059..979cbd4b56 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -3486,17 +3486,17 @@ standard.") (define-public python-eventlet (package (name "python-eventlet") - (version "0.33.0") + (version "0.33.3") (source (origin (method url-fetch) (uri (pypi-uri "eventlet" version)) (sha256 (base32 - "07qlyhcm0f28sxdizawvdf3d50m3hnbzz5kg3fjp7chvki44y540")))) + "1nngffz21afhfi266smf4s5mn5dfd0ykdnirfls9bwnzxbkh6a3j")))) (build-system python-build-system) (propagated-inputs - (list python-dnspython python-greenlet python-monotonic python-six)) + (list python-dnspython python-greenlet python-six)) (native-inputs (list python-nose)) (arguments @@ -3521,7 +3521,9 @@ standard.") ;; . "-e" "test_patcher_existing_locks_locked" ;; And see . - "-e" "test_017_ssl_zeroreturnerror"))))))) + "-e" "test_017_ssl_zeroreturnerror" + ;; This test is failing on some architectures + "-e" "test_fork_after_monkey_patch"))))))) (home-page "https://eventlet.net") (synopsis "Concurrent networking library for Python") (description From 17b8f3d2595ab4fed65194b044c0a24ddc242848 Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Fri, 8 Sep 2023 09:58:25 +0300 Subject: [PATCH 012/268] gnu: python-hacking: Update to 5.0.0. * gnu/packages/openstack.scm (python-hacking): Update to 5.0.0. [propagated-inputs]: Remove python-flake8-3.8; add python-flake8. [native-inputs]: Remove python-dnspython, python-mock, and python-monotonic. --- gnu/packages/openstack.scm | 15 ++++++--------- 1 file changed, 6 insertions(+), 9 deletions(-) diff --git a/gnu/packages/openstack.scm b/gnu/packages/openstack.scm index 169df27f7c..0937dc2e4f 100644 --- a/gnu/packages/openstack.scm +++ b/gnu/packages/openstack.scm @@ -1,6 +1,6 @@ ;;; GNU Guix --- Functional package management for GNU ;;; Copyright © 2015 Cyril Roelandt -;;; Copyright © 2015, 2016 Efraim Flashner +;;; Copyright © 2015, 2016, 2023 Efraim Flashner ;;; Copyright © 2016, 2017, 2019, 2021 Clément Lassieur ;;; Copyright © 2018, 2019 Tobias Geerinckx-Rice ;;; Copyright © 2018, 2022 Marius Bakke @@ -138,26 +138,23 @@ manner.") (define-public python-hacking (package (name "python-hacking") - (version "4.1.0") + (version "5.0.0") (source (origin (method url-fetch) (uri (pypi-uri "hacking" version)) (sha256 (base32 - "0fg19rlcky3n1y1ri61xyjp7534yzf8r102z9dw3zqg93f4kj20m")))) + "09p0avmz914asszvdknc46n43bl070f369wmjmppl51zmw4b4ddb")))) (build-system python-build-system) - (propagated-inputs - (list python-flake8-3.8)) + (propagated-inputs + (list python-flake8)) (native-inputs (list ;; Tests python-coverage python-ddt - python-dnspython - python-fixtures python-eventlet - python-mock - python-monotonic + python-fixtures python-subunit python-stestr python-testscenarios From 7646ea8270b12dd8630b5c7128241855b871f9b4 Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Fri, 8 Sep 2023 09:59:57 +0300 Subject: [PATCH 013/268] gnu: Remove python-flake8-3.8. * gnu/packages/python-xyz.scm (python-flake8-3.8): Delete variable. --- gnu/packages/python-xyz.scm | 14 -------------- 1 file changed, 14 deletions(-) diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index 979cbd4b56..8a7943915f 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -12592,20 +12592,6 @@ cyclomatic complexity of Python source code.") "Flake8 is a wrapper around PyFlakes, pep8 and python-mccabe.") (license license:expat))) -(define-public python-flake8-3.8 - (package - (inherit python-flake8) - (version "3.8.4") - (source (origin - (method url-fetch) - (uri (pypi-uri "flake8" version)) - (sha256 - (base32 - "0fvcrsbyzjpcli8ldbpsdbpmf238nkvwc1dy4hy82lf63rvfinma")))) - (propagated-inputs - (list python-pycodestyle-2.6 python-entrypoints python-pyflakes-2.2 - python-mccabe)))) - (define-public python-flake8-blind-except (package (name "python-flake8-blind-except") From 7525396c1ea205f70d3e095f51e50f1d80827bff Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Fri, 8 Sep 2023 10:00:36 +0300 Subject: [PATCH 014/268] gnu: Remove python-pycodestyle-2.6. * gnu/packages/python-xyz.scm (python-pycodestyle-2.6): Delete variable. --- gnu/packages/python-xyz.scm | 11 ----------- 1 file changed, 11 deletions(-) diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index 8a7943915f..325ff8b822 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -8358,17 +8358,6 @@ Python code against some of the style conventions in @url{http://www.python.org/dev/peps/pep-0008/,PEP 8}.") (license license:expat))) -(define-public python-pycodestyle-2.6 - (package - (inherit python-pycodestyle) - (version "2.6.0") - (source (origin - (method url-fetch) - (uri (pypi-uri "pycodestyle" version)) - (sha256 - (base32 - "0bhr6ia0hmgx3nhgibc9pmkzhlh1zcqk707i5fbxgs702ll7v2n5")))))) - (define-public python-multidict (package (name "python-multidict") From 67ffb90dcbc88694fea4a1cbfc01c49aec4d1808 Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Fri, 8 Sep 2023 10:01:02 +0300 Subject: [PATCH 015/268] gnu: Remove python-pyflakes-2.2. * gnu/packages/python-xyz.scm (python-pyflakes-2.2): Delete variable. * gnu/packages/patches/python-pyflakes-test-location.patch: Remove file. * gnu/local.mk (dist_patch_DATA): Remove it. --- gnu/local.mk | 1 - .../python-pyflakes-test-location.patch | 42 ------------------- gnu/packages/python-xyz.scm | 13 ------ 3 files changed, 56 deletions(-) delete mode 100644 gnu/packages/patches/python-pyflakes-test-location.patch diff --git a/gnu/local.mk b/gnu/local.mk index f58d04cf91..2b20606ca1 100644 --- a/gnu/local.mk +++ b/gnu/local.mk @@ -1835,7 +1835,6 @@ dist_patch_DATA = \ %D%/packages/patches/python-piexif-fix-tests-with-pillow-7.2.patch \ %D%/packages/patches/python-pillow-CVE-2022-45199.patch \ %D%/packages/patches/python-pyfakefs-remove-bad-test.patch \ - %D%/packages/patches/python-pyflakes-test-location.patch \ %D%/packages/patches/python-flint-includes.patch \ %D%/packages/patches/python-libxml2-utf8.patch \ %D%/packages/patches/python-memcached-syntax-warnings.patch \ diff --git a/gnu/packages/patches/python-pyflakes-test-location.patch b/gnu/packages/patches/python-pyflakes-test-location.patch deleted file mode 100644 index ea2c50c82e..0000000000 --- a/gnu/packages/patches/python-pyflakes-test-location.patch +++ /dev/null @@ -1,42 +0,0 @@ -This patch fixes test failure related to reported source code locations. -It is a backport of this patch: - - commit 6a5f38b5ab12260fde8a0463acd433bc2d34dbcf - Author: Louis Sautier - Date: Sat Oct 3 02:37:53 2020 +0200 - - Fix tests with Python 3.9, closes #549 (#586) - - Stop allowing failures on Python nightly. - -diff --git a/pyflakes/test/test_api.py b/pyflakes/test/test_api.py -index 128aa69..b728e65 100644 ---- a/pyflakes/test/test_api.py -+++ b/pyflakes/test/test_api.py -@@ -515,6 +515,8 @@ def foo(bar=baz, bax): - if ERROR_HAS_LAST_LINE: - if PYPY and sys.version_info >= (3,): - column = 7 -+ elif sys.version_info >= (3, 9): -+ column = 21 - elif sys.version_info >= (3, 8): - column = 9 - else: -@@ -543,6 +545,8 @@ foo(bar=baz, bax) - if ERROR_HAS_LAST_LINE: - if PYPY and sys.version_info >= (3,): - column = 12 -+ elif sys.version_info >= (3, 9): -+ column = 17 - elif sys.version_info >= (3, 8): - column = 14 - else: -@@ -577,6 +581,8 @@ foo(bar=baz, bax) - position_end = 1 - if PYPY: - column = 6 -+ elif ver >= (3, 9): -+ column = 13 - else: - column = 7 - # Column has been "fixed" since 3.2.4 and 3.3.1 diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index 325ff8b822..a540c6367d 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -12493,19 +12493,6 @@ file (e.g. @file{PKG-INFO}).") "Pyflakes statically checks Python source code for common errors.") (license license:expat))) -(define-public python-pyflakes-2.2 - (package - (inherit python-pyflakes) - (version "2.2.0") - (source (origin - (method url-fetch) - (uri (pypi-uri "pyflakes" version)) - (sha256 - (base32 - "1j3zqbiwkyicvww499bblq33x0bjpzdrxajhaysr7sk7x5gdgcim")) - (patches - (search-patches "python-pyflakes-test-location.patch")))))) - (define-public python-mccabe (package (name "python-mccabe") From 420d51fa02d5eeea441f8b9bc0395cf0bb68a2fb Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Fri, 8 Sep 2023 12:14:46 +0300 Subject: [PATCH 016/268] gnu: python-numcodecs: Remove another cythonized file. * gnu/packages/python-xyz.scm (python-numcodecs)[source]: Remove another cythonized file. --- gnu/packages/python-xyz.scm | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index a540c6367d..32fa9500e9 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -25144,7 +25144,8 @@ tool).") (snippet '(begin (delete-file-recursively "c-blosc") - (for-each delete-file '("numcodecs/blosc.c" + (for-each delete-file '("numcodecs/_shuffle.c" + "numcodecs/blosc.c" "numcodecs/compat_ext.c" "numcodecs/lz4.c" "numcodecs/vlen.c" From 68132407da0105ea7598e903f54b5096792ca17c Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Fri, 8 Sep 2023 12:15:38 +0300 Subject: [PATCH 017/268] gnu: python-numcodecs: Fix building on non x86 machines. * gnu/packages/python-xyz.scm (python-numcodecs)[source]: Adjust snippet to prevent setup.py adding unsupported architecture specific CFLAGS. --- gnu/packages/python-xyz.scm | 7 +++++++ 1 file changed, 7 insertions(+) diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index 32fa9500e9..408c370adf 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -25143,6 +25143,13 @@ tool).") (modules '((guix build utils))) (snippet '(begin + ;; Only add CFLAGS on architectures where they are supported + (substitute* "setup.py" + (("import sys") + "import sys\nimport platform") + (("os\\.name == 'posix'") + (string-append "os.name + platform.machine() == 'posixx86_64' or" + " os.name + platform.machine() == 'posixx86'"))) (delete-file-recursively "c-blosc") (for-each delete-file '("numcodecs/_shuffle.c" "numcodecs/blosc.c" From d4645d5d25c9de0def9745c48a96504e500ec850 Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Fri, 8 Sep 2023 12:24:21 +0300 Subject: [PATCH 018/268] gnu: python-fasteners: Update to 0.17.3. * gnu/packages/python-xyz.scm (python-fasteners): Update to 0.17.3. [build-system]: Switch to pyproject-build-system. [arguments]: Add custom 'check phase. [propagated-inputs]: Remove python-monotonic and python-six. [native-inputs]: Remove python-testtools; add python-diskcache, python-more-itertools, and python-pytest. --- gnu/packages/python-xyz.scm | 32 +++++++++++++++++++------------- 1 file changed, 19 insertions(+), 13 deletions(-) diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index 408c370adf..a3b7b9fa60 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -24763,19 +24763,25 @@ and corruption checks.") (define-public python-fasteners (package (name "python-fasteners") - (version "0.15") - (source - (origin - (method url-fetch) - (uri (pypi-uri "fasteners" version)) - (sha256 - (base32 - "1vzmz1xh38b84dv0f4hlp7arwmx8wjlih6lf964bpy8dnyk6s5rs")))) - (build-system python-build-system) - (propagated-inputs - (list python-monotonic python-six)) - (native-inputs - (list python-testtools)) + (version "0.17.3") + (source (origin + ;; No tests in the pypi tarball + (method git-fetch) + (uri (git-reference + (url "https://github.com/harlowja/fasteners") + (commit version))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "0m0dxv8ljpkq99s3d1mib1zfb0ppx3h74h5yr8809zsrq2klfn0m")))) + (build-system pyproject-build-system) + (arguments + `(#:phases (modify-phases %standard-phases + (replace 'check + (lambda* (#:key tests? #:allow-other-keys) + (when tests? + (invoke "pytest"))))))) + (native-inputs (list python-diskcache python-more-itertools python-pytest)) (home-page "https://github.com/harlowja/fasteners") (synopsis "Python package that provides useful locks") (description From b41ea5dcd4a70af3b5efdcac939b56a0e2243a69 Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Sun, 30 Apr 2023 19:03:42 +0800 Subject: [PATCH 019/268] gnu: ganeti: Fix build. * gnu/packages/patches/ganeti-lens-compat.patch, gnu/packages/patches/ganeti-procps-compat.patch, gnu/packages/patches/ganeti-relax-dependencies.patch, gnu/packages/patches/ganeti-reorder-arbitrary-definitions.patch, gnu/packages/patches/ganeti-template-haskell-2.17.patch, gnu/packages/patches/ganeti-template-haskell-2.18.patch: New files. * gnu/local.mk (dist_patch_DATA): Adjust accordingly. * gnu/packages/virtualization.scm (ganeti)[source](patches): Add them. --- gnu/local.mk | 6 + gnu/packages/patches/ganeti-lens-compat.patch | 40 ++++ .../patches/ganeti-procps-compat.patch | 45 +++++ .../patches/ganeti-relax-dependencies.patch | 28 +++ ...ganeti-reorder-arbitrary-definitions.patch | 90 +++++++++ .../ganeti-template-haskell-2.17.patch | 69 +++++++ .../ganeti-template-haskell-2.18.patch | 179 ++++++++++++++++++ gnu/packages/virtualization.scm | 8 +- 8 files changed, 464 insertions(+), 1 deletion(-) create mode 100644 gnu/packages/patches/ganeti-lens-compat.patch create mode 100644 gnu/packages/patches/ganeti-procps-compat.patch create mode 100644 gnu/packages/patches/ganeti-relax-dependencies.patch create mode 100644 gnu/packages/patches/ganeti-reorder-arbitrary-definitions.patch create mode 100644 gnu/packages/patches/ganeti-template-haskell-2.17.patch create mode 100644 gnu/packages/patches/ganeti-template-haskell-2.18.patch diff --git a/gnu/local.mk b/gnu/local.mk index 2b20606ca1..8a3c93c1c1 100644 --- a/gnu/local.mk +++ b/gnu/local.mk @@ -1178,9 +1178,15 @@ dist_patch_DATA = \ %D%/packages/patches/gajim-honour-GAJIM_PLUGIN_PATH.patch \ %D%/packages/patches/ganeti-disable-version-symlinks.patch \ %D%/packages/patches/ganeti-haskell-pythondir.patch \ + %D%/packages/patches/ganeti-lens-compat.patch \ %D%/packages/patches/ganeti-pyyaml-compat.patch \ + %D%/packages/patches/ganeti-procps-compat.patch \ + %D%/packages/patches/ganeti-reorder-arbitrary-definitions.patch \ + %D%/packages/patches/ganeti-relax-dependencies.patch \ %D%/packages/patches/ganeti-shepherd-master-failover.patch \ %D%/packages/patches/ganeti-shepherd-support.patch \ + %D%/packages/patches/ganeti-template-haskell-2.17.patch \ + %D%/packages/patches/ganeti-template-haskell-2.18.patch \ %D%/packages/patches/gawk-shell.patch \ %D%/packages/patches/gcc-arm-bug-71399.patch \ %D%/packages/patches/gcc-arm-link-spec-fix.patch \ diff --git a/gnu/packages/patches/ganeti-lens-compat.patch b/gnu/packages/patches/ganeti-lens-compat.patch new file mode 100644 index 0000000000..1b9108d78f --- /dev/null +++ b/gnu/packages/patches/ganeti-lens-compat.patch @@ -0,0 +1,40 @@ +Fix building against Lens 5 by commenting out type signatures(!). + +Taken from upstream: + + https://github.com/ganeti/ganeti/commit/5e30bad1bba63c9f6c782003ef2560f107a0ba24 + +diff --git a/src/Ganeti/Network.hs b/src/Ganeti/Network.hs +index 1cb6aa1ec..696c1cd1b 100644 +--- a/src/Ganeti/Network.hs ++++ b/src/Ganeti/Network.hs +@@ -87,11 +87,11 @@ data PoolPart = PoolInstances | PoolExt + addressPoolIso :: Iso' AddressPool BA.BitArray + addressPoolIso = iso apReservations AddressPool + +-poolLens :: PoolPart -> Lens' Network (Maybe AddressPool) ++--poolLens :: PoolPart -> Lens' Network (Maybe AddressPool) + poolLens PoolInstances = networkReservationsL + poolLens PoolExt = networkExtReservationsL + +-poolArrayLens :: PoolPart -> Lens' Network (Maybe BA.BitArray) ++--poolArrayLens :: PoolPart -> Lens' Network (Maybe BA.BitArray) + poolArrayLens part = poolLens part . mapping addressPoolIso + + netIpv4NumHosts :: Network -> Integer +diff --git a/src/Ganeti/Utils/MultiMap.hs b/src/Ganeti/Utils/MultiMap.hs +index d54da3ab0..279e9335a 100644 +--- a/src/Ganeti/Utils/MultiMap.hs ++++ b/src/Ganeti/Utils/MultiMap.hs +@@ -91,7 +91,7 @@ multiMap :: (Ord k, Ord v) => M.Map k (S.Set v) -> MultiMap k v + multiMap = MultiMap . M.filter (not . S.null) + + -- | A 'Lens' that allows to access a set under a given key in a multi-map. +-multiMapL :: (Ord k, Ord v) => k -> Lens' (MultiMap k v) (S.Set v) ++--multiMapL :: (Ord k, Ord v) => k -> Lens' (MultiMap k v) (S.Set v) + multiMapL k f = fmap MultiMap + . at k (fmap (mfilter (not . S.null) . Just) + . f . fromMaybe S.empty) +-- +2.41.0 + diff --git a/gnu/packages/patches/ganeti-procps-compat.patch b/gnu/packages/patches/ganeti-procps-compat.patch new file mode 100644 index 0000000000..a2145274cb --- /dev/null +++ b/gnu/packages/patches/ganeti-procps-compat.patch @@ -0,0 +1,45 @@ +Fix compatibility with procps 4. + +Negative UIDs are no longer allowed. Use a very high one instead. + +Taken from upstream: + + https://github.com/ganeti/ganeti/commit/9cd67e6a81c66ed326d68ea8c3241d14eea6550b + +diff --git a/test/py/ganeti.uidpool_unittest.py b/test/py/ganeti.uidpool_unittest.py +index b2f5bc5cf2..2d9227cbf5 100755 +--- a/test/py/ganeti.uidpool_unittest.py ++++ b/test/py/ganeti.uidpool_unittest.py +@@ -106,23 +106,24 @@ def testRequestUnusedUid(self): + + # Check with a single, known unused user-id + # +- # We use "-1" here, which is not a valid user-id, so it's +- # guaranteed that it's unused. +- uid = uidpool.RequestUnusedUid(set([-1])) +- self.assertEqualValues(uid.GetUid(), -1) ++ # We use 2^30+42 here, which is a valid UID, but unlikely to be used on ++ # most systems (even as a subuid). ++ free_uid = 2**30 + 42 ++ uid = uidpool.RequestUnusedUid(set([free_uid])) ++ self.assertEqualValues(uid.GetUid(), free_uid) + + # Check uid-pool exhaustion + # +- # uid "-1" is locked now, so RequestUnusedUid is expected to fail ++ # free_uid is locked now, so RequestUnusedUid is expected to fail + self.assertRaises(errors.LockError, + uidpool.RequestUnusedUid, +- set([-1])) ++ set([free_uid])) + + # Check unlocking + uid.Unlock() + # After unlocking, "-1" should be available again +- uid = uidpool.RequestUnusedUid(set([-1])) +- self.assertEqualValues(uid.GetUid(), -1) ++ uid = uidpool.RequestUnusedUid(set([free_uid])) ++ self.assertEqualValues(uid.GetUid(), free_uid) + + + if __name__ == "__main__": diff --git a/gnu/packages/patches/ganeti-relax-dependencies.patch b/gnu/packages/patches/ganeti-relax-dependencies.patch new file mode 100644 index 0000000000..521b410b9e --- /dev/null +++ b/gnu/packages/patches/ganeti-relax-dependencies.patch @@ -0,0 +1,28 @@ +Relax version constraints to work with Stackage LTS 19. + +Taken from upstream: + + https://github.com/ganeti/ganeti/commit/4f8d61ea0101721eae1c6f43be8430d819e5e611 + +diff --git a/cabal/ganeti.template.cabal b/cabal/ganeti.template.cabal +index bb4ff8053..98491dd9f 100644 +--- a/cabal/ganeti.template.cabal ++++ b/cabal/ganeti.template.cabal +@@ -63,14 +63,14 @@ library + , unix >= 2.5.1.0 + , utf8-string >= 0.3.7 + +- , attoparsec >= 0.10.1.1 && < 0.14 +- , base64-bytestring >= 1.0.0.1 && < 1.2 ++ , attoparsec >= 0.10.1.1 && < 0.15 ++ , base64-bytestring >= 1.0.0.1 && < 1.3 + , case-insensitive >= 0.4.0.1 && < 1.3 + , curl >= 1.3.7 && < 1.4 + , hinotify >= 0.3.2 && < 0.5 + , hslogger >= 1.1.4 && < 1.4 + , json >= 0.5 && < 1.0 +- , lens >= 3.10 && < 5.0 ++ , lens >= 3.10 && < 6.0 + , lifted-base >= 0.2.0.3 && < 0.3 + , monad-control >= 0.3.1.3 && < 1.1 + , parallel >= 3.2.0.2 && < 3.3 diff --git a/gnu/packages/patches/ganeti-reorder-arbitrary-definitions.patch b/gnu/packages/patches/ganeti-reorder-arbitrary-definitions.patch new file mode 100644 index 0000000000..ba34c0bdd6 --- /dev/null +++ b/gnu/packages/patches/ganeti-reorder-arbitrary-definitions.patch @@ -0,0 +1,90 @@ +Fix ordering of Arbitrary definitions for GHC 9 compatibility. + +Taken from upstream: + + https://github.com/ganeti/ganeti/commit/feab8faa8fe055c89205497e4f277ae4c7b8caad + +diff --git a/test/hs/Test/Ganeti/Objects.hs b/test/hs/Test/Ganeti/Objects.hs +index 97ceb36dca..8d80be9e80 100644 +--- a/test/hs/Test/Ganeti/Objects.hs ++++ b/test/hs/Test/Ganeti/Objects.hs +@@ -93,8 +93,14 @@ instance Arbitrary (Container DataCollectorConfig) where + instance Arbitrary BS.ByteString where + arbitrary = genPrintableByteString + ++instance Arbitrary a => Arbitrary (Private a) where ++ arbitrary = Private <$> arbitrary ++ + $(genArbitrary ''PartialNDParams) + ++instance Arbitrary (Container J.JSValue) where ++ arbitrary = return $ GenericContainer Map.empty ++ + instance Arbitrary Node where + arbitrary = Node <$> genFQDN <*> genFQDN <*> genFQDN + <*> arbitrary <*> arbitrary <*> arbitrary <*> genFQDN +@@ -297,10 +303,6 @@ genDisk = genDiskWithChildren 3 + -- validation rules. + $(genArbitrary ''PartialISpecParams) + +--- | FIXME: This generates completely random data, without normal +--- validation rules. +-$(genArbitrary ''PartialIPolicy) +- + $(genArbitrary ''FilledISpecParams) + $(genArbitrary ''MinMaxISpecs) + $(genArbitrary ''FilledIPolicy) +@@ -309,6 +311,10 @@ $(genArbitrary ''FilledNDParams) + $(genArbitrary ''FilledNicParams) + $(genArbitrary ''FilledBeParams) + ++-- | FIXME: This generates completely random data, without normal ++-- validation rules. ++$(genArbitrary ''PartialIPolicy) ++ + -- | No real arbitrary instance for 'ClusterHvParams' yet. + instance Arbitrary ClusterHvParams where + arbitrary = return $ GenericContainer Map.empty +@@ -331,18 +337,12 @@ instance Arbitrary OsParams where + instance Arbitrary Objects.ClusterOsParamsPrivate where + arbitrary = (GenericContainer . Map.fromList) <$> arbitrary + +-instance Arbitrary a => Arbitrary (Private a) where +- arbitrary = Private <$> arbitrary +- + instance Arbitrary ClusterOsParams where + arbitrary = (GenericContainer . Map.fromList) <$> arbitrary + + instance Arbitrary ClusterBeParams where + arbitrary = (GenericContainer . Map.fromList) <$> arbitrary + +-instance Arbitrary IAllocatorParams where +- arbitrary = return $ GenericContainer Map.empty +- + $(genArbitrary ''Cluster) + + instance Arbitrary ConfigData where +diff --git a/test/hs/Test/Ganeti/Query/Language.hs b/test/hs/Test/Ganeti/Query/Language.hs +index 04fb8c3898..fa50196f00 100644 +--- a/test/hs/Test/Ganeti/Query/Language.hs ++++ b/test/hs/Test/Ganeti/Query/Language.hs +@@ -59,6 +59,9 @@ import Ganeti.Query.Language + instance Arbitrary (Filter FilterField) where + arbitrary = genFilter + ++instance Arbitrary FilterRegex where ++ arbitrary = genName >>= mkRegex -- a name should be a good regex ++ + -- | Custom 'Filter' generator (top-level), which enforces a + -- (sane) limit on the depth of the generated filters. + genFilter :: Gen (Filter FilterField) +@@ -97,9 +100,6 @@ $(genArbitrary ''QueryTypeLuxi) + + $(genArbitrary ''ItemType) + +-instance Arbitrary FilterRegex where +- arbitrary = genName >>= mkRegex -- a name should be a good regex +- + $(genArbitrary ''ResultStatus) + + $(genArbitrary ''FieldType) diff --git a/gnu/packages/patches/ganeti-template-haskell-2.17.patch b/gnu/packages/patches/ganeti-template-haskell-2.17.patch new file mode 100644 index 0000000000..be5948bb96 --- /dev/null +++ b/gnu/packages/patches/ganeti-template-haskell-2.17.patch @@ -0,0 +1,69 @@ +Handle GHC 9 changes in a backwards compatible manner. + +Taken from upstream: + + https://github.com/ganeti/ganeti/commit/b279fa738fd5b30320584f79f4d2f0e894315aab + +diff --git a/src/Ganeti/THH.hs b/src/Ganeti/THH.hs +index 818c11f84..9ab93d5e3 100644 +--- a/src/Ganeti/THH.hs ++++ b/src/Ganeti/THH.hs +@@ -884,7 +884,7 @@ genLoadOpCode opdefs fn = do + ) $ zip mexps opdefs + defmatch = Match WildP (NormalB fails) [] + cst = NoBindS $ CaseE (VarE opid) $ mpats++[defmatch] +- body = DoE [st, cst] ++ body = mkDoE [st, cst] + -- include "OP_ID" to the list of used keys + bodyAndOpId <- [| $(return body) + <* tell (mkUsedKeys . S.singleton . T.pack $ opidKey) |] +@@ -1541,7 +1541,7 @@ loadExcConstructor inname sname fields = do + [x] -> BindS (ListP [VarP x]) + _ -> BindS (TupP (map VarP f_names)) + cval = appCons name $ map VarE f_names +- return $ DoE [binds read_args, NoBindS (AppE (VarE 'return) cval)] ++ return $ mkDoE [binds read_args, NoBindS (AppE (VarE 'return) cval)] + + {-| Generates the loadException function. + +diff --git a/src/Ganeti/THH/Compat.hs b/src/Ganeti/THH/Compat.hs +index d29e30d18..1f51e49d7 100644 +--- a/src/Ganeti/THH/Compat.hs ++++ b/src/Ganeti/THH/Compat.hs +@@ -40,9 +40,11 @@ module Ganeti.THH.Compat + , extractDataDConstructors + , myNotStrict + , nonUnaryTupE ++ , mkDoE + ) where + + import Language.Haskell.TH ++import Language.Haskell.TH.Syntax + + -- | Convert Names to DerivClauses + -- +@@ -61,7 +63,11 @@ derivesFromNames names = map ConT names + -- + -- Handle TH 2.11 and 2.12 changes in a transparent manner using the pre-2.11 + -- API. ++#if MIN_VERSION_template_haskell(2,17,0) ++gntDataD :: Cxt -> Name -> [TyVarBndr ()] -> [Con] -> [Name] -> Dec ++#else + gntDataD :: Cxt -> Name -> [TyVarBndr] -> [Con] -> [Name] -> Dec ++#endif + gntDataD x y z a b = + #if MIN_VERSION_template_haskell(2,12,0) + DataD x y z Nothing a $ derivesFromNames b +@@ -114,3 +120,12 @@ nonUnaryTupE es = TupE $ map Just es + #else + nonUnaryTupE es = TupE $ es + #endif ++ ++-- | DoE is now qualified with an optional ModName ++mkDoE :: [Stmt] -> Exp ++mkDoE s = ++#if MIN_VERSION_template_haskell(2,17,0) ++ DoE Nothing s ++#else ++ DoE s ++#endif diff --git a/gnu/packages/patches/ganeti-template-haskell-2.18.patch b/gnu/packages/patches/ganeti-template-haskell-2.18.patch new file mode 100644 index 0000000000..e7be869636 --- /dev/null +++ b/gnu/packages/patches/ganeti-template-haskell-2.18.patch @@ -0,0 +1,179 @@ +Fix compatibility with Template Haskell 2.18 and GHC 9.2. + + +diff --git a/src/Ganeti/BasicTypes.hs b/src/Ganeti/BasicTypes.hs +index 10d0426cd..d68bc7d5b 100644 +--- a/src/Ganeti/BasicTypes.hs ++++ b/src/Ganeti/BasicTypes.hs +@@ -206,12 +206,12 @@ instance MonadTrans (ResultT a) where + instance (MonadIO m, Error a) => MonadIO (ResultT a m) where + liftIO = ResultT . liftIO + . liftM (either (failError . show) return) +- . (try :: IO a -> IO (Either IOError a)) ++ . (try :: IO α -> IO (Either IOError α)) + + instance (MonadBase IO m, Error a) => MonadBase IO (ResultT a m) where + liftBase = ResultT . liftBase + . liftM (either (failError . show) return) +- . (try :: IO a -> IO (Either IOError a)) ++ . (try :: IO α -> IO (Either IOError α)) + + instance (Error a) => MonadTransControl (ResultT a) where + #if MIN_VERSION_monad_control(1,0,0) +diff --git a/src/Ganeti/Lens.hs b/src/Ganeti/Lens.hs +index faa5900ed..747366e6a 100644 +--- a/src/Ganeti/Lens.hs ++++ b/src/Ganeti/Lens.hs +@@ -93,14 +93,14 @@ makeCustomLenses' name lst = makeCustomLensesFiltered f name + -- Most often the @g@ functor is @(,) r@ and 'traverseOf2' is used to + -- traverse an effectful computation that also returns an additional output + -- value. +-traverseOf2 :: Over (->) (Compose f g) s t a b +- -> (a -> f (g b)) -> s -> f (g t) ++-- traverseOf2 :: Over (->) (Compose f g) s t a b ++-- -> (a -> f (g b)) -> s -> f (g t) + traverseOf2 k f = getCompose . traverseOf k (Compose . f) + + -- | Traverses over a composition of a monad and a functor. + -- See 'traverseOf2'. +-mapMOf2 :: Over (->) (Compose (WrappedMonad m) g) s t a b +- -> (a -> m (g b)) -> s -> m (g t) ++-- mapMOf2 :: Over (->) (Compose (WrappedMonad m) g) s t a b ++-- -> (a -> m (g b)) -> s -> m (g t) + mapMOf2 k f = unwrapMonad . traverseOf2 k (WrapMonad . f) + + -- | A helper lens over sets. +diff --git a/src/Ganeti/THH.hs b/src/Ganeti/THH.hs +index 9ab93d5e3..9a10a9a07 100644 +--- a/src/Ganeti/THH.hs ++++ b/src/Ganeti/THH.hs +@@ -996,8 +996,8 @@ buildAccessor fnm fpfx rnm rpfx nm pfx field = do + f_body = AppE (VarE fpfx_name) $ VarE x + return $ [ SigD pfx_name $ ArrowT `AppT` ConT nm `AppT` ftype + , FunD pfx_name +- [ Clause [ConP rnm [VarP x]] (NormalB r_body) [] +- , Clause [ConP fnm [VarP x]] (NormalB f_body) [] ++ [ Clause [myConP rnm [VarP x]] (NormalB r_body) [] ++ , Clause [myConP fnm [VarP x]] (NormalB f_body) [] + ]] + + -- | Build lense declartions for a field. +@@ -1037,10 +1037,10 @@ buildLens (fnm, fdnm) (rnm, rdnm) nm pfx ar (field, i) = do + (ConE cdn) + $ zip [0..] vars + let setterE = LamE [VarP context, VarP var] $ CaseE (VarE context) +- [ Match (ConP fnm [ConP fdnm . set (element i) WildP ++ [ Match (myConP fnm [myConP fdnm . set (element i) WildP + $ map VarP vars]) + (body (not isSimple) fnm fdnm) [] +- , Match (ConP rnm [ConP rdnm . set (element i) WildP ++ , Match (myConP rnm [myConP rdnm . set (element i) WildP + $ map VarP vars]) + (body False rnm rdnm) [] + ] +@@ -1098,9 +1098,9 @@ buildObjectWithForthcoming sname field_pfx fields = do + $ JSON.showJSON $(varE x) |] + let rdjson = FunD 'JSON.readJSON [Clause [] (NormalB read_body) []] + shjson = FunD 'JSON.showJSON +- [ Clause [ConP (mkName real_nm) [VarP x]] ++ [ Clause [myConP (mkName real_nm) [VarP x]] + (NormalB show_real_body) [] +- , Clause [ConP (mkName forth_nm) [VarP x]] ++ , Clause [myConP (mkName forth_nm) [VarP x]] + (NormalB show_forth_body) [] + ] + instJSONdecl = gntInstanceD [] (AppT (ConT ''JSON.JSON) (ConT name)) +@@ -1121,9 +1121,9 @@ buildObjectWithForthcoming sname field_pfx fields = do + (fromDictWKeys $(varE xs)) |] + todictx_r <- [| toDict $(varE x) |] + todictx_f <- [| ("forthcoming", JSON.JSBool True) : toDict $(varE x) |] +- let todict = FunD 'toDict [ Clause [ConP (mkName real_nm) [VarP x]] ++ let todict = FunD 'toDict [ Clause [myConP (mkName real_nm) [VarP x]] + (NormalB todictx_r) [] +- , Clause [ConP (mkName forth_nm) [VarP x]] ++ , Clause [myConP (mkName forth_nm) [VarP x]] + (NormalB todictx_f) [] + ] + fromdict = FunD 'fromDictWKeys [ Clause [VarP xs] +@@ -1136,9 +1136,9 @@ buildObjectWithForthcoming sname field_pfx fields = do + let forthPredDecls = [ SigD forthPredName + $ ArrowT `AppT` ConT name `AppT` ConT ''Bool + , FunD forthPredName +- [ Clause [ConP (mkName real_nm) [WildP]] ++ [ Clause [myConP (mkName real_nm) [WildP]] + (NormalB $ ConE 'False) [] +- , Clause [ConP (mkName forth_nm) [WildP]] ++ , Clause [myConP (mkName forth_nm) [WildP]] + (NormalB $ ConE 'True) [] + ] + ] +@@ -1412,9 +1412,9 @@ savePParamField fvar field = do + normalexpr <- saveObjectField actualVal field + -- we have to construct the block here manually, because we can't + -- splice-in-splice +- return $ CaseE (VarE fvar) [ Match (ConP 'Nothing []) ++ return $ CaseE (VarE fvar) [ Match (myConP 'Nothing []) + (NormalB (ConE '[])) [] +- , Match (ConP 'Just [VarP actualVal]) ++ , Match (myConP 'Just [VarP actualVal]) + (NormalB normalexpr) [] + ] + +@@ -1440,9 +1440,9 @@ fillParam sname field_pfx fields = do + -- due to apparent bugs in some older GHC versions, we need to add these + -- prefixes to avoid "binding shadows ..." errors + fbinds <- mapM (newName . ("f_" ++) . nameBase) fnames +- let fConP = ConP name_f (map VarP fbinds) ++ let fConP = myConP name_f (map VarP fbinds) + pbinds <- mapM (newName . ("p_" ++) . nameBase) pnames +- let pConP = ConP name_p (map VarP pbinds) ++ let pConP = myConP name_p (map VarP pbinds) + -- PartialParams instance -------- + -- fillParams + let fromMaybeExp fn pn = AppE (AppE (VarE 'fromMaybe) (VarE fn)) (VarE pn) +@@ -1462,7 +1462,7 @@ fillParam sname field_pfx fields = do + memptyClause = Clause [] (NormalB memptyExp) [] + -- mappend + pbinds2 <- mapM (newName . ("p2_" ++) . nameBase) pnames +- let pConP2 = ConP name_p (map VarP pbinds2) ++ let pConP2 = myConP name_p (map VarP pbinds2) + -- note the reversal of 'l' and 'r' in the call to <|> + -- as we want the result to be the rightmost value + let altExp = zipWith (\l r -> AppE (AppE (VarE '(<|>)) (VarE r)) (VarE l)) +@@ -1575,9 +1575,9 @@ genLoadExc tname sname opdefs = do + opdefs + -- the first function clause; we can't use [| |] due to TH + -- limitations, so we have to build the AST by hand +- let clause1 = Clause [ConP 'JSON.JSArray +- [ListP [ConP 'JSON.JSString [VarP exc_name], +- VarP exc_args]]] ++ let clause1 = Clause [myConP 'JSON.JSArray ++ [ListP [myConP 'JSON.JSString [VarP exc_name], ++ VarP exc_args]]] + (NormalB (CaseE (AppE (VarE 'JSON.fromJSString) + (VarE exc_name)) + (str_matches ++ [defmatch]))) [] +diff --git a/src/Ganeti/THH/Compat.hs b/src/Ganeti/THH/Compat.hs +index 1f51e49d7..9b07c47ef 100644 +--- a/src/Ganeti/THH/Compat.hs ++++ b/src/Ganeti/THH/Compat.hs +@@ -41,6 +41,7 @@ module Ganeti.THH.Compat + , myNotStrict + , nonUnaryTupE + , mkDoE ++ , myConP + ) where + + import Language.Haskell.TH +@@ -129,3 +130,11 @@ mkDoE s = + #else + DoE s + #endif ++ ++-- | ConP is now qualified with an optional [Type]. ++myConP :: Name -> [Pat] -> Pat ++myConP n patterns = ConP n ++#if MIN_VERSION_template_haskell(2,18,0) ++ [] ++#endif ++ patterns diff --git a/gnu/packages/virtualization.scm b/gnu/packages/virtualization.scm index 4ae0049269..5c5225b694 100644 --- a/gnu/packages/virtualization.scm +++ b/gnu/packages/virtualization.scm @@ -668,7 +668,13 @@ firmware blobs. You can "ganeti-shepherd-master-failover.patch" "ganeti-haskell-pythondir.patch" "ganeti-pyyaml-compat.patch" - "ganeti-disable-version-symlinks.patch")))) + "ganeti-procps-compat.patch" + "ganeti-disable-version-symlinks.patch" + "ganeti-lens-compat.patch" + "ganeti-template-haskell-2.17.patch" + "ganeti-template-haskell-2.18.patch" + "ganeti-reorder-arbitrary-definitions.patch" + "ganeti-relax-dependencies.patch")))) (build-system gnu-build-system) (arguments `(#:imported-modules (,@%gnu-build-system-modules From a71ce15c73b211512e7eafbe325894a2be98845f Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Thu, 7 Sep 2023 21:39:28 +0800 Subject: [PATCH 020/268] services: ganeti: Fix tests. * gnu/tests/ganeti.scm (run-ganeti-test)["force-start wconfd"]: Don't use INVOKE. ["gnt-os list"]: Import (ice-9 textual-ports). --- gnu/tests/ganeti.scm | 9 +++++---- 1 file changed, 5 insertions(+), 4 deletions(-) diff --git a/gnu/tests/ganeti.scm b/gnu/tests/ganeti.scm index b5624b7598..29eb354044 100644 --- a/gnu/tests/ganeti.scm +++ b/gnu/tests/ganeti.scm @@ -165,9 +165,9 @@ (marionette-eval '(begin (setenv "PATH" "/run/current-system/profile/bin") - (invoke "herd" "stop" "ganeti-wconfd") - (invoke "herd" "disable" "ganeti-wconfd") - (invoke "herd" "force-start" "ganeti-wconfd")) + (and (zero? (system* "herd" "stop" "ganeti-wconfd")) + (zero? (system* "herd" "disable" "ganeti-wconfd")) + (zero? (system* "herd" "force-start" "ganeti-wconfd")))) marionette)) ;; Verify that the cluster is healthy. @@ -230,7 +230,8 @@ "debootstrap+default\nguix+default\n" (marionette-eval '(begin - (use-modules (ice-9 popen)) + (use-modules (ice-9 popen) + (ice-9 textual-ports)) (let* ((port (open-pipe* OPEN_READ #$(file-append ganeti "/sbin/gnt-os") From 6add22db1e6ceebc987f9f1dce865a6a06d7e973 Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Thu, 7 Sep 2023 21:44:56 +0800 Subject: [PATCH 021/268] gnu: varnish: Update to 7.3.0. * gnu/packages/web.scm (varnish): Update to 7.3.0. --- 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 96dc5d9301..1b4eafeab8 100644 --- a/gnu/packages/web.scm +++ b/gnu/packages/web.scm @@ -6110,13 +6110,13 @@ deployments.") (package (name "varnish") (home-page "https://varnish-cache.org/") - (version "7.2.1") + (version "7.3.0") (source (origin (method url-fetch) (uri (string-append home-page "_downloads/varnish-" version ".tgz")) (sha256 (base32 - "0h590kr7rhp57a4kfx6apyvqk60w78qdjwpr6g2ikv5840bpv4sd")))) + "1rsay4vrg0dvf8d7bpj8dvaax4v949p6x1l6qd3hdabhq87bpnz2")))) (build-system gnu-build-system) (arguments `(#:configure-flags (list (string-append "LDFLAGS=-Wl,-rpath=" %output "/lib") From c14e115b8a927ffded33e5377b890d78672e9023 Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Thu, 7 Sep 2023 22:00:29 +0800 Subject: [PATCH 022/268] gnu: drbd-utils: Update to 9.25.0. * gnu/packages/cluster.scm (drbd-utils): Update to 9.25.0. --- gnu/packages/cluster.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/cluster.scm b/gnu/packages/cluster.scm index 6d10d73859..1b38015372 100644 --- a/gnu/packages/cluster.scm +++ b/gnu/packages/cluster.scm @@ -46,14 +46,14 @@ (define-public drbd-utils (package (name "drbd-utils") - (version "9.22.0") + (version "9.25.0") (source (origin (method url-fetch) (uri (list (string-append "https://pkg.linbit.com/downloads/drbd" "/utils/drbd-utils-" version ".tar.gz"))) (sha256 (base32 - "02zdfd9xg5xdxps2bg9ch3vkrs800whsycazkvgi29p80nihq1vm")) + "01vbghs4vyl3jvxkid59bqv73dya98k6jx5zhni2yx2xf8msynvf")) (modules '((guix build utils))) (snippet '(begin From 963abdf05de996f3f18133b8f06ab457ecdd1848 Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Thu, 7 Sep 2023 22:06:11 +0800 Subject: [PATCH 023/268] gnu: python-bitarray: Update to 2.8.1. * gnu/packages/python-xyz.scm (python-bitarray): Update to 2.8.1. --- 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 a3b7b9fa60..304258b811 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -2040,13 +2040,13 @@ and a list of words that are easier to remember for humans (the (define-public python-bitarray (package (name "python-bitarray") - (version "2.6.1") + (version "2.8.1") (source (origin (method url-fetch) (uri (pypi-uri "bitarray" version)) (sha256 (base32 - "0c4jli872nzix81n1xirnrghlq2fdsxb570d9rnfvxi1694sah44")))) + "1wy80bmhg33bpzn28g1n7s8r8f4drj7pcl4m2qb5sql8bbryx376")))) (build-system python-build-system) (arguments (list #:phases From 51939d19c14bbc755417d4a4ef98e21fd1b6d690 Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Thu, 7 Sep 2023 23:24:02 +0800 Subject: [PATCH 024/268] gnu: iputils: Update to 20221126. * gnu/packages/networking.scm (iputils): Update to 20221126. [source](patches): Remove. [arguments]: Remove obsolete phase. Disable one new test. [description]: Adjust for removed commands. * gnu/packages/patches/iputils-libcap-compat.patch: Delete file. * gnu/local.mk (dist_patch_DATA): Adjust accordingly. --- gnu/local.mk | 1 - gnu/packages/networking.scm | 39 ++++++------------- .../patches/iputils-libcap-compat.patch | 37 ------------------ 3 files changed, 12 insertions(+), 65 deletions(-) delete mode 100644 gnu/packages/patches/iputils-libcap-compat.patch diff --git a/gnu/local.mk b/gnu/local.mk index 8a3c93c1c1..b603e4a9c6 100644 --- a/gnu/local.mk +++ b/gnu/local.mk @@ -1416,7 +1416,6 @@ dist_patch_DATA = \ %D%/packages/patches/inkscape-poppler-compat.patch \ %D%/packages/patches/instead-use-games-path.patch \ %D%/packages/patches/intltool-perl-compatibility.patch \ - %D%/packages/patches/iputils-libcap-compat.patch \ %D%/packages/patches/irrlicht-use-system-libs.patch \ %D%/packages/patches/irrlicht-link-against-needed-libs.patch \ %D%/packages/patches/isl-0.11.1-aarch64-support.patch \ diff --git a/gnu/packages/networking.scm b/gnu/packages/networking.scm index dd3c7485d0..1403bab363 100644 --- a/gnu/packages/networking.scm +++ b/gnu/packages/networking.scm @@ -1564,35 +1564,25 @@ intended as a substitute for the PPPStatus and EthStatus projects.") (define-public iputils (package (name "iputils") - (version "20190709") + (version "20221126") (home-page "https://github.com/iputils/iputils") (source (origin (method git-fetch) - (uri (git-reference (url home-page) - (commit (string-append "s" version)))) + (uri (git-reference (url home-page) (commit version))) (file-name (git-file-name name version)) - (patches (search-patches "iputils-libcap-compat.patch")) (sha256 (base32 - "04bp4af15adp79ipxmiakfp0ij6hx5qam266flzbr94pr8z8l693")))) + "1qfdvr60mlwh5kr4p27wjknz1cvrwfi6iadh9ny45661v22i0njx")))) (build-system meson-build-system) (arguments - `(#:configure-flags '("-DBUILD_RARPD=true") - #:phases + `(#:phases (modify-phases %standard-phases - (add-after 'unpack 'fix-docbook-url - (lambda* (#:key inputs #:allow-other-keys) - (let* ((docbook-xsl (assoc-ref inputs "docbook-xsl")) - (uri (string-append docbook-xsl "/xml/xsl/docbook-xsl-" - ,(package-version docbook-xsl)))) - (for-each - (lambda (file) - (substitute* file - (("http://docbook\\.sourceforge\\.net/release/xsl-ns/current") - uri))) - (cons "doc/meson.build" - (find-files "doc" "\\.xsl$"))) - #t)))))) + (add-after 'unpack 'disable-ping-test + (lambda _ + ;; Disable ping test, as it requires root or raw socket capabilities. + (substitute* "test/meson.build" + (("if build_ping == true") + "if false"))))))) (native-inputs `(("gettext" ,gettext-minimal) ("pkg-config" ,pkg-config) @@ -1611,20 +1601,15 @@ configuration, troubleshooting, or servers. Utilities included are: @item @command{arping}: Ping hosts using the @dfn{Address Resolution Protocol}. @item @command{clockdiff}: Compute time difference between network hosts using ICMP TSTAMP messages. -@item @command{ninfod}: Daemon that responds to IPv6 Node Information Queries. @item @command{ping}: Use ICMP ECHO messages to measure round-trip delays and packet loss across network paths. -@item @command{rarpd}: Answer RARP requests from clients. -@item @command{rdisc}: Populate network routing tables with information from -the ICMP router discovery protocol. -@item @command{tftpd}: Trivial file transfer protocol server. @item @command{tracepath}: Trace network path to an IPv4 or IPv6 address and discover MTU along the way. @end itemize") ;; The various utilities are covered by different licenses, see LICENSE ;; for details. - (license (list license:gpl2+ ;arping, rarpd, tracepath - license:bsd-3 ;clockdiff, ninfod, ping, tftpd + (license (list license:gpl2+ ;arping, tracepath + license:bsd-3 ;clockdiff, ping (license:non-copyleft "https://spdx.org/licenses/Rdisc.html" "Sun Microsystems license, see rdisc.c for details"))))) diff --git a/gnu/packages/patches/iputils-libcap-compat.patch b/gnu/packages/patches/iputils-libcap-compat.patch deleted file mode 100644 index dc6da310ce..0000000000 --- a/gnu/packages/patches/iputils-libcap-compat.patch +++ /dev/null @@ -1,37 +0,0 @@ -Fix name clash with libcap 2.29. - -Taken from upstream: -https://github.com/iputils/iputils/commit/18f9a84e0e702841d6cc4d5f593de4fbd1348e83 - -diff --git a/ninfod/ninfod.c b/ninfod/ninfod.c ---- a/ninfod/ninfod.c -+++ b/ninfod/ninfod.c -@@ -455,7 +455,7 @@ static void do_daemonize(void) - /* --------- */ - #ifdef HAVE_LIBCAP - static const cap_value_t cap_net_raw = CAP_NET_RAW; --static const cap_value_t cap_setuid = CAP_SETUID; -+static const cap_value_t cap_setuserid = CAP_SETUID; - static cap_flag_value_t cap_ok; - #else - static uid_t euid; -@@ -487,7 +487,7 @@ static void limit_capabilities(void) - - cap_get_flag(cap_cur_p, CAP_SETUID, CAP_PERMITTED, &cap_ok); - if (cap_ok != CAP_CLEAR) -- cap_set_flag(cap_p, CAP_PERMITTED, 1, &cap_setuid, CAP_SET); -+ cap_set_flag(cap_p, CAP_PERMITTED, 1, &cap_setuserid, CAP_SET); - - if (cap_set_proc(cap_p) < 0) { - DEBUG(LOG_ERR, "cap_set_proc: %s\n", strerror(errno)); -@@ -520,8 +520,8 @@ static void drop_capabilities(void) - - /* setuid / setuid */ - if (cap_ok != CAP_CLEAR) { -- cap_set_flag(cap_p, CAP_PERMITTED, 1, &cap_setuid, CAP_SET); -- cap_set_flag(cap_p, CAP_EFFECTIVE, 1, &cap_setuid, CAP_SET); -+ cap_set_flag(cap_p, CAP_PERMITTED, 1, &cap_setuserid, CAP_SET); -+ cap_set_flag(cap_p, CAP_EFFECTIVE, 1, &cap_setuserid, CAP_SET); - - if (cap_set_proc(cap_p) < 0) { - DEBUG(LOG_ERR, "cap_set_proc: %s\n", strerror(errno)); From 0007b45437a3d1e5db2098b9954b83aa28dcb7f6 Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Thu, 7 Sep 2023 23:27:08 +0800 Subject: [PATCH 025/268] gnu: iputils: Use new style. * gnu/packages/networking.scm (iputils)[arguments]: Use G-expression. [native-inputs]: Remove labels. --- gnu/packages/networking.scm | 29 +++++++++++++++-------------- 1 file changed, 15 insertions(+), 14 deletions(-) diff --git a/gnu/packages/networking.scm b/gnu/packages/networking.scm index 1403bab363..b349bfe096 100644 --- a/gnu/packages/networking.scm +++ b/gnu/packages/networking.scm @@ -1575,21 +1575,22 @@ intended as a substitute for the PPPStatus and EthStatus projects.") "1qfdvr60mlwh5kr4p27wjknz1cvrwfi6iadh9ny45661v22i0njx")))) (build-system meson-build-system) (arguments - `(#:phases - (modify-phases %standard-phases - (add-after 'unpack 'disable-ping-test - (lambda _ - ;; Disable ping test, as it requires root or raw socket capabilities. - (substitute* "test/meson.build" - (("if build_ping == true") - "if false"))))))) + (list + #:phases + #~(modify-phases %standard-phases + (add-after 'unpack 'disable-ping-test + (lambda _ + ;; Disable ping test, as it requires root or raw socket capabilities. + (substitute* "test/meson.build" + (("if build_ping == true") + "if false"))))))) (native-inputs - `(("gettext" ,gettext-minimal) - ("pkg-config" ,pkg-config) - ("docbook-xsl" ,docbook-xsl) - ("docbook-xml" ,docbook-xml) - ("libxml2" ,libxml2) ;for XML_CATALOG_FILES - ("xsltproc" ,libxslt))) + (list gettext-minimal + pkg-config + docbook-xsl + docbook-xml + libxml2 ;for XML_CATALOG_FILES + libxslt)) (inputs (list libcap libidn2 openssl)) (synopsis "Collection of network utilities") From 41c7e74d970a19495f72be5148c906ab64e27f81 Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Fri, 8 Sep 2023 10:35:08 +0800 Subject: [PATCH 026/268] gnu: openvswitch: Update to 3.2.0. * gnu/packages/networking.scm (openvswitch): Update to 3.2.0. --- gnu/packages/networking.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/networking.scm b/gnu/packages/networking.scm index b349bfe096..6c22129a98 100644 --- a/gnu/packages/networking.scm +++ b/gnu/packages/networking.scm @@ -2754,7 +2754,7 @@ procedure calls (RPCs).") (define-public openvswitch (package (name "openvswitch") - (version "3.0.3") + (version "3.2.0") (source (origin (method url-fetch) (uri (string-append @@ -2762,7 +2762,7 @@ procedure calls (RPCs).") version ".tar.gz")) (sha256 (base32 - "0qwlpnwjcyb7fpw6yp65mdqg20i1851z70xmvzxwxwpifq56a1pm")))) + "1i0lb40lwbakmmqklmfcgr01l1ymsawgdi7k9a1zzp8ariw7x4ff")))) (build-system gnu-build-system) (arguments '(#:configure-flags From 0fbeeee7e9f173b9e3143eb460a1102b9ea71533 Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Fri, 8 Sep 2023 11:36:49 +0800 Subject: [PATCH 027/268] services: Open vSwitch: Depend on 'user-processes' target. * gnu/services/networking.scm (openvswitch-shepherd-service)[ovsdb](requirement): Add user-processes. --- gnu/services/networking.scm | 1 + 1 file changed, 1 insertion(+) diff --git a/gnu/services/networking.scm b/gnu/services/networking.scm index 5657b141d9..e2f6e6c0ca 100644 --- a/gnu/services/networking.scm +++ b/gnu/services/networking.scm @@ -1709,6 +1709,7 @@ simulation." (ovs-vswitchd (file-append package "/sbin/ovs-vswitchd"))) (list (shepherd-service (provision '(ovsdb)) + (requirement '(user-processes)) (documentation "Run the Open vSwitch database server.") (start #~(make-forkexec-constructor (list #$ovsdb-server "--pidfile" From 3228dcd7dbb532293d451d4d411df59f462e0287 Mon Sep 17 00:00:00 2001 From: Hilton Chain Date: Fri, 25 Aug 2023 16:59:36 +0800 Subject: [PATCH 028/268] gnu: font-chiron-sung-hk: Update to 1.010. * gnu/packages/fonts.scm (font-chiron-sung-hk): Update to 1.010. Signed-off-by: Efraim Flashner --- gnu/packages/fonts.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/fonts.scm b/gnu/packages/fonts.scm index 93c1308d54..c51679c273 100644 --- a/gnu/packages/fonts.scm +++ b/gnu/packages/fonts.scm @@ -3192,7 +3192,7 @@ dialects in Hong Kong and Taiwan."))) (define-public font-chiron-sung-hk (package (name "font-chiron-sung-hk") - (version "1.008") + (version "1.010") (source (origin (method git-fetch) (uri (git-reference @@ -3201,7 +3201,7 @@ dialects in Hong Kong and Taiwan."))) (file-name (git-file-name name version)) (sha256 (base32 - "19rabzmy4ywam4r5kgnqbgbmqzvhsagzddbyis5iicc6y8jrmd1j")))) + "065p1gc5xjwc4kfw8bqpsbhaf1p4w0k4l0j04vjsjhcl4k9vyvfz")))) (build-system font-build-system) (home-page "https://chiron-fonts.github.io/") (synopsis "Traditional Chinese Song typeface") From e65ae376715676c39c70cad58a3c7803192cfcc6 Mon Sep 17 00:00:00 2001 From: Michael Ford Date: Tue, 22 Aug 2023 11:59:29 +0100 Subject: [PATCH 029/268] gnu: libupnp: Update to 1.14.18. * gnu/packages/upnp.scm (libupnp): Update to 1.14.18. Signed-off-by: Efraim Flashner --- gnu/packages/upnp.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/upnp.scm b/gnu/packages/upnp.scm index bc93f51563..1602136e29 100644 --- a/gnu/packages/upnp.scm +++ b/gnu/packages/upnp.scm @@ -96,14 +96,14 @@ over IRC, instant messaging, network games, and most server software.") (define-public libupnp (package (name "libupnp") - (version "1.14.17") + (version "1.14.18") (source (origin (method url-fetch) (uri (string-append "https://github.com/pupnp/pupnp/releases/download" "/release-" version "/libupnp-" version".tar.bz2")) (sha256 - (base32 "1yvgrfdhvsz6br3i7k37pigcw25rnzkxdx4sjizqqhm0xd1751wv")))) + (base32 "1sywi1l0sc9s55hryfwqb5y5fhyyqx6ida5i7bk8m1p27klwx9qn")))) (native-inputs (list pkg-config)) (build-system gnu-build-system) From 45af7b89239d4bbdc145a5c9cc03356f31d5a20e Mon Sep 17 00:00:00 2001 From: Andy Tai Date: Fri, 25 Aug 2023 20:57:11 -0700 Subject: [PATCH 030/268] gnu: parallel: Update to 20230822. * gnu/packages/parallel.scm (parallel): Update to 20230822. Signed-off-by: Efraim Flashner --- gnu/packages/parallel.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/parallel.scm b/gnu/packages/parallel.scm index 569e98430c..a2d63b0be7 100644 --- a/gnu/packages/parallel.scm +++ b/gnu/packages/parallel.scm @@ -64,14 +64,14 @@ (define-public parallel (package (name "parallel") - (version "20230622") + (version "20230822") (source (origin (method url-fetch) (uri (string-append "mirror://gnu/parallel/parallel-" version ".tar.bz2")) (sha256 - (base32 "13i3himpq1gzhn3b0hl8vp34kz950ql9pssw251ad611f2nj8fny")) + (base32 "0ppwdgp9j7r0a5l5zb0mla70jq24wmy1n33b5naw44y1lfclanab")) (snippet '(begin (use-modules (guix build utils)) From 05f44bbeb40686599827cbe0df7fcc80122fe152 Mon Sep 17 00:00:00 2001 From: "Paul A. Patience" Date: Fri, 2 Sep 2022 20:34:29 +0000 Subject: [PATCH 031/268] gnu: Add asli. MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * gnu/packages/graphics.scm (asli): New variable. * gnu/packages/patches/asli-use-system-libs.patch: New file. * gnu/local.mk (dist_patch_DATA): Register patch. Signed-off-by: Ludovic Courtès --- gnu/local.mk | 1 + gnu/packages/graphics.scm | 74 +++++++++++++++++++ .../patches/asli-use-system-libs.patch | 72 ++++++++++++++++++ 3 files changed, 147 insertions(+) create mode 100644 gnu/packages/patches/asli-use-system-libs.patch diff --git a/gnu/local.mk b/gnu/local.mk index b603e4a9c6..4f8637418a 100644 --- a/gnu/local.mk +++ b/gnu/local.mk @@ -913,6 +913,7 @@ dist_patch_DATA = \ %D%/packages/patches/apr-skip-getservbyname-test.patch \ %D%/packages/patches/ark-skip-xar-test.patch \ %D%/packages/patches/arpack-ng-propagate-rng-state.patch \ + %D%/packages/patches/asli-use-system-libs.patch \ %D%/packages/patches/aspell-CVE-2019-25051.patch \ %D%/packages/patches/aspell-default-dict-dir.patch \ %D%/packages/patches/ath9k-htc-firmware-binutils.patch \ diff --git a/gnu/packages/graphics.scm b/gnu/packages/graphics.scm index 24ed547782..8edc93f702 100644 --- a/gnu/packages/graphics.scm +++ b/gnu/packages/graphics.scm @@ -2655,6 +2655,80 @@ anything from rendering scalable icons in an editor application to prototyping a game.") (license license:zlib)))) +(define-public asli + (package + (name "asli") + (version "0.1") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/tpms-lattice/ASLI") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 "02hwdavpsy3vmivd6prp03jn004ykrl11lbkvksy5i2zm38zbknr")) + (patches (search-patches "asli-use-system-libs.patch")) + (modules '((guix build utils))) + (snippet + ;; Remove bundled libraries except (the ones missing from Guix and) + ;; KU Leuven's mTT, which is an obscure (i.e., unfindable by searching + ;; online for “mTT KU Leuven”), BSD-3 licensed, header-only library. + #~(begin + ;;(delete-file-recursively "libs/AdaptTools") ; Missing from Guix + (delete-file-recursively "libs/CGAL") + ;;(delete-file-recursively "libs/alglib") ; Missing from Guix + (delete-file-recursively "libs/eigen") + (delete-file-recursively "libs/mmg") + ;;(delete-file-recursively "libs/tetgen") ; Missing from Guix + (delete-file-recursively "libs/yaml"))))) + (build-system cmake-build-system) + (inputs + (list boost + cgal + eigen + gmp + `(,mmg "lib") + mpfr + tbb-2020 + yaml-cpp)) + (arguments + (list #:tests? #f ; No tests + #:configure-flags + #~(list "-DCGAL_ACTIVATE_CONCURRENT_MESH_3=ON" + (string-append "-DEIGEN3_INCLUDE_DIR=" + #$(this-package-input "eigen") + "/include/eigen3") + (string-append "-DMMG_INCLUDE_DIR=" + (ungexp (this-package-input "mmg") "lib") + "/include") + (string-append "-DMMG_LIBRARY_DIR=" + (ungexp (this-package-input "mmg") "lib") + "/lib")) + #:phases + #~(modify-phases %standard-phases + (replace 'install ; No install phase + (lambda _ + (with-directory-excursion "../source/bin" + (install-file "ASLI" (string-append #$output "/bin")) + ;; The manual is included in the repository. + ;; Building it requires -DASLI_DOC=ON, but this is marked + ;; as unsupported (presumably for users). + ;; Besides, some of the LaTeX packages it uses are + ;; missing from Guix, for example emptypage, fvextra and + ;; menukeys. + (install-file "docs/ASLI [User Manual].pdf" + (string-append #$output "/share/doc/" + #$name "-" #$version)))))))) + (home-page "http://www.biomech.ulg.ac.be/ASLI/") + (synopsis "Create lattice infills with varying unit cell type, size and feature") + (description "ASLI (A Simple Lattice Infiller) is a command-line tool that +allows users to fill any 3D geometry with a functionally graded lattice. The +lattice infill is constructed out of unit cells, described by implicit +functions, whose type, size and feature can be varied locally to obtain the +desired local properties.") + (license license:agpl3+))) + (define-public f3d (package (name "f3d") diff --git a/gnu/packages/patches/asli-use-system-libs.patch b/gnu/packages/patches/asli-use-system-libs.patch new file mode 100644 index 0000000000..6c4518e04e --- /dev/null +++ b/gnu/packages/patches/asli-use-system-libs.patch @@ -0,0 +1,72 @@ +Adjust CMakeLists.txt to use system-provided mmg and yaml-cpp libraries. + +diff --git a/CMakeLists.txt b/CMakeLists.txt +index b11c5ba..702423e 100755 +--- a/CMakeLists.txt ++++ b/CMakeLists.txt +@@ -122,28 +122,8 @@ if(MMG_MESH) + add_definitions(-DMMG_MESH) + + # MMG +- set(MMG_PREFIX mmg3d) +- set(MMG_PREFIX_DIR ${CMAKE_CURRENT_BINARY_DIR}/${MMG_PREFIX}) +- set(MMG_INSTALL_DIR ${CMAKE_CURRENT_BINARY_DIR}/${MMG_PREFIX}) +- ExternalProject_Add(${MMG_PREFIX} +- PREFIX ${MMG_PREFIX_DIR} +- SOURCE_DIR ${CMAKE_CURRENT_SOURCE_DIR}/libs/mmg +- +- BUILD_ALWAYS OFF +- INSTALL_DIR ${MMG_INSTALL_DIR} +- +- CMAKE_ARGS(-DCMAKE_BUILD_TYPE=Release -DBUILD=MMG3D -DLIBMMG3D_STATIC=ON +- -DLIBMMG3D_SHARED=OFF -DCMAKE_INSTALL_PREFIX=) +- +- BUILD_COMMAND make +- INSTALL_COMMAND make install +- ) +- set(MMG3D_INCLUDE_DIRS "${MMG_INSTALL_DIR}/include") +- set(MMG3D_LIBRARIES "${MMG_INSTALL_DIR}/${CMAKE_INSTALL_LIBDIR}/${CMAKE_STATIC_LIBRARY_PREFIX}${MMG_PREFIX}${CMAKE_STATIC_LIBRARY_SUFFIX}") +- +- include_directories(${MMG3D_INCLUDE_DIRS}) +- #add_library(MMG3D STATIC IMPORTED) +- #set_target_properties(MMG3D PROPERTIES IMPORTED_LOCATION "${MMG3D_LIBRARIES}") ++ include_directories(${MMG_INCLUDE_DIR}) ++ set(MMG3D_LIBRARIES ${MMG_LIBRARY_DIR}/libmmg3d.so) + + # MshMet + set(MSHMET_PREFIX mshmet) +@@ -192,14 +172,8 @@ target_include_directories(tet PUBLIC ${CMAKE_CURRENT_SOURCE_DIR}/libs/tetgen) + target_compile_definitions(tet PUBLIC TETLIBRARY) # -DTETLIBRARY: flag to compile tetgen as a library + + # yaml +-file(GLOB yaml_SRC CONFIGURE_DEPENDS ${CMAKE_CURRENT_SOURCE_DIR}/libs/yaml/src/*.cpp) # Using file GLOB is not recomended! +-add_library(yaml STATIC) +-target_include_directories(yaml +- PUBLIC ${CMAKE_CURRENT_SOURCE_DIR}/libs/yaml/include +- PRIVATE ${CMAKE_CURRENT_SOURCE_DIR}/libs/yaml/src +-) +-target_sources(yaml PRIVATE ${yaml_SRC}) +-set_target_properties(yaml PROPERTIES CXX_STANDARD 11) ++find_package(yaml-cpp REQUIRED) ++include_directories(${YAML_CPP_INCLUDE_DIRS}) + + # Compile options for debuging + if(CMAKE_BUILD_TYPE MATCHES Debug) +@@ -259,7 +233,7 @@ if(MARCH_NATIVE) + endif() + + # Create entries for C++ files in "ASLI" routine +-target_link_libraries(ASLI PUBLIC alg tet yaml) ++target_link_libraries(ASLI PUBLIC alg tet ${YAML_CPP_LIBRARIES}) + if(NOT MSVC) + target_link_libraries(ASLI PUBLIC stdc++fs) + endif() +@@ -272,7 +246,7 @@ if(CGAL_MESH) + endif() + + if(MMG_MESH) +- add_dependencies(ASLI ${MMG_PREFIX} ${MSHMET_PREFIX}) ++ add_dependencies(ASLI ${MSHMET_PREFIX}) + target_link_libraries(ASLI PUBLIC ${MMG3D_LIBRARIES} ${MSHMET_LIBRARIES}) + if(SCOTCH_FOUND) + target_link_libraries(ASLI PUBLIC ${SCOTCH_LIBRARIES} scotch) From 96eda590e1eb288359532d92bbfc4795c60f3df5 Mon Sep 17 00:00:00 2001 From: Maxime Devos Date: Mon, 21 Aug 2023 15:59:53 +0200 Subject: [PATCH 032/268] lint: Check that (cc-for-target) and friends are used. MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit "CC=gcc" is almost always incorrect; people often just don't notice the incorrectness because they are compiling natively. For an exception, see tzdata. "guix style" partially made things worse, so I partially ignored it. * guix/lint.scm (check-compiler-for-target): New linter. * tests/lint.scm ("compiler-for-target: unconditional CC=gcc is unacceptable") ("compiler-for-target: looks through G-expressions") ("compiler-for-target: (cc-for-target) is acceptable") ("compiler-for-target: CC=gcc is acceptable when target=#false"): Test it. Signed-off-by: Ludovic Courtès --- guix/lint.scm | 56 +++++++++++++++++++++++++++++++++++++++++++++++++- tests/lint.scm | 32 ++++++++++++++++++++++++++++- 2 files changed, 86 insertions(+), 2 deletions(-) diff --git a/guix/lint.scm b/guix/lint.scm index d173563e51..7ccf52dec1 100644 --- a/guix/lint.scm +++ b/guix/lint.scm @@ -12,7 +12,7 @@ ;;; Copyright © 2020 Chris Marusich ;;; Copyright © 2020 Timothy Sample ;;; Copyright © 2021 Xinglu Chen -;;; Copyright © 2021, 2022 Maxime Devos +;;; Copyright © 2021-2023 Maxime Devos ;;; Copyright © 2021 Brice Waegeneire ;;; ;;; This file is part of GNU Guix. @@ -114,6 +114,7 @@ check-profile-collisions check-haskell-stackage check-tests-true + check-compiler-for-target lint-warning lint-warning? @@ -311,6 +312,55 @@ superfluous when building natively and incorrect when cross-compiling." #:field 'arguments)) '())) +(define (check-compiler-for-target package) + "Check that cross-compilers are used when cross-compiling, by inspecting +#:make-flags." + (define (make-compiler-warning variable=value) + (define =-index (string-index variable=value #\=)) + (define variable (substring variable=value 0 =-index)) + (define value (substring variable=value (+ =-index 1))) + (make-warning package + (G_ "'~0@*~a' should be set to '~1@*~a' instead of '~2@*~a'") + (list variable + (match variable + ("AR" "(ar-for-target)") + ("AS" "(as-for-target)") + ("CC" "(cc-for-target)") + ("CXX" "(cxx-for-target)") + ("LD" "(ld-for-target)") + ("PKG_CONFIG" "(pkg-config-for-target)")) + value) + #:field 'arguments)) + (define (find-incorrect-compilers l) + (match l + ((or "AR=ar" + "AS=as" + ;; 'cc' doesn't actually exist in Guix, but if it did, + ;; it would be incorrect to use it w.r.t. cross-compilation. + "CC=cc" "CC=gcc" "CC=clang" + "CXX=g++" + "LD=ld" + "PKG_CONFIG=pkg-config") + (list (make-compiler-warning l))) + ((x . y) + (append (find-incorrect-compilers x) + (find-incorrect-compilers y))) + (_ '()))) + (parameterize ((%current-target-system "aarch64-linux-gnu")) + (apply (lambda* (#:key (target 'not-set) + make-flags #:allow-other-keys) + (define make-flags/sexp + (if (gexp? make-flags/sexp) + (gexp->approximate-sexp make-flags) + make-flags)) + ;; Some packages like 'tzdata' are never cross-compiled; + ;; the compilers are only used to build tools for + ;; compiling the rest of the package. + (if (eq? target '#false) + '() + (find-incorrect-compilers make-flags/sexp))) + (package-arguments package)))) + (define (properly-starts-sentence? s) (string-match "^[(\"'`[:upper:][:digit:]]" s)) @@ -1864,6 +1914,10 @@ them for PACKAGE." (name 'tests-true) (description "Check if tests are explicitly enabled") (check check-tests-true)) + (lint-checker + (name 'compiler-for-target) + (description "Check that cross-compilers are used when cross-compiling") + (check check-compiler-for-target)) (lint-checker (name 'description) (description "Validate package descriptions") diff --git a/tests/lint.scm b/tests/lint.scm index b91bd053c5..a52a82237b 100644 --- a/tests/lint.scm +++ b/tests/lint.scm @@ -10,7 +10,7 @@ ;;; Copyright © 2020 Timothy Sample ;;; Copyright © 2020 Tobias Geerinckx-Rice ;;; Copyright © 2021 Xinglu Chen -;;; Copyright © 2021 Maxime Devos +;;; Copyright © 2021, 2023 Maxime Devos ;;; ;;; This file is part of GNU Guix. ;;; @@ -342,6 +342,36 @@ `(#:tests? ,(not (%current-target-system))))))) (check-tests-true pkg))) +(test-equal "compiler-for-target: unconditional CC=gcc is unacceptable" + "'CC' should be set to '(cc-for-target)' instead of 'gcc'" + (single-lint-warning-message + (check-compiler-for-target + (dummy-package "x" (arguments '(#:make-flags '("CC=gcc"))))))) + + +(test-equal "compiler-for-target: looks through G-expressions" + "'CC' should be set to '(cc-for-target)' instead of 'gcc'" + (single-lint-warning-message + (check-compiler-for-target + (dummy-package "x" (arguments '(#:make-flags #~'("CC=gcc"))))))) + +(test-equal "compiler-for-target: (cc-for-target) is acceptable" + '() + (check-compiler-for-target + (dummy-package "x" + (arguments + (list #:make-flags + #~(list (string-append "CC=" (cc-for-target)))))))) + +(test-equal "compiler-for-target: CC=gcc is acceptable when target=#false" + '() + (check-compiler-for-target + ;; This (dummy) package consists purely of architecture-independent data. + (dummy-package "tzdata" + (arguments + (list #:target #false + #:make-flags #~(list "CC=gcc")))))) + ;; The emacs-build-system sets #:tests? #f by default. (test-equal "tests-true: #:tests? #t acceptable for emacs packages" '() From d936ed6f084ac68507b322b93558e97c586f587a Mon Sep 17 00:00:00 2001 From: "Artyom V. Poptsov" Date: Tue, 15 Aug 2023 23:39:25 +0300 Subject: [PATCH 033/268] gnu: guile-dsv: Update to 0.7.0. MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * gnu/packages/guile-xyz.scm (guile-dsv): Update to 0.7.0. Improve the package style. [inputs]: Add "bash-minimal". [native-inputs]: Add "guile-smc". [description}: Update. (guile2.2-dsv) [inputs]: Add "bash-minimal". Signed-off-by: Ludovic Courtès --- gnu/packages/guile-xyz.scm | 44 ++++++++++++++++++++++---------------- 1 file changed, 25 insertions(+), 19 deletions(-) diff --git a/gnu/packages/guile-xyz.scm b/gnu/packages/guile-xyz.scm index 123845a3f1..5c6b106001 100644 --- a/gnu/packages/guile-xyz.scm +++ b/gnu/packages/guile-xyz.scm @@ -728,7 +728,7 @@ you send to a FIFO file.") (define-public guile-dsv (package (name "guile-dsv") - (version "0.6.0") + (version "0.7.0") (source (origin (method git-fetch) (uri (git-reference @@ -737,12 +737,17 @@ you send to a FIFO file.") (file-name (string-append name "-" version "-checkout")) (sha256 (base32 - "0llivcgb7idglsapcmvb2qscds7768f2xfgr4lns8mzl2xf5hwvv")))) + "0shrzmbh6x3n3xzpcijkxk3f73z6m1i50zgc2dnnccwf4j1c78p2")))) (build-system gnu-build-system) - (native-inputs - (list autoconf automake pkg-config texinfo help2man)) - (inputs (list guile-3.0)) - (propagated-inputs (list guile-lib)) + (native-inputs (list autoconf + automake + pkg-config + texinfo + help2man + ;; needed when cross-compiling. + guile-smc)) + (inputs (list bash-minimal guile-3.0)) + (propagated-inputs (list guile-lib guile-smc)) (arguments `(#:modules (((guix build guile-build-system) #:select (target-guile-effective-version)) @@ -756,31 +761,32 @@ you send to a FIFO file.") (bin (string-append out "/bin")) (guile-lib (assoc-ref inputs "guile-lib")) (version (target-guile-effective-version)) - (scm (string-append "/share/guile/site/" - version)) - (go (string-append "/lib/guile/" - version "/site-ccache"))) + (scm (string-append "/share/guile/site/" version)) + (go (string-append "/lib/guile/" version + "/site-ccache"))) (wrap-program (string-append bin "/dsv") `("GUILE_LOAD_PATH" prefix - (,(string-append out scm) - ,(string-append guile-lib scm))) + (,(string-append out scm) ,(string-append + guile-lib scm))) `("GUILE_LOAD_COMPILED_PATH" prefix - (,(string-append out go) - ,(string-append guile-lib go))))) - #t))))) + (,(string-append out go) ,(string-append guile-lib + go))))) #t))))) (home-page "https://github.com/artyom-poptsov/guile-dsv") (synopsis "DSV module for Guile") (description - "Guile-DSV is a GNU Guile module for working with the -delimiter-separated values (DSV) data format. Guile-DSV supports the -Unix-style DSV format and RFC 4180 format.") + "Guile-DSV is a GNU Guile module for working with the delimiter-separated +values (DSV) data format. Guile-DSV supports the Unix-style DSV format and RFC 4180 +style format. Also Guile-DSV includes a console program named @code{dsv} that allows +to view and process DSV data, including such operations as delimiter change, +conversion from one DSV standard to another and printing the data as pseudographics +tables.") (license license:gpl3+))) (define-public guile2.2-dsv (package (inherit guile-dsv) (name "guile2.2-dsv") - (inputs (list guile-2.2)) + (inputs (list bash-minimal guile-2.2)) (propagated-inputs `(("guile-lib" ,guile2.2-lib))))) (define-public guile-fibers-1.3 From 23cbb464abbaf35463e41885ac5ea6fb7876845f Mon Sep 17 00:00:00 2001 From: "Artyom V. Poptsov" Date: Wed, 23 Aug 2023 21:12:55 +0300 Subject: [PATCH 034/268] gnu: guile-smc: Fix build with Guile 2.2. MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * gnu/packages/guile-xyz.scm (guile-smc): Fix build with Guile 2.2. [native-inputs]: Replace "guile" with "guile-2.2" and "guile-lib" with "guile2.2-lib". Signed-off-by: Ludovic Courtès --- gnu/packages/guile-xyz.scm | 3 +++ 1 file changed, 3 insertions(+) diff --git a/gnu/packages/guile-xyz.scm b/gnu/packages/guile-xyz.scm index 5c6b106001..16c59948b3 100644 --- a/gnu/packages/guile-xyz.scm +++ b/gnu/packages/guile-xyz.scm @@ -5419,6 +5419,9 @@ with a FSM is being built (for example, from a Makefile.)") (package (inherit guile-smc) (name "guile2.2-smc") + (native-inputs (modify-inputs (package-native-inputs guile-smc) + (replace "guile" guile-2.2) + (replace "guile-lib" guile2.2-lib))) (inputs (modify-inputs (package-inputs guile-smc) (replace "guile" guile-2.2) (replace "guile-lib" guile2.2-lib))))) From 470ebff87b21d7673c82203f679f0dcfe5e8d284 Mon Sep 17 00:00:00 2001 From: "Artyom V. Poptsov" Date: Wed, 23 Aug 2023 21:17:02 +0300 Subject: [PATCH 035/268] gnu: guile2.2-dsv: Fix build. MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * gnu/packages/guile-xyz.scm (guile2.2-dsv): [native-inputs]: Replace "guile-smc" with "guile2.2-smc" and add "guile2.2-lib". [inputs]: Replace "guile" with "guile-2.2" and "guile-smc" with "guile2.2-smc". [propagated-inputs]: Replace "guile-lib" with "guile2.2-lib" and "guile-smc" with "guile2.2-smc". Signed-off-by: Ludovic Courtès --- gnu/packages/guile-xyz.scm | 11 +++++++++-- 1 file changed, 9 insertions(+), 2 deletions(-) diff --git a/gnu/packages/guile-xyz.scm b/gnu/packages/guile-xyz.scm index 16c59948b3..25fb76ba31 100644 --- a/gnu/packages/guile-xyz.scm +++ b/gnu/packages/guile-xyz.scm @@ -786,8 +786,15 @@ tables.") (package (inherit guile-dsv) (name "guile2.2-dsv") - (inputs (list bash-minimal guile-2.2)) - (propagated-inputs `(("guile-lib" ,guile2.2-lib))))) + (native-inputs (modify-inputs (package-native-inputs guile-dsv) + (replace "guile-smc" guile2.2-smc) + (append guile2.2-lib))) + (inputs (modify-inputs (package-inputs guile-dsv) + (replace "guile" guile-2.2) + (replace "guile-lib" guile2.2-lib))) + (propagated-inputs (modify-inputs (package-propagated-inputs guile-dsv) + (replace "guile-lib" guile2.2-lib) + (replace "guile-smc" guile2.2-smc))))) (define-public guile-fibers-1.3 (package From f4f92dd778574305608a02162026e3d5f575daf8 Mon Sep 17 00:00:00 2001 From: "Artyom V. Poptsov" Date: Wed, 23 Aug 2023 21:28:37 +0300 Subject: [PATCH 036/268] gnu: guile-dsv: Fix cross-compiling. MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * gnu/packages/guile-xyz.scm (guile-dsv): Fix cross-compiling. [native-inputs]: Add "guile-3.0" and "guile-lib". (guile2.2-dsv) [native-inputs]: Replace "guile" with "guile-2.2" and "guile-lib" with "guile2.2-lib". Signed-off-by: Ludovic Courtès --- gnu/packages/guile-xyz.scm | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/gnu/packages/guile-xyz.scm b/gnu/packages/guile-xyz.scm index 25fb76ba31..b40079c383 100644 --- a/gnu/packages/guile-xyz.scm +++ b/gnu/packages/guile-xyz.scm @@ -745,6 +745,8 @@ you send to a FIFO file.") texinfo help2man ;; needed when cross-compiling. + guile-3.0 + guile-lib guile-smc)) (inputs (list bash-minimal guile-3.0)) (propagated-inputs (list guile-lib guile-smc)) @@ -788,7 +790,8 @@ tables.") (name "guile2.2-dsv") (native-inputs (modify-inputs (package-native-inputs guile-dsv) (replace "guile-smc" guile2.2-smc) - (append guile2.2-lib))) + (replace "guile" guile-2.2) + (replace "guile-lib" guile2.2-lib))) (inputs (modify-inputs (package-inputs guile-dsv) (replace "guile" guile-2.2) (replace "guile-lib" guile2.2-lib))) From 4dd33fc62899134606f36f92594cf160b972f685 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ludovic=20Court=C3=A8s?= Date: Fri, 8 Sep 2023 18:48:11 +0200 Subject: [PATCH 037/268] gnu: shepherd: Switch back to Fibers 1.1 on Arm machines. MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Fixes . * gnu/packages/admin.scm (shepherd-0.10)[native-inputs]: Use GUILE-FIBERS-1.1 when ‘target-arm?’ is true. Reported-by: Timotej Lazar Reported-by: Liliana Marie Prikler Reported-by: Denis 'GNUtoo' Carikli --- gnu/packages/admin.scm | 13 +++++++++++-- 1 file changed, 11 insertions(+), 2 deletions(-) diff --git a/gnu/packages/admin.scm b/gnu/packages/admin.scm index 604cd70c02..5d586e6f36 100644 --- a/gnu/packages/admin.scm +++ b/gnu/packages/admin.scm @@ -385,9 +385,18 @@ interface and is based on GNU Guile.") (base32 "0v9ld9gbqdp5ya380fbkdsxa0iqr90gi6yk004ccz3n792nq6wlj")))) (native-inputs (modify-inputs (package-native-inputs shepherd-0.9) - (replace "guile-fibers" guile-fibers-1.3))) + (replace "guile-fibers" + ;; Work around + ;; . This + ;; affects any system without a functional real-time + ;; clock (RTC), but in practice these are typically Arm + ;; single-board computers. + (if (target-arm?) + guile-fibers-1.1 + guile-fibers-1.3)))) (inputs (modify-inputs (package-inputs shepherd-0.9) - (replace "guile-fibers" guile-fibers-1.3))))) + (replace "guile-fibers" + (this-package-native-input "guile-fibers")))))) (define-public shepherd shepherd-0.9) From 1ef4974be94d75d935d98399dcda44199a1fca47 Mon Sep 17 00:00:00 2001 From: Janneke Nieuwenhuizen Date: Wed, 6 Sep 2023 10:52:17 +0200 Subject: [PATCH 038/268] guix: shell: Don't whitelist / by typo in `shell-authorized-directories'. Fixes . * guix/scripts/shell.scm (authorized-shell-directory?): After warning, continue LOOP to return valid query result for DIRECTORY. --- guix/scripts/shell.scm | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/guix/scripts/shell.scm b/guix/scripts/shell.scm index d67152cef7..83888eee1d 100644 --- a/guix/scripts/shell.scm +++ b/guix/scripts/shell.scm @@ -1,5 +1,6 @@ ;;; GNU Guix --- Functional package management for GNU ;;; Copyright © 2021-2023 Ludovic Courtès +;;; Copyright © 2023 Janneke Nieuwenhuizen ;;; ;;; This file is part of GNU Guix. ;;; @@ -232,7 +233,8 @@ a hash-prefixed comment, or a blank line." (port-line port) (port-column port)))) (warning loc (G_ "ignoring invalid file name: '~a'~%") - line)))))))))) + line) + (loop)))))))))) (const #f))) (define (options-with-caching opts) From e2e5df596f5e682d78043b12463cc47d14291ba9 Mon Sep 17 00:00:00 2001 From: Janneke Nieuwenhuizen Date: Fri, 8 Sep 2023 23:09:11 +0200 Subject: [PATCH 039/268] gnu: dezyne: Update to 2.17.6. * gnu/packages/dezyne.scm (dezyne): Update to 2.17.6. --- gnu/packages/dezyne.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/dezyne.scm b/gnu/packages/dezyne.scm index 23b51274a5..db3523ac3e 100644 --- a/gnu/packages/dezyne.scm +++ b/gnu/packages/dezyne.scm @@ -32,14 +32,14 @@ (define-public dezyne (package (name "dezyne") - (version "2.17.5") + (version "2.17.6") (source (origin (method url-fetch) (uri (string-append "https://dezyne.org/download/dezyne/" name "-" version ".tar.gz")) (sha256 - (base32 "15jhi17f0aqnlznvpf6lkz2y837xkzf8chi9rhhb55920vqf6cgg")))) + (base32 "0z019yyvf1ac1l95j29wlayi2gmwa9sjqg31a4r89za1bijmk19k")))) (inputs (list bash-minimal guile-3.0-latest guile-json-4 From 12d8efb1a98a803c4de4368cb0890dbffeb2f619 Mon Sep 17 00:00:00 2001 From: Liliana Marie Prikler Date: Sat, 2 Sep 2023 08:52:02 +0200 Subject: [PATCH 040/268] gnu: capypdf: Update to 0.5.0. MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * gnu/packages/pdf.scm (capypdf): Update to 0.5.0. [arguments]<#:configure-flags>: Add “-Dcpp_std=c++23” <#:phases>: Drop ‘add-missing-header’. --- gnu/packages/pdf.scm | 10 +++------- 1 file changed, 3 insertions(+), 7 deletions(-) diff --git a/gnu/packages/pdf.scm b/gnu/packages/pdf.scm index e270bdf27f..b71add6f25 100644 --- a/gnu/packages/pdf.scm +++ b/gnu/packages/pdf.scm @@ -117,7 +117,7 @@ (define-public capypdf (package (name "capypdf") - (version "0.4.0") + (version "0.5.0") (source (origin (method git-fetch) (uri (git-reference @@ -125,18 +125,14 @@ (commit version))) (file-name (git-file-name name version)) (sha256 - (base32 "1kn46n3j5fygivmd6ldnv8vdwfv48ffaizq61yy4z9w2jm6fgxim")))) + (base32 "1mb3i0jq04gg5cm1l07mn9kal5s748miql97j6fpaf1x1j2lcrsx")))) (build-system meson-build-system) (arguments (list #:meson meson/newer + #:configure-flags #~(list "-Dcpp_std=c++23") #:test-options '(list "plainc") #:phases #~(modify-phases %standard-phases - (add-after 'unpack 'add-missing-header - (lambda _ - (substitute* "src/pdfgen.cpp" - (("#include " all) - (string-append all "\n#include "))))) (add-after 'unpack 'fix-glib-application-flags (lambda _ ;; XXX: remove when bumping glib From db61bdd7f52270a35bd0a3a88650d98276dab20b Mon Sep 17 00:00:00 2001 From: Liliana Marie Prikler Date: Sat, 2 Sep 2023 15:11:24 +0200 Subject: [PATCH 041/268] gnu: portfolio: Update to 1.0.0. MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * gnu/packages/gnome-xyz.scm (portfolio): Update to 1.0.0. [#:phases]: Add ‘skip-gtk-update-icon-cache’. [inputs]: Replace gtk+ with gtk. Replace libhandy with libadwaita. [native-inputs]: Remove gtk+:bin. Add pkg-config. --- gnu/packages/gnome-xyz.scm | 12 ++++++++---- 1 file changed, 8 insertions(+), 4 deletions(-) diff --git a/gnu/packages/gnome-xyz.scm b/gnu/packages/gnome-xyz.scm index 6ba0ee0092..8b5dc3030e 100644 --- a/gnu/packages/gnome-xyz.scm +++ b/gnu/packages/gnome-xyz.scm @@ -484,7 +484,7 @@ takes advantage of modern hardware using OpenGL.") (define-public portfolio (package (name "portfolio") - (version "0.9.14") + (version "1.0.0") (source (origin (method git-fetch) (uri (git-reference @@ -493,7 +493,7 @@ takes advantage of modern hardware using OpenGL.") (file-name (git-file-name name version)) (sha256 (base32 - "0h09v8lhz3kv6qmwjhx3gr7rp6ccfhrzm54gjnaixl4dcg9zddls")))) + "1ai9mx801m5lngkljg42vrpvhbvc3071sp4jypsvbzw55hxnn5ba")))) (arguments (list #:glib-or-gtk? #t #:imported-modules `(,@%meson-build-system-modules @@ -508,6 +508,10 @@ takes advantage of modern hardware using OpenGL.") (with-directory-excursion (string-append #$output "/bin") (symlink "dev.tchx84.Portfolio" "portfolio")))) + (add-after 'unpack 'skip-gtk-update-icon-cache + (lambda _ + (substitute* "build-aux/meson/postinstall.py" + (("gtk-update-icon-cache") "true")))) (add-after 'glib-or-gtk-wrap 'python-and-gi-wrap (lambda* (#:key inputs outputs #:allow-other-keys) (wrap-program (search-input-file outputs @@ -519,12 +523,12 @@ takes advantage of modern hardware using OpenGL.") `("GI_TYPELIB_PATH" = (,(getenv "GI_TYPELIB_PATH"))))))))) (build-system meson-build-system) - (inputs (list bash-minimal python-pygobject gtk+ libhandy)) + (inputs (list bash-minimal python-pygobject gtk libadwaita)) (native-inputs (list desktop-file-utils gettext-minimal `(,glib "bin") - `(,gtk+ "bin") + pkg-config python)) (home-page "https://github.com/tchx84/Portfolio") (synopsis "Minimalist file manager for Linux mobile devices") From 8d9bb5408a5088304ec8662bb53b9c3ded9ca725 Mon Sep 17 00:00:00 2001 From: Mathieu Othacehe Date: Sat, 9 Sep 2023 11:00:42 +0200 Subject: [PATCH 042/268] gnu: linux-libre: Fix cross-compilation. Fix generic aarch64 kernel cross-compilation by providing the missing hexdump binary. * gnu/packages/linux.scm (linux-libre)[native-inputs]: Add util-linux. --- gnu/packages/linux.scm | 1 + 1 file changed, 1 insertion(+) diff --git a/gnu/packages/linux.scm b/gnu/packages/linux.scm index 36354b4d82..bc1fedaad5 100644 --- a/gnu/packages/linux.scm +++ b/gnu/packages/linux.scm @@ -1071,6 +1071,7 @@ ARCH and optionally VARIANT, or #f if there is no such configuration." elfutils ;needed to enable CONFIG_STACK_VALIDATION flex bison + util-linux ;needed for hexdump ;; These are needed to compile the GCC plugins. gmp mpfr From f85c6ee26a5e693aaaebdab33b156938e10fb060 Mon Sep 17 00:00:00 2001 From: Guillaume Le Vaillant Date: Sat, 9 Sep 2023 11:24:27 +0200 Subject: [PATCH 043/268] gnu: qgis: Fix build. * gnu/packages/geo.scm (qgis)[arguments]: Add test_core_authconfig to disabled tests in 'check' phase. --- gnu/packages/geo.scm | 1 + 1 file changed, 1 insertion(+) diff --git a/gnu/packages/geo.scm b/gnu/packages/geo.scm index 0a823353fa..d702046865 100644 --- a/gnu/packages/geo.scm +++ b/gnu/packages/geo.scm @@ -2775,6 +2775,7 @@ growing set of geoscientific methods.") "ProcessingGrass7AlgorithmsRasterTestPt1" "ProcessingGrass7AlgorithmsRasterTestPt2" "ProcessingGrass7AlgorithmsVectorTest" + "test_core_authconfig" "test_core_authmanager" "test_core_compositionconverter" "test_core_expression" From 9f6fa3a9580a43d7406ac5b61c2fba0878a67edf Mon Sep 17 00:00:00 2001 From: Cayetano Santos Date: Sun, 30 Jul 2023 17:52:58 +0200 Subject: [PATCH 044/268] gnu: Add emacs-chatgpt-shell. * gnu/packages/emacs-xyz.scm (emacs-chatgpt-shell): New variable. Signed-off-by: Liliana Marie Prikler --- gnu/packages/emacs-xyz.scm | 19 +++++++++++++++++++ 1 file changed, 19 insertions(+) diff --git a/gnu/packages/emacs-xyz.scm b/gnu/packages/emacs-xyz.scm index baa67eefbb..1cce55bce9 100644 --- a/gnu/packages/emacs-xyz.scm +++ b/gnu/packages/emacs-xyz.scm @@ -493,6 +493,25 @@ just one-off queries and multiple independent sessions. It requires an OpenAI API key.") (license license:gpl3+))) +(define-public emacs-chatgpt-shell + (package + (name "emacs-chatgpt-shell") + (version "0.74.1") + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/xenodium/chatgpt-shell") + (commit "1de7bfa6a34f20cca813006282d9a8f2ef291f95"))) + (sha256 + (base32 + "1rabpp70qlmc47lmp2v7ckvfjhy6wkk881fxpbv2dchzhn77qk5r")))) + (build-system emacs-build-system) + (home-page "https://github.com/xenodium/chatgpt-shell") + (synopsis "ChatGPT and DALL-E Emacs shells + Org Babel") + (description + "chatgpt-shell is a comint-based ChatGPT shell for Emacs.") + (license license:gpl3+))) + (define-public emacs-geiser-guile (package (name "emacs-geiser-guile") From 5e72bb5c67943fecf690190bdccbda2bf16d12b0 Mon Sep 17 00:00:00 2001 From: Reily Siegel Date: Mon, 28 Aug 2023 11:11:23 -0400 Subject: [PATCH 045/268] services: vpn: Fix broken format string for wireguard dns. * gnu/services/vpn.scm (wireguard-configuration-file): Fix broken format string. Signed-off-by: Liliana Marie Prikler --- gnu/services/vpn.scm | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/gnu/services/vpn.scm b/gnu/services/vpn.scm index 9c8243d131..7fb4775757 100644 --- a/gnu/services/vpn.scm +++ b/gnu/services/vpn.scm @@ -820,7 +820,7 @@ strongSwan."))) (format #f "~@[ListenPort = ~a~]" #$port) #$@(if (null? dns) '() - (list (format #f "~{DNS = ~{~a~^, ~}" dns))))) + (list (format #f "DNS = ~{~a~^, ~}" dns))))) (mkdir #$output) (chdir #$output) From cab7ae94ec5e6e2c49946c82847d27499facc09a Mon Sep 17 00:00:00 2001 From: Mekeor Melire Date: Sun, 18 Jun 2023 23:17:18 +0000 Subject: [PATCH 046/268] gnu: Add emacs-jinx. * gnu/packages/emacs-xyz.scm (emacs-jinx): New variable. Signed-off-by: Liliana Marie Prikler --- gnu/packages/emacs-xyz.scm | 61 ++++++++++++++++++++++++++++++++++++++ 1 file changed, 61 insertions(+) diff --git a/gnu/packages/emacs-xyz.scm b/gnu/packages/emacs-xyz.scm index 1cce55bce9..e971edb676 100644 --- a/gnu/packages/emacs-xyz.scm +++ b/gnu/packages/emacs-xyz.scm @@ -181,6 +181,7 @@ #:use-module (gnu packages djvu) #:use-module (gnu packages ebook) #:use-module (gnu packages emacs) + #:use-module (gnu packages enchant) #:use-module (gnu packages fonts) #:use-module (gnu packages freedesktop) #:use-module (gnu packages games) @@ -10349,6 +10350,66 @@ insertion mode. When enabled all keys are implicitly prefixed with sgml/html integration, and indentation (working with sgml).") (license license:gpl3+))) +(define-public emacs-jinx + (package + (name "emacs-jinx") + (version "0.8") + (source + (origin + (method git-fetch) + (uri + (git-reference + (url "https://github.com/minad/jinx") + (commit version))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "1y097rnf9zg26jf4vh74a0laddfp4x6pp1fjqs3xqgwc0cmdq59w")))) + (build-system emacs-build-system) + (arguments + (list + #:phases + #~(modify-phases %standard-phases + (add-after 'expand-load-path 'build-jinx-mod + (lambda* _ + (invoke + "emacs" "--batch" "-L" "." + "-l" "jinx.el" + "-f" "jinx--load-module"))) + (add-after 'expand-load-path 'build-info + (lambda _ + (invoke "emacs" "--batch" + "--eval=(require 'ox-texinfo)" + "--eval=(find-file \"README.org\")" + "--eval=(org-texinfo-export-to-info)"))) + (add-after 'build-jinx-mod 'patch-path-to-jinx-mod + (lambda _ + (let ((file "jinx.el")) + (make-file-writable file) + (emacs-substitute-sexps file + ("\"Compile and load dynamic module.\"" + `(module-load + ,(string-append #$output + "/lib/emacs/jinx-mod.so"))))))) + (add-after 'install 'install-jinx-mod + (lambda _ + (install-file "jinx-mod.so" + (string-append #$output "/lib/emacs")))) + (add-after 'install 'install-info + (lambda _ + (install-file "jinx.info" + (string-append #$output "/share/info"))))))) + (inputs (list enchant)) + (propagated-inputs (list emacs-compat)) + (native-inputs (list emacs-compat enchant pkg-config texinfo)) + (home-page "https://github.com/minad/jinx") + (synopsis "Emacs Enchanted Spell Checker") + (description "Jinx is a just-in-time spell-checker for Emacs +based on the enchant library. It lazily highlights misspelled words in the +text of the visible portion of the buffer by honouring window boundaries as +well as text folding, if any.") + (license license:gpl3+))) + (define-public emacs-jit-spell (package (name "emacs-jit-spell") From 859928fc99015c64202eef6231c721e026925aec Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ludovic=20Court=C3=A8s?= Date: Fri, 8 Sep 2023 22:10:36 +0200 Subject: [PATCH 047/268] gnu: cuirass: Update to 6131880. * gnu/packages/ci.scm (cuirass): Update to 6131880. --- gnu/packages/ci.scm | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/gnu/packages/ci.scm b/gnu/packages/ci.scm index 25566bc0fa..f38dd4383d 100644 --- a/gnu/packages/ci.scm +++ b/gnu/packages/ci.scm @@ -58,8 +58,8 @@ #:use-module ((guix search-paths) #:select ($SSL_CERT_DIR))) (define-public cuirass - (let ((commit "7416bb916315730cd1ea74e7914f7532a1aba193") - (revision "17")) + (let ((commit "613188072c468fe2ffa4e8f83b48aefeb2488a2c") + (revision "18")) (package (name "cuirass") (version (git-version "1.1.0" revision commit)) @@ -72,7 +72,7 @@ (file-name (git-file-name name version)) (sha256 (base32 - "1wc39c7aqva5sp3gpdxq2kqa17ywy21yn5w8r66qgxjinvj21a68")))) + "13ai3xmf62kx9ijc5imapcjwyvkhj2kxnh36chh3vbh3sxbbanzz")))) (build-system gnu-build-system) (arguments `(#:modules ((guix build utils) From 4cf4bd1ebe1c4b206ffd686058acd69261672536 Mon Sep 17 00:00:00 2001 From: Thomas Albers Date: Tue, 8 Aug 2023 18:37:10 +0200 Subject: [PATCH 048/268] =?UTF-8?q?services:=20cgit:=20Allow=20file-like?= =?UTF-8?q?=20objects=20for=20=E2=80=98root-readme=E2=80=99.?= MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * gnu/services/cgit.scm (cgit-configuration)[root-readme]: Accept 'file-object' instead of only 'string' Signed-off-by: Ludovic Courtès --- gnu/services/cgit.scm | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/gnu/services/cgit.scm b/gnu/services/cgit.scm index e33cb9e7db..684ab73f76 100644 --- a/gnu/services/cgit.scm +++ b/gnu/services/cgit.scm @@ -581,7 +581,7 @@ removed for the URL and name.") (string "a fast webinterface for the git dscm") "Text printed below the heading on the repository index page.") (root-readme - (string "") + (file-object "") "The content of the file specified with this option will be included verbatim below the \"about\" link on the repository index page.") (root-title From 58fe4574a97046ffb3b015034a50119ffc04792d Mon Sep 17 00:00:00 2001 From: Distopico Date: Wed, 30 Aug 2023 14:58:13 -0500 Subject: [PATCH 049/268] gnu: Add rust-notify-5-pre.13. MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * gnu/packages/crates-io.scm (rust-notify-5-pre.13): New variable. This pinned version is required by `rust-analyzer` version `2022-01-10`. Signed-off-by: Ludovic Courtès --- gnu/packages/crates-io.scm | 13 +++++++++++++ 1 file changed, 13 insertions(+) diff --git a/gnu/packages/crates-io.scm b/gnu/packages/crates-io.scm index 77a41a5116..b6e2ac4507 100644 --- a/gnu/packages/crates-io.scm +++ b/gnu/packages/crates-io.scm @@ -41724,6 +41724,19 @@ with all line endings.") notification library.") (license (list license:cc0 license:artistic2.0)))) +(define-public rust-notify-5-pre.13 + (package + (inherit rust-notify-5) + (name "rust-notify") + (version "5.0.0-pre.13") + (source (origin + (method url-fetch) + (uri (crate-uri "notify" version)) + (file-name (string-append name "-" version ".tar.gz")) + (sha256 + (base32 + "0za8mpacxkr62fii5h7ny4h396y0m8myd3hf08njqdg2h21kap94")))))) + (define-public rust-notify-4 (package (inherit rust-notify-5) From a4514556df4e3138544def7286c6ecf640634a57 Mon Sep 17 00:00:00 2001 From: Distopico Date: Wed, 30 Aug 2023 14:58:14 -0500 Subject: [PATCH 050/268] gnu: rust-analyzer: Fix build of version 2022-01-10. MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * gnu/packages/rust-apps.scm (rust-analyzer): Update dependency rust-notify-5-pre.13. This fixes the build of `rust-analyzer@2022-01-10`, which required a pinned version of `rust-notify` (`rust-notify-5-pre.13`) to compile and rust >= 1.64. Signed-off-by: Ludovic Courtès --- gnu/packages/rust-apps.scm | 22 +++++++++++++++------- gnu/packages/rust.scm | 6 +++--- 2 files changed, 18 insertions(+), 10 deletions(-) diff --git a/gnu/packages/rust-apps.scm b/gnu/packages/rust-apps.scm index a291282325..8c7d8006cc 100644 --- a/gnu/packages/rust-apps.scm +++ b/gnu/packages/rust-apps.scm @@ -1780,9 +1780,10 @@ background agent taking care of maintaining the necessary state.") "1ci85bp8xwqrk8nqr8sh6yj8njgd98nhgnhaks2g00c77wwyra41")))) (build-system cargo-build-system) (arguments - `(#:install-source? #f ; virtual manifest + `(#:rust ,rust-1.64 + #:install-source? #f ; virtual manifest #:cargo-test-flags - '("--release" "--" + '("--release" "--lib" "--tests" "--" "--skip=tests::test_version_check" ;it need rustc's version ;; FIXME: Guix's rust does not install source in ;; %out/lib/rustlib/src/rust so "can't load standard library from @@ -1793,12 +1794,19 @@ background agent taking care of maintaining the necessary state.") "--skip=tests::sourcegen::sourcegen_assists_docs" ;need rustfmt "--skip=tests::sourcegen_ast::sourcegen_ast" ;same - "--skip=tidy::cargo_files_are_tidy" ;not needed "--skip=tidy::check_licenses" ;it runs cargo metadata "--skip=tidy::check_merge_commits" ;it runs git rev-list "--skip=tidy::check_code_formatting" ;need rustfmt as cargo fmt - "--skip=tidy::generate_grammar" ;same - "--skip=tidy::generate_assists_tests") ;same + + ;; These tests require rust <= 1.60 and too many packages + ;; has as dependency rust-serde-json-1 that use indexmap2 + ;; and it need rust >= 1.64 + "--skip=tests::list_test_macros" + "--skip=tests::test_derive_empty" + "--skip=tests::test_attr_macro" + "--skip=tests::test_fn_like_macro" + "--skip=tests::test_fn_like_macro2" + "--skip=tests::test_derive_error") #:cargo-development-inputs (("rust-arbitrary" ,rust-arbitrary-1) ("rust-derive-arbitrary" ,rust-derive-arbitrary-1) @@ -1845,7 +1853,7 @@ background agent taking care of maintaining the necessary state.") ("rust-memmap2" ,rust-memmap2-0.5) ("rust-mimalloc" ,rust-mimalloc-0.1) ("rust-miow" ,rust-miow-0.4) - ("rust-notify" ,rust-notify-5) + ("rust-notify" ,rust-notify-5-pre.13) ("rust-object" ,rust-object-0.28) ("rust-once-cell" ,rust-once-cell-1) ("rust-parking-lot" ,rust-parking-lot-0.11) @@ -1927,7 +1935,7 @@ exec -a \"$0\" \"~a\" \"$@\"" (chdir "../..") (install-file "LICENSE-MIT" doc) (install-file "LICENSE-APACHE" doc))))))) - (native-inputs (list rust-src)) + (native-inputs (list rust-src-1.64)) (home-page "https://rust-analyzer.github.io/") (synopsis "Experimental Rust compiler front-end for IDEs") (description "Rust-analyzer is a modular compiler frontend for the Rust diff --git a/gnu/packages/rust.scm b/gnu/packages/rust.scm index 4ee5ded5de..5cfdeffa81 100644 --- a/gnu/packages/rust.scm +++ b/gnu/packages/rust.scm @@ -652,7 +652,7 @@ safety and thread safety guarantees.") (rust-bootstrapped-package rust-1.62 "1.63.0" "1l4rrbzhxv88pnfq94nbyb9m6lfnjwixma3mwjkmvvs2aqlq158z")) -(define rust-1.64 +(define-public rust-1.64 (let ((base-rust (rust-bootstrapped-package rust-1.63 "1.64.0" "018j720b2n12slp4xk64jc6shkncd46d621qdyzh2a8s3r49zkdk"))) @@ -891,10 +891,10 @@ safety and thread safety guarantees.") `("procps" ,procps) (package-native-inputs base-rust)))))) -(define-public rust-src +(define-public rust-src-1.64 (hidden-package (package - (inherit rust) + (inherit rust-1.64) (name "rust-src") (build-system copy-build-system) (native-inputs '()) From 26c10ac9bf373475f08442d52e2162ec2504f265 Mon Sep 17 00:00:00 2001 From: Distopico Date: Wed, 30 Aug 2023 14:58:15 -0500 Subject: [PATCH 051/268] gnu: Add rust-either-1.6.0. MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * gnu/packages/crates-io.scm (rust-either-1.6.0): New variable. Signed-off-by: Ludovic Courtès --- gnu/packages/crates-io.scm | 18 ++++++++++++++++++ 1 file changed, 18 insertions(+) diff --git a/gnu/packages/crates-io.scm b/gnu/packages/crates-io.scm index b6e2ac4507..6a0f4e187d 100644 --- a/gnu/packages/crates-io.scm +++ b/gnu/packages/crates-io.scm @@ -21557,6 +21557,24 @@ signing, and verification in pure Rust.") @code{Right} is a general purpose sum type with two cases.") (license (list license:expat license:asl2.0)))) +(define-public rust-either-1.6.0 + (package + (inherit rust-either-1) + (name "rust-either") + (version "1.6.1") + (source + (origin + (method url-fetch) + (uri (crate-uri "either" version)) + (file-name + (string-append name "-" version ".tar.gz")) + (sha256 + (base32 + "0mwl9vngqf5jvrhmhn9x60kr5hivxyjxbmby2pybncxfqhf4z3g7")))) + (arguments + `(#:cargo-inputs (("rust-serde" ,rust-serde-1)) + #:cargo-development-inputs (("rust-serde-json" ,rust-serde-json-1.0.73)))))) + (define-public rust-elf-0.0.10 (package (name "rust-elf") From 63eddbb920e847129affce3ea17880fd699dd06f Mon Sep 17 00:00:00 2001 From: Distopico Date: Wed, 30 Aug 2023 14:58:16 -0500 Subject: [PATCH 052/268] gnu: Add rust-proc-macro2-1.0.34. MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * gnu/packages/crates-io.scm (rust-proc-macro2-1.0.34): New variable. Signed-off-by: Ludovic Courtès --- gnu/packages/crates-io.scm | 21 +++++++++++++++++++++ 1 file changed, 21 insertions(+) diff --git a/gnu/packages/crates-io.scm b/gnu/packages/crates-io.scm index 6a0f4e187d..70918d16d0 100644 --- a/gnu/packages/crates-io.scm +++ b/gnu/packages/crates-io.scm @@ -49419,6 +49419,27 @@ in your code.") in terms of the upstream unstable API.") (license (list license:asl2.0 license:expat)))) +(define-public rust-proc-macro2-1.0.34 + (package + (inherit rust-proc-macro2-1) + (name "rust-proc-macro2") + (version "1.0.34") + (source + (origin + (method url-fetch) + (uri (crate-uri "proc-macro2" version)) + (file-name (string-append name "-" version ".tar.gz")) + (sha256 + (base32 + "1c93jhwl8lv3hiqqvdhd2d2xhjryh5bqb9w5icr5i7bw1wnfk11g")))) + (arguments + `(#:cargo-test-flags '("--lib") + #:cargo-inputs + (("rust-unicode-ident" ,rust-unicode-ident-1)) + #:cargo-development-inputs + (("rust-quote" ,rust-quote-1.0.10) + ("rust-rustversion" ,rust-rustversion-1)))))) + (define-public rust-proc-macro2-0.4 (package (inherit rust-proc-macro2-1) From e32ae2fbf6f3c52d849036026ecc09a94d57fbb7 Mon Sep 17 00:00:00 2001 From: Distopico Date: Wed, 30 Aug 2023 14:58:17 -0500 Subject: [PATCH 053/268] gnu: Add rust-quote-1.0.10. MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * gnu/packages/crates-io.scm (rust-quote-1.0.10): New variable. Signed-off-by: Ludovic Courtès --- gnu/packages/crates-io.scm | 19 +++++++++++++++++++ 1 file changed, 19 insertions(+) diff --git a/gnu/packages/crates-io.scm b/gnu/packages/crates-io.scm index 70918d16d0..d245b32959 100644 --- a/gnu/packages/crates-io.scm +++ b/gnu/packages/crates-io.scm @@ -51640,6 +51640,25 @@ transport protocol in Rust.") (description "Quasi-quoting macro quote!(...)") (license (list license:asl2.0 license:expat)))) +(define-public rust-quote-1.0.10 + (package + (inherit rust-quote-1) + (name "rust-quote") + (version "1.0.10") + (source (origin + (method url-fetch) + (uri (crate-uri "quote" version)) + (file-name (string-append name "-" version ".tar.gz")) + (sha256 + (base32 + "01ff7a76f871ggnby57iagw6499vci4bihcr11g6bqzjlp38rg1q")))) + (arguments + `(#:cargo-inputs + (("rust-proc-macro2" ,rust-proc-macro2-1.0.34)) + #:cargo-development-inputs + (("rust-rustversion" ,rust-rustversion-1) + ("rust-trybuild" ,rust-trybuild-1.0.19)))))) + (define-public rust-quote-0.6 (package (inherit rust-quote-1) From 590d408c56bd63a429d51e8a47862e08e8862fb1 Mon Sep 17 00:00:00 2001 From: Distopico Date: Wed, 30 Aug 2023 14:58:18 -0500 Subject: [PATCH 054/268] gnu: Add rust-serde-json-1.0.73. MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * gnu/packages/crates-io.scm (rust-serde-json-1.0.73): New variable. Signed-off-by: Ludovic Courtès --- gnu/packages/crates-io.scm | 26 ++++++++++++++++++++++++++ 1 file changed, 26 insertions(+) diff --git a/gnu/packages/crates-io.scm b/gnu/packages/crates-io.scm index d245b32959..a89db5ba46 100644 --- a/gnu/packages/crates-io.scm +++ b/gnu/packages/crates-io.scm @@ -59866,6 +59866,32 @@ data. This crate provides a wrapper that works with any existing Serde "This package provides a JSON serialization file format.") (license (list license:expat license:asl2.0)))) +(define-public rust-serde-json-1.0.73 + (package + (inherit rust-serde-json-1) + (name "rust-serde-json") + (version "1.0.73") + (source + (origin + (method url-fetch) + (uri (crate-uri "serde-json" version)) + (file-name (string-append name "-" version ".tar.gz")) + (sha256 + (base32 "1xbwmzc5j6r1nz62a20w6l9bkwbhzd11vwbdqmzbqcv5pi207gdw")))) + (arguments + `(#:cargo-inputs + (("rust-indexmap" ,rust-indexmap-1.7) + ("rust-itoa" ,rust-itoa-1) + ("rust-ryu" ,rust-ryu-1) + ("rust-serde" ,rust-serde-1)) + #:cargo-development-inputs + (("rust-automod" ,rust-automod-1) + ("rust-rustversion" ,rust-rustversion-1) + ("rust-serde-bytes" ,rust-serde-bytes-0.11) + ("rust-serde-derive" ,rust-serde-derive-1) + ("rust-serde-stacker" ,rust-serde-stacker-0.1) + ("rust-trybuild" ,rust-trybuild-1)))))) + (define-public rust-serde-json-0.9 (package (inherit rust-serde-json-1) From bf7fcedbdfb2695f0f9197cfa812ce74033f36ae Mon Sep 17 00:00:00 2001 From: Distopico Date: Wed, 30 Aug 2023 14:58:19 -0500 Subject: [PATCH 055/268] gnu: Add rust-trybuild-1.0.19. MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * gnu/packages/crates-io.scm (rust-trybuild-1.0.19): New variable. Signed-off-by: Ludovic Courtès --- gnu/packages/crates-io.scm | 23 +++++++++++++++++++++++ 1 file changed, 23 insertions(+) diff --git a/gnu/packages/crates-io.scm b/gnu/packages/crates-io.scm index a89db5ba46..019afc010a 100644 --- a/gnu/packages/crates-io.scm +++ b/gnu/packages/crates-io.scm @@ -73245,6 +73245,29 @@ the Trust-DNS client to use rustls for TLS.") "Test harness for ui tests of compiler diagnostics.") (license (list license:expat license:asl2.0)))) +(define-public rust-trybuild-1.0.19 + (package + (inherit rust-trybuild-1) + (name "rust-trybuild") + (version "1.0.19") + (source + (origin + (method url-fetch) + (uri (crate-uri "trybuild" version)) + (file-name (string-append name "-" version ".tar.gz")) + (sha256 + (base32 "0ab7ahdx563n6kbm14pm3qnxq4fp06pz42nh5ii4acvlzycnwdh4")))) + (arguments + `(#:cargo-inputs + (("rust-toml" ,rust-toml-0.5) + ("rust-dissimilar" ,rust-dissimilar-1) + ("rust-glob" ,rust-glob-0.3) + ("rust-lazy-static" ,rust-lazy-static-1) + ("rust-serde" ,rust-serde-1) + ("rust-serde-json" ,rust-serde-json-1.0.73) + ("rust-termcolor" ,rust-termcolor-1)) + #:cargo-development-inputs (("rust-automod" ,rust-automod-1)))))) + (define-public rust-trybuild2-1 (package (name "rust-trybuild2") From 6fa720831f3337e729fdd50ef6ed44cd152cc698 Mon Sep 17 00:00:00 2001 From: Distopico Date: Wed, 30 Aug 2023 14:58:20 -0500 Subject: [PATCH 056/268] gnu: rust-analyzer: Update required dependencies version. MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Use pinned versions of different dependencies required by rust-analyzer@2022-01-10. * gnu/packages/crates-io.scm (rust-salsa-0.17): Require RUST-INDEXMAP-1.7. (rust-serde-path-to-error-0.1): Require RUST-SERDE-JSON-1.0.73. (rust-serde-repr-0.1): Require RUST-QUOTE-1.0.10, RUST-PROC-MACRO2-1.0.34, RUST-SERDE-JSON-1.0.73, RUST-TRYBUILD-1.0.19. * gnu/packages/rust-apps.scm (rust-analyzer): Adjust versions similarly. Signed-off-by: Ludovic Courtès --- gnu/packages/crates-io.scm | 12 ++++++------ gnu/packages/rust-apps.scm | 12 +++++------- 2 files changed, 11 insertions(+), 13 deletions(-) diff --git a/gnu/packages/crates-io.scm b/gnu/packages/crates-io.scm index 019afc010a..3c83563c45 100644 --- a/gnu/packages/crates-io.scm +++ b/gnu/packages/crates-io.scm @@ -57560,7 +57560,7 @@ in pure Rust.") #:cargo-inputs (("rust-crossbeam-utils" ,rust-crossbeam-utils-0.8) - ("rust-indexmap" ,rust-indexmap-1) + ("rust-indexmap" ,rust-indexmap-1.7) ("rust-lock-api" ,rust-lock-api-0.4) ("rust-log" ,rust-log-0.4) ("rust-oorandom" ,rust-oorandom-11.1) @@ -59960,7 +59960,7 @@ programs in rust.") (("rust-serde" ,rust-serde-1)) #:cargo-development-inputs (("rust-serde-derive" ,rust-serde-derive-1) - ("rust-serde-json" ,rust-serde-json-1)))) + ("rust-serde-json" ,rust-serde-json-1.0.73)))) (home-page "https://github.com/dtolnay/path-to-error") (synopsis @@ -60018,14 +60018,14 @@ commonly used by Ruby on Rails via Rack.") (build-system cargo-build-system) (arguments `(#:cargo-inputs - (("rust-proc-macro2" ,rust-proc-macro2-1) - ("rust-quote" ,rust-quote-1) + (("rust-proc-macro2" ,rust-proc-macro2-1.0.34) + ("rust-quote" ,rust-quote-1.0.10) ("rust-syn" ,rust-syn-1)) #:cargo-development-inputs (("rust-rustversion" ,rust-rustversion-1) ("rust-serde" ,rust-serde-1) - ("rust-serde-json" ,rust-serde-json-1) - ("rust-trybuild" ,rust-trybuild-1)))) + ("rust-serde-json" ,rust-serde-json-1.0.73) + ("rust-trybuild" ,rust-trybuild-1.0.19)))) (home-page "https://github.com/dtolnay/serde-repr") (synopsis "Serialize and deserialize C-like enum as underlying repr") (description diff --git a/gnu/packages/rust-apps.scm b/gnu/packages/rust-apps.scm index 8c7d8006cc..76d48e55f1 100644 --- a/gnu/packages/rust-apps.scm +++ b/gnu/packages/rust-apps.scm @@ -1812,7 +1812,7 @@ background agent taking care of maintaining the necessary state.") ("rust-derive-arbitrary" ,rust-derive-arbitrary-1) ("rust-expect-test" ,rust-expect-test-1) ("rust-oorandom" ,rust-oorandom-11.1) - ("rust-quote" ,rust-quote-1) + ("rust-quote" ,rust-quote-1.0.10) ("rust-rayon" ,rust-rayon-1) ("rust-tracing" ,rust-tracing-0.1) ("rust-tracing-subscriber" ,rust-tracing-subscriber-0.3) @@ -1823,7 +1823,6 @@ background agent taking care of maintaining the necessary state.") ("rust-anyhow" ,rust-anyhow-1) ("rust-anymap" ,rust-anymap-0.12) ("rust-arrayvec" ,rust-arrayvec-0.7) - ("rust-backtrace" ,rust-backtrace-0.3) ("rust-cargo-metadata" ,rust-cargo-metadata-0.14) ("rust-cfg-if" ,rust-cfg-if-1) ("rust-chalk-ir" ,rust-chalk-ir-0.75) @@ -1832,17 +1831,16 @@ background agent taking care of maintaining the necessary state.") ("rust-countme" ,rust-countme-3) ("rust-cov-mark" ,rust-cov-mark-2) ("rust-crossbeam-channel" ,rust-crossbeam-channel-0.5) - ("rust-dashmap" ,rust-dashmap-4) ("rust-dissimilar" ,rust-dissimilar-1) ("rust-dot" ,rust-dot-0.1) ("rust-drop-bomb" ,rust-drop-bomb-0.1) - ("rust-either" ,rust-either-1) + ("rust-either" ,rust-either-1.6.0) ("rust-ena" ,rust-ena-0.14) ("rust-env-logger" ,rust-env-logger-0.8) ("rust-flate2" ,rust-flate2-1) ("rust-fst" ,rust-fst-0.4) ("rust-home" ,rust-home-0.5) - ("rust-indexmap" ,rust-indexmap-1) + ("rust-indexmap" ,rust-indexmap-1.7) ("rust-itertools" ,rust-itertools-0.10) ("rust-jod-thread" ,rust-jod-thread-0.1) ("rust-libc" ,rust-libc-0.2) @@ -1858,7 +1856,7 @@ background agent taking care of maintaining the necessary state.") ("rust-once-cell" ,rust-once-cell-1) ("rust-parking-lot" ,rust-parking-lot-0.11) ("rust-perf-event" ,rust-perf-event-0.4) - ("rust-proc-macro2" ,rust-proc-macro2-1) + ("rust-proc-macro2" ,rust-proc-macro2-1.0.34) ("rust-pulldown-cmark" ,rust-pulldown-cmark-0.8) ("rust-pulldown-cmark-to-cmark" ,rust-pulldown-cmark-to-cmark-7) ("rust-rowan" ,rust-rowan-0.15) @@ -1867,7 +1865,7 @@ background agent taking care of maintaining the necessary state.") ("rust-salsa" ,rust-salsa-0.17) ("rust-scoped-tls" ,rust-scoped-tls-1) ("rust-serde" ,rust-serde-1) - ("rust-serde-json" ,rust-serde-json-1) + ("rust-serde-json" ,rust-serde-json-1.0.73) ("rust-serde-path-to-error" ,rust-serde-path-to-error-0.1) ("rust-typed-arena" ,rust-typed-arena-2) ("rust-smallvec" ,rust-smallvec-1) From 9aed82fe05b41ae37737bf741c85d030cf20d345 Mon Sep 17 00:00:00 2001 From: Yovan Naumovski Date: Sun, 27 Aug 2023 13:10:59 +0300 Subject: [PATCH 057/268] gnu: vcmi: Update to 1.3.1. MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * gnu/packages/games.scm (vcmi): Update to 1.3.1. Signed-off-by: Ludovic Courtès --- gnu/packages/games.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/games.scm b/gnu/packages/games.scm index 760234b031..4d5b85248a 100644 --- a/gnu/packages/games.scm +++ b/gnu/packages/games.scm @@ -11059,7 +11059,7 @@ play; it will look for them at @file{~/.local/share/fheroes2} folder.") (define-public vcmi (package (name "vcmi") - (version "1.2.1") + (version "1.3.1") (source (origin (method git-fetch) (uri (git-reference @@ -11068,7 +11068,7 @@ play; it will look for them at @file{~/.local/share/fheroes2} folder.") (file-name (git-file-name name version)) (sha256 (base32 - "0f3fk1fc2wb7f2j4pxz89dzr8zjnrdh435mijia483a3bq59w7pk")) + "0jq84i6lxp96xkzq9mq8n2bbmincjzi39vijj9ws8i59c7xvjw5f")) (patches (search-patches "vcmi-disable-privacy-breach.patch")))) (build-system cmake-build-system) (arguments From cd469932758bf2bec1ff9c82aeb373e18730d0c4 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?S=C3=B6ren=20Tempel?= Date: Sat, 26 Aug 2023 09:00:37 +0200 Subject: [PATCH 058/268] daemon: Fix build with GCC 13. MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit The sqlite.hh file uses fixed-width integer types from stdint.h. As such, it needs to include . Without this include, the file doesn't compile successfully with GCC13. See: https://gcc.gnu.org/gcc-13/porting_to.html#header-dep-changes * nix/libstore/sqlite.hh: include Signed-off-by: Sören Tempel Signed-off-by: Ludovic Courtès --- nix/libstore/sqlite.hh | 1 + 1 file changed, 1 insertion(+) diff --git a/nix/libstore/sqlite.hh b/nix/libstore/sqlite.hh index 326e4a4855..6cadba6849 100644 --- a/nix/libstore/sqlite.hh +++ b/nix/libstore/sqlite.hh @@ -2,6 +2,7 @@ #include #include +#include #include "types.hh" From d4bd5bc799e2face0b30bdb3a6ec3c347c0d1e22 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ludovic=20Court=C3=A8s?= Date: Sat, 9 Sep 2023 19:33:11 +0200 Subject: [PATCH 059/268] time-travel-manifest: Add 1.4.0. * etc/time-travel-manifest.scm (%release-commits): Add 1.4.0. --- etc/time-travel-manifest.scm | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/etc/time-travel-manifest.scm b/etc/time-travel-manifest.scm index ab890dd903..43d6708a0a 100644 --- a/etc/time-travel-manifest.scm +++ b/etc/time-travel-manifest.scm @@ -66,7 +66,8 @@ (define %release-commits ;; Release commits: the list of version/commit pairs. - '(("1.3.0" . "a0178d34f582b50e9bdbb0403943129ae5b560ff") + '(("1.4.0" . "8e2f32cee982d42a79e53fc1e9aa7b8ff0514714") + ("1.3.0" . "a0178d34f582b50e9bdbb0403943129ae5b560ff") ("1.2.0" . "a099685659b4bfa6b3218f84953cbb7ff9e88063") ("1.1.0" . "d62c9b2671be55ae0305bebfda17b595f33797f2") ("1.0.1" . "d68de958b60426798ed62797ff7c96c327a672ac") From a4c35c607cfd7d6b0bad90cfcc46188d489e1754 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ludovic=20Court=C3=A8s?= Date: Sat, 9 Sep 2023 19:36:05 +0200 Subject: [PATCH 060/268] time-travel-manifest: Comment out versions older than 1.3.0 for now. * etc/time-travel-manifest.scm (%release-commits): Comment out revisions older than 1.3.0. --- etc/time-travel-manifest.scm | 18 +++++++++++++----- 1 file changed, 13 insertions(+), 5 deletions(-) diff --git a/etc/time-travel-manifest.scm b/etc/time-travel-manifest.scm index 43d6708a0a..80c4c7c346 100644 --- a/etc/time-travel-manifest.scm +++ b/etc/time-travel-manifest.scm @@ -68,11 +68,19 @@ ;; Release commits: the list of version/commit pairs. '(("1.4.0" . "8e2f32cee982d42a79e53fc1e9aa7b8ff0514714") ("1.3.0" . "a0178d34f582b50e9bdbb0403943129ae5b560ff") - ("1.2.0" . "a099685659b4bfa6b3218f84953cbb7ff9e88063") - ("1.1.0" . "d62c9b2671be55ae0305bebfda17b595f33797f2") - ("1.0.1" . "d68de958b60426798ed62797ff7c96c327a672ac") - ("1.0.0" . "6298c3ffd9654d3231a6f25390b056483e8f407c") - ("0.16.0" . "4a0b87f0ec5b6c2dcf82b372dd20ca7ea6acdd9c"))) + + ;; FIXME: To merely compute the derivation of these revisions, we need to + ;; be able to build their dependencies. However, pre-built binaries are + ;; currently missing and some of these no longer build from source due to + ;; time bombs like . Thus, comment + ;; them output until we have substitutes for these old things. + + ;; ("1.2.0" . "a099685659b4bfa6b3218f84953cbb7ff9e88063") + ;; ("1.1.0" . "d62c9b2671be55ae0305bebfda17b595f33797f2") + ;; ("1.0.1" . "d68de958b60426798ed62797ff7c96c327a672ac") + ;; ("1.0.0" . "6298c3ffd9654d3231a6f25390b056483e8f407c") + ;; ("0.16.0" . "4a0b87f0ec5b6c2dcf82b372dd20ca7ea6acdd9c") + )) (manifest (map (match-lambda From 62ea0a0d3a921a25593b2a8db97d744fd2c53c08 Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Sat, 9 Sep 2023 21:23:30 +0300 Subject: [PATCH 061/268] gnu: global: Fix ctags creation using pygments. * gnu/packages/code.scm (global)[arguments]: Adjust configure-flags to use a specific python interpreter. --- gnu/packages/code.scm | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/gnu/packages/code.scm b/gnu/packages/code.scm index 9cdda2b751..1c21ad475b 100644 --- a/gnu/packages/code.scm +++ b/gnu/packages/code.scm @@ -200,6 +200,10 @@ highlighting your own code that seemed comprehensible when you wrote it.") (string-append "--with-universal-ctags=" #$(this-package-input "universal-ctags") "/bin/ctags") + ;; Otherwise this gets overridden in the 'configure phase. + (string-append "--with-python-interpreter=" + #$(this-package-input "python-wrapper") + "/bin/python") (string-append "--sysconfdir=" #$output "/share/gtags") "--localstatedir=/var" ; This needs to be a writable location. From 1bc09757868c26f14c119e3ce9842b86cb446f92 Mon Sep 17 00:00:00 2001 From: Leo Famulari Date: Wed, 6 Sep 2023 23:39:03 -0400 Subject: [PATCH 062/268] gnu: linux-libre: Update to 6.4.15. * gnu/packages/linux.scm (linux-libre-6.4-version): Update to 6.4.15. (linux-libre-6.4-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 bc1fedaad5..a347b8e8d2 100644 --- a/gnu/packages/linux.scm +++ b/gnu/packages/linux.scm @@ -490,7 +490,7 @@ corresponding UPSTREAM-SOURCE (an origin), using the given DEBLOB-SCRIPTS." ;; The current "stable" kernels. That is, the most recently released major ;; versions that are still supported upstream. -(define-public linux-libre-6.4-version "6.4.14") +(define-public linux-libre-6.4-version "6.4.15") (define-public linux-libre-6.4-gnu-revision "gnu") (define deblob-scripts-6.4 (linux-libre-deblob-scripts @@ -500,7 +500,7 @@ corresponding UPSTREAM-SOURCE (an origin), using the given DEBLOB-SCRIPTS." (base32 "1rwm09anyn4py1g877f9vh6ya86y2hfvlqx51bpa53dci5k0b0ds"))) (define-public linux-libre-6.4-pristine-source (let ((version linux-libre-6.4-version) - (hash (base32 "1rjh0jrn5qvxwzmyg478n08vckkld8r52nkc102ppqvsfhiy7skm"))) + (hash (base32 "1phlx375ln5pslw5vjqm029cdv6pzf4ang10xlrf90x5sb4fgy93"))) (make-linux-libre-source version (%upstream-linux-source version hash) deblob-scripts-6.4))) From ea8a92701102a31d0c6923693834575192e7caa3 Mon Sep 17 00:00:00 2001 From: Leo Famulari Date: Wed, 6 Sep 2023 23:39:17 -0400 Subject: [PATCH 063/268] gnu: linux-libre 6.1: Update to 6.1.52. * gnu/packages/linux.scm (linux-libre-6.1-version): Update to 6.1.52. (linux-libre-6.1-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 a347b8e8d2..04bcdd94d0 100644 --- a/gnu/packages/linux.scm +++ b/gnu/packages/linux.scm @@ -508,7 +508,7 @@ corresponding UPSTREAM-SOURCE (an origin), using the given DEBLOB-SCRIPTS." ;; The "longterm" kernels — the older releases with long-term upstream support. ;; Here are the support timelines: ;; -(define-public linux-libre-6.1-version "6.1.51") +(define-public linux-libre-6.1-version "6.1.52") (define-public linux-libre-6.1-gnu-revision "gnu") (define deblob-scripts-6.1 (linux-libre-deblob-scripts @@ -518,7 +518,7 @@ corresponding UPSTREAM-SOURCE (an origin), using the given DEBLOB-SCRIPTS." (base32 "1c73516nbhnz0cxjz38b5794dxygb8sznv9idiibw7ablmjbhd11"))) (define-public linux-libre-6.1-pristine-source (let ((version linux-libre-6.1-version) - (hash (base32 "0fqhmb6v28rssd44z7jw57mwvvskpl4kabjylck0pg54irnl9c2q"))) + (hash (base32 "0lis73mxnl7hxz8lyja6sfgmbym944l3k1h7dab6b4mw1nckfxsn"))) (make-linux-libre-source version (%upstream-linux-source version hash) deblob-scripts-6.1))) From 5db78e7c1b06d1b4892bdb3e153b95b21577271e Mon Sep 17 00:00:00 2001 From: Leo Famulari Date: Wed, 6 Sep 2023 23:39:43 -0400 Subject: [PATCH 064/268] gnu: linux-libre 5.15: Update to 5.15.131. * gnu/packages/linux.scm (linux-libre-5.15-version): Update to 5.15.131. (linux-libre-5.15-pristine-source): Update hash. --- gnu/packages/linux.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/linux.scm b/gnu/packages/linux.scm index 04bcdd94d0..67edc98013 100644 --- a/gnu/packages/linux.scm +++ b/gnu/packages/linux.scm @@ -523,7 +523,7 @@ corresponding UPSTREAM-SOURCE (an origin), using the given DEBLOB-SCRIPTS." (%upstream-linux-source version hash) deblob-scripts-6.1))) -(define-public linux-libre-5.15-version "5.15.130") +(define-public linux-libre-5.15-version "5.15.131") (define-public linux-libre-5.15-gnu-revision "gnu") (define deblob-scripts-5.15 (linux-libre-deblob-scripts @@ -533,7 +533,7 @@ corresponding UPSTREAM-SOURCE (an origin), using the given DEBLOB-SCRIPTS." (base32 "1c3lm0j401lv2lk39dmr4mlf5ic173snm7cc0cckl6czyvxr5ysy"))) (define-public linux-libre-5.15-pristine-source (let ((version linux-libre-5.15-version) - (hash (base32 "0qix62jsn3z9yccakac7fvqnip19zi05qn0w5wkgb7rj0x0lwimb"))) + (hash (base32 "0sacnbw48lblnqaj56nybh588sq4k84gwf0r5zinzyrryj8k6z4r"))) (make-linux-libre-source version (%upstream-linux-source version hash) deblob-scripts-5.15))) From 610752ac1ae8cef027c0c0afcef3e73b7747ef49 Mon Sep 17 00:00:00 2001 From: Olivier Dion Date: Thu, 7 Sep 2023 11:20:52 -0400 Subject: [PATCH 065/268] gnu: multipath-tools: Update to 0.9.6. * gnu/packages/linux.scm (multipath-tools): Update to 0.9.6. [#:make-flags]: Set systemd_prefix to output and remove SYSTEMDPATH. [#:phases]: Add phase 'no-fortfify-3 before 'build. [inputs]: Add util-linux "lib" output for libmount. Signed-off-by: Maxim Cournoyer --- gnu/packages/linux.scm | 20 ++++++++++++++++---- 1 file changed, 16 insertions(+), 4 deletions(-) diff --git a/gnu/packages/linux.scm b/gnu/packages/linux.scm index 67edc98013..b1bcda5e70 100644 --- a/gnu/packages/linux.scm +++ b/gnu/packages/linux.scm @@ -5548,7 +5548,7 @@ arrays when needed.") (define-public multipath-tools (package (name "multipath-tools") - (version "0.9.3") + (version "0.9.6") (home-page "https://github.com/opensvc/multipath-tools") (source (origin (method git-fetch) @@ -5556,7 +5556,7 @@ arrays when needed.") (file-name (git-file-name name version)) (sha256 (base32 - "0zcnr1135znizbnfqhqv3by9i2qwn5vg6kgmj6ma3yy1x1krx0d4")) + "1933iqh9r54pdl95yck0n4bw7jiiblymc964vlc1787qd4q012sz")) (modules '((guix build utils))) (snippet '(begin @@ -5574,7 +5574,7 @@ arrays when needed.") (string-append "prefix=" #$output) ;; Install Udev rules below this directory, relative ;; to the prefix. - "SYSTEMDPATH=lib") + (string-append "systemd_prefix=" #$output)) #:phases #~(modify-phases %standard-phases (add-after 'unpack 'patch-source @@ -5606,6 +5606,16 @@ arrays when needed.") (("CFLAGS \\+= " match) (string-append match "-Wno-error=unused-function "))))) (delete 'configure) ;no configure script + (add-before 'build 'no-fortify-3 + (lambda _ + ;; NOTE: The check made seems to wrongly assume the + ;; FORTIFY_SOURCE=3 is valid. However, when compiling, warnings + ;; are emitted from glibc, resulting in failed build. Fix this + ;; by forcing the usage of FORTIFY_SOURCE=2. + (substitute* "create-config.mk" + (("FORTIFY_SOURCE=3") + "FORTIFY_SOURCE=2")) + )) (add-before 'build 'set-LDFLAGS (lambda _ ;; Note: this cannot be passed as a make flag because that will @@ -5623,7 +5633,9 @@ arrays when needed.") liburcu lvm2 readline - eudev)) + eudev + ;; For libmount. + `(,util-linux "lib"))) (synopsis "Access block devices through multiple paths") (description "This package provides the following binaries to drive the From ff3eb851171f20654b8d6462c6b01ff3198a60e5 Mon Sep 17 00:00:00 2001 From: Olivier Dion Date: Thu, 7 Sep 2023 11:20:53 -0400 Subject: [PATCH 066/268] gnu: liburcu: Update to 0.14.0. * gnu/packages/datastructures.scm (liburcu): Update to 0.14.0. Signed-off-by: Maxim Cournoyer --- gnu/packages/datastructures.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/datastructures.scm b/gnu/packages/datastructures.scm index bd4f099d94..0689ef4259 100644 --- a/gnu/packages/datastructures.scm +++ b/gnu/packages/datastructures.scm @@ -213,14 +213,14 @@ allows multiple concurrent reader and writer threads.") (define-public liburcu (package (name "liburcu") - (version "0.13.1") + (version "0.14.0") (source (origin (method url-fetch) (uri (string-append "https://www.lttng.org/files/urcu/" "userspace-rcu-" version ".tar.bz2")) (sha256 (base32 - "10rh6v9j13622cjlzx31cfpghjy0kqkvn6pb42whwwcg5cyz64rj")))) + "0kwx4fi3gn4p4sdxqkz2zh4z0fv06q449bnz43zjqfad3lkbyhya")))) (build-system gnu-build-system) (native-inputs (list perl)) ; for tests From 2eb6df537c36da8bf8e81ff698421f6fb1bfd1ab Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Sun, 10 Sep 2023 09:19:18 -0400 Subject: [PATCH 067/268] gnu: Remove extraneous imports. * gnu/packages/perl.scm: Remove (gnu packages hurd) import. * gnu/packages/boost.scm: Likewise. Remove (srfi srfi-1). --- gnu/packages/boost.scm | 4 +--- gnu/packages/perl.scm | 1 - 2 files changed, 1 insertion(+), 4 deletions(-) diff --git a/gnu/packages/boost.scm b/gnu/packages/boost.scm index d2b676cc73..98dccf7f16 100644 --- a/gnu/packages/boost.scm +++ b/gnu/packages/boost.scm @@ -45,14 +45,12 @@ #:use-module (guix build-system trivial) #:use-module (gnu packages) #:use-module (gnu packages compression) - #:use-module (gnu packages hurd) #:use-module (gnu packages icu4c) #:use-module (gnu packages llvm) #:use-module (gnu packages perl) #:use-module (gnu packages python) #:use-module (gnu packages shells) - #:use-module (gnu packages mpi) - #:use-module (srfi srfi-1)) + #:use-module (gnu packages mpi)) (define (version-with-underscores version) (string-map (lambda (x) (if (eq? x #\.) #\_ x)) version)) diff --git a/gnu/packages/perl.scm b/gnu/packages/perl.scm index 6175a38365..8b82c272fc 100644 --- a/gnu/packages/perl.scm +++ b/gnu/packages/perl.scm @@ -76,7 +76,6 @@ #:use-module (gnu packages gd) #:use-module (gnu packages gl) #:use-module (gnu packages gtk) - #:use-module (gnu packages hurd) #:use-module (gnu packages image) #:use-module (gnu packages language) #:use-module (gnu packages less) From ab971e9c1922ae6eeec47401cb589ae15f29e15f Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Mon, 11 Sep 2023 10:56:03 +0300 Subject: [PATCH 068/268] system: vm-image: Remove duplicate packages. * gnu/system/examples/vm-image.tmpl (use-package-modules): Remove unneeded modules. (operating-system)[packages]: Remove nvi, wget. --- gnu/system/examples/vm-image.tmpl | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/gnu/system/examples/vm-image.tmpl b/gnu/system/examples/vm-image.tmpl index 343287eaf6..b68183a023 100644 --- a/gnu/system/examples/vm-image.tmpl +++ b/gnu/system/examples/vm-image.tmpl @@ -7,8 +7,8 @@ (use-modules (gnu) (guix) (srfi srfi-1)) (use-service-modules desktop mcron networking spice ssh xorg sddm) -(use-package-modules bootloaders certs fonts nvi - package-management wget xorg) +(use-package-modules bootloaders certs fonts + package-management xorg) (define vm-image-motd (plain-file "motd" " \x1b[1;37mThis is the GNU system. Welcome!\x1b[0m @@ -77,7 +77,7 @@ accounts.\x1b[0m root ALL=(ALL) ALL %wheel ALL=NOPASSWD: ALL\n")) - (packages (append (list font-bitstream-vera nss-certs nvi wget) + (packages (append (list font-bitstream-vera nss-certs) %base-packages)) (services From 3f76970fda82057f12429f81c41a47d8d8c3b954 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ludovic=20Court=C3=A8s?= Date: Sat, 2 Sep 2023 23:18:48 +0200 Subject: [PATCH 069/268] gnu: yelp: Provide dependencies to display "man:" URIs. MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Previously a command like the following one would fail to display the expected man page: guix shell yelp coreutils -C \ --expose=/tmp/.X11-unix --expose=/run/user \ --expose=/var/run/dbus --expose=/etc/machine-id -E ^DISPLAY -- \ /bin/sh -c \ 'export MANPATH=$GUIX_ENVIRONMENT/share/man; echo $MANPATH; yelp man:ls' * gnu/packages/gnome.scm (yelp)[arguments]: New field. [inputs]: Add ‘man-db’ and ‘groff-minimal’. Reported-by: Luis Felipe --- gnu/packages/gnome.scm | 25 +++++++++++++++++++++++++ 1 file changed, 25 insertions(+) diff --git a/gnu/packages/gnome.scm b/gnu/packages/gnome.scm index 3b80692e90..36fe1a80a1 100644 --- a/gnu/packages/gnome.scm +++ b/gnu/packages/gnome.scm @@ -142,6 +142,7 @@ #:use-module (gnu packages geo) #:use-module (gnu packages gperf) #:use-module (gnu packages graphviz) + #:use-module (gnu packages groff) #:use-module (gnu packages gstreamer) #:use-module (gnu packages gtk) #:use-module (gnu packages guile) @@ -7336,6 +7337,28 @@ jQuery.Syntax JavaScript libraries.") (base32 "0h9vf4fx056imjf8ibmn03wg1c3hniipy1nsm2jqi62lp1m19c95")))) (build-system glib-or-gtk-build-system) + (arguments + (list #:phases + #~(modify-phases %standard-phases + (add-after 'unpack 'set-man-file-name + (lambda* (#:key inputs #:allow-other-keys) + ;; Invoke 'man' directly instead of searching $PATH. + (substitute* '("libyelp/yelp-man-parser.c" + "libyelp/yelp-uri.c") + (("\"man\"") + (string-append "\"" + (search-input-file inputs "bin/man") + "\"")) + (("G_SPAWN_SEARCH_PATH") + "0")))) + (add-after 'install 'help-man-find-its-dependencies + (lambda* (#:key inputs outputs #:allow-other-keys) + ;; XXX: Currently 'man' looks for 'groff' in $PATH in one + ;; case. This should be fixed in 'man-db' proper. + (wrap-program (string-append (assoc-ref outputs "out") + "/bin/yelp") + `("PATH" ":" prefix + (,(dirname (search-input-file inputs "bin/groff")))))))))) (native-inputs (list `(,glib "bin") ; for glib-genmarshal, etc. intltool @@ -7347,6 +7370,8 @@ jQuery.Syntax JavaScript libraries.") (list gsettings-desktop-schemas libhandy libxslt + man-db ;for URIs like "man:ls" + groff-minimal ;ditto sqlite webkitgtk yelp-xsl)) From d514b7b4adf9aef198e5aedecffaf6f7014c0044 Mon Sep 17 00:00:00 2001 From: Thanos Apollo Date: Mon, 14 Aug 2023 12:38:19 +0300 Subject: [PATCH 070/268] gnu: Add emacs-yeetube. MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * gnu/packages/emacs-xyz.scm (emacs-yeetube): New variable. Signed-off-by: Ludovic Courtès --- gnu/packages/emacs-xyz.scm | 28 ++++++++++++++++++++++++++++ 1 file changed, 28 insertions(+) diff --git a/gnu/packages/emacs-xyz.scm b/gnu/packages/emacs-xyz.scm index e971edb676..355afbf8fb 100644 --- a/gnu/packages/emacs-xyz.scm +++ b/gnu/packages/emacs-xyz.scm @@ -134,6 +134,7 @@ ;;; Copyright © 2023 Ahmad Draidi ;;; Copyright © 2023 Sergiu Ivanov ;;; Copyright © 2023 Camilo Q.S. (Distopico) +;;; Copyright © 2023 Thanos Apollo ;;; ;;; This file is part of GNU Guix. ;;; @@ -27896,6 +27897,33 @@ as playing them in some video player, or downloading them.") and comments.") (license license:gpl3+)))) +(define-public emacs-yeetube + (package + (name "emacs-yeetube") + (version "1.4.2") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://git.sr.ht/~thanosapollo/yeetube.el") + (commit version))) + (sha256 + (base32 + "0vfap6sri6qnswrjsp6qvmrp98bvrfh58gwdqbjiakq1fzvcrm03")) + (file-name (git-file-name name version)))) + (build-system emacs-build-system) + (inputs + (list mpv yt-dlp)) + (home-page "https://sr.ht/~thanosapollo/yeetube.el") + (synopsis "Youtube & Invidious front-end for Emacs") + (description + "This package offers an Emacs interface that allows you to search YouTube +or an Invidious instance for a specific query. The search results are shown as +links in an org-mode buffer. The videos can be opened to a user-defined video +player(by default mpv) or downloaded using yt-dlp. This package also includes +a yt-dlp front-end.") + (license license:gpl3+))) + (define-public emacs-org-web-tools (package (name "emacs-org-web-tools") From 251bf55f507860d9775b520585c0fdd7ede7d534 Mon Sep 17 00:00:00 2001 From: Fabio Natali Date: Sun, 13 Aug 2023 16:16:15 +0100 Subject: [PATCH 071/268] gnu: Add emacs-notmuch-indicator. MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * gnu/packages/emacs-xyz.scm (emacs-notmuch-indicator): New variable. Signed-off-by: Ludovic Courtès --- gnu/packages/emacs-xyz.scm | 21 +++++++++++++++++++++ 1 file changed, 21 insertions(+) diff --git a/gnu/packages/emacs-xyz.scm b/gnu/packages/emacs-xyz.scm index 355afbf8fb..4a4aa85dbc 100644 --- a/gnu/packages/emacs-xyz.scm +++ b/gnu/packages/emacs-xyz.scm @@ -30302,6 +30302,27 @@ displays as you type thanks to Helm, though @command{notmuch-search} does the real search.") (license license:gpl3+))) +(define-public emacs-notmuch-indicator + (package + (name "emacs-notmuch-indicator") + (version "1.0.1") + (home-page "https://git.sr.ht/~protesilaos/notmuch-indicator") + (source (origin + (method url-fetch) + (uri (string-append + "https://elpa.gnu.org/packages/notmuch-indicator-" version + ".tar")) + (sha256 + (base32 + "1n5k2ikk93mdwqqysf6l7gd8i6iazk8yvbqpf8xnz5zny248cc2x")))) + (build-system emacs-build-system) + (synopsis "Display a mode line indicator with @code{notmuch-count} output") + (description "This package renders an indicator with an email count of the +@code{notmuch} index on the Emacs mode line. The underlying mechanism is that of +@code{notmuch-count}, which is used to find the number of items that match the +given search terms.") + (license license:gpl3+))) + (define-public emacs-notmuch-maildir (package (name "emacs-notmuch-maildir") From 1cca04d7cff75fc1fe8913b23096109a17d43a97 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ludovic=20Court=C3=A8s?= Date: Mon, 11 Sep 2023 23:35:28 +0200 Subject: [PATCH 072/268] gnu: emacs-php-mode: Update URL. * gnu/packages/emacs-xyz.scm (emacs-php-mode)[source, home-page]: Update URL and factorize it. Co-authored-by: Piotr Kwiecinski --- gnu/packages/emacs-xyz.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/emacs-xyz.scm b/gnu/packages/emacs-xyz.scm index 4a4aa85dbc..a380abc4ed 100644 --- a/gnu/packages/emacs-xyz.scm +++ b/gnu/packages/emacs-xyz.scm @@ -18304,11 +18304,12 @@ in Emacs.") (package (name "emacs-php-mode") (version "1.25.0") + (home-page "https://github.com/emacs-php/php-mode") (source (origin (method git-fetch) (uri (git-reference - (url "https://github.com/ejmr/php-mode") + (url home-page) (commit (string-append "v" version)))) (file-name (git-file-name name version)) (sha256 @@ -18331,7 +18332,6 @@ in Emacs.") (lambda _ (chdir "lisp")))))) (propagated-inputs (list emacs-projectile)) - (home-page "https://github.com/ejmr/php-mode") (synopsis "Major mode for editing PHP code") (description "PHP mode is a major mode for editing PHP source code. It's an extension From a35bfb61168ee706a94556a5bf834d27c022d2bd Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Sergio=20Pastor=20P=C3=A9rez?= Date: Sun, 10 Sep 2023 17:42:05 +0200 Subject: [PATCH 073/268] gnu: Add mini. MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * gnu/packages/image.scm (mini): New variable. Co-authored-by: Ludovic Courtès --- gnu/packages/image.scm | 39 +++++++++++++++++++++++++++++++++++++++ 1 file changed, 39 insertions(+) diff --git a/gnu/packages/image.scm b/gnu/packages/image.scm index 75f9e3c691..b41c1eac73 100644 --- a/gnu/packages/image.scm +++ b/gnu/packages/image.scm @@ -1931,6 +1931,45 @@ medical image data, e.g. magnetic resonance image (MRI) and functional MRI (home-page "https://niftilib.sourceforge.net") (license license:public-domain))) +(define-public mini + (package + (name "mini") + (version "0.9.14") + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/pulzed/mINI") + (commit version))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "01wn7h9rjz9h6cr11dd62jsb3315d1h6c33pdmwi2l7d8a4n3h8d")))) + (build-system gnu-build-system) + (arguments + (list #:phases + #~(modify-phases %standard-phases + (delete 'build) + (delete 'configure) + (replace 'check + (lambda* (#:key tests? #:allow-other-keys) + (when tests? + (with-directory-excursion "tests" + (for-each (lambda (test) + (let ((test-name (basename test + ".cpp"))) + (invoke "./build.sh" test-name) + (invoke "./run.sh" test-name))) + (find-files "." ".cpp")))))) + (replace 'install + (lambda _ + (install-file "src/mini/ini.h" + (string-append #$output "/include/mini"))))))) + (home-page "https://github.com/pulzed/mINI") + (synopsis "INI file reader and writer header library") + (description + "This is a tiny, header-only C++ library for manipulating INI files.") + (license license:expat))) + (define-public gpick (package (name "gpick") From 3235bfa25a82c1dbe6a8a0ec83ae98f840d1deb4 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Sergio=20Pastor=20P=C3=A9rez?= Date: Sun, 10 Sep 2023 17:42:06 +0200 Subject: [PATCH 074/268] gnu: Add picket. MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * gnu/packages/image.scm (picket): New variable. Signed-off-by: Ludovic Courtès --- gnu/packages/image.scm | 46 ++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 46 insertions(+) diff --git a/gnu/packages/image.scm b/gnu/packages/image.scm index b41c1eac73..403409975a 100644 --- a/gnu/packages/image.scm +++ b/gnu/packages/image.scm @@ -1970,6 +1970,52 @@ medical image data, e.g. magnetic resonance image (MRI) and functional MRI "This is a tiny, header-only C++ library for manipulating INI files.") (license license:expat))) +(define-public picket + (package + (name "picket") + (version "1.3") + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/rajter/picket") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "1zhpynyakjx9nc51b1j80b4y3138p3l380kp1cqmmjx2n9430144")) + (snippet '(begin + ;; bundled mINI header library. + (delete-file "src/cfg/ini.h"))))) + (native-inputs (list pkg-config)) + (inputs (list gtkmm-3 mini)) + (arguments + (list #:tests? #f + #:phases #~(modify-phases %standard-phases + (add-after 'unpack 'fix-mini-includes + (lambda _ + (substitute* '("src/cfg/config.h" + "src/cfg/config.cpp") + (("#include \"ini.h\"") + "#include \"mini/ini.h\"")) + (substitute* "src/main.cpp" + (("/usr") + #$output)))) + (add-after 'unpack 'fix-cmake-paths + (lambda* (#:key inputs #:allow-other-keys) + (substitute* "CMakeLists.txt" + (("src/cfg/ini.h") + (search-input-file inputs + "/include/mini/ini.h")) + (("/usr/") + #$output))))))) + (build-system cmake-build-system) + (home-page "https://github.com/rajter/picket") + (synopsis "Screen color picker with custom format output") + (description + "Picket is a screen color picker that includes a magnifier and supports +custom formats for representing color values..") + (license license:gpl3+))) + (define-public gpick (package (name "gpick") From 5ff9afb5fdc6e34936683524907343859976a805 Mon Sep 17 00:00:00 2001 From: Cayetano Santos Date: Mon, 21 Aug 2023 09:46:34 +0200 Subject: [PATCH 075/268] gnu: emacs-mastodon: Update to 1.0.0-1.20dec88. MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * gnu/packages/emacs-xyz.scm (emacs-mastodon): Update to 1.0.0-1.20dec88. Signed-off-by: Ludovic Courtès --- gnu/packages/emacs-xyz.scm | 63 ++++++++++++++++++++------------------ 1 file changed, 33 insertions(+), 30 deletions(-) diff --git a/gnu/packages/emacs-xyz.scm b/gnu/packages/emacs-xyz.scm index a380abc4ed..6063dc8958 100644 --- a/gnu/packages/emacs-xyz.scm +++ b/gnu/packages/emacs-xyz.scm @@ -32794,37 +32794,40 @@ time.") (license license:gpl3+))) (define-public emacs-mastodon - (package - (name "emacs-mastodon") - (version "1.0.0") - (source (origin - (method git-fetch) - (uri (git-reference - (url "https://codeberg.org/martianh/mastodon.el") - (commit version))) - (file-name (git-file-name name version)) - (sha256 - (base32 - "13swcbvwhjl8ksrgzvmfafkgd3iz8znk49bs1n48w3g9qvh097w7")))) - (build-system emacs-build-system) - (arguments - (list #:phases - #~(modify-phases %standard-phases - ;; Move the source files to the top level, which is included in - ;; the EMACSLOADPATH. - (add-after 'unpack 'move-source-files - (lambda _ - (let ((el-files (find-files "./lisp" ".*\\.el$"))) - (for-each (lambda (f) - (rename-file f (basename f))) - el-files))))))) - (propagated-inputs - (list emacs-request)) - (home-page "https://codeberg.org/martianh/mastodon.el") - (synopsis "Emacs client for Mastodon") - (description "@code{mastodon.el} is an Emacs client for Mastodon, the + ;; No release in ~1 year, hence this snapshot. + (let ((commit "20dec8871c9bb5f5e418bfc197e7533b5e3065e3") + (revision "1")) + (package + (name "emacs-mastodon") + (version (git-version "1.0.0" revision commit)) + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://codeberg.org/martianh/mastodon.el") + (commit commit))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "15cfjny99yw5frdp8nlyazlwgscvfvbinsj0fbdfprxf50k2zjs6")))) + (build-system emacs-build-system) + (arguments + (list #:phases + #~(modify-phases %standard-phases + ;; Move the source files to the top level, which is included in + ;; the EMACSLOADPATH. + (add-after 'unpack 'move-source-files + (lambda _ + (let ((el-files (find-files "./lisp" ".*\\.el$"))) + (for-each (lambda (f) + (rename-file f (basename f))) + el-files))))))) + (propagated-inputs + (list emacs-request emacs-ts emacs-persist)) + (home-page "https://codeberg.org/martianh/mastodon.el") + (synopsis "Emacs client for Mastodon") + (description "@code{mastodon.el} is an Emacs client for Mastodon, the federated microblogging social network.") - (license license:gpl3+))) + (license license:gpl3+)))) (define-public emacs-ebdb (package From a5b5df7f7fbbb98487b2e7a59941efee6492bc7f Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Mon, 11 Sep 2023 15:46:47 -0400 Subject: [PATCH 076/268] gnu-maintenance: Support URI list of mixed mirrors, HTTP URLs. Fixes . * guix/gnu-maintenance.scm (import-html-updatable-release): Update doc. : New nested procedure. Apply it to the origin URI. Reported-by: kiasoc5 --- guix/gnu-maintenance.scm | 29 ++++++++++++++++++----------- 1 file changed, 18 insertions(+), 11 deletions(-) diff --git a/guix/gnu-maintenance.scm b/guix/gnu-maintenance.scm index 5a84fcb117..302243559d 100644 --- a/guix/gnu-maintenance.scm +++ b/guix/gnu-maintenance.scm @@ -975,17 +975,24 @@ updater." ((url-predicate http-url?) package))) (define* (import-html-updatable-release package #:key (version #f)) - "Return the latest release of PACKAGE. Do that by crawling the HTML page of -the directory containing its source tarball. Optionally include a VERSION -string to fetch a specific version." - (let* ((uri (string->uri - (match (origin-uri (package-source package)) - ((and (? string?) - (? (cut string-prefix? "mirror://" <>) url)) - ;; Retrieve the authoritative HTTP URL from a mirror. - (http-url? url)) - ((? string? url) url) - ((url _ ...) url)))) + "Return the latest release of PACKAGE else #f. Do that by crawling the HTML +page of the directory containing its source tarball. Optionally include a +VERSION string to fetch a specific version." + + (define (expand-uri uri) + (string->uri + (match uri + ((and (? string?) (? (cut string-prefix? "mirror://" <>) url)) + ;; Retrieve the authoritative HTTP URL from a mirror. + (http-url? url)) + ((? string? url) + url) + ((url _ ...) + ;; This case is for when the URI is a list of possibly mirror URLs as + ;; well as HTTP URLs. + (expand-uri url))))) + + (let* ((uri (expand-uri (origin-uri (package-source package)))) (custom (assoc-ref (package-properties package) 'release-monitoring-url)) (base (or custom From a9d5d1d9dd186ab21ee44ccf9b5c777e79f83c5b Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Mon, 11 Sep 2023 23:30:43 -0400 Subject: [PATCH 077/268] Revert "gnu-maintenance: Support URI list of mixed mirrors, HTTP URLs." This reverts commit a5b5df7f7fbbb98487b2e7a59941efee6492bc7f. Pushed too early. --- guix/gnu-maintenance.scm | 29 +++++++++++------------------ 1 file changed, 11 insertions(+), 18 deletions(-) diff --git a/guix/gnu-maintenance.scm b/guix/gnu-maintenance.scm index 302243559d..5a84fcb117 100644 --- a/guix/gnu-maintenance.scm +++ b/guix/gnu-maintenance.scm @@ -975,24 +975,17 @@ updater." ((url-predicate http-url?) package))) (define* (import-html-updatable-release package #:key (version #f)) - "Return the latest release of PACKAGE else #f. Do that by crawling the HTML -page of the directory containing its source tarball. Optionally include a -VERSION string to fetch a specific version." - - (define (expand-uri uri) - (string->uri - (match uri - ((and (? string?) (? (cut string-prefix? "mirror://" <>) url)) - ;; Retrieve the authoritative HTTP URL from a mirror. - (http-url? url)) - ((? string? url) - url) - ((url _ ...) - ;; This case is for when the URI is a list of possibly mirror URLs as - ;; well as HTTP URLs. - (expand-uri url))))) - - (let* ((uri (expand-uri (origin-uri (package-source package)))) + "Return the latest release of PACKAGE. Do that by crawling the HTML page of +the directory containing its source tarball. Optionally include a VERSION +string to fetch a specific version." + (let* ((uri (string->uri + (match (origin-uri (package-source package)) + ((and (? string?) + (? (cut string-prefix? "mirror://" <>) url)) + ;; Retrieve the authoritative HTTP URL from a mirror. + (http-url? url)) + ((? string? url) url) + ((url _ ...) url)))) (custom (assoc-ref (package-properties package) 'release-monitoring-url)) (base (or custom From 2a7f031ca9d6d16fe0264023d8beca02b3ac0050 Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Mon, 11 Sep 2023 23:37:34 -0400 Subject: [PATCH 078/268] gnu-maintenance: Support URI list of mixed mirrors, HTTP URLs. This reinstate commit a5b5df7f7fbbb98487b2e7a59941efee6492bc7f with a fix to the inner expand-uri procedure. --- guix/gnu-maintenance.scm | 29 ++++++++++++++++++----------- 1 file changed, 18 insertions(+), 11 deletions(-) diff --git a/guix/gnu-maintenance.scm b/guix/gnu-maintenance.scm index 5a84fcb117..881e941fbf 100644 --- a/guix/gnu-maintenance.scm +++ b/guix/gnu-maintenance.scm @@ -975,17 +975,24 @@ updater." ((url-predicate http-url?) package))) (define* (import-html-updatable-release package #:key (version #f)) - "Return the latest release of PACKAGE. Do that by crawling the HTML page of -the directory containing its source tarball. Optionally include a VERSION -string to fetch a specific version." - (let* ((uri (string->uri - (match (origin-uri (package-source package)) - ((and (? string?) - (? (cut string-prefix? "mirror://" <>) url)) - ;; Retrieve the authoritative HTTP URL from a mirror. - (http-url? url)) - ((? string? url) url) - ((url _ ...) url)))) + "Return the latest release of PACKAGE else #f. Do that by crawling the HTML +page of the directory containing its source tarball. Optionally include a +VERSION string to fetch a specific version." + + (define (expand-uri uri) + (match uri + ((and (? string?) (? (cut string-prefix? "mirror://" <>) url)) + ;; Retrieve the authoritative HTTP URL from a mirror. + (http-url? url)) + ((? string? url) + url) + ((url _ ...) + ;; This case is for when the URI is a list of possibly + ;; mirror URLs as well as HTTP URLs. + (expand-uri url)))) + + (let* ((uri (string->uri + (expand-uri (origin-uri (package-source package))))) (custom (assoc-ref (package-properties package) 'release-monitoring-url)) (base (or custom From daeeaa221605726d8853b00261619ba039bd6db7 Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Mon, 11 Sep 2023 23:48:19 -0400 Subject: [PATCH 079/268] gnu: emacs-magit: Update to 3.3.0-6.7a1d503. * gnu/packages/emacs-xyz.scm (emacs-magit): Update to 3.3.0-6.7a1d503. --- gnu/packages/emacs-xyz.scm | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) diff --git a/gnu/packages/emacs-xyz.scm b/gnu/packages/emacs-xyz.scm index 6063dc8958..a4c6f45feb 100644 --- a/gnu/packages/emacs-xyz.scm +++ b/gnu/packages/emacs-xyz.scm @@ -1464,10 +1464,10 @@ libgit2 bindings for Emacs, intended to boost the performance of Magit.") (license license:gpl2+)))) (define-public emacs-magit - ;; Use this unreleased commit to benefit from a recent change needed to - ;; add Reviewed-by: tags for any contributor in commit messages. - (let ((commit "186414ae418a07a46c413f05c68413a76256a05e") - (revision "5")) + ;; Use this unreleased commit to benefit from a recent improvements with + ;; regard to adding git trailers such as "Reviewed-by". + (let ((commit "7a1d50347086678217cf90a32dda277b76ea3081") + (revision "6")) (package (name "emacs-magit") (version (git-version "3.3.0" revision commit)) @@ -1479,7 +1479,7 @@ libgit2 bindings for Emacs, intended to boost the performance of Magit.") (commit commit))) (file-name (git-file-name name version)) (sha256 - (base32 "0rhsbcjfjw0z3vy2ix30y4h55c0cx4lyvz6mbijwbbjryln71kpj")))) + (base32 "1yn3v24w0sx6r8jqw8blfvyjdjfz5xa7c3x8p6xw1lj7b81l8i0l")))) (build-system emacs-build-system) (arguments (list From 288799d3e8fa995a8bdc1f460378484124a30248 Mon Sep 17 00:00:00 2001 From: Christopher Baines Date: Tue, 5 Sep 2023 12:35:10 +0100 Subject: [PATCH 080/268] gnu: musl-cross: Remove i586-gnu from supported-systems. As I don't think musl supports the Hurd. * gnu/packages/heads.scm (musl-cross)[supported-systems]: Remove i586-gnu. --- gnu/packages/heads.scm | 1 + 1 file changed, 1 insertion(+) diff --git a/gnu/packages/heads.scm b/gnu/packages/heads.scm index 212849f2a9..268d4d0198 100644 --- a/gnu/packages/heads.scm +++ b/gnu/packages/heads.scm @@ -158,6 +158,7 @@ done (uri "http://www.musl-libc.org/releases/musl-1.1.24.tar.gz") (sha256 (base32 "18r2a00k82hz0mqdvgm7crzc7305l36109c0j9yjmkxj2alcjw0k")))))) + (supported-systems (delete "i586-gnu" %supported-systems)) (home-page "https://github.com/osresearch/heads") (synopsis "Musl-cross gcc 5 toolchain") (description "Musl-cross toolchain: binutils, gcc 5 and musl.") From 0e08ad7f19d5b29a4883468552b5d213a7bdb66e Mon Sep 17 00:00:00 2001 From: Christopher Baines Date: Tue, 5 Sep 2023 12:35:11 +0100 Subject: [PATCH 081/268] gnu: linux-libre-headers: Remove i586-gnu from supported-systems. As I don't think attempting to build for the Hurd is useful. * gnu/packages/heads.scm (make-linux-libre-headers*): Remove i586-gnu from supported-systems. --- gnu/packages/linux.scm | 1 + 1 file changed, 1 insertion(+) diff --git a/gnu/packages/linux.scm b/gnu/packages/linux.scm index b1bcda5e70..91109c41d9 100644 --- a/gnu/packages/linux.scm +++ b/gnu/packages/linux.scm @@ -739,6 +739,7 @@ corresponding UPSTREAM-SOURCE (an origin), using the given DEBLOB-SCRIPTS." (format p "~a-default~%" ,version))))))) #:allowed-references () #:tests? #f)) + (supported-systems (delete "i586-gnu" %supported-systems)) (home-page "https://www.gnu.org/software/linux-libre/") (synopsis "GNU Linux-Libre kernel headers") (description "Headers of the Linux-Libre kernel.") From 53f510dad6cc1b55b4abdbbfd55e507a9463a80f Mon Sep 17 00:00:00 2001 From: Christopher Baines Date: Tue, 5 Sep 2023 12:35:12 +0100 Subject: [PATCH 082/268] gnu: skalibs: Remove i586-gnu from %supported-systems. * gnu/packages/skarnet.scm (skalibs)[supported-systems]: Remove i586-gnu. --- gnu/packages/skarnet.scm | 1 + 1 file changed, 1 insertion(+) diff --git a/gnu/packages/skarnet.scm b/gnu/packages/skarnet.scm index 2c7b0f9c23..6781e2eb58 100644 --- a/gnu/packages/skarnet.scm +++ b/gnu/packages/skarnet.scm @@ -49,6 +49,7 @@ (substitute* "Makefile" (("\\$\\(wildcard src/lib\\*/\\*.c\\)") "$(sort $(wildcard src/lib*/*.c))"))))))) + (supported-systems (delete "i586-gnu" %supported-systems)) (home-page "https://skarnet.org/software/skalibs/") (synopsis "Platform abstraction libraries for skarnet.org software") (description From 93cb2880d6c45f113c3b18d3732049115ef08070 Mon Sep 17 00:00:00 2001 From: Christopher Baines Date: Tue, 12 Sep 2023 08:15:07 +0100 Subject: [PATCH 083/268] gnu: nar-herder: Use guile-next. As this provides suspendable soft/custom ports, which I'd like to use. * gnu/packages/package-management.scm (nar-herder)[native-inputs,inputs]: Use guile-next. --- gnu/packages/package-management.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/package-management.scm b/gnu/packages/package-management.scm index aa24798071..51a5d52131 100644 --- a/gnu/packages/package-management.scm +++ b/gnu/packages/package-management.scm @@ -1771,7 +1771,7 @@ in an isolated environment, in separate namespaces.") guile-gnutls ;; Guile libraries are needed here for cross-compilation. - (car (assoc-ref (package-native-inputs guix) "guile")) + guile-next guile-json-4 guile-gcrypt guix @@ -1783,7 +1783,7 @@ in an isolated environment, in separate namespaces.") guile-sqlite3)) (inputs (list bash-minimal - (car (assoc-ref (package-native-inputs guix) "guile")))) + guile-next)) (propagated-inputs (list guile-json-4 guile-gcrypt From 3acd355455a74a6e08bdcecc72e314c27e7c56b3 Mon Sep 17 00:00:00 2001 From: Andy Tai Date: Thu, 7 Sep 2023 18:27:09 +0800 Subject: [PATCH 084/268] gnu: svt-av1: Update to 1.7.0. MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * gnu/packages/video.scm (svt-av1): Update to 1.7.0. Signed-off-by: 宋文武 Signed-off-by: Christopher Baines --- gnu/packages/video.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/video.scm b/gnu/packages/video.scm index 153fe354d5..e8cee27382 100644 --- a/gnu/packages/video.scm +++ b/gnu/packages/video.scm @@ -5255,7 +5255,7 @@ transcode or reformat the videos in any way, producing perfect backups.") (define-public svt-av1 (package (name "svt-av1") - (version "1.3.0") + (version "1.7.0") (source (origin (method git-fetch) @@ -5264,7 +5264,7 @@ transcode or reformat the videos in any way, producing perfect backups.") (commit (string-append "v" version)))) (file-name (git-file-name name version)) (sha256 - (base32 "0blnla32yz665bx0xyx8lrjs2wqd2xhpbqwwpz72mq7zf341j8vv")))) + (base32 "1308g0nqxq65h76a7h91999cbglkwihgrpid64kdn0r9vh6399sq")))) (build-system cmake-build-system) (arguments ;; The test suite tries to download test data and git clone a 3rd-party From 8d51e31f862181c835dc75b74033be325d85d967 Mon Sep 17 00:00:00 2001 From: Hilton Chain Date: Tue, 12 Sep 2023 08:29:24 +0100 Subject: [PATCH 085/268] gnu: sqlite-next: Update to 3.42.0. * gnu/packages/sqlite.scm (sqlite-next): Update to 3.42.0. Signed-off-by: Christopher Baines --- gnu/packages/sqlite.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/sqlite.scm b/gnu/packages/sqlite.scm index 2e727bd933..a4db47270d 100644 --- a/gnu/packages/sqlite.scm +++ b/gnu/packages/sqlite.scm @@ -115,10 +115,10 @@ is in the public domain.") (define-public sqlite-next (package (inherit sqlite) - (version "3.40.0") + (version "3.42.0") (source (origin (method url-fetch) (uri (sqlite-uri version 2022)) (sha256 (base32 - "1rw0i63822pdkb3a16sqj4jdcp5zg0ffjmi26mshqw6jfqh5acq3")))))) + "19lc11fwl7jfv94hnjih0gr41jakz38ra23cbk5449vf3hbgvg3s")))))) From d6ad06cd6c9d96735aea5fe98c7dbf27adec25db Mon Sep 17 00:00:00 2001 From: Hilton Chain Date: Thu, 27 Jul 2023 22:37:14 +0800 Subject: [PATCH 086/268] gnu: python-apsw: Update to 3.42.0.1. * gnu/packages/databases.scm (python-apsw): Update to 3.42.0.1. Signed-off-by: Christopher Baines --- gnu/packages/databases.scm | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/gnu/packages/databases.scm b/gnu/packages/databases.scm index 3d41649f4d..8d87f238b5 100644 --- a/gnu/packages/databases.scm +++ b/gnu/packages/databases.scm @@ -3706,7 +3706,7 @@ PickleShare.") (define-public python-apsw (package (name "python-apsw") - (version "3.40.0.0") + (version "3.42.0.1") ;; The compressed release has fetching functionality disabled. (source (origin @@ -3716,11 +3716,11 @@ PickleShare.") version "/apsw-" version ".zip")) (sha256 (base32 - "02sgja00azvd08wi2wm105apmhp2644s7aw9b1zdg3dkcwjnsiad")))) + "0dr7zymn45x2793cilr709rnwn9g1c4n4vzln57y2lhj7420ykic")))) (build-system pyproject-build-system) (native-inputs (list python-cython unzip)) - (inputs (list sqlite-next)) ;SQLite 3.40 required. + (inputs (list sqlite-next)) ;SQLite 3.42 required. (arguments (list #:phases From 8294f45dfc849f3006ea362ce754d04c5ecf89db Mon Sep 17 00:00:00 2001 From: Hilton Chain Date: Thu, 27 Jul 2023 22:43:07 +0800 Subject: [PATCH 087/268] gnu: python-cgatcore: Update to 0.6.15. * gnu/packages/bioinformatics.scm (python-cgatcore): Update to 0.6.15. Signed-off-by: Christopher Baines --- 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 8968325e83..9500751a96 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -19134,7 +19134,7 @@ coordinates between different assemblies.") (define-public python-cgatcore (package (name "python-cgatcore") - (version "0.6.14") + (version "0.6.15") ;; The version of pypi does not include test data. (source (origin (method git-fetch) @@ -19144,7 +19144,7 @@ coordinates between different assemblies.") (file-name (git-file-name name version)) (sha256 (base32 - "0fjjaski39j8b7v21wldmbwwsfhicngajah7n4skafi56kdck33p")))) + "103hpdnkqr3a34blbicshk56j36g652s0g1zi9isppc5dngn0s18")))) (build-system pyproject-build-system) (arguments (list From cdddc6bc28e2026b78800533069688e510df42f2 Mon Sep 17 00:00:00 2001 From: "Artyom V. Poptsov" Date: Thu, 24 Aug 2023 09:05:04 +0300 Subject: [PATCH 088/268] gnu: guile-png: Update to 0.7.1 * gnu/packages/guile-xyz.scm (guile-png): Update to 0.7.1. [arguments]: Update style and delete "strip" phase. [description]: Update. Signed-off-by: Christopher Baines --- gnu/packages/guile-xyz.scm | 15 +++++++++------ 1 file changed, 9 insertions(+), 6 deletions(-) diff --git a/gnu/packages/guile-xyz.scm b/gnu/packages/guile-xyz.scm index b40079c383..01dbe9b3ad 100644 --- a/gnu/packages/guile-xyz.scm +++ b/gnu/packages/guile-xyz.scm @@ -3856,7 +3856,7 @@ debugging code.") (define-public guile-png (package (name "guile-png") - (version "0.7.0") + (version "0.7.1") (source (origin (method git-fetch) (uri (git-reference @@ -3865,10 +3865,13 @@ debugging code.") (file-name (string-append name "-" version "-checkout")) (sha256 (base32 - "0nkim662lb48y8n5hik8rrj76600v2inwaxwnfpdny7h2j0yq1wm")))) + "0y65795s9bs69msqvdbq8h34n00bkfs5v1d44wz21nwdffvq6557")))) (build-system gnu-build-system) (arguments - `(#:make-flags '("GUILE_AUTO_COMPILE=0"))) ;to prevent guild warnings + (list + #:make-flags #~(list "GUILE_AUTO_COMPILE=0") ;to prevent guild warnings + #:phases #~(modify-phases %standard-phases + (delete 'strip)))) (native-inputs (list autoconf automake pkg-config @@ -3884,9 +3887,9 @@ debugging code.") (synopsis "PNG file parsing library for Guile") (description "@code{guile-png} is a GNU Guile library for working with the -@url{https://en.wikipedia.org/wiki/PNG, PNG format}. This library provides -API for reading and writing PNG data, as well as some basic image processing -filters.") +@url{https://en.wikipedia.org/wiki/PNG, PNG format}. This library provides API for +reading and writing PNG data, as well as some graphic primitives and basic image +processing filters.") (license license:gpl3+))) (define-public nomad From e2a7c227dea5b361e2ebdbba24b923d1922a79d0 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?=E5=AE=8B=E6=96=87=E6=AD=A6?= Date: Sat, 2 Sep 2023 11:50:29 +0800 Subject: [PATCH 089/268] gnu: xfce4-terminal: Update to 1.1.0. * gnu/packages/xfce.scm (xfce4-terminal): Update to 1.1.0. Signed-off-by: Christopher Baines --- gnu/packages/xfce.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/xfce.scm b/gnu/packages/xfce.scm index 3292db4f58..cb2121f338 100644 --- a/gnu/packages/xfce.scm +++ b/gnu/packages/xfce.scm @@ -1082,7 +1082,7 @@ features playback of local media files, DVD/CD and live streams.") (define-public xfce4-terminal (package (name "xfce4-terminal") - (version "1.0.4") + (version "1.1.0") (source (origin (method url-fetch) (uri (string-append "https://archive.xfce.org/src/apps/" name "/" @@ -1090,7 +1090,7 @@ features playback of local media files, DVD/CD and live streams.") name "-" version ".tar.bz2")) (sha256 (base32 - "1x5saijxykxmn2hksf4qvaj965b6i0wy62z9hgrc2vvwmxbmkrbq")))) + "18yl792x617qa90g6caw4cy1arfl847majjxkxs0k6rb4ivk70j0")))) (build-system gnu-build-system) (arguments (list From 30ec6f2fb5bdac917df16d1efa122fad81518a0e Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Tue, 12 Sep 2023 12:26:41 +0200 Subject: [PATCH 090/268] gnu: macs: Update to 2.2.9.1. * gnu/packages/bioinformatics.scm (macs): Update to 2.2.9.1. [build-system]: Use pyproject-build-system. [arguments]: Remove custom 'check phase. [native-inputs]: Move python-cython from here... [inputs]: ...and python-numpy from here... [propagated-inputs]: ...to here. --- gnu/packages/bioinformatics.scm | 20 ++++++++------------ 1 file changed, 8 insertions(+), 12 deletions(-) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 9500751a96..0df5bbfad5 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -7023,7 +7023,7 @@ experiments.") (define-public macs (package (name "macs") - (version "2.2.7.1") + (version "2.2.9.1") (source (origin ;; The PyPi tarball does not contain tests. (method git-fetch) @@ -7033,7 +7033,7 @@ experiments.") (file-name (git-file-name name version)) (sha256 (base32 - "08zsgh65xbpv1md2s3wqmrk9g2mz6izmn59ryw5lbac54120p291")) + "10vwc09fq4nvbd39hax1949mvq2wvkgz0k3p2zqmqwq8hv9r5l0j")) (modules '((guix build utils))) ;; Remove files generated by Cython (snippet @@ -7048,21 +7048,17 @@ experiments.") ;; Python 3.10 is in fact more recent than 3.6. (substitute* "setup.py" (("float\\(sys.version\\[:3\\]\\)<3.6") "False")))))) - (build-system python-build-system) + (build-system pyproject-build-system) (arguments `(#:phases (modify-phases %standard-phases (add-before 'build 'set-HOME - (lambda _ (setenv "HOME" "/tmp"))) - (replace 'check - (lambda* (#:key tests? inputs outputs #:allow-other-keys) - (when tests? - (add-installed-pythonpath inputs outputs) - (invoke "pytest" "-v"))))))) - (inputs - (list python-numpy)) + (lambda _ (setenv "HOME" "/tmp")))))) + ;; Propagate these for use of macs as a library. + (propagated-inputs + (list python-cython python-numpy)) (native-inputs - (list python-cython python-pytest)) + (list python-pytest)) (home-page "https://github.com/macs3-project/MACS") (synopsis "Model based analysis for ChIP-Seq data") (description From 9996896dc252a02ba3b17473a685ce8957237546 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Tue, 12 Sep 2023 12:28:08 +0200 Subject: [PATCH 091/268] gnu: Add python-peaks2utr. * gnu/packages/bioinformatics.scm (python-peaks2utr): New variable. --- gnu/packages/bioinformatics.scm | 36 +++++++++++++++++++++++++++++++++ 1 file changed, 36 insertions(+) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 0df5bbfad5..e24d70e569 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -1945,6 +1945,42 @@ matplotlib Axes objects, making them easy to style and incorporate into multi-panel figures.") (license license:expat))) +(define-public python-peaks2utr + (package + (name "python-peaks2utr") + (version "1.2.0") + (source (origin + (method url-fetch) + (uri (pypi-uri "peaks2utr" version)) + (sha256 + (base32 + "1idp9cgwqxvryf4qqrc1xjsamfqn3jmr56kmjp2h1ysmckwmhw4v")))) + (build-system pyproject-build-system) + (arguments + (list + #:test-flags + ;; These two tests fail because file names are not URLs. + '(list "-k" "not test_annotation.py"))) + (propagated-inputs + (list python-asgiref + python-gffutils + python-importlib-resources + macs + python-numpy + python-psutil + python-pybedtools + python-pysam + python-requests + python-tqdm + python-typing-extensions + python-zipp)) + (home-page "https://github.com/haessar/peaks2utr") + (synopsis "Python CLI for annotating three prime UTR") + (description + "This package provides a robust, parallelized Python CLI for annotating +three prime UTR.") + (license license:gpl3+))) + (define-public python-pegasusio (package (name "python-pegasusio") From 076b3384dfa29ae118d0375d516376a7fe98a197 Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Tue, 12 Sep 2023 09:29:22 -0400 Subject: [PATCH 092/268] gnu: qemu: Reinstate the iothreads-commit-active test. * gnu/packages/virtualization.scm (qemu) [arguments]: Add set-SOCK_DIR phase. (qemu-minimal) [arguments]: Delete the disable-extra-tests phase. --- gnu/packages/virtualization.scm | 17 +++++++++-------- 1 file changed, 9 insertions(+), 8 deletions(-) diff --git a/gnu/packages/virtualization.scm b/gnu/packages/virtualization.scm index 5c5225b694..f5bdedd45e 100644 --- a/gnu/packages/virtualization.scm +++ b/gnu/packages/virtualization.scm @@ -385,6 +385,14 @@ (cut string-suffix? "-linux-user" <>)))))))) + (add-before 'check 'set-SOCK_DIR + (lambda _ + ;; The default value for SOCK_DIR is TMPDIR, which can be long + ;; in the build chroot (e.g.: + ;; /tmp/guix-build-qemu-minimal-drv-0); set it to SOCK_DIR to + ;; avoid using more than 109 characters for socket files (the + ;; limit when using the kernel Linux). + (setenv "SOCK_DIR" "/tmp"))) (add-after 'install 'delete-firmwares (lambda _ ;; Delete firmares that are accessible on --firmwarepath. @@ -542,14 +550,7 @@ server and embedded PowerPC, and S390 guests.") #~(modify-phases #$phases (delete 'configure-user-static) (delete 'build-user-static) - (delete 'install-user-static) - (add-after 'disable-unusable-tests 'disable-extra-tests - (lambda _ - ;; Interesting, the iothreads-commit-active test only fails in - ;; qemu-minimal, not the complete variant (see: - ;; https://gitlab.com/qemu-project/qemu/-/issues/1855). - (delete-file - "tests/qemu-iotests/tests/iothreads-commit-active"))))))) + (delete 'install-user-static))))) ;; Remove dependencies on optional libraries, notably GUI libraries. (native-inputs (filter (lambda (input) From f0e05411bdcb36f5adba493555c360799307f641 Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Tue, 12 Sep 2023 10:03:44 -0400 Subject: [PATCH 093/268] search-paths: Add $TZDIR. * guix/search-paths.scm ($TZDIR): New search path. --- guix/search-paths.scm | 11 +++++++++-- 1 file changed, 9 insertions(+), 2 deletions(-) diff --git a/guix/search-paths.scm b/guix/search-paths.scm index fcbe7b7953..8dc81861c9 100644 --- a/guix/search-paths.scm +++ b/guix/search-paths.scm @@ -37,6 +37,7 @@ $PKG_CONFIG_PATH $SSL_CERT_DIR $SSL_CERT_FILE + $TZDIR search-path-specification->sexp sexp->search-path-specification @@ -104,16 +105,22 @@ (define $SSL_CERT_DIR (search-path-specification (variable "SSL_CERT_DIR") - (separator #f) ;single entry + (separator #f) ;single entry (files '("etc/ssl/certs")))) (define $SSL_CERT_FILE (search-path-specification (variable "SSL_CERT_FILE") (file-type 'regular) - (separator #f) ;single entry + (separator #f) ;single entry (files '("etc/ssl/certs/ca-certificates.crt")))) +(define $TZDIR + (search-path-specification + (variable "TZDIR") + (files '("share/zoneinfo")) + (separator #f))) ;single entry + (define (search-path-specification->sexp spec) "Return an sexp representing SPEC, a . The sexp corresponds to the arguments expected by `set-path-environment-variable'." From 4cb2e08b8eb1acc824b72ec17b483d7d85b5af68 Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Tue, 12 Sep 2023 10:05:00 -0400 Subject: [PATCH 094/268] gnu: python-django-4.0: Use $TZDIR. * gnu/packages/django.scm (python-django-4.0) [native-search-paths]: Use $TZDIR. --- gnu/packages/django.scm | 5 ++--- 1 file changed, 2 insertions(+), 3 deletions(-) diff --git a/gnu/packages/django.scm b/gnu/packages/django.scm index b089954b6b..577789e988 100644 --- a/gnu/packages/django.scm +++ b/gnu/packages/django.scm @@ -34,6 +34,7 @@ #:use-module (guix gexp) #:use-module (guix build-system python) #:use-module (guix deprecation) + #:use-module (guix search-paths) #:use-module (gnu packages) #:use-module (gnu packages base) #:use-module (gnu packages compression) @@ -126,9 +127,7 @@ ;; Set TZDIR when 'tzdata' is available so that timezone functionality ;; works (mostly) out of the box in containerized environments. ;; Note: This search path actually belongs to 'glibc'. - (list (search-path-specification - (variable "TZDIR") - (files '("share/zoneinfo"))))) + (list $TZDIR)) (home-page "https://www.djangoproject.com/") (synopsis "High-level Python Web framework") (description From 07d43c66d5c11fef61f9846fefb97fa18e4764f1 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Tue, 12 Sep 2023 23:28:40 +0200 Subject: [PATCH 095/268] gnu: Add swineherd. * gnu/packages/admin.scm (swineherd): New variable. --- gnu/packages/admin.scm | 40 +++++++++++++++++++++++++++++++++++++++- 1 file changed, 39 insertions(+), 1 deletion(-) diff --git a/gnu/packages/admin.scm b/gnu/packages/admin.scm index 5d586e6f36..2492890ee5 100644 --- a/gnu/packages/admin.scm +++ b/gnu/packages/admin.scm @@ -8,7 +8,7 @@ ;;; Copyright © 2015 Eric Dvorsak ;;; Copyright © 2016, 2017, 2020 Leo Famulari ;;; Copyright © 2016 Pjotr Prins -;;; Copyright © 2016, 2017 Ricardo Wurmus +;;; Copyright © 2016, 2017, 2023 Ricardo Wurmus ;;; Copyright © 2016-2023 Efraim Flashner ;;; Copyright © 2016 Peter Feigl ;;; Copyright © 2016 John J. Foerch @@ -153,6 +153,7 @@ #:use-module (gnu packages ncurses) #:use-module (gnu packages networking) #:use-module (gnu packages openldap) + #:use-module (gnu packages package-management) #:use-module (gnu packages patchutils) #:use-module (gnu packages pciutils) #:use-module (gnu packages pcre) @@ -407,6 +408,43 @@ interface and is based on GNU Guile.") (native-inputs (list pkg-config guile-2.2)) (inputs (list guile-2.2 guile2.2-fibers)))) +(define-public swineherd + (package + (name "swineherd") + (version "0.0.1") + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/BIMSBbioinfo/swineherd") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "18nk0sy5s0dm2rhxnrrn8g0m098b110mxnnxa2vnl1dnvfdzszw8")))) + (build-system gnu-build-system) + (arguments + '(#:configure-flags '("--localstatedir=/var") + #:make-flags '("GUILE_AUTO_COMPILE=0"))) + (native-inputs + (list autoconf automake guile-3.0 pkg-config texinfo)) + (inputs + (list btrfs-progs + guile-config + guile-fibers-1.3 + guile-netlink + guile-3.0 + guix + shepherd-0.10)) + (home-page "https://github.com/BIMSBbioinfo/swineherd") + (synopsis "System container manager") + (description + "This project aims to provide an extension to the Shepherd, retraining it +as a swineherd, a manager of crude system containers. It does this by +providing a Shepherd service @code{swineherd} that talks to the Shepherd +process to create Guix System containers as Shepherd services. It also comes +with an optional HTTP API server.") + (license license:gpl3+))) + (define-public cfm (package (name "cfm") From 10bc07671e2a3a699d4f56e405f50d766323319a Mon Sep 17 00:00:00 2001 From: Valter Nazianzeno Date: Thu, 24 Aug 2023 08:08:25 -0300 Subject: [PATCH 096/268] gnu: emilua: Update to 0.4.3. * gnu/packages/lua.scm (emilua): Update to 0.4.3. [source]: Remove recursive? and replace with inputs. [arguments]: Update style, add patch phase, enable tests and enable some more features. [native-inputs]: Add gperf, gawk and xdd. [inputs]: Add emilua-http and trial-protocol as origin is no longer recursive, also add serd, sord, libcap and liburing. Signed-off-by: Christopher Baines --- gnu/packages/lua.scm | 151 +++++++++++++++++++++++++++---------------- 1 file changed, 97 insertions(+), 54 deletions(-) diff --git a/gnu/packages/lua.scm b/gnu/packages/lua.scm index 405f8511cb..3b58952911 100644 --- a/gnu/packages/lua.scm +++ b/gnu/packages/lua.scm @@ -19,6 +19,7 @@ ;;; Copyright © 2022 Luis Henrique Gomes Higino ;;; Copyright © 2022 Leo Nikkilä ;;; Copyright © 2023 Yovan Naumovski +;;; Copyright © 2023 Valter Nazianzeno ;;; ;;; This file is part of GNU Guix. ;;; @@ -50,14 +51,18 @@ #:use-module (gnu packages bash) #:use-module (gnu packages boost) #:use-module (gnu packages build-tools) + #:use-module (gnu packages gcc) #:use-module (gnu packages glib) + #:use-module (gnu packages gperf) #:use-module (gnu packages gtk) #:use-module (gnu packages libevent) #:use-module (gnu packages libffi) + #:use-module (gnu packages linux) #:use-module (gnu packages m4) #:use-module (gnu packages ncurses) #:use-module (gnu packages pkg-config) #:use-module (gnu packages pretty-print) + #:use-module (gnu packages rdf) #:use-module (gnu packages re2c) #:use-module (gnu packages readline) #:use-module (gnu packages tls) @@ -1129,63 +1134,101 @@ shell command executions.") (define-public emilua (package - (name "emilua") - (version "0.3.2") - (source (origin - (method git-fetch) - (uri (git-reference - (url "https://gitlab.com/emilua/emilua.git") - (commit (string-append "v" version)) - ;; Current version requires Trial.Protocol and the HTTP lib - ;; developed as part of GSoC 2014 for Boost, and these are - ;; dependencies unlikely to be "unbundled" in future releases. - (recursive? #t))) - (file-name (git-file-name name version)) - (sha256 - (base32 - "1999bgrh52124a5g4qizav3x257ff2brjr855srpm1jv1nxzbygv")))) - (build-system meson-build-system) - (arguments - `(;; Tests are disabled for now due to an issue that affecs guix: - ;; + (name "emilua") + (version "0.4.3") + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://gitlab.com/emilua/emilua.git") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "1dwag2pyqc0g86rris4w4fzafmz9a6kiqd47vdq7hl3a1lyi74mx")))) + (build-system meson-build-system) + (arguments + (list + #:phases + #~(modify-phases %standard-phases + (add-after 'unpack 'patch + (lambda* (#:key inputs #:allow-other-keys) + (substitute* "src/emilua_gperf.awk" + (("/usr/bin/env") (which "env"))) + (substitute* "src/system.cpp" + (("P_PIDFD") "P_PID")) + + (copy-recursively + (assoc-ref inputs "emilua-http") + "emilua-http") + (copy-recursively + (assoc-ref inputs "trial-protocol") + "trial-protocol") + + (with-directory-excursion "subprojects" + (symlink "../emilua-http" "emilua-http") + (copy-file "packagefiles/emilua-http/meson.build" + "emilua-http/meson.build") + (symlink "../trial-protocol" "trial-protocol") + (copy-file "packagefiles/trial.protocol/meson.build" + "trial-protocol/meson.build"))))) #:configure-flags - (list "-Denable_http=true" - "-Denable_tests=false" - "-Denable_manpages=false" - "-Dversion_suffix=-guix1"))) - (native-inputs - (list luajit-lua52-openresty - pkg-config - re2c - xxd)) - (inputs - (list boost - boost-static - fmt-7 - ;; LuaJIT has a 2GiB addressing limit[1] that has been fixed on OpenResty - ;; fork. Emilua is severely affected by this limit, so the upstream package - ;; is avoided. Emilua also depends on the -DLUAJIT_ENABLE_LUA52COMPAT - ;; configure flag[2] for some features to work (e.g. __pairs on HTTP - ;; headers). - ;; - ;; [1] - ;; [2] - luajit-lua52-openresty - ncurses - openssl)) - (native-search-paths - (list - (search-path-specification - (variable "EMILUA_PATH") - (files - (list (string-append "lib/emilua-" (version-major+minor version))))))) - (home-page "https://gitlab.com/emilua/emilua") - (synopsis "Lua execution engine") - (description - "Emilua is a LuaJIT-based Lua execution engine that supports async IO, + #~(list "-Denable_http=true" + "-Denable_file_io=true" + "-Denable_io_uring=true" + ;; TODO: Linux namespaces are disabled for now due to conflict + ;; with some packages in guix. + "-Denable_linux_namespaces=false" + "-Denable_manpages=false" + "-Dversion_suffix=-guix1"))) + (native-inputs + (list luajit-lua52-openresty + re2c + gperf + xxd + pkg-config)) + (inputs + `(("emilua-http" + ,(origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/BoostGSoC14/boost.http") + (commit "93ae527c89ffc517862e1f5f54c8a257278f1195"))) + (sha256 + (base32 + "0jm7fw0cjd3s9zkkvyh6mcj6z32hcy7l9bszv74l92qk15ivvp9h")))) + ("trial-protocol" + ,(origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/breese/trial.protocol") + (commit "79149f604a49b8dfec57857ca28aaf508069b669"))) + (sha256 + (base32 + "0k42i5b4v3zz5x0r3dssiymgmn2x8zg4fzdksya9aggxgigippsx")))) + ("boost" ,boost) + ("boost-static" ,boost-static) + ("fmt" ,fmt-8) + ("gcc" ,gcc-12) + ("luajit-lua52-openresty" ,luajit-lua52-openresty) + ("ncurses" ,ncurses) + ("serd" ,serd) + ("sord" ,sord) + ("libcap" ,libcap) + ("liburing" ,liburing) + ("openssl" ,openssl))) + (native-search-paths + (list + (search-path-specification + (variable "EMILUA_PATH") + (files + (list (string-append "lib/emilua-" (version-major+minor version))))))) + (home-page "https://gitlab.com/emilua/emilua") + (synopsis "Lua execution engine") + (description + "Emilua is a LuaJIT-based Lua execution engine that supports async IO, fibers and actor-inspired threading. The experimental builtin HTTP module is enabled.") - (license license:boost1.0))) + (license license:boost1.0))) (define-public fennel (package From de2ee9cae67079daf380f09c095f2a4b37be40e6 Mon Sep 17 00:00:00 2001 From: Sharlatan Hellseher Date: Tue, 5 Sep 2023 23:24:29 +0100 Subject: [PATCH 097/268] gnu: python-libsass: Update to 0.22.0. * gnu/packages/python-xyz.scm (python-libsass): Update to 0.22.0. [phases]: Add new phase 'silent-failing-tests and disable 2 failing tests to complete build. Signed-off-by: Christopher Baines --- gnu/packages/python-xyz.scm | 15 +++++++++++++-- 1 file changed, 13 insertions(+), 2 deletions(-) diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index 304258b811..5ba51ca654 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -14314,7 +14314,7 @@ specification.") (define-public python-libsass (package (name "python-libsass") - (version "0.20.1") + (version "0.22.0") (source (origin ;; PyPI tarball is missing some test files. @@ -14324,7 +14324,7 @@ specification.") (commit version))) (file-name (git-file-name name version)) (sha256 - (base32 "1r0kgl7i6nnhgjl44sjw57k08gh2qr7l8slqih550dyxbf1akbxh")))) + (base32 "0j6c7jb1bnpmz76gs5za41qwgrs7v1yd1jkgvsy5ql6dg2ph9vp4")))) (build-system python-build-system) (arguments '(#:phases @@ -14332,6 +14332,17 @@ specification.") ;; Use Guix package of libsass instead of compiling from a checkout. (add-before 'build 'set-libsass (lambda _ (setenv "SYSTEM_SASS" "indeed"))) + ;; XXX: Silent 2 failing tests, reported to upstream (closed), see + ;; https://github.com/sass/libsass-python/issues/440. It passed with + ;; libsass@3.6.5 which requires rebuild the world (1200+ packages), + ;; remove when v3.6.5 is available. + (add-before 'check 'silent-failing-tests + (lambda _ + (substitute* "sasstests.py" + (("def test_build_one") + "def __off_test_build_one") + (("def test_stack_trace_formatting") + "def __off_test_stack_trace_formatting")))) (replace 'check (lambda* (#:key tests? #:allow-other-keys) (when tests? From 7f150a18957daddb53caf11e23eb12122198d65c Mon Sep 17 00:00:00 2001 From: Sharlatan Hellseher Date: Tue, 5 Sep 2023 23:24:30 +0100 Subject: [PATCH 098/268] gnu: python-qtsass: Update to 0.4.0. This also fixes test failures preventing the package from building. * gnu/packages/python-xyz.scm (python-qtsass): Update to 0.4.0, fix build. [native-inputs]: Add python-flaky. Signed-off-by: Christopher Baines --- gnu/packages/python-xyz.scm | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index 5ba51ca654..dd43fb3cd1 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -29978,7 +29978,7 @@ applications and daemons.") (define-public python-qtsass (package (name "python-qtsass") - (version "0.3.0") + (version "0.4.0") (source (origin ;; There are no tests in the PyPI tarball. @@ -29988,7 +29988,7 @@ applications and daemons.") (commit (string-append "v" version)))) (file-name (git-file-name name version)) (sha256 - (base32 "09s04aa14d8jqbh71clrb5y7vcmkxlp94mwmvzrkxahry3bk03cb")))) + (base32 "1skdihfby2f41zxgwa5zv44vdxjrw301rh88rjmzj4xbdlix6cig")))) (build-system python-build-system) (arguments `(#:test-target "pytest" @@ -30000,7 +30000,7 @@ applications and daemons.") (for-each make-file-writable (find-files ".")) #t))))) (native-inputs - (list python-pytest python-pytest-cov python-pytest-runner)) + (list python-flaky python-pytest python-pytest-cov python-pytest-runner)) (propagated-inputs (list python-libsass)) (home-page "https://github.com/spyder-ide/qtsass") From 901eaca92becd99d297a09a4480f7095278b22b5 Mon Sep 17 00:00:00 2001 From: Hendursaga Date: Mon, 4 Sep 2023 19:09:12 -0400 Subject: [PATCH 099/268] gnu: tennix: Update to 1.3.4. * gnu/packages/games.scm (tennix): Update to 1.3.4. [arguments]<#:phases>: Update style and remove fix-include phase. [inputs]: Remove labels, update to SDL2, add SDL2_gfx dependency. [license]: Remove LGPL license, as SDL_rotozoom is no longer included. Signed-off-by: Christopher Baines --- gnu/packages/games.scm | 96 +++++++++++++++++++----------------------- 1 file changed, 44 insertions(+), 52 deletions(-) diff --git a/gnu/packages/games.scm b/gnu/packages/games.scm index 4d5b85248a..78063fa625 100644 --- a/gnu/packages/games.scm +++ b/gnu/packages/games.scm @@ -5571,65 +5571,57 @@ fullscreen, use F5 or Alt+Enter.") (define-public tennix (package (name "tennix") - (version "1.3.1") - (source - (origin - (method git-fetch) - (uri (git-reference - (url "https://repo.or.cz/tennix.git") - (commit (string-append "tennix-" version)))) - (file-name (git-file-name name version)) - (sha256 - (base32 "02cj4lrdrisal5s9pnbf2smx7qz9czczjzndfkhfx0qy67b957sk")) - ;; Remove non-free images. - (modules '((guix build utils))) - (snippet - '(begin - (for-each delete-file - '("data/loc_training_camp.png" - "data/loc_austrian_open.png" - "data/loc_olympic_green_tennis.png")) - #t)))) + (version "1.3.4") + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://repo.or.cz/tennix.git") + (commit (string-append "tennix-" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "1fmg0vw8c2spyxy4k64nwky80jsw9mc3vnlch49q6cagjsg9y8dj")) + ;; Remove non-free images. + (modules '((guix build utils))) + (snippet '(begin + (for-each delete-file + '("data/loc_training_camp.png" + "data/loc_austrian_open.png" + "data/loc_olympic_green_tennis.png")) #t)))) (build-system gnu-build-system) (arguments - `(#:tests? #f ;no test - #:phases - (modify-phases %standard-phases - (add-after 'unpack 'fix-include - (lambda _ - (substitute* '("src/graphics.h" "src/sound.h") - (("#include \"(SDL_(image|ttf|mixer)\\.h)\"" _ header) - (string-append "#include \"SDL/" header "\""))) - (substitute* '("src/tennix.h" "src/network.h" "src/SDL_rotozoom.h") - (("#include ") "#include ") - (("#include ") "#include ")) - #t)) - (add-after 'unpack 'locate-install - ;; Build process cannot expand "$(INSTALL)" in Makefile. - (lambda _ - (substitute* "makefile" - (("^CONFIGURE_OUTPUT :=.*" all) - (string-append "INSTALL := install -c\n" all))) - #t)) - (replace 'configure - ;; The "configure" script is picky about the arguments it - ;; gets. Call it ourselves. - (lambda _ - (invoke "./configure" "--prefix" (assoc-ref %outputs "out"))))))) - (native-inputs - (list which)) - (inputs - `(("python" ,python-wrapper) - ("sdl" ,(sdl-union (list sdl sdl-image sdl-mixer sdl-ttf sdl-net))))) + (list + #:tests? #f ;no tests + #:phases #~(modify-phases %standard-phases + (add-after 'unpack 'locate-install + ;; Build process cannot expand "$(INSTALL)" in Makefile. + (lambda _ + (substitute* "makefile" + (("^CONFIGURE_OUTPUT :=.*" all) + (string-append "INSTALL := install -c\n" all))) #t)) + (replace 'configure + ;; The "configure" script is picky about the arguments it + ;; gets. Call it ourselves. + (lambda _ + (invoke "./configure" "--prefix" + (assoc-ref %outputs "out"))))))) + (native-inputs (list which)) + (inputs (list python + (sdl-union (list sdl2 + sdl2-image + sdl2-mixer + sdl2-ttf + sdl2-net + sdl2-gfx)))) (home-page "https://icculus.org/tennix/") (synopsis "Play tennis against the computer or a friend") - (description "Tennix is a 2D tennis game. You can play against the + (description + "Tennix is a 2D tennis game. You can play against the computer or against another player using the keyboard. The game runs in-window at 640x480 resolution or fullscreen.") ;; Project is licensed under GPL2+ terms. It includes images - ;; released under Public Domain terms, and SDL_rotozoom, released - ;; under LGPL2.1 terms. - (license (list license:gpl2+ license:public-domain license:lgpl2.1)))) + ;; released under Public Domain terms. + (license (list license:gpl2+ license:public-domain)))) (define-public warzone2100 (package From 8d5304b143eee34e1998fca8f0c9f2fad7599d1a Mon Sep 17 00:00:00 2001 From: Zheng Junjie Date: Wed, 6 Sep 2023 16:55:39 +0800 Subject: [PATCH 100/268] gnu: libvterm: Update to 0.3.3. * gnu/packages/terminals.scm (libvterm): Update to 0.3.3. [source]: Use launchpad.net url. [arguments]: Use CC-FOR-TARGET. Signed-off-by: Christopher Baines --- gnu/packages/terminals.scm | 19 +++++++++++++------ 1 file changed, 13 insertions(+), 6 deletions(-) diff --git a/gnu/packages/terminals.scm b/gnu/packages/terminals.scm index 43aeac9fd7..1f72393593 100644 --- a/gnu/packages/terminals.scm +++ b/gnu/packages/terminals.scm @@ -35,6 +35,7 @@ ;;; Copyright © 2022 jgart ;;; Copyright © 2023 Aaron Covrig ;;; Copyright © 2023 Foundation Devices, Inc. +;;; Copyright © 2023 Zheng Junjie <873216071@qq.com> ;;; ;;; This file is part of GNU Guix. ;;; @@ -629,19 +630,25 @@ should be thread-safe.") (define-public libvterm (package (name "libvterm") - (version "0.3.1") + (version "0.3.3") (source (origin (method url-fetch) - (uri (string-append "https://www.leonerd.org.uk/code/libvterm/" - "libvterm-" version ".tar.gz")) + (uri (string-append + "https://launchpad.net/libvterm/trunk/v" + (version-major+minor version) + "/+download/libvterm-" version ".tar.gz")) (sha256 - (base32 "15y3y23kfpcda7n79ym3gp1abzn8mshxrad8s3gnhls82nfava15")))) + (base32 "1q16fbznm54p24hqvw8c9v3347apk86ybsxyghsbsa11vm1ny589")))) (build-system gnu-build-system) (arguments `(#:make-flags - (list "CC=gcc" - (string-append "PREFIX=" (assoc-ref %outputs "out"))) + (list + ;; FIXME: cross build fails. + ;; ld: src/.libs/encoding.o: error adding symbols: file in wrong format + ;; collect2: error: ld returned 1 exit status + (string-append "CC=" ,(cc-for-target)) + (string-append "PREFIX=" (assoc-ref %outputs "out"))) #:test-target "test" #:phases (modify-phases %standard-phases From 79988ab742fdb8b13ab61269ed11c0144593f320 Mon Sep 17 00:00:00 2001 From: Zheng Junjie Date: Wed, 6 Sep 2023 16:55:40 +0800 Subject: [PATCH 101/268] gnu: libvterm: Update arguments style. * gnu/packages/terminals.scm (libvterm)[arguments]: Update arguments style. Signed-off-by: Christopher Baines --- gnu/packages/terminals.scm | 22 +++++++++++----------- 1 file changed, 11 insertions(+), 11 deletions(-) diff --git a/gnu/packages/terminals.scm b/gnu/packages/terminals.scm index 1f72393593..a67ec97859 100644 --- a/gnu/packages/terminals.scm +++ b/gnu/packages/terminals.scm @@ -642,17 +642,17 @@ should be thread-safe.") (base32 "1q16fbznm54p24hqvw8c9v3347apk86ybsxyghsbsa11vm1ny589")))) (build-system gnu-build-system) (arguments - `(#:make-flags - (list - ;; FIXME: cross build fails. - ;; ld: src/.libs/encoding.o: error adding symbols: file in wrong format - ;; collect2: error: ld returned 1 exit status - (string-append "CC=" ,(cc-for-target)) - (string-append "PREFIX=" (assoc-ref %outputs "out"))) - #:test-target "test" - #:phases - (modify-phases %standard-phases - (delete 'configure)))) + (list #:make-flags + #~(list + ;; FIXME: cross build fails. + ;; ld: src/.libs/encoding.o: error adding symbols: file in wrong format + ;; collect2: error: ld returned 1 exit status + (string-append "CC=" #$(cc-for-target)) + (string-append "PREFIX=" #$output)) + #:test-target "test" + #:phases + #~(modify-phases %standard-phases + (delete 'configure)))) (native-inputs (list libtool perl)) (home-page "https://www.leonerd.org.uk/code/libvterm/") From c30c9df5e9eb2d28e1b593128f05a0aae1919826 Mon Sep 17 00:00:00 2001 From: Munyoki Kilyungi Date: Wed, 6 Sep 2023 14:12:10 +0300 Subject: [PATCH 102/268] gnu: yoyo-migrations: Update to 8.2.0. * gnu/packages/databases.scm (yoyo-migrations): Update to 8.2.0. [propagated-inputs]: Add python-importlib-metadata. Signed-off-by: Christopher Baines --- gnu/packages/databases.scm | 9 +++++---- 1 file changed, 5 insertions(+), 4 deletions(-) diff --git a/gnu/packages/databases.scm b/gnu/packages/databases.scm index 8d87f238b5..d0f8ce2001 100644 --- a/gnu/packages/databases.scm +++ b/gnu/packages/databases.scm @@ -59,7 +59,8 @@ ;;; Copyright © 2022 muradm ;;; Copyright © 2022 Thomas Albers Raviola ;;; Copyright © 2021, 2022 jgart -;;; Copyright © 2023 Felix Gruber +;;; Copyright © 2023 Felix Gruber ;;; ;;; This file is part of GNU Guix. ;;; @@ -3963,7 +3964,7 @@ database).") (define-public yoyo-migrations (package (name "yoyo-migrations") - (version "7.2.0") + (version "8.2.0") (source (origin ;; We use the upstream repository, as the tests are not included in the @@ -3974,14 +3975,14 @@ database).") (changeset (string-append "v" version "-release")))) (file-name (string-append name "-" version "-checkout")) (sha256 - (base32 "0q2z9bgdj3wyix7yvqsayfs21grp5av8ilh411lgmjhigszkvhcq")))) + (base32 "1al030ix0w63hr4s3mqry6s0mlqdj8p242pdqks06br7c25nx3yj")))) (build-system python-build-system) (arguments ;; XXX: Tests require a connection to some pgsql database and psycopg ;; fails to connect to it. '(#:tests? #f)) (propagated-inputs - (list python-sqlparse python-tabulate)) + (list python-sqlparse python-tabulate python-importlib-metadata)) (home-page "https://ollycope.com/software/yoyo/latest/") (synopsis "Database migrations with SQL") (description From 6a01c1142b0099bc5ccff6550c2dd24b90ec6aad Mon Sep 17 00:00:00 2001 From: Andreas Enge Date: Mon, 21 Aug 2023 22:12:28 +0200 Subject: [PATCH 103/268] gnu: hdf4, hdf4-alt: Update to 4.2.16-2. * gnu/packages/maths.scm (hdf4)[source]: Update to 4.2.16-2. Drop patches that do not apply any more. [arguments]: Drop configure flag related to libtirpc. Add configure flag to build xdr library and drop unneeded substitutions. * gnu/packages/patches/hdf4-architectures.patch, gnu/packages/patches/hdf4-tirpc.patch: Remove files. * gnu/local.mk (dist_patch_DATA): Unregister patches. --- gnu/local.mk | 2 - gnu/packages/maths.scm | 28 +- gnu/packages/patches/hdf4-architectures.patch | 632 ------------------ gnu/packages/patches/hdf4-tirpc.patch | 33 - 4 files changed, 8 insertions(+), 687 deletions(-) delete mode 100644 gnu/packages/patches/hdf4-architectures.patch delete mode 100644 gnu/packages/patches/hdf4-tirpc.patch diff --git a/gnu/local.mk b/gnu/local.mk index 4f8637418a..924d497057 100644 --- a/gnu/local.mk +++ b/gnu/local.mk @@ -1372,10 +1372,8 @@ dist_patch_DATA = \ %D%/packages/patches/gtksourceview-2-add-default-directory.patch \ %D%/packages/patches/gzdoom-search-in-installed-share.patch \ %D%/packages/patches/gzdoom-find-system-libgme.patch \ - %D%/packages/patches/hdf4-architectures.patch \ %D%/packages/patches/hdf4-reproducibility.patch \ %D%/packages/patches/hdf4-shared-fortran.patch \ - %D%/packages/patches/hdf4-tirpc.patch \ %D%/packages/patches/hdf5-config-date.patch \ %D%/packages/patches/hdf-eos2-build-shared.patch \ %D%/packages/patches/hdf-eos2-remove-gctp.patch \ diff --git a/gnu/packages/maths.scm b/gnu/packages/maths.scm index 38e71e18f8..e3cd0762be 100644 --- a/gnu/packages/maths.scm +++ b/gnu/packages/maths.scm @@ -1,5 +1,5 @@ ;;; GNU Guix --- Functional package management for GNU -;;; Copyright © 2013, 2014, 2015, 2016, 2019, 2020 Andreas Enge +;;; Copyright © 2013, 2014, 2015, 2016, 2019, 2020, 2023 Andreas Enge ;;; Copyright © 2013 Nikita Karetnikov ;;; Copyright © 2014, 2016, 2017 John Darrington ;;; Copyright © 2014-2022 Eric Bavier @@ -1321,18 +1321,16 @@ computations.") (define-public hdf4 (package (name "hdf4") - (version "4.2.14") + (version "4.2.16-2") (source (origin (method url-fetch) (uri (string-append "https://support.hdfgroup.org/ftp/HDF/releases/HDF" version "/src/hdf-" version ".tar.bz2")) (sha256 - (base32 "0n29klrrbwan9307np0d9hr128dlpc4nnlf57a140080ll3jmp8l")) - (patches (search-patches "hdf4-architectures.patch" - "hdf4-reproducibility.patch" - "hdf4-shared-fortran.patch" - "hdf4-tirpc.patch")))) + (base32 "0b395czhqr43mmbiifmg2mhb488wnd4zccj45vpql98ja15j7hy5")) + (patches (search-patches "hdf4-reproducibility.patch" + "hdf4-shared-fortran.patch")))) (build-system gnu-build-system) (native-inputs (list gfortran bison flex)) @@ -1345,9 +1343,7 @@ computations.") #:configure-flags (list "--enable-shared" "FCFLAGS=-fallow-argument-mismatch" "FFLAGS=-fallow-argument-mismatch" - (string-append "CPPFLAGS=-I" - (assoc-ref %build-inputs "libtirpc") - "/include/tirpc")) + "--enable-hdf4-xdr") #:phases (modify-phases %standard-phases ;; This is inspired by two of Debian's patches. @@ -1362,14 +1358,7 @@ computations.") (substitute* '("mfhdf/hdfimport/testutil.sh.in" "hdf/util/testutil.sh.in") (("/bin/rm") "rm") - (("/bin/mkdir") "mkdir")) - (substitute* (find-files "." "^Makefile\\.in$") - (("@HDF_BUILD_XDR_TRUE@XDR_ADD = \ --R\\$\\(abs_top_builddir\\)/mfhdf/xdr/\\.libs") "") - (("@HDF_BUILD_SHARED_TRUE@AM_LDFLAGS = \ --R\\$\\(abs_top_builddir\\)/mfhdf/libsrc/\\.libs \ --R\\$\\(abs_top_builddir\\)/hdf/src/\\.libs \\$\\(XDR_ADD\\)") "")) - #t)) + (("/bin/mkdir") "mkdir")))) (add-after 'configure 'patch-settings (lambda _ ;; libhdf4.settings contains the full path of the @@ -1389,8 +1378,7 @@ computations.") ;; files. Fix it manually to avoid having to propagate it. (substitute* (find-files (string-append out "/lib") "\\.la$") (("-ljpeg") - (string-append "-L" libjpeg "/lib -ljpeg"))) - #t)))))) + (string-append "-L" libjpeg "/lib -ljpeg"))))))))) (home-page "https://www.hdfgroup.org/products/hdf4/") (synopsis "Library and multi-object file format for storing and managing data") diff --git a/gnu/packages/patches/hdf4-architectures.patch b/gnu/packages/patches/hdf4-architectures.patch deleted file mode 100644 index aa71d5a383..0000000000 --- a/gnu/packages/patches/hdf4-architectures.patch +++ /dev/null @@ -1,632 +0,0 @@ -Copied from Debian. - -Description: Support additional architectures. -Author: Francesco Paolo Lovergine - ---- a/hdf/src/hdfi.h -+++ b/hdf/src/hdfi.h -@@ -48,6 +48,7 @@ - /* 8 - Cray IEEE */ - /* (i.e. Big-Endian, all 64-bit architecture w/IEEE Floats) */ - /*--------------------------------------------------------------------------*/ -+#define DFMT_S390 0x1111 - #define DFMT_SUN 0x1111 - #define DFMT_SUN_INTEL 0x4441 - #define DFMT_ALLIANT 0x1111 -@@ -62,6 +63,7 @@ - #define DFMT_CTSS 0x3331 - #define DFMT_VAX 0x2221 - #define DFMT_MIPSEL 0x4441 -+#define DFMT_MIPSEB 0x1111 - #define DFMT_PC 0x4441 - #define DFMT_APPLE 0x1111 - #define DFMT_APPLE_INTEL 0x4441 -@@ -75,6 +77,13 @@ - #define DFMT_IA64 0x4441 - #define DFMT_LINUX64 0x4441 - #define DFMT_POWERPC64 0x1111 -+#define DFMT_POWERPC64LE 0x4441 -+#define DFMT_ARMV4L 0x4441 -+#define DFMT_AARCH64 0x4441 -+#define DFMT_X86_64 0x4441 -+#define DFMT_SH 0x4441 -+#define DFMT_SHEB 0x1111 -+#define DFMT_RISCV64 0x4441 - - /* I/O library constants */ - #define UNIXUNBUFIO 1 -@@ -288,7 +297,7 @@ typedef int hdf_pint_t; - - #endif /* IBM6000 */ - --#if defined(HP9000) || (!defined(__convexc__) && (defined(hpux) || defined(__hpux))) -+#if defined(HP9000) || (!defined(__convexc__) && (defined(hpux) || defined(__hpux) || defined(__hppa__))) - - #ifndef HP9000 - #define HP9000 -@@ -347,6 +356,10 @@ typedef int hdf_pint_t; - /* what each does */ - #define JMEMSYS MEM_ANSI - -+#ifdef __linux__ -+#define FNAME_POST_UNDERSCORE -+#endif -+ - #endif /* HP9000 */ - - -@@ -670,6 +683,462 @@ typedef int hdf_pint_t; - #endif /* !(defined(__APPLE__)) */ - - /*-----------------------------------------------------*/ -+#if defined (__linux__) && defined (__mc68000__) -+ -+#ifdef GOT_MACHINE -+If you get an error on this line more than one machine type has been defined. -+Please check your Makefile. -+#endif -+#define GOT_MACHINE 1 -+ -+#include -+#include /* for unbuffered file I/O */ -+#include -+#include -+#include /* for character macros */ -+ -+#define DF_MT DFMT_MOTOROLA -+ -+#ifndef VOID /* The stupid windows.h header file uses a #define instead of a typedef */ -+typedef void VOID; -+#endif /* end VOID */ -+typedef void * VOIDP; -+typedef char * _fcd; -+typedef char char8; -+typedef unsigned char uchar8; -+typedef char int8; -+typedef unsigned char uint8; -+typedef short int int16; -+typedef unsigned short int uint16; -+typedef long int int32; -+typedef unsigned long int uint32; -+typedef int intn; -+typedef unsigned int uintn; -+typedef float float32; -+typedef double float64; -+typedef long intf; /* size of INTEGERs in Fortran compiler */ -+typedef int hdf_pint_t; /* an integer the same size as a pointer */ -+#define FNAME_POST_UNDERSCORE -+#define _fcdtocp(desc) (desc) -+ -+#ifdef HAVE_FMPOOL -+#define FILELIB PAGEBUFIO /* enable page buffering */ -+#else -+#define FILELIB UNIXBUFIO -+#endif -+ -+/* JPEG #define's - Look in the JPEG docs before changing - (Q) */ -+ -+/* Determine the memory manager we are going to use. Valid values are: */ -+/* MEM_DOS, MEM_ANSI, MEM_NAME, MEM_NOBS. See the JPEG docs for details on */ -+/* what each does */ -+#define JMEMSYS MEM_ANSI -+#define HAVE_STDC -+#define INCLUDES_ARE_ANSI -+ -+#endif /* Linux/m68k */ -+ -+#if defined (__linux__) && defined (__sparc__) -+ -+#ifdef GOT_MACHINE -+If you get an error on this line more than one machine type has been defined. -+Please check your Makefile. -+#endif -+#define GOT_MACHINE 1 -+ -+#include -+#include /* for unbuffered file I/O */ -+#include -+#include -+#include /* for character macros */ -+ -+#define DF_MT DFMT_SUN -+ -+#ifndef VOID /* The stupid windows.h header file uses a #define instead of a typedef */ -+typedef void VOID; -+#endif /* end VOID */ -+typedef void * VOIDP; -+typedef char * _fcd; -+typedef char char8; -+typedef unsigned char uchar8; -+typedef char int8; -+typedef unsigned char uint8; -+typedef short int int16; -+typedef unsigned short int uint16; -+#ifdef _LP64 /* 64-bit environment */ -+typedef int int32; -+typedef unsigned int uint32; -+#else /* 32-bit environment */ -+typedef long int int32; -+typedef unsigned long int uint32; -+#endif -+typedef int intn; -+typedef unsigned int uintn; -+typedef float float32; -+typedef double float64; -+typedef long intf; /* size of INTEGERs in Fortran compiler */ -+#ifdef _LP64 /* 64-bit environment */ -+typedef long hdf_pint_t; /* an integer the same size as a pointer */ -+#else /* 32-bit environment */ -+typedef int hdf_pint_t; /* an integer the same size as a pointer */ -+#endif -+#define FNAME_POST_UNDERSCORE -+#define _fcdtocp(desc) (desc) -+ -+#ifdef HAVE_FMPOOL -+#define FILELIB PAGEBUFIO /* enable page buffering */ -+#else -+#define FILELIB UNIXBUFIO -+#endif -+ -+/* JPEG #define's - Look in the JPEG docs before changing - (Q) */ -+ -+/* Determine the memory manager we are going to use. Valid values are: */ -+/* MEM_DOS, MEM_ANSI, MEM_NAME, MEM_NOBS. See the JPEG docs for details on */ -+/* what each does */ -+#define JMEMSYS MEM_ANSI -+#define HAVE_STDC -+#define INCLUDES_ARE_ANSI -+ -+#endif /* Linux/Sparc */ -+ -+#if defined (__linux__) && defined (__powerpc__) && !defined(__powerpc64__) -+ -+#ifdef GOT_MACHINE -+If you get an error on this line more than one machine type has been defined. -+Please check your Makefile. -+#endif -+#define GOT_MACHINE 1 -+ -+#include -+#include /* for unbuffered file I/O */ -+#include -+#include -+#include /* for character macros */ -+ -+#define DF_MT DFMT_MOTOROLA -+ -+#ifndef VOID /* The stupid windows.h header file uses a #define instead of a typedef */ -+typedef void VOID; -+#endif /* end VOID */ -+typedef void * VOIDP; -+typedef char * _fcd; -+typedef char char8; -+typedef unsigned char uchar8; -+typedef signed char int8; -+typedef unsigned char uint8; -+typedef short int int16; -+typedef unsigned short int uint16; -+typedef long int int32; -+typedef unsigned long int uint32; -+typedef int intn; -+typedef unsigned int uintn; -+typedef float float32; -+typedef double float64; -+typedef long intf; /* size of INTEGERs in Fortran compiler */ -+typedef int hdf_pint_t; /* an integer the same size as a pointer */ -+#define FNAME_POST_UNDERSCORE -+#define _fcdtocp(desc) (desc) -+ -+#ifdef HAVE_FMPOOL -+#define FILELIB PAGEBUFIO /* enable page buffering */ -+#else -+#define FILELIB UNIXBUFIO -+#endif -+ -+/* JPEG #define's - Look in the JPEG docs before changing - (Q) */ -+ -+/* Determine the memory manager we are going to use. Valid values are: */ -+/* MEM_DOS, MEM_ANSI, MEM_NAME, MEM_NOBS. See the JPEG docs for details on */ -+/* what each does */ -+#define JMEMSYS MEM_ANSI -+#define HAVE_STDC -+#define INCLUDES_ARE_ANSI -+ -+#endif /* Linux/powerpc */ -+ -+#if defined (__linux__) && defined (__s390__) -+ -+#ifdef GOT_MACHINE -+If you get an error on this line more than one machine type has been defined. -+Please check your Makefile. -+#endif -+#define GOT_MACHINE 1 -+ -+#include -+#include /* for unbuffered file I/O */ -+#include -+#include -+#include /* for character macros */ -+ -+#define DF_MT DFMT_S390 -+ -+#ifndef VOID /* The stupid windows.h header file uses a #define instead of a typedef */ -+typedef void VOID; -+#endif /* end VOID */ -+typedef void * VOIDP; -+typedef char * _fcd; -+typedef char char8; -+typedef unsigned char uchar8; -+typedef signed char int8; -+typedef unsigned char uint8; -+typedef short int int16; -+typedef unsigned short int uint16; -+#ifdef _LP64 /* 64-bit environment */ -+typedef int int32; -+typedef unsigned int uint32; -+#else /* 32-bit environment */ -+typedef long int int32; -+typedef unsigned long int uint32; -+#endif -+typedef int intn; -+typedef unsigned int uintn; -+typedef float float32; -+typedef double float64; -+typedef long intf; /* size of INTEGERs in Fortran compiler */ -+#ifdef _LP64 /* 64-bit environment */ -+typedef long hdf_pint_t; /* an integer the same size as a pointer */ -+#else /* 32-bit environment */ -+typedef int hdf_pint_t; /* an integer the same size as a pointer */ -+#endif -+#define FNAME_POST_UNDERSCORE -+#define _fcdtocp(desc) (desc) -+ -+#ifdef HAVE_FMPOOL -+#define FILELIB PAGEBUFIO /* enable page buffering */ -+#else -+#define FILELIB UNIXBUFIO -+#endif -+ -+/* JPEG #define's - Look in the JPEG docs before changing - (Q) */ -+ -+/* Determine the memory manager we are going to use. Valid values are: */ -+/* MEM_DOS, MEM_ANSI, MEM_NAME, MEM_NOBS. See the JPEG docs for details on */ -+/* what each does */ -+#define JMEMSYS MEM_ANSI -+#define HAVE_STDC -+#define INCLUDES_ARE_ANSI -+ -+#endif /* Linux/s390 */ -+ -+#if defined (__linux__) && (defined (__MIPSEB__) || defined(__MIPSEL__)) -+ -+#ifdef GOT_MACHINE -+If you get an error on this line more than one machine type has been defined. -+Please check your Makefile. -+#endif -+#define GOT_MACHINE 1 -+ -+#include -+#include /* for unbuffered file I/O */ -+#include -+#include -+#include /* for character macros */ -+ -+#if defined (__MIPSEB__) -+#define DF_MT DFMT_MIPSEB -+#elif defined(__MIPSEL__) -+#define DF_MT DFMT_MIPSEL -+#endif -+ -+#ifndef VOID /* The stupid windows.h header file uses a #define instead of a typedef */ -+typedef void VOID; -+#endif /* end VOID */ -+typedef void * VOIDP; -+typedef char * _fcd; -+typedef char char8; -+typedef unsigned char uchar8; -+typedef signed char int8; -+typedef unsigned char uint8; -+typedef short int int16; -+typedef unsigned short int uint16; -+typedef int int32; -+typedef unsigned int uint32; -+typedef int intn; -+typedef unsigned int uintn; -+typedef float float32; -+typedef double float64; -+typedef long intf; /* size of INTEGERs in Fortran compiler */ -+typedef long int hdf_pint_t; /* an integer the same size as a pointer */ -+#define FNAME_POST_UNDERSCORE -+#define _fcdtocp(desc) (desc) -+ -+#ifdef HAVE_FMPOOL -+#define FILELIB PAGEBUFIO /* enable page buffering */ -+#else -+#define FILELIB UNIXBUFIO -+#endif -+ -+/* JPEG #define's - Look in the JPEG docs before changing - (Q) */ -+ -+/* Determine the memory manager we are going to use. Valid values are: */ -+/* MEM_DOS, MEM_ANSI, MEM_NAME, MEM_NOBS. See the JPEG docs for details on */ -+/* what each does */ -+#define JMEMSYS MEM_ANSI -+#define HAVE_STDC -+#define INCLUDES_ARE_ANSI -+ -+#endif /* Linux/mips */ -+ -+#if defined (__linux__) && defined (__arm__) -+ -+#ifdef GOT_MACHINE -+If you get an error on this line more than one machine type has been defined. -+Please check your Makefile. -+#endif -+#define GOT_MACHINE 1 -+ -+#include -+#include /* for unbuffered file I/O */ -+#include -+#include -+#include /* for character macros */ -+ -+#define DF_MT DFMT_ARMV4L -+ -+#ifndef VOID /* The stupid windows.h header file uses a #define instead of a typedef */ -+typedef void VOID; -+#endif /* end VOID */ -+typedef void * VOIDP; -+typedef char * _fcd; -+typedef char char8; -+typedef unsigned char uchar8; -+typedef signed char int8; -+typedef unsigned char uint8; -+typedef short int int16; -+typedef unsigned short int uint16; -+typedef int int32; -+typedef unsigned int uint32; -+typedef int intn; -+typedef unsigned int uintn; -+typedef float float32; -+typedef double float64; -+typedef long intf; /* size of INTEGERs in Fortran compiler */ -+typedef long hdf_pint_t; /* an integer the same size as a pointer */ -+#define FNAME_POST_UNDERSCORE -+#define _fcdtocp(desc) (desc) -+ -+#ifdef HAVE_FMPOOL -+#define FILELIB PAGEBUFIO /* enable page buffering */ -+#else -+#define FILELIB UNIXBUFIO -+#endif -+ -+/* JPEG #define's - Look in the JPEG docs before changing - (Q) */ -+ -+/* Determine the memory manager we are going to use. Valid values are: */ -+/* MEM_DOS, MEM_ANSI, MEM_NAME, MEM_NOBS. See the JPEG docs for details on */ -+/* what each does */ -+#define JMEMSYS MEM_ANSI -+#define HAVE_STDC -+#define INCLUDES_ARE_ANSI -+ -+#endif /* Linux/arm */ -+ -+#if defined (__linux__) && defined (__aarch64__) -+ -+#ifdef GOT_MACHINE -+If you get an error on this line more than one machine type has been defined. -+Please check your Makefile. -+#endif -+#define GOT_MACHINE 1 -+ -+#include -+#include /* for unbuffered file I/O */ -+#include -+#include -+#include /* for character macros */ -+ -+#define DF_MT DFMT_AARCH64 -+ -+typedef void VOID; -+typedef void * VOIDP; -+typedef char * _fcd; -+typedef char char8; -+typedef unsigned char uchar8; -+typedef signed char int8; -+typedef unsigned char uint8; -+typedef short int int16; -+typedef unsigned short int uint16; -+typedef int int32; -+typedef unsigned int uint32; -+typedef int intn; -+typedef unsigned int uintn; -+typedef float float32; -+typedef double float64; -+typedef int intf; /* size of INTEGERs in Fortran compiler */ -+typedef long hdf_pint_t; /* an integer the same size as a pointer */ -+#define FNAME_POST_UNDERSCORE -+#define _fcdtocp(desc) (desc) -+#define FILELIB UNIXBUFIO -+ -+#ifndef BIG_LONGS -+#define BIG_LONGS -+#endif -+ -+/* JPEG #define's - Look in the JPEG docs before changing - (Q) */ -+ -+/* Determine the memory manager we are going to use. Valid values are: */ -+/* MEM_DOS, MEM_ANSI, MEM_NAME, MEM_NOBS. See the JPEG docs for details on */ -+/* what each does */ -+#define JMEMSYS MEM_ANSI -+#define HAVE_STDC -+#define INCLUDES_ARE_ANSI -+ -+#endif /* Linux/aarch64 */ -+ -+#if defined (__linux__) && defined (__riscv) && (__riscv_xlen == 64) -+ -+#ifdef GOT_MACHINE -+If you get an error on this line more than one machine type has been defined. -+Please check your Makefile. -+#endif -+#define GOT_MACHINE 1 -+ -+#include -+#include /* for unbuffered file I/O */ -+#include -+#include -+#include /* for character macros */ -+ -+#define DF_MT DFMT_RISCV64 -+ -+typedef void VOID; -+typedef void * VOIDP; -+typedef char * _fcd; -+typedef char char8; -+typedef unsigned char uchar8; -+typedef signed char int8; -+typedef unsigned char uint8; -+typedef short int int16; -+typedef unsigned short int uint16; -+typedef int int32; -+typedef unsigned int uint32; -+typedef int intn; -+typedef unsigned int uintn; -+typedef float float32; -+typedef double float64; -+typedef int intf; /* size of INTEGERs in Fortran compiler */ -+typedef long hdf_pint_t; /* an integer the same size as a pointer */ -+#define FNAME_POST_UNDERSCORE -+#define _fcdtocp(desc) (desc) -+#define FILELIB UNIXBUFIO -+ -+#ifndef BIG_LONGS -+#define BIG_LONGS -+#endif -+ -+/* JPEG #define's - Look in the JPEG docs before changing - (Q) */ -+ -+/* Determine the memory manager we are going to use. Valid values are: */ -+/* MEM_DOS, MEM_ANSI, MEM_NAME, MEM_NOBS. See the JPEG docs for details on */ -+/* what each does */ -+#define JMEMSYS MEM_ANSI -+#define HAVE_STDC -+#define INCLUDES_ARE_ANSI -+ -+#endif /* Linux/riscv64 */ -+ - #if defined(NEXT) || defined(NeXT) - - #ifndef NEXT -@@ -932,7 +1401,11 @@ Please check your Makefile. - - #include /* for unbuffered i/o stuff */ - #include --#define DF_MT DFMT_POWERPC64 -+#ifdef __LITTLE_ENDIAN__ -+#define DF_MT DFMT_POWERPC64LE -+#else -+#define DF_MT DFMT_POWERPC64 -+#endif - typedef void VOID; - typedef void *VOIDP; - typedef char *_fcd; -@@ -956,6 +1429,11 @@ typedef long hdf_pint_t; - #define _fcdtocp(desc) (desc) - #define FILELIB UNIXBUFIO - -+#ifndef BIG_LONGS -+#define BIG_LONGS -+#endif -+ -+ - /* JPEG #define's - Look in the JPEG docs before changing - (Q) */ - - /* Determine the memory manager we are going to use. Valid values are: */ -@@ -1101,6 +1579,8 @@ typedef long hdf_pint_t; - #define _fcdtocp(desc) (desc) - #define FILELIB UNIXBUFIO - -+#define BIG_LONGS -+ - /* JPEG #define's - Look in the JPEG docs before changing - (Q) */ - - /* Determine the memory manager we are going to use. Valid values are: */ -@@ -1115,6 +1595,66 @@ typedef long hdf_pint_t; - - #endif /* IA64 */ - -+/* Renesas SuperH SH3(little/big)/SH4(little/big) */ -+#if defined (__linux__) && defined(__sh__) -+ -+#ifdef GOT_MACHINE -+If you get an error on this line more than one machine type has been defined. -+Please check your Makefile. -+#endif -+#define GOT_MACHINE 1 -+ -+#include -+#include /* for unbuffered file I/O */ -+#include -+#include -+#include /* for character macros */ -+ -+#if defined (__LITTLE_ENDIAN__) -+#define DF_MT DFMT_SH -+#elif defined(__BIG_ENDIAN__) -+#define DF_MT DFMT_SHEB -+#endif -+ -+#ifndef VOID /* The stupid windows.h header file uses a #define instead of a typedef */ -+typedef void VOID; -+#endif /* end VOID */ -+ -+typedef void * VOIDP; -+typedef char * _fcd; -+typedef char char8; -+typedef unsigned char uchar8; -+typedef signed char int8; -+typedef unsigned char uint8; -+typedef short int int16; -+typedef unsigned short int uint16; -+typedef long int int32; -+typedef unsigned long int uint32; -+typedef int intn; -+typedef unsigned int uintn; -+typedef float float32; -+typedef double float64; -+typedef long intf; -+typedef int hdf_pint_t; -+#define FNAME_POST_UNDERSCORE -+#define _fcdtocp(desc) (desc) -+ -+#ifdef HAVE_FMPOOL -+#define FILELIB PAGEBUFIO /* enable page buffering */ -+#else -+#define FILELIB UNIXBUFIO -+#endif -+ -+/* JPEG #define's - Look in the JPEG docs before changing - (Q) */ -+/* Determine the memory manager we are going to use. Valid values are: */ -+/* MEM_DOS, MEM_ANSI, MEM_NAME, MEM_NOBS. See the JPEG docs for details on */ -+/* what each does */ -+#define JMEMSYS MEM_ANSI -+#define HAVE_STDC -+#define INCLUDES_ARE_ANSI -+ -+#endif /* Linux/sh */ -+ - #ifndef GOT_MACHINE - No machine type has been defined. Your Makefile needs to have someing like - -DSUN or -DUNICOS in order for the HDF internal structures to be defined ---- a/hdf/src/hconv.h -+++ b/hdf/src/hconv.h -@@ -59,7 +59,7 @@ - /* CONSTANT DEFINITIONS */ - /*****************************************************************************/ - /* Generally Big-Endian machines */ --#if !defined(INTEL86) && !defined(MIPSEL) && !defined(DEC_ALPHA) && !defined(I860) && !defined(SUN386) && !(defined(__ia64) && !(defined(hpux) || defined(__hpux))) && !defined(__x86_64__) -+#if !defined(INTEL86) && !defined(MIPSEL) && !defined(DEC_ALPHA) && !defined(I860) && !defined(SUN386) && !(defined(__ia64) && !(defined(hpux) || defined(__hpux))) && !defined(__x86_64__) && !(defined(__powerpc__) && defined(__LITTLE_ENDIAN__)) && !defined(__aarch64__) && !defined(__ARM_EABI__) && !defined(__riscv) - # define UI8_IN DFKnb1b /* Unsigned Integer, 8 bits */ - # define UI8_OUT DFKnb1b - # define SI16_IN DFKnb2b /* S = Signed */ diff --git a/gnu/packages/patches/hdf4-tirpc.patch b/gnu/packages/patches/hdf4-tirpc.patch deleted file mode 100644 index 3f436e3887..0000000000 --- a/gnu/packages/patches/hdf4-tirpc.patch +++ /dev/null @@ -1,33 +0,0 @@ -Build with libtirpc on all architectures because glibc no longer provides -SunRPC support. - -diff --git a/configure b/configure ---- a/configure -+++ b/configure -@@ -23635,10 +23635,13 @@ - *-pc-cygwin*) - LIBS="$LIBS -ltirpc" - CPPFLAGS="$CPPFLAGS -I/usr/include/tirpc" ;; -+ *-linux-gnu) -+ LIBS="$LIBS -ltirpc" -+ CPPFLAGS="$CPPFLAGS" ;; - *) ;; - esac - --if test "X$BUILD_XDR" != "Xyes"; then -+if test "X$BUILD_XDR" = "Xyes"; then - cat confdefs.h - <<_ACEOF >conftest.$ac_ext - /* end confdefs.h. */ - -@@ -23693,9 +23696,9 @@ - ## but we need to make sure that it is present on the system. Do that here, - ## The SunRPC of the glibc has been replaced by a TI-RPC (Transport Independent RPC) library for IPv6 support - case "$host" in -- *-pc-cygwin*) -+ *) - HAVE_RPC="yes" -- ac_fn_c_check_header_mongrel "$LINENO" "rpc.h" "ac_cv_header_rpc_h" "$ac_includes_default" -+ ac_fn_c_check_header_mongrel "$LINENO" "rpc/rpc.h" "ac_cv_header_rpc_h" "$ac_includes_default" - if test "x$ac_cv_header_rpc_h" = xyes; then : - : - else From cda20190bccf9bd55c264b1084eab8b6499c15cc Mon Sep 17 00:00:00 2001 From: Navid Afkhami Date: Sat, 2 Sep 2023 21:56:44 +0000 Subject: [PATCH 104/268] gnu: Add r-interactivedisplay. * gnu/packages/bioconductor.scm (r-interactivedisplay): New variable. Co-authored-by: Ricardo Wurmus --- gnu/packages/bioconductor.scm | 85 +++++++++++++++++++++++++++++++++++ 1 file changed, 85 insertions(+) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index c913232680..e5e9c80291 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -51,6 +51,7 @@ #:use-module (gnu packages haskell-xyz) #:use-module (gnu packages image) #:use-module (gnu packages java) + #:use-module (gnu packages javascript) #:use-module (gnu packages maths) #:use-module (gnu packages netpbm) #:use-module (gnu packages python) @@ -7734,6 +7735,90 @@ of other R packages who wish to make use of HTSlib.") microarray data, using nearest neighbor averaging.") (license license:gpl2+))) +(define-public r-interactivedisplay + (package + (name "r-interactivedisplay") + (version "1.38.0") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "interactiveDisplay" version)) + (sha256 + (base32 + "1y9fdnpz1bagrwhyj8jikp2q5fd9y74j48l5z7f0s88v88sa7szl")) + (snippet + '(for-each delete-file + '("inst/www/js/jquery.js" + "inst/www/js/jquery.min.js" + "inst/www/js/jquery.dataTables.min.js"))))) + (properties `((upstream-name . "interactiveDisplay"))) + (build-system r-build-system) + (arguments + (list + #:modules '((guix build utils) + (guix build r-build-system) + (srfi srfi-1)) + #:phases + '(modify-phases %standard-phases + (add-after 'unpack 'process-javascript + (lambda* (#:key inputs #:allow-other-keys) + (call-with-values + (lambda () + (unzip2 + `((,(assoc-ref inputs "js-jquery-1.8.2") + "inst/www/js/jquery.js") + (,(assoc-ref inputs "js-jquery-1.9.1") + "inst/www/js/jquery.min.js") + (,(search-input-file inputs + "/share/javascript/jquery.dataTables.min.js") + "inst/www/js/jquery.dataTables.min.js")))) + (lambda (sources targets) + (for-each (lambda (source target) + (format #true "Processing ~a --> ~a~%" + source target) + (invoke "esbuild" source "--minify" + (string-append "--outfile=" target))) + sources targets)))))))) + (propagated-inputs + (list r-annotationdbi + r-biocgenerics + r-biocmanager + r-category + r-dt + r-ggplot2 + r-gridsvg + r-interactivedisplaybase + r-plyr + r-rcolorbrewer + r-reshape2 + r-shiny + r-zlibbioc + r-xml)) + (native-inputs + `(("esbuild" ,esbuild) + ("r-knitr" ,r-knitr) + ("js-datatables" ,js-datatables) + ("js-jquery-1.8.2" + ,(origin + (method url-fetch) + (uri "https://code.jquery.com/jquery-1.8.2.js") + (sha256 + (base32 + "0nikk2clbnyi02k0brvhbd8m43lfh4l1zrya35jya9sy6wb9b9ng")))) + ("js-jquery-1.9.1" + ,(origin + (method url-fetch) + (uri "https://code.jquery.com/jquery-1.9.1.js") + (sha256 + (base32 + "0h4dk67yc9d0kadqxb6b33585f3x3559p6qmp70l00qwq030vn3v")))))) + (home-page "https://bioconductor.org/packages/interactiveDisplay") + (synopsis "Package for Shiny web displays of Bioconductor objects") + (description + "This package offers interactive Shiny displays for Bioconductor +objects. In addition, this package empowers users to develop engaging +visualizations and interfaces for working with Bioconductor data.") + (license license:artistic2.0))) + (define-public r-interactivedisplaybase (package (name "r-interactivedisplaybase") From 3007f77596a19608e4216ada575bec374da63f6f Mon Sep 17 00:00:00 2001 From: Artyom Bologov Date: Wed, 13 Sep 2023 02:37:08 +0400 Subject: [PATCH 105/268] gnu: cl-njson: Update to 1.2.0. * gnu/packages/lisp-xyz.scm (sbcl-njson): Update to 1.2.0. Signed-off-by: Guillaume Le Vaillant --- gnu/packages/lisp-xyz.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/lisp-xyz.scm b/gnu/packages/lisp-xyz.scm index 69686dbed9..e43bda9c5f 100644 --- a/gnu/packages/lisp-xyz.scm +++ b/gnu/packages/lisp-xyz.scm @@ -26603,7 +26603,7 @@ instead of #'FOO. (define-public sbcl-njson (package (name "sbcl-njson") - (version "1.1.1") + (version "1.2.0") (source (origin (method git-fetch) (uri (git-reference @@ -26612,7 +26612,7 @@ instead of #'FOO. (file-name (git-file-name "cl-njson" version)) (sha256 (base32 - "0zdf6mlbpc2j95qm000ljf642af18sfz45yxh6rnxrbf8m4laxxa")))) + "1zsf7sm88wjrd4da5bvpxi8fvsx01cv51p8820fnj062x6hlhg38")))) (build-system asdf-build-system/sbcl) (inputs (list sbcl-cl-json sbcl-jzon)) (native-inputs (list sbcl-lisp-unit2)) From 828b08d58526cf242e121da3f0e3a3524aa507c8 Mon Sep 17 00:00:00 2001 From: "Andre A. Gomes" Date: Mon, 11 Sep 2023 17:44:38 +0300 Subject: [PATCH 106/268] gnu: cl-nasdf: Update to 0.1.8. * gnu/packages/lisp-xyz.scm (sbcl-nasdf): Update to 0.1.8. Signed-off-by: Guillaume Le Vaillant --- gnu/packages/lisp-xyz.scm | 7 +++---- 1 file changed, 3 insertions(+), 4 deletions(-) diff --git a/gnu/packages/lisp-xyz.scm b/gnu/packages/lisp-xyz.scm index e43bda9c5f..1d88654962 100644 --- a/gnu/packages/lisp-xyz.scm +++ b/gnu/packages/lisp-xyz.scm @@ -25824,12 +25824,11 @@ change since last write. (inputs (cons (list "iolib" cl-iolib) (package-inputs sbcl-nfiles))))) - (define-public sbcl-nasdf - (let ((commit "dd9fb2df7174464b54561b2a2f3c3e00fdd5d4f7")) + (let ((commit "ab7a018f3a67a999c72710644b10b4545130c139")) (package (name "sbcl-nasdf") - (version "0.1.7") + (version "0.1.8") (source (origin (method git-fetch) @@ -25838,7 +25837,7 @@ change since last write. (commit commit))) (file-name (git-file-name "cl-ntemplate" version)) (sha256 - (base32 "1q8ky8hz8xrr37h7yyc6ysvrcwlsp1i6r2x44c060drspgjbqj70")))) + (base32 "15j7kqxvn0blr0i2xgk0il0ia91p28clfqxdh00vlp423v9a2wbx")))) (build-system asdf-build-system/sbcl) (arguments `(#:phases From 4f933f977dd8aa61ca3e50b194d3b56e298a3e30 Mon Sep 17 00:00:00 2001 From: "Andre A. Gomes" Date: Mon, 11 Sep 2023 17:44:45 +0300 Subject: [PATCH 107/268] gnu: nyxt: Update to 3.7.0. * gnu/packages/web-browsers.scm (nyxt): Update to 3.7.0. Signed-off-by: Guillaume Le Vaillant --- gnu/packages/web-browsers.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/web-browsers.scm b/gnu/packages/web-browsers.scm index 5fb43d0ee9..a8ef7099f5 100644 --- a/gnu/packages/web-browsers.scm +++ b/gnu/packages/web-browsers.scm @@ -586,7 +586,7 @@ driven and does not detract you from your daily work.") (define-public nyxt (package (name "nyxt") - (version "3.6.1") + (version "3.7.0") (source (origin (method git-fetch) @@ -595,7 +595,7 @@ driven and does not detract you from your daily work.") (commit version))) (sha256 (base32 - "0gf4akrkp15c3z3v3i5c94ga282ygqxb0rqxwm9ivchby0xv9lmd")) + "0mar3y69b62jby4kfdsm2xsnb830v1d468zspa3frpnphwxv4a5y")) (file-name (git-file-name "nyxt" version)) (modules '((guix build utils))) (snippet From 67268d9a8109936d9e7e486394fcc021880c6a28 Mon Sep 17 00:00:00 2001 From: Andy Tai Date: Mon, 11 Sep 2023 01:15:37 -0700 Subject: [PATCH 108/268] gnu: octave-cli: Update to 8.3.0 * gnu/packages/maths.scm (octave-cli): Update to 8.3.0 Signed-off-by: Eric Bavier --- gnu/packages/maths.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/maths.scm b/gnu/packages/maths.scm index e3cd0762be..6141c09886 100644 --- a/gnu/packages/maths.scm +++ b/gnu/packages/maths.scm @@ -2779,7 +2779,7 @@ can solve two kinds of problems: (define-public octave-cli (package (name "octave-cli") - (version "8.2.0") + (version "8.3.0") (source (origin (method url-fetch) @@ -2787,7 +2787,7 @@ can solve two kinds of problems: version ".tar.xz")) (sha256 (base32 - "1pkh4vmq4hcrmyl2gybd54i3qamyvmcjmpgy1i2kkw2g03jxdfdp")))) + "1aav8i88y2yl11g5d44wpjngkpldvzk90ja7wghkb91cy2a9974i")))) (build-system gnu-build-system) (inputs (list alsa-lib From b6441f7bd0257783fffecfc6b6b3c6f2950204c2 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 13 Sep 2023 14:06:19 +0200 Subject: [PATCH 109/268] upstream: Compare symbols to symbols. The UNCHANGED? comparison would always yield #FALSE, because we have been comparing lists of strings with lists of symbols. * guix/upstream.scm (update-package-inputs): Convert string labels to symbols before comparison. --- guix/upstream.scm | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/guix/upstream.scm b/guix/upstream.scm index 33248d645c..e28ae12f3f 100644 --- a/guix/upstream.scm +++ b/guix/upstream.scm @@ -1,7 +1,7 @@ ;;; GNU Guix --- Functional package management for GNU ;;; Copyright © 2010-2023 Ludovic Courtès ;;; Copyright © 2015 Alex Kost -;;; Copyright © 2019, 2022 Ricardo Wurmus +;;; Copyright © 2019, 2022, 2023 Ricardo Wurmus ;;; Copyright © 2021 Sarah Morgensen ;;; Copyright © 2021, 2022 Maxime Devos ;;; Copyright © 2022 Hartmut Goebel @@ -534,7 +534,8 @@ specified in SOURCE, an ." (define old (match (package-inputs package) (((labels (? package? packages)) ...) - labels) + labels + (map string->symbol labels)) (_ '()))) From dc172966ba88895096f2c71dcdc3c4083f412dff Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 13 Sep 2023 15:03:59 +0200 Subject: [PATCH 110/268] gnu: Add r-quickjsr. * gnu/packages/cran.scm (r-quickjsr): New variable. --- gnu/packages/cran.scm | 21 +++++++++++++++++++++ 1 file changed, 21 insertions(+) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index b6a01a99b0..21eaa6fbea 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -15583,6 +15583,27 @@ estimation problem.") ;; The CRAN page only says GPL-3. (license license:gpl3+))) +(define-public r-quickjsr + (package + (name "r-quickjsr") + (version "1.0.6") + (source (origin + (method url-fetch) + (uri (cran-uri "QuickJSR" version)) + (sha256 + (base32 + "1n09jivw1qvsniyap0ki5ablvkwgggh981hcs7k5wx3lp3qxxlnk")))) + (properties `((upstream-name . "QuickJSR"))) + (build-system r-build-system) + (propagated-inputs (list r-jsonlite r-r6 r-rcpp)) + (home-page "https://cran.r-project.org/package=QuickJSR") + (synopsis "Interface for the QuickJS lightweight JavaScript engine") + (description + "This package provides an R interface to the @code{QuickJS} portable +@code{JavaScript} engine. The engine is bundled entirely within the package, +requiring no external system dependencies beyond a C compiler.") + (license license:expat))) + (define-public r-abundant (package (name "r-abundant") From 2c1d86e2e0b52ce9ff916d4e6fd0f37998c9e430 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?M=C4=83d=C4=83lin=20Ionel=20Patra=C8=99cu?= Date: Wed, 13 Sep 2023 15:39:18 +0200 Subject: [PATCH 111/268] gnu: python-hicmatrix: Remove syntax error in setup.py. * gnu/packages/bioinformatics.scm (python-hicmatrix)[arguments]: Add phase remove-invalid-syntax. Signed-off-by: Ricardo Wurmus --- gnu/packages/bioinformatics.scm | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index e24d70e569..1ceb429169 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -16229,6 +16229,10 @@ includes operations like compartment, insulation or peak calling.") (list #:phases '(modify-phases %standard-phases + (add-after 'unpack 'remove-invalid-syntax + (lambda _ + (substitute* "setup.py" + ((".\\*\"") "\"")))) (replace 'check (lambda* (#:key tests? #:allow-other-keys) (when tests? From 4e8ec5a16b8334218e588b0e23924b796378f598 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 13 Sep 2023 15:20:09 +0200 Subject: [PATCH 112/268] gnu: r-dt: Update to 0.29. * gnu/packages/statistics.scm (r-dt): Update to 0.29. [propagated-inputs]: Add r-httpuv. --- gnu/packages/statistics.scm | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm index db99f4c7f2..67837a8e62 100644 --- a/gnu/packages/statistics.scm +++ b/gnu/packages/statistics.scm @@ -3837,13 +3837,13 @@ using the multicore functionality of the parallel package.") extensions))))) (package (name "r-dt") - (version "0.28") + (version "0.29") (source (origin (method url-fetch) (uri (cran-uri "DT" version)) (sha256 (base32 - "0khdl21kvgi9k7dlpfshk1xz9bkly5lq6p41plfh4g2jv1yxaxfr")) + "1b9qshrjv9xaak92rvg65vkak4pyci9js4j7nkfcg0p19ghnvlm8")) (modules '((guix build utils) (ice-9 match))) (snippet @@ -3917,6 +3917,7 @@ using the multicore functionality of the parallel package.") (list r-crosstalk r-htmltools r-htmlwidgets + r-httpuv r-jquerylib r-jsonlite r-magrittr From aaaaa2ea074526c5b036fa6aa77e1c519a6e4d6a Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 13 Sep 2023 15:20:43 +0200 Subject: [PATCH 113/268] gnu: r-minqa: Update to 1.2.6. * gnu/packages/statistics.scm (r-minqa): Update to 1.2.6. [inputs]: Move gfortran from here... [native-inputs]: ...to here. --- gnu/packages/statistics.scm | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm index 67837a8e62..1f4d76af60 100644 --- a/gnu/packages/statistics.scm +++ b/gnu/packages/statistics.scm @@ -5826,18 +5826,18 @@ showing the progress is useful e.g. bootstrap.") (define-public r-minqa (package (name "r-minqa") - (version "1.2.5") + (version "1.2.6") (source (origin (method url-fetch) (uri (cran-uri "minqa" version)) (sha256 (base32 - "1gpli7f3piz3jqjj63a6bk9v1jlygjdaqqqvqsr083crj0imd0wv")))) + "0421b4ysslaqmdgwlz080abis8m4xkcvjq7lx1wywbsz1s2vi9si")))) (build-system r-build-system) (propagated-inputs (list r-rcpp)) - (inputs + (native-inputs (list gfortran)) (home-page "https://optimizer.r-forge.r-project.org") (synopsis "Derivative-free optimization algorithms by quadratic approximation") From 6739c534f8f0035dbfd18ecbec15a0173e409d03 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 13 Sep 2023 15:35:19 +0200 Subject: [PATCH 114/268] gnu: apache-arrow: Update to 13.0.0. * gnu/packages/databases.scm (apache-arrow): Update to 13.0.0. --- gnu/packages/databases.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/databases.scm b/gnu/packages/databases.scm index d0f8ce2001..2b8e80e1b0 100644 --- a/gnu/packages/databases.scm +++ b/gnu/packages/databases.scm @@ -4305,7 +4305,7 @@ the SQL language using a syntax that reflects the resulting query.") (define-public apache-arrow (package (name "apache-arrow") - (version "12.0.1") + (version "13.0.0") (source (origin (method git-fetch) @@ -4315,7 +4315,7 @@ the SQL language using a syntax that reflects the resulting query.") (file-name (git-file-name name version)) (sha256 (base32 - "03flvb4xj6a7mfphx68ndrqr6g5jphmzb75m16fx7rnbzira2zpz")))) + "03ykynzz01ar2y4blhcxjh6xsi0gqv380h5m669dddfz2isplsf8")))) (build-system cmake-build-system) (arguments (list From 080d0880166aac172268c187a54aa843305430ff Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 13 Sep 2023 15:35:50 +0200 Subject: [PATCH 115/268] gnu: r-arrow: Update to 13.0.0. * gnu/packages/cran.scm (r-arrow): Update to 13.0.0. --- 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 21eaa6fbea..2968742f99 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -24338,14 +24338,14 @@ colored by the number of neighboring points. This is useful to visualize the (define-public r-arrow (package (name "r-arrow") - (version "12.0.1.1") + (version "13.0.0") (source (origin (method url-fetch) (uri (cran-uri "arrow" version)) (sha256 (base32 - "18c864ingckbi3v2xhigaiv72sc2c4x3zps60z0v22slkpz5ba0s")))) + "0s29xw9r9hxyvcgdasw95qa7q8zvs79ffhfnlpnzsvb523d2cb6l")))) (properties `((upstream-name . "arrow"))) (build-system r-build-system) (inputs From bf982837412f271f74b148b22ff5ec4d107e045f Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 13 Sep 2023 15:47:15 +0200 Subject: [PATCH 116/268] gnu: r-radiant-data: Update to 1.6.1. * gnu/packages/cran.scm (r-radiant-data): Update to 1.6.1. [propagated-inputs]: Add r-arrow. --- gnu/packages/cran.scm | 11 ++++++----- 1 file changed, 6 insertions(+), 5 deletions(-) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 2968742f99..d79c70170c 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -10939,14 +10939,14 @@ local smoothers and many more.") (define-public r-radiant-data (package (name "r-radiant-data") - (version "1.5.6") + (version "1.6.1") (source (origin (method url-fetch) (uri (cran-uri "radiant.data" version)) (sha256 (base32 - "1dd18brwgcpkqbnxg6jqk4r7aw1i2d7lg9mnfw59q95n6jk86lr5")) + "00bjq3zpxhd6yjq3jwizgiyzp2qf557ms6mhlz74d0wcm0l3vd72")) (modules '((guix build utils))) (snippet '(begin @@ -10978,15 +10978,16 @@ local smoothers and many more.") (string-append "--outfile=" target))) sources targets))))))))) (propagated-inputs - (list r-base64enc + (list r-arrow + r-base64enc r-broom r-bslib r-car r-curl r-dplyr r-dt - r-glue r-ggplot2 + r-glue r-import r-jsonlite r-knitr @@ -11006,8 +11007,8 @@ local smoothers and many more.") r-rstudioapi r-scales r-shiny - r-shinyfiles r-shinyace + r-shinyfiles r-stringi r-tibble r-tidyr From 9049506d8b11a4f77f207827cd8667e0dedeaeb2 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 13 Sep 2023 22:19:23 +0200 Subject: [PATCH 117/268] gnu: python-hicmatrix: Remove custom 'check phase. * gnu/packages/bioinformatics.scm (python-hicmatrix)[arguments]: Remove custom 'check phase. --- gnu/packages/bioinformatics.scm | 6 +----- 1 file changed, 1 insertion(+), 5 deletions(-) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 1ceb429169..aa88692204 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -16232,11 +16232,7 @@ includes operations like compartment, insulation or peak calling.") (add-after 'unpack 'remove-invalid-syntax (lambda _ (substitute* "setup.py" - ((".\\*\"") "\"")))) - (replace 'check - (lambda* (#:key tests? #:allow-other-keys) - (when tests? - (invoke "python" "-m" "pytest" "-v"))))))) + ((".\\*\"") "\""))))))) (propagated-inputs (list python-cooler python-intervaltree From f2d690c6c54a6cbea49bf4ac997125f81074ae57 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 13 Sep 2023 22:41:25 +0200 Subject: [PATCH 118/268] gnu: r-leaflet: Update to 2.2.0. * gnu/packages/cran.scm (r-leaflet): Update to 2.2.0. [source]: Do not delete jquery.min.js, because it is no longer included. [arguments]: Adjust minification accordingly. [native-inputs]: Remove js-jquery. [propagated-inputs]: Remove r-base64enc and r-markdown; add r-jquerylib and r-xfun. --- gnu/packages/cran.scm | 22 ++++++---------------- 1 file changed, 6 insertions(+), 16 deletions(-) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index d79c70170c..a3d70f2852 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -9912,20 +9912,19 @@ information between package updates.") (define-public r-leaflet (package (name "r-leaflet") - (version "2.1.2") + (version "2.2.0") (source (origin (method url-fetch) (uri (cran-uri "leaflet" version)) (sha256 - (base32 "0fa0f9fcrxbqhmcm45l0byws56d8gg0bi3vx4m65mn4rihg6gn16")) + (base32 "0k0zplbhmvld6q1id17s827z1230kvnz16c4hlvp6jn9g26yy0dq")) (snippet '(for-each delete-file (list "inst/htmlwidgets/lib/leaflet/leaflet.js" "inst/htmlwidgets/lib/leaflet-measure/leaflet-measure.min.js" "inst/htmlwidgets/lib/leaflet-omnivore/leaflet-omnivore.min.js" - "inst/htmlwidgets/lib/jquery/jquery.min.js" "inst/htmlwidgets/plugins/Leaflet-MiniMap/Control.MiniMap.min.js" "inst/htmlwidgets/plugins/Leaflet.awesome-markers/bootstrap.min.js" "inst/htmlwidgets/plugins/Leaflet.awesome-markers/leaflet.awesome-markers.min.js" @@ -9956,8 +9955,6 @@ information between package updates.") "htmlwidgets/lib/leaflet-measure/leaflet-measure.min.js") (,(assoc-ref inputs "js-leaflet-omnivore") "htmlwidgets/lib/leaflet-omnivore/leaflet-omnivore.min.js") - (,(assoc-ref inputs "js-jquery") - "htmlwidgets/lib/jquery/jquery.min.js") ("htmlwidgets/plugins/Leaflet-MiniMap/Control.MiniMap.js" "htmlwidgets/plugins/Leaflet-MiniMap/Control.MiniMap.min.js") (,(assoc-ref inputs "js-bootstrap3") @@ -9992,13 +9989,6 @@ information between package updates.") (sha256 (base32 "1j1qjagwj0m3q322z9wxxnpkd8zbk6g3kl047dsbmqad6gmqvgha")))) - ("js-jquery" - ,(origin - (method url-fetch) - (uri "https://code.jquery.com/jquery-1.12.4.js") - (sha256 - (base32 - "0x9mrc1668icvhpwzvgafm8xm11x9lfai9nwr66aw6pjnpwkc3s3")))) ("js-leaflet" ,(origin (method url-fetch) @@ -10061,19 +10051,19 @@ information between package updates.") (base32 "0vyrbf6gv2lyh4c2bzp5349ivwvvg28gpn87y52a7jdb13rlkpab")))))) (propagated-inputs - (list r-base64enc - r-crosstalk + (list r-crosstalk r-htmltools r-htmlwidgets + r-jquerylib r-leaflet-providers r-magrittr - r-markdown r-png r-raster r-rcolorbrewer r-scales r-sp - r-viridis)) + r-viridis + r-xfun)) (home-page "https://rstudio.github.io/leaflet/") (synopsis "Create interactive web maps with the JavaScript Leaflet library") (description From 455dadc41a706cdde336a01225c9846e67340dbe Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 13 Sep 2023 22:51:14 +0200 Subject: [PATCH 119/268] gnu: r-iheatmapr: Update to 0.7.0. * gnu/packages/cran.scm (r-iheatmapr): Update to 0.7.0. [source]: Delete minified plotly JavaScript. [native-inputs]: Add esbuild and js-plotly. [arguments]: Add phase to minify plotly.js. --- gnu/packages/cran.scm | 29 ++++++++++++++++++++++++++--- 1 file changed, 26 insertions(+), 3 deletions(-) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index a3d70f2852..a7f3b91207 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -31098,16 +31098,29 @@ Haberman's interaction model when all items are dichotomously scored.") (define-public r-iheatmapr (package (name "r-iheatmapr") - (version "0.5.1") + (version "0.7.0") (source (origin (method url-fetch) (uri (cran-uri "iheatmapr" version)) (sha256 (base32 - "1pwkwh7ljlpr6zyz6j8knpz3iw60xzkw8amc98x4pc2mw148jvzx")))) + "0ym796kf6d8cwd7nmgzy3ga7r8fyywddl3rr2hbn4cfmwhggv02l")) + (snippet + '(delete-file + "inst/htmlwidgets/lib/plotlyjs/plotly-latest.min.js")))) (properties `((upstream-name . "iheatmapr"))) (build-system r-build-system) + (arguments + (list + #:phases + '(modify-phases %standard-phases + (add-after 'unpack 'process-javascript + (lambda* (#:key inputs #:allow-other-keys) + (with-directory-excursion "inst/htmlwidgets/lib/plotlyjs/" + (invoke "esbuild" (assoc-ref inputs "js-plotly") + "--minify" + "--outfile=plotly-latest.min.js"))))))) (propagated-inputs (list r-fastcluster r-ggdendro @@ -31118,7 +31131,17 @@ Haberman's interaction model when all items are dichotomously scored.") r-rcolorbrewer r-scales)) (native-inputs - (list r-knitr)) + `(("esbuild" ,esbuild) + ("r-knitr" ,r-knitr) + ("js-plotly" + ,(let ((version "2.10.1")) + (origin + (method url-fetch) + (uri (string-append "https://raw.githubusercontent.com/plotly/plotly.js/v" + version "/dist/plotly.js")) + (sha256 + (base32 + "1cg2q681yjsrpjmm4nkfia7752wxnszi3c94nq9a91zpnfkm22yb"))))))) (home-page "https://docs.ropensci.org/iheatmapr") (synopsis "Interactive, Complex Heatmaps") (description From ab1f8495f92641402e68de83f3f03630f6331d9a Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 13 Sep 2023 22:57:03 +0200 Subject: [PATCH 120/268] gnu: r-rstan: Update to 2.26.23. * gnu/packages/cran.scm (r-rstan): Update to 2.26.23. [native-inputs]: Remove pandoc. [propagated-inputs]: Add r-quickjsr. --- 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 a7f3b91207..5d693f26c7 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -31391,14 +31391,14 @@ techniques to average Bayesian predictive distributions.") (define-public r-rstan (package (name "r-rstan") - (version "2.21.8") + (version "2.26.23") (source (origin (method url-fetch) (uri (cran-uri "rstan" version)) (sha256 (base32 - "0xah8wl4lg8zh5982m20ipc6cjck1dsfi8lz1jbkg4212p1yvm5j")))) + "08hdwrpxbxp2wdnfk2jj2xsdgl7q9nbalz5wgwmy0m878swxxzci")))) (properties `((upstream-name . "rstan"))) (build-system r-build-system) (arguments @@ -31412,7 +31412,7 @@ techniques to average Bayesian predictive distributions.") (search-input-directory inputs "share/zoneinfo"))))))) (native-inputs - (list tzdata-for-tests pandoc r-knitr)) + (list r-knitr tzdata-for-tests)) (propagated-inputs (list r-bh r-ggplot2 @@ -31420,6 +31420,7 @@ techniques to average Bayesian predictive distributions.") r-inline r-loo r-pkgbuild + r-quickjsr r-rcpp r-rcppeigen r-rcppparallel From b3b369f9903222d4db426fcbe356a633a6a68224 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 13 Sep 2023 22:58:18 +0200 Subject: [PATCH 121/268] gnu: r-hmisc: Update to 5.1-1. * gnu/packages/statistics.scm (r-hmisc): Update to 5.1-1. --- gnu/packages/statistics.scm | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm index 1f4d76af60..c3444560fd 100644 --- a/gnu/packages/statistics.scm +++ b/gnu/packages/statistics.scm @@ -4876,13 +4876,13 @@ package instead.") (define-public r-hmisc (package (name "r-hmisc") - (version "5.1-0") + (version "5.1-1") (source (origin (method url-fetch) (uri (cran-uri "Hmisc" version)) (sha256 - (base32 "0y10hnglid78gnaapmdy3ihjih4i2kvaycn2c60r2wr43nv7wl0q")))) + (base32 "0laan26ja6m9k3spkk1ymalwb181ramzjq6ii3b0404xv2kfywa9")))) (properties `((upstream-name . "Hmisc"))) (build-system r-build-system) (native-inputs @@ -4897,9 +4897,9 @@ package instead.") r-ggplot2 r-gridextra r-gtable - r-knitr r-htmltable r-htmltools + r-knitr r-nnet r-rmarkdown r-rpart From 4676f07f6d17df7d36dbcfaf76db24f7c8929e07 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 13 Sep 2023 23:02:37 +0200 Subject: [PATCH 122/268] gnu: r-glmnetutils: Update to 1.1.9. * gnu/packages/cran.scm (r-glmnetutils): Update to 1.1.9. --- gnu/packages/cran.scm | 7 +++---- 1 file changed, 3 insertions(+), 4 deletions(-) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 5d693f26c7..679a37f9f3 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -5558,18 +5558,17 @@ Docstrings (PEP-0257) and Julia's Triple-Quoted String Literals.") (define-public r-glmnetutils (package (name "r-glmnetutils") - (version "1.1.8") + (version "1.1.9") (source (origin (method url-fetch) (uri (cran-uri "glmnetUtils" version)) (sha256 (base32 - "1k8ivzjgpkm2a948qxx3wmkhlppbk31qc76spv2pscmp24x0lxyn")))) + "0rh07i9j6bxiqcl84d8jnn7dzqdwfdzak7w8bf4j4521r24mwm01")))) (properties `((upstream-name . "glmnetUtils"))) (build-system r-build-system) (propagated-inputs - (list r-glmnet - r-matrix)) + (list r-glmnet r-matrix)) (native-inputs (list r-knitr)) (home-page "https://github.com/hongooi73/glmnetUtils") (synopsis From 8f59ac151fc39a7dbad2c90a04d2c6c0fe5d3980 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 13 Sep 2023 23:14:38 +0200 Subject: [PATCH 123/268] gnu: r-abn: Update to 3.0.0. * gnu/packages/bioconductor.scm (r-abn): Update to 3.0.0. [propagated-inputs]: Add r-mclogit and r-stringi. --- gnu/packages/bioconductor.scm | 8 +++++--- 1 file changed, 5 insertions(+), 3 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index e5e9c80291..68463f1f33 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -21193,14 +21193,14 @@ on the plot.") (define-public r-abn (package (name "r-abn") - (version "2.7-5") + (version "3.0.0") (source (origin (method url-fetch) (uri (cran-uri "abn" version)) (sha256 (base32 - "0ibznjhy7vmh2myarvmxy06rvddbpbarbp201px62mig2pb9aq4y")))) + "100nafmyddz0c1h01fbqw5q6pji7zhg2196rkyak88za6s5ms0s4")))) (build-system r-build-system) (inputs (list gsl)) @@ -21209,11 +21209,13 @@ on the plot.") r-foreach r-graph r-lme4 + r-mclogit r-nnet r-rcpp r-rcpparmadillo r-rgraphviz - r-rjags)) + r-rjags + r-stringi)) (native-inputs (list r-r-rsp)) (home-page "https://r-bayesian-networks.org/") From bf9cd9521a75eb928d70b39a30f7b19edb89089b Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 14 Sep 2023 00:04:05 +0200 Subject: [PATCH 124/268] gnu: r-htscluster: Update to 2.0.11. * gnu/packages/bioconductor.scm (r-htscluster): Update to 2.0.11. --- 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 68463f1f33..0b44257b16 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -12649,14 +12649,14 @@ abnormal copy number.") (define-public r-htscluster (package (name "r-htscluster") - (version "2.0.10") + (version "2.0.11") (source (origin (method url-fetch) (uri (cran-uri "HTSCluster" version)) (sha256 (base32 - "0scn4fsfmlkzxibfhsh6krm2cl9c8hsmyjgn48k9dyjf0ylyxg9n")))) + "0x9shhyla9bldkkh367gfdmf0k72l1ppixb8gzsa6nf8jx8qdpbp")))) (properties `((upstream-name . "HTSCluster"))) (build-system r-build-system) (propagated-inputs From 34d08dc157b8ca611805720c2119e214fc3c8d31 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 14 Sep 2023 00:04:06 +0200 Subject: [PATCH 125/268] gnu: r-ggfittext: Update to 0.10.1. * gnu/packages/cran.scm (r-ggfittext): Update to 0.10.1. --- 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 679a37f9f3..f55ce23af9 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -782,13 +782,13 @@ text annotations.") (define-public r-ggfittext (package (name "r-ggfittext") - (version "0.10.0") + (version "0.10.1") (source (origin (method url-fetch) (uri (cran-uri "ggfittext" version)) (sha256 (base32 - "06xfv552nhw13wc8dixyqhhmw5zh8hphrabw090nzb33cpfwzin8")))) + "1z06q55igv6nibc72hll93cpp80mfg3yqfqbi967832nfj7wll7a")))) (properties `((upstream-name . "ggfittext"))) (build-system r-build-system) (propagated-inputs (list r-ggplot2 r-gridtext r-shades r-stringi)) From 4e2c4c5d4d682b71567a26dcfce5d4a14afdc4cd Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 14 Sep 2023 00:04:06 +0200 Subject: [PATCH 126/268] gnu: r-climaemet: Update to 1.2.0. * gnu/packages/cran.scm (r-climaemet): Update to 1.2.0. --- 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 f55ce23af9..af22783233 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -1714,13 +1714,13 @@ size and can be easily tested locally before being sent to a remote.") (define-public r-climaemet (package (name "r-climaemet") - (version "1.1.1") + (version "1.2.0") (source (origin (method url-fetch) (uri (cran-uri "climaemet" version)) (sha256 (base32 - "17g55shqsgpv9vpm41r5lc7ihqhfqj0phbsgv9ghpql9z1nxjy19")))) + "1276pxs3w610v6m8j5h206xxgwvm2wwma73jpvn7s3rcxycs32m5")))) (properties `((upstream-name . "climaemet"))) (build-system r-build-system) (propagated-inputs From 1af29b5f275604f975ffa662e73a303266afc289 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 14 Sep 2023 00:04:06 +0200 Subject: [PATCH 127/268] gnu: r-mboost: Update to 2.9-8. * gnu/packages/cran.scm (r-mboost): Update to 2.9-8. --- 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 af22783233..d8e407b10c 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -3018,13 +3018,13 @@ objects.") (define-public r-mboost (package (name "r-mboost") - (version "2.9-7") + (version "2.9-8") (source (origin (method url-fetch) (uri (cran-uri "mboost" version)) (sha256 (base32 - "01ln0vxbbx1fq77q17sx61si82lhfibbchsnf2yw9032cn8wnhh2")))) + "1jyigxi5lzcaa6psc8lyvw2b6ylldqlnps3jlvjrl9zr6336nk6n")))) (build-system r-build-system) (propagated-inputs (list r-lattice From f5bc3727de04cc0398f500b4526cb4dd719943f9 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 14 Sep 2023 00:04:06 +0200 Subject: [PATCH 128/268] gnu: r-askpass: Update to 1.2.0. * gnu/packages/cran.scm (r-askpass): Update to 1.2.0. --- 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 d8e407b10c..5952062fba 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -3168,14 +3168,14 @@ large-scale hypothesis testing and false discovery rate estimation.") (define-public r-askpass (package (name "r-askpass") - (version "1.1") + (version "1.2.0") (source (origin (method url-fetch) (uri (cran-uri "askpass" version)) (sha256 (base32 - "07q0ik8jzk44vpwh48rr3fnpd7dzsdhjjsl4l850rffv3dyq4h6v")))) + "1vrcb69gf5hc8rggc9m7wv19crz5mkl7f08cipy0ykckh6bkc8mr")))) (build-system r-build-system) (propagated-inputs (list r-sys)) (home-page "https://github.com/jeroen/askpass") From d0928fe95caaf4cc2ebc30646d4b9d9bd10a85d6 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 14 Sep 2023 00:04:06 +0200 Subject: [PATCH 129/268] gnu: r-rcppnumerical: Update to 0.6-0. * gnu/packages/cran.scm (r-rcppnumerical): 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 5952062fba..41265e26d1 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -5938,13 +5938,13 @@ safely be interrupted from R.") (define-public r-rcppnumerical (package (name "r-rcppnumerical") - (version "0.5-0") + (version "0.6-0") (source (origin (method url-fetch) (uri (cran-uri "RcppNumerical" version)) (sha256 (base32 - "15hb08vwdvjrhzq1pyalv3qv946jnlk0w77nn654zcmmsns2fqar")))) + "11nph9fz1bzb0pcvh6xx4cb94090ahwpj21zmbi06m4pibb1a1rg")))) (build-system r-build-system) (propagated-inputs (list r-rcpp r-rcppeigen)) From 273b193782f6e1e9afae81de83b2a90bfc7838af Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 14 Sep 2023 00:04:06 +0200 Subject: [PATCH 130/268] gnu: r-ctrdata: Update to 1.15.1. * gnu/packages/cran.scm (r-ctrdata): Update to 1.15.1. --- 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 41265e26d1..f4e9823a6c 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -6157,13 +6157,13 @@ graphics packages that comes with the base installation.") (define-public r-ctrdata (package (name "r-ctrdata") - (version "1.15.0") + (version "1.15.1") (source (origin (method url-fetch) (uri (cran-uri "ctrdata" version)) (sha256 (base32 - "16j44mzfllpp7il0kz3j4a6mi2k939yndgwxki01rqlmf8lrj15j")))) + "1yzn7cxsxbldnfhk83kw8p9qv0154lf2207qvlgjhpc6lzka4lic")))) (properties `((upstream-name . "ctrdata"))) (build-system r-build-system) (propagated-inputs From d530d51c395064e92983e67db8406c39b7e6a7f9 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 14 Sep 2023 00:04:06 +0200 Subject: [PATCH 131/268] gnu: r-lambertw: Update to 0.6.8. * gnu/packages/cran.scm (r-lambertw): Update to 0.6.8. --- 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 f4e9823a6c..02d3cd1e81 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -6680,13 +6680,13 @@ print, summary, etc.") (define-public r-lambertw (package (name "r-lambertw") - (version "0.6.7-1") + (version "0.6.8") (source (origin (method url-fetch) (uri (cran-uri "LambertW" version)) (sha256 (base32 - "0cdrq2nrvji8l5blswkffymm7cbjk5jzzx16js2a516cm3gjwxk4")))) + "10lqsz44ndm8pl8z75j35fzd1s313q09rs9bs3lkym8d43k50pha")))) (properties `((upstream-name . "LambertW"))) (build-system r-build-system) (propagated-inputs (list r-ggplot2 From 96841f9b22aac0ed66c8a14a5a7bb81f267a17d1 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 14 Sep 2023 00:04:06 +0200 Subject: [PATCH 132/268] gnu: r-lpsolve: Update to 5.6.19. * gnu/packages/cran.scm (r-lpsolve): Update to 5.6.19. --- 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 02d3cd1e81..212b33578d 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -7144,14 +7144,14 @@ topics for ecologists (ISBN 978-0-691-12522-0).") (define-public r-lpsolve (package (name "r-lpsolve") - (version "5.6.18") + (version "5.6.19") (source (origin (method url-fetch) (uri (cran-uri "lpSolve" version)) (sha256 (base32 - "04p71mcpksighyvl74ffvgxzc7iiv7nafphddhmqa6yqzhk1j7km")))) + "06sqjj69gp2ja2hgzfxii00js6pjbmhyp07a9jya5sy6cjgb9ma9")))) (properties `((upstream-name . "lpSolve"))) (build-system r-build-system) (home-page "https://cran.r-project.org/web/packages/lpSolve") From ad05f415537ab0a34957d62e146e97dd0bbecd14 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 14 Sep 2023 00:04:07 +0200 Subject: [PATCH 133/268] gnu: r-prodlim: Update to 2023.08.28. * gnu/packages/cran.scm (r-prodlim): Update to 2023.08.28. --- gnu/packages/cran.scm | 11 ++++++++--- 1 file changed, 8 insertions(+), 3 deletions(-) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 212b33578d..3de5546a39 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -7577,17 +7577,22 @@ regression using Kernel Ridge Regression.") (define-public r-prodlim (package (name "r-prodlim") - (version "2023.03.31") + (version "2023.08.28") (source (origin (method url-fetch) (uri (cran-uri "prodlim" version)) (sha256 (base32 - "003qg4apcayj5kr3730qcs8npibmv1vznzgjcrk9bjhihm7la42m")))) + "1s2xalxfq2q6a9ssz01vzpldpa98q3cl5icap0k2xr5v72gj40l0")))) (build-system r-build-system) (propagated-inputs - (list r-data-table r-diagram r-kernsmooth r-lava r-rcpp r-survival)) + (list r-data-table + r-diagram + r-kernsmooth + r-lava + r-rcpp + r-survival)) (home-page "https://cran.r-project.org/web/packages/prodlim") (synopsis "Product-limit estimation for censored event history analysis") (description From a8c112e212eee1fe3995d228e3c5098b676458d4 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 14 Sep 2023 00:04:07 +0200 Subject: [PATCH 134/268] gnu: r-statsexpressions: Update to 1.5.2. * gnu/packages/cran.scm (r-statsexpressions): Update to 1.5.2. --- gnu/packages/cran.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 3de5546a39..405a1d1209 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -8249,13 +8249,13 @@ functions for: (define-public r-statsexpressions (package (name "r-statsexpressions") - (version "1.5.1") + (version "1.5.2") (source (origin (method url-fetch) (uri (cran-uri "statsExpressions" version)) (sha256 (base32 - "1lq4h3a8yr7wnmjkg2rgr8524vdpfacr73pv4wxj44dbg9yh8l3x")))) + "1lqx6wcip0vzlrlhj8yg09009r1r12xg1wxkq93hrlkvya6wm66k")))) (properties `((upstream-name . "statsExpressions"))) (build-system r-build-system) (propagated-inputs (list r-afex From 4d0b8b39a7c7162a4a50b0b1ed619ef3717c35b7 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 14 Sep 2023 00:04:07 +0200 Subject: [PATCH 135/268] gnu: r-rio: Update to 0.5.30. * gnu/packages/cran.scm (r-rio): Update to 0.5.30. --- gnu/packages/cran.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 405a1d1209..98110625b8 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -11663,14 +11663,14 @@ dependency on Java.") (define-public r-rio (package (name "r-rio") - (version "0.5.29") + (version "0.5.30") (source (origin (method url-fetch) (uri (cran-uri "rio" version)) (sha256 (base32 - "04jlrhyl0791yxwcpp1s8p1hhkljnijlc5iaxpk56h41w63k39lz")))) + "0ihpdwixzkpm3qqh7iy6xm9mmvka2hx50qdidhxnav72nx5b31w0")))) (build-system r-build-system) (propagated-inputs (list r-curl From 28d1e102b671f9642ded97d467946951284c0e87 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 14 Sep 2023 00:04:07 +0200 Subject: [PATCH 136/268] gnu: r-reticulate: Update to 1.32.0. * gnu/packages/cran.scm (r-reticulate): Update to 1.32.0. --- 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 98110625b8..f9f7060648 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -12357,14 +12357,14 @@ always locate the files relative to your project root.") (define-public r-reticulate (package (name "r-reticulate") - (version "1.31") + (version "1.32.0") (source (origin (method url-fetch) (uri (cran-uri "reticulate" version)) (sha256 (base32 - "19yrxn99xwv5pfn3rnp4ahnp4wfkavj0chqp3zkn223azsigz5cj")))) + "0r9rycwin4yv5k2n1lzybwblb8529yhw5xnl46if6yvxm3bcra9s")))) (build-system r-build-system) (arguments (list From e371d89fa466e07f71e24dda3b62185d73559d84 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 14 Sep 2023 00:04:07 +0200 Subject: [PATCH 137/268] gnu: r-insight: Update to 0.19.4. * gnu/packages/cran.scm (r-insight): Update to 0.19.4. --- gnu/packages/cran.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index f9f7060648..ee512e7ba7 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -13254,14 +13254,14 @@ Decomposition in R (Beaton et al 2014) .") (define-public r-insight (package (name "r-insight") - (version "0.19.3") + (version "0.19.4") (source (origin (method url-fetch) (uri (cran-uri "insight" version)) (sha256 (base32 - "0zl8in5mvqjq58kprn1slrgc5wfh8vv7wprfc3qp3xl4bsqkj7zz")))) + "1v9555c4rrq91gkpy995f4p6gzcmw7xir73pvi70jwy81agc99g1")))) (build-system r-build-system) (native-inputs (list r-knitr)) From 00a4e351ebdbc5fea36df0ddccdb681dd73ed589 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 14 Sep 2023 00:04:07 +0200 Subject: [PATCH 138/268] gnu: r-flextable: Update to 0.9.3. * gnu/packages/cran.scm (r-flextable): Update to 0.9.3. --- gnu/packages/cran.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index ee512e7ba7..d3beb12a64 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -13413,14 +13413,14 @@ functions.") (define-public r-flextable (package (name "r-flextable") - (version "0.9.2") + (version "0.9.3") (source (origin (method url-fetch) (uri (cran-uri "flextable" version)) (sha256 (base32 - "0gcjkw35dlhf71djkvmlz0rp62sy3zd45vm8qhk1v3z5ka8m7kdw")))) + "1jdikfiswxi63vj9xr9a24p8fv50h91pvhv3xllgwwfbs1wqyq4x")))) (build-system r-build-system) (propagated-inputs (list r-data-table From 52c69229f894a347502f7979ec68d2416d67e9b6 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 14 Sep 2023 00:04:07 +0200 Subject: [PATCH 139/268] gnu: r-phyclust: Update to 0.1-34. * gnu/packages/cran.scm (r-phyclust): Update to 0.1-34. --- 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 d3beb12a64..9e71f33d8f 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -15090,13 +15090,13 @@ singular or ill-conditioned Jacobian.") (define-public r-phyclust (package (name "r-phyclust") - (version "0.1-33") + (version "0.1-34") (source (origin (method url-fetch) (uri (cran-uri "phyclust" version)) (sha256 (base32 - "04x4ymqnmc20pns89i4zs2yp75vchdgjszsinnpddjiv3446cy1q")))) + "1wzmd02ng7zphn97xdra3hgivrxqpizqcy5kpg45sk7jx4q7016j")))) (properties `((upstream-name . "phyclust"))) (build-system r-build-system) (propagated-inputs (list r-ape)) From c4d627396f467b2e8d3fdc260663d4713f765b8f Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 14 Sep 2023 00:04:08 +0200 Subject: [PATCH 140/268] gnu: r-tarchetypes: Update to 0.7.8. * gnu/packages/cran.scm (r-tarchetypes): Update to 0.7.8. --- 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 9e71f33d8f..de746ebcb5 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -15368,13 +15368,13 @@ handle data from simple random samples as well as complex surveys.") (define-public r-tarchetypes (package (name "r-tarchetypes") - (version "0.7.7") + (version "0.7.8") (source (origin (method url-fetch) (uri (cran-uri "tarchetypes" version)) (sha256 (base32 - "1vqyabk04kpskx1ny7c4knzg90ri99x17vfnwcb6syjbzpcfg444")))) + "1m43f2c2rrwnmsbhzfl97fvgjnfm4xwip09saia0dmp84lml26n1")))) (properties `((upstream-name . "tarchetypes"))) (build-system r-build-system) (propagated-inputs (list r-digest From 73eec30f7cc3f1537d3206cb958a2522d27625f4 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 14 Sep 2023 00:04:08 +0200 Subject: [PATCH 141/268] gnu: r-targets: Update to 1.3.0. * gnu/packages/cran.scm (r-targets): Update to 1.3.0. --- 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 de746ebcb5..0bc8c3c858 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -15405,13 +15405,13 @@ were influenced by the drake R package by Will Landau (2018) (define-public r-targets (package (name "r-targets") - (version "1.2.2") + (version "1.3.0") (source (origin (method url-fetch) (uri (cran-uri "targets" version)) (sha256 (base32 - "13znvv0qxdmad4rdxjm7zv1wayzj71m35vj8xxshf4fy55a1d59f")))) + "146ylh76sc5vzfgh2xp5mfpgdxvm3j9b2hzh0wqgih6d9d11n8pk")))) (properties `((upstream-name . "targets"))) (build-system r-build-system) (propagated-inputs (list r-base64url From b0a59e175c03c0a51ac61ebc4a392c4a4ea1c184 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 14 Sep 2023 00:04:08 +0200 Subject: [PATCH 142/268] gnu: r-performance: Update to 0.10.5. * gnu/packages/cran.scm (r-performance): Update to 0.10.5. --- 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 0bc8c3c858..0194dd7f00 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -16116,14 +16116,14 @@ ROPE percentage and pd).") (define-public r-performance (package (name "r-performance") - (version "0.10.4") + (version "0.10.5") (source (origin (method url-fetch) (uri (cran-uri "performance" version)) (sha256 (base32 - "0ddwfkrzwbj1bykvifzrb11hs5kh2a6ykr3ac1hi7cqpqikymfna")))) + "1bwcdz2iah6ya1p9ykbj5ybvzwlq9spv6mq3fn68cckymg0hs76r")))) (build-system r-build-system) (propagated-inputs (list r-bayestestr r-datawizard r-insight)) From 2085788215c959fda22561aa017c4410b6d50052 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 14 Sep 2023 00:04:08 +0200 Subject: [PATCH 143/268] gnu: r-ggeffects: Update to 1.3.1. * gnu/packages/cran.scm (r-ggeffects): Update to 1.3.1. --- gnu/packages/cran.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 0194dd7f00..642c139cf8 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -16142,14 +16142,14 @@ effects models and Bayesian models.") (define-public r-ggeffects (package (name "r-ggeffects") - (version "1.3.0") + (version "1.3.1") (source (origin (method url-fetch) (uri (cran-uri "ggeffects" version)) (sha256 (base32 - "145lqfkbawfm9nb23znd80v80j4a5jj8fgyilxqf8pxbqdbwmqql")))) + "0cw9j08qqck1gbfqsfyl3nb4rgi5cwsydxazqw8ppfnjqzw3nwmp")))) (build-system r-build-system) (propagated-inputs (list r-insight)) From 27be02ef17c44763f5cd3d5559d2d498863b6718 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 14 Sep 2023 00:04:08 +0200 Subject: [PATCH 144/268] gnu: r-credentials: Update to 2.0.1. * gnu/packages/cran.scm (r-credentials): Update to 2.0.1. --- gnu/packages/cran.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 642c139cf8..89128ee0a5 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -16405,14 +16405,14 @@ terminals that do not support Unicode.") (define-public r-credentials (package (name "r-credentials") - (version "1.3.2") + (version "2.0.1") (source (origin (method url-fetch) (uri (cran-uri "credentials" version)) (sha256 (base32 - "1f18j3zrq8c9kah57xwahmmljsjg5qphlgamvx507ynvpq8pryig")))) + "12rm7hjrbl3vfcbvdqc1hx3a6b91gf83xm455cn9myjapm2zqz1c")))) (properties `((upstream-name . "credentials"))) (build-system r-build-system) (arguments From d502c65bd4ee5ee27d5aa45861c96cce68c69ae0 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 14 Sep 2023 00:04:08 +0200 Subject: [PATCH 145/268] gnu: r-circular: Update to 0.5-0. * gnu/packages/cran.scm (r-circular): Update to 0.5-0. --- gnu/packages/cran.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 89128ee0a5..7c2fbec0d1 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -17493,14 +17493,14 @@ University Press, 2007.") (define-public r-circular (package (name "r-circular") - (version "0.4-95") + (version "0.5-0") (source (origin (method url-fetch) (uri (cran-uri "circular" version)) (sha256 (base32 - "1qmwj1pf37lc2s5r83y7nqckscznqhbsv66bdfgfbby7x4qkwga8")))) + "14kvkbmvdfzh8j4hgw93qkjkg86xlpw69sp7g8d5smcyw9fxmx2b")))) (build-system r-build-system) (propagated-inputs (list r-boot r-mvtnorm)) From b7b579dce4635d7db5d3ea0ad9f96c816b0558bd Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 14 Sep 2023 00:04:08 +0200 Subject: [PATCH 146/268] gnu: r-fmri: Update to 1.9.12. * gnu/packages/cran.scm (r-fmri): Update to 1.9.12. --- 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 7c2fbec0d1..d506b01df7 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -17561,13 +17561,13 @@ for evolution along a phylogenetic tree.") (define-public r-fmri (package (name "r-fmri") - (version "1.9.11") + (version "1.9.12") (source (origin (method url-fetch) (uri (cran-uri "fmri" version)) (sha256 (base32 - "07lk24jandnlxn6b8q8acnc4v6r2x2vsl734cpzhwxfjky119sz5")))) + "1cv5mxcdpyf05n5pcjdawl59j7f4k40386r4m38qf15vcy45zdfq")))) (properties `((upstream-name . "fmri"))) (build-system r-build-system) (propagated-inputs (list r-aws r-metafor r-nlme r-oro-nifti)) From d9b671a96ecff954238918321cd767551a5dd345 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 14 Sep 2023 00:04:08 +0200 Subject: [PATCH 147/268] gnu: r-adimpro: Update to 0.9.6. * gnu/packages/cran.scm (r-adimpro): Update to 0.9.6. --- gnu/packages/cran.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index d506b01df7..60883e4314 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -17669,13 +17669,13 @@ Anderson-Darling Distribution\".") (define-public r-adimpro (package (name "r-adimpro") - (version "0.9.5") + (version "0.9.6") (source (origin (method url-fetch) (uri (cran-uri "adimpro" version)) (sha256 (base32 - "1w3zcazbxkn1vq37vm4zz4mcmmk1bhxy22gkmv1v9bkv63b46kzm")))) + "0d5viz9ayywpp1pas1yzmhllzn9rjrl8a3k7bj7h46f95l5x1586")))) (properties `((upstream-name . "adimpro"))) (build-system r-build-system) (propagated-inputs From 2dac269403ab6d0bf4bbf9e8c5170236f3683f43 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 14 Sep 2023 00:04:09 +0200 Subject: [PATCH 148/268] gnu: r-qmri: Update to 1.2.6. * gnu/packages/cran.scm (r-qmri): Update to 1.2.6. --- gnu/packages/cran.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 60883e4314..5580331c46 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -18278,13 +18278,13 @@ while other are highly specific for the special data format used for (define-public r-qmri (package (name "r-qmri") - (version "1.2") + (version "1.2.6") (source (origin (method url-fetch) (uri (cran-uri "qMRI" version)) (sha256 (base32 - "10x59g8awxjib5j5mc1yd5wsibk3z6ki6zifxsg8azl0zblxbscf")))) + "1laslvp1h6xh73lbxvjysznazafcbl7bz0pw4h85n6mp3gsnlvcj")))) (properties `((upstream-name . "qMRI"))) (build-system r-build-system) (propagated-inputs (list r-adimpro r-aws r-awsmethods r-oro-nifti From 7dd9d99f717380b916b743ffe3995f35fd531974 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 14 Sep 2023 00:04:09 +0200 Subject: [PATCH 149/268] gnu: r-nnls: Update to 1.5. * gnu/packages/cran.scm (r-nnls): Update to 1.5. --- 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 5580331c46..84d3913bc9 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -18882,14 +18882,14 @@ inventor of the SOM.") (define-public r-nnls (package (name "r-nnls") - (version "1.4") + (version "1.5") (source (origin (method url-fetch) (uri (cran-uri "nnls" version)) (sha256 (base32 - "07vcrrxvswrvfiha6f3ikn640yg0m2b4yd9lkmim1g0jmsmpfp8f")))) + "0lilga63p7k5mkkfcf5p3swx76vwysl979jxszm6svzqhsrgww6d")))) (build-system r-build-system) (native-inputs (list gfortran)) (home-page "https://cran.r-project.org/web/packages/nnls") From 982487c0fe4e6cbfdfdf12eea5ce1a8e9f3345af Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 14 Sep 2023 00:04:09 +0200 Subject: [PATCH 150/268] gnu: r-minpack-lm: Update to 1.2-4. * gnu/packages/cran.scm (r-minpack-lm): Update to 1.2-4. --- gnu/packages/cran.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 84d3913bc9..224a2ebccf 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -21157,14 +21157,14 @@ user-defined patterns.") (define-public r-minpack-lm (package (name "r-minpack-lm") - (version "1.2-3") + (version "1.2-4") (source (origin (method url-fetch) (uri (cran-uri "minpack.lm" version)) (sha256 (base32 - "1w7f9zhqjzayppbd5r6wmlkzlv72nvg74cdjajd2qfq2kxkh59xz")))) + "0cg7arnmb7x6v5x487gkc2k4i5gchgdwblrrd0k0vw1w6pza83z3")))) (properties `((upstream-name . "minpack.lm"))) (build-system r-build-system) (native-inputs (list gfortran)) From ebd91f1bb4d2c53b3f28e8d78ba367780f9f789e Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 14 Sep 2023 00:04:09 +0200 Subject: [PATCH 151/268] gnu: r-pbdzmq: Update to 0.3-10. * gnu/packages/cran.scm (r-pbdzmq): Update to 0.3-10. --- gnu/packages/cran.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 224a2ebccf..528274c741 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -21387,14 +21387,14 @@ graphs.") (define-public r-pbdzmq (package (name "r-pbdzmq") - (version "0.3-9") + (version "0.3-10") (source (origin (method url-fetch) (uri (cran-uri "pbdZMQ" version)) (sha256 (base32 - "1dhg9sakfz4mivwvyfv5hnjrbi6gcd9cgis0dcgmh44q1a6j6cyh")))) + "14fi1bcvc77k5qjh0vb5r44p9rzlzrbzbw2c99psnzq2wic018ir")))) (properties `((upstream-name . "pbdZMQ"))) (build-system r-build-system) (inputs From d4dd9c352d7a4ac1fe1ae1a267c13c786bfe7578 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 14 Sep 2023 00:04:09 +0200 Subject: [PATCH 152/268] gnu: r-classint: Update to 0.4-10. * gnu/packages/cran.scm (r-classint): Update to 0.4-10. --- gnu/packages/cran.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 528274c741..400538ed24 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -22011,14 +22011,14 @@ classes.") (define-public r-classint (package (name "r-classint") - (version "0.4-9") + (version "0.4-10") (source (origin (method url-fetch) (uri (cran-uri "classInt" version)) (sha256 (base32 - "1hz1436apcnqvfyhmlv5f4127jviwfw6hz7f8xxkqygq11ysy4av")))) + "12rbwh7g0a6abvy423xjiv53gx1f9lg4y78r80lc0fj9pjpiwmn3")))) (properties `((upstream-name . "classInt"))) (build-system r-build-system) (propagated-inputs From c4084fb9d5a32969a7f41bf78c7e0f7652cf647f Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 14 Sep 2023 00:04:09 +0200 Subject: [PATCH 153/268] gnu: r-rms: Update to 6.7-1. * gnu/packages/cran.scm (r-rms): Update to 6.7-1. --- gnu/packages/cran.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 400538ed24..bc5bca8ce5 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -22440,13 +22440,13 @@ lspec, polyclass, and polymars.") (define-public r-rms (package (name "r-rms") - (version "6.7-0") + (version "6.7-1") (source (origin (method url-fetch) (uri (cran-uri "rms" version)) (sha256 - (base32 "1zxv7njzaxh6ivrxcszcn128pfxqyh5ga1q8kx6v5brfgv218flb")))) + (base32 "199xb98zxsbd8wa9g33bgrvbcpq79glnfmq060ic8f9vjw96r0qz")))) (build-system r-build-system) (propagated-inputs (list r-cluster From 6589c5fab61f799edf9b98d9f12418d163375a02 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 14 Sep 2023 00:04:09 +0200 Subject: [PATCH 154/268] gnu: r-bqtl: Update to 1.0-35. * gnu/packages/cran.scm (r-bqtl): Update to 1.0-35. --- 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 bc5bca8ce5..5aed60dc1c 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -22554,14 +22554,14 @@ examples in the vignette.") (define-public r-bqtl (package (name "r-bqtl") - (version "1.0-34") + (version "1.0-35") (source (origin (method url-fetch) (uri (cran-uri "bqtl" version)) (sha256 (base32 - "1xlkgyhlgrwqfzph4sbhh49pjzfnw5zdr3y4786rsnr3faksnxns")))) + "107yq7mk4gdr1wm20i751682jlj172bzbdjgqwviwgjxzbd0c2xa")))) (build-system r-build-system) (native-inputs (list gfortran)) (home-page "http://famprevmed.ucsd.edu/faculty/cberry/bqtl/") From d92372b3fad2a3eeaa6bbb6f24c734440736835f Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 14 Sep 2023 00:04:09 +0200 Subject: [PATCH 155/268] gnu: r-yulab-utils: Update to 0.0.9. * gnu/packages/cran.scm (r-yulab-utils): Update to 0.0.9. --- gnu/packages/cran.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 5aed60dc1c..df0b9b05fe 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -23248,14 +23248,14 @@ package.") (define-public r-yulab-utils (package (name "r-yulab-utils") - (version "0.0.8") + (version "0.0.9") (source (origin (method url-fetch) (uri (cran-uri "yulab.utils" version)) (sha256 (base32 - "1bb2rxpwisvb5a670n65k24rdd4aba2xx27dxb9wgj8swqc1rc6y")))) + "0y8594xmsg59p7pgz9bnjdc0bi50y6nmzvvzmjk8wyn4v5rz09ln")))) (properties `((upstream-name . "yulab.utils"))) (build-system r-build-system) (propagated-inputs From 961a3a81ca4bccf60320c343f870b704cce1b294 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 14 Sep 2023 00:04:10 +0200 Subject: [PATCH 156/268] gnu: r-ggcorrplot: Update to 0.1.4.1. * gnu/packages/cran.scm (r-ggcorrplot): Update to 0.1.4.1. --- gnu/packages/cran.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index df0b9b05fe..7ab8c18857 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -23901,14 +23901,14 @@ in-memory raw vectors.") (define-public r-ggcorrplot (package (name "r-ggcorrplot") - (version "0.1.4") + (version "0.1.4.1") (source (origin (method url-fetch) (uri (cran-uri "ggcorrplot" version)) (sha256 (base32 - "186a0mpdpipp24fjbd52l1gdgpqm6vl83ff8069d8nngyqbrx0jr")))) + "0yd865lfs4144jqh9ilznqa69rj0183ashnhvmjmis87zw69a45q")))) (build-system r-build-system) (propagated-inputs (list r-ggplot2 r-reshape2)) From 6b25da59a10b4b3d41c17332ccd5cb3df93ac62e Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 14 Sep 2023 00:04:10 +0200 Subject: [PATCH 157/268] gnu: r-cyclocomp: Update to 1.1.1. * gnu/packages/cran.scm (r-cyclocomp): Update to 1.1.1. --- 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 7ab8c18857..8f749f9dae 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -24566,14 +24566,14 @@ provided.") (define-public r-cyclocomp (package (name "r-cyclocomp") - (version "1.1.0") + (version "1.1.1") (source (origin (method url-fetch) (uri (cran-uri "cyclocomp" version)) (sha256 (base32 - "0gky3svk02wiajw7nfjh30684h3qxili4bvsab0m7b6cggw6bgyd")))) + "0kdinnn6cgkfc94japyyp5qr7imjxddajds3qqxf4q5higahdzws")))) (properties `((upstream-name . "cyclocomp"))) (build-system r-build-system) (propagated-inputs From ae07546906b23cf1a570e73456e372b0909588a6 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 14 Sep 2023 00:04:10 +0200 Subject: [PATCH 158/268] gnu: r-styler: Update to 1.10.2. * gnu/packages/cran.scm (r-styler): Update to 1.10.2. --- gnu/packages/cran.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 8f749f9dae..2a8316c81b 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -24724,14 +24724,14 @@ batch correction, and data correction.") (define-public r-styler (package (name "r-styler") - (version "1.10.1") + (version "1.10.2") (source (origin (method url-fetch) (uri (cran-uri "styler" version)) (sha256 (base32 - "0rswg2habyk38hcx0gn9hnvb200bq0dc4fy4k3gqhfhwjq9l7a1b")))) + "043v9xwm72jqrrzzmjgrkf34lncjnn69650ks72z7rjb1wqmbh56")))) (build-system r-build-system) ;; This is needed by R.cache. (arguments From 99f4f47c8f5372bd08e5ff49a696a20d52d9ae5b Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 14 Sep 2023 00:04:10 +0200 Subject: [PATCH 159/268] gnu: r-dqrng: Update to 0.3.1. * gnu/packages/cran.scm (r-dqrng): Update to 0.3.1. --- gnu/packages/cran.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 2a8316c81b..4041e942be 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -24907,14 +24907,14 @@ dimensional low-discrepancy sequence.") (define-public r-dqrng (package (name "r-dqrng") - (version "0.3.0") + (version "0.3.1") (source (origin (method url-fetch) (uri (cran-uri "dqrng" version)) (sha256 (base32 - "1fwsldqcri2lccna4icbmmlqic3w4xyjm7rn0xmikrsw4kzapvjb")))) + "0vmrbnix05a9h1bc4b7d999qkzkk63i1arzyblyhmvydv4m8cc72")))) (build-system r-build-system) (propagated-inputs (list r-bh r-rcpp r-sitmo)) From 331045a386a35f19824bd4f26b09cee8cc35b6bc Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 14 Sep 2023 00:04:10 +0200 Subject: [PATCH 160/268] gnu: r-leidenalg: Update to 1.1.2. * gnu/packages/cran.scm (r-leidenalg): Update to 1.1.2. --- gnu/packages/cran.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 4041e942be..c43cdcd112 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -25672,13 +25672,13 @@ guaranteeing well-connected communities.\" .") (define-public r-leidenalg (package (name "r-leidenalg") - (version "1.1.0") + (version "1.1.2") (source (origin (method url-fetch) (uri (cran-uri "leidenAlg" version)) (sha256 - (base32 "1hn5fps5m5am4s82wvhr4fgfw49h0jar4i687czbkab3l9x1dr68")))) + (base32 "0wqay0rf28pgaf88bsvmrwgggzbma93rv9nqbydhjf1lc96ay1lz")))) (properties `((upstream-name . "leidenAlg") (updater-extra-inputs . ("gmp")))) From 53d902a9d4844475400b695ac00f52f8cdf2ec83 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 14 Sep 2023 00:04:10 +0200 Subject: [PATCH 161/268] gnu: r-terra: Update to 1.7-46. * gnu/packages/cran.scm (r-terra): Update to 1.7-46. --- 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 c43cdcd112..cb3c0ee397 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -26013,14 +26013,14 @@ emphasize hidden group structures in networks or focus on specific nodes.") (define-public r-terra (package (name "r-terra") - (version "1.7-39") + (version "1.7-46") (source (origin (method url-fetch) (uri (cran-uri "terra" version)) (sha256 (base32 - "03kc2m89236qh50qfxl1101ys466ddhgjwp80x6hjpmd9fz5jf5l")))) + "0jpni25g9rhsqh71pgr2d3221r9xacsw3kz5qqnifj0jz5g3wyh1")))) (properties `((upstream-name . "terra"))) (build-system r-build-system) (inputs From adb7d031270f9f5c0a70b32884e2ccc9afca8d67 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 14 Sep 2023 00:04:10 +0200 Subject: [PATCH 162/268] gnu: r-desolve: Update to 1.38. * gnu/packages/cran.scm (r-desolve): Update to 1.38. --- 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 cb3c0ee397..3824517b3c 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -26303,13 +26303,13 @@ programming problems.") (define-public r-desolve (package (name "r-desolve") - (version "1.36") + (version "1.38") (source (origin (method url-fetch) (uri (cran-uri "deSolve" version)) (sha256 - (base32 "1ygijjvmi7igk3xmm2mzfnbw05kynjdqbwddifg798awk7mfffjw")))) + (base32 "0sc933g0jx25b7fm5bl6is95mn4fn1sf8cgb6qzhlmmf8rfgxd50")))) (properties `((upstream-name . "deSolve"))) (build-system r-build-system) (native-inputs From aec1073ee7c44436c9b083cf778cfe57a30bac6e Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 14 Sep 2023 00:04:11 +0200 Subject: [PATCH 163/268] gnu: r-gamlss: Update to 5.4-18. * gnu/packages/cran.scm (r-gamlss): Update to 5.4-18. --- 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 3824517b3c..7c71183105 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -27506,14 +27506,14 @@ models.") (define-public r-gamlss (package (name "r-gamlss") - (version "5.4-12") + (version "5.4-18") (source (origin (method url-fetch) (uri (cran-uri "gamlss" version)) (sha256 (base32 - "1w5630hzir49nacpvmx28hqc8hcc9acmba9dd8zwzhz5ywwi0ycz")))) + "1wj6hx6z48zpwkqz3w68dfsf2nfj8clhwqykq5ln94vrarqaim7g")))) (properties `((upstream-name . "gamlss"))) (build-system r-build-system) (propagated-inputs From 39c45564506c8b387aa392abf7853843ba04ec3d Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 14 Sep 2023 00:04:11 +0200 Subject: [PATCH 164/268] gnu: r-acopula: Update to 0.9.4. * gnu/packages/cran.scm (r-acopula): Update to 0.9.4. --- gnu/packages/cran.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 7c71183105..233fe04f1c 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -27821,14 +27821,14 @@ and may be used to generate realistic data sets with known truth.") (define-public r-acopula (package (name "r-acopula") - (version "0.9.3") + (version "0.9.4") (source (origin (method url-fetch) (uri (cran-uri "acopula" version)) (sha256 (base32 - "0vvbbw8pfs9jwfz5c57lw48pr0qj661r0ys007q6zf9jmlrhx1ln")))) + "0asxfcjrsr9d7ab59pdajs0zvdjgwfswk9rdlpfdr51535wpjrfy")))) (properties `((upstream-name . "acopula"))) (build-system r-build-system) (home-page "https://cran.r-project.org/web/packages/acopula/") From cd57a3ec9fd9bd0d522191b24c11f1f38edfd21c Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 14 Sep 2023 00:04:11 +0200 Subject: [PATCH 165/268] gnu: r-emplik: Update to 1.3-1. * gnu/packages/cran.scm (r-emplik): Update to 1.3-1. --- gnu/packages/cran.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 233fe04f1c..d6b19f95e7 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -29788,14 +29788,14 @@ OpenMP.") (define-public r-emplik (package (name "r-emplik") - (version "1.3") + (version "1.3-1") (source (origin (method url-fetch) (uri (cran-uri "emplik" version)) (sha256 (base32 - "14jgwwxvsglkbq7kwjl34lyax45qn4hkra4qmmv4ybnvvcmbcag1")))) + "1f6v0bg9sl8kn4y8bpgjyc1b18xkmfbs86gbbmbh198v335lgcrb")))) (properties `((upstream-name . "emplik"))) (build-system r-build-system) (propagated-inputs From 2b40d9b13afde321a3139502c622aa1ef5bb3a9e Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 14 Sep 2023 00:04:11 +0200 Subject: [PATCH 166/268] gnu: r-forecast: Update to 8.21.1. * gnu/packages/cran.scm (r-forecast): Update to 8.21.1. --- 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 d6b19f95e7..4923efd05e 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -30047,14 +30047,14 @@ Raftery, Appl.Statistics, 1989); it includes inference and basic methods.") (define-public r-forecast (package (name "r-forecast") - (version "8.21") + (version "8.21.1") (source (origin (method url-fetch) (uri (cran-uri "forecast" version)) (sha256 (base32 - "1hn60p88jq9qprgwgh4ymb53fri71imad6kasycv6gwxb9wk3lgx")))) + "09w1vh96cf9wz071why5f4265cvvwqi2b3wb0khrjvkzgkiaq7l1")))) (properties `((upstream-name . "forecast"))) (build-system r-build-system) (propagated-inputs From 3c3dbf219660c8a1e3b29c2ee0681af8f130afaa Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 14 Sep 2023 00:04:11 +0200 Subject: [PATCH 167/268] gnu: r-stanheaders: Update to 2.26.28. * gnu/packages/cran.scm (r-stanheaders): Update to 2.26.28. --- 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 4923efd05e..d2c7cad995 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -30637,14 +30637,14 @@ perform @dfn{exploratory mediation} (XMed).") (define-public r-stanheaders (package (name "r-stanheaders") - (version "2.26.27") + (version "2.26.28") (source (origin (method url-fetch) (uri (cran-uri "StanHeaders" version)) (sha256 (base32 - "1cf9hc7z3d8b70jck37j3lc2ml040di91dylfb18yi6wx936bq3h")))) + "1s1xgvn5c1vjikm1dx9g0qm2k8m24clylgp7zssmfhx6sfb8v2lk")))) (properties `((upstream-name . "StanHeaders"))) (build-system r-build-system) (inputs (list pandoc)) From b40994d97d893090f47c566aaa2e0855b778b3a7 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 14 Sep 2023 00:04:11 +0200 Subject: [PATCH 168/268] gnu: r-packrat: Update to 0.9.2. * gnu/packages/cran.scm (r-packrat): Update to 0.9.2. --- gnu/packages/cran.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index d2c7cad995..87a8644602 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -31163,14 +31163,14 @@ interesting features. iheatmapr uses the plotly library for interactivity.") (define-public r-packrat (package (name "r-packrat") - (version "0.9.1") + (version "0.9.2") (source (origin (method url-fetch) (uri (cran-uri "packrat" version)) (sha256 (base32 - "0i1kzmjzks6g673jkcqmra0nysviab0r915wkgk8aaad0k316h21")))) + "1mvj2s78n2r66nlqq5bjrvgdwlwbcqdj81yryc34sv3y4m1mkpv9")))) (properties `((upstream-name . "packrat"))) (build-system r-build-system) (home-page "https://github.com/rstudio/packrat/") From d471fd760d8bd9eacd326719d56cdd759343713b Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 14 Sep 2023 00:04:11 +0200 Subject: [PATCH 169/268] gnu: r-rsconnect: Update to 1.1.0. * gnu/packages/cran.scm (r-rsconnect): Update to 1.1.0. --- 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 87a8644602..060eb2122b 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -31184,14 +31184,14 @@ and reproducible way.") (define-public r-rsconnect (package (name "r-rsconnect") - (version "1.0.2") + (version "1.1.0") (source (origin (method url-fetch) (uri (cran-uri "rsconnect" version)) (sha256 (base32 - "1cni5sc4qgvd3vvn2jy0saxsxz144yl2jahhbf0bhix35blgzlp1")))) + "1jpz9cx2fqj3cp69xd2vi9gc5wdfrs4rbpy81mm7hq1iaq5nd7pc")))) (properties `((upstream-name . "rsconnect"))) (build-system r-build-system) (propagated-inputs From f8fdfb731f1f2523852f445e094e13b5908447e0 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 14 Sep 2023 00:04:12 +0200 Subject: [PATCH 170/268] gnu: r-directlabels: Update to 2023.8.25. * gnu/packages/cran.scm (r-directlabels): Update to 2023.8.25. --- gnu/packages/cran.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 060eb2122b..eb4ad4195d 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -32664,14 +32664,14 @@ permuted copies (shadows).") (define-public r-directlabels (package (name "r-directlabels") - (version "2021.1.13") + (version "2023.8.25") (source (origin (method url-fetch) (uri (cran-uri "directlabels" version)) (sha256 (base32 - "0415kh9k2qzdwi8zb32fh2icl5wf5335kyj11cyfdmfxji39zv2w")))) + "0p7as0yvvywbdqjpng70sdiy0xyczac4qbv534cwqxiqyx81vp8j")))) (build-system r-build-system) (propagated-inputs (list r-quadprog)) From 9cf2cf4c9a44726bd467e1b7bf10babbcf2f81a7 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 14 Sep 2023 00:04:12 +0200 Subject: [PATCH 171/268] gnu: r-spatstat-explore: Update to 3.2-3. * gnu/packages/cran.scm (r-spatstat-explore): Update to 3.2-3. --- gnu/packages/cran.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index eb4ad4195d..91d3d549e9 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -33231,13 +33231,13 @@ diagonals. This package allows you to compute the tensor product of arrays.") (define-public r-spatstat-explore (package (name "r-spatstat-explore") - (version "3.2-1") + (version "3.2-3") (source (origin (method url-fetch) (uri (cran-uri "spatstat.explore" version)) (sha256 (base32 - "02n64bml361xakfbj71m7mgkb0p6szqc55lijjsnwa3z69pwwshb")))) + "18zhpspq07rcnpmnkc82hzjvjp39fsb06g73gin4x5bwzbi22kgr")))) (properties `((upstream-name . "spatstat.explore"))) (build-system r-build-system) (propagated-inputs From 1e6db67bc176b3d14f31f838529090511adf4819 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 14 Sep 2023 00:04:12 +0200 Subject: [PATCH 172/268] gnu: r-spatstat-model: Update to 3.2-6. * gnu/packages/cran.scm (r-spatstat-model): Update to 3.2-6. --- gnu/packages/cran.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 91d3d549e9..bfd989ef87 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -33271,13 +33271,13 @@ Kolmogorov-Smirnov, ANOVA) are also supported.") (define-public r-spatstat-model (package (name "r-spatstat-model") - (version "3.2-4") + (version "3.2-6") (source (origin (method url-fetch) (uri (cran-uri "spatstat.model" version)) (sha256 (base32 - "0vcxwwc4kjfmjd80sk7rbv8a9yg9v2m94brgww8fiibrm6m9psi6")))) + "1lvs6ns4hna7w6b0nvzsx2rw699ampdm8jmxdzlfpk4hla2lf7wq")))) (properties `((upstream-name . "spatstat.model"))) (build-system r-build-system) (propagated-inputs From 3bf11b1eea2cfcd978df968b69ee96a8d1ed5fe7 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 14 Sep 2023 00:04:12 +0200 Subject: [PATCH 173/268] gnu: r-spatstat-geom: Update to 3.2-5. * gnu/packages/cran.scm (r-spatstat-geom): Update to 3.2-5. --- 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 bfd989ef87..5f9bba3ac2 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -33382,14 +33382,14 @@ package.") (define-public r-spatstat-geom (package (name "r-spatstat-geom") - (version "3.2-4") + (version "3.2-5") (source (origin (method url-fetch) (uri (cran-uri "spatstat.geom" version)) (sha256 (base32 - "09x2z2jqgbmilqg2kx4sgzrz54hbkyfpv9hm759075i2hkaza796")))) + "13xlp88yfp61kl0c3vaqs7lrckkc4ixpp0mpf89h5ggmjyf57nxx")))) (properties `((upstream-name . "spatstat.geom"))) (build-system r-build-system) (propagated-inputs From 9de7344c48d2c1315a38c017fae7ad313a11325f Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 14 Sep 2023 00:04:12 +0200 Subject: [PATCH 174/268] gnu: r-spatstat-random: Update to 3.1-6. * gnu/packages/cran.scm (r-spatstat-random): Update to 3.1-6. --- gnu/packages/cran.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 5f9bba3ac2..38513e0a4f 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -33468,13 +33468,13 @@ for spatial data on a linear network.") (define-public r-spatstat-random (package (name "r-spatstat-random") - (version "3.1-5") + (version "3.1-6") (source (origin (method url-fetch) (uri (cran-uri "spatstat.random" version)) (sha256 - (base32 "128rm8k4b5rklddmnhbsv93jj6qym0fngir9nb65cawg3zb991m6")))) + (base32 "0vrx0mxzcd6yr6rzn9jk2wj5d2l7yn0ij1n58yb3hw2g7nasad06")))) (properties `((upstream-name . "spatstat.random"))) (build-system r-build-system) (propagated-inputs (list r-spatstat-data r-spatstat-geom r-spatstat-utils)) From eb0ba6f4948cd5e224fa5f4650e1e54d3e8f955f Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 14 Sep 2023 00:04:12 +0200 Subject: [PATCH 175/268] gnu: r-config: Update to 0.3.2. * gnu/packages/cran.scm (r-config): Update to 0.3.2. --- gnu/packages/cran.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 38513e0a4f..a6746b9efb 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -34222,14 +34222,14 @@ coerce and verify the types and shapes of values for input checking.") (define-public r-config (package (name "r-config") - (version "0.3.1") + (version "0.3.2") (source (origin (method url-fetch) (uri (cran-uri "config" version)) (sha256 (base32 - "0l2zp7v6qaz72dclcbjrlis633zlwp8rsi5azr7iw127iyz7i26l")))) + "0r8hjg7jrhr9lncb82xmq2slygv3slacd2w8ds6shnvdp3122p3v")))) (properties `((upstream-name . "config"))) (build-system r-build-system) (propagated-inputs From 09b6be49e82515d64c188f8946b9d6ab139979c1 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 14 Sep 2023 00:04:12 +0200 Subject: [PATCH 176/268] gnu: r-infer: Update to 1.0.5. * gnu/packages/cran.scm (r-infer): Update to 1.0.5. [propagated-inputs]: Add r-vctrs. --- gnu/packages/cran.scm | 7 ++++--- 1 file changed, 4 insertions(+), 3 deletions(-) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index a6746b9efb..bdb65b8497 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -35088,14 +35088,14 @@ functions or computational engines (e.g. R, Spark, Stan, etc).") (define-public r-infer (package (name "r-infer") - (version "1.0.4") + (version "1.0.5") (source (origin (method url-fetch) (uri (cran-uri "infer" version)) (sha256 (base32 - "1s4q0nslykl0pb2w1i6ni6hkpp7awvp0wks79br3gk5wa1qkvs19")))) + "1zs1c22zc255m23in99cqp2chpdkski002rywmkdzwf6nd96mly7")))) (properties `((upstream-name . "infer"))) (build-system r-build-system) (propagated-inputs @@ -35109,7 +35109,8 @@ functions or computational engines (e.g. R, Spark, Stan, etc).") r-purrr r-rlang r-tibble - r-tidyr)) + r-tidyr + r-vctrs)) (native-inputs (list r-knitr)) (home-page "https://github.com/tidymodels/infer") From 8da144981873f8febaa9fa0fa0ff70606dc5ea6e Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 14 Sep 2023 00:04:13 +0200 Subject: [PATCH 177/268] gnu: r-seqminer: Update to 9.1. * gnu/packages/cran.scm (r-seqminer): Update to 9.1. --- 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 bdb65b8497..51ef53414d 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -35438,14 +35438,14 @@ designs. Broman et al. (2018) .") (define-public r-seqminer (package (name "r-seqminer") - (version "8.9") + (version "9.1") (source (origin (method url-fetch) (uri (cran-uri "seqminer" version)) (sha256 (base32 - "1cnsy1cjz4rcm32hzcvr1d43y4m7sdkzim1mwsn3490mf3xmi3i1")))) + "0vdprasxy4dc9p5k43xgcmi0q50iapgcam43qzbh1kr0vi6fgqkr")))) (build-system r-build-system) (inputs (list zlib)) From fe2a36ed5bb962420284500d562db59e5cc5a5f6 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 14 Sep 2023 00:04:13 +0200 Subject: [PATCH 178/268] gnu: r-diversitree: Update to 0.9-20. * gnu/packages/cran.scm (r-diversitree): Update to 0.9-20. --- gnu/packages/cran.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 51ef53414d..c522afa7fa 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -35820,14 +35820,14 @@ Maximum Parsimony, distance methods and Hadamard conjugation.") (define-public r-diversitree (package (name "r-diversitree") - (version "0.9-19") + (version "0.9-20") (source (origin (method url-fetch) (uri (cran-uri "diversitree" version)) (sha256 (base32 - "1z3lzqphswb4r3rdh2jmi1pfagqs38dbccm9li02sc8aasdqk0if")))) + "0lm098ysk6np4dy1cifbhd85jd1f1iz4bqhgzlcx7x8qnhh3zc1c")))) (build-system r-build-system) (native-inputs (list gfortran)) From d8ac99ec8ee98ec8174337e56b20da9f9dade285 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 14 Sep 2023 00:04:13 +0200 Subject: [PATCH 179/268] gnu: r-readods: Update to 2.1.0. * gnu/packages/cran.scm (r-readods): Update to 2.1.0. [propagated-inputs]: Remove r-xml2. --- gnu/packages/cran.scm | 5 ++--- 1 file changed, 2 insertions(+), 3 deletions(-) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index c522afa7fa..2af0435bdb 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -37190,14 +37190,14 @@ functionalities in strex.") (define-public r-readods (package (name "r-readods") - (version "2.0.0") + (version "2.1.0") (source (origin (method url-fetch) (uri (cran-uri "readODS" version)) (sha256 (base32 - "09b0z5fbl09inygbmbgprj8v6cd8z8zw9r3j68rlmi7mivxzbqk4")))) + "1znp039wfbq8bbjj9pdkl8hwnhm9x5n8c7y5b53xmpnaqxx5agiz")))) (properties `((upstream-name . "readODS"))) (build-system r-build-system) (propagated-inputs @@ -37207,7 +37207,6 @@ functionalities in strex.") r-stringi r-tibble r-vctrs - r-xml2 r-zip)) (native-inputs (list r-knitr)) (home-page From 6287891b2ad77b3aa2c29c301f0d49570845574f Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 14 Sep 2023 00:04:13 +0200 Subject: [PATCH 180/268] gnu: r-pbdmpi: Update to 0.5-0. * gnu/packages/cran.scm (r-pbdmpi): Update to 0.5-0. [propagated-inputs]: Remove r-rlecuyer. --- gnu/packages/cran.scm | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 2af0435bdb..828f1cc149 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -37260,13 +37260,13 @@ data you need the @code{pdftools} package.") (define-public r-pbdmpi (package (name "r-pbdmpi") - (version "0.4-6") + (version "0.5-0") (source (origin (method url-fetch) (uri (cran-uri "pbdMPI" version)) (sha256 (base32 - "0r6kbrvc0z4mb2dhrz1iqdyx0c03f682b5xfi1igp7z3rszd1va1")))) + "0wfx33jhdrwp97chsp9v8z2yf49shycvky8dwl9pgwqd9l69aw7x")))) (properties `((upstream-name . "pbdMPI"))) (build-system r-build-system) (arguments @@ -37275,7 +37275,7 @@ data you need the @code{pdftools} package.") (add-before 'install 'mpi-setup ,%openmpi-setup)))) (inputs (list openmpi)) - (propagated-inputs (list r-float r-rlecuyer)) + (propagated-inputs (list r-float)) (native-inputs (list pkg-config)) (home-page "https://pbdr.org/") (synopsis "Programming with Big Data -- Interface to MPI") From 1b2d3cf25d22aa7319c0ae006577ecda2887805d Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 14 Sep 2023 00:04:13 +0200 Subject: [PATCH 181/268] gnu: r-packcircles: Update to 0.3.6. * gnu/packages/cran.scm (r-packcircles): Update to 0.3.6. --- gnu/packages/cran.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 828f1cc149..1202d009c1 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -37393,14 +37393,14 @@ and formatted text files with additional meta-data, such including @code{.csv}, (define-public r-packcircles (package (name "r-packcircles") - (version "0.3.5") + (version "0.3.6") (source (origin (method url-fetch) (uri (cran-uri "packcircles" version)) (sha256 (base32 - "0m8ivgc5y1f9ramqw6sxb02ri6aqxz3av0l5csl32mdldrb126nc")))) + "0fjc575i1vxjp2v4niv2syqqk0d609wm86gkq9rvgmch841x40ps")))) (properties `((upstream-name . "packcircles"))) (build-system r-build-system) (propagated-inputs (list r-rcpp)) From 6bf5162b1d0f8fa0fc981085af4fae9b435ecd73 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 14 Sep 2023 00:04:14 +0200 Subject: [PATCH 182/268] gnu: r-stars: Update to 0.6-4. * gnu/packages/cran.scm (r-stars): Update to 0.6-4. [propagated-inputs]: Remove r-lwgeom. --- gnu/packages/cran.scm | 11 +++-------- 1 file changed, 3 insertions(+), 8 deletions(-) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 1202d009c1..88aae7ee9b 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -37443,23 +37443,18 @@ light-weight geometry library used by @url{http://postgis.net/,PostGIS}.") (define-public r-stars (package (name "r-stars") - (version "0.6-3") + (version "0.6-4") (source (origin (method url-fetch) (uri (cran-uri "stars" version)) (sha256 (base32 - "08i5m46plkwkxwgzpy6srvn69jchp364vj3sg1isp2lj9pxhzfwc")))) + "0mqd2dfa8jhxjmfphvv3rkw2lri5sz49042asj5lyln3wkylqjj2")))) (properties `((upstream-name . "stars"))) (build-system r-build-system) (propagated-inputs - (list r-abind - r-classint - r-lwgeom - r-rlang - r-sf - r-units)) + (list r-abind r-classint r-rlang r-sf r-units)) (native-inputs (list r-knitr)) (home-page "https://r-spatial.github.io/stars/") (synopsis From 0285844e14b6ef15e3f8afd01171c249fbb1f540 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 14 Sep 2023 00:04:14 +0200 Subject: [PATCH 183/268] gnu: r-distributionutils: Update to 0.6-1. * gnu/packages/cran.scm (r-distributionutils): Update to 0.6-1. --- gnu/packages/cran.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 88aae7ee9b..1a03e362c8 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -38491,14 +38491,14 @@ carrying out economic experiments.") (define-public r-distributionutils (package (name "r-distributionutils") - (version "0.6-0") + (version "0.6-1") (source (origin (method url-fetch) (uri (cran-uri "DistributionUtils" version)) (sha256 (base32 - "08vq54pyqxlqsj6q6gsg5ikqa0z3x842j52ld5dxaq272p6xchvl")))) + "1mv3p7hm02q3mhrw5165gc2d77ighnykyfn6ibxvkc3ii2m9xrri")))) (properties `((upstream-name . "DistributionUtils"))) (build-system r-build-system) From a2afbbed24fe0aa35d6de31ceababd61e98d226e Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 14 Sep 2023 00:04:14 +0200 Subject: [PATCH 184/268] gnu: r-paws-common: Update to 0.6.0. * gnu/packages/cran.scm (r-paws-common): 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 1a03e362c8..b5cad45fb1 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -38709,14 +38709,14 @@ fully reproducible.") (define-public r-paws-common (package (name "r-paws-common") - (version "0.5.8") + (version "0.6.0") (source (origin (method url-fetch) (uri (cran-uri "paws.common" version)) (sha256 (base32 - "1vx74lxgzsl1yl4ak5zympkgwza023qbjwskp19nm2dvxhz75cfh")))) + "1451705w30lb33msi4qgzpfmw6xnwh2ffh30fwb9im8g47fqm2bw")))) (properties `((upstream-name . "paws.common"))) (build-system r-build-system) (propagated-inputs From 067f519a4d2486d5dd91101acacdcb6f3e31bfe6 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 14 Sep 2023 00:04:14 +0200 Subject: [PATCH 185/268] gnu: r-paws-customer-engagement: Update to 0.4.0. * gnu/packages/cran.scm (r-paws-customer-engagement): Update to 0.4.0. --- gnu/packages/cran.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index b5cad45fb1..c487dc674b 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -38740,14 +38740,14 @@ Service (S3).") (define-public r-paws-customer-engagement (package (name "r-paws-customer-engagement") - (version "0.3.0") + (version "0.4.0") (source (origin (method url-fetch) (uri (cran-uri "paws.customer.engagement" version)) (sha256 (base32 - "18gkr3272jj1pkksm6fy6qz5s5jn0yvb12pz29k204xrzmqwdwgm")))) + "0skfya3m9i36dd0jqvnnc72k1h3lb4s3fjkvg7na6aq6xgpjh4jv")))) (properties `((upstream-name . "paws.customer.engagement"))) (build-system r-build-system) From 6a6c29efb55fc30d3d061f5aaebf4b405078041d Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 14 Sep 2023 00:04:14 +0200 Subject: [PATCH 186/268] gnu: r-paws-cost-management: Update to 0.4.0. * gnu/packages/cran.scm (r-paws-cost-management): Update to 0.4.0. --- gnu/packages/cran.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index c487dc674b..faccc2d50b 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -38764,14 +38764,14 @@ service, and more.") (define-public r-paws-cost-management (package (name "r-paws-cost-management") - (version "0.3.1") + (version "0.4.0") (source (origin (method url-fetch) (uri (cran-uri "paws.cost.management" version)) (sha256 (base32 - "0v0s8wwx2j3a6s0pl9vnvbpgdyhn3jlxri0b2fl3gc3zx6qh07dl")))) + "1j9zi73y9ng5m6wlws4crfv4j6b8qxk1m9g1hd286g4gg852g80y")))) (properties `((upstream-name . "paws.cost.management"))) (build-system r-build-system) From ab20ed6424435a131aa8aa93b79521fd0e0ea3cb Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 14 Sep 2023 00:04:14 +0200 Subject: [PATCH 187/268] gnu: r-paws-developer-tools: Update to 0.4.0. * gnu/packages/cran.scm (r-paws-developer-tools): Update to 0.4.0. --- gnu/packages/cran.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index faccc2d50b..d0798be66a 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -38788,13 +38788,13 @@ more.") (define-public r-paws-developer-tools (package (name "r-paws-developer-tools") - (version "0.3.1") + (version "0.4.0") (source (origin (method url-fetch) (uri (cran-uri "paws.developer.tools" version)) (sha256 - (base32 "1b661gpg7rsdkgpriwczj4cvqg9rh1ajz9ma457bw4p3lv7n53x2")))) + (base32 "13i5yi23xsrks1dsw0k3cqzr2gqj8p23yajb3a7drim6d4rpsaxl")))) (properties `((upstream-name . "paws.developer.tools"))) (build-system r-build-system) (propagated-inputs From 4052f7d113b17d917956f1bc86c5a37d19aa1726 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 14 Sep 2023 00:04:14 +0200 Subject: [PATCH 188/268] gnu: r-paws-end-user-computing: Update to 0.4.0. * gnu/packages/cran.scm (r-paws-end-user-computing): Update to 0.4.0. --- gnu/packages/cran.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index d0798be66a..05c2e0cb1d 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -38810,13 +38810,13 @@ deployment, and more.") (define-public r-paws-end-user-computing (package (name "r-paws-end-user-computing") - (version "0.3.0") + (version "0.4.0") (source (origin (method url-fetch) (uri (cran-uri "paws.end.user.computing" version)) (sha256 - (base32 "0as9ix46rsa7sg8k96v6l3ibxqc95pf7swrij31ljmwfy82z2rq3")))) + (base32 "0v3ng20vrp5cvpbgipwwpvyhi995n2rp8jls0kklkrjax41x62cn")))) (properties `((upstream-name . "paws.end.user.computing"))) (build-system r-build-system) (propagated-inputs From 90aa4f2afe7833c7891dfba54fd8bc91c2f510d8 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 14 Sep 2023 00:04:14 +0200 Subject: [PATCH 189/268] gnu: r-paws-application-integration: Update to 0.4.0. * gnu/packages/cran.scm (r-paws-application-integration): Update to 0.4.0. --- gnu/packages/cran.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 05c2e0cb1d..42dc5e057f 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -38832,14 +38832,14 @@ and more.") (define-public r-paws-application-integration (package (name "r-paws-application-integration") - (version "0.3.1") + (version "0.4.0") (source (origin (method url-fetch) (uri (cran-uri "paws.application.integration" version)) (sha256 (base32 - "19lz1vcvb1bn405saxx4zjsmm1q4zaw77z08iw4xbyny5xhkgyvi")))) + "0hilnczvamdv3bi1v6hdki05h8qqh0wlgvh5ilh09113005fpz98")))) (properties `((upstream-name . "paws.application.integration"))) (build-system r-build-system) From 6e8f6654d79e8ac9c7f026b21d9c645380155e4f Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 14 Sep 2023 00:04:15 +0200 Subject: [PATCH 190/268] gnu: r-paws-security-identity: Update to 0.4.0. * gnu/packages/cran.scm (r-paws-security-identity): Update to 0.4.0. --- gnu/packages/cran.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 42dc5e057f..b8f8c111d4 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -38856,14 +38856,14 @@ Simple Notification Service (SNS) publish/subscribe messaging, and more.") (define-public r-paws-security-identity (package (name "r-paws-security-identity") - (version "0.3.1") + (version "0.4.0") (source (origin (method url-fetch) (uri (cran-uri "paws.security.identity" version)) (sha256 (base32 - "02k15skswd58icafydrbjrp7br5x8l93lwi5z1pwqak6xasi0vqh")))) + "081339201j19y8y28h0dhr876ii82zpfyqddc21lvmg27z53hj4x")))) (properties `((upstream-name . "paws.security.identity"))) (build-system r-build-system) From ba2fa58be01da4f6e4abee2e2831a55ac368aaff Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 14 Sep 2023 00:04:15 +0200 Subject: [PATCH 191/268] gnu: r-paws-analytics: Update to 0.4.0. * gnu/packages/cran.scm (r-paws-analytics): Update to 0.4.0. --- gnu/packages/cran.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index b8f8c111d4..f90803b949 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -38881,14 +38881,14 @@ more.") (define-public r-paws-analytics (package (name "r-paws-analytics") - (version "0.3.0") + (version "0.4.0") (source (origin (method url-fetch) (uri (cran-uri "paws.analytics" version)) (sha256 (base32 - "0qjk1gn4p41l4ryqf9xppiphfakypl0xdjk23c9c8xdhqkbw0lcw")))) + "1x7ix8x0ks357b7gf2skixsd0najjbn8hnq7p6a354p5h7bz39b4")))) (properties `((upstream-name . "paws.analytics"))) (build-system r-build-system) From 9497c4dbff01bbdbef9e6f235d92ca92f657e601 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 14 Sep 2023 00:04:15 +0200 Subject: [PATCH 192/268] gnu: r-paws-machine-learning: Update to 0.4.0. * gnu/packages/cran.scm (r-paws-machine-learning): Update to 0.4.0. --- gnu/packages/cran.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index f90803b949..dfc5d31e88 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -38905,14 +38905,14 @@ Elasticsearch search engine, and more.") (define-public r-paws-machine-learning (package (name "r-paws-machine-learning") - (version "0.3.0") + (version "0.4.0") (source (origin (method url-fetch) (uri (cran-uri "paws.machine.learning" version)) (sha256 (base32 - "092n5p5hjwaqkdnw4r7n71znabfazc2pg19raja69jgk6zh6csvy")))) + "0cwmriprwrz446q4d5ljkpvwdhmamnl98g1ks6p35vbjiv4imk21")))) (properties `((upstream-name . "paws.machine.learning"))) (build-system r-build-system) From 98c8da964f680d4ad900a145987125f50b9bb90a Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 14 Sep 2023 00:04:15 +0200 Subject: [PATCH 193/268] gnu: r-paws-management: Update to 0.4.0. * gnu/packages/cran.scm (r-paws-management): Update to 0.4.0. --- gnu/packages/cran.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index dfc5d31e88..d78109c6af 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -38929,14 +38929,14 @@ natural language processing, speech recognition, translation, and more.") (define-public r-paws-management (package (name "r-paws-management") - (version "0.3.1") + (version "0.4.0") (source (origin (method url-fetch) (uri (cran-uri "paws.management" version)) (sha256 (base32 - "0hdmc07i75hbk2fh580p7q7p3pk8ykr5m1jibnfk8azc4flikwv6")))) + "0lp8s4caxppwxsra6ijcz1dzkmnznwrrs92y87387vq53y3icc6m")))) (properties `((upstream-name . "paws.management"))) (build-system r-build-system) From 2e8126e3baa07c370504f73af4a452b033a4defc Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 14 Sep 2023 00:04:15 +0200 Subject: [PATCH 194/268] gnu: r-paws-networking: Update to 0.4.0. * gnu/packages/cran.scm (r-paws-networking): Update to 0.4.0. --- gnu/packages/cran.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index d78109c6af..f8cb25fdfb 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -38953,14 +38953,14 @@ monitoring, Auto Scaling for automatically scaling resources, and more.") (define-public r-paws-networking (package (name "r-paws-networking") - (version "0.3.0") + (version "0.4.0") (source (origin (method url-fetch) (uri (cran-uri "paws.networking" version)) (sha256 (base32 - "0pf1vvwmgsz65bq5diabybnsgyxfbjq1f64srf3qk49ycfh2sc7h")))) + "1imq29nxy5hxz2vlijdj2jl0lllvm3plb3jwpvsx1wlcvhpz0in3")))) (properties `((upstream-name . "paws.networking"))) (build-system r-build-system) From 30bd163d01a271ec439fc9c9326562e10e551087 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 14 Sep 2023 00:04:15 +0200 Subject: [PATCH 195/268] gnu: r-paws-database: Update to 0.4.0. * gnu/packages/cran.scm (r-paws-database): Update to 0.4.0. --- gnu/packages/cran.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index f8cb25fdfb..38f971d94a 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -38977,14 +38977,14 @@ CloudFront content delivery, load balancing, and more.") (define-public r-paws-database (package (name "r-paws-database") - (version "0.3.0") + (version "0.4.0") (source (origin (method url-fetch) (uri (cran-uri "paws.database" version)) (sha256 (base32 - "08ak299kyr6dr8idcna7i433aab1bis2b9zqmwm1yma3m3xk4n8i")))) + "1rnjjdb4l7a943cawkkzfjkg8shy2vy5d9mcl2p5ms191lw056bn")))) (properties `((upstream-name . "paws.database"))) (build-system r-build-system) (propagated-inputs From c165a1fa9b624a530399e8ea34cdb4bc45075226 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 14 Sep 2023 00:04:15 +0200 Subject: [PATCH 196/268] gnu: r-paws-storage: Update to 0.4.0. * gnu/packages/cran.scm (r-paws-storage): Update to 0.4.0. --- gnu/packages/cran.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 38f971d94a..d047884fc7 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -39001,14 +39001,14 @@ database, and more.") (define-public r-paws-storage (package (name "r-paws-storage") - (version "0.3.0") + (version "0.4.0") (source (origin (method url-fetch) (uri (cran-uri "paws.storage" version)) (sha256 (base32 - "0z693wawgm975lw54xkbg9hwsf1lz69a4dsg85ywjpjcfvl1g1b7")))) + "0yr99328rwm6i95xhp4yds6dzfvrvbr7ys2hy17iqbyij958j0m4")))) (properties `((upstream-name . "paws.storage"))) (build-system r-build-system) (propagated-inputs From b2610240c4ec3c35abb988531523bcf0c8ce181a Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 14 Sep 2023 00:04:15 +0200 Subject: [PATCH 197/268] gnu: r-paws-compute: Update to 0.4.0. * gnu/packages/cran.scm (r-paws-compute): Update to 0.4.0. --- gnu/packages/cran.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index d047884fc7..0b1185e4c6 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -39023,14 +39023,14 @@ services, including Simple Storage Service (S3).") (define-public r-paws-compute (package (name "r-paws-compute") - (version "0.3.1") + (version "0.4.0") (source (origin (method url-fetch) (uri (cran-uri "paws.compute" version)) (sha256 (base32 - "17xzc1ngir4v043xclw6c1qs092aicj83qmn8sydn9apmlzcps1r")))) + "0q0xikrq7095l8fhii2jyjxfbihhnlm7nzzbspfqdh8xbr7g4kld")))) (properties `((upstream-name . "paws.compute"))) (build-system r-build-system) (propagated-inputs From 772f00b171f6ad3f497f4609defddf175cf6a773 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 14 Sep 2023 00:04:16 +0200 Subject: [PATCH 198/268] gnu: r-mlearning: Update to 1.2.1. * gnu/packages/cran.scm (r-mlearning): Update to 1.2.1. [propagated-inputs]: Add r-rpart. --- 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 0b1185e4c6..9c93a5477b 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -39191,14 +39191,14 @@ large datasets.") (define-public r-mlearning (package (name "r-mlearning") - (version "1.1.1") + (version "1.2.1") (source (origin (method url-fetch) (uri (cran-uri "mlearning" version)) (sha256 (base32 - "1zjnh4gcw068li1bks60gazn3205xhmqz67hbkb1san33lmlxya3")))) + "0fh28i36smpybhzd2kni435m7wf20i3yib6h7jy173r1v5adzkba")))) (properties `((upstream-name . "mlearning"))) (build-system r-build-system) (propagated-inputs @@ -39207,7 +39207,8 @@ large datasets.") r-ipred r-mass r-nnet - r-randomforest)) + r-randomforest + r-rpart)) (home-page "https://www.sciviews.org/zooimage") (synopsis "Machine learning algorithms with unified interface") (description From b832880b1e220148fc81a758e1439de400c35658 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 14 Sep 2023 00:04:16 +0200 Subject: [PATCH 199/268] gnu: r-ggh4x: Update to 0.2.6. * gnu/packages/cran.scm (r-ggh4x): Update to 0.2.6. --- gnu/packages/cran.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 9c93a5477b..6166b0d006 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -39852,14 +39852,14 @@ be efficient and easy to use.") (define-public r-ggh4x (package (name "r-ggh4x") - (version "0.2.5") + (version "0.2.6") (source (origin (method url-fetch) (uri (cran-uri "ggh4x" version)) (sha256 (base32 - "0xj4nlxrpmwzdlj4q3vnhwy7gd1634ff7yjsnaf609ap0q23mxb1")))) + "0frbkdylyz630y7rjyif0whf74r89ca5bmhk9djcwz8nqfs2jygb")))) (properties `((upstream-name . "ggh4x"))) (build-system r-build-system) (propagated-inputs From 1a7612a64cbe923a68b9f26b9cc81ce38fdbf9e6 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 14 Sep 2023 00:04:16 +0200 Subject: [PATCH 200/268] gnu: r-foreign: Update to 0.8-85. * gnu/packages/statistics.scm (r-foreign): Update to 0.8-85. --- 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 c3444560fd..f5268bb0b6 100644 --- a/gnu/packages/statistics.scm +++ b/gnu/packages/statistics.scm @@ -603,14 +603,14 @@ code for possible problems.") (define-public r-foreign (package (name "r-foreign") - (version "0.8-84") + (version "0.8-85") (source (origin (method url-fetch) (uri (cran-uri "foreign" version)) (sha256 (base32 - "0jc5r5wiqqbkni2xjdd24hic1xvfi151m9lnqhni52jnqw1g7v8p")))) + "1azca97fhwb1pzgrjw2xscfh2k7bfryp6wjsdcx2y4h7305d4ych")))) (build-system r-build-system) (home-page "https://cran.r-project.org/web/packages/foreign") (synopsis "Read data stored by other statistics software") From 8f68be3264004b17ae9e2bef0c878fab07462d8f Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 14 Sep 2023 00:04:16 +0200 Subject: [PATCH 201/268] gnu: r-labeling: Update to 0.4.3. * gnu/packages/statistics.scm (r-labeling): Update to 0.4.3. --- 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 f5268bb0b6..4b1d7ef896 100644 --- a/gnu/packages/statistics.scm +++ b/gnu/packages/statistics.scm @@ -1005,13 +1005,13 @@ non-estimable cases correctly.") (define-public r-labeling (package (name "r-labeling") - (version "0.4.2") + (version "0.4.3") (source (origin (method url-fetch) (uri (cran-uri "labeling" version)) (sha256 - (base32 "0rfikd9gy70b8qz87q9axcwv8nmn9mbxfdwypxi0sghpfs9df8p0")))) + (base32 "1wk4wa1s8f17b5lf8vs5hxsmyadp2ccmyg4hamq7sdvlrk14yby6")))) (build-system r-build-system) (home-page "https://cran.r-project.org/web/packages/labeling") (synopsis "Axis labeling algorithms") From 44dfcc013a9af9de179b821f8bf71d6949ce8703 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 14 Sep 2023 00:04:16 +0200 Subject: [PATCH 202/268] gnu: r-knitr: Update to 1.44. * gnu/packages/statistics.scm (r-knitr): Update to 1.44. --- 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 4b1d7ef896..c9b4cc518a 100644 --- a/gnu/packages/statistics.scm +++ b/gnu/packages/statistics.scm @@ -1576,13 +1576,13 @@ emitter (http://pyyaml.org/wiki/LibYAML) for R.") (define-public r-knitr (package (name "r-knitr") - (version "1.43") + (version "1.44") (source (origin (method url-fetch) (uri (cran-uri "knitr" version)) (sha256 (base32 - "0g6m9s53qyf34ba4db97k31sxg2ikndfp747229sm6ilikmbla9x")))) + "015ylljvx0q2himch4k813021nvh0l7p5x3aqdkj3w0ax8x8k3ki")))) (build-system r-build-system) (propagated-inputs (list r-evaluate r-highr r-xfun r-yaml)) From 800aab705c802dda1c10eee0104a0a1e8513c961 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 14 Sep 2023 00:04:16 +0200 Subject: [PATCH 203/268] gnu: r-dplyr: Update to 1.1.3. * gnu/packages/statistics.scm (r-dplyr): Update to 1.1.3. --- 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 c9b4cc518a..e78744d15d 100644 --- a/gnu/packages/statistics.scm +++ b/gnu/packages/statistics.scm @@ -1827,13 +1827,13 @@ and printing capabilities than traditional data frames.") (define-public r-dplyr (package (name "r-dplyr") - (version "1.1.2") + (version "1.1.3") (source (origin (method url-fetch) (uri (cran-uri "dplyr" version)) (sha256 (base32 - "1qwn00ai7k6km0z9kl6aa1qjkfz8j3prlgdfxr1pr5s47a5c6862")))) + "0hhpzv66rqz7z8vdryzjdkp4flmjvzxrx1pwpxnbmjqgvd3s4hv8")))) (build-system r-build-system) (propagated-inputs (list r-cli From fcf5c595e2989cdeaf8d08414118b47adbb9e5da Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 14 Sep 2023 00:04:16 +0200 Subject: [PATCH 204/268] gnu: r-rcpparmadillo: Update to 0.12.6.4.0. * gnu/packages/statistics.scm (r-rcpparmadillo): Update to 0.12.6.4.0. --- 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 e78744d15d..27e9f95e73 100644 --- a/gnu/packages/statistics.scm +++ b/gnu/packages/statistics.scm @@ -2963,13 +2963,13 @@ well as additional utilities such as panel and axis annotation functions.") (define-public r-rcpparmadillo (package (name "r-rcpparmadillo") - (version "0.12.6.1.0") + (version "0.12.6.4.0") (source (origin (method url-fetch) (uri (cran-uri "RcppArmadillo" version)) (sha256 (base32 - "0saga8anaahyrvvynggg168756rv8d9gyq8sryjgnx5pp4jbz6ck")))) + "1k7xq2yl4pkc7krz1bcdnx5kfj6n4zjmnm40nly2da2ji87agv49")))) (properties `((upstream-name . "RcppArmadillo"))) (build-system r-build-system) (propagated-inputs From 894c89b1d87b2c9c30df79d5f038f1c0df1802be Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 14 Sep 2023 00:04:16 +0200 Subject: [PATCH 205/268] gnu: r-rematch: Update to 2.0.0. * gnu/packages/statistics.scm (r-rematch): Update to 2.0.0. --- 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 27e9f95e73..843d0d9992 100644 --- a/gnu/packages/statistics.scm +++ b/gnu/packages/statistics.scm @@ -4717,14 +4717,14 @@ distribution).") (define-public r-rematch (package (name "r-rematch") - (version "1.0.1") + (version "2.0.0") (source (origin (method url-fetch) (uri (cran-uri "rematch" version)) (sha256 (base32 - "0y3mshvpvz9csmq8hk8jbabx4nxlv5sckvfzvm6920ndg34xw2d4")))) + "09jwg3glp32q4ml4khhzi8j7bzg9zhqqdg1m6r8gibh756zzgnhm")))) (build-system r-build-system) (home-page "https://github.com/MangoTheCat/rematch") (synopsis "Match regular expressions with a nicer API") From fd1d1e11a29e7d2cd674c1c51f3499234bbf4bc4 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 14 Sep 2023 00:04:16 +0200 Subject: [PATCH 206/268] gnu: r-deoptimr: Update to 1.1-2. * gnu/packages/statistics.scm (r-deoptimr): Update to 1.1-2. --- gnu/packages/statistics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm index 843d0d9992..791b811eff 100644 --- a/gnu/packages/statistics.scm +++ b/gnu/packages/statistics.scm @@ -5586,14 +5586,14 @@ data for species delimitation, nearest neighbor based noise detection.") (define-public r-deoptimr (package (name "r-deoptimr") - (version "1.1-1") + (version "1.1-2") (source (origin (method url-fetch) (uri (cran-uri "DEoptimR" version)) (sha256 (base32 - "1appp5xgayafda6f5pcdsxaskqs831rb21znx44r8nyb9gvg0f6z")))) + "0swycypiyxkvhn1438q0wysz2c4ky6zjw89w62dggbciqwk8xdbq")))) (properties `((upstream-name . "DEoptimR"))) (build-system r-build-system) (home-page "https://cran.r-project.org/web/packages/DEoptimR") From 97e5c897c4ba22ce8b9955eec4a683fdcf9a7ef6 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 14 Sep 2023 00:04:16 +0200 Subject: [PATCH 207/268] gnu: r-lmom: Update to 3.0. * gnu/packages/statistics.scm (r-lmom): Update to 3.0. --- 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 791b811eff..b647ec0b61 100644 --- a/gnu/packages/statistics.scm +++ b/gnu/packages/statistics.scm @@ -7232,13 +7232,13 @@ Annealing\" @url{doi:10.1145/3025453.3025912}.") (define-public r-lmom (package (name "r-lmom") - (version "2.9") + (version "3.0") (source (origin (method url-fetch) (uri (cran-uri "lmom" version)) (sha256 - (base32 "145va4dhl767mywk36xcmqilm21sfkqhcqi0s07qgq3k39sn4gin")))) + (base32 "1482kbb4cm65m2d1xlxml93yjd3d43iiap6nvzg5vd33i9iyh2jb")))) (properties `((upstream-name . "lmom"))) (build-system r-build-system) (native-inputs (list gfortran)) From 3d402fbf1d950c1d7c194d5cdd1bc17e884ab6eb Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 14 Sep 2023 00:04:16 +0200 Subject: [PATCH 208/268] gnu: r-desctools: Update to 0.99.50. * gnu/packages/statistics.scm (r-desctools): Update to 0.99.50. --- 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 b647ec0b61..00eb6c7f1b 100644 --- a/gnu/packages/statistics.scm +++ b/gnu/packages/statistics.scm @@ -7316,13 +7316,13 @@ Calculates confidence intervals for the difference in proportion.") (define-public r-desctools (package (name "r-desctools") - (version "0.99.49") + (version "0.99.50") (source (origin (method url-fetch) (uri (cran-uri "DescTools" version)) (sha256 - (base32 "0s2zh8xz06c45rbwcypgsa8shby66nm6sj90cb9d1bwb60mws8j5")))) + (base32 "1awfhbv7klvkwxki4lvxj086yiwqyys95jnss8q5qqn7wyfz170v")))) (properties `((upstream-name . "DescTools"))) (build-system r-build-system) (propagated-inputs From 2afa9353a0f69dabf4ddec54b58b60308092c794 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 14 Sep 2023 00:04:16 +0200 Subject: [PATCH 209/268] gnu: r-reghelper: Update to 1.1.2. * gnu/packages/statistics.scm (r-reghelper): Update to 1.1.2. [propagated-inputs]: Add r-rlang. --- gnu/packages/statistics.scm | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm index 00eb6c7f1b..d8fde36cd3 100644 --- a/gnu/packages/statistics.scm +++ b/gnu/packages/statistics.scm @@ -7553,16 +7553,16 @@ generating and manipulating colors in R.") (define-public r-reghelper (package (name "r-reghelper") - (version "1.1.1") + (version "1.1.2") (source (origin (method url-fetch) (uri (cran-uri "reghelper" version)) (sha256 (base32 - "0v1987rs6kcpizfhrp3hxsyx9arn5vsbapjfgj9478j73mm844ji")))) + "1vd8kd719kyjp65zym6zx3vax1q2kbhpl6la71d5aa59s54ylri3")))) (properties `((upstream-name . "reghelper"))) (build-system r-build-system) - (propagated-inputs (list r-ggplot2 r-lme4 r-mass r-nlme)) + (propagated-inputs (list r-ggplot2 r-lme4 r-mass r-nlme r-rlang)) (home-page "https://github.com/jeff-hughes/reghelper") (synopsis "Helper Functions for Regression Analysis") (description From 028ebb8edb133bec27c6c7ae1f604dcb090ed127 Mon Sep 17 00:00:00 2001 From: Julien Lepiller Date: Thu, 14 Sep 2023 06:50:42 +0200 Subject: [PATCH 210/268] gnu: libwebp: Replace with 1.3.2. [fixes CVE-2023-4863] * gnu/packages/image.scm (libwebp/fixed): Update to 1.3.2. --- gnu/packages/image.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/image.scm b/gnu/packages/image.scm index 403409975a..a632a02139 100644 --- a/gnu/packages/image.scm +++ b/gnu/packages/image.scm @@ -1475,7 +1475,7 @@ channels.") (package (inherit libwebp) (name "libwebp") - (version "1.3.1") + (version "1.3.2") (source (origin (method git-fetch) @@ -1485,7 +1485,7 @@ channels.") (file-name (git-file-name name version)) (sha256 (base32 - "1aas6gwy7kfcq34cil781kcsl286khh9grwcx7k4d2n1g7zcpl3m")))))) + "1x37795gpc63g1ma9kqw4q3dikwhrjklixqzjjsj6viqksa19z41")))))) (define-public libmng (package From 6e06c0032cd0f4f3b49d38b226b082e1c4e4d429 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 14 Sep 2023 08:57:19 +0200 Subject: [PATCH 211/268] gnu: r-genomeinfodb: Update to 1.36.3. * gnu/packages/bioconductor.scm (r-genomeinfodb): Update to 1.36.3. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 0b44257b16..0fd32ddacb 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -7195,13 +7195,13 @@ genomic intervals. In addition, it can use BAM or BigWig files as input.") (define-public r-genomeinfodb (package (name "r-genomeinfodb") - (version "1.36.2") + (version "1.36.3") (source (origin (method url-fetch) (uri (bioconductor-uri "GenomeInfoDb" version)) (sha256 (base32 - "0bd46s7ch4j70n0snjf2nyx8gzkxn7d563jh5i3i0wzb647f5hbg")))) + "04bh4481jcj91xdh11ic4519jczck6zmysbpnpbbhykanp31z4pf")))) (properties `((upstream-name . "GenomeInfoDb"))) (build-system r-build-system) From a1245f559d1291cac1b8578157fbbb0f565f0219 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 14 Sep 2023 08:57:19 +0200 Subject: [PATCH 212/268] gnu: r-genomicdatacommons: Update to 1.24.3. * gnu/packages/bioconductor.scm (r-genomicdatacommons): Update to 1.24.3. [propagated-inputs]: Add r-tidyr. --- gnu/packages/bioconductor.scm | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 0fd32ddacb..165f704934 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -7254,13 +7254,13 @@ alignments.") (define-public r-genomicdatacommons (package (name "r-genomicdatacommons") - (version "1.24.2") + (version "1.24.3") (source (origin (method url-fetch) (uri (bioconductor-uri "GenomicDataCommons" version)) (sha256 (base32 - "0dgvhi6nbc1qvrdwww2r39gxd2xmbadvy03lxh5nny9pyhhdlz3l")))) + "1grvria7lx7p0py3w8yi0j41bpfx951lds5db7jdiq0j8l75fh38")))) (properties `((upstream-name . "GenomicDataCommons"))) (build-system r-build-system) (propagated-inputs (list r-dplyr @@ -7273,6 +7273,7 @@ alignments.") r-readr r-rlang r-tibble + r-tidyr r-xml2)) (native-inputs (list r-knitr)) (home-page "https://bioconductor.org/packages/GenomicDataCommons") From 7f983fb73024a3f0429b8a78bde74a8fdd059ff4 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 14 Sep 2023 08:57:19 +0200 Subject: [PATCH 213/268] gnu: r-shinymethyl: Update to 1.36.1. * gnu/packages/bioconductor.scm (r-shinymethyl): Update to 1.36.1. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 165f704934..aa7b491191 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -9813,13 +9813,13 @@ and advanced quality control routines.") (define-public r-shinymethyl (package (name "r-shinymethyl") - (version "1.36.0") + (version "1.36.1") (source (origin (method url-fetch) (uri (bioconductor-uri "shinyMethyl" version)) (sha256 (base32 - "1rqwwglj0475gr14bxazfmcvsy7rq6nlw2zcswa684751wy15w0r")))) + "0hq1q66vjd9pwdwm9zx8q45ws65bn6cm87zmjmyc3md8dwvb8cck")))) (properties `((upstream-name . "shinyMethyl"))) (build-system r-build-system) (propagated-inputs From 8fe9e14917973c2039079be9440f0acd9b91cfe5 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 14 Sep 2023 08:57:19 +0200 Subject: [PATCH 214/268] gnu: r-tcgautils: Update to 1.20.4. * gnu/packages/bioconductor.scm (r-tcgautils): Update to 1.20.4. [propagated-inputs]: Add r-biocbaseutils. --- gnu/packages/bioconductor.scm | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index aa7b491191..43952be0aa 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -9963,16 +9963,17 @@ level.") (define-public r-tcgautils (package (name "r-tcgautils") - (version "1.20.2") + (version "1.20.4") (source (origin (method url-fetch) (uri (bioconductor-uri "TCGAutils" version)) (sha256 (base32 - "0nnfrd5x3mii9adizvz79jinlxn2lhg4civ9v0wwygmdhk7rrm1n")))) + "02mkijvh2h58wg7hsi76ycw6gapl0ai190agckaw4l54sqpsx91q")))) (properties `((upstream-name . "TCGAutils"))) (build-system r-build-system) (propagated-inputs (list r-annotationdbi + r-biocbaseutils r-biocgenerics r-genomeinfodb r-genomicdatacommons From 8cfd6e804ab5917d161f3880bd1f9d70b2d1fb4b Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 14 Sep 2023 08:57:19 +0200 Subject: [PATCH 215/268] gnu: r-greylistchip: Update to 1.32.1. * gnu/packages/bioconductor.scm (r-greylistchip): Update to 1.32.1. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 43952be0aa..2f2d649e4f 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -11110,13 +11110,13 @@ posterior for individual coefficients.") (define-public r-greylistchip (package (name "r-greylistchip") - (version "1.32.0") + (version "1.32.1") (source (origin (method url-fetch) (uri (bioconductor-uri "GreyListChIP" version)) (sha256 (base32 - "1sfpf9msnzyrc8b0xzc2406bq2gkcwrrhv7fa9ynqv2ip6xwsc8s")))) + "0z89yikglx077x18qhq6f8f2fa9xni12jz8my9p5sa6zmvnj4dnm")))) (properties `((upstream-name . "GreyListChIP"))) (build-system r-build-system) (propagated-inputs From 9232ef79865439cc6584e8942550f8d6fb70a1c8 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 14 Sep 2023 08:57:19 +0200 Subject: [PATCH 216/268] gnu: r-clusterprofiler: Update to 4.8.3. * gnu/packages/bioconductor.scm (r-clusterprofiler): Update to 4.8.3. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 2f2d649e4f..69795311a7 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -14422,14 +14422,14 @@ attempts to assess their statistical significance.") (define-public r-clusterprofiler (package (name "r-clusterprofiler") - (version "4.8.2") + (version "4.8.3") (source (origin (method url-fetch) (uri (bioconductor-uri "clusterProfiler" version)) (sha256 (base32 - "0iijby2j9i6sbdc3iwhqqb8xlz25k3dpiyq91p7yybggpr2p1nw4")))) + "1kihrpa8cb2bqk5dck0w6yzgfpl72qxlrxwpidg1ar27q3ivz8w3")))) (properties `((upstream-name . "clusterProfiler"))) (build-system r-build-system) From ebaf944cddd7a7fd5e9ba825a9c17dfda2cfe223 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 14 Sep 2023 08:57:19 +0200 Subject: [PATCH 217/268] gnu: r-s4arrays: Update to 1.0.6. * gnu/packages/bioconductor.scm (r-s4arrays): Update to 1.0.6. --- 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 69795311a7..e37ce4d424 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -19663,13 +19663,13 @@ routines.") (define-public r-s4arrays (package (name "r-s4arrays") - (version "1.0.5") + (version "1.0.6") (source (origin (method url-fetch) (uri (bioconductor-uri "S4Arrays" version)) (sha256 (base32 - "01xlccybhdgas9pnx88ll9q56qb2xd687xvfrc7bd5r9sf72b81c")))) + "011n4lyznlrya5l8d7m30x81k7h81wbp07b12s6a4s5sy9fzd5jb")))) (properties `((upstream-name . "S4Arrays"))) (build-system r-build-system) (propagated-inputs From c8e7ea8a8be82ac9296e0bcea9b4b83c0a656179 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 14 Sep 2023 08:57:20 +0200 Subject: [PATCH 218/268] gnu: r-rhdf5lib: Update to 1.22.1. * gnu/packages/bioconductor.scm (r-rhdf5lib): Update to 1.22.1. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index e37ce4d424..abf35d72fb 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -19927,14 +19927,14 @@ block processing.") (define-public r-rhdf5lib (package (name "r-rhdf5lib") - (version "1.22.0") + (version "1.22.1") (source (origin (method url-fetch) (uri (bioconductor-uri "Rhdf5lib" version)) (sha256 (base32 - "1j8i4rmq85n7jys86a9zyj1n4qn7bhc1sqgcq8dyh7zqfdvb9bcw")) + "1007i2rzz86k04kswa4h53p8zzh52k31m9d8im6iw0n91inqbcj9")) (modules '((guix build utils))) (snippet '(begin From cf5cb0875b06b5823e9de8bbd01ddd8c0b0d15a7 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 14 Sep 2023 08:57:20 +0200 Subject: [PATCH 219/268] gnu: r-delayedmatrixstats: Update to 1.22.6. * gnu/packages/bioconductor.scm (r-delayedmatrixstats): Update to 1.22.6. --- 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 abf35d72fb..8e13044b1a 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -20550,14 +20550,14 @@ Visium platform.") (define-public r-delayedmatrixstats (package (name "r-delayedmatrixstats") - (version "1.22.5") + (version "1.22.6") (source (origin (method url-fetch) (uri (bioconductor-uri "DelayedMatrixStats" version)) (sha256 (base32 - "1bzbsfds5zki6iazj53y6kps8bvn7zdysbmpf9359sv6zshk18fv")))) + "0jaaqa2fm61dmsphm5y4rlwf2dm1l5rs0vpq0f5r35iyw2m12lh8")))) (properties `((upstream-name . "DelayedMatrixStats"))) (build-system r-build-system) From 180502f28fbed79228549738fd550894dbdc2dc7 Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Thu, 14 Sep 2023 11:08:54 +0300 Subject: [PATCH 220/268] gnu: debootstrap: Update to 1.0.132. * gnu/packages/debian.scm (debootstrap): Update to 1.0.132. --- gnu/packages/debian.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/debian.scm b/gnu/packages/debian.scm index ef3c5f1f2c..78cdd0d3f4 100644 --- a/gnu/packages/debian.scm +++ b/gnu/packages/debian.scm @@ -190,7 +190,7 @@ contains the archive keys used for that.") (define-public debootstrap (package (name "debootstrap") - (version "1.0.128") + (version "1.0.132") (source (origin (method git-fetch) @@ -199,7 +199,7 @@ contains the archive keys used for that.") (commit version))) (file-name (git-file-name name version)) (sha256 - (base32 "0hc7xc6qvnmjlpf3j6bm25kf0j1ifvv5j7a0iljfmbag4idxc9jv")))) + (base32 "1l6mc3i2wqfhmhj85x9qiiqchqp9br6gg54hv1xs08h8xndmfchf")))) (build-system gnu-build-system) (arguments (list From 6226b8f72d87583322b075d4c51f253f9b13bc07 Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Thu, 14 Sep 2023 11:12:28 +0300 Subject: [PATCH 221/268] gnu: debootstrap: Hardcode location of archive keyrings. * gnu/packages/debian.scm (debootstrap)[arguments]: Adjust custom 'patch-source phase to hardcode the location of the archive keyrings. --- gnu/packages/debian.scm | 6 ++++++ 1 file changed, 6 insertions(+) diff --git a/gnu/packages/debian.scm b/gnu/packages/debian.scm index 78cdd0d3f4..f011802ed3 100644 --- a/gnu/packages/debian.scm +++ b/gnu/packages/debian.scm @@ -226,6 +226,12 @@ contains the archive keys used for that.") (substitute* "debootstrap" (("=/usr") (string-append "=" #$output)) (("/usr/bin/dpkg") (search-input-file inputs "/bin/dpkg"))) + ;; Include the keyring locations by default. + (substitute* (find-files "scripts") + (("keyring.*(debian-archive-keyring.gpg)"_ keyring) + (string-append "keyring " debian "/share/keyrings/" keyring)) + (("keyring.*(ubuntu-archive-keyring.gpg)" _ keyring) + (string-append "keyring " ubuntu "/share/keyrings/" keyring))) ;; Ensure PATH works both in guix and within the debian chroot ;; workaround for: https://bugs.debian.org/929889 (substitute* "functions" From 0ce57ea4a17139038c79a00057635e89103c76f6 Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Thu, 14 Sep 2023 11:31:41 +0300 Subject: [PATCH 222/268] gnu: dpkg: Update to 1.22.0. * gnu/packages/debian.scm (dpkg): Update to 1.22.0. [arguments]: Wrap another script in the custom 'wrap-scripts phase. --- gnu/packages/debian.scm | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/gnu/packages/debian.scm b/gnu/packages/debian.scm index f011802ed3..6e40096199 100644 --- a/gnu/packages/debian.scm +++ b/gnu/packages/debian.scm @@ -341,7 +341,7 @@ distributions such as Debian and Trisquel.") (define-public dpkg (package (name "dpkg") - (version "1.21.22") + (version "1.22.0") (source (origin (method git-fetch) @@ -350,7 +350,7 @@ distributions such as Debian and Trisquel.") (commit version))) (file-name (git-file-name name version)) (sha256 - (base32 "0b5czgif5g6pdjzcw60hzzj0i1llxvajf3nlx115axmpa3y4iynd")))) + (base32 "1p7f2mgrn2iy0xfysxfq4pjbbhbhb2rp649bsik0x25jrck4if83")))) (build-system gnu-build-system) (arguments (list #:modules @@ -388,6 +388,7 @@ distributions such as Debian and Trisquel.") `("PATH" ":" prefix (,(string-append #$output "/bin"))))) (list "dpkg-architecture" + "dpkg-buildapi" "dpkg-buildflags" "dpkg-buildpackage" "dpkg-checkbuilddeps" From c36d4760c6a32864c10809b996e1c093928a3653 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 14 Sep 2023 11:16:29 +0200 Subject: [PATCH 223/268] gnu: perl-cworld-dekker: Drop labels from inputs. * gnu/packages/bioinformatics.scm (perl-cworld-dekker)[arguments]: Use G-expression and avoid references to labeled inputs. [inputs]: Drop labels. --- gnu/packages/bioinformatics.scm | 134 ++++++++++++++++---------------- 1 file changed, 67 insertions(+), 67 deletions(-) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index aa88692204..c78f017a24 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -19246,77 +19246,77 @@ large-scale data-analysis.") "1dvh23fx52m59y6304xi2j2pl2hiqadlqg8jyv2pm14j1hy71ych")))) (build-system perl-build-system) (arguments - `(#:modules ((guix build perl-build-system) + (list + #:modules '((guix build perl-build-system) (guix build utils) (srfi srfi-26)) - #:phases - (modify-phases %standard-phases - (add-after 'unpack 'hardcode-references - (lambda* (#:key inputs #:allow-other-keys) - (let ((bedtools (assoc-ref inputs "bedtools")) - (r (assoc-ref inputs "r-minimal"))) - (substitute* '("scripts/python/getEigenVectors.py" - "scripts/python/matrix2EigenVectors.py") - (("bedtools intersect") - (string-append bedtools "/bin/bedtools intersect"))) - (substitute* "lib/cworld/dekker.pm" - (("bedtools --version") - (string-append bedtools "/bin/bedtools --version"))) - (substitute* '("scripts/perl/correlateMatrices.pl" - "scripts/perl/matrix2scaling.pl" - "scripts/perl/matrix2distance.pl" - "scripts/perl/coverageCorrect.pl" - "scripts/perl/matrix2anchorPlot.pl" - "scripts/python/matrix2EigenVectors.py" - "scripts/python/matrix2insulation-lite.py" - "scripts/perl/matrix2compartment.pl" - "scripts/perl/anchorPurge.pl" - "scripts/perl/applyCorrection.pl" - "scripts/perl/compareInsulation.pl" - "scripts/perl/fillMissingData.pl" - "scripts/perl/matrix2loess.pl" - "scripts/python/getEigenVectors.py" - "scripts/perl/aggregateBED.pl" - "scripts/perl/collapseMatrix.pl" - "scripts/perl/matrix2direction.pl" - "scripts/perl/singletonRemoval.pl" - "lib/cworld/dekker.pm" - "scripts/perl/matrix2insulation.pl") - (("(`|\")Rscript" _ pre) - (string-append pre r "/bin/Rscript")))))) - (add-after 'install 'install-scripts - (lambda* (#:key outputs #:allow-other-keys) - (let* ((out (assoc-ref outputs "out")) - (share (string-append out "/share/cworld-dekker"))) - (mkdir-p share) - (copy-recursively "scripts" share) + #:phases + #~(modify-phases %standard-phases + (add-after 'unpack 'hardcode-references + (lambda* (#:key inputs #:allow-other-keys) + (let ((bedtools #$(this-package-input "bedtools")) + (r #$(this-package-input "r-minimal"))) + (substitute* '("scripts/python/getEigenVectors.py" + "scripts/python/matrix2EigenVectors.py") + (("bedtools intersect") + (string-append bedtools "/bin/bedtools intersect"))) + (substitute* "lib/cworld/dekker.pm" + (("bedtools --version") + (string-append bedtools "/bin/bedtools --version"))) + (substitute* '("scripts/perl/correlateMatrices.pl" + "scripts/perl/matrix2scaling.pl" + "scripts/perl/matrix2distance.pl" + "scripts/perl/coverageCorrect.pl" + "scripts/perl/matrix2anchorPlot.pl" + "scripts/python/matrix2EigenVectors.py" + "scripts/python/matrix2insulation-lite.py" + "scripts/perl/matrix2compartment.pl" + "scripts/perl/anchorPurge.pl" + "scripts/perl/applyCorrection.pl" + "scripts/perl/compareInsulation.pl" + "scripts/perl/fillMissingData.pl" + "scripts/perl/matrix2loess.pl" + "scripts/python/getEigenVectors.py" + "scripts/perl/aggregateBED.pl" + "scripts/perl/collapseMatrix.pl" + "scripts/perl/matrix2direction.pl" + "scripts/perl/singletonRemoval.pl" + "lib/cworld/dekker.pm" + "scripts/perl/matrix2insulation.pl") + (("(`|\")Rscript" _ pre) + (string-append pre r "/bin/Rscript")))))) + (add-after 'install 'install-scripts + (lambda _ + (let ((share (string-append #$output "/share/cworld-dekker"))) + (mkdir-p share) + (copy-recursively "scripts" share) - ;; Make all scripts executable and wrap them. - (let ((r (find-files share "\\.R$")) - (py (find-files share "\\.py$")) - (pl (find-files share "\\.pl$")) - (wrap (lambda* (script var #:optional (extra "")) - (let ((path (string-append (getenv var) - extra))) - (wrap-program script - `(,var ":" prefix (,path))))))) - (for-each (cut chmod <> #o555) (append r py pl)) - (for-each (cut wrap <> "PERL5LIB" - (string-append ":" out - "/lib/perl5/site_perl")) - pl) - (for-each (cut wrap <> "GUIX_PYTHONPATH") py)))))))) + ;; Make all scripts executable and wrap them. + (let ((r (find-files share "\\.R$")) + (py (find-files share "\\.py$")) + (pl (find-files share "\\.pl$")) + (wrap (lambda* (script var #:optional (extra "")) + (let ((path (string-append (getenv var) + extra))) + (wrap-program script + `(,var ":" prefix (,path))))))) + (for-each (cut chmod <> #o555) (append r py pl)) + (for-each (cut wrap <> "PERL5LIB" + (string-append ":" #$output + "/lib/perl5/site_perl")) + pl) + (for-each (cut wrap <> "GUIX_PYTHONPATH") py)))))))) (inputs - `(("libgd" ,gd) - ("perl-gd" ,perl-gd) - ("bedtools" ,bedtools) - ("python" ,python-wrapper) - ("python-scipy" ,python-scipy) - ("python-numpy" ,python-numpy) - ("python-matplotlib" ,python-matplotlib) - ("python-h5py" ,python-h5py) - ("python-scikit-learn" ,python-scikit-learn) - ("r-minimal" ,r-minimal))) + (list gd + perl-gd + bedtools + python-wrapper + python-scipy + python-numpy + python-matplotlib + python-h5py + python-scikit-learn + r-minimal)) (native-inputs (list perl-module-build)) (home-page "https://github.com/dekkerlab/cworld-dekker") From e5f7c14ef6c951f02ca710fad1869db3aedff4b5 Mon Sep 17 00:00:00 2001 From: c4droid Date: Thu, 14 Sep 2023 17:29:26 +0800 Subject: [PATCH 224/268] gnu: python-requests_ntlm: Update to 1.2.0. * gnu/packages/python-web.scm (python-requests_ntlm): Update to 1.2.0. Signed-off-by: Efraim Flashner --- gnu/packages/python-web.scm | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/gnu/packages/python-web.scm b/gnu/packages/python-web.scm index 93fd2d2278..12f0ce6208 100644 --- a/gnu/packages/python-web.scm +++ b/gnu/packages/python-web.scm @@ -3215,17 +3215,17 @@ HTTP via a UNIX domain socket.") (define-public python-requests_ntlm (package (name "python-requests_ntlm") - (version "1.1.0") + (version "1.2.0") (source (origin (method url-fetch) (uri (pypi-uri "requests_ntlm" version)) (sha256 (base32 - "0wgbqzaq9w7bas16b7brdb75f91bh3275fb459093bk1ihpck2ci")))) + "1a0np7lk8ma1plv1s4aw5q9h2z3aljprkl9qsfypqcaf0zsqbhik")))) (build-system python-build-system) (propagated-inputs - (list python-cryptography python-ntlm-auth python-requests)) + (list python-cryptography python-pyspnego python-requests)) (home-page "https://github.com/requests/requests-ntlm") (synopsis "NTLM authentication support for Requests") From 2643fa3513ef93fc98a1bbf368f456b163fcf191 Mon Sep 17 00:00:00 2001 From: Kjartan Oli Agustsson Date: Wed, 23 Aug 2023 22:35:11 +0000 Subject: [PATCH 225/268] home: services: redshift: Use redshift package specified in configuration MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * gnu/home/services/desktop.scm (redshift-shepherd-service): Use the redshift package specified by config. Signed-off-by: Ludovic Courtès --- gnu/home/services/desktop.scm | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/gnu/home/services/desktop.scm b/gnu/home/services/desktop.scm index 626918fd9e..c4da116100 100644 --- a/gnu/home/services/desktop.scm +++ b/gnu/home/services/desktop.scm @@ -172,7 +172,7 @@ format.")) ;; FIXME: This fails to start if Home is first activated from a ;; non-X11 session. (start #~(make-forkexec-constructor - (list #$(file-append redshift "/bin/redshift") + (list #$(file-append (home-redshift-configuration-redshift config) "/bin/redshift") "-c" #$config-file))) (stop #~(make-kill-destructor)) (actions (list (shepherd-configuration-action config-file)))))) From e645a53d87be1132bb7f8c3c0afc5967e061fb94 Mon Sep 17 00:00:00 2001 From: Ramin Honary Date: Thu, 24 Aug 2023 17:57:51 +0900 Subject: [PATCH 226/268] gnu: Add stklos. MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * gnu/packages/scheme.scm (stklos): New variable. Co-authored-by: Ludovic Courtès --- gnu/packages/scheme.scm | 45 +++++++++++++++++++++++++++++++++++++++-- 1 file changed, 43 insertions(+), 2 deletions(-) diff --git a/gnu/packages/scheme.scm b/gnu/packages/scheme.scm index 44e0130573..ad06d7db06 100644 --- a/gnu/packages/scheme.scm +++ b/gnu/packages/scheme.scm @@ -42,8 +42,8 @@ (define-module (gnu packages scheme) #:use-module (gnu packages) #:use-module ((guix licenses) - #:select (gpl2+ lgpl2.0+ lgpl2.1 lgpl2.1+ lgpl3+ asl2.0 bsd-3 - cc-by-sa4.0 non-copyleft expat public-domain)) + #:select (gpl2 gpl2+ lgpl2.0+ lgpl2.1 lgpl2.1+ lgpl3+ asl2.0 + bsd-3 cc-by-sa4.0 non-copyleft expat public-domain)) #:use-module (guix gexp) #:use-module (guix packages) #:use-module (guix download) @@ -1235,3 +1235,44 @@ time compilation and compiled macros.") (description "Gerbil mode provides font-lock, indentation, navigation, and REPL for Gerbil code within Emacs."))) + +(define-public stklos + (package + (name "stklos") + (version "1.70") + (source (origin + (method url-fetch) + ;; TODO: Unbundle pcre, libgc, and libffi. + (uri (string-append "https://stklos.net/download/stklos-" + version ".tar.gz")) + (sha256 + (base32 + "1iw3pgycjz3kz3jd1855v2ngf8ib2almpf8v058n1mkj1qd2b88m")))) + (build-system gnu-build-system) + (arguments + (list + #:modules `((ice-9 ftw) + ,@%gnu-build-system-modules) + #:phases + #~(modify-phases %standard-phases + (add-before 'configure 'patch-sh-references + (lambda* (#:key inputs #:allow-other-keys) + (let ((bash (which "bash"))) + (substitute* "configure" + (("/bin/sh") bash))))) + (add-after 'configure 'patch-rm-references + (lambda _ + (let ((rm (which "rm"))) + (substitute* (find-files "." "^Makefile$") + (("/bin/rm") rm)))))))) + (properties + '((release-monitoring-url . "https://stklos.net/download.html"))) + (home-page "https://stklos.net") + (synopsis "R7RS Scheme with CLOS-like object system") + (description + "STklos is a free Scheme system mostly compliant with the languages +features defined in R7RS small. The aim of this implementation is to be fast +as well as light. The implementation is based on an ad-hoc Virtual +Machine. STklos can also be compiled as a library and embedded in an +application.") + (license gpl2+))) From 08e8c3483fa16b4fc9b1fbd92f52bbc778f65249 Mon Sep 17 00:00:00 2001 From: Timotej Lazar Date: Fri, 25 Aug 2023 14:31:23 +0200 Subject: [PATCH 227/268] gnu: syncthing: Update to 1.23.7. MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit The uraggregate binary was merged into ursrv, so don’t attempt to install it. * gnu/packages/syncthing.scm (syncthing): Update to 1.23.7. [arguments]: Build with go-1.20. Signed-off-by: Ludovic Courtès --- gnu/packages/syncthing.scm | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/gnu/packages/syncthing.scm b/gnu/packages/syncthing.scm index 414395251b..fd30360006 100644 --- a/gnu/packages/syncthing.scm +++ b/gnu/packages/syncthing.scm @@ -46,7 +46,7 @@ (define-public syncthing (package (name "syncthing") - (version "1.23.6") + (version "1.23.7") (source (origin (method url-fetch) (uri (string-append "https://github.com/syncthing/syncthing" @@ -54,7 +54,7 @@ "/syncthing-source-v" version ".tar.gz")) (sha256 (base32 - "03myinspq61aiis29mq0xjigj5rh5jd8m0d9xakf43vi7pqgwjbc")))) + "1891dqcsg5r034bw19qjm6qg0zi1g0djcllp2c550zq7v1sdvn0q")))) (build-system go-build-system) ;; The primary Syncthing executable goes to "out", while the auxiliary ;; server programs and utility tools go to "utils". This reduces the size @@ -64,7 +64,7 @@ (list #:modules '((srfi srfi-26) ; for cut (guix build utils) (guix build go-build-system)) - #:go go-1.19 + #:go go-1.20 #:import-path "github.com/syncthing/syncthing" ;; We don't need to install the source code for end-user applications. #:install-source? #f @@ -101,7 +101,7 @@ "stdisco" "stdiscosrv" "stevents" "stfileinfo" "stfinddevice" "stfindignored" "stgenfiles" "strelaypoolsrv" "strelaysrv" "stsigtool" - "stvanity" "stwatchfile" "uraggregate" "ursrv"))))) + "stvanity" "stwatchfile" "ursrv"))))) (add-after 'install 'install-docs (lambda _ From de64e412f3684d54bd2a485920cd3287a551f793 Mon Sep 17 00:00:00 2001 From: fanquake Date: Thu, 24 Aug 2023 09:47:33 +0100 Subject: [PATCH 228/268] gnu: tor: Update to 0.4.8.5. MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * gnu/packages/tor.scm (tor): Update to 0.4.8.5. * gnu/packages/tor.scm (tor)[arguments]<#:configure-flags>: Add "--enable-gpl". * gnu/packages/patches/tor-remove-defensive-assert.patch: New file. * gnu/local.mk (dist_patch_DATA): Register it. * gnu/packages/tor.scm (tor)[source]: Add patch to remove defensive assert. Signed-off-by: Ludovic Courtès --- gnu/local.mk | 1 + .../patches/tor-remove-defensive-assert.patch | 28 +++++++++++++++++++ gnu/packages/tor.scm | 8 ++++-- 3 files changed, 34 insertions(+), 3 deletions(-) create mode 100644 gnu/packages/patches/tor-remove-defensive-assert.patch diff --git a/gnu/local.mk b/gnu/local.mk index 924d497057..8dd363dd79 100644 --- a/gnu/local.mk +++ b/gnu/local.mk @@ -2018,6 +2018,7 @@ dist_patch_DATA = \ %D%/packages/patches/tofi-32bit-compat.patch \ %D%/packages/patches/tootle-glib-object-naming.patch \ %D%/packages/patches/tootle-reason-phrase.patch \ + %D%/packages/patches/tor-remove-defensive-assert.patch \ %D%/packages/patches/transcode-ffmpeg.patch \ %D%/packages/patches/transfig-gcc10-fno-common.patch \ %D%/packages/patches/trytond-add-egg-modules-to-path.patch \ diff --git a/gnu/packages/patches/tor-remove-defensive-assert.patch b/gnu/packages/patches/tor-remove-defensive-assert.patch new file mode 100644 index 0000000000..7207ec867a --- /dev/null +++ b/gnu/packages/patches/tor-remove-defensive-assert.patch @@ -0,0 +1,28 @@ +This patch removes a call to `tor_assert_nonfatal_unreached()` in +`relay_key_is_unavailable_()` that is only called when Tor is compiled +without relay support. + +Unfortunately, the non-fatal assertion causes a BUG log +message to appear for clients when they start up without relay support +for each CPU worker we spawn. This makes it spotting issues during +bootstrap harder particularly for our iOS developers. + +Since the call sites to `get_master_identity_key()` handles `NULL` +values already, we do not think this will be an issue later on. + +Reported by Benjamin Erhart (@tla) from Guardian Project. + +Fixes tpo/core/tor#40848. + +diff --git a/src/feature/relay/routerkeys.h b/src/feature/relay/routerkeys.h +index 7b6d80773c..b97615a9c9 100644 +--- a/src/feature/relay/routerkeys.h ++++ b/src/feature/relay/routerkeys.h +@@ -53,7 +53,6 @@ void routerkeys_free_all(void); + static inline void * + relay_key_is_unavailable_(void) + { +- tor_assert_nonfatal_unreached(); + return NULL; + } + #define relay_key_is_unavailable(type) \ diff --git a/gnu/packages/tor.scm b/gnu/packages/tor.scm index 7fec88656f..44e62b63cc 100644 --- a/gnu/packages/tor.scm +++ b/gnu/packages/tor.scm @@ -63,18 +63,20 @@ (define-public tor (package (name "tor") - (version "0.4.7.14") + (version "0.4.8.5") (source (origin (method url-fetch) (uri (string-append "https://dist.torproject.org/tor-" version ".tar.gz")) (sha256 (base32 - "1y2xwrji1rvk6h0k15705yra5s74h72h2g84x02zr0338vv6gb55")))) + "06g1awb4piqvgxa97pyswxgjzkpj8rx3iy2jbiaygvi99b8wymv9")) + (patches (search-patches "tor-remove-defensive-assert.patch")))) (build-system gnu-build-system) (arguments (list #:configure-flags - #~(list "--enable-lzma" + #~(list "--enable-gpl" + "--enable-lzma" "--enable-zstd") #:phases #~(modify-phases %standard-phases From 6c72db7314b6c355a2bd956da840e9a07a5b1929 Mon Sep 17 00:00:00 2001 From: Zheng Junjie Date: Sat, 9 Sep 2023 17:26:00 +0800 Subject: [PATCH 229/268] gnu: neofetch: Fix cross-compiling. MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * gnu/packages/admin.scm (neofetch): Fix cross-compiling. [arguments]: Use Gexp. Signed-off-by: Ludovic Courtès --- gnu/packages/admin.scm | 14 +++++++------- 1 file changed, 7 insertions(+), 7 deletions(-) diff --git a/gnu/packages/admin.scm b/gnu/packages/admin.scm index 2492890ee5..98ed3d4e61 100644 --- a/gnu/packages/admin.scm +++ b/gnu/packages/admin.scm @@ -36,7 +36,7 @@ ;;; Copyright © 2020 Vincent Legoll ;;; Copyright © 2020 Morgan Smith ;;; Copyright © 2021, 2022, 2023 Maxim Cournoyer -;;; Copyright © 2021 Zheng Junjie <873216071@qq.com> +;;; Copyright © 2021, 2023 Zheng Junjie <873216071@qq.com> ;;; Copyright © 2021 Stefan Reichör ;;; Copyright © 2021 qblade ;;; Copyright © 2021 Hyunseok Kim @@ -4008,12 +4008,12 @@ Intel DRM Driver.") "0i7wpisipwzk0j62pzaigbiq42y1mn4sbraz4my2jlz6ahwf00kv")))) (build-system gnu-build-system) (arguments - `(#:tests? #f ; there are no tests - #:make-flags - (list (string-append "PREFIX=" %output)) - #:phases - (modify-phases %standard-phases - (delete 'configure)))) ; no configure script + (list #:tests? #f ; there are no tests + #:make-flags + #~(list (string-append "PREFIX=" #$output)) + #:phases + #~(modify-phases %standard-phases + (delete 'configure)))) ; no configure script (home-page "https://github.com/dylanaraps/neofetch") (synopsis "System information script") (description "Neofetch is a command-line system information tool written in From 9aeb9e7cc83d5d0e1aed7b34fb5a357645fd86a9 Mon Sep 17 00:00:00 2001 From: Skyler Date: Thu, 7 Sep 2023 02:01:51 +0000 Subject: [PATCH 230/268] gnu: rottlog: Add gawk as an input. MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit This avoids an issue where rottlog will delete the entire /tmp directory if gawk is not installed. See . * gnu/packages/admin.scm (rottlog): Add gawk input, also update the patch-paths build phase for awk invocations. Signed-off-by: Ludovic Courtès --- gnu/packages/admin.scm | 8 ++++++-- 1 file changed, 6 insertions(+), 2 deletions(-) diff --git a/gnu/packages/admin.scm b/gnu/packages/admin.scm index 98ed3d4e61..1b2324bfc7 100644 --- a/gnu/packages/admin.scm +++ b/gnu/packages/admin.scm @@ -1978,7 +1978,11 @@ at once based on a Perl regular expression.") (lambda* (#:key inputs #:allow-other-keys) (substitute* "rc/rc" (("/usr/sbin/sendmail") - (search-input-file inputs "/bin/mail"))))) + (search-input-file inputs "/bin/mail"))) + (with-fluids ((%default-port-encoding "ISO-8859-1")) + (substitute* "src/rottlog" + (("awk") + (search-input-file inputs "/bin/awk")))))) (add-after 'build 'set-packdir (lambda _ ;; Set a default location for archived logs. @@ -1997,7 +2001,7 @@ at once based on a Perl regular expression.") (lambda _ (invoke "make" "install-info")))))) (native-inputs (list autoconf automake texinfo util-linux)) ; for 'cal' - (inputs (list coreutils mailutils)) + (inputs (list coreutils gawk mailutils)) (home-page "https://www.gnu.org/software/rottlog/") (synopsis "Log rotation and management") (description From 40a76a7750586c05b85619a8a6e69610005edbc8 Mon Sep 17 00:00:00 2001 From: Zheng Junjie Date: Wed, 6 Sep 2023 17:46:48 +0800 Subject: [PATCH 231/268] gnu: npiet: Fix cross-compilation. MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * gnu/packages/piet.scm (npiet)[arguments]<#:phases>: Use SEARCH-INPUT-FILE replace WHICH. Signed-off-by: Ludovic Courtès --- gnu/packages/piet.scm | 7 +++++-- 1 file changed, 5 insertions(+), 2 deletions(-) diff --git a/gnu/packages/piet.scm b/gnu/packages/piet.scm index 824efe59de..8e5a313e82 100644 --- a/gnu/packages/piet.scm +++ b/gnu/packages/piet.scm @@ -1,6 +1,7 @@ ;;; GNU Guix --- Functional package management for GNU ;;; Copyright © 2020 Jesse Gibbons ;;; Copyright © 2020 Tobias Geerinckx-Rice +;;; Copyright © 2023 Zheng Junjie <873216071@qq.com> ;;; ;;; This file is part of GNU Guix. ;;; @@ -46,10 +47,12 @@ `(#:phases (modify-phases %standard-phases (add-after 'install 'wrap-binaries - (lambda* (#:key outputs #:allow-other-keys) + (lambda* (#:key inputs outputs #:allow-other-keys) (let ((out (assoc-ref outputs "out"))) (wrap-program (string-append out "/bin/npietedit") - `("PATH" ":" prefix (,(dirname (which "wish"))))) + `("PATH" ":" prefix + (,(dirname + (search-input-file inputs "bin/wish"))))) #t)))))) (inputs (list gd giflib libpng tk)) From 62e138706507bab7e342c2b75fcaaa92f9440597 Mon Sep 17 00:00:00 2001 From: Zheng Junjie Date: Wed, 6 Sep 2023 17:46:49 +0800 Subject: [PATCH 232/268] gnu: npiet: Use gexps. MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * gnu/packages/piet.scm (npiet): Use Gexp. [arguments]: Use Gexp and remove tail #t. Signed-off-by: Ludovic Courtès --- gnu/packages/piet.scm | 22 ++++++++++++---------- 1 file changed, 12 insertions(+), 10 deletions(-) diff --git a/gnu/packages/piet.scm b/gnu/packages/piet.scm index 8e5a313e82..0b16299482 100644 --- a/gnu/packages/piet.scm +++ b/gnu/packages/piet.scm @@ -21,6 +21,7 @@ (define-module (gnu packages piet) #:use-module (guix packages) #:use-module (guix download) + #:use-module (guix gexp) #:use-module (guix git-download) #:use-module ((guix licenses) #:prefix license:) #:use-module (guix build-system gnu) @@ -44,16 +45,17 @@ "0nl59fhdqqr7nslxdirdn8nvlq5wws67c7jyx2ckbmxbc9h8bv9d")))) (build-system gnu-build-system) (arguments - `(#:phases - (modify-phases %standard-phases - (add-after 'install 'wrap-binaries - (lambda* (#:key inputs outputs #:allow-other-keys) - (let ((out (assoc-ref outputs "out"))) - (wrap-program (string-append out "/bin/npietedit") - `("PATH" ":" prefix - (,(dirname - (search-input-file inputs "bin/wish"))))) - #t)))))) + (list #:phases + #~(modify-phases %standard-phases + (add-after 'install 'wrap-binaries + (lambda* (#:key inputs outputs #:allow-other-keys) + (let ((out (assoc-ref outputs "out"))) + (wrap-program (string-append out + "/bin/npietedit") + `("PATH" ":" prefix + (,(dirname + (search-input-file + inputs "bin/wish"))))))))))) (inputs (list gd giflib libpng tk)) (native-inputs (list groff)) From 6d12c16299c1654a909c69d52bcb99b02cca0962 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ludovic=20Court=C3=A8s?= Date: Thu, 14 Sep 2023 17:18:09 +0200 Subject: [PATCH 233/268] =?UTF-8?q?doc:=20Make=20=E2=80=9Ccrash=20course?= =?UTF-8?q?=E2=80=9D=20xref=20more=20visible.?= MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * doc/guix.texi (Using the Configuration System): Move the “Do not panic” note right after the first example. Clarify wording. --- doc/guix.texi | 35 ++++++++++++++++++++--------------- 1 file changed, 20 insertions(+), 15 deletions(-) diff --git a/doc/guix.texi b/doc/guix.texi index 339dcb2a41..7e42a7151c 100644 --- a/doc/guix.texi +++ b/doc/guix.texi @@ -16834,24 +16834,37 @@ instance to support new system services. The operating system is configured by providing an @code{operating-system} declaration in a file that can then be passed to the @command{guix system} command (@pxref{Invoking guix system}). A -simple setup, with the default system services, the default Linux-Libre -kernel, initial RAM disk, and boot loader looks like this: +simple setup, with the default Linux-Libre +kernel, initial RAM disk, and a couple of system services added to those +provided by default looks like this: @findex operating-system @lisp @include os-config-bare-bones.texi @end lisp -This example should be self-describing. Some of the fields defined +The configuration is declarative and hopefully mostly self-describing. +It is actually code in the Scheme programming language; the whole +@code{(operating-system @dots{})} expression produces a @dfn{record} +with a number of @dfn{fields}. +Some of the fields defined above, such as @code{host-name} and @code{bootloader}, are mandatory. Others, such as @code{packages} and @code{services}, can be omitted, in -which case they get a default value. +which case they get a default value. @xref{operating-system Reference}, +for details about all the available fields. -Below we discuss the effect of some of the most important fields -(@pxref{operating-system Reference}, for details about all the available -fields), and how to @dfn{instantiate} the operating system using +Below we discuss the effect of some of the most important fields, +and how to @dfn{instantiate} the operating system using @command{guix system}. +@quotation Do not panic +@cindex Scheme programming language, getting started +Intimidated by the Scheme language or curious about it? The Cookbook +has a short section to get started that explains the fundamentals, which +you will find helpful when hacking your configuration. @xref{A Scheme +Crash Course,,, guix-cookbook, GNU Guix Cookbook}. +@end quotation + @unnumberedsubsec Bootloader @cindex legacy boot, on Intel machines @@ -17025,14 +17038,6 @@ Alternatively, the @code{modify-services} macro can be used: (delete avahi-service-type)) @end lisp -@quotation Do not panic -@cindex Scheme programming language, getting started -Intimidated by the Scheme language or curious about it? The Cookbook -has a short section to get started that explains the fundamentals, which -you will find helpful when hacking your configuration. @xref{A Scheme -Crash Course,,, guix-cookbook, GNU Guix Cookbook}. -@end quotation - @unnumberedsubsec Instantiating the System Assuming the @code{operating-system} declaration From 55da0930e30e0ee1b3da1b9aee5851e9ccfca32c Mon Sep 17 00:00:00 2001 From: Lars Bilke Date: Thu, 7 Sep 2023 15:06:03 +0200 Subject: [PATCH 234/268] gnu: openmpi: Enable PMIx. MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * gnu/packages/mpi.scm (openmpi)[arguments]: Pass “--with-pmix=internal”. Signed-off-by: Ludovic Courtès --- gnu/packages/mpi.scm | 6 ++++++ 1 file changed, 6 insertions(+) diff --git a/gnu/packages/mpi.scm b/gnu/packages/mpi.scm index 4d2458344f..baf6ce11e0 100644 --- a/gnu/packages/mpi.scm +++ b/gnu/packages/mpi.scm @@ -247,6 +247,12 @@ bind processes, and much more.") "--enable-openib-rdmacm" "--enable-openib-rdmacm-ibaddr" + ;; Enable support for the 'Process Management + ;; Interface for Exascale' (PMIx) used e.g. by + ;; Slurm for the management communication and + ;; coordination of MPI processes. + "--with-pmix=internal" + ;; Enable support for SLURM's Process Manager ;; Interface (PMI). ,(string-append "--with-pmi=" From 258729b928e14f0349a109d0a9a1d56a8e68e139 Mon Sep 17 00:00:00 2001 From: Zheng Junjie Date: Wed, 6 Sep 2023 18:25:53 +0800 Subject: [PATCH 235/268] gnu: makefile2graph: fix cross-compile. MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * gnu/packages/code.scm (makefile2graph): fix cross-compile. [arguments]: Use gexp and CC-FOR-TARGET. Signed-off-by: Ludovic Courtès --- gnu/packages/code.scm | 13 ++++++++----- 1 file changed, 8 insertions(+), 5 deletions(-) diff --git a/gnu/packages/code.scm b/gnu/packages/code.scm index 1c21ad475b..4335c57150 100644 --- a/gnu/packages/code.scm +++ b/gnu/packages/code.scm @@ -17,6 +17,7 @@ ;;; Copyright © 2021 lu hui ;;; Copyright © 2021, 2022 Foo Chuan Wei ;;; Copyright © 2022 Michael Rohleder +;;; Copyright © 2023 Zheng Junjie <873216071@qq.com> ;;; ;;; This file is part of GNU Guix. ;;; @@ -773,11 +774,13 @@ produce colored output.") (base32 "1gjfk3d8qg3cla7qd2y7r9s03whlfwy83q8k76xfcnqrjjfavdgk")))) (build-system gnu-build-system) (arguments - '(#:test-target "test" - #:make-flags (list "CC=gcc" (string-append "prefix=" %output)) - #:phases - (modify-phases %standard-phases - (delete 'configure)))) + (list + #:test-target "test" + #:make-flags #~(list (string-append "CC=" #$(cc-for-target)) + (string-append "prefix=" #$output)) + #:phases + #~(modify-phases %standard-phases + (delete 'configure)))) (native-inputs (list graphviz)) (home-page "https://github.com/lindenb/makefile2graph") From ca5fae4f26f2f35412a96fe2042883341ca62182 Mon Sep 17 00:00:00 2001 From: Zheng Junjie Date: Wed, 6 Sep 2023 18:51:08 +0800 Subject: [PATCH 236/268] gnu: uncrustify: Update to 0.77.1. MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * gnu/packages/code.scm (uncrustify): Update to 0.77.1. Signed-off-by: Ludovic Courtès --- gnu/packages/code.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/code.scm b/gnu/packages/code.scm index 4335c57150..a9e94dab25 100644 --- a/gnu/packages/code.scm +++ b/gnu/packages/code.scm @@ -794,7 +794,7 @@ independent targets.") (define-public uncrustify (package (name "uncrustify") - (version "0.75.1") + (version "0.77.1") (source (origin (method git-fetch) (uri (git-reference @@ -803,7 +803,7 @@ independent targets.") (file-name (git-file-name name version)) (sha256 (base32 - "1mzzzd4alajjdshbjd2a5mddqcpag8yyss72n09mfpialzyf7g60")))) + "17x9p5pqgzjchi9xhskp4kq7ag4chmsgbkvwym5m2b9zwm6qykpm")))) (build-system cmake-build-system) (native-inputs `(("python" ,python-wrapper))) From c0bfa12666cc6dc706981c76b9ee5c7f9006932d Mon Sep 17 00:00:00 2001 From: Zheng Junjie Date: Wed, 6 Sep 2023 18:51:09 +0800 Subject: [PATCH 237/268] gnu: uncrustify: use new style and gexp. MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * gnu/packages/code.scm (uncrustify): use new style and gexp. [native-inputs]: remove label. [arguments]: use gexp and remove tail #t. Signed-off-by: Ludovic Courtès --- gnu/packages/code.scm | 24 +++++++++++------------- 1 file changed, 11 insertions(+), 13 deletions(-) diff --git a/gnu/packages/code.scm b/gnu/packages/code.scm index a9e94dab25..b716f32599 100644 --- a/gnu/packages/code.scm +++ b/gnu/packages/code.scm @@ -805,20 +805,18 @@ independent targets.") (base32 "17x9p5pqgzjchi9xhskp4kq7ag4chmsgbkvwym5m2b9zwm6qykpm")))) (build-system cmake-build-system) - (native-inputs - `(("python" ,python-wrapper))) + (native-inputs (list python-wrapper)) (arguments - `(#:phases - (modify-phases %standard-phases - (add-after 'unpack 'unpack-etc - (lambda* (#:key inputs outputs #:allow-other-keys) - ;; Configuration samples are not installed by default. - (let* ((output (assoc-ref outputs "out")) - (etcdir (string-append output "/etc"))) - (for-each (lambda (l) - (install-file l etcdir)) - (find-files "etc" "\\.cfg$"))) - #t))))) + (list #:phases + #~(modify-phases %standard-phases + (add-after 'unpack 'unpack-etc + (lambda* (#:key inputs outputs #:allow-other-keys) + ;; Configuration samples are not installed by default. + (let* ((output (assoc-ref outputs "out")) + (etcdir (string-append output "/etc"))) + (for-each (lambda (l) + (install-file l etcdir)) + (find-files "etc" "\\.cfg$")))))))) (home-page "https://uncrustify.sourceforge.net/") (synopsis "Code formatter for C and other related languages") (description From 50725212f0578b98ad4bac9786ca954ae22125cc Mon Sep 17 00:00:00 2001 From: Sughosha Date: Fri, 16 Jun 2023 14:44:00 +0000 Subject: [PATCH 238/268] gnu: dpf-plugins: Update to 1.7. MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Message-Id: <23da89c3cbf2358ac70d387ebd714abe03b6758e.1686926462.git.sughosha@proton.me> From: Sughosha Date: Fri, 16 Jun 2023 16:22:57 +0200 Subject: [PATCH 1/2] gnu: dpf-plugins: Update to 1.7. * gnu/packages/music.scm (dpf-plugins): Update to 1.7. Signed-off-by: Ludovic Courtès --- gnu/packages/music.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/music.scm b/gnu/packages/music.scm index cf74a2cd36..3f17a054ca 100644 --- a/gnu/packages/music.scm +++ b/gnu/packages/music.scm @@ -6517,7 +6517,7 @@ curl/include/curl/curl.h") (define-public dpf-plugins (package (name "dpf-plugins") - (version "1.4") + (version "1.7") (source (origin (method git-fetch) @@ -6527,7 +6527,7 @@ curl/include/curl/curl.h") (commit (string-append "v" version)))) (file-name (git-file-name name version)) (sha256 - (base32 "0y7qvpfm34g6f7d786c6c9043dlbg5c4h71l2s24dsc9m8i7x2ww")))) + (base32 "082f3f78x6k58j78mqr57qhw40f5s8fmcbkhl36nn3vbcsa07bzg")))) (build-system gnu-build-system) (arguments `(#:tests? #f ; no "check" target From 0a6ad454a3ec01e402403f500bb90fe55fc232b7 Mon Sep 17 00:00:00 2001 From: "Artyom V. Poptsov" Date: Sat, 8 Jul 2023 11:50:16 +0300 Subject: [PATCH 239/268] gnu: nanosvg: Add a patch for PrusaSlicer 2.6. MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * gnu/packages/graphics.scm (nanosvg): Add a patch that is required to build PrusaSlicer 2.6. * gnu/packages/patches/nanosvg-prusa-slicer.patch: New file. * gnu/local.mk (dist_patch_DATA): Add it. Signed-off-by: Ludovic Courtès --- gnu/local.mk | 1 + gnu/packages/graphics.scm | 8 +- .../patches/nanosvg-prusa-slicer.patch | 248 ++++++++++++++++++ 3 files changed, 256 insertions(+), 1 deletion(-) create mode 100644 gnu/packages/patches/nanosvg-prusa-slicer.patch diff --git a/gnu/local.mk b/gnu/local.mk index 8dd363dd79..0d6e6846ee 100644 --- a/gnu/local.mk +++ b/gnu/local.mk @@ -1636,6 +1636,7 @@ dist_patch_DATA = \ %D%/packages/patches/mutter-fix-inverted-test.patch \ %D%/packages/patches/mutt-store-references.patch \ %D%/packages/patches/m17n-lib-1.8.0-use-pkg-config-for-freetype.patch \ + %D%/packages/patches/nanosvg-prusa-slicer.patch \ %D%/packages/patches/nautilus-extension-search-path.patch \ %D%/packages/patches/ncompress-fix-softlinks.patch \ %D%/packages/patches/ncftp-reproducible.patch \ diff --git a/gnu/packages/graphics.scm b/gnu/packages/graphics.scm index 8edc93f702..9362666274 100644 --- a/gnu/packages/graphics.scm +++ b/gnu/packages/graphics.scm @@ -36,6 +36,7 @@ ;;; Copyright © 2023 Sharlatan Hellseher ;;; Copyright © 2023 David Thompson ;;; Copyright © 2023 Eric Bavier +;;; Copyright © 2023 Artyom V. Poptsov ;;; ;;; This file is part of GNU Guix. ;;; @@ -2643,7 +2644,12 @@ a tetrahedral mesh, isovalue discretization and Lagrangian movement; (file-name (git-file-name name version)) (sha256 (base32 - "1pkzv75kavkhrbdd2kvq755jyr0vamgrfr7lc33dq3ipkzmqvs2l")))) + "1pkzv75kavkhrbdd2kvq755jyr0vamgrfr7lc33dq3ipkzmqvs2l")) + ;; This patch required to build PrusaSlicer 2.6. + ;; + ;; It is taken from + ;; + (patches (search-patches "nanosvg-prusa-slicer.patch")))) (build-system cmake-build-system) (arguments (list #:tests? #f ;no test suite #:configure-flags #~(list "-DBUILD_SHARED_LIBS=ON"))) diff --git a/gnu/packages/patches/nanosvg-prusa-slicer.patch b/gnu/packages/patches/nanosvg-prusa-slicer.patch new file mode 100644 index 0000000000..dc11e9365c --- /dev/null +++ b/gnu/packages/patches/nanosvg-prusa-slicer.patch @@ -0,0 +1,248 @@ +From abcd277ea45e9098bed752cf9c6875b533c0892f Mon Sep 17 00:00:00 2001 +From: AlbrechtS +Date: Sun, 4 Feb 2018 23:47:38 +0100 +Subject: [PATCH] Modify rasterizer to support non-square X,Y axes scaling. + +Add new function nsvgRasterizeXY() similar to nsvgRasterize() but with +separate scaling factors for x-axis and y-axis. +--- + src/nanosvgrast.h | 78 +++++++++++++++++++++++++++++++---------------- + 1 file changed, 51 insertions(+), 27 deletions(-) + +diff --git a/src/nanosvgrast.h b/src/nanosvgrast.h +index 17ba3b0..a83db27 100644 +--- a/src/nanosvgrast.h ++++ b/src/nanosvgrast.h +@@ -22,6 +22,12 @@ + * + */ + ++/* Modified by FLTK to support non-square X,Y axes scaling. ++ * ++ * Added: nsvgRasterizeXY() ++*/ ++ ++ + #ifndef NANOSVGRAST_H + #define NANOSVGRAST_H + +@@ -46,6 +52,9 @@ typedef struct NSVGrasterizer NSVGrasterizer; + unsigned char* img = malloc(w*h*4); + // Rasterize + nsvgRasterize(rast, image, 0,0,1, img, w, h, w*4); ++ ++ // For non-square X,Y scaling, use ++ nsvgRasterizeXY(rast, image, 0,0,1,1, img, w, h, w*4); + */ + + // Allocated rasterizer context. +@@ -55,7 +64,7 @@ NSVGrasterizer* nsvgCreateRasterizer(void); + // r - pointer to rasterizer context + // image - pointer to image to rasterize + // tx,ty - image offset (applied after scaling) +-// scale - image scale ++// scale - image scale (assumes square aspect ratio) + // dst - pointer to destination image data, 4 bytes per pixel (RGBA) + // w - width of the image to render + // h - height of the image to render +@@ -64,6 +73,12 @@ void nsvgRasterize(NSVGrasterizer* r, + NSVGimage* image, float tx, float ty, float scale, + unsigned char* dst, int w, int h, int stride); + ++// As above, but allow X and Y axes to scale independently for non-square aspects ++void nsvgRasterizeXY(NSVGrasterizer* r, ++ NSVGimage* image, float tx, float ty, ++ float sx, float sy, ++ unsigned char* dst, int w, int h, int stride); ++ + // Deletes rasterizer context. + void nsvgDeleteRasterizer(NSVGrasterizer*); + +@@ -370,7 +385,7 @@ static void nsvg__flattenCubicBez(NSVGrasterizer* r, + nsvg__flattenCubicBez(r, x1234,y1234, x234,y234, x34,y34, x4,y4, level+1, type); + } + +-static void nsvg__flattenShape(NSVGrasterizer* r, NSVGshape* shape, float scale) ++static void nsvg__flattenShape(NSVGrasterizer* r, NSVGshape* shape, float sx, float sy) + { + int i, j; + NSVGpath* path; +@@ -378,13 +393,13 @@ static void nsvg__flattenShape(NSVGrasterizer* r, NSVGshape* shape, float scale) + for (path = shape->paths; path != NULL; path = path->next) { + r->npoints = 0; + // Flatten path +- nsvg__addPathPoint(r, path->pts[0]*scale, path->pts[1]*scale, 0); ++ nsvg__addPathPoint(r, path->pts[0]*sx, path->pts[1]*sy, 0); + for (i = 0; i < path->npts-1; i += 3) { + float* p = &path->pts[i*2]; +- nsvg__flattenCubicBez(r, p[0]*scale,p[1]*scale, p[2]*scale,p[3]*scale, p[4]*scale,p[5]*scale, p[6]*scale,p[7]*scale, 0, 0); ++ nsvg__flattenCubicBez(r, p[0]*sx,p[1]*sy, p[2]*sx,p[3]*sy, p[4]*sx,p[5]*sy, p[6]*sx,p[7]*sy, 0, 0); + } + // Close path +- nsvg__addPathPoint(r, path->pts[0]*scale, path->pts[1]*scale, 0); ++ nsvg__addPathPoint(r, path->pts[0]*sx, path->pts[1]*sy, 0); + // Build edges + for (i = 0, j = r->npoints-1; i < r->npoints; j = i++) + nsvg__addEdge(r, r->points[j].x, r->points[j].y, r->points[i].x, r->points[i].y); +@@ -734,7 +749,7 @@ static void nsvg__prepareStroke(NSVGrasterizer* r, float miterLimit, int lineJoi + } + } + +-static void nsvg__flattenShapeStroke(NSVGrasterizer* r, NSVGshape* shape, float scale) ++static void nsvg__flattenShapeStroke(NSVGrasterizer* r, NSVGshape* shape, float sx, float sy) + { + int i, j, closed; + NSVGpath* path; +@@ -742,15 +757,16 @@ static void nsvg__flattenShapeStroke(NSVGrasterizer* r, NSVGshape* shape, float + float miterLimit = shape->miterLimit; + int lineJoin = shape->strokeLineJoin; + int lineCap = shape->strokeLineCap; +- float lineWidth = shape->strokeWidth * scale; ++ const float sw = (sx + sy) / 2; // average scaling factor ++ const float lineWidth = shape->strokeWidth * sw; // FIXME (?) + + for (path = shape->paths; path != NULL; path = path->next) { + // Flatten path + r->npoints = 0; +- nsvg__addPathPoint(r, path->pts[0]*scale, path->pts[1]*scale, NSVG_PT_CORNER); ++ nsvg__addPathPoint(r, path->pts[0]*sx, path->pts[1]*sy, NSVG_PT_CORNER); + for (i = 0; i < path->npts-1; i += 3) { + float* p = &path->pts[i*2]; +- nsvg__flattenCubicBez(r, p[0]*scale,p[1]*scale, p[2]*scale,p[3]*scale, p[4]*scale,p[5]*scale, p[6]*scale,p[7]*scale, 0, NSVG_PT_CORNER); ++ nsvg__flattenCubicBez(r, p[0]*sx,p[1]*sy, p[2]*sx,p[3]*sy, p[4]*sx,p[5]*sy, p[6]*sx,p[7]*sy, 0, NSVG_PT_CORNER); + } + if (r->npoints < 2) + continue; +@@ -796,7 +812,7 @@ static void nsvg__flattenShapeStroke(NSVGrasterizer* r, NSVGshape* shape, float + dashOffset -= shape->strokeDashArray[idash]; + idash = (idash + 1) % shape->strokeDashCount; + } +- dashLen = (shape->strokeDashArray[idash] - dashOffset) * scale; ++ dashLen = (shape->strokeDashArray[idash] - dashOffset) * sw; + + for (j = 1; j < r->npoints2; ) { + float dx = r->points2[j].x - cur.x; +@@ -818,7 +834,7 @@ static void nsvg__flattenShapeStroke(NSVGrasterizer* r, NSVGshape* shape, float + // Advance dash pattern + dashState = !dashState; + idash = (idash+1) % shape->strokeDashCount; +- dashLen = shape->strokeDashArray[idash] * scale; ++ dashLen = shape->strokeDashArray[idash] * sw; + // Restart + cur.x = x; + cur.y = y; +@@ -987,7 +1003,7 @@ static inline int nsvg__div255(int x) + } + + static void nsvg__scanlineSolid(unsigned char* dst, int count, unsigned char* cover, int x, int y, +- float tx, float ty, float scale, NSVGcachedPaint* cache) ++ float tx, float ty, float sx, float sy, NSVGcachedPaint* cache) + { + + if (cache->type == NSVG_PAINT_COLOR) { +@@ -1028,9 +1044,9 @@ static void nsvg__scanlineSolid(unsigned char* dst, int count, unsigned char* co + int i, cr, cg, cb, ca; + unsigned int c; + +- fx = ((float)x - tx) / scale; +- fy = ((float)y - ty) / scale; +- dx = 1.0f / scale; ++ fx = ((float)x - tx) / sx; ++ fy = ((float)y - ty) / sy; ++ dx = 1.0f / sx; + + for (i = 0; i < count; i++) { + int r,g,b,a,ia; +@@ -1073,9 +1089,9 @@ static void nsvg__scanlineSolid(unsigned char* dst, int count, unsigned char* co + int i, cr, cg, cb, ca; + unsigned int c; + +- fx = ((float)x - tx) / scale; +- fy = ((float)y - ty) / scale; +- dx = 1.0f / scale; ++ fx = ((float)x - tx) / sx; ++ fy = ((float)y - ty) / sy; ++ dx = 1.0f / sx; + + for (i = 0; i < count; i++) { + int r,g,b,a,ia; +@@ -1114,7 +1130,7 @@ static void nsvg__scanlineSolid(unsigned char* dst, int count, unsigned char* co + } + } + +-static void nsvg__rasterizeSortedEdges(NSVGrasterizer *r, float tx, float ty, float scale, NSVGcachedPaint* cache, char fillRule) ++static void nsvg__rasterizeSortedEdges(NSVGrasterizer *r, float tx, float ty, float sx, float sy, NSVGcachedPaint* cache, char fillRule) + { + NSVGactiveEdge *active = NULL; + int y, s; +@@ -1196,7 +1212,7 @@ static void nsvg__rasterizeSortedEdges(NSVGrasterizer *r, float tx, float ty, fl + if (xmin < 0) xmin = 0; + if (xmax > r->width-1) xmax = r->width-1; + if (xmin <= xmax) { +- nsvg__scanlineSolid(&r->bitmap[y * r->stride] + xmin*4, xmax-xmin+1, &r->scanline[xmin], xmin, y, tx,ty, scale, cache); ++ nsvg__scanlineSolid(&r->bitmap[y * r->stride] + xmin*4, xmax-xmin+1, &r->scanline[xmin], xmin, y, tx,ty, sx, sy, cache); + } + } + +@@ -1364,8 +1380,9 @@ static void dumpEdges(NSVGrasterizer* r, const char* name) + } + */ + +-void nsvgRasterize(NSVGrasterizer* r, +- NSVGimage* image, float tx, float ty, float scale, ++void nsvgRasterizeXY(NSVGrasterizer* r, ++ NSVGimage* image, float tx, float ty, ++ float sx, float sy, + unsigned char* dst, int w, int h, int stride) + { + NSVGshape *shape = NULL; +@@ -1396,7 +1413,7 @@ void nsvgRasterize(NSVGrasterizer* r, + r->freelist = NULL; + r->nedges = 0; + +- nsvg__flattenShape(r, shape, scale); ++ nsvg__flattenShape(r, shape, sx, sy); + + // Scale and translate edges + for (i = 0; i < r->nedges; i++) { +@@ -1414,14 +1431,14 @@ void nsvgRasterize(NSVGrasterizer* r, + // now, traverse the scanlines and find the intersections on each scanline, use non-zero rule + nsvg__initPaint(&cache, &shape->fill, shape->opacity); + +- nsvg__rasterizeSortedEdges(r, tx,ty,scale, &cache, shape->fillRule); ++ nsvg__rasterizeSortedEdges(r, tx,ty, sx, sy, &cache, shape->fillRule); + } +- if (shape->stroke.type != NSVG_PAINT_NONE && (shape->strokeWidth * scale) > 0.01f) { ++ if (shape->stroke.type != NSVG_PAINT_NONE && (shape->strokeWidth * sx) > 0.01f) { + nsvg__resetPool(r); + r->freelist = NULL; + r->nedges = 0; + +- nsvg__flattenShapeStroke(r, shape, scale); ++ nsvg__flattenShapeStroke(r, shape, sx, sy); + + // dumpEdges(r, "edge.svg"); + +@@ -1441,7 +1458,7 @@ void nsvgRasterize(NSVGrasterizer* r, + // now, traverse the scanlines and find the intersections on each scanline, use non-zero rule + nsvg__initPaint(&cache, &shape->stroke, shape->opacity); + +- nsvg__rasterizeSortedEdges(r, tx,ty,scale, &cache, NSVG_FILLRULE_NONZERO); ++ nsvg__rasterizeSortedEdges(r, tx,ty,sx, sy, &cache, NSVG_FILLRULE_NONZERO); + } + } + +@@ -1453,6 +1470,13 @@ void nsvgRasterize(NSVGrasterizer* r, + r->stride = 0; + } + ++void nsvgRasterize(NSVGrasterizer* r, ++ NSVGimage* image, float tx, float ty, float scale, ++ unsigned char* dst, int w, int h, int stride) ++{ ++ nsvgRasterizeXY(r,image, tx, ty, scale, scale, dst, w, h, stride); ++} ++ + #endif // NANOSVGRAST_IMPLEMENTATION + + #endif // NANOSVGRAST_H From a5d207f0db20933501712c037703cb7cb27adbbc Mon Sep 17 00:00:00 2001 From: Zheng Junjie Date: Wed, 6 Sep 2023 23:43:53 +0800 Subject: [PATCH 240/268] gnu: kwin: Unwrap executable name for desktop file search. MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit see https://github.com/NixOS/nixpkgs/pull/116549 * gnu/packages/patches/kwin-unwrap-executable-name-for-dot-desktop-search.patch: New file. * gnu/local.mk (dist_patch_DATA): Add it. * gnu/packages/kde-plasma.scm (kwin)[origin]: Use it. Signed-off-by: Ludovic Courtès --- gnu/local.mk | 1 + gnu/packages/kde-plasma.scm | 1 + ...ecutable-name-for-dot-desktop-search.patch | 89 +++++++++++++++++++ 3 files changed, 91 insertions(+) create mode 100644 gnu/packages/patches/kwin-unwrap-executable-name-for-dot-desktop-search.patch diff --git a/gnu/local.mk b/gnu/local.mk index 0d6e6846ee..a94fce9248 100644 --- a/gnu/local.mk +++ b/gnu/local.mk @@ -1479,6 +1479,7 @@ dist_patch_DATA = \ %D%/packages/patches/kobodeluxe-midicon-segmentation-fault.patch \ %D%/packages/patches/kobodeluxe-graphics-window-signed-char.patch \ %D%/packages/patches/kodi-set-libcurl-ssl-parameters.patch \ + %D%/packages/patches/kwin-unwrap-executable-name-for-dot-desktop-search.patch\ %D%/packages/patches/kodi-mesa-eglchromium.patch \ %D%/packages/patches/laby-make-install.patch \ %D%/packages/patches/laby-use-tmpdir-from-runtime.patch \ diff --git a/gnu/packages/kde-plasma.scm b/gnu/packages/kde-plasma.scm index 11586a6ce2..331ab28cd1 100644 --- a/gnu/packages/kde-plasma.scm +++ b/gnu/packages/kde-plasma.scm @@ -1210,6 +1210,7 @@ KDE Frameworks components.") (method url-fetch) (uri (string-append "mirror://kde/stable/plasma/" version "/" name "-" version ".tar.xz")) + (patches (search-patches "kwin-unwrap-executable-name-for-dot-desktop-search.patch")) (sha256 (base32 "0bssp76lzqqlan5pfg6wjf4z9c6pl6p66ri8p82vqqw406x5bzyb")))) diff --git a/gnu/packages/patches/kwin-unwrap-executable-name-for-dot-desktop-search.patch b/gnu/packages/patches/kwin-unwrap-executable-name-for-dot-desktop-search.patch new file mode 100644 index 0000000000..8f67553138 --- /dev/null +++ b/gnu/packages/patches/kwin-unwrap-executable-name-for-dot-desktop-search.patch @@ -0,0 +1,89 @@ +origin patch from nixos. + +see https://github.com/NixOS/nixpkgs/blob/2457551a54ffbd93b7d8f84af8b8fb3aac5cbdd5/pkgs/desktops/plasma-5/kwin/0001-NixOS-Unwrap-executable-name-for-.desktop-search.patch + +--- + src/guix_utils.h | 41 +++++++++++++++++++++++++++++++++++++++++ + src/service_utils.h | 4 +++- + src/waylandwindow.cpp | 5 ++++- + 3 files changed, 48 insertions(+), 2 deletions(-) + create mode 100644 src/guix_utils.h + +diff a/src/guix_utils.h b/src/guix_utils.h +new file mode 100644 +index 0000000..726065d +--- /dev/null ++++ b/src/guix_utils.h +@@ -0,0 +1,24 @@ ++#ifndef GUIX_UTILS_H ++#define GUIX_UTILS_H ++ ++// kwin ++#include ++ ++namespace KWin ++{ ++ ++static QString unwrapExecutablePath(const QString &in_executablePath) ++{ ++ QString executablePath(in_executablePath); ++ ++ while (executablePath.endsWith("-real") && executablePath[executablePath.lastIndexOf("/")+1] == QChar('.')) { ++ executablePath.remove(executablePath.length() - 5, 5); ++ executablePath.remove(executablePath.lastIndexOf("/")+1, 1); ++ } ++ ++ return executablePath; ++} ++ ++}// namespace ++ ++#endif // GUIX_UTILS_H +diff a/src/utils/serviceutils.h b/src/utils/serviceutils.h +index 8a70c1f..475b15d 100644 +--- a/src/utils/serviceutils.h ++++ b/src/utils/serviceutils.h +@@ -19,6 +19,7 @@ + #include + //KF + #include ++#include "guix_utils.h" + + namespace KWin + { +@@ -26,8 +27,9 @@ namespace KWin + const static QString s_waylandInterfaceName = QStringLiteral("X-KDE-Wayland-Interfaces"); + const static QString s_dbusRestrictedInterfaceName = QStringLiteral("X-KDE-DBUS-Restricted-Interfaces"); + +-static QStringList fetchProcessServiceField(const QString &executablePath, const QString &fieldName) ++static QStringList fetchProcessServiceField(const QString &in_executablePath, const QString &fieldName) + { ++ const QString executablePath = unwrapExecutablePath(in_executablePath); + // needed to be able to use the logging category in a header static function + static QLoggingCategory KWIN_UTILS ("KWIN_UTILS", QtWarningMsg); + const auto servicesFound = KApplicationTrader::query([&executablePath] (const KService::Ptr &service) { +diff a/src/waylandwindow.cpp b/src/waylandwindow.cpp +index fd2c0c1..ae8cf96 100644 +--- a/src/waylandwindow.cpp ++++ b/src/waylandwindow.cpp +@@ -10,6 +10,7 @@ + #include "screens.h" + #include "wayland_server.h" + #include "workspace.h" ++#include "guix_utils.h" + + #include + #include +@@ -173,7 +174,9 @@ void WaylandWindow::updateIcon() + + void WaylandWindow::updateResourceName() + { +- const QFileInfo fileInfo(surface()->client()->executablePath()); ++ const QString in_path = surface()->client()->executablePath(); ++ const QString path = unwrapExecutablePath(in_path); ++ const QFileInfo fileInfo(path); + if (fileInfo.exists()) { + const QByteArray executableFileName = fileInfo.fileName().toUtf8(); + setResourceClass(executableFileName, executableFileName); +-- +2.32.0 \ No newline at end of file From f59a1dc924f6cfd3bddb3dae2e56ffb585097b4e Mon Sep 17 00:00:00 2001 From: Hendursaga Date: Wed, 6 Sep 2023 14:38:56 -0400 Subject: [PATCH 241/268] gnu: armagetronad: Update to 0.2.9.1.1. MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * gnu/packages/games.scm (armagetronad): Update to 0.2.9.1.1. [inputs]: Add sdl-mixer to fix game audio. Signed-off-by: Ludovic Courtès --- gnu/packages/games.scm | 22 ++++++++++------------ 1 file changed, 10 insertions(+), 12 deletions(-) diff --git a/gnu/packages/games.scm b/gnu/packages/games.scm index 78063fa625..1167443825 100644 --- a/gnu/packages/games.scm +++ b/gnu/packages/games.scm @@ -491,27 +491,25 @@ Doom clone shooter game.") (define-public armagetronad (package (name "armagetronad") - (version "0.2.9.1.0") + (version "0.2.9.1.1") (source (origin (method url-fetch) (uri (string-append "mirror://sourceforge/armagetronad/stable/" version "/armagetronad-" version ".tbz")) (sha256 (base32 - "18gn4sg4j5sw38ngb90sl50raliplrsgjcvy8fjwry733k0cgdjr")))) + "0cpxvzbssyf45fmanp1d6l992wln8zkjx4z2flgx27fg1rqdw5zn")))) (build-system gnu-build-system) - (native-inputs - (list pkg-config)) - (inputs - (list libxml2 - sdl - sdl-image - freeglut - libpng - libjpeg-turbo)) + (native-inputs (list pkg-config)) + (inputs (list libxml2 + (sdl-union (list sdl sdl-image sdl-mixer)) + freeglut + libpng + libjpeg-turbo)) (home-page "https://www.armagetronad.org") (synopsis "Tron clone in 3D") - (description "Armagetron Advanced is a multiplayer game in 3d that + (description + "Armagetron Advanced is a multiplayer game in 3d that attempts to emulate and expand on the lightcycle sequence from the movie Tron. It's an old school arcade game slung into the 21st century. Highlights include a customizable playing arena, HUD, unique graphics, and AI bots. For From c057507a0bac3ee5885a4ef055c9fea44683a1c3 Mon Sep 17 00:00:00 2001 From: Andy Tai Date: Wed, 6 Sep 2023 20:56:20 -0700 Subject: [PATCH 242/268] gnu: icewm: Update to 3.4.1 MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * gnu/packages/wm.scm (icewm): Update to 3.4.1 Signed-off-by: Ludovic Courtès --- 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 aaff618248..9ef60ec668 100644 --- a/gnu/packages/wm.scm +++ b/gnu/packages/wm.scm @@ -789,7 +789,7 @@ desktop environment.") (define-public icewm (package (name "icewm") - (version "3.3.4") + (version "3.4.1") (source (origin (method url-fetch) (uri (string-append @@ -797,7 +797,7 @@ desktop environment.") version "/icewm-" version ".tar.lz")) (sha256 (base32 - "124w00yq35mj859nf321bpy36ij7a0kblcg95axxahz4l6fhxfxf")))) + "0fr79i6r2sjr27lv4wik8lvcnrrapd28lzhy4gnqffzds0sqx64r")))) (build-system gnu-build-system) (native-inputs (list pkg-config)) (inputs (list fontconfig From 9620b9d29858c05c774c15c3011bd610ce7ab671 Mon Sep 17 00:00:00 2001 From: Simon South Date: Thu, 7 Sep 2023 12:37:50 -0400 Subject: [PATCH 243/268] gnu: libftdi: Update package style. MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * gnu/packages/libftdi.scm: Re-order #:use-module statements. (libftdi): Wrap long lines; reformat gently. [license]: Use "license:" prefix. Signed-off-by: Ludovic Courtès --- gnu/packages/libftdi.scm | 19 +++++++++---------- 1 file changed, 9 insertions(+), 10 deletions(-) diff --git a/gnu/packages/libftdi.scm b/gnu/packages/libftdi.scm index e39e0b3d71..4cfa1d3424 100644 --- a/gnu/packages/libftdi.scm +++ b/gnu/packages/libftdi.scm @@ -18,12 +18,12 @@ ;;; along with GNU Guix. If not, see . (define-module (gnu packages libftdi) - #:use-module (guix licenses) + #:use-module (guix build-system cmake) #:use-module (guix download) + #:use-module ((guix licenses) #:prefix license:) #:use-module (guix packages) #:use-module (gnu packages) - #:use-module (gnu packages libusb) - #:use-module (guix build-system cmake)) + #:use-module (gnu packages libusb)) (define-public libftdi (package @@ -32,18 +32,17 @@ (source (origin (method url-fetch) (uri (string-append - "http://www.intra2net.com/en/developer/libftdi/download/libftdi1-" - version ".tar.bz2")) + "http://www.intra2net.com/en/developer/libftdi/download/" + "libftdi1-" version ".tar.bz2")) (sha256 (base32 "0x0vncf6i92slgrn0h7ghkskqbglbs534220qa84d0qg114zndpc")))) (build-system cmake-build-system) (propagated-inputs - (list libusb)) ; required by libftdi1.pc + (list libusb)) ; required by libftdi1.pc (home-page "https://www.intra2net.com/en/developer/libftdi/") (synopsis "FTDI USB driver with bitbang mode") (description - "libFTDI is a library to talk to FTDI chips: FT232BM, -FT245BM, FT2232C, FT2232D, FT245R and FT232H including the popular -bitbangmode.") - (license lgpl2.1))) + "libFTDI is a library to talk to FTDI chips: FT232BM, FT245BM, FT2232C, +FT2232D, FT245R and FT232H including the popular bitbangmode.") + (license license:lgpl2.1))) From ea2376a4f5f0bd82ac0b74521b656123fc39fba5 Mon Sep 17 00:00:00 2001 From: Simon South Date: Thu, 7 Sep 2023 12:37:51 -0400 Subject: [PATCH 244/268] gnu: libftdi: Use HTTPS for package source. MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * gnu/packages/libftdi.scm (libftdi)[source]: Use HTTPS. Signed-off-by: Ludovic Courtès --- gnu/packages/libftdi.scm | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/gnu/packages/libftdi.scm b/gnu/packages/libftdi.scm index 4cfa1d3424..b881aa5cc2 100644 --- a/gnu/packages/libftdi.scm +++ b/gnu/packages/libftdi.scm @@ -32,7 +32,7 @@ (source (origin (method url-fetch) (uri (string-append - "http://www.intra2net.com/en/developer/libftdi/download/" + "https://www.intra2net.com/en/developer/libftdi/download/" "libftdi1-" version ".tar.bz2")) (sha256 (base32 From dcef5c7179816583bc008f4719092a0171d791dd Mon Sep 17 00:00:00 2001 From: Simon South Date: Thu, 7 Sep 2023 12:37:52 -0400 Subject: [PATCH 245/268] gnu: libftdi: Do not build example programs. MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * gnu/packages/libftdi.scm (libftdi)[arguments]: Add with "-DEXAMPLES" configure flag. Signed-off-by: Ludovic Courtès --- gnu/packages/libftdi.scm | 3 +++ 1 file changed, 3 insertions(+) diff --git a/gnu/packages/libftdi.scm b/gnu/packages/libftdi.scm index b881aa5cc2..74df12a354 100644 --- a/gnu/packages/libftdi.scm +++ b/gnu/packages/libftdi.scm @@ -20,6 +20,7 @@ (define-module (gnu packages libftdi) #:use-module (guix build-system cmake) #:use-module (guix download) + #:use-module (guix gexp) #:use-module ((guix licenses) #:prefix license:) #:use-module (guix packages) #:use-module (gnu packages) @@ -38,6 +39,8 @@ (base32 "0x0vncf6i92slgrn0h7ghkskqbglbs534220qa84d0qg114zndpc")))) (build-system cmake-build-system) + (arguments + (list #:configure-flags #~(list "-DEXAMPLES=OFF"))) (propagated-inputs (list libusb)) ; required by libftdi1.pc (home-page "https://www.intra2net.com/en/developer/libftdi/") From ea67b8571d0ed2132956d0c2857b26faf835f0c9 Mon Sep 17 00:00:00 2001 From: Simon South Date: Thu, 7 Sep 2023 12:37:53 -0400 Subject: [PATCH 246/268] gnu: libftdi: Install libraries to /lib instead of /lib64. MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * gnu/packages/libftdi.scm (libftdi)[arguments]<#:configure-flags>: Add "-DLIB_SUFFIX". Signed-off-by: Ludovic Courtès --- gnu/packages/libftdi.scm | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/gnu/packages/libftdi.scm b/gnu/packages/libftdi.scm index 74df12a354..1e97793a93 100644 --- a/gnu/packages/libftdi.scm +++ b/gnu/packages/libftdi.scm @@ -40,7 +40,10 @@ "0x0vncf6i92slgrn0h7ghkskqbglbs534220qa84d0qg114zndpc")))) (build-system cmake-build-system) (arguments - (list #:configure-flags #~(list "-DEXAMPLES=OFF"))) + (list + #:configure-flags + #~(list "-DEXAMPLES=OFF" + "-DLIB_SUFFIX=''"))) ; place libraries in /lib, not /lib64 (propagated-inputs (list libusb)) ; required by libftdi1.pc (home-page "https://www.intra2net.com/en/developer/libftdi/") From d92c71f1d63cd89e4805c4dfde8f4deed9d037cf Mon Sep 17 00:00:00 2001 From: Simon South Date: Thu, 7 Sep 2023 12:37:54 -0400 Subject: [PATCH 247/268] gnu: libftdi: Build ftdi_eeprom. MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * gnu/packages/libftdi.scm (libftdi)[arguments]<#:configure-flags>: Add "-DCMAKE_INSTALL_DOCDIR". [native-inputs]: Add with pkg-config. [inputs]: Add with libconfuse. [license]: Add GPL version 2. Signed-off-by: Ludovic Courtès --- gnu/packages/libftdi.scm | 15 ++++++++++++--- 1 file changed, 12 insertions(+), 3 deletions(-) diff --git a/gnu/packages/libftdi.scm b/gnu/packages/libftdi.scm index 1e97793a93..b3fb717905 100644 --- a/gnu/packages/libftdi.scm +++ b/gnu/packages/libftdi.scm @@ -24,7 +24,9 @@ #:use-module ((guix licenses) #:prefix license:) #:use-module (guix packages) #:use-module (gnu packages) - #:use-module (gnu packages libusb)) + #:use-module (gnu packages libusb) + #:use-module (gnu packages pkg-config) + #:use-module (gnu packages textutils)) (define-public libftdi (package @@ -42,8 +44,14 @@ (arguments (list #:configure-flags - #~(list "-DEXAMPLES=OFF" + #~(list (string-append "-DCMAKE_INSTALL_DOCDIR=" + #$output "/share/doc/" #$name "-" #$version) + "-DEXAMPLES=OFF" "-DLIB_SUFFIX=''"))) ; place libraries in /lib, not /lib64 + (native-inputs + (list pkg-config)) + (inputs + (list libconfuse)) (propagated-inputs (list libusb)) ; required by libftdi1.pc (home-page "https://www.intra2net.com/en/developer/libftdi/") @@ -51,4 +59,5 @@ (description "libFTDI is a library to talk to FTDI chips: FT232BM, FT245BM, FT2232C, FT2232D, FT245R and FT232H including the popular bitbangmode.") - (license license:lgpl2.1))) + (license (list license:gpl2 ; ftdi_eeprom + license:lgpl2.1)))) ; main library From fce3d00cdb045fe8714be62d67ba3a0c303f4ea0 Mon Sep 17 00:00:00 2001 From: Simon South Date: Thu, 7 Sep 2023 12:37:55 -0400 Subject: [PATCH 248/268] gnu: libftdi: Build C++ bindings. MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Enabling the C++ bindings allows the test suite to be run, although this fails without access to the host's USB interface. * gnu/packages/libftdi.scm (libftdi)[arguments]: Add #:test-target, #:tests?. (inputs): Add boost. Signed-off-by: Ludovic Courtès --- gnu/packages/libftdi.scm | 9 ++++++--- 1 file changed, 6 insertions(+), 3 deletions(-) diff --git a/gnu/packages/libftdi.scm b/gnu/packages/libftdi.scm index b3fb717905..0a996b05e7 100644 --- a/gnu/packages/libftdi.scm +++ b/gnu/packages/libftdi.scm @@ -24,6 +24,7 @@ #:use-module ((guix licenses) #:prefix license:) #:use-module (guix packages) #:use-module (gnu packages) + #:use-module (gnu packages boost) #:use-module (gnu packages libusb) #:use-module (gnu packages pkg-config) #:use-module (gnu packages textutils)) @@ -47,11 +48,13 @@ #~(list (string-append "-DCMAKE_INSTALL_DOCDIR=" #$output "/share/doc/" #$name "-" #$version) "-DEXAMPLES=OFF" - "-DLIB_SUFFIX=''"))) ; place libraries in /lib, not /lib64 + "-DLIB_SUFFIX=''") ; place libraries in /lib, not /lib64 + #:test-target "check" + #:tests? #f)) ; tests fail without access to USB (native-inputs (list pkg-config)) (inputs - (list libconfuse)) + (list boost libconfuse)) (propagated-inputs (list libusb)) ; required by libftdi1.pc (home-page "https://www.intra2net.com/en/developer/libftdi/") @@ -59,5 +62,5 @@ (description "libFTDI is a library to talk to FTDI chips: FT232BM, FT245BM, FT2232C, FT2232D, FT245R and FT232H including the popular bitbangmode.") - (license (list license:gpl2 ; ftdi_eeprom + (license (list license:gpl2 ; ftdi_eeprom, C++ bindings license:lgpl2.1)))) ; main library From 856eeedcbc65add655a40878ebed81aecd44a377 Mon Sep 17 00:00:00 2001 From: Simon South Date: Thu, 7 Sep 2023 12:37:56 -0400 Subject: [PATCH 249/268] gnu: libftdi: Build Python bindings. MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * gnu/packages/libftdi.scm (libftdi)[outputs]: Add "python". [arguments]<#:phases>: Add with "install-python-binding" phase. [native-inputs]: Add python, swig. Signed-off-by: Ludovic Courtès --- gnu/packages/libftdi.scm | 24 +++++++++++++++++++++++- 1 file changed, 23 insertions(+), 1 deletion(-) diff --git a/gnu/packages/libftdi.scm b/gnu/packages/libftdi.scm index 0a996b05e7..773b0ec73e 100644 --- a/gnu/packages/libftdi.scm +++ b/gnu/packages/libftdi.scm @@ -1,6 +1,7 @@ ;;; GNU Guix --- Functional package management for GNU ;;; Copyright © 2014 Manolis Fragkiskos Ragkousis ;;; Copyright © 2018 Tobias Geerinckx-Rice +;;; Copyright © 2023 Simon South ;;; ;;; This file is part of GNU Guix. ;;; @@ -18,15 +19,19 @@ ;;; along with GNU Guix. If not, see . (define-module (gnu packages libftdi) + #:use-module (guix build utils) #:use-module (guix build-system cmake) #:use-module (guix download) #:use-module (guix gexp) #:use-module ((guix licenses) #:prefix license:) #:use-module (guix packages) + #:use-module (guix utils) #:use-module (gnu packages) #:use-module (gnu packages boost) #:use-module (gnu packages libusb) #:use-module (gnu packages pkg-config) + #:use-module (gnu packages python) + #:use-module (gnu packages swig) #:use-module (gnu packages textutils)) (define-public libftdi @@ -42,6 +47,7 @@ (base32 "0x0vncf6i92slgrn0h7ghkskqbglbs534220qa84d0qg114zndpc")))) (build-system cmake-build-system) + (outputs '("out" "python")) (arguments (list #:configure-flags @@ -49,10 +55,26 @@ #$output "/share/doc/" #$name "-" #$version) "-DEXAMPLES=OFF" "-DLIB_SUFFIX=''") ; place libraries in /lib, not /lib64 + #:phases + #~(modify-phases %standard-phases + (add-after 'install 'install-python-binding + (lambda _ + (let* ((python-version + #$(version-major+minor (package-version python))) + (python-lib-path + (string-append "/lib/python" python-version))) + (mkdir-p (string-append #$output:python "/lib")) + (mkdir-p (string-append #$output:python "/share/libftdi")) + (rename-file (string-append #$output python-lib-path) + (string-append #$output:python python-lib-path)) + (rename-file (string-append #$output + "/share/libftdi/examples") + (string-append #$output:python + "/share/libftdi/examples")))))) #:test-target "check" #:tests? #f)) ; tests fail without access to USB (native-inputs - (list pkg-config)) + (list pkg-config python swig)) (inputs (list boost libconfuse)) (propagated-inputs From 6c4868aca9e098fd7c830ba681ae0735aa752bdd Mon Sep 17 00:00:00 2001 From: Simon South Date: Thu, 7 Sep 2023 12:37:57 -0400 Subject: [PATCH 250/268] gnu: libftdi: Update to 1.5. MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * gnu/packages/patches/libftdi-fix-paths-when-FTDIPP-set.patch: New file. * gnu/local.mk (dist_patch_DATA): Add it. * gnu/packages/libftdi.scm (libftdi): Update to 1.5. [source]: Apply patch. [arguments]<#:configure-flags>: Add "-DFTDIPP", "-DPYTHON_BINDINGS". Signed-off-by: Ludovic Courtès --- gnu/local.mk | 1 + gnu/packages/libftdi.scm | 10 +++-- .../libftdi-fix-paths-when-FTDIPP-set.patch | 39 +++++++++++++++++++ 3 files changed, 47 insertions(+), 3 deletions(-) create mode 100644 gnu/packages/patches/libftdi-fix-paths-when-FTDIPP-set.patch diff --git a/gnu/local.mk b/gnu/local.mk index a94fce9248..4c3de24d73 100644 --- a/gnu/local.mk +++ b/gnu/local.mk @@ -1449,6 +1449,7 @@ dist_patch_DATA = \ %D%/packages/patches/json-c-0.12-CVE-2020-12762.patch \ %D%/packages/patches/julia-SOURCE_DATE_EPOCH-mtime.patch \ %D%/packages/patches/julia-Use-MPFR-4.2.patch \ + %D%/packages/patches/libftdi-fix-paths-when-FTDIPP-set.patch \ %D%/packages/patches/libgeotiff-fix-tests-with-proj-9.1.1.patch \ %D%/packages/patches/libobjc2-unbundle-robin-map.patch \ %D%/packages/patches/librime-fix-build-with-gcc10.patch \ diff --git a/gnu/packages/libftdi.scm b/gnu/packages/libftdi.scm index 773b0ec73e..bdfc635379 100644 --- a/gnu/packages/libftdi.scm +++ b/gnu/packages/libftdi.scm @@ -37,7 +37,7 @@ (define-public libftdi (package (name "libftdi") - (version "1.4") + (version "1.5") (source (origin (method url-fetch) (uri (string-append @@ -45,7 +45,9 @@ "libftdi1-" version ".tar.bz2")) (sha256 (base32 - "0x0vncf6i92slgrn0h7ghkskqbglbs534220qa84d0qg114zndpc")))) + "0jdh5r499wbz83vmpskczq5m3cfc1mcv8xqisj5i95k1r3lr2w3w")) + (patches + (search-patches "libftdi-fix-paths-when-FTDIPP-set.patch")))) (build-system cmake-build-system) (outputs '("out" "python")) (arguments @@ -54,7 +56,9 @@ #~(list (string-append "-DCMAKE_INSTALL_DOCDIR=" #$output "/share/doc/" #$name "-" #$version) "-DEXAMPLES=OFF" - "-DLIB_SUFFIX=''") ; place libraries in /lib, not /lib64 + "-DFTDIPP=ON" + "-DLIB_SUFFIX=''" ; place libraries in /lib, not /lib64 + "-DPYTHON_BINDINGS=ON") #:phases #~(modify-phases %standard-phases (add-after 'install 'install-python-binding diff --git a/gnu/packages/patches/libftdi-fix-paths-when-FTDIPP-set.patch b/gnu/packages/patches/libftdi-fix-paths-when-FTDIPP-set.patch new file mode 100644 index 0000000000..0a81cceb26 --- /dev/null +++ b/gnu/packages/patches/libftdi-fix-paths-when-FTDIPP-set.patch @@ -0,0 +1,39 @@ +commit cdb28383402d248dbc6062f4391b038375c52385 +Author: Fabrice Fontaine +Date: Fri Jul 17 21:25:03 2020 +0200 + + CMakeLists.txt: fix paths when FTDIPP is set + + Use the same project name (i.e. libftdi1 and not libftdipp1) when FTDIPP + is enabled as suggested by Aurelien Jarno in + http://developer.intra2net.com/mailarchive/html/libftdi/2020/msg00044.html + + Without this change, the libftdi1.pc config file defines the include + path as /usr/local/include/libftdipp1 while the ftdi.h file is actually + installed in /usr/local/include/libftdi1 + + This is an issue for example for libsigrok which will fail on: + + In file included from src/hardware/asix-sigma/protocol.c:27: + src/hardware/asix-sigma/protocol.h:28:10: fatal error: ftdi.h: No such file or directory + 28 | #include + | ^~~~~~~~ + + Fixes: + - http://autobuild.buildroot.org/results/1427f44e36752c337791597fab47a1889552a2fe + + Signed-off-by: Fabrice Fontaine + +diff --git a/CMakeLists.txt b/CMakeLists.txt +index 5aecafc..3b0b87c 100644 +--- a/CMakeLists.txt ++++ b/CMakeLists.txt +@@ -136,7 +136,7 @@ endif () + + add_subdirectory(src) + if ( FTDIPP ) +- project(libftdipp1 C CXX) ++ project(libftdi1 C CXX) + add_subdirectory(ftdipp) + endif () + if ( PYTHON_BINDINGS ) From a5bc9f233f630e06b05f3029b181ba951502c00d Mon Sep 17 00:00:00 2001 From: Simon South Date: Thu, 7 Sep 2023 12:37:58 -0400 Subject: [PATCH 251/268] gnu: libftdi: Build API documentation. MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * gnu/packages/libftdi.scm (libftdi)[outputs]: Add "doc" output. [arguments]<#:configure-flags>: Add "-DDOCUMENTATION". <#:phases>: Add "install-documentation" phase. [native-inputs]: Add doxygen, graphviz. Signed-off-by: Ludovic Courtès --- gnu/packages/libftdi.scm | 18 +++++++++++++++--- 1 file changed, 15 insertions(+), 3 deletions(-) diff --git a/gnu/packages/libftdi.scm b/gnu/packages/libftdi.scm index bdfc635379..02efcbbbc0 100644 --- a/gnu/packages/libftdi.scm +++ b/gnu/packages/libftdi.scm @@ -28,6 +28,8 @@ #:use-module (guix utils) #:use-module (gnu packages) #:use-module (gnu packages boost) + #:use-module (gnu packages documentation) + #:use-module (gnu packages graphviz) #:use-module (gnu packages libusb) #:use-module (gnu packages pkg-config) #:use-module (gnu packages python) @@ -49,12 +51,13 @@ (patches (search-patches "libftdi-fix-paths-when-FTDIPP-set.patch")))) (build-system cmake-build-system) - (outputs '("out" "python")) + (outputs '("out" "doc" "python")) (arguments (list #:configure-flags #~(list (string-append "-DCMAKE_INSTALL_DOCDIR=" #$output "/share/doc/" #$name "-" #$version) + "-DDOCUMENTATION=ON" "-DEXAMPLES=OFF" "-DFTDIPP=ON" "-DLIB_SUFFIX=''" ; place libraries in /lib, not /lib64 @@ -74,11 +77,20 @@ (rename-file (string-append #$output "/share/libftdi/examples") (string-append #$output:python - "/share/libftdi/examples")))))) + "/share/libftdi/examples"))))) + (add-after 'install-python-binding 'install-documentation + (lambda _ + (let ((share (string-append #$output:doc "/share"))) + (copy-recursively "doc/man" + (string-append share "/man")) + (copy-recursively "doc/html" + (string-append share "/doc/" + #$name "-" #$version + "/html")))))) #:test-target "check" #:tests? #f)) ; tests fail without access to USB (native-inputs - (list pkg-config python swig)) + (list doxygen graphviz pkg-config python swig)) (inputs (list boost libconfuse)) (propagated-inputs From 1149cc1b9f2f3124f890c76497b826d7f959cec2 Mon Sep 17 00:00:00 2001 From: "Artyom V. Poptsov" Date: Sun, 10 Sep 2023 10:18:44 +0300 Subject: [PATCH 252/268] gnu: go-ipfs: Update to 0.13.0. MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * gnu/packages/ipfs.scm (go-ipfs): Update to 0.13.0. [inputs]: Add GO-GOLANG-ORG-X-{EXP,TEXT}. Signed-off-by: Ludovic Courtès --- gnu/packages/ipfs.scm | 7 +++++-- 1 file changed, 5 insertions(+), 2 deletions(-) diff --git a/gnu/packages/ipfs.scm b/gnu/packages/ipfs.scm index 141653176b..1e4a7cca3a 100644 --- a/gnu/packages/ipfs.scm +++ b/gnu/packages/ipfs.scm @@ -4,6 +4,7 @@ ;;; Copyright © 2019, 2020 Martin Becze ;;; Copyright © 2020, 2021, 2022 Michael Rohleder ;;; Copyright © 2022 Maxime Devos +;;; Copyright © 2023 Artyom V. Poptsov ;;; ;;; This file is part of GNU Guix. ;;; @@ -220,7 +221,7 @@ written in Go.") (define-public go-ipfs (package (name "go-ipfs") - (version "0.11.0") + (version "0.13.0") (source (origin (method url-fetch/tarbomb) @@ -228,7 +229,7 @@ written in Go.") "https://dist.ipfs.io/go-ipfs/v" version "/go-ipfs-source.tar.gz")) (sha256 - (base32 "13pmj83hwpz6mk7x52qn0cjnfqxqw2qri3r0k4b270w3bafcccwm")) + (base32 "1cx47ais2zn62c0r7lmrpfzia2gjyr61qi8my5wg3pj3dfr0fhkq")) (file-name (string-append name "-" version "-source")) (modules '((guix build utils))) (snippet '(for-each delete-file-recursively @@ -350,6 +351,8 @@ written in Go.") go-golang-org-x-term go-golang-org-x-tools go-golang-org-x-xerrors + go-golang-org-x-exp + go-golang-org-x-text go-lukechampine-com-blake3)) (native-inputs (append (if (%current-target-system) From b2cc649999ed97b62517dcfb7cf21ee731c97487 Mon Sep 17 00:00:00 2001 From: Janneke Nieuwenhuizen Date: Sun, 10 Sep 2023 15:21:24 +0200 Subject: [PATCH 253/268] gnu: glibc/hurd: Add unsubmitted getauxval patch from upstream. This support building of gdk-pixbuf, gobject-introspection. * gnu/packages/patches/glibc-hurd-getauxval.patch: New file. * gnu/local.mk (dist_patch_DATA): Add it. * gnu/packages/base.scm (glibc/hurd)[source]: Use it. --- gnu/local.mk | 1 + gnu/packages/base.scm | 3 +- .../patches/glibc-hurd-getauxval.patch | 34 +++++++++++++++++++ 3 files changed, 37 insertions(+), 1 deletion(-) create mode 100644 gnu/packages/patches/glibc-hurd-getauxval.patch diff --git a/gnu/local.mk b/gnu/local.mk index 4c3de24d73..8862fbfbb9 100644 --- a/gnu/local.mk +++ b/gnu/local.mk @@ -1287,6 +1287,7 @@ dist_patch_DATA = \ %D%/packages/patches/glibc-2.37-hurd-local-clock_gettime_MONOTONIC.patch \ %D%/packages/patches/glibc-2.37-versioned-locpath.patch \ %D%/packages/patches/glibc-hurd-clock_t_centiseconds.patch \ + %D%/packages/patches/glibc-hurd-getauxval.patch \ %D%/packages/patches/glibc-hurd-gettyent.patch \ %D%/packages/patches/glibc-hurd-mach-print.patch \ %D%/packages/patches/glibc-hurd-signal-sa-siginfo.patch \ diff --git a/gnu/packages/base.scm b/gnu/packages/base.scm index 5a3d5aced5..786b080ae4 100644 --- a/gnu/packages/base.scm +++ b/gnu/packages/base.scm @@ -1463,7 +1463,8 @@ command.") "glibc-2.37-hurd-clock_t_centiseconds.patch" "glibc-2.37-hurd-local-clock_gettime_MONOTONIC.patch" "glibc-hurd-mach-print.patch" - "glibc-hurd-gettyent.patch")))) + "glibc-hurd-gettyent.patch" + "glibc-hurd-getauxval.patch")))) (supported-systems %hurd-systems))) (define-public glibc/hurd-headers diff --git a/gnu/packages/patches/glibc-hurd-getauxval.patch b/gnu/packages/patches/glibc-hurd-getauxval.patch new file mode 100644 index 0000000000..815371b2d0 --- /dev/null +++ b/gnu/packages/patches/glibc-hurd-getauxval.patch @@ -0,0 +1,34 @@ +Taken from https://salsa.debian.org/glibc-team/glibc/-/blob/5af8e3701c63ad202b652b5051bec592b8385820/debian/patches/hurd-i386/unsubmitted-getaux_at_secure.diff + +This fixes gdk-pixbuf, gobject-introspection. + +FIXME: sysdeps/mach/hurd/i386/init-first.c should instead pass an auxv +to __libc_start_main + +Index: glibc-2.33/misc/getauxval.c +=================================================================== +--- glibc-2.33.orig/misc/getauxval.c ++++ glibc-2.33/misc/getauxval.c +@@ -19,6 +19,7 @@ + #include + #include + #include ++#include + + bool + __getauxval2 (unsigned long int type, unsigned long int *result) +@@ -27,6 +28,14 @@ __getauxval2 (unsigned long int type, un + ElfW(auxv_t) *p; + #endif + ++#ifdef AT_SECURE ++ if (type == AT_SECURE) ++ { ++ *result = __libc_enable_secure; ++ return true; ++ } ++#endif ++ + if (type == AT_HWCAP) + { + *result = GLRO(dl_hwcap); From 1d5f1a5462491bf877999525466fb83c55e7e66d Mon Sep 17 00:00:00 2001 From: Janneke Nieuwenhuizen Date: Thu, 14 Sep 2023 19:14:21 +0200 Subject: [PATCH 254/268] gnu: glib-next: Disable failing tests on the Hurd. * gnu/packages/glib.scm (glib-next)[arguments]: In phase `disable-tests', disable four extra failing tests when building on the Hurd. --- gnu/packages/glib.scm | 16 +++++++++++++++- 1 file changed, 15 insertions(+), 1 deletion(-) diff --git a/gnu/packages/glib.scm b/gnu/packages/glib.scm index e2a0bbdcdf..b5eb4602da 100644 --- a/gnu/packages/glib.scm +++ b/gnu/packages/glib.scm @@ -532,7 +532,21 @@ functions for strings and common data structures.") (string-append "//" all "\n")) (("^ g_assert_cmpfloat \\(elapsed, ==.*" all) (string-append "//" all "\n")))) - '()))))))) + '()) + #$@(if (system-hurd?) + '((with-directory-excursion "gio/tests" + ;; FAIL + (substitute* '("appmonitor.c" + "gdbus-server-auth.c" + "live-g-file.c" + "socket.c") + (("return (g_test_run|session_bus_run)" all call) + (string-append "return 0;// " call)) + ((" (ret|rtv|result) = (g_test_run|session_bus_run)" + all var call) + (string-append " " var " = 0;// " call)) + (("[ \t]*g_test_add_func.*;") "")))) + '()))))))) (native-inputs (modify-inputs (package-native-inputs glib) (append desktop-file-utils))) From 0c1aa354048f82023e6d2043bfecc4fd58bc9b58 Mon Sep 17 00:00:00 2001 From: Janneke Nieuwenhuizen Date: Thu, 14 Sep 2023 23:12:23 +0200 Subject: [PATCH 255/268] gnu: python-cython: Support building on the Hurd. * gnu/packages/python-xyz.scm (python-cython)[arguments]: In phase `check', skip failing tests on the Hurd. --- gnu/packages/python-xyz.scm | 6 ++++++ 1 file changed, 6 insertions(+) diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index dd43fb3cd1..2230310a03 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -142,6 +142,7 @@ ;;; Copyright © 2023 Parnikkapore ;;; Copyright © 2023 Foundation Devices, Inc. ;;; Copyright © c4droid +;;; Copyright © 2023 Janneke Nieuwenhuizen ;;; ;;; This file is part of GNU Guix. ;;; @@ -7129,6 +7130,11 @@ provides additional functionality on the produced Mallard documents.") ,@(if (not (target-64bit?)) '("-x" "run.parallel") '()) + ,@(if (system-hurd?) + '("-x" "test_class_ref" + "-x" "test_compiler_directives" + "-x" "test_lang_version") + '()) ;; This test fails when running on 24 cores. "-x" "cpp_stl_conversion"))))))) (home-page "https://cython.org/") From dca96f27ed5b870109c26836d32d991fcfbedaab Mon Sep 17 00:00:00 2001 From: Christopher Baines Date: Wed, 12 Jul 2023 14:57:58 +0100 Subject: [PATCH 256/268] gnu: Add bffe. * gnu/packages/package-management.scm (bffe): New variable. --- gnu/packages/package-management.scm | 53 +++++++++++++++++++++++++++++ 1 file changed, 53 insertions(+) diff --git a/gnu/packages/package-management.scm b/gnu/packages/package-management.scm index 51a5d52131..daf2d3b0c0 100644 --- a/gnu/packages/package-management.scm +++ b/gnu/packages/package-management.scm @@ -961,6 +961,59 @@ transactions from C or Python.") ;; The whole is GPLv2+; librpm itself is dual-licensed LGPLv2+ | GPLv2+. (license license:gpl2+))) +(define-public bffe + (let ((commit "634d3444c094dd594bdf2b15b9a71055462ae676") + (revision "1")) + (package + (name "bffe") + (version (git-version "0" revision commit)) + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://git.cbaines.net/guix/bffe") + (commit commit))) + (sha256 + (base32 + "0z13hyaq6bs2j3hnr7ys2vsyx2554zy69ka21savywx0ci3hhfk3")) + (file-name (string-append name "-" version "-checkout")))) + (build-system gnu-build-system) + (native-inputs + (list pkg-config + autoconf + automake + + ;; Guile libraries are needed here for cross-compilation. + guile-next + guile-gnutls + guile-json-4 + guix + guix-data-service + guix-build-coordinator + guile-fibers-1.3 + guile-prometheus + guile-lib)) + (inputs + (list guile-next)) + (propagated-inputs + (list guile-gnutls + guile-json-4 + guix + guix-data-service + guix-build-coordinator + guile-fibers-1.3 + guile-prometheus + guile-lib)) + (home-page "https://git.cbaines.net/guix/bffe") + (synopsis "Build Farm Front-end for Guix") + (description + "The BFFE of Build Farm Front-end is an experimental frontend for Guix +build farms. It works together with the Guix Data Service and Guix Build +Coordinator to submit builds and monitor the activity. + +It functions as a Guile library, with the @code{run-bffe-service} procedure in +the @code{(bffe)} module as the entry point.") + (license license:gpl3+)))) + (define-public python-anaconda-client (package (name "python-anaconda-client") From 82abf6ddadc6139148660440a064e60ae68f238e Mon Sep 17 00:00:00 2001 From: Christopher Baines Date: Sat, 26 Aug 2023 10:08:56 +0100 Subject: [PATCH 257/268] services: guix: Add bffe-service-type. This is intended to replace the functionality of the Guix Build Coordinator queue builds script, and also provide a web interface for build farms. * gnu/services/guix.scm (): New record type. (bffe-configuration, bffe-configuration?, bffe-configuration-package, bffe-configuration-user, bffe-configuration-group, bffe-configuration-arguments bffe-configuration-extra-environment-variables): New procedures. (bffe-service-type): New variable. * gnu/tests/guix.scm (%test-bffe): New variable. * doc/guix.texi (Guix Services): Document the new service. --- doc/guix.texi | 59 ++++++++++++++++++++ gnu/services/guix.scm | 127 +++++++++++++++++++++++++++++++++++++++++- gnu/tests/guix.scm | 81 ++++++++++++++++++++++++++- 3 files changed, 265 insertions(+), 2 deletions(-) diff --git a/doc/guix.texi b/doc/guix.texi index 7e42a7151c..46cc8e1b80 100644 --- a/doc/guix.texi +++ b/doc/guix.texi @@ -38088,6 +38088,65 @@ File name of the file system key for the target volume. @node Guix Services @subsection Guix Services +@subsubheading Build Farm Front-End (BFFE) +The @uref{https://git.cbaines.net/guix/bffe/,Build Farm Front-End} +assists with building Guix packages in bulk. It's responsible for +submitting builds and displaying the status of the build farm. + +@defvar bffe-service-type +Service type for the Build Farm Front-End. Its value must be a +@code{bffe-configuration} object. +@end defvar + +@deftp {Data Type} bffe-configuration +Data type representing the configuration of the Build Farm Front-End. + +@table @asis +@item @code{package} (default: @code{bffe}) +The Build Farm Front-End package to use. + +@item @code{user} (default: @code{"bffe"}) +The system user to run the service as. + +@item @code{group} (default: @code{"bffe"}) +The system group to run the service as. + +@item @code{arguments} +A list of arguments to the Build Farm Front-End. These are passed to +the @code{run-bffe-service} procedure when starting the service. + +For example, the following value directs the Build Farm Front-End to +submit builds for derivations available from @code{data.guix.gnu.org} to +the Build Coordinator instance assumed to be running on the same +machine. + +@example +(list + #:build + (list + (build-from-guix-data-service + (data-service-url "https://data.guix.gnu.org") + (build-coordinator-url "http://127.0.0.1:8746") + (branches '("master")) + (systems '("x86_64-linux" "i686-linux")) + (systems-and-targets + (map (lambda (target) + (cons "x86_64-linux" target)) + '("aarch64-linux-gnu" + "i586-pc-gnu"))) + (build-priority (const 0)))) + #:web-server-args + '(#:event-source "https://example.com" + #:controller-args + (#:title "example.com build farm"))) +@end example + +@item @code{extra-environment-variables} (default: @var{'()}) +Extra environment variables to set via the shepherd service. + +@end table +@end deftp + @subsubheading Guix Build Coordinator The @uref{https://git.cbaines.net/guix/build-coordinator/,Guix Build Coordinator} aids in distributing derivation builds among machines diff --git a/gnu/services/guix.scm b/gnu/services/guix.scm index 99b21f52d8..9b19a48cfd 100644 --- a/gnu/services/guix.scm +++ b/gnu/services/guix.scm @@ -140,7 +140,17 @@ nar-herder-cached-compression-configuration-type nar-herder-cached-compression-configuration-level nar-herder-cached-compression-configuration-directory - nar-herder-cached-compression-configuration-directory-max-size)) + nar-herder-cached-compression-configuration-directory-max-size + + bffe-configuration + bffe-configuration? + bffe-configuration-package + bffe-configuration-user + bffe-configuration-group + bffe-configuration-arguments + bffe-configuration-extra-environment-variables + + bffe-service-type)) ;;;; Commentary: ;;; @@ -1030,3 +1040,118 @@ ca-certificates.crt file in the system profile." nar-herder-account))) (description "Run a Nar Herder server."))) + + +;;; +;;; Build Farm Front-end (BFFE) +;;; + +(define-record-type* + bffe-configuration make-bffe-configuration + bffe-configuration? + (package bffe-configuration-package + (default bffe)) + (user bffe-configuration-user + (default "bffe")) + (group bffe-configuration-group + (default "bffe")) + (arguments bffe-configuration-arguments) + (extra-environment-variables + bffe-configuration-extra-environment-variables + (default '()))) + +(define (bffe-shepherd-services config) + (define bffe-package + (bffe-configuration-package config)) + + (define start-script + (program-file + "run-bffe" + (with-extensions (cons + bffe-package + ;; This is a poorly constructed Guile load path, + ;; since it contains things that aren't Guile + ;; libraries, but it means that the Guile + ;; libraries needed for BFFE don't need to be + ;; individually specified here. + (map second (package-transitive-propagated-inputs + bffe-package))) + #~(begin + (use-modules (bffe) + (bffe manage-builds)) + + (setvbuf (current-output-port) 'line) + (setvbuf (current-error-port) 'line) + + (simple-format #t "starting the bffe:\n ~A\n" + (current-filename)) + + (apply run-bffe-service + (append + (list #:pid-file "/var/run/bffe/pid") + #$(bffe-configuration-arguments config))))) + #:guile guile-3.0)) + + (match-record config + (package user group arguments extra-environment-variables) + + (list + (shepherd-service + (documentation "Build Farm Front-end") + (provision '(bffe)) + (requirement '(networking)) + (start #~(make-forkexec-constructor + (list #$start-script) + #:user #$user + #:group #$group + #:pid-file "/var/run/bffe/pid" + #:directory "/var/lib/bffe" + #:environment-variables + `(,(string-append + "GUIX_LOCPATH=" #$glibc-utf8-locales "/lib/locale") + "LC_ALL=en_US.utf8" + #$@extra-environment-variables) + #:log-file "/var/log/bffe/server.log")) + (stop #~(make-kill-destructor)))))) + +(define (bffe-activation config) + #~(begin + (use-modules (guix build utils)) + + (define %user + (getpw #$(bffe-configuration-user config))) + + (chmod "/var/lib/bffe" #o755) + + (mkdir-p "/var/log/bffe") + + ;; Allow writing the PID file + (mkdir-p "/var/run/bffe") + (chown "/var/run/bffe" (passwd:uid %user) (passwd:gid %user)))) + +(define (bffe-account config) + (match-record config + (user group) + (list (user-group + (name group) + (system? #t)) + (user-account + (name user) + (group group) + (system? #t) + (comment "BFFE user") + (home-directory "/var/lib/bffe") + (shell (file-append shadow "/sbin/nologin")))))) + +(define bffe-service-type + (service-type + (name 'bffe) + (extensions + (list (service-extension shepherd-root-service-type + bffe-shepherd-services) + (service-extension activation-service-type + bffe-activation) + (service-extension account-service-type + bffe-account))) + (description + "Run the Build Farm Front-end."))) diff --git a/gnu/tests/guix.scm b/gnu/tests/guix.scm index ad0980a10c..240ded4825 100644 --- a/gnu/tests/guix.scm +++ b/gnu/tests/guix.scm @@ -37,7 +37,8 @@ #:use-module (ice-9 match) #:export (%test-guix-build-coordinator %test-guix-data-service - %test-nar-herder)) + %test-nar-herder + %test-bffe)) ;;; ;;; Guix Build Coordinator @@ -325,3 +326,81 @@ host all all ::1/128 trust")))))) (name "nar-herder") (description "Connect to a running Nar Herder server.") (value (run-nar-herder-test)))) + + +;;; +;;; Build Farm Front-end +;;; + +(define %bffe-os + (simple-operating-system + (service dhcp-client-service-type) + (service guix-build-coordinator-service-type) + (service bffe-service-type + (bffe-configuration + (arguments + #~(list + #:web-server-args + '(#:port 8767 + #:controller-args + (#:title "Test title")))))))) + +(define (run-bffe-test) + (define os + (marionette-operating-system + %bffe-os + #:imported-modules '((gnu services herd) + (guix combinators)))) + + (define forwarded-port 8767) + + (define vm + (virtual-machine + (operating-system os) + (memory-size 1024) + (port-forwardings `((,forwarded-port . 8767))))) + + (define test + (with-imported-modules '((gnu build marionette)) + #~(begin + (use-modules (srfi srfi-11) (srfi srfi-64) + (gnu build marionette) + (web uri) + (web client) + (web response)) + + (define marionette + (make-marionette (list #$vm))) + + (test-runner-current (system-test-runner #$output)) + (test-begin "bffe") + + (test-assert "service running" + (marionette-eval + '(begin + (use-modules (gnu services herd)) + (match (start-service 'bffe) + (#f #f) + (('service response-parts ...) + (match (assq-ref response-parts 'running) + ((pid) (number? pid)))))) + marionette)) + + (test-equal "http-get" + 200 + (let-values + (((response text) + (http-get #$(simple-format + #f "http://localhost:~A/" forwarded-port) + #:decode-body? #t))) + (response-code response))) + + (test-end)))) + + (gexp->derivation "bffe-test" test)) + +(define %test-bffe + (system-test + (name "bffe") + (description "Connect to a running Build Farm Front-end.") + (value (run-bffe-test)))) From 92498fad27a304ab73f66bd4944007c150012a07 Mon Sep 17 00:00:00 2001 From: Vagrant Cascadian Date: Fri, 8 Sep 2023 12:51:53 -0700 Subject: [PATCH 258/268] gnu: diffoscope: Update to 250. * gnu/packages/diffoscope.scm (diffoscope): Update to 250. [native-inputs]: Add html2text and u-boot-tools. Signed-off-by: Christopher Baines --- gnu/packages/diffoscope.scm | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) diff --git a/gnu/packages/diffoscope.scm b/gnu/packages/diffoscope.scm index 86f0c779ef..1b8b77d7a4 100644 --- a/gnu/packages/diffoscope.scm +++ b/gnu/packages/diffoscope.scm @@ -74,7 +74,7 @@ (define-public diffoscope (package (name "diffoscope") - (version "247") + (version "250") (source (origin (method git-fetch) @@ -83,7 +83,7 @@ (commit version))) (file-name (git-file-name name version)) (sha256 - (base32 "0c81pvdq0bz47sk3gcgpm2l3g5hxdi2s1jz05krv1cr2bd0sfq4j")))) + (base32 "12cdsgxlva1gcry16w9x44ji9asar1n8p9q6rv2jd1gr9fi6l0sz")))) (build-system python-build-system) (arguments (list @@ -188,6 +188,7 @@ gnumeric gnupg hdf5 + html2text imagemagick libarchive llvm @@ -206,6 +207,7 @@ sqlite squashfs-tools tcpdump + u-boot-tools unzip wabt xxd From af1d2c031032b2b0330a3093a41b16f7699f29b9 Mon Sep 17 00:00:00 2001 From: Sergey Trofimov Date: Fri, 8 Sep 2023 17:57:39 +0200 Subject: [PATCH 259/268] gnu: squid: Update to 6.3. Signed-off-by: Christopher Baines --- gnu/packages/networking.scm | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/gnu/packages/networking.scm b/gnu/packages/networking.scm index 6c22129a98..1eb464673d 100644 --- a/gnu/packages/networking.scm +++ b/gnu/packages/networking.scm @@ -1998,14 +1998,14 @@ TCP connection, TLS handshake and so on) in the terminal.") (define-public squid (package (name "squid") - (version "4.17") + (version "6.3") (source (origin (method url-fetch) - (uri (string-append "http://www.squid-cache.org/Versions/v4/squid-" + (uri (string-append "http://www.squid-cache.org/Versions/v6/squid-" version ".tar.xz")) (sha256 - (base32 "060lwghn6q982bay11ia38c86kd8w6mjgy68n58v31kwik08m4nb")))) + (base32 "1yj869jnbdv1fb604j6g602dyvfnw7ahh9sh7mbqjpbsd9cgb83l")))) (build-system gnu-build-system) (arguments '(#:configure-flags From 4c031bb86f2a82c9e37ce37981abc2779fcd8b68 Mon Sep 17 00:00:00 2001 From: Jussi Timperi Date: Mon, 11 Sep 2023 12:06:48 +0300 Subject: [PATCH 260/268] gnu: pasystray: Update to 0.8.2. * gnu/packages/pulseaudio.scm (pasystray): Update to 0.8.2. Signed-off-by: Christopher Baines --- gnu/packages/pulseaudio.scm | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/gnu/packages/pulseaudio.scm b/gnu/packages/pulseaudio.scm index ef4f8ba8cf..dd0d3985c0 100644 --- a/gnu/packages/pulseaudio.scm +++ b/gnu/packages/pulseaudio.scm @@ -385,16 +385,16 @@ volume levels of the sinks (get, set, decrease, increase, toggle mute, etc).") (define-public pasystray (package (name "pasystray") - (version "0.7.1") + (version "0.8.2") (source (origin (method git-fetch) (uri (git-reference (url "https://github.com/christophgysin/pasystray") - (commit (string-append name "-" version)))) + (commit version))) (file-name (git-file-name name version)) (sha256 - (base32 "0xx1bm9kimgq11a359ikabdndqg5q54pn1d1dyyjnrj0s41168fk")))) + (base32 "1zf79pfmm7wa1l9yyab2g6lf0j81v1mrp406262rd21g4prx1921")))) (build-system gnu-build-system) (arguments `(#:phases From a0510561935e3327099df558e9dd9bdffe850441 Mon Sep 17 00:00:00 2001 From: Andrew Jose Date: Wed, 13 Sep 2023 13:24:35 +0530 Subject: [PATCH 261/268] gnu: delve: Update to 1.21.0. * gnu/packages/debug.scm (delve): Update to 1.21.0. [propagated-inputs]: Remove go. Signed-off-by: Christopher Baines --- gnu/packages/debug.scm | 6 ++---- 1 file changed, 2 insertions(+), 4 deletions(-) diff --git a/gnu/packages/debug.scm b/gnu/packages/debug.scm index e2a29a3ae9..febc041e53 100644 --- a/gnu/packages/debug.scm +++ b/gnu/packages/debug.scm @@ -892,11 +892,10 @@ to aid in debugging.") (home-page "https://www.gnu.org/software/ddd/") (license license:gpl3+))) - (define-public delve (package (name "delve") - (version "1.9.1") + (version "1.21.0") (source (origin (method git-fetch) @@ -906,14 +905,13 @@ to aid in debugging.") (file-name (git-file-name name version)) (sha256 (base32 - "07jch3yd1pgqviyy18amn23gazbzi7l51f210c3vmc707v3vbbqr")))) + "1gdynx4gp02lj47znnf638kkbmmsl24a9fis81a2fg3pdrg6jg3c")))) (build-system go-build-system) (arguments (list #:import-path "github.com/go-delve/delve/cmd/dlv" #:unpack-path "github.com/go-delve/delve" #:install-source? #f #:phases #~(modify-phases %standard-phases (delete 'check)))) - (propagated-inputs (list go)) (home-page "https://github.com/go-delve/delve") (synopsis "Debugger for the Go programming language") (description "Delve is a debugger for the Go programming language.") From 61a89de7d7e6517cd393dd1f3cf93004a5a3bdf2 Mon Sep 17 00:00:00 2001 From: Nicolas Graves Date: Thu, 14 Sep 2023 14:15:35 +0200 Subject: [PATCH 262/268] gnu: emacs-sway: Update to 0.7. * gnu/packages/emacs-xyz.scm (emacs-sway): Update to 0.7. Signed-off-by: Andrew Tropin --- gnu/packages/emacs-xyz.scm | 39 ++++++++++++++++++-------------------- 1 file changed, 18 insertions(+), 21 deletions(-) diff --git a/gnu/packages/emacs-xyz.scm b/gnu/packages/emacs-xyz.scm index a4c6f45feb..c4de0e1d1f 100644 --- a/gnu/packages/emacs-xyz.scm +++ b/gnu/packages/emacs-xyz.scm @@ -12440,30 +12440,27 @@ The following completions are currently available: (license license:gpl3+))) (define-public emacs-sway - ;; Commit from Nicola's fork (dash free version with various improvments) - (let ((commit "838ef531a30fe616f0141adbdabc132d4edfd374") - (revision "0")) - (package - (name "emacs-sway") - (version (git-version "0.6.1" revision commit)) - (source - (origin - (method git-fetch) - (uri (git-reference - (url "https://github.com/thblt/sway.el") - (commit commit))) - (file-name (git-file-name name version)) - (sha256 - (base32 "0ddaz8my3z4ca2z81kf1h8773pyx8h0l0ra3ssqd1rq5j0041wdh")))) - (build-system emacs-build-system) - (home-page "https://github.com/thblt/sway.el") - (synopsis "Communication with the Sway window manager") - (description - "This is a basic library to control the Sway window manager from Emacs. + (package + (name "emacs-sway") + (version "0.7") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/thblt/sway.el") + (commit version))) + (file-name (git-file-name name version)) + (sha256 + (base32 "1w29dkl7s835zgwnc4jx1cp84s6mmwbvlil8z2c31psy0rlajc6i")))) + (build-system emacs-build-system) + (home-page "https://github.com/thblt/sway.el") + (synopsis "Communication with the Sway window manager") + (description + "This is a basic library to control the Sway window manager from Emacs. Its main use case is in combination with popup managers like Shackle, to use frames instead of windows while still giving focus to existing frames instead of duplicating them.") - (license license:gpl3+)))) + (license license:gpl3+))) (define-public emacs-sweet-theme (let ((commit "78f741806ecebe01224bf54d09ad80e306652508") From 9549266ba42cc31a9442ddd78af592e824f2d061 Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Thu, 14 Sep 2023 13:18:43 +0300 Subject: [PATCH 263/268] gnu: julia-freetype2-jll: Update to 2.13.1+0. * gnu/packages/julia-jll.scm (julia-freetype2-jll): Update to 2.13.1+0. [arguments]: Remove trailing #t from phases. --- gnu/packages/julia-jll.scm | 7 +++---- 1 file changed, 3 insertions(+), 4 deletions(-) diff --git a/gnu/packages/julia-jll.scm b/gnu/packages/julia-jll.scm index 35e06c7124..753651cb9e 100644 --- a/gnu/packages/julia-jll.scm +++ b/gnu/packages/julia-jll.scm @@ -401,7 +401,7 @@ build tree Yggdrasil.") (define-public julia-freetype2-jll (package (name "julia-freetype2-jll") - (version "2.10.4+0") + (version "2.13.1+0") (source (origin (method git-fetch) @@ -410,7 +410,7 @@ build tree Yggdrasil.") (commit (string-append "FreeType2-v" version)))) (file-name (git-file-name name version)) (sha256 - (base32 "03lgmb59lipc3bi7z22j4a53bbjmcwkf0xzpwan889p1ix3ry1lr")))) + (base32 "1kngkk3kkf6dam8g4g2ajvzvydzxbgpgxlcpsg7nm7q6r5b4b4db")))) (build-system julia-build-system) (arguments '(#:tests? #f ; No runtests.jl @@ -426,8 +426,7 @@ build tree Yggdrasil.") "generate_wrapper_header(\"FreeType2\", \"" (assoc-ref inputs "freetype") "\")\n")))) ;; There's a Julia file for each platform, override them all - (find-files "src/wrappers/" "\\.jl$")) - #t))))) + (find-files "src/wrappers/" "\\.jl$"))))))) (inputs (list freetype)) (propagated-inputs From 69580997bd1b383659b990a5e1e46817e371fa8c Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Thu, 14 Sep 2023 13:28:57 +0300 Subject: [PATCH 264/268] gnu: julia-structarrays: Add missing input. * gnu/packages/julia-xyz.scm (julia-structarrays)[propagated-inputs]: Add julia-adapt. --- gnu/packages/julia-xyz.scm | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/gnu/packages/julia-xyz.scm b/gnu/packages/julia-xyz.scm index bbb8085492..a1e65332fa 100644 --- a/gnu/packages/julia-xyz.scm +++ b/gnu/packages/julia-xyz.scm @@ -6084,7 +6084,8 @@ with ANSI escape sequences.") "test/runtests.jl") (("Int64") "Int32")))))))) (propagated-inputs - (list julia-dataapi + (list julia-adapt + julia-dataapi julia-staticarrays julia-tables)) (native-inputs From 9c9d6c3dab0a3c83ca30664d0461807d0289579b Mon Sep 17 00:00:00 2001 From: Christopher Baines Date: Fri, 15 Sep 2023 10:50:31 +0100 Subject: [PATCH 265/268] services: bffe: Use guile from the package. Rather than hardcoding a particular guile in the service definition. * gnu/services/guix.scm (bffe-shepherd-services): Use guile from the package. * gnu/packages/package-management.scm (bffe)[inputs]: Remove unnecessary guile-next input. --- gnu/packages/package-management.scm | 2 -- gnu/services/guix.scm | 2 +- 2 files changed, 1 insertion(+), 3 deletions(-) diff --git a/gnu/packages/package-management.scm b/gnu/packages/package-management.scm index daf2d3b0c0..d2e0cdecd7 100644 --- a/gnu/packages/package-management.scm +++ b/gnu/packages/package-management.scm @@ -992,8 +992,6 @@ transactions from C or Python.") guile-fibers-1.3 guile-prometheus guile-lib)) - (inputs - (list guile-next)) (propagated-inputs (list guile-gnutls guile-json-4 diff --git a/gnu/services/guix.scm b/gnu/services/guix.scm index 9b19a48cfd..fe602efb99 100644 --- a/gnu/services/guix.scm +++ b/gnu/services/guix.scm @@ -1090,7 +1090,7 @@ ca-certificates.crt file in the system profile." (append (list #:pid-file "/var/run/bffe/pid") #$(bffe-configuration-arguments config))))) - #:guile guile-3.0)) + #:guile (lookup-package-native-input bffe-package "guile-next"))) (match-record config (package user group arguments extra-environment-variables) From eeeaf13984b96ca8856532559d5ab755c560e42c Mon Sep 17 00:00:00 2001 From: Vincent Prat Date: Mon, 26 Jun 2023 11:44:47 +0200 Subject: [PATCH 266/268] gnu: python-mypy: Update to 1.4.1. * gnu/packages/python-check.scm (python-mypy): Update to 1.4.1. [origin]: Switch to PyPI. [arguments]: Don't skip the testImports test. Signed-off-by: Christopher Baines --- gnu/packages/python-check.scm | 23 +++++------------------ 1 file changed, 5 insertions(+), 18 deletions(-) diff --git a/gnu/packages/python-check.scm b/gnu/packages/python-check.scm index 87e15b4560..3a718954c5 100644 --- a/gnu/packages/python-check.scm +++ b/gnu/packages/python-check.scm @@ -1834,24 +1834,14 @@ supported by the MyPy typechecker.") (define-public python-mypy (package (name "python-mypy") - (version "0.971") + (version "1.4.1") (source (origin - ;; Because of https://github.com/python/mypy/issues/9584, the - ;; mypyc/analysis directory is missing in the PyPI archive, leading to - ;; test failures. - (method git-fetch) - (uri (git-reference - (url "https://github.com/python/mypy") - (commit (string-append "v" version)) - ;; Fetch git submodules otherwise typeshed is not fetched. - ;; Typeshed is a collection of Python sources type annotation - ;; (data) files. - (recursive? #t))) - (file-name (git-file-name name version)) + (method url-fetch) + (uri (pypi-uri "mypy" version)) (sha256 (base32 - "0i8swdynms1wpiprgqn24za6mx8rlgxr2jash3cb5xi8jyf58n97")))) + "06svfmqbnb45pydy8lcrr12wqhhla5dl888w0g4f3wm1ismxkg4v")))) (build-system python-build-system) (arguments `(#:phases @@ -1859,10 +1849,7 @@ supported by the MyPy typechecker.") (replace 'check (lambda* (#:key tests? #:allow-other-keys) (when tests? - (invoke "pytest" "-vv" "mypyc" - ;; XXX: This test gets an unexpected DeprecationWarning - ;; from recent versions of setuptools. Ignore for now. - "-k" "not testImports"))))))) + (invoke "pytest" "mypyc"))))))) (native-inputs (list python-attrs python-lxml From 444cab7f05686c0b0ca75b61eb69866c6d7536dc Mon Sep 17 00:00:00 2001 From: Hilton Chain Date: Sun, 2 Jul 2023 18:01:32 +0800 Subject: [PATCH 267/268] gnu: go-github-com-tdewolff-minify-v2: Update to 2.12.7. * gnu/packages/golang.scm (go-github-com-tdewolff-minify-v2): Update to 2.12.7 Signed-off-by: Christopher Baines --- 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 cbd4bafd20..3d19b48e9f 100644 --- a/gnu/packages/golang.scm +++ b/gnu/packages/golang.scm @@ -3673,7 +3673,7 @@ per-goroutine.") (define-public go-github-com-tdewolff-minify-v2 (package (name "go-github-com-tdewolff-minify-v2") - (version "2.12.6") + (version "2.12.7") (source (origin (method git-fetch) (uri (git-reference @@ -3682,7 +3682,7 @@ per-goroutine.") (file-name (git-file-name name version)) (sha256 (base32 - "0h006wpfkl0ls0skqxblwcanrhmphgq5q0ii26l2ayh7s99cgmy3")))) + "0qhslaq885zbqs83nvbi29yh09b89kkb6ycami8lz28wkwrlayap")))) (build-system go-build-system) (arguments (list #:import-path "github.com/tdewolff/minify/v2" From b696fb41bc0dfcb7130a5aa6d69aff2ae191c283 Mon Sep 17 00:00:00 2001 From: kiasoc5 Date: Tue, 4 Jul 2023 14:28:56 -0400 Subject: [PATCH 268/268] gnu: libostree: Update to 2023.5. * gnu/packages/package-management.scm (libostree): Update to 2023.5. Signed-off-by: Christopher Baines --- gnu/packages/package-management.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/package-management.scm b/gnu/packages/package-management.scm index d2e0cdecd7..e899817093 100644 --- a/gnu/packages/package-management.scm +++ b/gnu/packages/package-management.scm @@ -1921,7 +1921,7 @@ for packaging and deployment of cross-compiled Windows applications.") (define-public libostree (package (name "libostree") - (version "2022.7") + (version "2023.5") (source (origin (method url-fetch) @@ -1929,7 +1929,7 @@ for packaging and deployment of cross-compiled Windows applications.") "https://github.com/ostreedev/ostree/releases/download/v" (version-major+minor version) "/libostree-" version ".tar.xz")) (sha256 - (base32 "07s14awf9ynlp84s08dkbwj9i18g93y0yf0k87nbks4l3hkakqlb")))) + (base32 "056v7bz40dx8k2j2pfypc4shl6ijzvx1gy8r0kaw66py67xklndw")))) (build-system gnu-build-system) (arguments '(#:phases