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Author SHA1 Message Date
Sharlatan Hellseher 74cab6cd03
gnu: go-github-com-blang-semver: Update to 3.8.0. 
* gnu/packages/golang-xyz.scm (go-github-com-blang-semver): Update to 3.8.0.

Change-Id: I5f1eec936236e4f8984d6aabbab9a9ce99e291a3
 2024-03-15 23:33:12 +00:00
Ilya Chernyshov 868e21bb76
gnu: guile-scheme-json-rpc: Update to 0.4.5a. 
Shift some inputs requiring during runtime.

* gnu/packages/guile-xyz.scm (guile-scheme-json-rpc): Update to 0.4.5a.
[inputs]: Remove guile-srfi-145 and guile-srfi-180.
[propagated-inputs]: Add guile-srfi-145 and guile-srfi-180.

Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
Change-Id: If1c6ffaf6269c36ec857fd6f0aec444869468d24
 2024-03-15 23:24:56 +00:00
Ricardo Wurmus 10345d2f63
gnu: r-clusterprofiler: Update to 4.10.1. 
* gnu/packages/bioconductor.scm (r-clusterprofiler): Update to 4.10.1.

Change-Id: I05b41c27d1e1ac8b2887845df5a4a75d45513929
 2024-03-15 23:54:35 +01:00
Ricardo Wurmus 48e458e662
gnu: r-zlibbioc: Update to 1.48.2. 
* gnu/packages/bioconductor.scm (r-zlibbioc): Update to 1.48.2.
[native-inputs]: Add r-knitr.

Change-Id: Iee1c599473d30532660eb3770cf471ff979530dd
 2024-03-15 23:54:35 +01:00
Ricardo Wurmus b11f7c18bd
gnu: r-stringdb: Update to 2.14.3. 
* gnu/packages/bioconductor.scm (r-stringdb): Update to 2.14.3.
[propagated-inputs]: Remove r-rcurl; add r-httr.

Change-Id: Id46873bee69cdd1047002db3505ff5420097e9e9
 2024-03-15 23:54:35 +01:00
Ricardo Wurmus 74066baa0b
gnu: r-gsva: Update to 1.50.1. 
* gnu/packages/bioconductor.scm (r-gsva): Update to 1.50.1.

Change-Id: Ib298992cb9ea4615fe3888e799c332e778a7b5be
 2024-03-15 23:54:35 +01:00
Ricardo Wurmus 7416d0f273
gnu: r-genomicfeatures: Update to 1.54.4. 
* gnu/packages/bioconductor.scm (r-genomicfeatures): Update to 1.54.4.
[propagated-inputs]: Remove r-rcurl; add r-httr and r-rjson.

Change-Id: Iaed5177d04bc1c292dfad607f82401f45cfd02bc
 2024-03-15 23:54:35 +01:00
Ricardo Wurmus df26e72fd6
gnu: r-genomeinfodb: Update to 1.38.7. 
* gnu/packages/bioconductor.scm (r-genomeinfodb): Update to 1.38.7.
[propagated-inputs]: Remove r-rcurl.

Change-Id: Ifc265a49ed946f3548ff279b930a8346c42025a8
 2024-03-15 23:54:35 +01:00
Ricardo Wurmus b49398487c
gnu: r-deseq2: Update to 1.42.1. 
* gnu/packages/bioconductor.scm (r-deseq2): Update to 1.42.1.

Change-Id: Ida0b7ad662c44b2b12af487bb6aa8364874ce3da
 2024-03-15 23:54:35 +01:00
Ricardo Wurmus db7d9e6cab
gnu: r-biostrings: Update to 2.70.3. 
* gnu/packages/bioconductor.scm (r-biostrings): Update to 2.70.3.

Change-Id: I4a921a148d9f54be13967ed0e3092353a683f20f
 2024-03-15 23:54:35 +01:00
Ricardo Wurmus f97a8a8650
gnu: r-coregx: Update to 2.6.1. 
* gnu/packages/bioconductor.scm (r-coregx): Update to 2.6.1.

Change-Id: Icb0eb5a7697811f4272cda3d42d3c428bb59bd23
 2024-03-15 23:54:35 +01:00
Ricardo Wurmus 900ad49572
gnu: r-asics: Update to 2.18.1. 
* gnu/packages/bioconductor.scm (r-asics): Update to 2.18.1.

Change-Id: I760771fd8fe57984ae1d0c96b72cb63562a1b43e
 2024-03-15 23:54:35 +01:00
Luis Felipe 999bfa0d54
doc: build: Update paths to style sheets. 
The Guix website style sheets are now organized in themes. This change
makes the documentation builder use the resources provided by a theme
called "initial" (See https://issues.guix.gnu.org/69783).

* doc/build.scm (syntax-highlighted-html): Update path to CSS.
(html-manual-indexes): Likewise.
(stylized-html): Likewise, and update path to language picker image.

Change-Id: Ib2d51fcfdec42ad827add1ead1cfee4c9c4e65b7
Signed-off-by: Florian Pelz <pelzflorian@pelzflorian.de>
 2024-03-15 23:22:45 +01:00
Clément Lassieur 93aefca7ba
gnu: alacritty: Fix loading of libxkbcommon-x11.so. 
* gnu/packages/terminals.scm (alacritty)[arguments]: Handle
libxkbcommon-x11.so in the ‘add-absolute-library-references’ phase.

This fixes this error:

thread 'main' panicked at /tmp/guix-build-alacritty-0.13.1.drv-0/source/guix-vendor/rust-xkbcommon-dl-0.4.1.tar.gz/src/x11.rs:59:28:
Library libxkbcommon-x11.so could not be loaded.
note: run with `RUST_BACKTRACE=1` environment variable to display a backtrace

Change-Id: Ifbf19b4962bc3d9eeba6acdf32ca66b0c662f493
Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
 2024-03-15 10:32:03 +02:00
Sharlatan Hellseher 646810ab6a
gnu: python-pycurl: Disable one failing test. 
* gnu/packages/python-web.com (python-pycurl) [arguments]
<#:test-flags>: Disable one more failing test which occurs on CI with
CPU thread count more than 16.

Change-Id: Ie772a7f096357b541cc8baa2349a524f05500e52
 2024-03-15 07:48:08 +00:00
Leo Famulari e1e6116e05
Revert "gnu: linux-libre-documentation: Fix compilation." 
This bug was fixed upstream in 6.7.6.

This reverts commit b6f82b9ef1.

Change-Id: Ia756a62b29ad1f342b0e7430a0cb88cc140974eb
 2024-03-15 01:41:23 -04:00
Leo Famulari f28802a813
gnu: linux-libre 4.19: Update to 4.19.309. 
* gnu/packages/linux.scm (linux-libre-4.19-version): Update to 4.19.309.
(linux-libre-4.19-pristine-source): Update hash.

Change-Id: If579a8179ded35cb4269e733bd96ee6f7c5d5360
 2024-03-15 01:41:23 -04:00
Leo Famulari 557fc25caa
gnu: linux-libre 5.4: Update to 5.4.271. 
* gnu/packages/linux.scm (linux-libre-5.4-version): Update to 5.4.271.
(linux-libre-5.4-pristine-source): Update hash.

Change-Id: Iaf7277f1f4ec3f106b8f0b82aef5a8be953972bd
 2024-03-15 01:41:22 -04:00
Leo Famulari 65d12a4a97
gnu: linux-libre 5.10: Update to 5.10.212. 
* gnu/packages/linux.scm (linux-libre-5.10-version): Update to 5.10.212.
(linux-libre-5.10-pristine-source): Update hash.

Change-Id: I620729ec22cd67bbe22dc808ba6b4d74d2c0479d
 2024-03-15 01:41:22 -04:00
Leo Famulari cc2b28975b
gnu: linux-libre 5.15: Update to 5.15.151. 
* gnu/packages/linux.scm (linux-libre-5.15-version): Update to 5.15.151.
(linux-libre-5.15-pristine-source): Update hash.

Change-Id: I83ddffad4f1ce05723faa5d243e8345b21e39edb
 2024-03-15 01:41:22 -04:00
Leo Famulari c6d2fa1139
gnu: linux-libre 6.1: Update to 6.1.81. 
* gnu/packages/linux.scm (linux-libre-6.1-version): Update to 6.1.81.
(linux-libre-6.1-pristine-source, deblob-scripts-6.1): Update hashes.

Change-Id: Iaec9f01a190d67bcab490c318456241ea8eabf22
 2024-03-15 01:41:22 -04:00
Leo Famulari 1e568b2ed3
gnu: linux-libre 6.6: Update to 6.6.21. 
* gnu/packages/linux.scm (linux-libre-6.6-version): Update to 6.6.21.
(linux-libre-6.6-pristine-source): Update hash.

Change-Id: Ic2f197add55f89196010c32957e10d3683cb8c01
 2024-03-15 01:41:21 -04:00
Leo Famulari 019fb14b1e
gnu: linux-libre: Update to 6.7.9. 
* gnu/packages/linux.scm (linux-libre-6.7-version): Update to 6.7.9.
(linux-libre-6.7-pristine-source): Update hash.

Change-Id: I9d3e3907623b17f1a47b78ea00e9b7a5cf428ff6
 2024-03-15 01:41:21 -04:00
Sharlatan Hellseher a862a99bb3
gnu: python-pycurl: Enable tests. 
* gnu/packages/python-web.scm (python-pycurl): Enable most of the tests.
[build-system]: Swap to pyproject-build-system.
[arguments] <#:tests?>: Enable them.
<#:test-arguments>: Disable some failing and hanging tests.
[native-inputs]: Add python-flaky, python-pytest, and
python-pytest-xdist.

Change-Id: Ie222aa1111720f2e39b950b79d9e707401be7e8f
 2024-03-14 23:29:02 +00:00
Sharlatan Hellseher 2187ac84d0
gnu: packages: python-web: Sort use-modules alphabetically. 
* gnu/packages/python-web.scm: Sort #:use-module alphabetically to ease
maintenance.

Change-Id: Id01b66ff7eaf610895c1275c2abfd9de2e537d8e
 2024-03-14 23:28:52 +00:00
Troy Figiel e22175655d
gnu: Add python-zodb. 
* gnu/packages/python-web.scm (python-zodb): New variable.

Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
 2024-03-14 22:49:59 +00:00
Troy Figiel 36da1ad73d
gnu: Add python-zodbpickle. 
* gnu/packages/python-web.scm (python-zodbpickle): New variable.

Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
 2024-03-14 22:49:51 +00:00
Troy Figiel fb377b4af7
gnu: Add python-zconfig. 
* gnu/packages/python-web.scm (python-zconfig): New variable.

Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
 2024-03-14 22:22:45 +00:00
Ricardo Wurmus efe62c5ed3
gnu: Add morpheus. 
* gnu/packages/bioinformatics.scm (morpheus): New variable.

Co-authored-by: Navid Afkhami <navid.afkhami@mdc-berlin.de>
Change-Id: I4bf14414f497ff17690b1d26420d442d236fd6b5
 2024-03-14 21:01:37 +01:00
Tanguy Le Carrour 7319b4d528
teams: Add Tanguy Le Carrour. 
* etc/teams.scm.in ("Tanguy Le Carrour"): New member.

Change-Id: Ic1b1588a5a8bc67ee8e135c3069966f139374529
Signed-off-by: Christopher Baines <mail@cbaines.net>
 2024-03-14 13:48:07 +00:00
Jean-Pierre De Jesus DIAZ 8166d5b81e
gnu: raspi-gpio: Make public. 
As it's unclear why it's not.

* gnu/packages/raspberry-pi.scm (raspi-gpio): Make variable public.

Change-Id: Iaf2789120a726d702d97c3a30a32e3b2cf5da3f1
Signed-off-by: Christopher Baines <mail@cbaines.net>
 2024-03-14 13:42:42 +00:00
Christopher Baines 0e00d2ced1
gnu: combinatorial-blas: Update source hash. 
Diffoscope shows there are changes, but they don't look significant.

* gnu/packages/maths.scm (combinatorial-blas): Update source hash.

Change-Id: I32db6df0ef7c652572b1e874fe22175a4b66af6e
 2024-03-14 13:40:31 +00:00
Fabio Natali 3bd795bc57
doc: Fix section on LUKS support. 
Only LUKS1 is supported in Guix at the time of this commit. Contrarily to what
reported in previous versions of this section, LUKS2 is not supported.

* doc/guix.texi (Keyboard Layout, Networking, and Partitioning)[Disk
Partitioning]: Fix section on LUKS support.

Signed-off-by: Christopher Baines <mail@cbaines.net>
Change-Id: Ia670963178810174d3ea4585c537defbaaeb0f25
 2024-03-14 13:31:13 +00:00
Greg Hogan b5bd0d3a7e
gnu: openjdk21: Update to 21.0.2. 
* gnu/packages/java.scm (openjdk21): Update to 21.0.2.

Signed-off-by: Christopher Baines <mail@cbaines.net>
 2024-03-14 13:27:14 +00:00
Greg Hogan 37073f9dd2
gnu: openjdk20: Update to 20.0.2. 
* gnu/packages/java.scm (openjdk20): Update to 20.0.2.

Signed-off-by: Christopher Baines <mail@cbaines.net>
 2024-03-14 13:27:13 +00:00
Greg Hogan 289666a09c
gnu: openjdk18: Update to 18.0.2.1. 
* gnu/packages/java.scm (openjdk18): Update to 18.0.2.1.

Signed-off-by: Christopher Baines <mail@cbaines.net>
 2024-03-14 13:27:13 +00:00
Greg Hogan b844b81dce
gnu: openjdk17: Update to 17.0.10. 
* gnu/packages/java.scm (openjdk17): Update to 17.0.10.

Signed-off-by: Christopher Baines <mail@cbaines.net>
 2024-03-14 13:27:13 +00:00
Greg Hogan 62c7f9947e
gnu: openjdk15: Update to 15.0.10. 
* gnu/packages/java.scm (openjdk15): Update to 15.0.10.

Signed-off-by: Christopher Baines <mail@cbaines.net>
 2024-03-14 13:27:13 +00:00
Greg Hogan 6d96d7c4e7
gnu: openjdk13: Update to 13.0.14. 
* gnu/packages/java.scm (openjdk13): Update to 13.0.14.

Signed-off-by: Christopher Baines <mail@cbaines.net>
 2024-03-14 13:27:13 +00:00
Greg Hogan d200159b8e
gnu: openjdk12: Update source hash. 
* gnu/packages/java.scm (openjdk12): Update source hash.

Signed-off-by: Christopher Baines <mail@cbaines.net>
Change-Id: I03cbaf3fc21c045c67cd89bb37e232716b03bb30
 2024-03-14 13:26:44 +00:00
Greg Hogan 59bd15a7c6
gnu: openjdk11: Update to 11.0.22. 
* gnu/packages/java.scm (openjdk11): Update to 11.0.22.

Signed-off-by: Christopher Baines <mail@cbaines.net>
 2024-03-14 13:26:30 +00:00
cage dc4842797b
gnu: tinmop: Update to 0.9.9.141421356. 
* gnu/packages/web-browsers.scm (tinmop): Update to 0.9.9.141421356.

Change-Id: Ibf43c33b2581a78d5a4050493049db73f77c896b
Signed-off-by: Guillaume Le Vaillant <glv@posteo.net>
 2024-03-14 11:09:03 +01:00
cage 6e4b1b450c
gnu: cl-croatoan: Update to 0.2-1.282145f. 
* gnu/packages/lisp-xyz.scm (sbcl-croatoan): Update to 0.2-1.282145f.

Change-Id: I8a7e93e9f0dabfa42e35845e610dd5bd2b63cec9
Signed-off-by: Guillaume Le Vaillant <glv@posteo.net>
 2024-03-14 11:04:18 +01:00
Andrew Tropin 507315643e
gnu: emacs-arei: Update to 0.9.3. 
* gnu/packages/emacs-xyz.scm (emacs-arei): Update to 0.9.3.

Change-Id: I4cbdc4d5b65038c34912575a4f106993972c2a6f
 2024-03-14 11:30:45 +03:00
Andrew Tropin bed706f1ff
gnu: guile-ares-rs: Update to 0.9.3. 
* gnu/packages/guile-xyz.scm (guile-ares-rs): Update to 0.9.3.

Change-Id: Iabe57fcb4f1947eb0908109333e4432b8e554cfe
 2024-03-14 11:30:44 +03:00
Nicolas Goaziou 76a3414a1b
gnu: emacs-hyperbole: Update to 9.0.1. 
Fixes <https://issues.guix.gnu.org/69776>.

* gnu/packages/emacs-xyz.scm (emacs-hyperbole): Update to 9.0.1.
[arguments]<#:include>: Add HY-NEWS.

Change-Id: I9d8c4be3d1a1af30f69ac87cf5d0f1db29d5d935
 2024-03-13 21:47:22 +01:00
Efraim Flashner cee74f3725
gnu: rust: Make all intermediate packages public. 
* gnu/packages/rust.scm (rust-1.74, rust-1.75): Make package public.

Change-Id: Id45d6e8c6e6c42811d4cbc3ab50c61045a7c9090
 2024-03-13 21:14:46 +02:00
Efraim Flashner 4e26331a5e
gnu: llvm-17: Fix building on riscv64-linux. 
* gnu/packages/llvm.scm (%llvm-patches): Add a patch for 17.0.6.
* gnu/packages/patches/clang-17.0-link-dsymutil-latomic.patch: New file.
* gnu/local.mk (dist_patch_DATA): Register it.

Change-Id: I9dfd23d2f0fb10620c4aa73a6480151d6e6daa9a
 2024-03-13 17:36:37 +02:00
cage 7b5c030684
gnu: cl-nodgui: Update to 0.6.0.2. 
* gnu/packages/lisp-xyz.scm (sbcl-nodgui): Update to 0.6.0.2.
[inputs]: Add sbcl-cl-opengl, sbcl-sdl2 and sbcl-zpng.

Change-Id: I6fc569d4a32b1f8fc256ae17de186145caa2ac30
Signed-off-by: Christopher Baines <mail@cbaines.net>
 2024-03-13 12:59:42 +00:00
Tomas Volf ca66f63600
gnu: cni-plugins: Update to 1.4.1. 
* gnu/packages/containers.scm (cni-plugins): Update to 1.4.1.

Change-Id: I770504d4f3cf2c74cb14ce8ea37055742529db94
Signed-off-by: Christopher Baines <mail@cbaines.net>
 2024-03-13 12:59:42 +00:00