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Author SHA1 Message Date
宋文武 8ce414a206 gnu: xfce: Add 'stable-version-regexp' property for packages.
* gnu/packages/xfce.scm (libxfce4util, xfconf, libxfce4ui, catfish, exo)
(garcon, tumbler, libxfce4windowing, xfce4-appfinder, xfce4-session)
(xfce4-settings, thunar, thunar-volman, xfwm4, xfdesktop, parole)
(xfce4-power-manager, orage, xfce4-screensaver, xfce4-dev-tools)
[properties]: Add stable-version-regexp.

Merges: guix/guix!5222
Change-Id: Ia296b1ea3dbca95b4c9e99c43a52b4503d5f481a
2026-05-30 10:02:03 +08:00
宋文武 5c41a431df import: git: Support 'stable-version-regexp' property.
Some packages (eg: xfce4-panel) use even number for minor version to indicate
a stable release, when refresh such packages to latest versions we'd like them
to be stable ones.  Introduce 'stable-version-regexp' as a package property,
so that unwanted releases can be filtered out.

* doc/guix.texi (Invoking guix refresh): Document 'stable-version-regexp'.
* guix/import/git.scm (import-git-release): Filter out unstable releases when
target-version is unset but 'stable-version-regexp' is available.

Change-Id: I7bbb2cb41b19175a7e3fb79e00cd8dbb20d049ad
2026-05-30 10:01:58 +08:00
Vagrant Cascadian 5863808183 gnu: linux-libre: Update default version to 7.0.
* gnu/packages/linux.scm (linux-libre-version, linux-libre-gnu-revision,
linux-libre-pristine-source, linux-libre-source, linux-libre,
linux-libre-arm64-mnt-reform): Update to 7.0.

Merges: guix/guix#8954
2026-05-29 14:29:00 -07:00
Cayetano Santos 0b083f0dc9 gnu: qucs-s: Update to 26.1.1.
* gnu/packages/electronics.scm (qucs-s): Update to 26.1.1.

Change-Id: I910a976a69230aac6bf99add71e07bdab122887e
2026-05-29 22:19:16 +02:00
Cayetano Santos 32328a29ce gnu: netgen: Update to 1.5.320.
* gnu/packages/electronics.scm (netgen): Update to 1.5.320.

Change-Id: I64efc82c9164211a063043e609f561033a94bf59
2026-05-29 22:19:16 +02:00
Cayetano Santos 5a889494d5 gnu: magic: Update to 8.3.652.
* gnu/packages/electronics.scm (magic): Update to 8.3.652.

Change-Id: I2aaaa407101952bcd19f869a7d6272488bcbda56
2026-05-29 22:19:16 +02:00
Cayetano Santos 31cbb38266 gnu: klayout: Update to 0.30.9.
* gnu/packages/electronics.scm (klayout): Update to 0.30.9.

Change-Id: If080a1f4ac14b724f5e2b729e6a71a62e40281c9
2026-05-29 22:19:15 +02:00
Jake Forster ac7d094687 gnu: insight-toolkit: Replace zlib with zlib-ng-compat.
* gnu/packages/image-processing.scm (insight-toolkit)[inputs]: Replace zlib
with zlib-ng-compat.

Change-Id: I2286a321420311a8260ce15b30a04519ea88fc90
Signed-off-by: Liliana Marie Prikler <liliana.prikler@gmail.com>
2026-05-29 20:42:08 +02:00
Jake Forster 4093bf9e95 gnu: Add zlib-ng-compat.
* gnu/packages/compression.scm (zlib-ng-compat): New variable.

Change-Id: I765cef93406dc975e93a1c87590abc61b2ef3bd2
Signed-off-by: Liliana Marie Prikler <liliana.prikler@gmail.com>
2026-05-29 20:42:08 +02:00
Jake Forster 66a8184c46 gnu: Add zlib-ng.
* gnu/packages/compression.scm (zlib-ng): New variable.

Change-Id: Ic4f5b9fa005ccc89160f4dc8a275ca6c9adadc30
Signed-off-by: Liliana Marie Prikler <liliana.prikler@gmail.com>
2026-05-29 20:42:08 +02:00
Sören Tempel 26368214a6 gnu: chicken: Refer to required programs by path, not name.
Fixes #8471

* gnu/packages/chicken.scm (chicken)[#:phases]<fix-paths>: Refer
to sh and cp by full path in the Scheme source, instead of by name.
[inputs]: Add bash-minimal.

Change-Id: Id5fc66044c4ae736d7c847d5c781d9317313d3ac
Signed-off-by: Liliana Marie Prikler <liliana.prikler@gmail.com>
2026-05-29 20:42:07 +02:00
Sören Tempel f032a41f41 gnu: chicken: Bootstrap from Scheme source code.
The CHICKEN compiler is itself written in CHICKEN.  To mitigate the
compiler bootstrapping problem, the CHICKEN release tarball includes
auto-generated C code, from which the CHICKEN compiler is build using
a C compiler.

However, if we want to patch the CHICKEN Scheme source (for  #8471), we
need to be able to build the CHICKEN compiler from its Scheme source
files.  This is achieved here by separate the build into two packages
chicken-bootstrap (build from the auto-generated C code) and chicken
(build from the Scheme source).

Note that this still isn't a full-source bootstrap, we still require
the auto-generated C source code, but at least we can now patch the
package based on the Scheme source. Hence, it improves the situation.

See also: https://issues.guix.gnu.org/22366

* gnu/packages/chicken.scm (chicken-bootstrap): Rename from chicken.
* gnu/packages/chicken.scm (chicken): New package.

Change-Id: Ie656e95e2112241b066158a62e55ac07c722c150
Signed-off-by: Liliana Marie Prikler <liliana.prikler@gmail.com>
2026-05-29 20:42:03 +02:00
bdunahu a13589b2b9 gnu: openrct2: Update to 0.5.0.
* gnu/packages/games.scm (openrct2): Update to 0.5.0.
[source]: Unbundle sfl-library and quickjs-ng.
[#:configure-flags]: Do not download music or sound effects.
Disable version checks on startup and Discord RPC.
[#:phases]<fix-usr-share-paths&data>: Also copy sfl includes.
[inputs]: Add flac, libvorbis, quickjs-ng, sfl-library, and ztsd:lib.
Remove duktape.
Replace nlohmann-json with nlohmann-json-no-char8-t.
[license]: Update comment.

Change-Id: I4a6b2952ba0425b8d25e52af78a0ccc9dcdca64e
Signed-off-by: Liliana Marie Prikler <liliana.prikler@gmail.com>
2026-05-29 20:41:32 +02:00
bdunahu 1f146dc38f gnu: openrct2-title-sequences: Update to 0.4.26.
* gnu/packages/games.scm (openrct2-title-sequences): Update to 0.4.26.
[source]: Adjust uri accordingly.

Change-Id: I55b2e7bbb4abc436e390ff89ae2be42613eeab36
Signed-off-by: Liliana Marie Prikler <liliana.prikler@gmail.com>
2026-05-29 20:41:13 +02:00
bdunahu 89d9027f18 gnu: openrct2-objects: Update to 1.7.9.
* gnu/packages/games.scm (openrct2-objects): Update to 1.7.9.

Change-Id: I24d33b3e1f804fb633ed903c8356cf03a93e7b41
Signed-off-by: Liliana Marie Prikler <liliana.prikler@gmail.com>
2026-05-29 20:41:11 +02:00
bdunahu c32a2a2e5d gnu: openrct2-title-sequences: Modernize package declaration.
* gnu/packages/games.scm (openrct2-title-sequences)[source]: Split uri to respect line size limit.
[build-system]: Switch to copy-build-system.
[native-inputs]: Remove bash and coreutils.  Remove input labels.
[homepage]: Use “https://openrct2.io”.

Change-Id: I66171fb3e594f27150d656edc1fc815a2d024ac7
Signed-off-by: Liliana Marie Prikler <liliana.prikler@gmail.com>
2026-05-29 20:40:50 +02:00
bdunahu e02071dae1 gnu: openrct2-objects: Modernize package declaration.
* gnu/packages/games.scm (openrct2-objects)[source]: Split uri to respect line size limit.
[build-system]: Switch to copy-build-system
[native-inputs]: Remove bash and coreutils.  Remove input labels.
[homepage]: Use “https://openrct2.io”

Change-Id: Id0477bde171420676a2f99c68a09f27b4bec5797
Signed-off-by: Liliana Marie Prikler <liliana.prikler@gmail.com>
2026-05-29 20:40:46 +02:00
bdunahu 255921621b gnu: openrct2: Modernize package declaration.
* gnu/packages/games.scm (openrct2)[arguments]: Change to list of
G-Expressions.
<#:phases>: Remove trailing #t.  Use #$output to refer to outputs.
[inputs]: Remove input labels.
[homepage]: Use “https://openrct2.io”.

Change-Id: I8b47d345cd82718d1a2bd40009c480aca7c2c5b3
Signed-off-by: Liliana Marie Prikler <liliana.prikler@gmail.com>
2026-05-29 20:40:44 +02:00
bdunahu 0853a1671f gnu: Add nlohmann-json-no-char8-t.
* gnu/packages/patches/nlohmann_json_fix_char8_t.patch: New file.
* gnu/local.mk: (dist_patch_DATA): Register it.
* gnu/packages/cpp.scm (nlohmann-json-no-char8-t): New variable.

Change-Id: I8b47d345cd82718d1a2bd40009c480aca7c2c5b3
Signed-off-by: Liliana Marie Prikler <liliana.prikler@gmail.com>
2026-05-29 20:40:42 +02:00
bdunahu 54d29defe0 gnu: Add sfl-library.
* gnu/packages/cpp.scm (sfl-library): New variable.

Change-Id: I4c4d054c2cc9fadd1c57996296e382f72ed84864
Signed-off-by: Liliana Marie Prikler <liliana.prikler@gmail.com>
2026-05-29 20:40:41 +02:00
Charles Roelli 42ab6a3899 gnu: Update default prometheus-node-exporter-configuration-package.
* gnu/services/monitoring.scm
(prometheus-node-exporter-configuration) [package]: Use the
non-deprecated prometheus-node-exporter package as a default value.

Merges: guix/guix!8935
Change-Id: I39a0c4eb3cf9e8d82ec0dc134c4f5abe40f1bc4d
Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
2026-05-29 16:41:42 +01:00
Lars Bilke 2c279760e4 gnu: ogs-serial: Update to 6.5.8
* gnu/packages/geo.scm (ogs-serial): Update to 6.5.8.
* gnu/packages/geo.scm (ogs-serial): Remove patch.
* gnu/packages/geo.scm (ogs-serial): Add xdmf input.
* packages/patches/ogs-6.5.7-netcdfconverter.patch: Removed.
* gnu/local.mk: Deregister patch.

Merges: guix/guix!8841
Change-Id: I9b4e502c37ca9470669296d6a038bb1b5e2de8b7
Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
2026-05-29 16:36:27 +01:00
Lars Bilke fa5a46958f gnu: Add xdmf.
* gnu/packages/math.scm (xdmf): New variable.
* gnu/packages/patches/xdmf-3.0.0-hdf5.patch: Patch for xdmf.
* gnu/local.mk: Register patch.

Relates-to: guix/guix!8841
Change-Id: I0606eaf8f6524f3efe71b442405438e4df070ff7
Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
2026-05-29 16:36:18 +01:00
orahcio e87c221cd2 gnu: Add whatscli.
* gnu/packages/messaging.scm (whatscli): New variable.

Merges: guix/guix!8655
Change-Id: I2c2f03afc93a538bdaf83424d3186665e9749e13
Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
2026-05-29 15:51:35 +01:00
orahcio a2b4e406b9 gnu: mautrix-whatsapp: Update to 0.2605.0.
* gnu/packages/matrix.scm (mautrix-whatsapp): Update to 0.2605.0.

Relates-to: guix/guix!8655
Change-Id: I39d044b02437d2b63f79e0ad9f19c7434c6acf9b
Modified-by: Sharlatan Hellseher <sharlatanus@gmail.com>
Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
2026-05-29 15:51:35 +01:00
orahcio 347d83f6b4 gnu: go-go-mau-fi-util: Update to 0.9.9.
* gnu/packages/golang-xyz.scm (go-go-mau-fi-util): Update to 0.9.9.

Relates-to: guix/guix!8655
Change-Id: Ibae7a9301e491c5e9b47937ee04862179ef536d9
Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
2026-05-29 15:51:34 +01:00
orahcio 50fde0c4f1 gnu: go-maunium-net-go-mautrix: Update to 0.28.0.
* gnu/packages/golang-web.scm (go-maunium-net-go-mautrix): Update to 0.28.0.
[arguments] <test-flags>: Rework skipped tests.
[propagated-inputs]: Remove go-github-com-gorilla-mux and
go-github-com-gorilla-websocket; add go-github-com-coder-websocket, and
olm.
[native-inputs]: olm move to [propagated-inputs].

Relates-to: guix/guix!8655
Change-Id: I1946010f414edb46caa38eb33f034f0e68ee1397
Modified-by: Sharlatan Hellseher <sharlatanus@gmail.com>
Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
2026-05-29 15:51:34 +01:00
orahcio 153c2aa234 gnu: go-go-mau-fi-whatsmeow: Update to 0.0.0-20260529101937-a7ea56383ec4.
* gnu/packages/golang-web.scm (go-go-mau-fi-whatsmeow): Update to
0.0.0-20260529101937-a7ea56383ec4.
[propagated-inputs]: Remove go-github-com-gorilla-websocket; add
go-github-com-beeper-argo-go, go-github-com-coder-websocket and
go-golang-org-x-sync.

Relates-to: guix/guix!8655
Change-Id: If0f2e561b68a91e30b5068558077f6d433e3c403
Modified-by: Sharlatan Hellseher <sharlatanus@gmail.com>
Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
2026-05-29 15:51:34 +01:00
orahcio dd96fdd983 gnu: go-go-mau-fi-libsignal: Update to 0.2.1.
* gnu/packages/golang-crypto.scm (go-go-mau-fi-libsignal): Update to 0.2.1.

Relates-to: guix/guix!8655
Change-Id: Ie89222a54e530c8336dcc41a30cc57d173669c78
Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
2026-05-29 15:51:34 +01:00
orahcio c1ad3df229 gnu: Add go-github-com-beeper-argo-go.
* gnu/packages/golang-web.scm (go-github-com-beeper-argo-go): New variable.

Relates-to: guix/guix!8655
Change-Id: Ic53a29ec2659c7d3c8abd8ac59853193212757ee
Modified-by: Sharlatan Hellseher <sharlatanus@gmail.com>
Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
2026-05-29 15:51:34 +01:00
orahcio 1099daf023 gnu: Add go-code-rocketnine-space-tslocum-cbind.
* gnu/packages/golang-xyz.scm (go-code-rocketnine-space-tslocum-cbind): New variable.

Relates-to: guix/guix!8655
Change-Id: I72febb98a17fb30372629542ccfbaacd28789dfe
Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
2026-05-29 15:51:34 +01:00
orahcio c82ff29e50 gnu: Add go-github-com-elliotchance-orderedmap-v3.
* gnu/packages/golang-xyz.scm (go-github-com-elliotchance-orderedmap-v3): New variable.

Relates-to: guix/guix!8655
Change-Id: I67e941a00316d44bed154472fa30dbd7f7388834
Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
2026-05-29 15:51:34 +01:00
orahcio 9b26838b93 gnu: Add go-github-com-gen2brain-beeep.
* gnu/packages/golang-xyz.scm (go-github-com-gen2brain-beeep): New variable.

Relates-to: guix/guix!8655
Change-Id: Ia67c794b6cf2697710f7dec39ffcaa662c7abdb0
Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
2026-05-29 15:51:34 +01:00
orahcio 7f676b2756 gnu: Add go-github-com-esiqveland-notify.
* gnu/packages/golang-xyz.scm (go-github-com-esiqveland-notify): New variable.

Relates-to: guix/guix!8655
Change-Id: I9711d42925dad3018872e8b5d52de6e3d9daf228
Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
2026-05-29 15:51:33 +01:00
orahcio a011ccb66a gnu: Add go-github-com-jackmordaunt-icns-v3.
* gnu/packages/golang-graphics.scm (go-github-com-jackmordaunt-icns-v3):
New variable.

Relates-to: guix/guix!8655
Change-Id: I306a31ec0ff372b29faa234be760b6cb60d46eff
Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
2026-05-29 15:51:33 +01:00
orahcio beee9fb721 gnu: Add go-github-com-sergeymakinen-go-ico.
* gnu/packages/golang-graphics.scm (go-github-com-sergeymakinen-go-ico):
New variable.

Relates-to: guix/guix!8655
Change-Id: I99edcfb5ab9ea430cbaf6f44547b1d8293da58f0
Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
2026-05-29 15:51:33 +01:00
orahcio 7bb3f86293 gnu: Add go-github-com-sergeymakinen-go-bmp.
* gnu/packages/golang-graphics.scm (go-github-com-sergeymakinen-go-bmp): New variable.

Relates-to: guix/guix!8655
Change-Id: Icfd72c90bdf55258d39632cb39a76384c2887919
Modified-by: Sharlatan Hellseher <sharlatanus@gmail.com>
Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
2026-05-29 15:51:33 +01:00
orahcio d668bc43ee gnu: Add go-github-com-zyedidia-clipboard.
* gnu/packages/golang-xyz.scm (go-github-com-zyedidia-clipboard): New variable.

Relates-to: guix/guix!8655
Change-Id: Ie9360b3944464cc6026794f09acccaaf562797da
Modified-by: Sharlatan Hellseher <sharlatanus@gmail.com>
Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
2026-05-29 15:51:31 +01:00
jgart a500ce3177 gnu: trealla: Update to 2.100.25.
* gnu/packages/prolog.scm (trealla): Update to 2.100.25.

Change-Id: Ie39bfe037c19902198b2ab066f6c36c5913e73d8
2026-05-29 10:27:37 -04:00
luca 77eb5a4a3c gnu: thunar: Update to 4.20.8.
* gnu/packages.xfce.scm (thunar): Update to 4.20.8.

Merges: guix/guix!8937
Change-Id: I0e95410bf2cc6548496170e17eb4ebc9f1ff16d0
Signed-off-by: 宋文武 <iyzsong@member.fsf.org>
2026-05-29 20:32:45 +08:00
Andreas Enge a7d4c7fe4b gnu: thunarx-python: Fix build.
* gnu/packages/xfce.scm (thunarx-python)[native-inputs]: Add
python-setuptools.

Merges: guix/guix!8931
Change-Id: Id3ebf04ce0a03b58e880bd1f0993c0a71e50f93c
Signed-off-by: 宋文武 <iyzsong@member.fsf.org>
2026-05-29 20:32:45 +08:00
Josep Bigorra 7134d139d4 gnu: Add guile-scriba.
* gnu/packages/guile-xyz.scm (guile-scriba): New variable.

Change-Id: I7ed365dedb307a8619b54f9978e135e0214a90bc
Signed-off-by: Ludovic Courtès <ludo@gnu.org>
Merges: #8868
2026-05-29 14:28:29 +02:00
Josep Bigorra 9591ab8c99 gnu: guile-veritas: Update to 0.3.0.
* gnu/packages/guile-xyz.scm (guile-veritas): Update to 0.3.0.

- Added guile-json-4 to propagated-inputs

add forgotten dependency

Change-Id: I9c9e195657217ebae4b5b4b00e96c6a728263a49
Signed-off-by: Ludovic Courtès <ludo@gnu.org>
Merges: #8815
2026-05-29 14:27:34 +02:00
Herman Rimm 4514f4cf19 scripts: lint: Add 'whole-file' option with ordering checker.
* guix/scripts/lint.scm (show-help): Describe option.
(%options): Add 'whole-file' option.
(guix-lint): Run checkers on packages defined in files.
* doc/guix.texi (Invoking guix lint): Document option.
* tests/guix-lint.sh: Define unordered package and invoke new option.

Change-Id: I52b48a9a6982d0c4a03416e3d070887c64716485
Signed-off-by: Ludovic Courtès <ludo@gnu.org>
Merges: #8796
2026-05-29 14:23:28 +02:00
Herman Rimm 1d3d136bb0 guix: Move ‘package-location<?’ to (guix packages).
* guix/scripts/style.scm (package-location<?): Move to…
* guix/packages.scm (package-location<?): … here.

Change-Id: I8ebb37c261a1bb3fa5772177b27fd62a2553e318
Signed-off-by: Ludovic Courtès <ludo@gnu.org>
2026-05-29 14:23:28 +02:00
Sergio Pastor Pérez b7a618f9f2 gnu: tensile: Set executable permissions for Tensile Python scripts.
* gnu/packages/rocm-libs.scm (tensile): Set executable permissions for Tensile
Python scripts.

Fixes: guix/guix#8553

Change-Id: I29c07898877325af5fd8f448e74ef8ea7111a640
Signed-off-by: Ludovic Courtès <ludo@gnu.org>
Merges: #8845
2026-05-29 14:17:27 +02:00
Ricardo Wurmus 33acdbdfb1 gnu: pigx-chipseq: Use latest Snakemake.
* gnu/packages/bioinformatics.scm (pigx-chipseq)[inputs]: Replace
snakemake-7 with snakemake.

Change-Id: I2b12fce7ed04be71643ae4b72931a123bbc63b36
2026-05-29 12:03:06 +02:00
Ricardo Wurmus ce49115168 gnu: pigx-bsseq: Update to 0.1.10-0.1b3a69b.
* gnu/packages/bioinformatics.scm (pigx-bsseq): Update to 0.1.10-0.1b3a69b.
[source]: Fetch git repository.
[arguments]: Add phase 'delete-GNUmakefile.
[native-inputs]: Add autoconf and automake.

Change-Id: I1be72e1016b57c0bc576de689a2edcc31a101d1e
2026-05-29 12:03:06 +02:00
Ricardo Wurmus 8be76ae944 gnu: pigx-sars-cov-2: Use latest Snakemake.
* gnu/packages/bioinformatics.scm (pigx-sars-cov-2)[inputs]: Replace
snakemake-7 with snakemake.

Change-Id: I3cd53aa84a3b49b4eabea2b93e40095d5ee957b6
2026-05-29 12:03:05 +02:00
Anderson Torres 72d813155f gnu: Add let-go.
* gnu/packages/clojure.scm (let-go): New variable.

Merges: guix/guix!8619
Change-Id: I7e2ba76758a16a6a60040582b07cca8d9c70833a
Modified-by: Sharlatan Hellseher <sharlatanus@gmail.com>
Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
2026-05-29 10:18:59 +01:00
Anderson Torres decfac5d56 gnu: clojure.scm: Reorder #:use-module directives alphabetically.
* gnu/packages/clojure.scm: Reorder #:use-module directives alphabetically.

Relates-to: guix/guix!8619
Change-Id: I2c73c5fd9902cff2222964b375544f42f711be5a
Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
2026-05-29 10:18:59 +01:00
Anderson Torres 7519fe23c0 gnu: Add go-github-com-zeebo-bencode.
* gnu/packages/golang-xyz.scm (go-github-com-zeebo-bencode): New variable.

Relates-to: guix/guix!8619
Change-Id: I43b6841b81f99afa1417367715cb492e4d34acb6
Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
2026-05-29 10:18:59 +01:00
Anderson Torres 01d66eb90b gnu: Add go-github-com-alimpfard-line.
* gnu/packages/golang-xyz.scm (go-github-com-alimpfard-line): New variable.

Relates-to: guix/guix!8619
Change-Id: I60ea28e595c1ae80db635449abcd360ca6cd6a8c
2026-05-29 10:18:59 +01:00
Andreas Enge 3288e2f586 gnu: sage: Update to 10.9.
* gnu/packages/sagemath.scm (sage): Update to 10.9.

Change-Id: If8f93389ffe8bb8449476e61bfcb83d61c2c3839
2026-05-29 10:58:23 +02:00
Arun Isaac b8354c2979 services: mumi: Make rsync and index timer event configurable.
* gnu/services/web.scm (<mumi-configuration>)[rsync-and-index-event]: New
field.
* gnu/services/web.scm (mumi-shepherd-services): Use it.
* doc/guix.texi (Web Services)[Mumi]: Document it.

Change-Id: I5910c4a93106b44eaf3900d6a72fb501c01b8773
2026-05-29 09:48:26 +01:00
Cayetano Santos 33036b2908 gnu: perl-gnupg-interface: Update to 1.06.
* gnu/packages/gnupg.scm (perl-gnupg-interface): Update to 1.06.

Merges guix/guix!8909

Change-Id: Ia60101846e415863d5f2f089ceeb5a84d52e8991
2026-05-29 10:44:55 +02:00
Cayetano Santos 01b64d3428 gnu: gpa: Update to 0.11.1.
* gnu/packages/gnupg.scm (gpa): Update to 0.11.1.

Merges guix/guix!8909

Change-Id: I83c5d8180ae5f50953c2c9f6a606c14e5b78b3b9
2026-05-29 10:44:47 +02:00
Cayetano Santos 1c7e2df756 gnu: gpa: Refresh package.
* gnu/packages/gnupg.scm (gpa)[arguments]: Switch to G-Expressions.

Merges guix/guix!8909

Change-Id: I2352a74b486729dcbaf548d497dcbaec0a85c85d
2026-05-29 10:44:39 +02:00
Cayetano Santos 062cd42d46 gnu: signing-party: Update to 2.12.
* gnu/packages/gnupg.scm (signing-party): Update to 2.12.

Merges guix/guix!8909

Change-Id: Icfeb77fca0f9a4f89bf726d4dbe00d5661b17821
2026-05-29 10:44:31 +02:00
Cayetano Santos 5764620de1 gnu: signing-party: Refresh package.
* gnu/packages/gnupg.scm (signing-party)[arguments]: Switch to
G-Expressions; apply max column.

Merges guix/guix!8909

Change-Id: I86de74da637d3484f37db90a7315ee37183d9177
2026-05-29 10:44:23 +02:00
Cayetano Santos 7c271adcee gnu: llama-cpp: Update to 0.0.0-9353.
* gnu/packages/machine-learning.scm (llama-cpp): Update to
0.0.0-9353.
[arguments]<#:configure-flags>: Retore build ui.
<#:phases>: Add ’get-ui; update ’fix-tests.
[inputs]: Add ui.

Merges guix/guix!8859

Change-Id: I34da043c207041e14ce97e92799f541da3ce862d
2026-05-29 10:42:09 +02:00
Cayetano Santos e8f0ac36a0 gnu: ggml: Update to 0.13.0.
* gnu/packages/machine-learning.scm (ggml): Update to 0.13.0.

Merges guix/guix!8859

Change-Id: I1a64b171c313f7b8217e20a347bba6548fd829e4
2026-05-29 10:42:08 +02:00
Nguyễn Gia Phong 728e54fbae Revert "gnu: node-typescript: Update to 6.0.3."
This reverts commit ba4943661a,
which was pushed by mistake.

Change-Id: I887a59c3fc67c9618ffb4f3d9e7e2314954a0050
2026-05-29 17:27:53 +09:00
Nguyễn Gia Phong 2cc6aacbd7 gnu: postgresql-14: Graft to 14.23 [security fixes].
PostgreSQL 14.23 contains fixes for CVE-2026-6472, CVE-2026-6473,
CVE-2026-6474, CVE-2026-6475, CVE-2026-6477, CVE-2026-6478,
CVE-2026-6479 and CVE-2026-6637.

* gnu/packages/databases.scm (postgresql-14): Update to 14.23.

Change-Id: I15229d938c5bfbd787d4b5f6a9328d79ba1b3626
2026-05-29 16:41:30 +09:00
Nguyễn Gia Phong 20dcd44484 gnu: postgresql-15: Update to 15.18.
PostgreSQL 14.23 contains fixes for CVE-2026-6472, CVE-2026-6473,
CVE-2026-6474, CVE-2026-6475, CVE-2026-6477, CVE-2026-6478,
CVE-2026-6479 and CVE-2026-6637.

* gnu/packages/databases.scm (postgresql-15): Update to 15.18.

Change-Id: I6435952609e84c232cf3ed092ff067f855f9a414
2026-05-29 16:41:30 +09:00
Nguyễn Gia Phong 75a84eaea6 gnu: postgresql-16: Update to 16.14.
PostgreSQL 16.14 contains fixes for CVE-2026-6472, CVE-2026-6473,
CVE-2026-6474, CVE-2026-6475, CVE-2026-6477, CVE-2026-6478,
CVE-2026-6479, CVE-2026-6637 and CVE-2026-6638.

* gnu/packages/databases.scm (postgresql-16): Update to 16.14.

Change-Id: Ifa8a9a86618a06d5ca6b4f34b542f05508b87b30
2026-05-29 16:41:30 +09:00
Nguyễn Gia Phong f15277c19a gnu: postgresql-17: Update to 17.10.
PostgreSQL 17.10 contains fixes for CVE-2026-6472, CVE-2026-6473,
CVE-2026-6474, CVE-2026-6475, CVE-2026-6476, CVE-2026-6477,
CVE-2026-6478, CVE-2026-6479, CVE-2026-6637 and CVE-2026-6638.

* gnu/packages/databases.scm (postgresql-17): Update to 17.10.

Change-Id: I761ff3cc28c7b21eb15a6cd7f5cb2e2c48a1915b
2026-05-29 16:41:29 +09:00
Kjartan Oli Agustsson ba4943661a gnu: node-typescript: Update to 6.0.3.
* gnu/packages/node-xyz.scm (node-typescript): Update to 6.0.3.

Change-Id: I1989b73d7ecabd2bfcfe6495f317776484d6ddbf
Merges: https://codeberg.org/guix/guix/pulls/8623
Signed-off-by: Nguyễn Gia Phong <cnx@loang.net>
2026-05-29 16:41:29 +09:00
Anderson Torres cf21d51433 gnu: Remove pending references to deprecated (gnu packages flex).
* gnu/packages/c.scm:  Remove references to (gnu packages flex).
* gnu/packages/video.scm: Likewise.
* gnu/packages/web.scm: Likewise.
* gnu/packages/admin.scm: Change (gnu packages flex)
  to (gnu packages compiler-tools).
* gnu/packages/algebra.scm: Likewise.
* gnu/packages/apparmor.scm: Likewise.
* gnu/packages/assembly.scm: Likewise.
* gnu/packages/astronomy.scm: Likewise.
* gnu/packages/audio.scm: Likewise.
* gnu/packages/bioinformatics.scm: Likewise.
* gnu/packages/bison.scm: Likewise.
* gnu/packages/bootloaders.scm: Likewise.
* gnu/packages/cdrom.scm: Likewise.
* gnu/packages/chemistry.scm: Likewise.
* gnu/packages/cluster.scm: Likewise.
* gnu/packages/cobol.scm: Likewise.
* gnu/packages/code.scm: Likewise.
* gnu/packages/commencement.scm: Likewise.
* gnu/packages/coq.scm: Likewise.
* gnu/packages/coreboot.scm: Likewise.
* gnu/packages/databases.scm: Likewise.
* gnu/packages/datalog.scm: Likewise.
* gnu/packages/debug.scm: Likewise.
* gnu/packages/dictionaries.scm: Likewise.
* gnu/packages/dns.scm: Likewise.
* gnu/packages/documentation.scm: Likewise.
* gnu/packages/dotnet.scm: Likewise.
* gnu/packages/education.scm: Likewise.
* gnu/packages/electronics.scm: Likewise.
* gnu/packages/embedded.scm: Likewise.
* gnu/packages/emulators.scm: Likewise.
* gnu/packages/engineering.scm: Likewise.
* gnu/packages/esolangs.scm: Likewise.
* gnu/packages/fabric-management.scm: Likewise.
* gnu/packages/file-systems.scm: Likewise.
* gnu/packages/finance.scm: Likewise.
* gnu/packages/firmware.scm: Likewise.
* gnu/packages/flashing-tools.scm: Likewise.
* gnu/packages/fontutils.scm: Likewise.
* gnu/packages/games.scm: Likewise.
* gnu/packages/gcc.scm: Likewise.
* gnu/packages/gdb.scm: Likewise.
* gnu/packages/geo.scm: Likewise.
* gnu/packages/gl.scm: Likewise.
* gnu/packages/glib.scm: Likewise.
* gnu/packages/gnome.scm: Likewise.
* gnu/packages/graph.scm: Likewise.
* gnu/packages/graphics.scm: Likewise.
* gnu/packages/groff.scm: Likewise.
* gnu/packages/gstreamer.scm: Likewise.
* gnu/packages/guile.scm: Likewise.
* gnu/packages/hardware.scm: Likewise.
* gnu/packages/haskell.scm: Likewise.
* gnu/packages/heads.scm: Likewise.
* gnu/packages/hurd.scm: Likewise.
* gnu/packages/image-processing.scm: Likewise.
* gnu/packages/instrumentation.scm: Likewise.
* gnu/packages/kde-frameworks.scm: Likewise.
* gnu/packages/kde-graphics.scm: Likewise.
* gnu/packages/kde-pim.scm: Likewise.
* gnu/packages/kde-sdk.scm: Likewise.
* gnu/packages/kerberos.scm: Likewise.
* gnu/packages/lego.scm: Likewise.
* gnu/packages/lesstif.scm: Likewise.
* gnu/packages/libreoffice.scm: Likewise.
* gnu/packages/lighting.scm: Likewise.
* gnu/packages/linux.scm: Likewise.
* gnu/packages/logging.scm: Likewise.
* gnu/packages/mail.scm: Likewise.
* gnu/packages/man.scm: Likewise.
* gnu/packages/maths.scm: Likewise.
* gnu/packages/mpi.scm: Likewise.
* gnu/packages/multiprecision.scm: Likewise.
* gnu/packages/music.scm: Likewise.
* gnu/packages/netpbm.scm: Likewise.
* gnu/packages/networking.scm: Likewise.
* gnu/packages/nickle.scm: Likewise.
* gnu/packages/ocaml.scm: Likewise.
* gnu/packages/package-management.scm: Likewise.
* gnu/packages/parallel.scm: Likewise.
* gnu/packages/plotutils.scm: Likewise.
* gnu/packages/pretty-print.scm: Likewise.
* gnu/packages/profiling.scm: Likewise.
* gnu/packages/qt.scm: Likewise.
* gnu/packages/radio.scm: Likewise.
* gnu/packages/rdesktop.scm: Likewise.
* gnu/packages/rpc.scm: Likewise.
* gnu/packages/rust.scm: Likewise.
* gnu/packages/security-token.scm: Likewise.
* gnu/packages/selinux.scm: Likewise.
* gnu/packages/shellutils.scm: Likewise.
* gnu/packages/simulation.scm: Likewise.
* gnu/packages/statistics.scm: Likewise.
* gnu/packages/telephony.scm: Likewise.
* gnu/packages/toys.scm: Likewise.
* gnu/packages/version-control.scm: Likewise.
* gnu/packages/virtualization.scm: Likewise.
* gnu/packages/vpn.scm: Likewise.
* gnu/packages/vulkan.scm: Likewise.
* gnu/packages/webkit.scm: Likewise.
* gnu/packages/wine.scm: Likewise.
* gnu/packages/wm.scm: Likewise.
* gnu/packages/xdisorg.scm: Likewise.
* gnu/packages/xorg.scm: Likewise.

Merges: https://codeberg.org/guix/guix/pulls/8483
Signed-off-by: Nguyễn Gia Phong <cnx@loang.net>
2026-05-29 16:41:06 +09:00
Anderson Torres c74733f035 gnu: Change (gnu packages re2c) to (gnu packages compiler-tools).
* gnu/packages/build-tools.scm: Change (gnu packages re2c)
  to (gnu packages compiler-tools).
* gnu/packages/lua.scm: Likewise.
* gnu/packages/perl-web.scm: Likewise.
* gnu/packages/potassco.scm: Likewise.
* gnu/packages/video.scm: Likewise.
* gnu/packages/web.scm: Likewise.

Change-Id: I8b95c1bd646fae34260a92f48038400eb97413fd
Signed-off-by: Nguyễn Gia Phong <cnx@loang.net>
2026-05-29 16:41:06 +09:00
Anderson Torres b25c0b62fe gnu: re2c: Migrate to (gnu packages compiler-tools).
* gnu/packages/compiler-tools.scm: Move to here...
* gnu/packages/re2c.scm (re2c): ...from here.  New deprecated variable.

Change-Id: I540e0d2cf0a1137e08f0278e2768b02b9d6fdfae
Signed-off-by: Nguyễn Gia Phong <cnx@loang.net>
2026-05-29 16:41:06 +09:00
Anderson Torres 1fcf978657 gnu: flex: Drop input label.
* gnu/packages/compiler-tools.scm (flex)[inputs]: Drop label.

Change-Id: I2fc83a76735bf66a68a0e56d3ca3558265cde872
Modified-by: Nguyễn Gia Phong <cnx@loang.net>
Signed-off-by: Nguyễn Gia Phong <cnx@loang.net>
2026-05-29 16:41:06 +09:00
Anderson Torres 7af7accf2f gnu: flex: Migrate to (gnu packages compiler-tools).
* gnu/packages/compiler-tools.scm (flex): Move to here...
* gnu/packages/flex.scm (flex): ...from here.  New deprecated variablle.

Change-Id: I505ce7660096fc6325b96eafe1e130d7a1f3924b
Signed-off-by: Nguyễn Gia Phong <cnx@loang.net>
2026-05-29 16:41:05 +09:00
Ricardo Wurmus f7c1f2cafe gnu: pigx-rnaseq: Update to 0.1.1-0.1605b54.
* gnu/packages/bioinformatics.scm (pigx-rnaseq): Update to 0.1.1-0.1605b54.
[source]: Fetch git repository.
[arguments]: Adjust phase 'disable-resource-intensive-test.
[inputs]: Replace snakemake-7 with snakemake.

Change-Id: I4aa4d681061ecc58cb819fe95c919da55eb34532
2026-05-29 09:29:40 +02:00
Cayetano Santos eec2d7a1c8 gnu: Remove emacs-flymake-shellcheck.
* gnu/packages/emacs-xyz.scm (emacs-flymake-shellcheck): Delete
variable.

Merges guix/guix!8463

Change-Id: I7ea08bf680f85b76ff6860dead6e59c940c268e8
2026-05-29 09:27:17 +02:00
Cayetano Santos d6d8b1bb4f gnu: Add emacs-emcp.
* gnu/packages/emacs-xyz.scm (emacs-emcp): New variable.

Merges guix/guix!8781

Change-Id: I629b6f723bcc68c4c9910662f1915e9852161067
Signed-off-by: Cayetano Santos <csantosb@inventati.org>
2026-05-29 09:21:56 +02:00
Cayetano Santos e1b33e1dd2 gnu: Add emacs-http-server.
* gnu/packages/emacs-xyz.scm (emacs-http-server): New variable.

Merges guix/guix!8781

Change-Id: I6d99fffb9ec9289cd7a92afbee9ce6eff0789e73
Signed-off-by: Cayetano Santos <csantosb@inventati.org>
2026-05-29 09:21:56 +02:00
Maxim Cournoyer 613e069b3f .dir-locals.el: Refine `bug-reference-bug-regexp' regular expression.
There is no need to special-case !NNN compared to #NNN, both are valid and
serve difference purposes (PRs vs issues).

* .dir-locals.el: Refine `bug-reference-bug-regexp' regular expression.

Change-Id: I8246203a11c338be02b7a731f477b3411aa23ece
2026-05-29 16:06:39 +09:00
Nicolas Goaziou f5302d3491 gnu: Add font-literata.
* gnu/packages/fonts.scm (font-literata): New variable.

Change-Id: Ia37f493b12221016b8348899871c2639df63100f
2026-05-29 09:03:16 +02:00
Ashish SHUKLA b3479e0f53 gnu: got: Update to 0.126
* gnu/packages/version-control.scm (got): Update to 0.126.

Change-Id: I35fef23587cf519e9c154673e28806ff9772b57d
Merges: https://codeberg.org/guix/guix/pulls/8847
Signed-off-by: Nguyễn Gia Phong <cnx@loang.net>
2026-05-29 15:54:32 +09:00
Ashish SHUKLA 1ec29241ef gnu: kakoune: Update to 2026.05.21
* gnu/packages/text-editors.scm (kakoune): Update to 2026.05.21.
  [inputs]: Add bash-minimal.

Change-Id: Idec5798eca8f962d0f01cabb847c9ca5bfdcac74
Merges: https://codeberg.org/guix/guix/pulls/8751
Reviewed-by: Sughosha <sughosha@disroot.org>
Signed-off-by: Nguyễn Gia Phong <cnx@loang.net>
2026-05-29 15:50:41 +09:00
luca 921621c78d gnu: Add zeptofetch.
* gnu/packages/admin.scm (zeptofetch): New variable.

Change-Id: I3b9cc1bd18152596520225eaaee4816a1a18b003
Merges: https://codeberg.org/guix/guix/pulls/8865
Signed-off-by: Nguyễn Gia Phong <cnx@loang.net>
2026-05-29 15:46:39 +09:00
Andy Tai 21e90a96c7 gnu: xrdp: Update to 0.10.6.
* gnu/packages/rdesktop.scm (xrdp): Update to 0.10.6.

Change-Id: I147247273a987311149563373ecea37b08fd782c
Merges: https://codeberg.org/guix/guix/pulls/8906
Reviewed-by: Sharlatan Hellseher <sharlatanus@gmail.com>
Signed-off-by: Nguyễn Gia Phong <cnx@loang.net>
2026-05-29 15:44:04 +09:00
Patrick Norton e59a793af1 gnu: widelands: Update to 1.3.1.
* gnu/packages/games.scm (widelands): Update to 1.3.1.

Change-Id: I53a028c09fda013fd8b26b4b6b66417a30757ab1
Merges: https://codeberg.org/guix/guix/pulls/8762
Reviewed-by: kestrel <kestrel.w@proton.me>
Signed-off-by: Nguyễn Gia Phong <cnx@loang.net>
2026-05-29 15:41:25 +09:00
Zhu Zihao 6028a2f7ed gnu: musl: Update to 1.2.6 [security-fixes].
This update contains fixes for:
- CVE-2025-26519: musl libc: input-controlled out-of-bounds
  write primitive in iconv()
- CVE-2026-6042: musl libc GB18030 4-byte Decoder iconv.c
  iconv algorithmic complexity
- CVE-2026-40200: musl libc: stack corruption in qsort
  with sufficiently large inputs

* gnu/packages/musl.scm (musl): Update to 1.2.6.
* gnu/packages/patches/musl-CVE-2026-40200.patch: New patch.
* gnu/packages/patches/musl-cross-locale.patch: Remove stale patch.
* gnu/local.mk (dist_DATA): Add entry for musl-CVE-2026-40200.patch,
  remove entry for musl-cross-locale.patch.

Change-Id: I52b60b119a3a3c720f3098ad5e89c2e1382153e5
Merges: https://codeberg.org/guix/guix/pulls/8878
Reviewed-by: Nicolas Graves <ngraves@ngraves.fr>
Signed-off-by: Nguyễn Gia Phong <cnx@loang.net>
2026-05-29 15:33:26 +09:00
Spencer King 380d705b4e gnu: Add python-cotengra.
* gnu/packages/python-science.scm (python-cotengra): New variable.

Merges guix/guix!8830

Change-Id: I414616ad579831498180578eb40682ac3c455df6
Signed-off-by: Cayetano Santos <csantosb@inventati.org>
2026-05-29 07:58:20 +02:00
Cayetano Santos 1b4fd88b07 gnu: emacs-forgejo: Update to 0.2.3.
* gnu/packages/emacs-xyz.scm (emacs-forgejo): Update to 0.2.3.

Change-Id: Iad79dab798dae40e4105cfde921ec0620c21fed6
2026-05-29 07:54:22 +02:00
Ashish SHUKLA 950bae548a gnu: sqlite-next: Update to 3.53.1
* gnu/packages/sqlite.scm (sqlite-next): Update to 3.53.1.

Change-Id: I624018963384d03bedf1cd73c5b8bb92373dcd54
Merges: https://codeberg.org/guix/guix/pulls/8853
Signed-off-by: Nguyễn Gia Phong <cnx@loang.net>
2026-05-29 14:26:27 +09:00
Maxim Cournoyer 39baeaa58f Update commit-msg hook.
Retrieved from <https://gerrit.googlesource.com/gerrit/+/refs/heads/master/resources/com/google/gerrit/server/tools/root/hooks/commit-msg>.

Fixes: <https://issues.guix.gnu.org/81044>
Change-Id: Ia0bbc6fac3354df6162c813fe94c344a041ffbaf
Reported-by: Tomas Volf <~@wolfsden.cz>
2026-05-29 14:09:15 +09:00
Maxim Cournoyer f9a8158580 gnu: mysql-connector-python: Update to 9.7.0.
* gnu/packages/databases.scm (mysql-connector-python): Update to 9.7.0.
[#:configure-flags]: Delete.
[#:phases] {chdir}: New phase.
{check}: Remove all substitutions.
[propagated-inputs]: Delete.
[inputs]: Add zstd:lib.  Remove protobuf-3.20.  Replace openssl-1.1 with
openssl.

Change-Id: Ic00e586a85988f4a4f8939842b2b6017b3f19160
2026-05-29 13:20:05 +09:00
Maxim Cournoyer 2c79f4d932 gnu: mysql: Update to 9.7.0 and make reproducible [security fixes].
Fixes a slew of security vulnerabilities, which can be consulted here:
<https://nvd.nist.gov/vuln/search#/nvd/home?cpeFilterMode=cpe&cpeName=cpe:2.3:a:oracle:mysql:5.7.33:*:*:*:-:*:*:*&resultType=records>

* gnu/packages/databases.scm (mysql): Remove stale comment.  Update to 9.7.0.
[source]: Adjust URI.  Delete most bundled library sources.
[#:tests?]: Set to #f.
[#:configure-flags]: Replace -DWITH_SSL=system and -DWITH_ZLIB=system with
-DWITH_SYSTEM_LIBS=ON.  Add -DWITH_AUTHENTICATION_LDAP=ON,
-DWITH_AUTHENTICATION_WEBAUTHN=ON, -DWITH_BENCHMARK=OFF
-DWITH_BUILD_ID=OFF, -DWITH_FIDO=system, -DWITH_SYSTEM_LIBS=ON,
-DREPRODUCIBLE_BUILD=ON.  Set -DINSTALL_INFODIR to share/info.
Set -DINSTALL_MYSQLTESTDIR to OFF.  Delete
-DINSTALL_SCRIPTDIR=bin, -DDEFAULT_CHARSET=utf8,
-DDEFAULT_COLLATION=utf8_general_ci and -DINSTALL_SQLBENCHDIR="".
[#:phases] {disable-broken-abi-check, fix-permissions}: New phases.
[inputs]: Replace boost-for-mysql with boost.  Replace openssl-1.1 with
openssl.  Add curl, cyrus-sasl, icu4c, libedit, libfido2, lz4, mit-krb5,
openldap, protobuf and zstd:lib.
[license]: Add comment.

Fixes: #7500
Fixes: #8897
Change-Id: Ia089e66064406d082de8b17e31ffdca6eaf42449
2026-05-29 13:20:05 +09:00
Julian Flake ffe6057e2a gnu: aqbanking: Update to 6.9.2.
* gnu/packages/gnucash.scm (aqbanking): Update to 6.9.2.

Change-Id: If4831653ac1d442633a75df77ef8554c118056e6
Merges: https://codeberg.org/guix/guix/pulls/8840
Signed-off-by: Nguyễn Gia Phong <cnx@loang.net>
2026-05-29 12:34:14 +09:00
Artyom V. Poptsov f6ed91ec35 gnu: igt-gpu-tools: Update to 2.4.
* gnu/packages/admin.scm (igt-gpu-tools): Update to 2.4.
[inputs]: Add pciutils.

Change-Id: I82aaa2425b064a3d04357a3283358ce10c7fda88
2026-05-29 06:28:13 +03:00
Artyom V. Poptsov 3a72fa155f gnu: stress-ng: Update to 0.21.01.
* gnu/packages/admin.scm (stress-ng): Update to 0.21.01.

Change-Id: If9072cac66b260756d7c3ec647ded1e0659c814f
2026-05-29 06:28:12 +03:00
Artyom V. Poptsov 4572918625 gnu: witr: Update to 0.3.2.
* gnu/packages/admin.scm (witr): Update to 0.3.2.

Change-Id: I68e69d4ab7e7715e346800c1d72257db85de9056
2026-05-29 06:28:11 +03:00
moksh 61a36beb4a gnu: librewolf: Update to 151.0.2-1.
* gnu/packages/librewolf.scm (librewolf): Update to 151.0.2-1.

Change-Id: I95a215401d1059035c448caa5847ef1d2b9143cf
2026-05-28 20:17:54 -07:00
moksh a7cc0cf504 gnu: firefox-l10n: Update to a8799feda04a221a2c552576501975662c5350bb.
* gnu/packages/librewolf.scm (firefox-l10n): Update to a8799feda04a221a2c552576501975662c5350bb.

Change-Id: I2c6bffd563c145b707e0039e0cc0b3fdc2dbcada
2026-05-28 20:17:54 -07:00
Nguyễn Gia Phong 13d24ec965 gnu: Remove snakemake-5.
* gnu/packages/python-science.scm (snakemake-5): Delete variable.

Change-Id: I5ed4ed815a0271680ae7c7862a8acc2827b9aff9
2026-05-29 12:00:51 +09:00
Nguyễn Gia Phong ab1cccf8d9 gnu: snakemake-6: Uninherit from snakemake-5.
* gnu/packages/python-science.scm (snakemake-6):
  Do not inherit from snakemake-5.
  [home-page, synopsis, description, license]: Copy from snakemake-5.

Change-Id: I01aadb93d2acf13ba227cb113bd5ef7002194403
2026-05-29 12:00:51 +09:00
Nguyễn Gia Phong c266426f15 gnu: pigx-scrnaseq: Switch to snakemake-6.
* gnu/packages/bioinformatics.scm (pigx-scrnaseq)[inputs]:
  Replace snakemake-5 with snakemake-6.

Change-Id: Ia9f5db13dca08274baab585a64227d1eba4d1e2e
2026-05-29 12:00:47 +09:00
Maxim Cournoyer dc64ec527c build: Ensure the installed pre-push git hook matches its source.
* Makefile.am ($(GIT_HOOKS_DIR)/pre-push): Make a phony target, and copy file
when the target differs from its prerequisite.

Fixes: #7645
Reported-by: Gábor Udvari <mail@gaborudvari.com>
Change-Id: I6b5f677afe59c25a4d8905da814af4bbd91fb401
2026-05-29 11:52:12 +09:00
Kaelyn Takata 9873d2c433 gnu: python@3.12: Support cross-compilation.
* gnu/packages/python.scm (python-3.12)[arguments]: Pass
‘--with-build-python’ when cross-compiling.

Fixes: guix/guix#8827
Merges: guix/guix!8826
Change-Id: Ibaea0cf3250ee0ce0b2d838a4edc30fa1ac59dbc
Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
2026-05-29 00:39:51 +01:00
Nicolas Goaziou a6c665b575 gnu: font-inter: Ensure all font files are installed.
* gnu/packages/fonts.scm (font-inter)[source]: Use release tarball.
[outputs]: Add "ttf" and "woff" outputs.

Fixes guix/guix#7993

Change-Id: I77aac4ee8ee73c8e3e360579d28a1691bd04880f
2026-05-28 22:56:25 +02:00
Andreas Enge 338915e54b gnu: libbigwig: Modernize.
* gnu/packages/bioinformatics.scm (libbigwig)[inputs]:
Replace python2 by python.
[arguments]: Use gexps.

Change-Id: Ica8343a3525cce5490b3112b077a6eab1c316992
2026-05-28 22:19:12 +02:00
luca a3335874f8 gnu: fzf: Update to 0.73.1.
* gnu/packages/terminals.scm (fzf): Update to 0.73.1.

Change-Id: Id5a90771622b8e707e1038ae57b259b250d1d8f9
Signed-off-by: Andreas Enge <andreas@enge.fr>
2026-05-28 20:06:50 +02:00
luca 61f6b51e4b gnu: go-github-com-charlievieth-fastwalk: Update to 1.0.14.
* gnu/packages/golang-xyz.scm (go-github-com-charlievieth-fastwalk):
  Update to 1.0.14.

Change-Id: I06ae18cd3532c2b97cb7b2615491e6872bac9fdd
Signed-off-by: Andreas Enge <andreas@enge.fr>
2026-05-28 20:06:42 +02:00
jgart c66c1023ef gnu: trealla: Update to 2.100.24.
* gnu/packages/prolog.scm (trealla): Update to 2.100.24.

Change-Id: Ia7575b164748d22e996c39af50fc339552a4da2b
2026-05-28 12:21:46 -04:00
Sören Tempel 0bf7964f68 gnu: loksh: Update to 7.9.
* gnu/packages/shells.scm (loksh): Update to 7.9.

Change-Id: Ie502be69ef93c1e5edde84107071b5ce2ced0ed1
2026-05-28 17:52:39 +02:00
Foster Hangdaan daa68f1713 gnu: font-mona-sans: Update to 2.0.27.
* gnu/packages/fonts.scm (font-mona-sans): Update to 2.0.27.

Merges: guix/guix!8818
Change-Id: I173038062a78c10647e42c1c040539d26dfbeeba
Signed-off-by: 宋文武 <iyzsong@member.fsf.org>
2026-05-28 22:54:10 +08:00
Nguyễn Gia Phong 7fdc5a4bad gnu: Rename ibus-libhangul to ibus-hangul.
* gnu/packages/ibus.scm (ibus-hangul): Rename from ibus-libhangul.
  (ibus-libhangul): Define as a deprecated alias of ibus-hangul.

Merges: guix/guix!8850
Change-Id: I80a8e107c97bfa7138bb367dfdb906335e0a96fe
Signed-off-by: 宋文武 <iyzsong@member.fsf.org>
2026-05-28 22:54:10 +08:00
Nguyễn Gia Phong 1d8c586d42 gnu: ibus-libhangul: Update to 1.5.5.
* gnu/packages/ibus.scm (ibus-libhangul): Update to 1.5.5.
  [arguments]: Switch to gexp.  <#:make-flags>: Set DISABLE_GUI_TESTS.
  [native-inputs]: Add autoconf, automake and libtool.

Change-Id: Ibe7a310ef50666f2b890dbf30fe44be08a4d3b9c
Signed-off-by: 宋文武 <iyzsong@member.fsf.org>
2026-05-28 22:54:10 +08:00
Sughosha f48fd06151 gnu: packages/image-viewers: Add missing copyright.
This is a following up 71f13e3a63 commit.

* gnu/packages/image-viewers.scm: Add copyright entry for Luis Guilherme Coelho
<lgcoelho@disroot.org>.

Change-Id: I60c77dd9c95e8c3d0470f780cbabc50a6d99733d
2026-05-28 20:00:49 +05:30
Nigko Yerden b7a2eb48b6 gnu: texmacs: Fix icon path in texmacs.desktop file.
* gnu/packages/text-editors.scm (texmacs)[arguments]{#:phases}
<fix-icon-directory>: Fix icon path in texmacs.desktop file.

Change-Id: I57b484a0b2c7b56852231d37a26ddba7fc309339
Signed-off-by: Sughosha <sughosha@disroot.org>
Merges: guix/guix!8908
2026-05-28 19:27:08 +05:30
Patrick Norton 245a5b7b3d gnu: Add go-github-com-tenntenn-text-transform.
* gnu/packages/golang-check.scm (go-github-com-tenntenn-text-transform):
New variable.

Relates-to: guix/guix!5417
Change-Id: I2525771a8adb13d8f5b05e2b3e93cecca27d1a48
Reviewed-by: Johannes Christ <jc@jchri.st>
Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
2026-05-28 14:49:38 +01:00
Patrick Norton 536cde5925 gnu: Add go-github-com-tenntenn-modver.
* gnu/packages/golang-check.scm (go-github-com-tenntenn-modver): New
variable.

Relates-to: guix/guix!5417
Change-Id: Ib996fb977d2fb4ae6851720ddaedce93d0442523
Reviewed-by: Johannes Christ <jc@jchri.st>
Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
2026-05-28 14:49:38 +01:00
Patrick Norton 029571fb86 gnu: Add go-github-com-tenntenn-golden.
* gnu/packages/golang-check.scm (go-github-com-tenntenn-golden): New
variable.

Relates-to: guix/guix!5417
Change-Id: I5a1b3b5d56aed143ffedb77402d64b500a649506
Reviewed-by: Johannes Christ <jc@jchri.st>
Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
2026-05-28 14:49:38 +01:00
Patrick Norton f75fe3892c gnu: Add go-github-com-newmo-oss-gotestingmock.
* gnu/packages/golang-check.scm (go-github-com-newmo-oss-gotestingmock):
New variable.

Relates-to: guix/guix!5417
Change-Id: I0e907b7dc1b9200a851122f2f60f3564dae72956
Reviewed-by: Johannes Christ <jc@jchri.st>
Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
2026-05-28 14:49:38 +01:00
Patrick Norton 8197800586 gnu: Add go-github-com-newmo-oss-go-caller.
* gnu/packages/golang-check.scm (go-github-com-newmo-oss-go-caller): New
variable.

Relates-to: guix/guix!5417
Change-Id: Idb7a4ff58ceb1973ae913c21124d610b9cee8628
Reviewed-by: Johannes Christ <jc@jchri.st>
Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
2026-05-28 14:49:38 +01:00
Patrick Norton 1adf73658f gnu: Add go-github-com-josharian-txtarfs.
* gnu/packages/golang-check.scm (go-github-com-josharian-txtarfs): New
variable.

Relates-to: guix/guix!5417
Change-Id: Ide2b2584b219448f75538fdc3f3a5e7caad55f69
Reviewed-by: Johannes Christ <jc@jchri.st>
Modified-by: Sharlatan Hellseher <sharlatanus@gmail.com>
Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
2026-05-28 14:49:38 +01:00
Patrick Norton a3a0c7da42 gnu: Add go-github-com-josharian-mapfs.
* gnu/packages/golang-check.scm (go-github-com-josharian-mapfs): New
variable.

Relates-to: guix/guix!5417
Change-Id: I73477f46cdfab03c192dfe86b75fe8624115e669
Reviewed-by: Johannes Christ <jc@jchri.st>
Modified-by: Sharlatan Hellseher <sharlatanus@gmail.com>
Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
2026-05-28 14:49:38 +01:00
Patrick Norton 5b073c6178 gnu: Add go-gitlab-com-bosi-decorder.
* gnu/packages/golang-check.scm (go-gitlab-com-bosi-decorder): New
variable.

Relates-to: guix/guix!5417
Change-Id: I27a1e1fb1837b1e0780f8316bd5c86024d8824f5
Reviewed-by: Johannes Christ <jc@jchri.st>
Modified-by: Sharlatan Hellseher <sharlatanus@gmail.com>
Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
2026-05-28 14:49:37 +01:00
Patrick Norton 0c648625b0 gnu: Add go-go-simpler-org-musttag.
* gnu/packages/golang-check.scm (go-go-simpler-org-musttag): New
variable.

Relates-to: guix/guix!5417
Change-Id: I57e07ab19a94db448c486f01220037e0b055eb85
Reviewed-by: Johannes Christ <jc@jchri.st>
Modified-by: Sharlatan Hellseher <sharlatanus@gmail.com>
Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
2026-05-28 14:49:37 +01:00
Patrick Norton 6b442402c2 gnu: Add go-go-simpler-org-assert.
* gnu/packages/golang-check.scm (go-go-simpler-org-assert): New
variable.

Relates-to: guix/guix!5417
Change-Id: I5baea5122063b3edf89dfd60496d635507883da4
Edited-by: Johannes Christ <jc@jchri.st>
Reviewed-by: Johannes Christ <jc@jchri.st>
Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
2026-05-28 14:49:37 +01:00
Gabriel Wicki 0ff409542b etc: teams: kernel: Rename team to `linux-libre'.
Since linux-libre is not the only kernel around in GNU Guix anymore.

* etc/teams.scm (kernel): Rename variable to linux-libre.
* CODEOWNERS: Regenerate file.

Change-Id: Ic8081f471ad7f6aa21e2830f294549460466249b
Signed-off-by: Gabriel Wicki <gabriel@erlikon.ch>
2026-05-28 15:47:42 +02:00
Luis Guilherme Coelho 71f13e3a63 gnu: Add ueberzugpp.
* gnu/packages/image-viewers.scm (ueberzugpp): New variable.

Change-Id: Icc8f64aaa5d0dd5d7289f8e92af2eff39d59747b
Signed-off-by: Sughosha <sughosha@disroot.org>
2026-05-28 18:38:31 +05:30
Ricardo Wurmus d426c0ef73 gnu: r-rhdf5filters: Define __ARM_NEON__ on aarch64-linux.
* gnu/packages/cran.scm (r-rhdf5filters)[arguments]: Conditionally define
__ARM_NEON__.

Change-Id: I0bd3353642044caba10ac9831d4ec6eeded825f9
2026-05-28 12:14:00 +02:00
Ricardo Wurmus a15f89137e gnu: r-lme4: Skip one more test on aarch64-linux.
* gnu/packages/cran.scm (r-lme4)[arguments]: Conditionally skip one more test
on aarch64-linux.

Change-Id: I82606670e2aa35e44594a0e99f03559341174b51
2026-05-28 12:14:00 +02:00
Ricardo Wurmus 9f1b386c79 gnu: nng-1.11: Fix build on aarch64-linux.
* gnu/packages/networking.scm (nng-1.11)[arguments]: Disable parallel tests;
disable one more test.

Change-Id: I979172b7c4749354242d6015ac7888fb7e8f3af9
2026-05-28 12:14:00 +02:00
Ricardo Wurmus f9074ee018 gnu: r-scater: Update to 1.40.1.
* gnu/packages/bioconductor.scm (r-scater): Update to 1.40.1.

Change-Id: Ic92c5632210b6b947780034770ae8da41af3c736
2026-05-28 12:14:00 +02:00
Ricardo Wurmus 27f6f2c794 gnu: r-biostrings: Update to 2.80.1.
* gnu/packages/bioconductor.scm (r-biostrings): Update to 2.80.1.

Change-Id: Ica55bf875302ff0f223dca08f670cf2c4a17d2ae
2026-05-28 12:14:00 +02:00
Ricardo Wurmus 2591e74702 gnu: r-bamsignals: Update to 1.44.1.
* gnu/packages/bioconductor.scm (r-bamsignals): Update to 1.44.1.

Change-Id: I4cf058281d479eca901c242443df9bcdd3a4a34d
2026-05-28 12:14:00 +02:00
Ricardo Wurmus f92a18b25d gnu: r-mlr3fselect: Update to 1.6.0.
* gnu/packages/cran.scm (r-mlr3fselect): Update to 1.6.0.
[native-inputs]: Remove r-processx and r-redux.

Change-Id: I3ad638a0afad3fdfd5d32ecbe42929b40cc0756f
2026-05-28 12:14:00 +02:00
Ricardo Wurmus 19e9449528 gnu: r-nanotime: Update to 0.3.15.
* gnu/packages/cran.scm (r-nanotime): Update to 0.3.15.

Change-Id: I47a8534c86a97ad52372bd8ad83c1fa39e2db4e6
2026-05-28 12:13:59 +02:00
Ricardo Wurmus 29fbcb971a gnu: r-spatstat-sparse: Update to 3.2-0.
* gnu/packages/cran.scm (r-spatstat-sparse): Update to 3.2-0.

Change-Id: I8d9c5237e8f72f78a62322566721d3a00545c69c
2026-05-28 12:13:59 +02:00
Ricardo Wurmus 0258c8b2e4 gnu: r-leidenbase: Update to 0.1.37.
* gnu/packages/cran.scm (r-leidenbase): Update to 0.1.37.

Change-Id: I5afc19e52f3d8afbb04dddba893381f21a61bd12
2026-05-28 12:13:59 +02:00
Ricardo Wurmus 38c3079e30 gnu: r-logging: Update to 0.10-111.
* gnu/packages/cran.scm (r-logging): Update to 0.10-111.

Change-Id: If0917c8bd94bb8db47d6468abb6f53a4dc656e9d
2026-05-28 12:13:59 +02:00
Ricardo Wurmus 429e983685 gnu: r-tweedie: Update to 3.1.0.
* gnu/packages/cran.scm (r-tweedie): Update to 3.1.0.

Change-Id: I92f9eb930c0d16e4319dccc0ba283054bbe35730
2026-05-28 12:13:59 +02:00
Ricardo Wurmus ebac77ac66 gnu: r-performance: Update to 0.17.0.
* gnu/packages/cran.scm (r-performance): Update to 0.17.0.

Change-Id: Ic2bd3ae23d9a99c0dd3f83a6d1e29bdf64c94c97
2026-05-28 12:13:59 +02:00
Ricardo Wurmus 5c309648bf gnu: r-bayestestr: Update to 0.18.0.
* gnu/packages/cran.scm (r-bayestestr): Update to 0.18.0.

Change-Id: I960d063ea5fd49bde0b2900fd086257538e2234a
2026-05-28 12:13:59 +02:00
Ricardo Wurmus 48e9e74851 gnu: r-dofuture: Update to 1.2.2.
* gnu/packages/cran.scm (r-dofuture): Update to 1.2.2.

Change-Id: I74eef243667c28bc57c2b5644aed481128ce8df1
2026-05-28 12:13:58 +02:00
Ricardo Wurmus 97471399c9 gnu: r-insight: Update to 1.5.1.
* gnu/packages/cran.scm (r-insight): Update to 1.5.1.

Change-Id: Ie66490bb8b9b315bcdc9ff85d9ee7724b87addf7
2026-05-28 12:13:58 +02:00
Ricardo Wurmus e1658e410d gnu: r-climatol: Update to 4.5-0.
* gnu/packages/cran.scm (r-climatol): Update to 4.5-0.

Change-Id: I054623610a0ad8418c8d9c1bcee1cc7a5fe1afd1
2026-05-28 12:13:58 +02:00
Ricardo Wurmus 1fc38e6bea gnu: r-ggpicrust2: Update to 2.5.16.
* gnu/packages/bioconductor.scm (r-ggpicrust2): Update to 2.5.16.

Change-Id: I91fc93449dca3072908d047051d6aa90b787dc38
2026-05-28 12:13:58 +02:00
Ricardo Wurmus 9859f913f1 gnu: r-tidyclust: Update to 0.3.0.
* gnu/packages/cran.scm (r-tidyclust): Update to 0.3.0.
[propagated-inputs]: Remove r-foreach; add r-lifecycle, r-mclust, r-purrr.
[native-inputs]: Add r-dbscan, r-future, r-knitr, r-mirai, and r-withr.

Change-Id: Iae381ac22030639b9334d112e8e7434d1a9999a9
2026-05-28 12:13:58 +02:00
Ricardo Wurmus fdfd9a36b7 gnu: r-bit64: Update to 4.8.2.
* gnu/packages/cran.scm (r-bit64): Update to 4.8.2.
[properties]: Record updater-ignored-native-inputs.

Change-Id: If3444b513ecbd7de08c6606b733b74a60be5c89e
2026-05-28 12:13:58 +02:00
Ricardo Wurmus 2130fd2ada gnu: r-chromvar: Update to 1.34.1.
* gnu/packages/bioconductor.scm (r-chromvar): Update to 1.34.1.
[propagated-inputs]: Add r-pwalign.

Change-Id: I8c41064c347b8b9f4b02c636531449305e4556b2
2026-05-28 12:13:57 +02:00
Ricardo Wurmus e0cddffc1d gnu: r-gdsfmt: Update to 1.48.1.
* gnu/packages/bioconductor.scm (r-gdsfmt): Update to 1.48.1.

Change-Id: Ida66602b7c96072aa2710cadd60f0b572f6a49b4
2026-05-28 12:13:57 +02:00
Ricardo Wurmus 173f1ada6f gnu: r-missmethyl: Update to 1.46.0.
* gnu/packages/bioconductor.scm (r-missmethyl): Update to 1.46.0.

Change-Id: I7f4ac17690791430db1df346c3acd48a20254f2b
2026-05-28 12:13:57 +02:00
Ricardo Wurmus 4f106bf9ae gnu: r-milor: Update to 2.8.1.
* gnu/packages/bioconductor.scm (r-milor): Update to 2.8.1.

Change-Id: Id1dc67683518598684a40d3662fa057b5e713e7b
2026-05-28 12:13:57 +02:00
Ricardo Wurmus f7c391e879 gnu: r-scrapper: Update to 1.6.3.
* gnu/packages/bioconductor.scm (r-scrapper): Update to 1.6.3.

Change-Id: Id6989e033eb0986d9bdc93e1ace798419af915fb
2026-05-28 12:13:57 +02:00
Ricardo Wurmus 8ecafbaa91 gnu: r-limma: Update to 3.68.3.
* gnu/packages/bioconductor.scm (r-limma): Update to 3.68.3.

Change-Id: Iafd34fdb4427b3eec6aec4e8efe9fc3664766e5d
2026-05-28 12:13:57 +02:00
Ricardo Wurmus 39a8e7cac3 gnu: r-gsva: Update to 2.6.2.
* gnu/packages/bioconductor.scm (r-gsva): Update to 2.6.2.

Change-Id: Ie8e087db7164578109bc9ed9de8aba4658674910
2026-05-28 12:13:57 +02:00
Ricardo Wurmus ebb3502bab gnu: r-biocgenerics: Update to 0.58.1.
* gnu/packages/bioconductor.scm (r-biocgenerics): Update to 0.58.1.

Change-Id: I778117374b060f155996808bede8204f72166cc2
2026-05-28 12:13:57 +02:00
Ricardo Wurmus f6333ac9c0 gnu: r-badregionfinder: Update to 1.40.0.
* gnu/packages/bioconductor.scm (r-badregionfinder): Update to 1.40.0.

Change-Id: Iab33618dd4e940a1063cbbb8e7df5f216c510e89
2026-05-28 12:13:56 +02:00
Ricardo Wurmus 3f287e40fa gnu: r-s4vectors: Update to 0.50.1.
* gnu/packages/bioconductor.scm (r-s4vectors): Update to 0.50.1.
[arguments]: Enable some tests; remove phase 'R-4.6.0-compatibility.
[native-inputs]: Add r-runit.

Change-Id: I03c03d8080e0d6daf43483921122d3ecd1b8981e
2026-05-28 12:13:56 +02:00
Ricardo Wurmus 0884fcb15a gnu: r-pdftools: Update to 3.9.0.
* gnu/packages/cran.scm (r-pdftools): Update to 3.9.0.

Change-Id: I63a3d9cc0cd25915f8612365774a7621028b790b
2026-05-28 12:13:56 +02:00
Ricardo Wurmus 174b60d152 gnu: r-parsnip: Update to 1.6.0.
* gnu/packages/cran.scm (r-parsnip): Update to 1.6.0.

Change-Id: I91c6a5374ec8642af2557751c75fa393cae8d675
2026-05-28 12:13:56 +02:00
Ricardo Wurmus da647acb56 gnu: r-spatstat-univar: Update to 3.2-0.
* gnu/packages/cran.scm (r-spatstat-univar): Update to 3.2-0.

Change-Id: I3dc15790f7152d258804fdfafb799ebcfc66eece
2026-05-28 12:13:56 +02:00
Ricardo Wurmus ec26dd90ca gnu: r-harmony: Update to 2.0.3.
* gnu/packages/cran.scm (r-harmony): Update to 2.0.3.

Change-Id: I5ab739d797d9209111ab49fc6488e7c6b1197d7b
2026-05-28 12:13:56 +02:00
Ricardo Wurmus 5c18bb5d36 gnu: r-bigrquery: Update to 1.6.2.
* gnu/packages/cran.scm (r-bigrquery): Update to 1.6.2.

Change-Id: If7c74183cb2bea59253c3d3cc1a08f6ee0ead010
2026-05-28 12:13:55 +02:00
Ricardo Wurmus a4dfc70450 gnu: r-feature: Update to 1.2.16.
* gnu/packages/cran.scm (r-feature): Update to 1.2.16.

Change-Id: Ibb660bfcabbd7f6b12535dc466a1e0f205102225
2026-05-28 12:13:55 +02:00
Ricardo Wurmus 0baf6604b8 gnu: r-lsei: Update to 1.3-1.
* gnu/packages/cran.scm (r-lsei): Update to 1.3-1.

Change-Id: I57f907854601e073315a6f64c57bac3df4b84322
2026-05-28 12:13:55 +02:00
Ricardo Wurmus 6428f41b12 gnu: r-quickjsr: Update to 1.10.0.
* gnu/packages/cran.scm (r-quickjsr): Update to 1.10.0.

Change-Id: I0a8276e0ff77c9d2b525d83b0dff82d033de578a
2026-05-28 12:13:55 +02:00
Ricardo Wurmus d35ebc17e8 gnu: r-mosaic: Update to 1.10.2.
* gnu/packages/cran.scm (r-mosaic): Update to 1.10.2.

Change-Id: I0a3b6c97cbda60e2a99391aae7100884337eb8d6
2026-05-28 12:13:55 +02:00
Ricardo Wurmus d4cadadaac gnu: r-renv: Update to 1.2.3.
* gnu/packages/cran.scm (r-renv): Update to 1.2.3.

Change-Id: Ie9a83255d48bd2212d46a522c5d783aa6ee8d78f
2026-05-28 12:13:55 +02:00
Ricardo Wurmus a6ed426e1f gnu: r-np: Update to 0.70-2.
* gnu/packages/cran.scm (r-np): Update to 0.70-2.
[native-inputs]: Add r-withr.

Change-Id: I5c3350a7b65eba18703480ce529f051178504e6d
2026-05-28 12:13:55 +02:00
Ricardo Wurmus 73993d585b gnu: r-aricode: Update to 1.1.0.
* gnu/packages/cran.scm (r-aricode): Update to 1.1.0.
[propagated-inputs]: Add r-lifecycle.
[native-inputs]: Add r-spelling.

Change-Id: I1525a3c89ac3068faea8494a1def48b8ba16a8ca
2026-05-28 12:13:55 +02:00
Ricardo Wurmus cda1265bda gnu: r-broom: Update to 1.0.13.
* gnu/packages/cran.scm (r-broom): Update to 1.0.13.

Change-Id: I623d20e29b43ac2b80183047d930c269d4965f7c
2026-05-28 12:13:54 +02:00
Ricardo Wurmus 8d6a0e2b28 gnu: r-readxl: Update to 1.5.0.
* gnu/packages/cran.scm (r-readxl): Update to 1.5.0.

Change-Id: I1ca2591487d5fcfb02b3dc59be2d7e1ff37fe809
2026-05-28 12:13:54 +02:00
Ricardo Wurmus 0326784f17 gnu: r-statmod: Update to 1.5.2.
* gnu/packages/cran.scm (r-statmod): Update to 1.5.2.

Change-Id: Ib78fea9a6ea90d1357c1651a4ed780345a113b22
2026-05-28 12:13:54 +02:00
Ricardo Wurmus e7fdea4d22 gnu: r-sfsmisc: Update to 1.1-24.
* gnu/packages/cran.scm (r-sfsmisc): Update to 1.1-24.

Change-Id: I7377c2ae0c9018b00e610b07d77fc734ea8289ac
2026-05-28 12:13:54 +02:00
Ricardo Wurmus 23c52b900b gnu: r-openssl: Update to 2.4.1.
* gnu/packages/cran.scm (r-openssl): Update to 2.4.1.

Change-Id: I35aff8361a10acd4b23c12d0887f4de89d26bb7c
2026-05-28 12:13:54 +02:00
Ricardo Wurmus 156de6111a gnu: r-epir: Update to 2.0.93.
* gnu/packages/cran.scm (r-epir): Update to 2.0.93.

Change-Id: I844b881f16eebc7e075910272023659aed0a2261
2026-05-28 12:13:54 +02:00
Ricardo Wurmus 7ba25068eb gnu: r-crs: Update to 0.15-43.
* gnu/packages/cran.scm (r-crs): Update to 0.15-43.

Change-Id: I7635a8c6f78721df344bed45097881342f59f9aa
2026-05-28 12:13:54 +02:00
Ricardo Wurmus cd35f0130b gnu: r-collapse: Update to 2.1.7.
* gnu/packages/cran.scm (r-collapse): Update to 2.1.7.
[native-inputs]: Add r-tibble.

Change-Id: Ieb29ba91721bfc5045baf779a03eb5b4be390550
2026-05-28 12:13:53 +02:00
Ricardo Wurmus badba86af0 gnu: r-infusion: Update to 2.3.12.
* gnu/packages/bioconductor.scm (r-infusion): Update to 2.3.12.

Change-Id: I49e982400816a7025bdf6da6203c6f3163de8189
2026-05-28 12:13:53 +02:00
Ricardo Wurmus 0495b1ab2e gnu: r-permute: Remove outdated comment.
* gnu/packages/cran.scm (r-permute): Remove outdated comment on tests.

Change-Id: I19e8883cbea32a98dc643da588e989166e49b5bf
2026-05-28 12:13:53 +02:00
Ricardo Wurmus bc1584918b gnu: r-rjsonio: Update to 2.0.5.
* gnu/packages/cran.scm (r-rjsonio): Update to 2.0.5.
[native-inputs]: Add r-knitr and r-testthat.

Change-Id: I027a3f916d35a92556667b542bea52788a5d8a44
2026-05-28 12:13:53 +02:00
Ricardo Wurmus eb5dabf6ba gnu: r-drr: Update to 0.0.5.
* gnu/packages/cran.scm (r-drr): Update to 0.0.5.
[native-inputs]: Add r-knitr.

Change-Id: I872a3d4d902d94c8f49eb66f180122f99d7ad851
2026-05-28 12:13:53 +02:00
Ricardo Wurmus 4f3fdea338 gnu: r-officer: Update to 0.7.5.
* gnu/packages/cran.scm (r-officer): Update to 0.7.5.

Change-Id: I355805caab1e6c65fc9d71231429d9e352ea70d7
2026-05-28 12:13:53 +02:00
Ricardo Wurmus bf5e93d398 gnu: r-lava: Update to 1.9.1.
* gnu/packages/cran.scm (r-lava): Update to 1.9.1.
[properties]: Record updater-ignored-native-inputs.
[arguments]: Update list of skipped tests.

Change-Id: I6d70db3763e0eb2092f255c8baa7729f505607b2
2026-05-28 12:13:53 +02:00
Ricardo Wurmus 2c2cc77477 gnu: r-extradistr: Update to 1.10.0.4.
* gnu/packages/cran.scm (r-extradistr): Update to 1.10.0.4.

Change-Id: I3ce812aebd7939ca817d7033e130cbfc9cd02822
2026-05-28 12:13:52 +02:00
Ricardo Wurmus b3521a6f9f gnu: r-psych: Update to 2.6.5.
* gnu/packages/cran.scm (r-psych): Update to 2.6.5.

Change-Id: I579fffc83ab0ee4215164ba9bab5039d1178f50f
2026-05-28 12:13:52 +02:00
Ricardo Wurmus 65558f3b06 gnu: r-boruta: Update to 10.0.0.
* gnu/packages/cran.scm (r-boruta): Update to 10.0.0.
[propagated-inputs]: Remove r-ranger; add r-fru.
[native-inputs]: Remove r-rferns and r-testthat.

Change-Id: I1d89dcf52bda0fcad9c599cb6109c57e45b52044
2026-05-28 12:13:52 +02:00
Ricardo Wurmus bb2e12eaf8 gnu: r-webfakes: Update to 1.5.0.
* gnu/packages/cran.scm (r-webfakes): Update to 1.5.0.
[arguments]: Remove phase 'disable-bad-tests in favor of #:skipped-tests.

Change-Id: I573afd303f12e46af5dc53ac6a2a94f84c35de68
2026-05-28 12:13:52 +02:00
Ricardo Wurmus 86af74249b gnu: r-testit: Update to 1.0.
* gnu/packages/cran.scm (r-testit): Update to 1.0.
[arguments]: Add phase 'delete-bad-test.

Change-Id: I4e234ade350b0c447af8159735a01c786bce24e8
2026-05-28 12:13:52 +02:00
Ricardo Wurmus 2c11859b76 gnu: r-bslib: Update to 0.11.0.
* gnu/packages/cran.scm (r-bslib): Update to 0.11.0.
[arguments]: Update skipped tests.
[native-inputs]: Drop input labels; add r-withr.

Change-Id: I60fd6f4e551fae126b32bfa88105a29a64a7c762
2026-05-28 12:13:52 +02:00
Ricardo Wurmus 5d3c2280de gnu: Add r-riskregression.
* gnu/packages/cran.scm (r-riskregression): New variable.

Change-Id: I8ae57d78a63bdc3398f0d728eafaecee3980f687
2026-05-28 12:13:52 +02:00
Ricardo Wurmus 178b76a80e gnu: Add r-publish.
* gnu/packages/cran.scm (r-publish): New variable.

Change-Id: I38fdc4546746ab5864d6b922a13fb8920f3f0183
2026-05-28 12:13:51 +02:00
Ricardo Wurmus d3ee79f694 gnu: Add r-smcfcs.
* gnu/packages/cran.scm (r-smcfcs): New variable.

Change-Id: I61524e39a7e204c32e884e94439cee74c65d8bd0
2026-05-28 12:13:51 +02:00
Ricardo Wurmus 2ce9a6acf4 gnu: Add r-mets.
* gnu/packages/cran.scm (r-mets): New variable.

Change-Id: Id2079ea76dc384b9175e2d3f58adf318e27dfb8f
2026-05-28 12:13:51 +02:00
Ricardo Wurmus 2e8c9f6f9d gnu: Add r-xactonomial.
* gnu/packages/cran.scm (r-xactonomial): New variable.

Change-Id: Ic57dc8058f8bf931b0d00b025cbd3b2b5b1feb51
2026-05-28 12:13:51 +02:00
Ricardo Wurmus 5ea2cf2c4b gnu: Add r-fru.
* gnu/packages/cran.scm (r-fru): New variable.

Change-Id: Ia51967630f494d4daf7342262cedb6c99ce8ac88
2026-05-28 12:13:51 +02:00
Ricardo Wurmus 0391196836 gnu: Add r-geodata.
* gnu/packages/cran.scm (r-geodata): New variable.

Change-Id: I7280b5a4f67f6ce8a462b742bd079817cdb153d2
2026-05-28 12:13:51 +02:00
Ricardo Wurmus 8619050966 gnu: Add r-gdalutilities.
* gnu/packages/cran.scm (r-gdalutilities): New variable.

Change-Id: Ieef95339f225d8474da7b61bf1cf1872dc14962d
2026-05-28 12:13:51 +02:00
Ricardo Wurmus a2dd50d593 gnu: Add r-elevatr.
* gnu/packages/cran.scm (r-elevatr): New variable.

Change-Id: I9a629ba791cacc2df0161cd57593f4b906c3f58a
2026-05-28 12:13:50 +02:00
Ricardo Wurmus e1dd7cba84 gnu: Add r-slippymath.
* gnu/packages/cran.scm (r-slippymath): New variable.

Change-Id: Id1b9eae74137df1bc913ae2c3e66b6864199ed5c
2026-05-28 12:13:50 +02:00
Ricardo Wurmus 4df14cbf9d gnu: r-logger: Update to 0.4.2.
* gnu/packages/cran.scm (r-logger): Update to 0.4.2.
[native-inputs]: Add r-shiny.

Change-Id: I3d39787a968487b2216960a4b83763c13e5e2cb0
2026-05-28 12:13:50 +02:00
Ricardo Wurmus e689d2cfc0 gnu: r-spatstat-utils: Update to 3.2-3.
* gnu/packages/cran.scm (r-spatstat-utils): Update to 3.2-3.

Change-Id: I61b165ae8a8f55afb970e2c3a9aa381d448cd444
2026-05-28 12:13:50 +02:00
Ricardo Wurmus 9c43c98fac gnu: r-r-devices: Update to 2.17.4.
* gnu/packages/cran.scm (r-r-devices): Update to 2.17.4.

Change-Id: I5418e240d315441b84a6bce4e1e76ede5daa1954
2026-05-28 12:13:50 +02:00
Ricardo Wurmus df254d3621 gnu: r-parameters: Update to 0.29.0.
* gnu/packages/cran.scm (r-parameters): Update to 0.29.0.

Change-Id: I78b5ab0ae4949318e03d5c58d64ed30e767942c7
2026-05-28 12:13:50 +02:00
Ricardo Wurmus a3cca25cee gnu: r-terra: Update to 1.9-27.
* gnu/packages/cran.scm (r-terra): Update to 1.9-27.

Change-Id: I36db1d2f7ab393e8d24f1afa7ca0c7a5ff5fc172
2026-05-28 12:13:49 +02:00
Ricardo Wurmus 5b6539f077 gnu: r-sftime: Update to 0.3.2.
* gnu/packages/cran.scm (r-sftime): Update to 0.3.2.

Change-Id: Ib48a13ce9ead087fdfe821e6f0158578dea73963
2026-05-28 12:13:49 +02:00
Ricardo Wurmus 572938f14c gnu: r-ks: Update to 1.15.2.
* gnu/packages/cran.scm (r-ks): Update to 1.15.2.

Change-Id: I0de8bc727cdf7d5032cf5df31053b4ec33129b62
2026-05-28 12:13:49 +02:00
Ricardo Wurmus 4b9ead4f84 gnu: r-rcppspdlog: Update to 0.0.29.
* gnu/packages/cran.scm (r-rcppspdlog): Update to 0.0.29.

Change-Id: I931f738153eacf3e0b67d4200a48b539f214b8a6
2026-05-28 12:13:49 +02:00
Ricardo Wurmus 541a48b01b gnu: r-rsqlite: Update to 3.52.0.
* gnu/packages/cran.scm (r-rsqlite): Update to 3.52.0.

Change-Id: Icdf2758aa7c3bd75c1e35937ef12f08a24f4285e
2026-05-28 12:13:49 +02:00
Ricardo Wurmus 5b616f1ebc gnu: r-rbiom: Update to 3.1.0.
* gnu/packages/cran.scm (r-rbiom): Update to 3.1.0.
[propagated-inputs]: Remove r-parallelly and r-slam; add r-ecodive.

Change-Id: I144e10fd2246b81924f53ae7f99550d97ce07da2
2026-05-28 12:13:49 +02:00
Ricardo Wurmus 44dc62e08e gnu: r-mirai: Update to 2.7.0.
* gnu/packages/cran.scm (r-mirai): Update to 2.7.0.

Change-Id: Iece8467c6ca16d7ded6f2836ab6a1818c6a5621b
2026-05-28 12:13:49 +02:00
Ricardo Wurmus 8f93204f92 gnu: r-rliger: Add missing test input.
* gnu/packages/bioconductor.scm (r-rliger)[native-inputs]: Add r-cowplot.

Change-Id: Ie4c36c393d5a5cd632d9b41cf77e23a7e93137a3
2026-05-28 12:13:48 +02:00
Ricardo Wurmus f75a1d1c0b gnu: r-a4: Update to 1.60.0.
* gnu/packages/bioconductor.scm (r-a4): Update to 1.60.0.

Change-Id: I6575fdc40b8d0f25088f44003b291f17bd3dab24
2026-05-28 12:13:48 +02:00
Ricardo Wurmus d5941e4504 gnu: r-a4base: Update to 1.60.0.
* gnu/packages/bioconductor.scm (r-a4base): Update to 1.60.0.

Change-Id: I8cac7ccc34bd37920e98ac0648bbc63dc591cbbf
2026-05-28 12:13:48 +02:00
Ricardo Wurmus e569396763 gnu: r-sva: Update to 3.60.0.
* gnu/packages/bioconductor.scm (r-sva): Update to 3.60.0.

Change-Id: I468c76a82259793047a3dea967d29aef627156af
2026-05-28 12:13:48 +02:00
Ricardo Wurmus 23456c1260 gnu: r-stager: Update to 1.34.0.
* gnu/packages/bioconductor.scm (r-stager): Update to 1.34.0.

Change-Id: I3af908b4b43a62577ff5e6679d39be21c0b99256
2026-05-28 12:13:48 +02:00
Ricardo Wurmus 29f6cb61ac gnu: r-limma: Update to 3.68.2.
* gnu/packages/bioconductor.scm (r-limma): Update to 3.68.2.

Change-Id: I75e13724760a5b1440458ddc05d67d63a5282998
2026-05-28 12:13:48 +02:00
Ricardo Wurmus a9e4ee9389 gnu: r-gsva: Update to 2.6.1.
* gnu/packages/bioconductor.scm (r-gsva): Update to 2.6.1.

Change-Id: I2c90547e4c7d7bdc0ab6d9da490bf38662111e59
2026-05-28 12:13:48 +02:00
Ricardo Wurmus bcf746d5c9 gnu: r-assorthead: Update to 1.6.1.
* gnu/packages/bioconductor.scm (r-assorthead): Update to 1.6.1.

Change-Id: I5f9ed214b1a80b89c6b56e16506d502c1f6f40f1
2026-05-28 12:13:47 +02:00
Ricardo Wurmus bdbcdacfbd gnu: Remove r-qs.
This package fails to build with R 4.6.0 as it depends on internal symbols
that have since been removed from R.  r-qs has been abandoned in favor of
r-qs2, which is not a drop-in replacement.

See https://github.com/qsbase/qs/issues/103

* gnu/packages/cran.scm (r-qs): Delete variable.

Change-Id: Ia1b0268cb8f6b74e3c2ab6446cd956aaffa7291e
2026-05-28 12:13:47 +02:00
Ricardo Wurmus 1240dc7006 gnu: Remove r-seurat-utils.
This package depends on r-qs, which fails to build with R 4.6.0.  r-qs has
been abandoned in favor of r-qs2, which is not a drop-in replacement.

* gnu/packages/bioinformatics.scm (r-seurat-utils): Delete variable.

Change-Id: I2b62a766e4784e25599329c86c49a1e059dd909f
2026-05-28 12:13:47 +02:00
Ricardo Wurmus bcbee6077b gnu: Remove r-seqbias.
This package was removed with Bioconductor 3.19 release.  It depends on R
internal symbols, which have been removed.

* gnu/packages/bioconductor.scm (r-seqbias): Delete variable.

Change-Id: Ib8a834c1d69f329281904e739c429448474d511b
2026-05-28 12:13:47 +02:00
Ricardo Wurmus 0d5d4cf8c7 gnu: Remove r-reqon.
This package was removed with Bioconductor 3.20 release.  It depends on
r-seqbias, which fails to build.

* gnu/packages/bioconductor.scm (r-reqon): Delete variable.

Change-Id: I7c9e731ebde3d2991b30140c7f2c26868e29664c
2026-05-28 12:13:47 +02:00
Ricardo Wurmus 0b0c6d9850 gnu: r-misha: Update to 5.6.23.
* gnu/packages/bioinformatics.scm (r-misha): Update to 5.6.23.
[source]: Remove obsolete snippet.
[arguments]: Remove phase 'do-not-use-bundled-bigWigToWig.
[inputs]: Remove kentutils.
[propagated-inputs]: Add r-curl, r-digest, r-magrittr, r-ps, and r-yaml.
[native-inputs]: Add r-knitr and r-testthat.

Change-Id: Ia3bf627976d5963757b7ac0cede1cd43cff7da3b
2026-05-28 12:13:47 +02:00
Ricardo Wurmus 48f4dbec9a gnu: r-muscat: Add missing test inputs.
* gnu/packages/bioconductor.scm (r-muscat)[native-inputs]: Add r-deseq2 and
r-sctransform.

Change-Id: Ib4d4829a0fdfb59243a4960ba98686af4817b4c5
2026-05-28 12:13:47 +02:00
Ricardo Wurmus 8dbddf3832 gnu: r-mvabund: Add missing input.
* gnu/packages/cran.scm (r-mvabund)[inputs]: Add gsl.
[properties]: Record updater-extra-inputs.

Change-Id: I19b1b683117b507843e615a32cdbb82c46dfceaa
2026-05-28 12:13:46 +02:00
Ricardo Wurmus e410f2b30a gnu: r-rcppziggurat: Add missing input.
* gnu/packages/cran.scm (r-rcppziggurat)[inputs]: Add gsl.
[properties]: Record updater-extra-inputs.

Change-Id: Ice7fe6bc3611cc45d14ef7c0475523a431be9a45
2026-05-28 12:13:46 +02:00
Ricardo Wurmus df6e13facc gnu: r-sf: Update to 1.1-1.
* gnu/packages/cran.scm (r-sf): Update to 1.1-1.
[propagated-inputs]: Remove r-magrittr.

Change-Id: If3dd9fb392a9b51179b1c0b4ca9bf7c756d6dcda
2026-05-28 12:13:46 +02:00
Ricardo Wurmus b97598040c gnu: r-data-table: Update to 1.18.4.
* gnu/packages/cran.scm (r-data-table): Update to 1.18.4.

Change-Id: I23c4df82d0380337af8acbbd9da34c435308e18d
2026-05-28 12:13:46 +02:00
Ricardo Wurmus 3f13c49e01 gnu: r-mgsub: Update to 2.0.0.
* gnu/packages/cran.scm (r-mgsub): Update to 2.0.0.

Change-Id: Ia967d86670673423df178ebb8a88d85f00a02284
2026-05-28 12:13:46 +02:00
Ricardo Wurmus f0e627fd0a gnu: r-cpp11: Update to 0.5.5.
* gnu/packages/cran.scm (r-cpp11): Update to 0.5.5.

Change-Id: I1857e893276bdb90c16ded39a3ac479d31634dbe
2026-05-28 12:13:46 +02:00
Ricardo Wurmus 59d56d830d gnu: r-exactextractr: Disable two tests.
* gnu/packages/cran.scm (r-exactextractr)[arguments]: Disable two tests.

Change-Id: I19933ae758c913e707b25e8e89c4132e5339b060
2026-05-28 12:13:46 +02:00
Ricardo Wurmus f94b2fa8b3 gnu: r-spectre: Update to 1.3.0.
* gnu/packages/bioinformatics.scm (r-spectre): Update to 1.3.0.
[propagated-inputs]: Replace r-qs with r-qs2.

Change-Id: Ia55fed95e05ab7acf5e43d4ff32569156f6e4e93
2026-05-28 12:13:45 +02:00
Ricardo Wurmus 41cefea1e0 gnu: r-terra: Update to 1.9-25.
* gnu/packages/cran.scm (r-terra): Update to 1.9-25.
[input]: Replace proj-9.3 with proj.

Change-Id: I6e9e07658fc8e3e92f638bcf632910e37f8340d7
2026-05-28 12:13:45 +02:00
Ricardo Wurmus 3ba4f6de9a gnu: r-pizzarr: Update to 0.2.0.
* gnu/packages/bioinformatics.scm (r-pizzarr): Update to 0.2.0.
[build-system]: Use cargo-build-system.
[arguments]: Add phases from the r-build-system; enable most tests.
[inputs]: Add openssl, zlib, and zstd:lib; add cargo inputs.
[native-inputs]: Add pkg-config and r-minimal.
[propagated-inputs]: Remove r-qs; add r-qs2.
* gnu/packages/rust-crates.scm (lookup-cargo-inputs): Add entries for extendr
and r-pizzarr.
* gnu/packages/rust-sources.scm (rust-extendr-0.8.1.93d7244): New variable.

Change-Id: Ibce9ce84bedac56978729513756b8476769126bb
2026-05-28 12:13:45 +02:00
Ricardo Wurmus 6c23765499 gnu: r-rstpm2: Add missing test input.
* gnu/packages/cran.scm (r-rstpm2)[native-inputs]: Add r-eha.

Change-Id: I8df4e0c06f4dcc147f4eb3a3b3f70840f1279ef2
2026-05-28 12:13:45 +02:00
Ricardo Wurmus d91ec342c6 gnu: Add r-eha.
* gnu/packages/cran.scm (r-eha): New variable.

Change-Id: I8cfe81ec60f57c10c17ddaede5f0f1369516bf80
2026-05-28 12:13:45 +02:00
Ricardo Wurmus 341381466f gnu: r-universalmotif: Update to 1.30.1.
* gnu/packages/bioconductor.scm (r-universalmotif): Update to 1.30.1.

Change-Id: I7e7cfe559bfdee2da0d2eb060021b765f71e1683
2026-05-28 12:13:44 +02:00
Ricardo Wurmus b0accc4fa4 gnu: r-scrapper: Update to 1.6.2.
* gnu/packages/bioconductor.scm (r-scrapper): Update to 1.6.2.

Change-Id: Ib93e9f1751db7fc9440486bf299362fb13ecee88
2026-05-28 12:13:44 +02:00
Ricardo Wurmus edb8d97aef gnu: r-scrnaseq: Update to 2.26.0.
* gnu/packages/bioconductor.scm (r-scrnaseq): Update to 2.26.0.

Change-Id: I9ddf947f97c5e5e41a3ab7b34fbe7619b92425c5
2026-05-28 12:13:44 +02:00
Ricardo Wurmus 0c676c2ca2 gnu: r-limma: Update to 3.68.1.
* gnu/packages/bioconductor.scm (r-limma): Update to 3.68.1.

Change-Id: Id51bfc31a6f3424677f86baf6cfd3cfb99f0a4df
2026-05-28 12:13:44 +02:00
Ricardo Wurmus ac6e193694 gnu: r-dmrcate: Update to 3.8.0.
* gnu/packages/bioconductor.scm (r-dmrcate): Update to 3.8.0.

Change-Id: I2dbc7ef5e40948a6c3d48c793acf026d1fd27e82
2026-05-28 12:13:44 +02:00
Ricardo Wurmus e0ffc36c4b gnu: r-zebrafishrnaseq: Update to 1.32.0.
* gnu/packages/bioconductor.scm (r-zebrafishrnaseq): Update to 1.32.0.

Change-Id: I94a96f87d8a9d672b673fcab16aea45e23de9636
2026-05-28 12:13:44 +02:00
Ricardo Wurmus cab200653a gnu: r-tximportdata: Update to 1.40.0.
* gnu/packages/bioconductor.scm (r-tximportdata): Update to 1.40.0.

Change-Id: I0e7142e2a6653de73e3d47d47fee7cbe294333bf
2026-05-28 12:13:44 +02:00
Ricardo Wurmus 801bb92a9a gnu: r-tcgabiolinksgui-data: Update to 1.32.0.
* gnu/packages/bioconductor.scm (r-tcgabiolinksgui-data): Update to 1.32.0.

Change-Id: I41f6e1a4ed50ea069939ba641dc6797eecb7cf7e
2026-05-28 12:13:43 +02:00
Ricardo Wurmus ea8503d0cd gnu: r-systempiperdata: Update to 2.16.0.
* gnu/packages/bioconductor.scm (r-systempiperdata): Update to 2.16.0.

Change-Id: Ie85d08f8923ac5381d25ed66da8f826cafbeabf4
2026-05-28 12:13:43 +02:00
Ricardo Wurmus 73d1f7ae6b gnu: r-sesamedata: Update to 1.30.0.
* gnu/packages/bioconductor.scm (r-sesamedata): Update to 1.30.0.

Change-Id: I9816045889e8bb115cc9726f7824989faedf4472
2026-05-28 12:13:43 +02:00
Ricardo Wurmus e06b634441 gnu: r-scpdata: Update to 1.20.0.
* gnu/packages/bioconductor.scm (r-scpdata): Update to 1.20.0.

Change-Id: If2ebd4ef53e99298329cfe49f1f55969133f281e
2026-05-28 12:13:43 +02:00
Ricardo Wurmus 46b795c279 gnu: r-rtcga-rnaseq: Update to 20151101.42.0.
* gnu/packages/bioconductor.scm (r-rtcga-rnaseq): Update to 20151101.42.0.

Change-Id: Ia84b23833e92749eb9892545be039a6cd6772016
2026-05-28 12:13:43 +02:00
Ricardo Wurmus 84dbefed24 gnu: r-rnbeads-hg19: Update to 1.44.0.
* gnu/packages/bioconductor.scm (r-rnbeads-hg19): Update to 1.44.0.

Change-Id: I44714670aa905ac0b0af539cdb7decb1362d1c5f
2026-05-28 12:13:43 +02:00
Ricardo Wurmus 8820c9f777 gnu: r-rnaseqdata-hnrnpc-bam-chr14: Update to 0.50.0.
* gnu/packages/bioconductor.scm (r-rnaseqdata-hnrnpc-bam-chr14): Update to 0.50.0.

Change-Id: I888b3ad8df394c819d923b690b9d4559320abfea
2026-05-28 12:13:43 +02:00
Ricardo Wurmus b0d3cd3089 gnu: r-rcistarget-hg19-motifdbs-cisbponly-500bp: Update to 1.32.0.
* gnu/packages/bioconductor.scm (r-rcistarget-hg19-motifdbs-cisbponly-500bp): Update to 1.32.0.

Change-Id: I3d7892df42c6e7541cfa11208114bd1dcf49ef19
2026-05-28 12:13:43 +02:00
Ricardo Wurmus aa5d03153e gnu: r-curatedtcgadata: Update to 1.34.0.
* gnu/packages/bioconductor.scm (r-curatedtcgadata): Update to 1.34.0.

Change-Id: I2938cb9e94d494b332480282b863cb32ddb2d91d
2026-05-28 12:13:42 +02:00
Ricardo Wurmus 5ae59b07a7 gnu: r-gagedata: Update to 2.50.0.
* gnu/packages/bioconductor.scm (r-gagedata): Update to 2.50.0.

Change-Id: I7d2878e3139ad9c773548230dbec1b70aebedcd1
2026-05-28 12:13:42 +02:00
Ricardo Wurmus 73cc9ab759 gnu: r-affydata: Update to 1.60.0.
* gnu/packages/bioconductor.scm (r-affydata): Update to 1.60.0.
[native-inputs]: Add r-biobase.

Change-Id: I4c0d4b588c5ea1b0c53b2424cc9a3b9b9d57da52
2026-05-28 12:13:42 +02:00
Ricardo Wurmus f03931b143 gnu: r-all: Update to 1.54.0.
* gnu/packages/bioconductor.scm (r-all): Update to 1.54.0.
[native-inputs]: Add r-rpart.

Change-Id: Ia95ed032df922768e631e8130e5b81f9e3043774
2026-05-28 12:13:42 +02:00
Ricardo Wurmus 2f7c9cb009 gnu: r-hsmmsinglecell: Update to 1.32.0.
* gnu/packages/bioconductor.scm (r-hsmmsinglecell): Update to 1.32.0.

Change-Id: If94fe35b407d636feecd2c6170895fbf2f750326
2026-05-28 12:13:42 +02:00
Ricardo Wurmus d871f2a06d gnu: r-prolocdata: Update to 1.50.0.
* gnu/packages/bioconductor.scm (r-prolocdata): Update to 1.50.0.

Change-Id: Ia6da02c40713ba068dcc5ab01b76f021e1f7a74a
2026-05-28 12:13:42 +02:00
Ricardo Wurmus 16c6c347f9 gnu: r-pasillabamsubset: Update to 0.50.0.
* gnu/packages/bioconductor.scm (r-pasillabamsubset): Update to 0.50.0.

Change-Id: I4aaf16a429c42fe87b4bbce76aa5d4af57cf0fa6
2026-05-28 12:13:42 +02:00
Ricardo Wurmus 7a4575a86c gnu: r-pasilla: Update to 1.40.0.
* gnu/packages/bioconductor.scm (r-pasilla): Update to 1.40.0.

Change-Id: I00a64ea1e76718e4f9bf6107894adf6280850dd6
2026-05-28 12:13:42 +02:00
Ricardo Wurmus 1c3c21134b gnu: r-msigdb: Update to 1.20.0.
* gnu/packages/bioconductor.scm (r-msigdb): Update to 1.20.0.

Change-Id: I144589804554930825a5a99a40ca8726c8e399dc
2026-05-28 12:13:41 +02:00
Ricardo Wurmus e4d202a332 gnu: r-msdata: Update to 0.52.0.
* gnu/packages/bioconductor.scm (r-msdata): Update to 0.52.0.

Change-Id: Ia24c626f9fe2e70c0f55ca70c866824df683e7ba
2026-05-28 12:13:41 +02:00
Ricardo Wurmus c986978dcc gnu: r-minionsummarydata: Update to 1.42.0.
* gnu/packages/bioconductor.scm (r-minionsummarydata): Update to 1.42.0.

Change-Id: Ic9ecb643982b30312642971ee96eaa60541fa34c
2026-05-28 12:13:41 +02:00
Ricardo Wurmus d48200b857 gnu: r-minfidataepic: Update to 1.38.0.
* gnu/packages/bioconductor.scm (r-minfidataepic): Update to 1.38.0.

Change-Id: I3f83498562edb9010d4627ac934d89f85e483048
2026-05-28 12:13:41 +02:00
Ricardo Wurmus c2181a6895 gnu: r-minfidata: Update to 0.58.0.
* gnu/packages/bioconductor.scm (r-minfidata): Update to 0.58.0.

Change-Id: If375e3486dfb1ac821a24784791607d94407c4d2
2026-05-28 12:13:41 +02:00
Ricardo Wurmus cbb3a1e21e gnu: r-mousegastrulationdata: Update to 1.26.0.
* gnu/packages/bioconductor.scm (r-mousegastrulationdata): Update to 1.26.0.

Change-Id: Ie7046d19a1ce3448bceeacb38447e96e1289775e
2026-05-28 12:13:41 +02:00
Ricardo Wurmus 9772ecc3fa gnu: r-methylclockdata: Update to 1.20.0.
* gnu/packages/bioconductor.scm (r-methylclockdata): Update to 1.20.0.

Change-Id: Id3fa6b8e36cf85ddadbb5a3b0de9a05ac21420ba
2026-05-28 12:13:41 +02:00
Ricardo Wurmus bfc17619b3 gnu: r-methylaiddata: Update to 1.44.0.
* gnu/packages/bioconductor.scm (r-methylaiddata): Update to 1.44.0.

Change-Id: I9962b7337510d27b978c923b85597b7d8bda9155
2026-05-28 12:13:41 +02:00
Ricardo Wurmus 86214dd9aa gnu: r-macrophage: Update to 1.28.0.
* gnu/packages/bioconductor.scm (r-macrophage): Update to 1.28.0.

Change-Id: I4d343235bb9413310fc12cbba4d6186cd3a5b88f
2026-05-28 12:13:41 +02:00
Ricardo Wurmus 3c7b290027 gnu: r-lungcancerlines: Update to 0.50.0.
* gnu/packages/bioconductor.scm (r-lungcancerlines): Update to 0.50.0.

Change-Id: I69741a4efe88e7b4a0714d1459112581527090cd
2026-05-28 12:13:40 +02:00
Ricardo Wurmus 471aff200e gnu: r-leukemiaseset: Update to 1.48.0.
* gnu/packages/bioconductor.scm (r-leukemiaseset): Update to 1.48.0.

Change-Id: Idf6212a41d1997c30672bd909534a7b8b87e4933
2026-05-28 12:13:40 +02:00
Ricardo Wurmus 143b9ebe65 gnu: r-jaspar2016: Update to 1.40.0.
* gnu/packages/bioconductor.scm (r-jaspar2016): Update to 1.40.0.

Change-Id: Id4ac234985d05a2d4594f380eb087d898c5a1d13
2026-05-28 12:13:40 +02:00
Ricardo Wurmus c4c7393d63 gnu: r-italicsdata: Update to 2.50.0.
* gnu/packages/bioconductor.scm (r-italicsdata): Update to 2.50.0.

Change-Id: Id4b2e07cba7f6d0ea7d6b55d6f3ba1739dd7e766
2026-05-28 12:13:40 +02:00
Ricardo Wurmus b5e09726c2 gnu: r-illuminadatatestfiles: Update to 1.50.0.
* gnu/packages/bioconductor.scm (r-illuminadatatestfiles): Update to 1.50.0.

Change-Id: I7be22b486866d0ee99d8f5acc811dd4a52b15401
2026-05-28 12:13:40 +02:00
Ricardo Wurmus 7a1b940058 gnu: r-illumina450probevariants-db: Update to 1.48.0.
* gnu/packages/bioconductor.scm (r-illumina450probevariants-db): Update to 1.48.0.

Change-Id: I5fffeecc93c7b0b2ee9364e513800ecfe33d800e
2026-05-28 12:13:40 +02:00
Ricardo Wurmus d403e3def7 gnu: r-hdcytodata: Update to 1.32.0.
* gnu/packages/bioconductor.scm (r-hdcytodata): Update to 1.32.0.

Change-Id: I1530b730094d920bd453fedbd2c4a805e4983b10
2026-05-28 12:13:40 +02:00
Ricardo Wurmus e8502d44c9 gnu: r-hellorangesdata: Update to 1.38.0.
* gnu/packages/bioconductor.scm (r-hellorangesdata): Update to 1.38.0.
[native-inputs]: Add r-biocstyle.

Change-Id: Ib67167eab2d3153d50190d06fd50bb664f5a904a
2026-05-28 12:13:40 +02:00
Ricardo Wurmus 95a291b4a7 gnu: r-gsvadata: Update to 1.48.0.
* gnu/packages/bioconductor.scm (r-gsvadata): Update to 1.48.0.

Change-Id: I1ba94ff805ff2d3479d363895bc686fe17550411
2026-05-28 12:13:39 +02:00
Ricardo Wurmus 03f59889d3 gnu: r-golubesets: Update to 1.54.0.
* gnu/packages/bioconductor.scm (r-golubesets): Update to 1.54.0.

Change-Id: I4f482e6a9234ec86568435798e74956619fcd20d
2026-05-28 12:13:39 +02:00
Ricardo Wurmus bdeb0d2ff1 gnu: r-genomationdata: Update to 1.44.0.
* gnu/packages/bioconductor.scm (r-genomationdata): Update to 1.44.0.

Change-Id: Id1f5facef39ec30827a674fc7324a6e639954eb3
2026-05-28 12:13:39 +02:00
Ricardo Wurmus 0c13657990 gnu: r-genelendatabase: Update to 1.48.0.
* gnu/packages/bioconductor.scm (r-genelendatabase): Update to 1.48.0.

Change-Id: I18b48f1d252a09e996eb4f1a75637bfcdeff1642
2026-05-28 12:13:39 +02:00
Ricardo Wurmus 13146988e2 gnu: r-flowworkspacedata: Update to 3.24.0.
* gnu/packages/bioconductor.scm (r-flowworkspacedata): Update to 3.24.0.

Change-Id: I084cc59e98f96ddb4158f0c129a76788201d1ec1
2026-05-28 12:13:39 +02:00
Ricardo Wurmus b6b9f525ee gnu: r-flowsorted-blood-epic: Update to 2.16.0.
* gnu/packages/bioconductor.scm (r-flowsorted-blood-epic): Update to 2.16.0.

Change-Id: Iae64b3b60f67a0730c8fd9a500aa36dbbe666021
2026-05-28 12:13:39 +02:00
Ricardo Wurmus ebefbf419d gnu: r-flowsorted-blood-450k: Update to 1.50.0.
* gnu/packages/bioconductor.scm (r-flowsorted-blood-450k): Update to 1.50.0.

Change-Id: Ieae0c2b96ce7dcaecabd5bc68eb5ea7c192c8636
2026-05-28 12:13:39 +02:00
Ricardo Wurmus ef3dfbd81a gnu: r-faahko: Update to 1.52.0.
* gnu/packages/bioconductor.scm (r-faahko): Update to 1.52.0.

Change-Id: I17eb4301da1fd220c3c438dfa4b88586da8b1aae
2026-05-28 12:13:39 +02:00
Ricardo Wurmus b40991f18e gnu: r-derfinderdata: Update to 2.30.0.
* gnu/packages/bioconductor.scm (r-derfinderdata): Update to 2.30.0.

Change-Id: I0f996f036cc4e65b42256ecac9c35cf23303cac9
2026-05-28 12:13:39 +02:00
Ricardo Wurmus 5dc582b98c gnu: r-copyhelper: Update to 1.44.0.
* gnu/packages/bioconductor.scm (r-copyhelper): Update to 1.44.0.
[native-inputs]: Add r-biocstyle.

Change-Id: I67e6c9c3864367b4f1ab29485bd35e4702fd62fc
2026-05-28 12:13:38 +02:00
Ricardo Wurmus a22391f07d gnu: r-chipexoqualexample: Update to 1.36.0.
* gnu/packages/bioconductor.scm (r-chipexoqualexample): Update to 1.36.0.

Change-Id: I97e1e1a3178c15d5e0659aa0d74c8fa633b96236
2026-05-28 12:13:38 +02:00
Ricardo Wurmus aa989fde12 gnu: r-champdata: Update to 2.44.0.
* gnu/packages/bioconductor.scm (r-champdata): Update to 2.44.0.

Change-Id: Iae761fee2a67fd3ff734eb325515588a86b3b47a
2026-05-28 12:13:38 +02:00
Ricardo Wurmus e88494594e gnu: r-celldex: Update to 1.22.0.
* gnu/packages/bioconductor.scm (r-celldex): Update to 1.22.0.

Change-Id: I73511647b21150f0b1cb358325858fa55bda294b
2026-05-28 12:13:38 +02:00
Ricardo Wurmus 74934f2a41 gnu: r-breastcancervdx: Update to 1.50.0.
* gnu/packages/bioconductor.scm (r-breastcancervdx): Update to 1.50.0.

Change-Id: I505bd02985aae88584ec1ece91a8f13c827023c2
2026-05-28 12:13:38 +02:00
Ricardo Wurmus f0372ee7a4 gnu: r-breakpointrdata: Update to 1.30.0.
* gnu/packages/bioconductor.scm (r-breakpointrdata): Update to 1.30.0.

Change-Id: Ia8a442a97d06a21a92dda3747b8686d025f48a72
2026-05-28 12:13:38 +02:00
Ricardo Wurmus 74b92ce075 gnu: r-biscuiteerdata: Update to 1.26.0.
* gnu/packages/bioconductor.scm (r-biscuiteerdata): Update to 1.26.0.

Change-Id: If58f7db24fb10b272744616099e61bb0d923c913
2026-05-28 12:13:38 +02:00
Ricardo Wurmus 75d4f8b43f gnu: r-bodymaprat: Update to 1.28.0.
* gnu/packages/bioconductor.scm (r-bodymaprat): Update to 1.28.0.

Change-Id: I4e0699b2cfe346a9f58cedf39fbed91fcac86b18
2026-05-28 12:13:38 +02:00
Ricardo Wurmus 13e2f76b0f gnu: r-bladderbatch: Update to 1.50.0.
* gnu/packages/bioconductor.scm (r-bladderbatch): Update to 1.50.0.

Change-Id: Ie9bde875c8e4b99ca8ea2cad866940894c433688
2026-05-28 12:13:37 +02:00
Ricardo Wurmus c598a8816e gnu: r-biotmledata: Update to 1.36.0.
* gnu/packages/bioconductor.scm (r-biotmledata): Update to 1.36.0.

Change-Id: I24af557034efa086db6a6115160448eed1938f67
2026-05-28 12:13:37 +02:00
Ricardo Wurmus bde1e4bebc gnu: r-bcellviper: Update to 1.48.0.
* gnu/packages/bioconductor.scm (r-bcellviper): Update to 1.48.0.

Change-Id: I41df72fbc87c2d795d8a8a65c1640878ba038bcc
2026-05-28 12:13:37 +02:00
Ricardo Wurmus c008a2bd06 gnu: r-arrmdata: Update to 1.48.0.
* gnu/packages/bioconductor.scm (r-arrmdata): Update to 1.48.0.

Change-Id: I8a7b1b84b8a638ee7c6177315312725d06a0ff66
2026-05-28 12:13:37 +02:00
Ricardo Wurmus 5e22e0a461 gnu: r-airway: Update to 1.32.0.
* gnu/packages/bioconductor.scm (r-airway): Update to 1.32.0.

Change-Id: Ia2d5e7c8aa88fdeafcd85c00a1048eba6b0c2c36
2026-05-28 12:13:37 +02:00
Ricardo Wurmus 5f2c20d830 gnu: r-adductdata: Update to 1.28.0.
* gnu/packages/bioconductor.scm (r-adductdata): Update to 1.28.0.

Change-Id: I3c95faa7e4757669126881a1b059f9201e5276b0
2026-05-28 12:13:37 +02:00
Ricardo Wurmus 1d77285b44 gnu: r-acfmperiod: Add missing input.
* gnu/packages/cran.scm (r-acfmperiod)[native-inputs]: Add r-knitr.

Change-Id: Id96c12db32a8481bdb3ddb540494ad8b07c7baab
2026-05-28 12:13:37 +02:00
Ricardo Wurmus c2e3b95e7e gnu: r-qs2: Update to 0.2.1.
* gnu/packages/cran.scm (r-qs2): Update to 0.2.1.

Change-Id: I59b6a094c1813fa61e56bcc817334a42bd956490
2026-05-28 12:13:37 +02:00
Ricardo Wurmus a21c4f8e6e gnu: r-lwgeom: Update to 0.2-16.
* gnu/packages/cran.scm (r-lwgeom): Update to 0.2-16.

Change-Id: Id971ef5c2c7811e5d3f6a76cb37d6948d97d6857
2026-05-28 12:13:36 +02:00
Ricardo Wurmus 24645a570b gnu: r-qtl2: Update to 0.40.
* gnu/packages/cran.scm (r-qtl2): Update to 0.40.
[native-inputs]: Add r-regress.

Change-Id: I780bf35eb59d772524a429c9815829c4837ee50d
2026-05-28 12:13:36 +02:00
Ricardo Wurmus 07d973a86f gnu: r-igraph: Update to 2.3.1.
* gnu/packages/cran.scm (r-igraph): Update to 2.3.1.

Change-Id: Ic5aab9866a0dc7bedea2609b18d7df0ceffacd0b
2026-05-28 12:13:36 +02:00
Ricardo Wurmus 886b0cbe61 gnu: r-exactranktests: Update to 0.8-37.
* gnu/packages/cran.scm (r-exactranktests): Update to 0.8-37.

Change-Id: I822540050eb692a2d80896dcbffd77da35a4cbbf
2026-05-28 12:13:36 +02:00
Ricardo Wurmus 0f271ff2d4 gnu: r-fds: Update to 1.9.
* gnu/packages/cran.scm (r-fds): Update to 1.9.

Change-Id: Id0c4d7b00e34cf47566a079749beb5edd7838e23
2026-05-28 12:13:36 +02:00
Ricardo Wurmus 8b1627e320 gnu: r-spdata: Update to 2.3.5.
* gnu/packages/cran.scm (r-spdata): Update to 2.3.5.

Change-Id: I0b68fd939a1fc1ef4c76a03c398e13eca3d512ac
2026-05-28 12:13:36 +02:00
Ricardo Wurmus 57385e0b22 gnu: r-fields: Update to 17.3.
* gnu/packages/cran.scm (r-fields): Update to 17.3.

Change-Id: If5bb82448bcad388690af1851a291f3ebf437cac
2026-05-28 12:13:36 +02:00
Ricardo Wurmus 67354fcd9e gnu: r-np: Update to 0.70-1.
* gnu/packages/cran.scm (r-np): Update to 0.70-1.
[native-inputs]: Remove r-gam, r-mass, and r-mgcv; add r-crs, r-knitr, r-pkgload, and
r-testthat.

Change-Id: I926f44b81efb61d6b1b8b73f181db98e594c6232
2026-05-28 12:13:36 +02:00
Ricardo Wurmus d4d046b2d1 gnu: r-fastglm: Update to 0.1.0.
* gnu/packages/cran.scm (r-fastglm): Update to 0.1.0.
[propagated-inputs]: Add r-formula and r-matrix.
[native-inputs]: Add r-logistf, r-mass, r-pscl, r-sandwich, r-statmod, r-testthat,
and r-tweedie.

Change-Id: I771f722105ad342f83b3bd54265b8b430d5453bc
2026-05-28 12:13:36 +02:00
Ricardo Wurmus 2db6cd2ab9 gnu: r-fixest: Update to 0.14.1.
* gnu/packages/cran.scm (r-fixest): Update to 0.14.1.

Change-Id: Ib9a9ac0917bddb0b5194e2d1e6fa556e1767333d
2026-05-28 12:13:35 +02:00
Ricardo Wurmus bb5572f9a6 gnu: r-glmnet: Update to 5.0.
* gnu/packages/cran.scm (r-glmnet): Update to 5.0.
[native-inputs]: Remove gfortran; add r-nnet and r-testthat.

Change-Id: I8353bb75fde34d29cbfdde9342246a1c6c8e7f3f
2026-05-28 12:13:35 +02:00
Ricardo Wurmus 78248184a3 gnu: r-fivethirtyeight: Update to 0.6.2.
* gnu/packages/cran.scm (r-fivethirtyeight): Update to 0.6.2.
[propagated-inputs]: Remove r-knitr, r-rmarkdown, r-dplyr, r-readr, r-ggplot2,
r-magrittr, and r-stringr.
[native-inputs]: Add r-knitr.

Change-Id: I641ced860ae6b8fa65ce346b2af07544973a9fa3
2026-05-28 12:13:35 +02:00
Ricardo Wurmus 716469fac5 gnu: r-clubsandwich: Update to 0.7.0.
* gnu/packages/cran.scm (r-clubsandwich): Update to 0.7.0.

Change-Id: I5afa87ef47311be6b0e3b2aabc23ac00fde1319f
2026-05-28 12:13:35 +02:00
Ricardo Wurmus a54a9f102a gnu: r-nanonext: Update to 1.9.0.
* gnu/packages/cran.scm (r-nanonext): Update to 1.9.0.
[source]: Remove bundled code.

Change-Id: I88213d91b997957dd5c08cdefd5629e8d75b678c
2026-05-28 12:13:35 +02:00
Ricardo Wurmus 0adb4d3cfa gnu: nng-1.10: Update to 1.11.
* gnu/packages/networking.scm (nng-1.10): Update to 1.11.
[arguments]: Enable one additional test.
* gnu/packages/cran.scm (r-nanonext)[inputs]: Update reference.

Change-Id: Id123b0a4e881824337fad74be3e297f3e92b7213
2026-05-28 12:13:35 +02:00
Ricardo Wurmus 828cecf25f gnu: Add r-crs.
* gnu/packages/cran.scm (r-crs): New variable.

Change-Id: I7d6a6ee02f7ce5f631a3e3da5a692064f9b45321
2026-05-28 12:13:35 +02:00
Ricardo Wurmus 5db662197f gnu: Add r-regress.
* gnu/packages/cran.scm (r-regress): New variable.

Change-Id: Iecbfbeda21bea0140e0b44fc631933c201f8405a
2026-05-28 12:13:35 +02:00
Ricardo Wurmus cd68997daa gnu: r-rserve: Update to 1.8-19.
* gnu/packages/cran.scm (r-rserve): Update to 1.8-19.
[source]: Remove bundled jars.
[arguments]: Pass configure flags to build client, server, and proxy; add
phase 'build-java-components; remove phase 'relax-gcc-14-strictness.
[propagated-inputs]: Remove r-checkmate, r-mime, r-jsonlite, r-knitr, r-r6,
r-rcpp, and r-uuid.
[inputs]: Add openjdk11:jdk.

Change-Id: I1e8204dbf55e76d7e7f4541328b99896db7d45d2
2026-05-28 12:13:34 +02:00
Ricardo Wurmus 9a5ba858ff gnu: r-liana: Make compatible with latest version of SeuratObject.
* gnu/packages/bioinformatics.scm (r-liana)[arguments]: Add phase
'seurat-compatibility.

Change-Id: Icbae60f26fae38e5c292c83235c32f544ba274b4
2026-05-28 12:13:34 +02:00
Ricardo Wurmus c6d301bd90 gnu: r-liana: Replace custom phase with #:skipped-tests.
* gnu/packages/bioinformatics.scm (r-liana)[arguments]: Remove phase
'disable-bad-tests; use #:skipped-tests instead.

Change-Id: I4b4c6627a314c267419349207d8c6c50f07d30b1
2026-05-28 12:13:34 +02:00
Ricardo Wurmus 95cb5879f5 gnu: Remove r-refgenome.
This package has been removed from CRAN on 2020-01-16.  It has failing tests
and now fails to build with R 4.6.0.

* gnu/packages/cran.scm (r-refgenome): Remove variable.

Change-Id: I4f20e670045865061d6d6e06f4b25472a834cf32
2026-05-28 12:13:34 +02:00
Ricardo Wurmus 724bc60ad3 gnu: Remove r-rbamtools.
This package has been removed from CRAN on 2020-01-16.  It has failing tests
and it depends on r-refgenome, which fails to build with R 4.6.0.

* gnu/packages/cran.scm (r-rbamtools): Remove variable.

Change-Id: Ie096b1a2ac100b0c3affbfda8d521ed0b8a2a5b7
2026-05-28 12:13:34 +02:00
Ricardo Wurmus b66a7e57f2 gnu: r-voltron: Update to 0.2.6.
* gnu/packages/bioinformatics.scm (r-voltron): Update to 0.2.6.
[propagated-inputs]: Remove r-pizzarr, r-reshape2, r-reticulate, and r-rhdf5;
add r-s4vectors.

Change-Id: Ie3f0661bf976fe63aa85bbcaea66e1f4478a5bca
2026-05-28 12:13:34 +02:00
Ricardo Wurmus 1cb339b691 gnu: simpleitk: Update to 2.5.4.
* gnu/packages/image-processing.scm (simpleitk): Update to 2.5.4.
[source]: Add patch.
* gnu/packages/patches/simpleitk-r-4.6.0.patch: New file.
* gnu/local.mk (dist_patch_DATA): Record it.

Change-Id: Id85b8a717046497bd8469c365c738ac984229e03
2026-05-28 12:13:34 +02:00
Ricardo Wurmus cb0eb58005 gnu: swig: Support R 4.6.0.
* gnu/packages/patches/swig-support-r-4.6.0.patch: New file.
* gnu/local.mk (dist_patch_DATA): Register it.
* gnu/packages/swig.scm (swig-4.4)[source]: Add patch.

Change-Id: I3e8b58e05537cbb12139ba463289be3cf19cab41
2026-05-28 12:13:34 +02:00
Ricardo Wurmus dd8bd87436 gnu: r-zarrdataframe: Update to 0.0.0-3.f5f6715.
* gnu/packages/bioinformatics.scm (r-zarrdataframe): Update to
0.0.0-3.f5f6715.
[propagated-inputs]: Add r-zarrarray.

Change-Id: Ibc8d188cf19180c57155f137aaf9822860a78f3b
2026-05-28 12:13:33 +02:00
Ricardo Wurmus 34a5a0744c gnu: python-pyarrow: Add missing input.
* gnu/packages/databases.scm (python-pyarrow)[native-inputs]: Add
python-scikit-build-core.

Change-Id: I28b982f309d7a3074fe29f1ea80abba7430ba2c7
2026-05-28 12:13:33 +02:00
Ricardo Wurmus a0a728072a gnu: r-imagearray: Update to 1.0.0.
* gnu/packages/bioinformatics.scm (r-imagearray): Update to 1.0.0.
[source]: Fetch from Bioconductor.
[arguments]: Disable test requiring RBiomFormats.
[propagated-inputs]: Add r-zarrarray.
[native-inputs]: Add r-ggplot2.

Change-Id: I945840930b2ba010754e63c7d43fcbcd9af550c5
2026-05-28 12:13:33 +02:00
Ricardo Wurmus b9720cd6f4 gnu: r-zarrarray: Update to 1.0.0.
* gnu/packages/bioinformatics.scm (r-zarrarray): Update to 1.0.0.
[source]: Fetch from Bioconductor.
[arguments]: Enable tests.
[properties]: Remove updater-extra-native-inputs.
[propagated-inputs]: Remove r-matrix.
[native-inputs]: Add r-knitr.
[home-page]: Use Bioconductor page.
[license]: Use Artistic 2.0.

Change-Id: Iaeda27401e8dede9cebc54979fc9ff109da54c51
2026-05-28 12:13:33 +02:00
Ricardo Wurmus 981d6b5c6a gnu: r-sparsearray: Update to 1.12.2.
* gnu/packages/bioconductor.scm (r-sparsearray): Update to 1.12.2.

Change-Id: I803a387686bcbe989c8b69cc9752b73ee4c1531c
2026-05-28 12:13:33 +02:00
Ricardo Wurmus bf032e87eb gnu: r-diffbind: Update to 3.22.1.
* gnu/packages/bioconductor.scm (r-diffbind): Update to 3.22.1.
[native-inputs]: Add r-deseq.

Change-Id: I975eb5aac4a06145629f46ba839cdf68d72ba8a7
2026-05-28 12:13:33 +02:00
Ricardo Wurmus f43bd8f4b3 gnu: apache-arrow: Update to 24.0.0.
* gnu/packages/databases.scm (apache-arrow): Update to 24.0.0.

Change-Id: I62f2f8f40d0914426c8cff9c639c64db71ba690b
2026-05-28 12:13:33 +02:00
Ricardo Wurmus ac086d271c gnu: r-metadat: Update to 1.6-0.
* gnu/packages/cran.scm (r-metadat): Update to 1.6-0.

Change-Id: I60842b83d2f3883ce1149d85f5e089939d912a54
2026-05-28 12:13:33 +02:00
Ricardo Wurmus 6bde614df2 gnu: r-bien: Update to 1.2.8.
* gnu/packages/cran.scm (r-bien): Update to 1.2.8.

Change-Id: Ic949cdf16101ca19bd030bcfb865308e08aa5e6f
2026-05-28 12:13:32 +02:00
Ricardo Wurmus a76bfe5741 gnu: r-altmeta: Update to 4.3.1.
* gnu/packages/cran.scm (r-altmeta): Update to 4.3.1.

Change-Id: Id4dba0d895c5b382bdc54e4894df0b0806377aa4
2026-05-28 12:13:32 +02:00
Ricardo Wurmus 556fcedc72 gnu: r-fracdiff: Update to 1.5-4.
* gnu/packages/cran.scm (r-fracdiff): Update to 1.5-4.

Change-Id: I9caa720b9f750bc3585e13463651f774484e1499
2026-05-28 12:13:32 +02:00
Ricardo Wurmus 1f3865b7c1 gnu: r-enrichwith: Update to 0.5.0.
* gnu/packages/cran.scm (r-enrichwith): Update to 0.5.0.

Change-Id: Ie4a31e08e871c8bdd9be8f411b2925cd19235047
2026-05-28 12:13:32 +02:00
Ricardo Wurmus d707a94190 gnu: r-arrow: Update to 24.0.0.
* gnu/packages/cran.scm (r-arrow): Update to 24.0.0.

Change-Id: Icbea4b39e724bfe2ae20b36b686d972edaad98da
2026-05-28 12:13:32 +02:00
Ricardo Wurmus f0c88b6029 gnu: r-seqinr: Update to 4.2-44.
* gnu/packages/cran.scm (r-seqinr): Update to 4.2-44.

Change-Id: Ib42fa3a82aa21d042af67f5892a973cde2e11241
2026-05-28 12:13:32 +02:00
Ricardo Wurmus 6e24ed1234 gnu: r-brglm2: Update to 1.1.0.
* gnu/packages/cran.scm (r-brglm2): Update to 1.1.0.

Change-Id: I19600e3a06020cc6f3b8bfaf5986a259576d33c6
2026-05-28 12:13:32 +02:00
Ricardo Wurmus 17a93faf3a gnu: r-secretbase: Update to 1.2.2.
* gnu/packages/cran.scm (r-secretbase): Update to 1.2.2.

Change-Id: Ibd47e9c71118cd7c3198e3dd9c0887b8b5e605ad
2026-05-28 12:13:32 +02:00
Ricardo Wurmus 85ffec17fe gnu: r-gparotation: Update to 2026.4-1.
* gnu/packages/cran.scm (r-gparotation): Update to 2026.4-1.

Change-Id: I24ea2913e3b84c5296bb90be8a92a5e196d0f89e
2026-05-28 12:13:31 +02:00
Ricardo Wurmus c23f4be208 gnu: r-roxygen2: Update to 8.0.0.
* gnu/packages/cran.scm (r-roxygen2): Update to 8.0.0.
[propagated-inputs]: Remove r-purrr, r-stringi, and r-stringr; add r-lifecycle.
[native-inputs]: Add r-s7.

Change-Id: I8da50c352702bb7d821582f931a6639ab396a829
2026-05-28 12:13:31 +02:00
Ricardo Wurmus cceefdfb9a gnu: r-devtools: Update to 2.5.2.
* gnu/packages/cran.scm (r-devtools): Update to 2.5.2.

Change-Id: I5855febaccbd87f89e74da7be85251c8946c4709
2026-05-28 12:13:31 +02:00
Ricardo Wurmus 343c478e1b gnu: r-descr: Update to 1.1.9.
* gnu/packages/cran.scm (r-descr): Update to 1.1.9.

Change-Id: Ie6ad4acf0c7cdd8a37c4674fd8907ddc0d136623
2026-05-28 12:13:31 +02:00
Ricardo Wurmus c2e950d22c gnu: r-metap: Update to 1.14.
* gnu/packages/bioconductor.scm (r-metap): Update to 1.14.

Change-Id: Id2c1de4226ac27359e101aba69e73a7e1df29196
2026-05-28 12:13:31 +02:00
Ricardo Wurmus d0c6062d12 gnu: r-ggpicrust2: Update to 2.5.14.
* gnu/packages/bioconductor.scm (r-ggpicrust2): Update to 2.5.14.
[native-inputs]: Add r-circlize, r-complexheatmap, and r-metagenomeseq.

Change-Id: I2b24e392d11e4941de6a28da965ac5533a8b2052
2026-05-28 12:13:31 +02:00
Ricardo Wurmus ac5fd6d21f gnu: r-basics: Update to 2.24.0.
* gnu/packages/bioconductor.scm (r-basics): Update to 2.24.0.

Change-Id: If8d77505ffcd4c8c70bdd63aa3a036ee8b98a011
2026-05-28 12:13:31 +02:00
Ricardo Wurmus 10507ced4f gnu: r-basic4cseq: Update to 1.48.0.
* gnu/packages/bioconductor.scm (r-basic4cseq): Update to 1.48.0.

Change-Id: I09116627f16d595160dc8483fff436b4cebe9751
2026-05-28 12:13:31 +02:00
Ricardo Wurmus a7d9ed0526 gnu: r-bgeedb: Update to 2.38.1.
* gnu/packages/bioconductor.scm (r-bgeedb): Update to 2.38.1.

Change-Id: I27752bbc32904e0a44d527a754bc8ecaaaae5e4c
2026-05-28 12:13:30 +02:00
Ricardo Wurmus 632c1238bd gnu: r-bioccheck: Update to 1.48.0.
* gnu/packages/bioconductor.scm (r-bioccheck): Update to 1.48.0.

Change-Id: I7dd3fcff5d53671a3203886ca57db1f1a2451ad9
2026-05-28 12:13:30 +02:00
Ricardo Wurmus 3a1d357de6 gnu: r-biocbaseutils: Update to 1.14.0.
* gnu/packages/bioconductor.scm (r-biocbaseutils): Update to 1.14.0.

Change-Id: I901f6e26f6c6e81c728e63dcb9f63a7709d84279
2026-05-28 12:13:30 +02:00
Ricardo Wurmus aedc29d32f gnu: r-aucell: Update to 1.34.0.
* gnu/packages/bioconductor.scm (r-aucell): Update to 1.34.0.

Change-Id: If8a672f7474bf5e1b319ff5fe5668741f7eda371
2026-05-28 12:13:30 +02:00
Ricardo Wurmus 46679a8bed gnu: r-treeio: Update to 1.36.1.
* gnu/packages/bioconductor.scm (r-treeio): Update to 1.36.1.

Change-Id: I5001544bed94430b064c5c3739b5e3e8946322db
2026-05-28 12:13:30 +02:00
Ricardo Wurmus 013a58dde7 gnu: r-zellkonverter: Update to 1.22.0.
* gnu/packages/bioconductor.scm (r-zellkonverter): Update to 1.22.0.

Change-Id: Id925a233522956bb02d7a29a98d150ab28e0c2c2
2026-05-28 12:13:30 +02:00
Ricardo Wurmus 2e045d6b61 gnu: r-metabocoreutils: Update to 1.20.1.
* gnu/packages/bioconductor.scm (r-metabocoreutils): Update to 1.20.1.

Change-Id: I80acc777d566de91508009da37ef7bb3152f3cff
2026-05-28 12:13:30 +02:00
Ricardo Wurmus 03795210b1 gnu: r-biocparallel: Update to 1.46.0.
* gnu/packages/bioconductor.scm (r-biocparallel): Update to 1.46.0.

Change-Id: I552f4ab632ebff047f7fdd824c16c2d9cecadbff
2026-05-28 12:13:30 +02:00
Ricardo Wurmus 615aa1c25c gnu: r-affycoretools: Update to 1.84.0.
* gnu/packages/bioconductor.scm (r-affycoretools): Update to 1.84.0.

Change-Id: If4b177f91acd3f365164c7ab151d2d9f13fb96a1
2026-05-28 12:13:29 +02:00
Ricardo Wurmus 2ad7d83367 gnu: r-delayedarray: Update to 0.38.1.
* gnu/packages/bioconductor.scm (r-delayedarray): Update to 0.38.1.

Change-Id: I3a37dcc3ee18558c214693328738272a72dd4459
2026-05-28 12:13:29 +02:00
Ricardo Wurmus b0f880e9b8 gnu: r-banocc: Update to 1.36.0.
* gnu/packages/bioconductor.scm (r-banocc): Update to 1.36.0.

Change-Id: Iadc186f67c81b217227b247000a3255d6c69d8fb
2026-05-28 12:13:29 +02:00
Ricardo Wurmus b102e3979d gnu: r-basespacer: Update to 1.56.0.
* gnu/packages/bioconductor.scm (r-basespacer): Update to 1.56.0.

Change-Id: I1baa89ddb99177d1715c433a9d9ce487092bf766
2026-05-28 12:13:29 +02:00
Ricardo Wurmus 6e5cadec5d gnu: r-baalchip: Update to 1.38.0.
* gnu/packages/bioconductor.scm (r-baalchip): Update to 1.38.0.

Change-Id: I6bab66a2f76246f39648c519e17f92cff0862770
2026-05-28 12:13:29 +02:00
Ricardo Wurmus e95131c15f gnu: r-awst: Update to 1.20.0.
* gnu/packages/bioconductor.scm (r-awst): Update to 1.20.0.

Change-Id: I5e835d3ab9188961249f5adc36069cef6866ba37
2026-05-28 12:13:29 +02:00
Ricardo Wurmus 0d2ed172d7 gnu: r-atsnp: Update to 1.28.0.
* gnu/packages/bioconductor.scm (r-atsnp): Update to 1.28.0.

Change-Id: I5a4e7731d562def6c8b8996d4db79d925ec40283
2026-05-28 12:13:29 +02:00
Ricardo Wurmus fe6d916d81 gnu: r-anvil: Update to 1.24.0.
* gnu/packages/bioconductor.scm (r-anvil): Update to 1.24.0.

Change-Id: Ia9540457b6a63a83ff951f1133fdf1c1a6bf77ec
2026-05-28 12:13:29 +02:00
Ricardo Wurmus 5aa2a75a51 gnu: r-agimicrorna: Update to 2.62.0.
* gnu/packages/bioconductor.scm (r-agimicrorna): Update to 2.62.0.

Change-Id: I631f2a563de07e3607fd6088c20949e3da1ae071
2026-05-28 12:13:28 +02:00
Ricardo Wurmus 1c1eafec80 gnu: r-anndatar: Update to 1.2.0.
* gnu/packages/bioconductor.scm (r-anndatar): Update to 1.2.0.
[arguments]: Skip one test.

Change-Id: I018f1df716807cac11c573330b570fb17456748c
2026-05-28 12:13:28 +02:00
Ricardo Wurmus 56f3f8fba7 gnu: r-rarr: Build with more compression libraries.
This prevents building of bundled static libraries, which causes problems in
dependents.

* gnu/packages/bioconductor.scm (r-rarr)[inputs]: Add c-blosc and zstd:lib.
[arguments]: Disable one test.

Change-Id: I9546f8f3f034cfe7a0c19cf37267fb3d2ca847c3
2026-05-28 12:13:28 +02:00
Ricardo Wurmus 175eee4db9 gnu: r-tximeta: Update to 1.30.0.
* gnu/packages/bioconductor.scm (r-tximeta): Update to 1.30.0.
[propagated-inputs]: Add r-dbi.

Change-Id: I2534471c34ad3dda237162de29d65eea499bd368
2026-05-28 12:13:28 +02:00
Ricardo Wurmus c58e6a7616 gnu: r-tricycle: Update to 1.20.0.
* gnu/packages/bioconductor.scm (r-tricycle): Update to 1.20.0.

Change-Id: I6007e98d3d56acab0cacfaa902d58bf640561660
2026-05-28 12:13:28 +02:00
Ricardo Wurmus 1e3e8931dd gnu: r-tcgabiolinks: Update to 2.40.0.
* gnu/packages/bioconductor.scm (r-tcgabiolinks): Update to 2.40.0.

Change-Id: I6df0b83b682f25e95ee6a9fa240c6306a38c79af
2026-05-28 12:13:28 +02:00
Ricardo Wurmus 24faedd459 gnu: r-biscuiteer: Update to 1.26.0.
* gnu/packages/bioconductor.scm (r-biscuiteer): Update to 1.26.0.

Change-Id: I27ca881f54d3f3021c73d8ba712fe3faa577a609
2026-05-28 12:13:28 +02:00
Ricardo Wurmus 9cc5d37c52 gnu: r-omicade4: Update to 1.52.0.
* gnu/packages/bioconductor.scm (r-omicade4): Update to 1.52.0.

Change-Id: I638e2ded88c167648111b2f197aace3656f048c8
2026-05-28 12:13:28 +02:00
Ricardo Wurmus 62e1900a3f gnu: r-dmrseq: Update to 1.32.0.
* gnu/packages/bioconductor.scm (r-dmrseq): Update to 1.32.0.

Change-Id: If0d449fbe9127ce2a5ace9e9fe83ee5393e215c7
2026-05-28 12:13:27 +02:00
Ricardo Wurmus a6230a7204 gnu: r-dada2: Update to 1.40.0.
* gnu/packages/bioconductor.scm (r-dada2): Update to 1.40.0.

Change-Id: I06ab8961ec4bc0e7005d62424141835a77d1220c
2026-05-28 12:13:27 +02:00
Ricardo Wurmus 939e5ddea9 gnu: r-bsseq: Update to 1.48.0.
* gnu/packages/bioconductor.scm (r-bsseq): Update to 1.48.0.

Change-Id: I4bc97cea071c168d7ea27fc2c8732635a6c5ebe9
2026-05-28 12:13:27 +02:00
Ricardo Wurmus 5dd4e09535 gnu: r-biotmle: Update to 1.36.0.
* gnu/packages/bioconductor.scm (r-biotmle): Update to 1.36.0.

Change-Id: I94b88adc935a272cbb6314aab31132990ef2cdef
2026-05-28 12:13:27 +02:00
Ricardo Wurmus 3b7d54af1a gnu: r-biotip: Update to 1.26.0.
* gnu/packages/bioconductor.scm (r-biotip): Update to 1.26.0.

Change-Id: I05a5f9ecdd2b7152a069dd6a786b983494c82e6b
2026-05-28 12:13:27 +02:00
Ricardo Wurmus c43ad69f93 gnu: r-bioqc: Update to 1.40.0.
* gnu/packages/bioconductor.scm (r-bioqc): Update to 1.40.0.

Change-Id: Ifbd7218aef3596f0c57a1ed4538778ef541823c6
2026-05-28 12:13:27 +02:00
Ricardo Wurmus 1cbd4239e6 gnu: r-bionet: Update to 1.72.0.
* gnu/packages/bioconductor.scm (r-bionet): Update to 1.72.0.

Change-Id: Ie66d9fc21ca73a4bc6ddcd5ac3807e43b6feb0d4
2026-05-28 12:13:27 +02:00
Ricardo Wurmus ad5c293a11 gnu: r-bionero: Update to 1.20.0.
* gnu/packages/bioconductor.scm (r-bionero): Update to 1.20.0.

Change-Id: If1ab45de014589e408b7da3c0b1c40d9a26e168c
2026-05-28 12:13:27 +02:00
Ricardo Wurmus b7287a6dde gnu: r-biomvrcns: Update to 1.52.0.
* gnu/packages/bioconductor.scm (r-biomvrcns): Update to 1.52.0.

Change-Id: Ida95b526e6beba5754597f851ebd821c9f6ac112
2026-05-28 12:13:26 +02:00
Ricardo Wurmus da87fa734e gnu: r-biomvcclass: Update to 1.80.0.
* gnu/packages/bioconductor.scm (r-biomvcclass): Update to 1.80.0.

Change-Id: I75d657557dc7e8a03b6e8ca10234c233d9600305
2026-05-28 12:13:26 +02:00
Ricardo Wurmus 49cbae164c gnu: r-mvcclass: Update to 1.86.0.
* gnu/packages/bioconductor.scm (r-mvcclass): Update to 1.86.0.

Change-Id: If208b24f5ff33cd9b9109756057a191005497e8b
2026-05-28 12:13:26 +02:00
Ricardo Wurmus e65800eb53 gnu: r-biodb: Update to 1.20.0.
* gnu/packages/bioconductor.scm (r-biodb): Update to 1.20.0.

Change-Id: I8a542771835379d4c5199966bd279c15d10ff9dc
2026-05-28 12:13:26 +02:00
Ricardo Wurmus 60a7a4364d gnu: r-biocthis: Update to 1.22.0.
* gnu/packages/bioconductor.scm (r-biocthis): Update to 1.22.0.

Change-Id: I8bda7567e5e18b23f26a983d9c99623d2d7c5abc
2026-05-28 12:13:26 +02:00
Ricardo Wurmus 2aa9bc5bdb gnu: r-bcrank: Update to 1.74.0.
* gnu/packages/bioconductor.scm (r-bcrank): Update to 1.74.0.

Change-Id: I1d4386670cf754e60b2738aa84377f665660d5f8
2026-05-28 12:13:26 +02:00
Ricardo Wurmus 3f6b891238 gnu: r-bbcanalyzer: Update to 1.42.0.
* gnu/packages/bioconductor.scm (r-bbcanalyzer): Update to 1.42.0.

Change-Id: Ic5080bda0b394038f07423ce21ec6a59cd473b38
2026-05-28 12:13:26 +02:00
Ricardo Wurmus 5c3a4fa696 gnu: r-baynorm: Update to 1.30.0.
* gnu/packages/bioconductor.scm (r-baynorm): Update to 1.30.0.

Change-Id: I72574c7e04f3cae81b0df9f565cccf464bc7b03c
2026-05-28 12:13:26 +02:00
Ricardo Wurmus 6266a027f6 gnu: r-bayesspace: Update to 1.22.0.
* gnu/packages/bioconductor.scm (r-bayesspace): Update to 1.22.0.

Change-Id: If5468bb49deab1d5e7326c5b3fd1447cf2a645a3
2026-05-28 12:13:25 +02:00
Ricardo Wurmus a21716eb03 gnu: r-bayesknockdown: Update to 1.38.0.
* gnu/packages/bioconductor.scm (r-bayesknockdown): Update to 1.38.0.

Change-Id: Ie077615c8f1e3454410bb927525a78df3303ba9b
2026-05-28 12:13:25 +02:00
Ricardo Wurmus 93e32699fe gnu: r-basilisk: Update to 1.24.0.
* gnu/packages/bioconductor.scm (r-basilisk): Update to 1.24.0.

Change-Id: I5866c704e411ba76f69103c7af9cabdbd0881e4f
2026-05-28 12:13:25 +02:00
Ricardo Wurmus 55b2f3532a gnu: r-basilisk-utils: Update to 1.24.0.
* gnu/packages/bioconductor.scm (r-basilisk-utils): Update to 1.24.0.

Change-Id: I203917bd82e8b038dce47fa463e8f981bc48f88b
2026-05-28 12:13:25 +02:00
Ricardo Wurmus 34531c86b0 gnu: r-basicstarrseq: Update to 1.40.0.
* gnu/packages/bioconductor.scm (r-basicstarrseq): Update to 1.40.0.

Change-Id: If31582a719484b6e99670cb7618a5e9829028c18
2026-05-28 12:13:25 +02:00
Ricardo Wurmus 9b5321e151 gnu: r-basics: Update to 2.23.2.
* gnu/packages/bioconductor.scm (r-basics): Update to 2.23.2.

Change-Id: I299b9dc56ccf1f0f0b0cbd4376087172a557e998
2026-05-28 12:13:25 +02:00
Ricardo Wurmus c58577793f gnu: r-basic4cseq: Update to 1.47.0.
* gnu/packages/bioconductor.scm (r-basic4cseq): Update to 1.47.0.

Change-Id: I59d812c8ba306d3a1345cde61b00a11603b86a33
2026-05-28 12:13:25 +02:00
Ricardo Wurmus 9725af2f08 gnu: r-dir-expiry: Update to 1.20.0.
* gnu/packages/bioconductor.scm (r-dir-expiry): Update to 1.20.0.

Change-Id: Ic3c30829fb4c632c006654b8684032d7f6899476
2026-05-28 12:13:25 +02:00
Ricardo Wurmus 9e6dfc0ed9 gnu: r-genetclassifier: Update to 1.52.0.
* gnu/packages/bioconductor.scm (r-genetclassifier): Update to 1.52.0.
[native-inputs]: Add r-biocmanager.

Change-Id: I91e6baad6f707aac84e65f372dd05ecb7044e1de
2026-05-28 12:13:24 +02:00
Ricardo Wurmus 6ff5b0369c gnu: r-minet: Update to 3.70.0.
* gnu/packages/bioconductor.scm (r-minet): Update to 3.70.0.

Change-Id: If95031b1dbc59af8520acf4a85bf8781457de3d8
2026-05-28 12:13:24 +02:00
Ricardo Wurmus f489374d59 gnu: r-bgeedb: Update to 2.38.0.
* gnu/packages/bioconductor.scm (r-bgeedb): Update to 2.38.0.

Change-Id: Ie7aa84bcb601d971714884109411462986155c70
2026-05-28 12:13:24 +02:00
Ricardo Wurmus 024f754902 gnu: r-beclear: Update to 2.28.0.
* gnu/packages/bioconductor.scm (r-beclear): Update to 2.28.0.
[propagated-inputs]: Remove r-futile-logger; add r-logger.

Change-Id: I61f82c9a2f9292d49d5ad41b3b4ca25fb164b244
2026-05-28 12:13:24 +02:00
Ricardo Wurmus bc4a12a2c1 gnu: r-megadepth: Update to 1.22.0.
* gnu/packages/bioconductor.scm (r-megadepth): Update to 1.22.0.

Change-Id: I4bdaaa9cfddf5679e878484c7dc37b7811fdbf7e
2026-05-28 12:13:24 +02:00
Ricardo Wurmus d1be3364cd gnu: r-ballgown: Update to 2.43.0.
* gnu/packages/bioconductor.scm (r-ballgown): Update to 2.43.0.

Change-Id: Iccfa61fd971c3120e66c004f5bfbf51da6df153a
2026-05-28 12:13:24 +02:00
Ricardo Wurmus 8c5c0d3df6 gnu: r-guitar: Update to 2.28.0.
* gnu/packages/bioconductor.scm (r-guitar): Update to 2.28.0.

Change-Id: I1efdaefc38c4cec199fc84272fc9e580935f64f5
2026-05-28 12:13:24 +02:00
Ricardo Wurmus ae056d417d gnu: r-snprelate: Update to 1.46.0.
* gnu/packages/bioconductor.scm (r-snprelate): Update to 1.46.0.

Change-Id: I3616ab0860de8d30738305a7de9c3808dac5336e
2026-05-28 12:13:24 +02:00
Ricardo Wurmus 1b82ad825e gnu: r-pathview: Update to 1.52.0.
* gnu/packages/bioconductor.scm (r-pathview): Update to 1.52.0.

Change-Id: Ibab684dafb9cf813a3ca69b6816cf02f402ed5a9
2026-05-28 12:13:24 +02:00
Ricardo Wurmus 7c5a3878af gnu: r-parody: Update to 1.70.0.
* gnu/packages/bioconductor.scm (r-parody): Update to 1.70.0.

Change-Id: Ifc2ae09d015221252446759eea245a63e147df64
2026-05-28 12:13:23 +02:00
Ricardo Wurmus bdfed4c393 gnu: r-ldblock: Update to 1.42.0.
* gnu/packages/bioconductor.scm (r-ldblock): Update to 1.42.0.

Change-Id: If1ad037f2588e0b8e801b8c055e4fa5ad216f1de
2026-05-28 12:13:23 +02:00
Ricardo Wurmus f88fdb3137 gnu: r-kegggraph: Update to 1.72.0.
* gnu/packages/bioconductor.scm (r-kegggraph): Update to 1.72.0.

Change-Id: If7c8891835c4f58bab765270b2cd288812c3bdad
2026-05-28 12:13:23 +02:00
Ricardo Wurmus b906046de7 gnu: r-gwastools: Update to 1.58.0.
* gnu/packages/bioconductor.scm (r-gwastools): Update to 1.58.0.

Change-Id: Ib8262f5de4394d9b566121c0a5915955f3d8632b
2026-05-28 12:13:23 +02:00
Ricardo Wurmus c3e74910ed gnu: r-gwascat: Update to 2.44.0.
* gnu/packages/bioconductor.scm (r-gwascat): Update to 2.44.0.
[propagated-inputs]: Add r-snpstats.

Change-Id: If5f4e618a168179e8aa35d2358aea1959bbf3aa5
2026-05-28 12:13:23 +02:00
Ricardo Wurmus 2d3086ade3 gnu: r-gviz: Update to 1.56.0.
* gnu/packages/bioconductor.scm (r-gviz): Update to 1.56.0.

Change-Id: I4b32aa1fdc066b83b6ba32e1a554c6a3ae6107a7
2026-05-28 12:13:23 +02:00
Ricardo Wurmus ba30784cb1 gnu: r-ggbio: Update to 1.60.0.
* gnu/packages/bioconductor.scm (r-ggbio): Update to 1.60.0.
[native-inputs]: Add r-biocstyle and r-rcolorbrewer.

Change-Id: Id11ced0d7455984ca91f46f4eaab0b899f1cbfff
2026-05-28 12:13:23 +02:00
Ricardo Wurmus 1edf490119 gnu: r-catalyst: Update to 1.36.0.
* gnu/packages/bioconductor.scm (r-catalyst): Update to 1.36.0.
[propagated-inputs]: Remove r-data-table and r-purrr.

Change-Id: I8042543a308cd568494d0646c23547a5205689a7
2026-05-28 12:13:22 +02:00
Ricardo Wurmus 343915eed2 gnu: r-msmstests: Update to 1.50.0.
* gnu/packages/bioconductor.scm (r-msmstests): Update to 1.50.0.

Change-Id: I378d20a86c1f73b125bd05b0d3c1d787f78cee33
2026-05-28 12:13:22 +02:00
Ricardo Wurmus ccd5379d7b gnu: r-msmseda: Update to 1.50.0.
* gnu/packages/bioconductor.scm (r-msmseda): Update to 1.50.0.

Change-Id: I027280e073141b98746889a588b4998fdb1af561
2026-05-28 12:13:22 +02:00
Ricardo Wurmus 6d63aeca7f gnu: r-biocio: Update to 1.22.0.
* gnu/packages/bioconductor.scm (r-biocio): Update to 1.22.0.

Change-Id: I9c7b2d6437ebd5f2b73acf7c4e439b3d96f8c06c
2026-05-28 12:13:22 +02:00
Ricardo Wurmus da596371a4 gnu: r-msfeatures: Update to 1.20.0.
* gnu/packages/bioconductor.scm (r-msfeatures): Update to 1.20.0.

Change-Id: I90898dd895dcf23aa21efa583535a01001d9eb34
2026-05-28 12:13:22 +02:00
Ricardo Wurmus 7991d0e5a3 gnu: r-delayedmatrixstats: Update to 1.34.0.
* gnu/packages/bioconductor.scm (r-delayedmatrixstats): Update to 1.34.0.

Change-Id: I0e6a5b59cbc30327a7dc7a0486bc2e1837767bcb
2026-05-28 12:13:22 +02:00
Ricardo Wurmus 1819bd1cbc gnu: r-spatialexperiment: Update to 1.22.0.
* gnu/packages/bioconductor.scm (r-spatialexperiment): Update to 1.22.0.

Change-Id: I5f3e3d1d4ca600dbd99815033aecec6235c37b47
2026-05-28 12:13:22 +02:00
Ricardo Wurmus 9419a14e62 gnu: r-sparsematrixstats: Update to 1.24.0.
* gnu/packages/bioconductor.scm (r-sparsematrixstats): Update to 1.24.0.

Change-Id: Icb0c0e52139882236a78b366828258dac4fa5eba
2026-05-28 12:13:22 +02:00
Ricardo Wurmus 4b98717384 gnu: r-scran: Update to 1.40.0.
* gnu/packages/bioconductor.scm (r-scran): Update to 1.40.0.

Change-Id: I76b0bfba7d2af09cbfff13e4fbac90f3a3310dcb
2026-05-28 12:13:21 +02:00
Ricardo Wurmus b856d1b28b gnu: r-scater: Update to 1.40.0.
* gnu/packages/bioconductor.scm (r-scater): Update to 1.40.0.

Change-Id: I74971e87f9f70de23efd14364810f37221406787
2026-05-28 12:13:21 +02:00
Ricardo Wurmus d3899855c9 gnu: r-scuttle: Update to 1.22.0.
* gnu/packages/bioconductor.scm (r-scuttle): Update to 1.22.0.
[propagated-inputs]: Add r-assorthead.

Change-Id: I91f9cf5648b99884a96bd3042bc5a1c87f4122d7
2026-05-28 12:13:21 +02:00
Ricardo Wurmus f7553c296d gnu: r-singler: Update to 2.14.0.
* gnu/packages/bioconductor.scm (r-singler): Update to 2.14.0.
[propagated-inputs]: Remove r-biocneighbors, r-biocparallel, and r-delayedmatrixstats;
add r-biocgenerics.
[native-inputs]: Remove r-biobase and r-scuttle; add r-biocparallel.

Change-Id: Ibc3c2213fd69c1f9aa39840400b8f97f48343600
2026-05-28 12:13:21 +02:00
Ricardo Wurmus 3666e14084 gnu: r-singlecellexperiment: Update to 1.34.0.
* gnu/packages/bioconductor.scm (r-singlecellexperiment): Update to 1.34.0.

Change-Id: I5a549efb4ad670eecf66adbc005da7a854c65407
2026-05-28 12:13:21 +02:00
Ricardo Wurmus 75e773067c gnu: r-motifmatchr: Update to 1.34.0.
* gnu/packages/bioconductor.scm (r-motifmatchr): Update to 1.34.0.

Change-Id: I801f3ad78f7d94f9e85696dfd69defd7016b6fa5
2026-05-28 12:13:21 +02:00
Ricardo Wurmus 28051950c3 gnu: r-maftools: Update to 2.28.0.
* gnu/packages/bioconductor.scm (r-maftools): Update to 2.28.0.

Change-Id: I2709cc7fd7992a623aa3f20e0ba83bcbebaef1ee
2026-05-28 12:13:21 +02:00
Ricardo Wurmus 4245542743 gnu: r-tfbstools: Update to 1.50.0.
* gnu/packages/bioconductor.scm (r-tfbstools): Update to 1.50.0.

Change-Id: Ie92a29acd359f39d7d44b482884493ff37e61a09
2026-05-28 12:13:21 +02:00
Ricardo Wurmus 49c850772d gnu: r-cner: Update to 1.48.0.
* gnu/packages/bioconductor.scm (r-cner): Update to 1.48.0.

Change-Id: I6b10effcbfd8fe424f89dba4bc29556516b33d4c
2026-05-28 12:13:21 +02:00
Ricardo Wurmus e6ed68e7b1 gnu: r-beaddatapackr: Update to 1.64.0.
* gnu/packages/bioconductor.scm (r-beaddatapackr): Update to 1.64.0.

Change-Id: I1ac4dac55f51c0897317aff4a9389565083ee9a2
2026-05-28 12:13:20 +02:00
Ricardo Wurmus 9bd003a26d gnu: r-beadarray: Update to 2.62.0.
* gnu/packages/bioconductor.scm (r-beadarray): Update to 2.62.0.
[propagated-inputs]: Remove r-illuminaio.

Change-Id: I871c2849374f8aed5683c56264df0348ad78b11a
2026-05-28 12:13:20 +02:00
Ricardo Wurmus c79aaed70f gnu: r-beachmat-hdf5: Update to 1.10.0.
* gnu/packages/bioconductor.scm (r-beachmat-hdf5): Update to 1.10.0.

Change-Id: I4c15298a04227bed60f6af87988103d010719eb3
2026-05-28 12:13:20 +02:00
Ricardo Wurmus 1ba5089bef gnu: r-beachmat: Update to 2.28.0.
* gnu/packages/bioconductor.scm (r-beachmat): Update to 2.28.0.

Change-Id: Iebaa15b6b866a7448ef2c449546961f2236c5ece
2026-05-28 12:13:20 +02:00
Ricardo Wurmus e527e07e95 gnu: r-hdf5array: Update to 1.40.0.
* gnu/packages/bioconductor.scm (r-hdf5array): Update to 1.40.0.

Change-Id: Ib7dab8421c9a4bddd8560c0c2e9b2a9eddf13ae7
2026-05-28 12:13:20 +02:00
Ricardo Wurmus 05996c87ee gnu: r-hitc: Update to 1.56.0.
* gnu/packages/bioconductor.scm (r-hitc): Update to 1.56.0.

Change-Id: I1ff7afb0f51e41f22d877ba345ff71bc28a5f7ae
2026-05-28 12:13:20 +02:00
Ricardo Wurmus 14e44bdc80 gnu: r-fithic: Update to 1.38.0.
* gnu/packages/bioconductor.scm (r-fithic): Update to 1.38.0.

Change-Id: I649151825f9284961ffad03f4de111450ae95d59
2026-05-28 12:13:20 +02:00
Ricardo Wurmus a42726ff2a gnu: r-fishpond: Update to 2.18.0.
* gnu/packages/bioconductor.scm (r-fishpond): Update to 2.18.0.

Change-Id: Ib2052e97f7cddde9f05040958139c18f1489b154
2026-05-28 12:13:20 +02:00
Ricardo Wurmus f276ea1d45 gnu: r-rgraphviz: Update to 2.56.0.
* gnu/packages/bioconductor.scm (r-rgraphviz): Update to 2.56.0.

Change-Id: Iff81797519822aff5ce0589f9601b9da282f8af8
2026-05-28 12:13:19 +02:00
Ricardo Wurmus d9e7528315 gnu: r-s4vectors: Update to 0.50.0.
* gnu/packages/bioconductor.scm (r-s4vectors): Update to 0.50.0.

Change-Id: I0be3306dadfd10022d48dbee7c7e1ad5e671ab24
2026-05-28 12:13:19 +02:00
Ricardo Wurmus c15b99d96d gnu: r-s4arrays: Update to 1.12.0.
* gnu/packages/bioconductor.scm (r-s4arrays): Update to 1.12.0.

Change-Id: I826489ead0c36cc1fdd4de078421c3a696b57d00
2026-05-28 12:13:19 +02:00
Ricardo Wurmus 6e5273e4f8 gnu: r-preprocesscore: Update to 1.74.0.
* gnu/packages/bioconductor.scm (r-preprocesscore): Update to 1.74.0.

Change-Id: I4a9fad7a3bad33a0c257bdbed31d8aae2fb2ab4f
2026-05-28 12:13:19 +02:00
Ricardo Wurmus 72a5b7b824 gnu: r-icens: Update to 1.84.0.
* gnu/packages/bioconductor.scm (r-icens): Update to 1.84.0.

Change-Id: Id16b6fef477670affc304fc175949eca1f032872
2026-05-28 12:13:19 +02:00
Ricardo Wurmus 225436b600 gnu: r-m3c: Update to 1.34.0.
* gnu/packages/bioconductor.scm (r-m3c): Update to 1.34.0.

Change-Id: I73cf3e75d836916828f4bbf03e39a695039b8b34
2026-05-28 12:13:19 +02:00
Ricardo Wurmus d90ad62349 gnu: r-rgreat: Update to 2.14.0.
* gnu/packages/bioconductor.scm (r-rgreat): Update to 2.14.0.

Change-Id: I9692ad2a4ce39d68c44aa4ad7458c06cecc3f1ba
2026-05-28 12:13:19 +02:00
Ricardo Wurmus 479a47ff01 gnu: r-pcatools: Update to 2.24.0.
* gnu/packages/bioconductor.scm (r-pcatools): Update to 2.24.0.

Change-Id: Ic6c01add82aa733e7e8138ca11397737c86476a8
2026-05-28 12:13:19 +02:00
Ricardo Wurmus cf3c5d1879 gnu: r-biodist: Update to 1.84.0.
* gnu/packages/bioconductor.scm (r-biodist): Update to 1.84.0.

Change-Id: I833c4b5244b1db79edf2899d78402c79b1f45e15
2026-05-28 12:13:18 +02:00
Ricardo Wurmus 9f23ca9b01 gnu: r-biocworkflowtools: Update to 1.38.0.
* gnu/packages/bioconductor.scm (r-biocworkflowtools): Update to 1.38.0.

Change-Id: I9bd4c3055365964b5d75808e3c30a795a6d9b9b7
2026-05-28 12:13:18 +02:00
Ricardo Wurmus ddd3ceed0f gnu: r-biocor: Update to 1.36.0.
* gnu/packages/bioconductor.scm (r-biocor): Update to 1.36.0.

Change-Id: I388378a9d35c9154a52eef290f2cef603edbca58
2026-05-28 12:13:18 +02:00
Ricardo Wurmus 4b63c7ca9e gnu: r-multiassayexperiment: Update to 1.38.0.
* gnu/packages/bioconductor.scm (r-multiassayexperiment): Update to 1.38.0.

Change-Id: I4c550d70ee68bd03bc2860968581b4d3434b4521
2026-05-28 12:13:18 +02:00
Ricardo Wurmus 05d9ae8ffe gnu: r-grohmm: Update to 1.46.0.
* gnu/packages/bioconductor.scm (r-grohmm): Update to 1.46.0.

Change-Id: I04b2f11a354d39c0f6977beff316e4b7da7a8fb1
2026-05-28 12:13:18 +02:00
Ricardo Wurmus cb4bf0057e gnu: r-experimenthubdata: Update to 1.38.0.
* gnu/packages/bioconductor.scm (r-experimenthubdata): Update to 1.38.0.

Change-Id: I1c9a9270363e8f0de65a42a4c7b3ce7e480e98d2
2026-05-28 12:13:18 +02:00
Ricardo Wurmus c32d88433e gnu: r-experimenthub: Update to 3.2.0.
* gnu/packages/bioconductor.scm (r-experimenthub): Update to 3.2.0.

Change-Id: I2d877e12f2b0825d3ab6e4c478cb28bb0f1335d9
2026-05-28 12:13:18 +02:00
Ricardo Wurmus c4f8ad44e0 gnu: r-biocviews: Update to 1.80.0.
* gnu/packages/bioconductor.scm (r-biocviews): Update to 1.80.0.

Change-Id: Ic25e070da97833ed10779bd4816a9b1c6ed075eb
2026-05-28 12:13:18 +02:00
Ricardo Wurmus ae94b45612 gnu: r-biocstyle: Update to 2.40.0.
* gnu/packages/bioconductor.scm (r-biocstyle): Update to 2.40.0.

Change-Id: Idae904cf7845ceb9c4017e6782a457aebb5504f5
2026-05-28 12:13:17 +02:00
Ricardo Wurmus 78b01d439e gnu: r-biocgraph: Update to 1.74.0.
* gnu/packages/bioconductor.scm (r-biocgraph): Update to 1.74.0.

Change-Id: Ic149a3b800a3459061cbdb30c379bbd970ad8c1d
2026-05-28 12:13:17 +02:00
Ricardo Wurmus 9983dbed4b gnu: r-bioccheck: Update to 1.47.26.
* gnu/packages/bioconductor.scm (r-bioccheck): Update to 1.47.26.
[propagated-inputs]: Add r-commonmark and r-xml2.

Change-Id: I706acdf765099c0debf9a8143768b64db5ff291c
2026-05-28 12:13:17 +02:00
Ricardo Wurmus a7c19bfd1f gnu: r-biocbaseutils: Update to 1.13.0.
* gnu/packages/bioconductor.scm (r-biocbaseutils): Update to 1.13.0.

Change-Id: I47c8a461d30e5e1c9bd237fd3d8d7667a75c0951
2026-05-28 12:13:17 +02:00
Ricardo Wurmus 150e82654e gnu: r-ebarrays: Update to 2.76.0.
* gnu/packages/bioconductor.scm (r-ebarrays): Update to 2.76.0.

Change-Id: Ib1a1e1b129cfe7711b03c0387fc7b16cd28afd06
2026-05-28 12:13:17 +02:00
Ricardo Wurmus 060d28af72 gnu: r-reactomepa: Update to 1.56.0.
* gnu/packages/bioconductor.scm (r-reactomepa): Update to 1.56.0.
[propagated-inputs]: Remove r-dose; add r-enrichit.

Change-Id: I2e73be776e405f09957b1daaf793ea2f6e9ec576
2026-05-28 12:13:17 +02:00
Ricardo Wurmus 2c2de0c790 gnu: r-graphite: Update to 1.58.0.
* gnu/packages/bioconductor.scm (r-graphite): Update to 1.58.0.
[native-inputs]: Add r-biocstyle.

Change-Id: I47c40ce388097ccc78a14f08e4b3862f03a86f8a
2026-05-28 12:13:17 +02:00
Ricardo Wurmus 11ec4286ed gnu: r-biobroom: Update to 1.43.0.
* gnu/packages/bioconductor.scm (r-biobroom): Update to 1.43.0.
[propagated-inputs]: Remove r-tibble.

Change-Id: I8e13cf556368bbb65a869a1d641ed227247150bc
2026-05-28 12:13:17 +02:00
Ricardo Wurmus 01fe991f3e gnu: r-bioassayr: Update to 1.50.0.
* gnu/packages/bioconductor.scm (r-bioassayr): Update to 1.50.0.

Change-Id: I383bd4069a1daf88a5dafe538c3434a057480aee
2026-05-28 12:13:16 +02:00
Ricardo Wurmus 01807e351c gnu: r-fmcsr: Update to 1.54.0.
* gnu/packages/bioconductor.scm (r-fmcsr): Update to 1.54.0.

Change-Id: Ic1b268165e5353d7716ea18d8278ab8166aa8c44
2026-05-28 12:13:16 +02:00
Ricardo Wurmus d49c9752fb gnu: r-chemminer: Update to 3.64.0.
* gnu/packages/bioconductor.scm (r-chemminer): Update to 3.64.0.
[native-inputs]: Add r-biocmanager and r-biocstyle.

Change-Id: Ia223b7fd87f274ed9ceb9efe2392503796606a15
2026-05-28 12:13:16 +02:00
Ricardo Wurmus cd33379110 gnu: r-chemmineob: Update to 1.50.0.
* gnu/packages/bioconductor.scm (r-chemmineob): Update to 1.50.0.

Change-Id: I15859f70af4595802b6c0058c6c7ae9fdfb8b3ee
2026-05-28 12:13:16 +02:00
Ricardo Wurmus 3cd7de0bcc gnu: r-hyperdraw: Update to 1.64.0.
* gnu/packages/bioconductor.scm (r-hyperdraw): Update to 1.64.0.

Change-Id: I5185943dc49f4eb3efc8adabb2aaa69691da7494
2026-05-28 12:13:16 +02:00
Ricardo Wurmus cdddf7468a gnu: r-hypergraph: Update to 1.84.0.
* gnu/packages/bioconductor.scm (r-hypergraph): Update to 1.84.0.

Change-Id: I1fc74067b36a40f0dc0a3323d1563a5fa401c418
2026-05-28 12:13:16 +02:00
Ricardo Wurmus 41b7883121 gnu: r-hybridmtest: Update to 1.56.0.
* gnu/packages/bioconductor.scm (r-hybridmtest): Update to 1.56.0.

Change-Id: I89f89cd7b750d67a3b9d20193933c78261adc4bf
2026-05-28 12:13:16 +02:00
Ricardo Wurmus 9a4bde4f58 gnu: r-rsbml: Update to 2.70.0.
* gnu/packages/bioconductor.scm (r-rsbml): Update to 2.70.0.

Change-Id: Ie1c777b54c761c98ee52270efaa085ece73a9198
2026-05-28 12:13:16 +02:00
Ricardo Wurmus f8b10f7601 gnu: r-bifet: Update to 1.32.0.
* gnu/packages/bioconductor.scm (r-bifet): Update to 1.32.0.

Change-Id: I12b75271ae842866f3a61f9a8a36a39ea40acf85
2026-05-28 12:13:15 +02:00
Ricardo Wurmus e3b0e03431 gnu: r-bicare: Update to 1.70.0.
* gnu/packages/bioconductor.scm (r-bicare): Update to 1.70.0.

Change-Id: I3b8e7ad3d7da99c49feb607ab0aab4629fcff618
2026-05-28 12:13:15 +02:00
Ricardo Wurmus 092c2e5356 gnu: r-acde: Update to 1.42.0.
* gnu/packages/bioconductor.scm (r-acde): Update to 1.42.0.

Change-Id: I037aedb2fbb676903ccbac94f1305de002474142
2026-05-28 12:13:15 +02:00
Ricardo Wurmus b9dd6d5121 gnu: r-acme: Update to 2.68.0.
* gnu/packages/bioconductor.scm (r-acme): Update to 2.68.0.

Change-Id: I6ca9bf34bf75a46c9321d88b4394ae5fc60b1914
2026-05-28 12:13:15 +02:00
Ricardo Wurmus 12cc1baf4a gnu: r-acgh: Update to 1.90.0.
* gnu/packages/bioconductor.scm (r-acgh): Update to 1.90.0.

Change-Id: I37837cd5284add2fb376a7a0016b95549ce48b57
2026-05-28 12:13:15 +02:00
Ricardo Wurmus 0b5a52bb20 gnu: r-ace: Update to 1.30.0.
* gnu/packages/bioconductor.scm (r-ace): Update to 1.30.0.

Change-Id: Iada388b15140a314d00f6f146f896a6498e4b977
2026-05-28 12:13:15 +02:00
Ricardo Wurmus 34d0093d89 gnu: r-universalmotif: Update to 1.30.0.
* gnu/packages/bioconductor.scm (r-universalmotif): Update to 1.30.0.

Change-Id: I4bc67e57851d0b0ec0c613b87794490699364e7c
2026-05-28 12:13:15 +02:00
Ricardo Wurmus d1cfbca865 gnu: r-unifiedwmwqpcr: Update to 1.48.0.
* gnu/packages/bioconductor.scm (r-unifiedwmwqpcr): Update to 1.48.0.

Change-Id: Ifbf4df4268ed22bcb8be5d3c3bba3474185d7b33
2026-05-28 12:13:15 +02:00
Ricardo Wurmus 1137ca46cf gnu: r-ucsc-utils: Update to 1.8.0.
* gnu/packages/bioconductor.scm (r-ucsc-utils): Update to 1.8.0.

Change-Id: I79c8da491828a02a90952858f8c23639b7130ad9
2026-05-28 12:13:14 +02:00
Ricardo Wurmus 859d76ab6c gnu: r-ucell: Update to 2.16.0.
* gnu/packages/bioconductor.scm (r-ucell): Update to 2.16.0.

Change-Id: I0b9e3a94c42640d2da265f31b8271a7632199578
2026-05-28 12:13:14 +02:00
Ricardo Wurmus f6a3cf6c49 gnu: r-htqpcr: Update to 1.66.0.
* gnu/packages/bioconductor.scm (r-htqpcr): Update to 1.66.0.

Change-Id: I8f12a5c43eb77d690eb6b65d235959569901772c
2026-05-28 12:13:14 +02:00
Ricardo Wurmus bb58bb2fe5 gnu: r-variancepartition: Update to 1.42.0.
* gnu/packages/bioconductor.scm (r-variancepartition): Update to 1.42.0.

Change-Id: Ia2d825df95ccf393b8e79f61c272038b9dfb446c
2026-05-28 12:13:14 +02:00
Ricardo Wurmus 4f495264a4 gnu: r-variantfiltering: Update to 1.48.0.
* gnu/packages/bioconductor.scm (r-variantfiltering): Update to 1.48.0.

Change-Id: I07935b31bd802d384ee9f87b55405d2b9a81b51c
2026-05-28 12:13:14 +02:00
Ricardo Wurmus 85f57b36b3 gnu: r-tilingarray: Update to 1.90.0.
* gnu/packages/bioconductor.scm (r-tilingarray): Update to 1.90.0.

Change-Id: I1ad70f6c5fb30f7ff0b26437b6351c0052da4181
2026-05-28 12:13:14 +02:00
Ricardo Wurmus e7543dc481 gnu: r-wavcluster: Update to 2.46.0.
* gnu/packages/bioconductor.scm (r-wavcluster): Update to 2.46.0.
[propagated-inputs]: Add r-txdbmaker.

Change-Id: I0071aa23f65eb8b3260aa8ce37fb688845590d40
2026-05-28 12:13:14 +02:00
Ricardo Wurmus 1271089d19 gnu: r-bigmelon: Update to 1.38.0.
* gnu/packages/bioconductor.scm (r-bigmelon): Update to 1.38.0.
[native-inputs]: Add r-biocmanager.

Change-Id: If9110b3d591a36b36210124e2e19b9555f44da46
2026-05-28 12:13:13 +02:00
Ricardo Wurmus ff124580f9 gnu: r-gdsfmt: Update to 1.48.0.
* gnu/packages/bioconductor.scm (r-gdsfmt): Update to 1.48.0.

Change-Id: I382d6fd244fd8036f24cf5b020a7e337da2b96fe
2026-05-28 12:13:13 +02:00
Ricardo Wurmus b9a0ac5c4d gnu: r-watermelon: Update to 2.18.0.
* gnu/packages/bioconductor.scm (r-watermelon): Update to 2.18.0.

Change-Id: I098e84c5617cb7ef5e7906c025aaf51a788e1df0
2026-05-28 12:13:13 +02:00
Ricardo Wurmus 2bc3ade8d8 gnu: r-roc: Update to 1.88.0.
* gnu/packages/bioconductor.scm (r-roc): Update to 1.88.0.

Change-Id: I8fb4382763a2c534810b97e8bb3f1b22fea07d2a
2026-05-28 12:13:13 +02:00
Ricardo Wurmus 069bc7fba2 gnu: r-genie3: Update to 1.34.0.
* gnu/packages/bioconductor.scm (r-genie3): Update to 1.34.0.

Change-Id: I2ef171059215e5db45b6de8191fe4c1989c74411
2026-05-28 12:13:13 +02:00
Ricardo Wurmus 713b7db75b gnu: r-circrnaprofiler: Update to 1.26.0.
* gnu/packages/bioconductor.scm (r-circrnaprofiler): Update to 1.26.0.

Change-Id: I190ace6eee0dad5a70fffb36b76d1b0ff0d37f1d
2026-05-28 12:13:13 +02:00
Ricardo Wurmus 709e1e12a1 gnu: r-cicero: Update to 1.30.0.
* gnu/packages/bioconductor.scm (r-cicero): Update to 1.30.0.

Change-Id: Ie509f0f6d81719373013f002f06156efb35506b4
2026-05-28 12:13:13 +02:00
Ricardo Wurmus 4ac147e013 gnu: r-chicago: Update to 1.40.0.
* gnu/packages/bioconductor.scm (r-chicago): Update to 1.40.0.

Change-Id: I5c3392564e459b13ae14bfcaf32080480a539619
2026-05-28 12:13:13 +02:00
Ricardo Wurmus 61a67383b4 gnu: r-depecher: Update to 1.28.0.
* gnu/packages/bioconductor.scm (r-depecher): Update to 1.28.0.

Change-Id: I7054b7407c18d2629d3885119c28faddd6c19c04
2026-05-28 12:13:13 +02:00
Ricardo Wurmus 01ef8bb547 gnu: r-mixomics: Update to 6.36.0.
* gnu/packages/bioconductor.scm (r-mixomics): Update to 6.36.0.
[propagated-inputs]: Remove r-gsignal; add r-rlang.

Change-Id: I8af455ea5a83133927b2cd8fcc215c556a335e14
2026-05-28 12:13:12 +02:00
Ricardo Wurmus e6e8eab70f gnu: r-flowsom: Update to 2.20.0.
* gnu/packages/bioconductor.scm (r-flowsom): Update to 2.20.0.
[native-inputs]: Add r-biocmanager, r-biocstyle, and r-flowworkspace.

Change-Id: Ic5072a8b7627e4ef44339651bdbd96257c0a0f97
2026-05-28 12:13:12 +02:00
Ricardo Wurmus 3ea37f32d4 gnu: r-cytoml: Update to 2.24.0.
* gnu/packages/bioconductor.scm (r-cytoml): Update to 2.24.0.

Change-Id: If21c1c99fe9bac63fd4c2ff7121d32174ac8694d
2026-05-28 12:13:12 +02:00
Ricardo Wurmus d381db6e55 gnu: r-opencyto: Update to 2.24.0.
* gnu/packages/bioconductor.scm (r-opencyto): Update to 2.24.0.

Change-Id: I71fa34b873802b11feedb6971761b619d88d4e2f
2026-05-28 12:13:12 +02:00
Ricardo Wurmus 58dbc672e8 gnu: r-flowstats: Update to 4.24.0.
* gnu/packages/bioconductor.scm (r-flowstats): Update to 4.24.0.

Change-Id: I7216cb0d538a976d7e19abc7b82c4b64394e33e1
2026-05-28 12:13:12 +02:00
Ricardo Wurmus d23601b7d9 gnu: r-flowworkspace: Update to 4.24.0.
* gnu/packages/bioconductor.scm (r-flowworkspace): Update to 4.24.0.

Change-Id: I839c2083355347816a5cfe7e33d8b6c9d975608f
2026-05-28 12:13:12 +02:00
Ricardo Wurmus 8c5510b720 gnu: r-rprotobuflib: Update to 2.24.0.
* gnu/packages/bioconductor.scm (r-rprotobuflib): Update to 2.24.0.

Change-Id: I6672c2d971898f0517f5ec47bc92fb77acfbd355
2026-05-28 12:13:12 +02:00
Ricardo Wurmus 75ffbb5771 gnu: r-flowclust: Update to 3.50.0.
* gnu/packages/bioconductor.scm (r-flowclust): Update to 3.50.0.

Change-Id: I1e5f3b59c7ca1d27069715881ea48fc6ef777141
2026-05-28 12:13:12 +02:00
Ricardo Wurmus a429d23bbc gnu: r-flowviz: Update to 1.76.0.
* gnu/packages/bioconductor.scm (r-flowviz): Update to 1.76.0.

Change-Id: If3f07d063f68c07684fa3efc9d61916dbfb54fe2
2026-05-28 12:13:11 +02:00
Ricardo Wurmus e96d280bc3 gnu: r-ggcyto: Update to 1.40.0.
* gnu/packages/bioconductor.scm (r-ggcyto): Update to 1.40.0.

Change-Id: I82c59d7327683548ac9b3b70fdfc88569419c428
2026-05-28 12:13:11 +02:00
Ricardo Wurmus f426729db4 gnu: r-ncdfflow: Update to 2.58.0.
* gnu/packages/bioconductor.scm (r-ncdfflow): Update to 2.58.0.

Change-Id: I4c4a52879c794eccbc57b3e336cf8cc975313adf
2026-05-28 12:13:11 +02:00
Ricardo Wurmus df87abe05e gnu: r-flowmeans: Update to 1.72.0.
* gnu/packages/bioconductor.scm (r-flowmeans): Update to 1.72.0.

Change-Id: If182f009f4a8045f76130efd8a97044d5a8c395d
2026-05-28 12:13:11 +02:00
Ricardo Wurmus da22aaf4c6 gnu: r-flowcore: Update to 2.24.0.
* gnu/packages/bioconductor.scm (r-flowcore): Update to 2.24.0.

Change-Id: I28bec604e253c59db8eaa4eee815d2f2722800f7
2026-05-28 12:13:11 +02:00
Ricardo Wurmus 5a80018d67 gnu: r-cytolib: Update to 2.24.0.
* gnu/packages/bioconductor.scm (r-cytolib): Update to 2.24.0.

Change-Id: I83b30b0f47f7b550401ffe90dbdc0ff9fb1918fb
2026-05-28 12:13:11 +02:00
Ricardo Wurmus bd0b6fe212 gnu: r-consensusclusterplus: Update to 1.76.0.
* gnu/packages/bioconductor.scm (r-consensusclusterplus): Update to 1.76.0.

Change-Id: I30612a5ad5e65ae825919f6b175f349e20518134
2026-05-28 12:13:11 +02:00
Ricardo Wurmus b4af97b291 gnu: r-flowai: Update to 1.42.0.
* gnu/packages/bioconductor.scm (r-flowai): Update to 1.42.0.

Change-Id: If675433364a0e7f4e1e7bf7015499508c61303d5
2026-05-28 12:13:10 +02:00
Ricardo Wurmus e7a6fb4304 gnu: r-flames: Update to 2.6.0.
* gnu/packages/bioconductor.scm (r-flames): Update to 2.6.0.
[propagated-inputs]: Remove r-ggbio; add r-scrapper.

Change-Id: I1740b98352b350f89fb1a73479984d96bdb5f85f
2026-05-28 12:13:10 +02:00
Ricardo Wurmus e775461e85 gnu: r-rsubread: Update to 2.26.0.
* gnu/packages/bioconductor.scm (r-rsubread): Update to 2.26.0.

Change-Id: I3261cce131ad0209bc2c934a084843742a978b36
2026-05-28 12:13:10 +02:00
Ricardo Wurmus ccca0607f9 gnu: r-annotatr: Update to 1.38.0.
* gnu/packages/bioconductor.scm (r-annotatr): Update to 1.38.0.

Change-Id: Ifd30d19346ed3032edfa0df0bd8a7a786af1b6cf
2026-05-28 12:13:10 +02:00
Ricardo Wurmus e87c901628 gnu: r-biosigner: Update to 1.40.0.
* gnu/packages/bioconductor.scm (r-biosigner): Update to 1.40.0.

Change-Id: I0eb9138b17a441d7dc2f509e4b797d3df5db384f
2026-05-28 12:13:10 +02:00
Ricardo Wurmus c5c9a6a9f9 gnu: r-ropls: Update to 1.44.0.
* gnu/packages/bioconductor.scm (r-ropls): Update to 1.44.0.

Change-Id: I6e618c6cad1ca46eb30718ebd343c064d138d729
2026-05-28 12:13:10 +02:00
Ricardo Wurmus 86c70bf66e gnu: r-multidataset: Update to 1.40.0.
* gnu/packages/bioconductor.scm (r-multidataset): Update to 1.40.0.

Change-Id: I8229d8a234f937462e92c7027225cc2e6cedf18c
2026-05-28 12:13:10 +02:00
Ricardo Wurmus e29550af60 gnu: r-rqc: Update to 1.46.0.
* gnu/packages/bioconductor.scm (r-rqc): Update to 1.46.0.

Change-Id: I1f78c23344685f1fbbbbeb7bc03d9a3f2c86e2fd
2026-05-28 12:13:10 +02:00
Ricardo Wurmus 9de1fd17f6 gnu: r-quasr: Update to 1.52.0.
* gnu/packages/bioconductor.scm (r-quasr): Update to 1.52.0.

Change-Id: Idd6ecd91345e2ce48cb46fcd93b69448639b43d2
2026-05-28 12:13:10 +02:00
Ricardo Wurmus c22e372df3 gnu: r-rhisat2: Update to 1.28.0.
* gnu/packages/bioconductor.scm (r-rhisat2): Update to 1.28.0.

Change-Id: I32390b3b80f67685c069f5572b9e69d5561b368b
2026-05-28 12:13:09 +02:00
Ricardo Wurmus cc42dd29d0 gnu: r-sgseq: Update to 1.46.0.
* gnu/packages/bioconductor.scm (r-sgseq): Update to 1.46.0.

Change-Id: Ie45c2879e6ed128774e54f634d82add1a4d8582e
2026-05-28 12:13:09 +02:00
Ricardo Wurmus 9f45b4cc4b gnu: r-rbowtie: Update to 1.52.0.
* gnu/packages/bioconductor.scm (r-rbowtie): Update to 1.52.0.

Change-Id: Id44ad26c77d30f8c35868bd1a7b1b5330e29792a
2026-05-28 12:13:09 +02:00
Ricardo Wurmus d695234667 gnu: r-biocfilecache: Update to 3.2.0.
* gnu/packages/bioconductor.scm (r-biocfilecache): Update to 3.2.0.

Change-Id: Ic0f6417d994b753b541b136bcb8219d27337c783
2026-05-28 12:13:09 +02:00
Ricardo Wurmus 2d641a748c gnu: r-arrmnormalization: Update to 1.52.0.
* gnu/packages/bioconductor.scm (r-arrmnormalization): Update to 1.52.0.

Change-Id: I71deeb3e1e5b751c6cee5f2a2586b7557364fc8c
2026-05-28 12:13:09 +02:00
Ricardo Wurmus 7ea07256fc gnu: r-progeny: Update to 1.34.0.
* gnu/packages/bioconductor.scm (r-progeny): Update to 1.34.0.

Change-Id: I3e4fc13f60f4cd66bf89e5a74fe8f2f2204f7ea1
2026-05-28 12:13:09 +02:00
Ricardo Wurmus 079ecc0734 gnu: r-rbowtie2: Update to 2.18.0.
* gnu/packages/bioconductor.scm (r-rbowtie2): Update to 2.18.0.

Change-Id: I0b15f8c72e78840976c0dc7dbfa8af08bdc5745b
2026-05-28 12:13:09 +02:00
Ricardo Wurmus ec8a1ae52b gnu: r-zfpkm: Update to 1.34.0.
* gnu/packages/bioconductor.scm (r-zfpkm): Update to 1.34.0.

Change-Id: I0f3a1d058da6b7d534b51d666bc555e096d79d24
2026-05-28 12:13:09 +02:00
Ricardo Wurmus 1a9d1f456a gnu: r-zinbwave: Update to 1.34.0.
* gnu/packages/bioconductor.scm (r-zinbwave): Update to 1.34.0.

Change-Id: I2fd2796e269df0de18bc0e3d844f57c6b63e5213
2026-05-28 12:13:08 +02:00
Ricardo Wurmus ae37bc5746 gnu: r-webbioc: Update to 1.84.0.
* gnu/packages/bioconductor.scm (r-webbioc): Update to 1.84.0.

Change-Id: I5fd957b8d0fba830f7196579e0cac2e5b04972fe
2026-05-28 12:13:08 +02:00
Ricardo Wurmus f34a0c3dd0 gnu: r-widgettools: Update to 1.90.0.
* gnu/packages/bioconductor.scm (r-widgettools): Update to 1.90.0.

Change-Id: Ie74aa3897e7516a947a925636ddcdf6a90b6112c
2026-05-28 12:13:08 +02:00
Ricardo Wurmus 036884a4a9 gnu: r-wiggleplotr: Update to 1.36.0.
* gnu/packages/bioconductor.scm (r-wiggleplotr): Update to 1.36.0.

Change-Id: Ie6121a0ddaffc6b70f3e0f2faa258bee72df8ff3
2026-05-28 12:13:08 +02:00
Ricardo Wurmus a33102ec20 gnu: r-wrench: Update to 1.30.0.
* gnu/packages/bioconductor.scm (r-wrench): Update to 1.30.0.

Change-Id: If759b76b880838ba86f51ff7e6c7e3ccb27fa55d
2026-05-28 12:13:08 +02:00
Ricardo Wurmus 90ae3a014e gnu: r-wppi: Update to 1.19.0.
* gnu/packages/bioconductor.scm (r-wppi): Update to 1.19.0.

Change-Id: I7d75a463a1e35eba9423a55f2ba7900f4f653670
2026-05-28 12:13:08 +02:00
Ricardo Wurmus 53c9c34d50 gnu: r-massspecwavelet: Update to 1.78.0.
* gnu/packages/bioconductor.scm (r-massspecwavelet): Update to 1.78.0.

Change-Id: Iafa74c27dba73fd63a8cd5a8c4b94ac55dedaaa7
2026-05-28 12:13:08 +02:00
Ricardo Wurmus ee6bc4e1a0 gnu: r-roar: Update to 1.48.0.
* gnu/packages/bioconductor.scm (r-roar): Update to 1.48.0.

Change-Id: I364fdec48252580647b8457a18af707356ddd944
2026-05-28 12:13:07 +02:00
Ricardo Wurmus 07c6424c90 gnu: r-yarn: Update to 1.38.0.
* gnu/packages/bioconductor.scm (r-yarn): Update to 1.38.0.

Change-Id: I61c5c5cd8564998f2f61ecee4285fec1adf44d28
2026-05-28 12:13:07 +02:00
Ricardo Wurmus 3caa3cc4bd gnu: r-quantro: Update to 1.46.0.
* gnu/packages/bioconductor.scm (r-quantro): Update to 1.46.0.

Change-Id: I06ba16b94af0e87e95c4d6c9bddbb05cbe89d7c2
2026-05-28 12:13:07 +02:00
Ricardo Wurmus bbeb7e6c7f gnu: r-gcrma: Update to 2.84.0.
* gnu/packages/bioconductor.scm (r-gcrma): Update to 2.84.0.

Change-Id: I5f7e428495860706dde229aa4542ca46b33c0360
2026-05-28 12:13:07 +02:00
Ricardo Wurmus 8aef253ffc gnu: r-yapsa: Update to 1.38.0.
* gnu/packages/bioconductor.scm (r-yapsa): Update to 1.38.0.

Change-Id: I770b3b2e9f383418d56cf3a2aa7274dfffe93250
2026-05-28 12:13:07 +02:00
Ricardo Wurmus 503c05b7ee gnu: r-somaticsignatures: Update to 2.48.0.
* gnu/packages/bioconductor.scm (r-somaticsignatures): Update to 2.48.0.

Change-Id: I9400682299fc4186518b17c35c9c59738376d904
2026-05-28 12:13:07 +02:00
Ricardo Wurmus c7ea47f139 gnu: r-gtrellis: Update to 1.44.0.
* gnu/packages/bioconductor.scm (r-gtrellis): Update to 1.44.0.

Change-Id: I779f0702edab40cc8c46803c65b97ab623f431e9
2026-05-28 12:13:07 +02:00
Ricardo Wurmus 7d1bb9e44c gnu: r-yamss: Update to 1.38.0.
* gnu/packages/bioconductor.scm (r-yamss): Update to 1.38.0.

Change-Id: I7584e0028a69a5771a4e9f7742df2b052213cd29
2026-05-28 12:13:07 +02:00
Ricardo Wurmus 52594f08e6 gnu: r-ebimage: Update to 4.54.0.
* gnu/packages/bioconductor.scm (r-ebimage): Update to 4.54.0.

Change-Id: Ic11576f8f2a19e457c64cba383284c00d240cca5
2026-05-28 12:13:06 +02:00
Ricardo Wurmus d603938ff6 gnu: r-aucell: Update to 1.33.0.
* gnu/packages/bioconductor.scm (r-aucell): Update to 1.33.0.

Change-Id: Ie5bf22a38261792887fdfce0083d9466b0a49714
2026-05-28 12:13:06 +02:00
Ricardo Wurmus 2e3f394133 gnu: r-allelicimbalance: Update to 1.50.0.
* gnu/packages/bioconductor.scm (r-allelicimbalance): Update to 1.50.0.

Change-Id: Ic682cc827cd96648086a13d279f9ca3ec88dc638
2026-05-28 12:13:06 +02:00
Ricardo Wurmus 0a585d7827 gnu: r-annotationtools: Update to 1.86.0.
* gnu/packages/bioconductor.scm (r-annotationtools): Update to 1.86.0.

Change-Id: Idef3f1eac0d0cddd1e885987258fcf5c9442e123
2026-05-28 12:13:06 +02:00
Ricardo Wurmus fd3c51410a gnu: r-gofuncr: Update to 1.31.0.
* gnu/packages/bioconductor.scm (r-gofuncr): Update to 1.31.0.
[native-inputs]: Remove r-homo-sapiens.

Change-Id: I24a3296056d9226819b3c1ff00bf106565db7a8c
2026-05-28 12:13:06 +02:00
Ricardo Wurmus 83bbe2ba2c gnu: r-atacseqqc: Update to 1.36.0.
* gnu/packages/bioconductor.scm (r-atacseqqc): Update to 1.36.0.

Change-Id: I09820330543281252b90279ea566466873c5d4a3
2026-05-28 12:13:06 +02:00
Ricardo Wurmus df86ef584a gnu: r-genomicscores: Update to 2.24.0.
* gnu/packages/bioconductor.scm (r-genomicscores): Update to 2.24.0.

Change-Id: I3c0f41917fd9bd6cde526838a21946edcea6ace2
2026-05-28 12:13:05 +02:00
Ricardo Wurmus b100eda9d3 gnu: r-motifstack: Update to 1.56.0.
* gnu/packages/bioconductor.scm (r-motifstack): Update to 1.56.0.

Change-Id: I0f72bb417a216812f18c4aa07fbf20b5c93581a2
2026-05-28 12:13:05 +02:00
Ricardo Wurmus b92b1d6ba3 gnu: r-motifdb: Update to 1.54.0.
* gnu/packages/bioconductor.scm (r-motifdb): Update to 1.54.0.

Change-Id: I776ce60285b09608713edc401c8f40a2982df0a2
2026-05-28 12:13:05 +02:00
Ricardo Wurmus ec4140c363 gnu: r-bacon: Update to 1.40.0.
* gnu/packages/bioconductor.scm (r-bacon): Update to 1.40.0.

Change-Id: I0e8f6dea31d96960fbe3a8ce0ca4f6e8b2f671f2
2026-05-28 12:13:05 +02:00
Ricardo Wurmus f31ad218dd gnu: r-abseqr: Update to 1.30.0.
* gnu/packages/bioconductor.scm (r-abseqr): Update to 1.30.0.

Change-Id: Ifcbd870cbd2c25c0ea4ddd3cbce08df95c3a4174
2026-05-28 12:13:05 +02:00
Ricardo Wurmus 842686d8b7 gnu: r-a4: Update to 1.59.0.
* gnu/packages/bioconductor.scm (r-a4): Update to 1.59.0.

Change-Id: I98f778d7d806cba1c240116bc861af4574310c66
2026-05-28 12:13:05 +02:00
Ricardo Wurmus 5c94196c43 gnu: r-a4base: Update to 1.59.0.
* gnu/packages/bioconductor.scm (r-a4base): Update to 1.59.0.

Change-Id: I1e143a64276c91aa8cb49902fa96d095971a4c80
2026-05-28 12:13:05 +02:00
Ricardo Wurmus b114fd5045 gnu: r-a4reporting: Update to 1.60.0.
* gnu/packages/bioconductor.scm (r-a4reporting): Update to 1.60.0.

Change-Id: Iec9eb6003c579ff71a7be2d4589f96118136ba27
2026-05-28 12:13:04 +02:00
Ricardo Wurmus c931f56de4 gnu: r-a4preproc: Update to 1.60.0.
* gnu/packages/bioconductor.scm (r-a4preproc): Update to 1.60.0.

Change-Id: Ic0b7cbe7d14fb11cf8eecb6b885a2bde8079d713
2026-05-28 12:13:04 +02:00
Ricardo Wurmus d1f9da02de gnu: r-a4classif: Update to 1.60.0.
* gnu/packages/bioconductor.scm (r-a4classif): Update to 1.60.0.

Change-Id: I9873d1921fcc86ca8496381a072d942434303a5f
2026-05-28 12:13:04 +02:00
Ricardo Wurmus a4113e8ed1 gnu: r-a4core: Update to 1.60.0.
* gnu/packages/bioconductor.scm (r-a4core): Update to 1.60.0.

Change-Id: Icbce46f0b4b596eb8eb8eb29e8b786c7bcadf2c9
2026-05-28 12:13:04 +02:00
Ricardo Wurmus e38fc06a71 gnu: r-annaffy: Update to 1.84.0.
* gnu/packages/bioconductor.scm (r-annaffy): Update to 1.84.0.

Change-Id: Ia97753b3bd65d99653ab1fc2f1f9e3871d0a9550
2026-05-28 12:13:04 +02:00
Ricardo Wurmus 391c5d3820 gnu: r-mlinterfaces: Update to 1.92.0.
* gnu/packages/bioconductor.scm (r-mlinterfaces): Update to 1.92.0.

Change-Id: I2b096e8f0e8b022ef6010bfb2387e04649a17555
2026-05-28 12:13:04 +02:00
Ricardo Wurmus b080c5f3ea gnu: r-clusterexperiment: Update to 2.32.0.
* gnu/packages/bioconductor.scm (r-clusterexperiment): Update to 2.32.0.

Change-Id: I29cf639e922b1140a3923203c7450699239410b7
2026-05-28 12:13:04 +02:00
Ricardo Wurmus 868f8c6a77 gnu: r-clusterprofiler: Update to 4.20.0.
* gnu/packages/bioconductor.scm (r-clusterprofiler): Update to 4.20.0.
[propagated-inputs]: Remove r-dose; add r-aisdk, r-enrichit, r-ggplot2, and r-jsonlite.

Change-Id: I5f886129cd807fb1fc4d846de389250fd0928a42
2026-05-28 12:13:03 +02:00
Ricardo Wurmus 4f44037054 gnu: r-enrichplot: Update to 1.32.0.
* gnu/packages/bioconductor.scm (r-enrichplot): Update to 1.32.0.
[propagated-inputs]: Remove r-plyr; add r-dplyr and r-enrichit.
[native-inputs]: Remove r-knitr; add r-quarto.

Change-Id: I9e6b251aad50bd6e4a0ef7d59ecc165b759a6b44
2026-05-28 12:13:03 +02:00
Ricardo Wurmus 83128b3400 gnu: r-enrichedheatmap: Update to 1.42.0.
* gnu/packages/bioconductor.scm (r-enrichedheatmap): Update to 1.42.0.

Change-Id: I302505e91afcff27f28a3180777a797931f03dd0
2026-05-28 12:13:03 +02:00
Ricardo Wurmus ed8d28e989 gnu: r-dose: Update to 4.6.0.
* gnu/packages/bioconductor.scm (r-dose): Update to 4.6.0.
[propagated-inputs]: Remove r-biocparallel, r-fgsea, and r-qvalue; add r-enrichit.

Change-Id: I6c95a1335c66b60b07b215ba1d2af185353ce0b5
2026-05-28 12:13:03 +02:00
Ricardo Wurmus 4d1383f6df gnu: r-fgsea: Update to 1.38.0.
* gnu/packages/bioconductor.scm (r-fgsea): Update to 1.38.0.

Change-Id: I971b3e898a35ef83881d668a16822ed081de0e78
2026-05-28 12:13:03 +02:00
Ricardo Wurmus 1ef766a97b gnu: r-fcscan: Update to 1.26.0.
* gnu/packages/bioconductor.scm (r-fcscan): Update to 1.26.0.

Change-Id: I61cec481f2d7ed16073724728fd3a4d614054bd0
2026-05-28 12:13:03 +02:00
Ricardo Wurmus 14c2ea02a3 gnu: r-anota2seq: Update to 1.34.0.
* gnu/packages/bioconductor.scm (r-anota2seq): Update to 1.34.0.
[native-inputs]: Add r-biocstyle.

Change-Id: Ifcac4e6e84f47ef2aaf08b148a04e07149209f79
2026-05-28 12:13:03 +02:00
Ricardo Wurmus cbe34b7be3 gnu: r-anota: Update to 1.60.0.
* gnu/packages/bioconductor.scm (r-anota): Update to 1.60.0.

Change-Id: Id8f77e949938bb56e845d0e00da608dbfc4f4856
2026-05-28 12:13:03 +02:00
Ricardo Wurmus 292eef1dcc gnu: r-gosemsim: Update to 2.38.0.
* gnu/packages/bioconductor.scm (r-gosemsim): Update to 2.38.0.
[propagated-inputs]: Remove r-r-utils.

Change-Id: I40388ad4ec03c2be3d406d6cbe4c6980d22fc4f8
2026-05-28 12:13:02 +02:00
Ricardo Wurmus 6ad7a58979 gnu: r-helloranges: Update to 1.38.0.
* gnu/packages/bioconductor.scm (r-helloranges): Update to 1.38.0.

Change-Id: I6c49b2f17ee0528949afc4362a75746b9d18decb
2026-05-28 12:13:02 +02:00
Ricardo Wurmus 20802c89c5 gnu: r-heatplus: Update to 3.20.0.
* gnu/packages/bioconductor.scm (r-heatplus): Update to 3.20.0.

Change-Id: Id8e0ce4d3d8a196f9e827df939d9b16de2efac57
2026-05-28 12:13:02 +02:00
Ricardo Wurmus 2742c58bb5 gnu: r-varianttools: Update to 1.54.0.
* gnu/packages/bioconductor.scm (r-varianttools): Update to 1.54.0.

Change-Id: I3520d034c76e8409790826cabbdce84ecae60374
2026-05-28 12:13:02 +02:00
Ricardo Wurmus ac18c066d5 gnu: r-tradeseq: Update to 1.26.0.
* gnu/packages/bioconductor.scm (r-tradeseq): Update to 1.26.0.

Change-Id: Ic34d1ac0b60f7ba58b26506ffe52d727bae25f44
2026-05-28 12:13:02 +02:00
Ricardo Wurmus 2977dc046f gnu: r-ioniser: Update to 2.35.0.
* gnu/packages/bioconductor.scm (r-ioniser): Update to 2.35.0.

Change-Id: Ic9a24dfce16310add892669a729fc6de17d754ae
2026-05-28 12:13:02 +02:00
Ricardo Wurmus 90390fbd84 gnu: r-linnorm: Update to 2.36.0.
* gnu/packages/bioconductor.scm (r-linnorm): Update to 2.36.0.

Change-Id: I0145e0163c5003cb1035938834e03ee3f560cb22
2026-05-28 12:13:02 +02:00
Ricardo Wurmus 767d454f27 gnu: r-lumi: Update to 2.64.0.
* gnu/packages/bioconductor.scm (r-lumi): Update to 2.64.0.

Change-Id: Ib53bb54074114f60f973c96fc044223ee7f13109
2026-05-28 12:13:02 +02:00
Ricardo Wurmus e6e496f18c gnu: r-lefser: Update to 1.22.0.
* gnu/packages/bioconductor.scm (r-lefser): Update to 1.22.0.

Change-Id: I34465a999b0cbcedf1af4c0ce1ea0a4d6a3cdfab
2026-05-28 12:13:01 +02:00
Ricardo Wurmus b264a33153 gnu: r-methylumi: Update to 2.58.0.
* gnu/packages/bioconductor.scm (r-methylumi): Update to 2.58.0.

Change-Id: Ifa438db01772285d7b496145826cb48fb56b10fe
2026-05-28 12:13:01 +02:00
Ricardo Wurmus f62ccb82a5 gnu: r-missmethyl: Update to 1.45.0.
* gnu/packages/bioconductor.scm (r-missmethyl): Update to 1.45.0.

Change-Id: I8ce89c6832ad29bf62c88db0c976405cc4c7f4a3
2026-05-28 12:13:01 +02:00
Ricardo Wurmus b2171d3e90 gnu: r-minfi: Update to 1.58.0.
* gnu/packages/bioconductor.scm (r-minfi): Update to 1.58.0.
[native-inputs]: Add r-biocstyle.

Change-Id: I16173d8cbe1ef9999450bd6656d0ae5f1549dfa5
2026-05-28 12:13:01 +02:00
Ricardo Wurmus 0d125b22d7 gnu: r-milor: Update to 2.7.2.
* gnu/packages/bioconductor.scm (r-milor): Update to 2.7.2.
[propagated-inputs]: Remove r-rcppeigen and r-rcppml.

Change-Id: I14a95ec6dd2b0aefa423e93cbaaf402faa842a60
2026-05-28 12:13:01 +02:00
Ricardo Wurmus bd254211a1 gnu: r-microbiome: Update to 1.34.0.
* gnu/packages/bioconductor.scm (r-microbiome): Update to 1.34.0.

Change-Id: I28ea43221e9567474aabab38ac229615871e37bf
2026-05-28 12:13:01 +02:00
Ricardo Wurmus d8fbc7f639 gnu: r-mia: Update to 1.20.0.
* gnu/packages/bioconductor.scm (r-mia): Update to 1.20.0.
[propagated-inputs]: Remove r-rbiom and r-scuttle; add r-ecodive.
[native-inputs]: Add r-scuttle.

Change-Id: Ie8f1ef7ba2430034d68cb82e15558f4c890c6b19
2026-05-28 12:13:01 +02:00
Ricardo Wurmus 7a9d2ce26b gnu: r-bumpymatrix: Update to 1.20.0.
* gnu/packages/bioconductor.scm (r-bumpymatrix): Update to 1.20.0.

Change-Id: I47065c642760afcdfd983b767406f3a4b6e2bddf
2026-05-28 12:13:00 +02:00
Ricardo Wurmus e766992ec3 gnu: r-bumphunter: Update to 1.54.0.
* gnu/packages/bioconductor.scm (r-bumphunter): Update to 1.54.0.

Change-Id: Id786be5c7b418a9b6fe55d2c58bd76b2536a0341
2026-05-28 12:13:00 +02:00
Ricardo Wurmus 3a74be9fcb gnu: r-siggenes: Update to 1.86.0.
* gnu/packages/bioconductor.scm (r-siggenes): Update to 1.86.0.

Change-Id: Icda2d33409c2b2b7ff0c8cd7d0637d4e8bc4a7b6
2026-05-28 12:13:00 +02:00
Ricardo Wurmus 779b99b8e9 gnu: r-illuminaio: Update to 0.54.0.
* gnu/packages/bioconductor.scm (r-illuminaio): Update to 0.54.0.

Change-Id: Idaff70f251e55f066e1bfab1f18daa7ce3787872
2026-05-28 12:13:00 +02:00
Ricardo Wurmus 385cf7a7a0 gnu: r-geoquery: Update to 2.80.0.
* gnu/packages/bioconductor.scm (r-geoquery): Update to 2.80.0.

Change-Id: I54d53ca9a1cac28d8b6716ab6999c85ef8a8d05f
2026-05-28 12:13:00 +02:00
Ricardo Wurmus b7374aee0b gnu: r-scone: Update to 1.36.0.
* gnu/packages/bioconductor.scm (r-scone): Update to 1.36.0.

Change-Id: I8583498c5cd1d2b5897d7053f65b98c64b114ba0
2026-05-28 12:13:00 +02:00
Ricardo Wurmus 4f36ee2b93 gnu: r-scdd: Update to 1.36.0.
* gnu/packages/bioconductor.scm (r-scdd): Update to 1.36.0.
[native-inputs]: Add r-biocstyle.

Change-Id: I6c6bc67764994f216d9c68abdf1f990d4bb3a5d2
2026-05-28 12:13:00 +02:00
Ricardo Wurmus b81cbd4e26 gnu: r-noiseq: Update to 2.56.0.
* gnu/packages/bioconductor.scm (r-noiseq): Update to 2.56.0.

Change-Id: I949e145dea70dc5e51ad67c12ac22e4031aeadcd
2026-05-28 12:13:00 +02:00
Ricardo Wurmus b387993885 gnu: r-sangerseqr: Update to 1.48.0.
* gnu/packages/bioconductor.scm (r-sangerseqr): Update to 1.48.0.

Change-Id: I7e56d65388e0c8a4322704f41ec11a97935220d5
2026-05-28 12:12:59 +02:00
Ricardo Wurmus 7b9f266c9e gnu: r-monocle: Update to 2.40.0.
* gnu/packages/bioconductor.scm (r-monocle): Update to 2.40.0.

Change-Id: I2ef42b62d39e3d10b48b783084a11df028cd1d6c
2026-05-28 12:12:59 +02:00
Ricardo Wurmus 4fe3811dc9 gnu: r-batchelor: Update to 1.28.0.
* gnu/packages/bioconductor.scm (r-batchelor): Update to 1.28.0.

Change-Id: I78a3e9b06fd89b854cf8ec3be859211ebf94642d
2026-05-28 12:12:59 +02:00
Ricardo Wurmus 905e04b0db gnu: r-residualmatrix: Update to 1.22.0.
* gnu/packages/bioconductor.scm (r-residualmatrix): Update to 1.22.0.

Change-Id: I4977d2ef4e85f9bde8e378f7c9f95a5ec5eeb65f
2026-05-28 12:12:59 +02:00
Ricardo Wurmus ee38e6e29b gnu: r-icobra: Update to 1.40.0.
* gnu/packages/bioconductor.scm (r-icobra): Update to 1.40.0.
[propagated-inputs]: Remove r-shinybs; add r-prompter.

Change-Id: Ib07a583660c06acb473ce93920d7f3fd7bfdd9af
2026-05-28 12:12:59 +02:00
Ricardo Wurmus bfaec75511 gnu: r-ihw: Update to 1.40.0.
* gnu/packages/bioconductor.scm (r-ihw): Update to 1.40.0.

Change-Id: I98e0a03634dc32be0d07c03131ca31f7b7bbee63
2026-05-28 12:12:59 +02:00
Ricardo Wurmus 9d68a6fcc8 gnu: r-lpsymphony: Update to 1.40.0.
* gnu/packages/bioconductor.scm (r-lpsymphony): Update to 1.40.0.

Change-Id: I4e69c89ac484d21dfc42e11c0d6d6d0b66a2fcd2
2026-05-28 12:12:59 +02:00
Ricardo Wurmus 1b9422d7cb gnu: r-karyoploter: Update to 1.38.0.
* gnu/packages/bioconductor.scm (r-karyoploter): Update to 1.38.0.

Change-Id: I00851d2622d243c2af6c5a381c72975e1793c4c1
2026-05-28 12:12:59 +02:00
Ricardo Wurmus 5b81cf623b gnu: r-ebseq: Update to 2.10.0.
* gnu/packages/bioconductor.scm (r-ebseq): Update to 2.10.0.

Change-Id: I7bbea8dbf5fa53d05c3d47cff49760534297cb2e
2026-05-28 12:12:58 +02:00
Ricardo Wurmus 7a9bf9a1a7 gnu: r-hmmcopy: Update to 1.54.0.
* gnu/packages/bioconductor.scm (r-hmmcopy): Update to 1.54.0.

Change-Id: Ice9463e4624c3caabf8300f6ff79b812d74c4c8c
2026-05-28 12:12:58 +02:00
Ricardo Wurmus c927418e81 gnu: r-dnacopy: Update to 1.86.0.
* gnu/packages/bioconductor.scm (r-dnacopy): Update to 1.86.0.

Change-Id: Iae7fe86ab3f99ab15eab94fc13eddd2839eecf10
2026-05-28 12:12:58 +02:00
Ricardo Wurmus d65173d784 gnu: r-chipexoqual: Update to 1.36.0.
* gnu/packages/bioconductor.scm (r-chipexoqual): Update to 1.36.0.

Change-Id: Ice70fb965485b174bb83c6f3184055f23e901a4a
2026-05-28 12:12:58 +02:00
Ricardo Wurmus 82b0fd19ca gnu: r-destiny: Update to 3.26.0.
* gnu/packages/bioconductor.scm (r-destiny): Update to 3.26.0.
[propagated-inputs]: Remove r-smoother.

Change-Id: I69ef33d13f8fecefd48687dcc7bf5ee76aee975f
2026-05-28 12:12:58 +02:00
Ricardo Wurmus 71d3f87194 gnu: r-biocsingular: Update to 1.28.0.
* gnu/packages/bioconductor.scm (r-biocsingular): Update to 1.28.0.

Change-Id: I5767f2eb74832412932896bf7c2f6579482954ba
2026-05-28 12:12:58 +02:00
Ricardo Wurmus 61b81af0b3 gnu: r-metapod: Update to 1.20.0.
* gnu/packages/bioconductor.scm (r-metapod): Update to 1.20.0.

Change-Id: I1db72e025c83e1b3051cf8e40cac6a1ea36a9528
2026-05-28 12:12:58 +02:00
Ricardo Wurmus 44d013de7c gnu: r-ggtree: Update to 4.2.0.
* gnu/packages/bioconductor.scm (r-ggtree): Update to 4.2.0.

Change-Id: I3f9e4071e8a8e12c2746722177e959aa6b292db4
2026-05-28 12:12:57 +02:00
Ricardo Wurmus 40f61a009c gnu: r-treesummarizedexperiment: Update to 2.20.0.
* gnu/packages/bioconductor.scm (r-treesummarizedexperiment): Update to 2.20.0.

Change-Id: I961b4244378abd67d57d13895fcacf6a9f8985f2
2026-05-28 12:12:57 +02:00
Ricardo Wurmus c7b0f378e6 gnu: r-treeio: Update to 1.36.0.
* gnu/packages/bioconductor.scm (r-treeio): Update to 1.36.0.

Change-Id: I1a5bada4f476e9880a682a273b6554914780b846
2026-05-28 12:12:57 +02:00
Ricardo Wurmus 3084e6733e gnu: r-scaledmatrix: Update to 1.20.0.
* gnu/packages/bioconductor.scm (r-scaledmatrix): Update to 1.20.0.

Change-Id: I54d4adc9707caa7c9d6fded660d94501e9017485
2026-05-28 12:12:57 +02:00
Ricardo Wurmus 90f0049190 gnu: r-biocneighbors: Update to 2.6.0.
* gnu/packages/bioconductor.scm (r-biocneighbors): Update to 2.6.0.
[propagated-inputs]: Add r-beachmat.
[native-inputs]: Add r-delayedarray.

Change-Id: I40ba3ad52df7e24c8354a97512400e7ea178de81
2026-05-28 12:12:57 +02:00
Ricardo Wurmus f6c83a095e gnu: r-ruvseq: Update to 1.46.0.
* gnu/packages/bioconductor.scm (r-ruvseq): Update to 1.46.0.

Change-Id: I3463baef38b9618a6e65127eccc3a26aff6de04d
2026-05-28 12:12:57 +02:00
Ricardo Wurmus 1ae421a2eb gnu: r-dnabarcodes: Update to 1.42.0.
* gnu/packages/bioconductor.scm (r-dnabarcodes): Update to 1.42.0.

Change-Id: If1b3eb0bc04fb9c2a6216934440749a2cd1cc683
2026-05-28 12:12:57 +02:00
Ricardo Wurmus 0c412ec512 gnu: r-inspect: Update to 1.42.0.
* gnu/packages/bioconductor.scm (r-inspect): Update to 1.42.0.

Change-Id: Ica8d57edeeefd23f6a99dc9598d811fcf9dad279
2026-05-28 12:12:57 +02:00
Ricardo Wurmus c618e31e80 gnu: r-plyranges: Update to 1.32.0.
* gnu/packages/bioconductor.scm (r-plyranges): Update to 1.32.0.

Change-Id: I77bebfcd5256810cd3e5b83fa2ec266cce5f9a31
2026-05-28 12:12:56 +02:00
Ricardo Wurmus c7267e7792 gnu: r-plgem: Update to 1.84.0.
* gnu/packages/bioconductor.scm (r-plgem): Update to 1.84.0.

Change-Id: If4cfd6d1b409a9b9a4b7e5ca72caaf3df5f390df
2026-05-28 12:12:56 +02:00
Ricardo Wurmus 4ce53711fe gnu: r-rots: Update to 2.4.0.
* gnu/packages/bioconductor.scm (r-rots): Update to 2.4.0.
[propagated-inputs]: Add r-survival.

Change-Id: If77bea8e51327567fef20d9053ab8b1774eeec9b
2026-05-28 12:12:56 +02:00
Ricardo Wurmus 8f42c87b47 gnu: r-glmgampoi: Update to 1.24.0.
* gnu/packages/bioconductor.scm (r-glmgampoi): Update to 1.24.0.

Change-Id: I0f3532b94ed911f0cb3eecf74c54b31023e7ac27
2026-05-28 12:12:56 +02:00
Ricardo Wurmus 4accf00521 gnu: r-goseq: Update to 1.64.0.
* gnu/packages/bioconductor.scm (r-goseq): Update to 1.64.0.

Change-Id: I4cd5d02a68ae85a179218705851b65e0ffaf354d
2026-05-28 12:12:56 +02:00
Ricardo Wurmus d3ab47e4b8 gnu: r-ctc: Update to 1.86.0.
* gnu/packages/bioconductor.scm (r-ctc): Update to 1.86.0.

Change-Id: Id47387657c7fd1e25d5f142b79a92a2e7a32b565
2026-05-28 12:12:56 +02:00
Ricardo Wurmus adf62555af gnu: r-genomicinteractions: Update to 1.46.0.
* gnu/packages/bioconductor.scm (r-genomicinteractions): Update to 1.46.0.

Change-Id: I1364f32d2481831d6d60d317e3f66fb88608013c
2026-05-28 12:12:56 +02:00
Ricardo Wurmus 0eeb59be99 gnu: r-interactionset: Update to 1.40.0.
* gnu/packages/bioconductor.scm (r-interactionset): Update to 1.40.0.

Change-Id: I4255836270f2218f6a9e32e55e2483b1aacb5280
2026-05-28 12:12:55 +02:00
Ricardo Wurmus 26432ce6f7 gnu: r-riboseqr: Update to 1.46.0.
* gnu/packages/bioconductor.scm (r-riboseqr): Update to 1.46.0.

Change-Id: I1ab5cabac33ba7319c0ba3d6db3f437a68b37bbb
2026-05-28 12:12:55 +02:00
Ricardo Wurmus a9b706cddc gnu: r-chipcomp: Update to 1.41.0.
* gnu/packages/bioconductor.scm (r-chipcomp): Update to 1.41.0.

Change-Id: I5594c19f9f86ed8aaceccf5b1287b22a64a0eb06
2026-05-28 12:12:55 +02:00
Ricardo Wurmus 917a5d0aa1 gnu: r-bayseq: Update to 2.46.0.
* gnu/packages/bioconductor.scm (r-bayseq): Update to 2.46.0.

Change-Id: Ia8f2ea4de195f1b406ba4f1aad0043534d237de5
2026-05-28 12:12:55 +02:00
Ricardo Wurmus 25ac169bf1 gnu: r-qdnaseq: Update to 1.48.0.
* gnu/packages/bioconductor.scm (r-qdnaseq): Update to 1.48.0.
[native-inputs]: Add r-digest.

Change-Id: Icec793bae7b9278b7d36c20eed0cbf42809542ce
2026-05-28 12:12:55 +02:00
Ricardo Wurmus 18996e4cbd gnu: r-cghcall: Update to 2.74.0.
* gnu/packages/bioconductor.scm (r-cghcall): Update to 2.74.0.

Change-Id: I2803c869d9a91f92739899f7a16ee48f5969eb34
2026-05-28 12:12:55 +02:00
Ricardo Wurmus 91fc46e2a6 gnu: r-cghbase: Update to 1.72.0.
* gnu/packages/bioconductor.scm (r-cghbase): Update to 1.72.0.

Change-Id: Ia04679c46483ac00a36b657026cb11e0b382b1ef
2026-05-28 12:12:55 +02:00
Ricardo Wurmus b6d4f3197b gnu: r-marray: Update to 1.90.0.
* gnu/packages/bioconductor.scm (r-marray): Update to 1.90.0.

Change-Id: I7e4ca265203dc4ad3d10a97a93f4212efee76427
2026-05-28 12:12:55 +02:00
Ricardo Wurmus d83ecef726 gnu: r-matrixgenerics: Update to 1.24.0.
* gnu/packages/bioconductor.scm (r-matrixgenerics): Update to 1.24.0.

Change-Id: Id7d36ed869c8adab3b41016fc306b4e93cedab12
2026-05-28 12:12:54 +02:00
Ricardo Wurmus 67f3e3e5b6 gnu: r-chippeakanno: Update to 3.46.0.
* gnu/packages/bioconductor.scm (r-chippeakanno): Update to 3.46.0.

Change-Id: I8cb3cfe74183da00ef995ee30e9d689d4d3081a1
2026-05-28 12:12:54 +02:00
Ricardo Wurmus 2262722173 gnu: r-pepsnmr: Update to 1.30.0.
* gnu/packages/bioconductor.scm (r-pepsnmr): Update to 1.30.0.

Change-Id: I03ce39f2dbd35d7d8f176594915c74869d51c2ec
2026-05-28 12:12:54 +02:00
Ricardo Wurmus 31a30c26dc gnu: r-ggtreeextra: Update to 1.22.0.
* gnu/packages/bioconductor.scm (r-ggtreeextra): Update to 1.22.0.

Change-Id: If99a822f7f04db79cfeb03e4c786a498b0a9dd0f
2026-05-28 12:12:54 +02:00
Ricardo Wurmus 10b1193c99 gnu: r-graph: Update to 1.90.0.
* gnu/packages/bioconductor.scm (r-graph): Update to 1.90.0.

Change-Id: I911298b5a23559582883024dc07056da5d0939a4
2026-05-28 12:12:54 +02:00
Ricardo Wurmus 47449d3570 gnu: r-multtest: Update to 2.68.0.
* gnu/packages/bioconductor.scm (r-multtest): Update to 2.68.0.

Change-Id: I7d53182922e10a9d60f835a9ec9c6e6d1d415246
2026-05-28 12:12:54 +02:00
Ricardo Wurmus 2548c6348d gnu: r-multibac: Update to 1.22.0.
* gnu/packages/bioconductor.scm (r-multibac): Update to 1.22.0.

Change-Id: Id204674331caa6fa755ca5f0880eb1711c6d980e
2026-05-28 12:12:54 +02:00
Ricardo Wurmus 1ad302ea8f gnu: r-mbkmeans: Update to 1.28.0.
* gnu/packages/bioconductor.scm (r-mbkmeans): Update to 1.28.0.

Change-Id: Ib66b9ff7df6482bac9e7f47ef4a93913d4a28df3
2026-05-28 12:12:54 +02:00
Ricardo Wurmus 490782506c gnu: r-mbecs: Update to 1.16.0.
* gnu/packages/bioconductor.scm (r-mbecs): Update to 1.16.0.

Change-Id: I0b092c4e567b26f4dcdd606eb23fd0586b7c1490
2026-05-28 12:12:53 +02:00
Ricardo Wurmus 12998163e8 gnu: r-greylistchip: Update to 1.44.0.
* gnu/packages/bioconductor.scm (r-greylistchip): Update to 1.44.0.

Change-Id: I8cc4e4480dfc80c73bc1dd06bd0787dafdb72a8f
2026-05-28 12:12:53 +02:00
Ricardo Wurmus f5d12c9942 gnu: r-apeglm: Update to 1.34.0.
* gnu/packages/bioconductor.scm (r-apeglm): Update to 1.34.0.

Change-Id: I337736b86a1add9e0f49c044e909d436c35dbe5d
2026-05-28 12:12:53 +02:00
Ricardo Wurmus 249c6daa8b gnu: r-apcomplex: Update to 2.78.0.
* gnu/packages/bioconductor.scm (r-apcomplex): Update to 2.78.0.

Change-Id: I86709899c548f231c534634d126c59128a89c2fb
2026-05-28 12:12:53 +02:00
Ricardo Wurmus ef2d03b13d gnu: r-qvalue: Update to 2.44.0.
* gnu/packages/bioconductor.scm (r-qvalue): Update to 2.44.0.

Change-Id: I92e18a3993fa8edeb08284fb7f15d5c5a885424a
2026-05-28 12:12:53 +02:00
Ricardo Wurmus 4fc29f0db3 gnu: r-quantsmooth: Update to 1.78.0.
* gnu/packages/bioconductor.scm (r-quantsmooth): Update to 1.78.0.

Change-Id: Ie37f2ee45e53d16534a6f0b25cb05bcd426fec29
2026-05-28 12:12:53 +02:00
Ricardo Wurmus be18548bfd gnu: r-qfeatures: Update to 1.22.0.
* gnu/packages/bioconductor.scm (r-qfeatures): Update to 1.22.0.

Change-Id: Ia79b67d186b393dc2997129f274b79d6449a917b
2026-05-28 12:12:53 +02:00
Ricardo Wurmus 62f00ad6a0 gnu: r-oligo: Update to 1.76.0.
* gnu/packages/bioconductor.scm (r-oligo): Update to 1.76.0.

Change-Id: I8f96318a56bc01ddba91fea3638b0e7c6966636e
2026-05-28 12:12:53 +02:00
Ricardo Wurmus 2280a73a73 gnu: r-oligoclasses: Update to 1.74.0.
* gnu/packages/bioconductor.scm (r-oligoclasses): Update to 1.74.0.

Change-Id: Ia0a00ed3cf39c6e0badf374eaf5861a804364543
2026-05-28 12:12:52 +02:00
Ricardo Wurmus eed5bb66bb gnu: r-geneplotter: Update to 1.90.0.
* gnu/packages/bioconductor.scm (r-geneplotter): Update to 1.90.0.

Change-Id: Id5529c9877ec9d1352d6d85c407a28b0414303fc
2026-05-28 12:12:52 +02:00
Ricardo Wurmus b43274a345 gnu: r-zellkonverter: Update to 1.21.2.
* gnu/packages/bioconductor.scm (r-zellkonverter): Update to 1.21.2.

Change-Id: I5dee56dbc9b876494b46b3135c060e063e4f432e
2026-05-28 12:12:52 +02:00
Ricardo Wurmus c394241386 gnu: r-xvector: Update to 0.52.0.
* gnu/packages/bioconductor.scm (r-xvector): Update to 0.52.0.

Change-Id: Ia2eb13b6ae737e6fe04542cfd5cd37118b7007f7
2026-05-28 12:12:52 +02:00
Ricardo Wurmus ec6360871d gnu: r-xmapbridge: Update to 1.70.0.
* gnu/packages/bioconductor.scm (r-xmapbridge): Update to 1.70.0.

Change-Id: I0bcf8be304b4c322c6eab4b65e8a7beb1ef9ed1c
2026-05-28 12:12:52 +02:00
Ricardo Wurmus 414d72796d gnu: r-xina: Update to 1.30.0.
* gnu/packages/bioconductor.scm (r-xina): Update to 1.30.0.

Change-Id: I4771e26372536979264a05223f42cf43257c80a8
2026-05-28 12:12:52 +02:00
Ricardo Wurmus 71fbb069de gnu: r-vsn: Update to 3.80.0.
* gnu/packages/bioconductor.scm (r-vsn): Update to 3.80.0.

Change-Id: I0057a51af1dd20347168e5ad3c1337aa744f28f2
2026-05-28 12:12:52 +02:00
Ricardo Wurmus 4b3b8511e3 gnu: r-variantannotation: Update to 1.58.0.
* gnu/packages/bioconductor.scm (r-variantannotation): Update to 1.58.0.

Change-Id: If013f63e96874debfdb32a3ccd6712ee8b70d3a5
2026-05-28 12:12:52 +02:00
Ricardo Wurmus 85fa538ae5 gnu: r-tximport: Update to 1.40.0.
* gnu/packages/bioconductor.scm (r-tximport): Update to 1.40.0.

Change-Id: I9177e4193d563edfc4bebbf32312c83671de1ea0
2026-05-28 12:12:51 +02:00
Ricardo Wurmus b921720d41 gnu: r-txdbmaker: Update to 1.8.0.
* gnu/packages/bioconductor.scm (r-txdbmaker): Update to 1.8.0.

Change-Id: I2f18fe62e3c9de64346077152f9f72cf7db74526
2026-05-28 12:12:51 +02:00
Ricardo Wurmus 77dba29d8a gnu: r-topgo: Update to 2.64.0.
* gnu/packages/bioconductor.scm (r-topgo): Update to 2.64.0.

Change-Id: I11ae642244fc728eeebf5bd20e1f798d2ef66bf6
2026-05-28 12:12:51 +02:00
Ricardo Wurmus 0da1077af7 gnu: r-systempiper: Update to 2.18.0.
* gnu/packages/bioconductor.scm (r-systempiper): Update to 2.18.0.

Change-Id: I42eb87b5b1ce98b308f15aa0534562177d22f9eb
2026-05-28 12:12:51 +02:00
Ricardo Wurmus e872bbcef9 gnu: r-survcomp: Update to 1.62.0.
* gnu/packages/bioconductor.scm (r-survcomp): Update to 1.62.0.

Change-Id: I62b263dbf58017f5438dc3469a4dd20392b78462
2026-05-28 12:12:51 +02:00
Ricardo Wurmus 2f75108cd7 gnu: r-summarizedexperiment: Update to 1.42.0.
* gnu/packages/bioconductor.scm (r-summarizedexperiment): Update to 1.42.0.

Change-Id: Idda38768d32ca3ffc3ab9bc2a8730483c1e8ce6f
2026-05-28 12:12:51 +02:00
Ricardo Wurmus cf76fc2bdd gnu: r-structuralvariantannotation: Update to 1.28.0.
* gnu/packages/bioconductor.scm (r-structuralvariantannotation): Update to 1.28.0.

Change-Id: I57f64250496b6cc8bdde0701f276f617e517d03e
2026-05-28 12:12:51 +02:00
Ricardo Wurmus aa34954ecc gnu: r-structstrings: Update to 1.28.0.
* gnu/packages/bioconductor.scm (r-structstrings): Update to 1.28.0.

Change-Id: I635acc62069235ff2697291739d6d1a2e0864484
2026-05-28 12:12:51 +02:00
Ricardo Wurmus 3b222765d1 gnu: r-stringdb: Update to 2.24.0.
* gnu/packages/bioconductor.scm (r-stringdb): Update to 2.24.0.

Change-Id: I4a2adb394592e3bcd545603aaa849d7753ad0cd0
2026-05-28 12:12:50 +02:00
Ricardo Wurmus 2bc5e1abb5 gnu: r-stager: Update to 1.33.0.
* gnu/packages/bioconductor.scm (r-stager): Update to 1.33.0.

Change-Id: If98316e830b09a46a164897d51418c34f72720f6
2026-05-28 12:12:50 +02:00
Ricardo Wurmus 0e9915db03 gnu: r-spectra: Update to 1.22.0.
* gnu/packages/bioconductor.scm (r-spectra): Update to 1.22.0.
[propagated-inputs]: Add r-data-table.
[native-inputs]: Add r-msdatahub.

Change-Id: I2513b8e715235377d0674559dbe7c09824289648
2026-05-28 12:12:50 +02:00
Ricardo Wurmus 97ae7219e7 gnu: r-slingshot: Update to 2.20.0.
* gnu/packages/bioconductor.scm (r-slingshot): Update to 2.20.0.

Change-Id: I0dd3cd768e9652e18bb1c8e46ae60e4d08d82029
2026-05-28 12:12:50 +02:00
Ricardo Wurmus d64e1009df gnu: r-scds: Update to 2.0.0.
* gnu/packages/bioconductor.scm (r-scds): Update to 2.0.0.

Change-Id: Id7d419f6ec4b4aef39cf1f28af5e7040e8dedd2b
2026-05-28 12:12:50 +02:00
Ricardo Wurmus f99fe9b65e gnu: r-trnadbimport: Update to 1.30.0.
* gnu/packages/bioconductor.scm (r-trnadbimport): Update to 1.30.0.

Change-Id: I844b7e251f5e8184e86a1b2d782754e7a08de908
2026-05-28 12:12:50 +02:00
Ricardo Wurmus c952bca307 gnu: r-trna: Update to 1.30.0.
* gnu/packages/bioconductor.scm (r-trna): Update to 1.30.0.

Change-Id: I4cd18de89cdf883cbd30b4ff753f195f48c813f4
2026-05-28 12:12:50 +02:00
Ricardo Wurmus 8a1401843d gnu: r-trajectoryutils: Update to 1.20.0.
* gnu/packages/bioconductor.scm (r-trajectoryutils): Update to 1.20.0.

Change-Id: I6d8555a56eced8b82d4e51bbd30c85f9fba3d90a
2026-05-28 12:12:50 +02:00
Ricardo Wurmus ec413ec3b1 gnu: r-transcriptr: Update to 1.40.0.
* gnu/packages/bioconductor.scm (r-transcriptr): Update to 1.40.0.

Change-Id: Ib3f873b26d7807eddaa91067219db82c7d47ef32
2026-05-28 12:12:49 +02:00
Ricardo Wurmus fc1230f6ef gnu: r-trackviewer: Update to 1.48.0.
* gnu/packages/bioconductor.scm (r-trackviewer): Update to 1.48.0.

Change-Id: I85ba4da8fea1537d448718e7adac4209b364d54d
2026-05-28 12:12:49 +02:00
Ricardo Wurmus e037c0a307 gnu: r-toast: Update to 1.26.0.
* gnu/packages/bioconductor.scm (r-toast): Update to 1.26.0.

Change-Id: I7b27d3e863752c1d4511d85ba67ca4710c92f4cd
2026-05-28 12:12:49 +02:00
Ricardo Wurmus 0340ce6876 gnu: r-tkwidgets: Update to 1.90.0.
* gnu/packages/bioconductor.scm (r-tkwidgets): Update to 1.90.0.

Change-Id: I4fb96ddbb01cad62b164f022d632f851f116bd19
2026-05-28 12:12:49 +02:00
Ricardo Wurmus 2fb18f0010 gnu: r-tcgautils: Update to 1.32.0.
* gnu/packages/bioconductor.scm (r-tcgautils): Update to 1.32.0.
[propagated-inputs]: Add r-glue.

Change-Id: I2d3dc457e5631ff2a702a84f562b5474e6c11124
2026-05-28 12:12:49 +02:00
Ricardo Wurmus a3ab25372a gnu: r-singscore: Update to 1.32.0.
* gnu/packages/bioconductor.scm (r-singscore): Update to 1.32.0.

Change-Id: I2aeb9c31d57441382db4f21cc77a3db8627d28eb
2026-05-28 12:12:49 +02:00
Ricardo Wurmus 95c5bba70f gnu: r-simplifyenrichment: Update to 2.6.0.
* gnu/packages/bioconductor.scm (r-simplifyenrichment): Update to 2.6.0.

Change-Id: Id95754b8eb7dba34474576c7d99c3fe61c065bb5
2026-05-28 12:12:49 +02:00
Ricardo Wurmus 2c79ada894 gnu: r-simona: Update to 1.10.0.
* gnu/packages/bioconductor.scm (r-simona): Update to 1.10.0.

Change-Id: I74b4913be31e88ac75c62ded449cbe8dd5082479
2026-05-28 12:12:49 +02:00
Ricardo Wurmus 09a3f9685d gnu: r-sictools: Update to 1.42.0.
* gnu/packages/bioconductor.scm (r-sictools): Update to 1.42.0.

Change-Id: I67555db24016092b859576fe48913aa174d549b2
2026-05-28 12:12:48 +02:00
Ricardo Wurmus d351bb0b74 gnu: r-shinymethyl: Update to 1.48.0.
* gnu/packages/bioconductor.scm (r-shinymethyl): Update to 1.48.0.

Change-Id: I6bc429b6703816955e7dec41e0eedc99030f8ca4
2026-05-28 12:12:48 +02:00
Ricardo Wurmus 34115cb44a gnu: r-sesame: Update to 1.30.0.
* gnu/packages/bioconductor.scm (r-sesame): Update to 1.30.0.

Change-Id: Id06f859c1dcad94c5f48fab5a7f60fa7fedba87e
2026-05-28 12:12:48 +02:00
Ricardo Wurmus b014a042c5 gnu: r-seqpattern: Update to 1.44.0.
* gnu/packages/bioconductor.scm (r-seqpattern): Update to 1.44.0.

Change-Id: I2f330791f34d90405b7000f2f7862d80067b0bbf
2026-05-28 12:12:48 +02:00
Ricardo Wurmus 67606c9602 gnu: r-seqlogo: Update to 1.78.0.
* gnu/packages/bioconductor.scm (r-seqlogo): Update to 1.78.0.

Change-Id: I525f7a00a543d3591706fffd33b99a5c16436a97
2026-05-28 12:12:48 +02:00
Ricardo Wurmus 8cb49a24d1 gnu: r-seqinfo: Update to 1.2.0.
* gnu/packages/bioconductor.scm (r-seqinfo): Update to 1.2.0.

Change-Id: I4501eb8ba4b6b93b770c447328d317cf3b78a8dd
2026-05-28 12:12:48 +02:00
Ricardo Wurmus ce2a1e1523 gnu: r-seqarray: Update to 1.52.0.
* gnu/packages/bioconductor.scm (r-seqarray): Update to 1.52.0.

Change-Id: Id63264b691b100a5709065437c9a0eacaa4aa99e
2026-05-28 12:12:48 +02:00
Ricardo Wurmus 79a9103fb0 gnu: r-scry: Update to 1.24.0.
* gnu/packages/bioconductor.scm (r-scry): Update to 1.24.0.

Change-Id: I28b77074a6bd963bee24b21a91b98cad3ee87627
2026-05-28 12:12:47 +02:00
Ricardo Wurmus 58680ecfc8 gnu: r-scrnaseq: Update to 2.25.0.
* gnu/packages/bioconductor.scm (r-scrnaseq): Update to 2.25.0.

Change-Id: I50a9a47e5cc78ed944e9b68d40baaa00287e1756
2026-05-28 12:12:47 +02:00
Ricardo Wurmus 49499c24b1 gnu: r-screpertoire: Update to 2.8.0.
* gnu/packages/bioconductor.scm (r-screpertoire): Update to 2.8.0.

Change-Id: Ib21c4dd741c72aaf07eb20171f3ce6ec6d573661
2026-05-28 12:12:47 +02:00
Ricardo Wurmus 7934ddb8a0 gnu: r-scp: Update to 1.22.0.
* gnu/packages/bioconductor.scm (r-scp): Update to 1.22.0.

Change-Id: I53367b3b1b267cfd6a7927556ddd94d8c9f14198
2026-05-28 12:12:47 +02:00
Ricardo Wurmus cde9b06df5 gnu: r-scmap: Update to 1.34.0.
* gnu/packages/bioconductor.scm (r-scmap): Update to 1.34.0.

Change-Id: Ie04816dbda5f8d68a25fa882d8efdcd831350965
2026-05-28 12:12:47 +02:00
Ricardo Wurmus 76fbb6f67c gnu: r-scdblfinder: Update to 1.26.0.
* gnu/packages/bioconductor.scm (r-scdblfinder): Update to 1.26.0.

Change-Id: I8b9a7ceb0812106eb2221f82a87320bc1ad9a0aa
2026-05-28 12:12:47 +02:00
Ricardo Wurmus a5ddac534b gnu: r-scannotatr: Update to 1.18.0.
* gnu/packages/bioconductor.scm (r-scannotatr): Update to 1.18.0.

Change-Id: Ie657f95598648aec8dd0cad64b0c1d54cf6711be
2026-05-28 12:12:47 +02:00
Ricardo Wurmus bd52e338cb gnu: r-saturn: Update to 1.20.0.
* gnu/packages/bioconductor.scm (r-saturn): Update to 1.20.0.

Change-Id: I77f6e238a85d2333c96b7ef35caf8257c1a6b96b
2026-05-28 12:12:47 +02:00
Ricardo Wurmus 2c46f2ce72 gnu: r-rtracklayer: Update to 1.72.0.
* gnu/packages/bioconductor.scm (r-rtracklayer): Update to 1.72.0.

Change-Id: I55f3fcfa0818a95d52ebdfb80b7e68d172b422a6
2026-05-28 12:12:46 +02:00
Ricardo Wurmus 714907e8f2 gnu: r-rtcgatoolbox: Update to 2.42.0.
* gnu/packages/bioconductor.scm (r-rtcgatoolbox): Update to 2.42.0.

Change-Id: I328dc0307a8d12c948221c390daed9b25b2aa561
2026-05-28 12:12:46 +02:00
Ricardo Wurmus 2233cec7b4 gnu: r-rtcga: Update to 1.41.0.
* gnu/packages/bioconductor.scm (r-rtcga): Update to 1.41.0.

Change-Id: I531673b22e24fefa1a10d029f94ea3b50fcb7771
2026-05-28 12:12:46 +02:00
Ricardo Wurmus 8de87fbae1 gnu: r-rnaagecalc: Update to 1.24.0.
* gnu/packages/bioconductor.scm (r-rnaagecalc): Update to 1.24.0.

Change-Id: Ia7db2714427777f9f840ebf2f2725d8b16e228e3
2026-05-28 12:12:46 +02:00
Ricardo Wurmus 34c8ce4fa2 gnu: r-rhdf5filters: Update to 1.24.0.
* gnu/packages/bioconductor.scm (r-rhdf5filters): Update to 1.24.0.
[native-inputs]: Remove r-tinytest; add r-testthat.

Change-Id: I132247f8f9026b95b719dbb4337bf639c56db3c7
2026-05-28 12:12:46 +02:00
Ricardo Wurmus 214a1d8445 gnu: r-rhdf5: Update to 2.56.0.
* gnu/packages/bioconductor.scm (r-rhdf5): Update to 2.56.0.

Change-Id: I90c98a394401101b2ec0416d3d514567f1128b61
2026-05-28 12:12:46 +02:00
Ricardo Wurmus 1f351671be gnu: r-reportingtools: Update to 2.52.0.
* gnu/packages/bioconductor.scm (r-reportingtools): Update to 2.52.0.

Change-Id: Ib7738d984d5c3a67f7773a524a9e0ea00472f4c5
2026-05-28 12:12:46 +02:00
Ricardo Wurmus 23187dda7f gnu: r-regioner: Update to 1.44.0.
* gnu/packages/bioconductor.scm (r-regioner): Update to 1.44.0.

Change-Id: I06bf50727305b238052408f5c4cc1e6f73a79f34
2026-05-28 12:12:46 +02:00
Ricardo Wurmus 76c4d45784 gnu: r-recount: Update to 1.38.0.
* gnu/packages/bioconductor.scm (r-recount): Update to 1.38.0.

Change-Id: I7be0ff77b3eace63ed0241a8c7c45b9ad1312506
2026-05-28 12:12:45 +02:00
Ricardo Wurmus 12ad8b9b99 gnu: r-rcy3: Update to 2.32.0.
* gnu/packages/bioconductor.scm (r-rcy3): Update to 2.32.0.

Change-Id: I8a55bc7ed0b26240f0b40814052a9f08293a103c
2026-05-28 12:12:45 +02:00
Ricardo Wurmus a53ba86cc2 gnu: r-rcas: Update to 1.38.0.
* gnu/packages/bioconductor.scm (r-rcas): Update to 1.38.0.

Change-Id: I47e4fb23b52ff8b0ae3d110881fb6f3ef13d2f6a
2026-05-28 12:12:45 +02:00
Ricardo Wurmus a511aa8dd3 gnu: r-rbgl: Update to 1.88.0.
* gnu/packages/bioconductor.scm (r-rbgl): Update to 1.88.0.

Change-Id: Icf53bd937a206300f03740a5c4fc4670ae61779e
2026-05-28 12:12:45 +02:00
Ricardo Wurmus ba3a3dfd98 gnu: r-pwalign: Update to 1.8.0.
* gnu/packages/bioconductor.scm (r-pwalign): Update to 1.8.0.

Change-Id: I876eb1518a8f8c0b41fd41c56ba5e295c2abb2ab
2026-05-28 12:12:45 +02:00
Ricardo Wurmus f65da6d839 gnu: r-ptmods: Update to 1.0.0.
* gnu/packages/bioconductor.scm (r-ptmods): Update to 1.0.0.

Change-Id: If21b048160de8db7e7979bd7e3b9b5ac99562d4a
2026-05-28 12:12:45 +02:00
Ricardo Wurmus 56a2658226 gnu: r-protgenerics: Update to 1.44.0.
* gnu/packages/bioconductor.scm (r-protgenerics): Update to 1.44.0.

Change-Id: Id36cb73f3b7342a683239fa353fe1cd3e1d92485
2026-05-28 12:12:45 +02:00
Ricardo Wurmus 36680dbfa2 gnu: r-protgear: Update to 1.16.0.
* gnu/packages/bioconductor.scm (r-protgear): Update to 1.16.0.

Change-Id: I5693d960cbff8bc334006cbab39fc593e19307b2
2026-05-28 12:12:45 +02:00
Ricardo Wurmus 9b442b2e03 gnu: r-psmatch: Update to 1.16.0.
* gnu/packages/bioconductor.scm (r-psmatch): Update to 1.16.0.
[propagated-inputs]: Remove r-iranges; add r-ptmods.
[native-inputs]: Remove r-msdata; add r-iranges and r-msdatahub.

Change-Id: Id5853b32f7585912c127dcbf5f9be0f9d8bdcbc5
2026-05-28 12:12:44 +02:00
Ricardo Wurmus f460c9ef60 gnu: r-powertcr: Update to 1.32.0.
* gnu/packages/bioconductor.scm (r-powertcr): Update to 1.32.0.

Change-Id: I7379120677e8271c99b636fb91ea9f1ebfa87a26
2026-05-28 12:12:44 +02:00
Ricardo Wurmus 71e732d064 gnu: r-piano: Update to 2.28.0.
* gnu/packages/bioconductor.scm (r-piano): Update to 2.28.0.
[native-inputs]: Add r-biocmanager.

Change-Id: I954b563d8e2d0a4da588060d1d987c2f4153d3ec
2026-05-28 12:12:44 +02:00
Ricardo Wurmus b332faca7c gnu: r-pfamanalyzer: Update to 1.12.0.
* gnu/packages/bioconductor.scm (r-pfamanalyzer): Update to 1.12.0.

Change-Id: Id1c7cea657392c506de3208672925d6ff6097e94
2026-05-28 12:12:44 +02:00
Ricardo Wurmus f815def29a gnu: r-pcamethods: Update to 2.4.0.
* gnu/packages/bioconductor.scm (r-pcamethods): Update to 2.4.0.

Change-Id: I52119838eea4bb060ce1a3f627bcd45e7c39e7af
2026-05-28 12:12:44 +02:00
Ricardo Wurmus e5d1a4f386 gnu: r-pcaexplorer: Update to 3.6.0.
* gnu/packages/bioconductor.scm (r-pcaexplorer): Update to 3.6.0.

Change-Id: Ia2a1a7e0de27a1316089a8afc9608b244f0ce2d3
2026-05-28 12:12:44 +02:00
Ricardo Wurmus fef35535ea gnu: r-oscope: Update to 1.42.0.
* gnu/packages/bioconductor.scm (r-oscope): Update to 1.42.0.
[native-inputs]: Add r-biocstyle.

Change-Id: Ia7e3ab1009a86793517a0646a36f420b38694b41
2026-05-28 12:12:44 +02:00
Ricardo Wurmus df1d0e66fc gnu: r-organismdbi: Update to 1.54.0.
* gnu/packages/bioconductor.scm (r-organismdbi): Update to 1.54.0.

Change-Id: I7d528d0acafab2e720a1559817f9f1dff2449a59
2026-05-28 12:12:44 +02:00
Ricardo Wurmus bc5a3647ad gnu: r-mzr: Update to 2.46.0.
* gnu/packages/bioconductor.scm (r-mzr): Update to 2.46.0.
[native-inputs]: Remove r-msdata; add r-msdatahub.

Change-Id: I215f88b9ddbaa72c9b92c5aa08c11ee3f0e4cf0a
2026-05-28 12:12:43 +02:00
Ricardo Wurmus f355731f45 gnu: r-mzid: Update to 1.50.0.
* gnu/packages/bioconductor.scm (r-mzid): Update to 1.50.0.

Change-Id: I4a9fc46435fe9e068619e2dfd86bdc3c03cf5158
2026-05-28 12:12:43 +02:00
Ricardo Wurmus 50dc55adeb gnu: r-msnid: Update to 1.46.0.
* gnu/packages/bioconductor.scm (r-msnid): Update to 1.46.0.

Change-Id: Ibf481b8e6a0a8ebffd420d9e3167da1c355bc26c
2026-05-28 12:12:43 +02:00
Ricardo Wurmus 451484a8ab gnu: r-msdatahub: Update to 1.12.0.
* gnu/packages/bioconductor.scm (r-msdatahub): Update to 1.12.0.

Change-Id: I869825fcb536f468b5345d7fd99f6b57e696b899
2026-05-28 12:12:43 +02:00
Ricardo Wurmus 372b9ba4b4 gnu: r-msa: Update to 1.44.0.
* gnu/packages/bioconductor.scm (r-msa): Update to 1.44.0.
[native-inputs]: Add r-biocmanager.

Change-Id: Ibd43e66252013bdb8d9e0cf2daf1ce6e3820b635
2026-05-28 12:12:43 +02:00
Ricardo Wurmus 09a234bc9d gnu: r-mutationalpatterns: Update to 3.22.0.
* gnu/packages/bioconductor.scm (r-mutationalpatterns): Update to 3.22.0.

Change-Id: I86c8518867a0ec3064f7b3a7801ebf03412df8fa
2026-05-28 12:12:43 +02:00
Ricardo Wurmus 143eba5258 gnu: r-muscat: Update to 1.26.0.
* gnu/packages/bioconductor.scm (r-muscat): Update to 1.26.0.
[propagated-inputs]: Remove r-data-table, r-deseq2, r-ihw, r-purrr, and r-sctransform;
add r-matrixgenerics.

Change-Id: Iba29e4cf4640e07c98343a3a6aa979fb882d69e3
2026-05-28 12:12:43 +02:00
Ricardo Wurmus 39e3756291 gnu: r-mosdef: Update to 1.8.0.
* gnu/packages/bioconductor.scm (r-mosdef): Update to 1.8.0.

Change-Id: Icd747ccb0dfa57f19baba2ac5792ce49ed5679d8
2026-05-28 12:12:42 +02:00
Ricardo Wurmus 6777068d16 gnu: r-modstrings: Update to 1.28.0.
* gnu/packages/bioconductor.scm (r-modstrings): Update to 1.28.0.

Change-Id: I5ca89d72a6225bdb62272988d7bf105ccc8e6a2e
2026-05-28 12:12:42 +02:00
Ricardo Wurmus 8a43a38b7e gnu: r-mmuphin: Update to 2.0.0.
* gnu/packages/bioconductor.scm (r-mmuphin): Update to 2.0.0.

Change-Id: I623fbd4952eeb6791e116d81e9a2ca4b326f018f
2026-05-28 12:12:42 +02:00
Ricardo Wurmus 6253c85e15 gnu: r-mfuzz: Update to 2.72.0.
* gnu/packages/bioconductor.scm (r-mfuzz): Update to 2.72.0.

Change-Id: I09abbb594a9928c61851c0e068ed174aa1f7b667
2026-05-28 12:12:42 +02:00
Ricardo Wurmus 67f341f0ef gnu: r-methylkit: Update to 1.38.0.
* gnu/packages/bioconductor.scm (r-methylkit): Update to 1.38.0.

Change-Id: I2d77375a092731b9c51e5726115a5f748f432a12
2026-05-28 12:12:42 +02:00
Ricardo Wurmus 0e756bce67 gnu: r-methylaid: Update to 1.46.0.
* gnu/packages/bioconductor.scm (r-methylaid): Update to 1.46.0.
[native-inputs]: Add r-biocstyle.

Change-Id: I52106bdae1e90f72dd2f2543812d7e7ad0747ec8
2026-05-28 12:12:42 +02:00
Ricardo Wurmus 0a60e65c96 gnu: r-metagenomeseq: Update to 1.54.0.
* gnu/packages/bioconductor.scm (r-metagenomeseq): Update to 1.54.0.
[native-inputs]: Add r-annotate.

Change-Id: Ief784933d47bc5b773533f4586d6927f4fbabc1e
2026-05-28 12:12:42 +02:00
Ricardo Wurmus d662e32cf9 gnu: r-metabocoreutils: Update to 1.20.0.
* gnu/packages/bioconductor.scm (r-metabocoreutils): Update to 1.20.0.

Change-Id: I257cbd5ac0dc2440cc4db0542d8a66930d364d62
2026-05-28 12:12:42 +02:00
Ricardo Wurmus eaa6089618 gnu: r-mdqc: Update to 1.74.0.
* gnu/packages/bioconductor.scm (r-mdqc): Update to 1.74.0.

Change-Id: I2fc2d45aec66a6f08fce76cd7acb785d2ac1a944
2026-05-28 12:12:41 +02:00
Ricardo Wurmus 1acf4e8f1f gnu: r-maser: Update to 1.30.0.
* gnu/packages/bioconductor.scm (r-maser): Update to 1.30.0.

Change-Id: I115d758528b8cd0136a91d9b860681f34f5dea4e
2026-05-28 12:12:41 +02:00
Ricardo Wurmus 0dbbcea0ed gnu: r-manor: Update to 1.84.0.
* gnu/packages/bioconductor.scm (r-manor): Update to 1.84.0.

Change-Id: I155c6c67b20266d9825e49bfde35a35a93cb2bb9
2026-05-28 12:12:41 +02:00
Ricardo Wurmus 71a57aa1df gnu: r-makecdfenv: Update to 1.88.0.
* gnu/packages/bioconductor.scm (r-makecdfenv): Update to 1.88.0.

Change-Id: If26aa6b4c5c6a73378428195dbe751e57b2743eb
2026-05-28 12:12:41 +02:00
Ricardo Wurmus d4131695e0 gnu: r-made4: Update to 1.86.0.
* gnu/packages/bioconductor.scm (r-made4): Update to 1.86.0.

Change-Id: I87aa8fa50ecd42113ecd9191b4171450c09aa683
2026-05-28 12:12:41 +02:00
Ricardo Wurmus 09c9c6bd51 gnu: r-maaslin3: Update to 1.4.0.
* gnu/packages/bioconductor.scm (r-maaslin3): Update to 1.4.0.

Change-Id: I1b4d611dbe1b8cd31ff086fd70ae20b9533dd65c
2026-05-28 12:12:41 +02:00
Ricardo Wurmus 643402fdf9 gnu: r-maaslin2: Update to 1.26.0.
* gnu/packages/bioconductor.scm (r-maaslin2): Update to 1.26.0.

Change-Id: Id36d88f30a281da933943fc68e00e79a3408a46b
2026-05-28 12:12:41 +02:00
Ricardo Wurmus 4acdd91115 gnu: r-limma: Update to 3.68.0.
* gnu/packages/bioconductor.scm (r-limma): Update to 3.68.0.

Change-Id: I6773a28b254215c68edc859394c38d81121c5b91
2026-05-28 12:12:41 +02:00
Ricardo Wurmus 93556d3484 gnu: r-lfa: Update to 2.12.0.
* gnu/packages/bioconductor.scm (r-lfa): Update to 2.12.0.
[propagated-inputs]: Add r-bedmatrix and r-genio.
[native-inputs]: Remove r-ggplot2.

Change-Id: I06b6975cdb126a757d6b2a7b65ee9361d9234083
2026-05-28 12:12:40 +02:00
Ricardo Wurmus 472b7ce9ce gnu: r-lea: Update to 3.24.0.
* gnu/packages/bioconductor.scm (r-lea): Update to 3.24.0.

Change-Id: I0feedcef9749fa29cb8b6c5f9db8c0fd05efe96c
2026-05-28 12:12:40 +02:00
Ricardo Wurmus d6b15e1276 gnu: r-keggrest: Update to 1.52.0.
* gnu/packages/bioconductor.scm (r-keggrest): Update to 1.52.0.

Change-Id: Idd4525e2e53fe66292d65f204f8819b1960ffc3c
2026-05-28 12:12:40 +02:00
Ricardo Wurmus de60baf04f gnu: r-impute: Update to 1.86.0.
* gnu/packages/bioconductor.scm (r-impute): Update to 1.86.0.

Change-Id: If868fd51052773acd23751fb6bceed5738306e7d
2026-05-28 12:12:40 +02:00
Ricardo Wurmus 6eb42e308a gnu: r-rpx: Update to 2.20.0.
* gnu/packages/bioconductor.scm (r-rpx): Update to 2.20.0.

Change-Id: I24e443d0488ec7d95cb133418e10c799bf3f8283
2026-05-28 12:12:40 +02:00
Ricardo Wurmus 5d9a3a5eac gnu: r-rnbeads: Update to 2.30.0.
* gnu/packages/bioconductor.scm (r-rnbeads): Update to 2.30.0.
[native-inputs]: Add r-biocmanager.

Change-Id: Ic844ed1f9a33d17ae9f63955373cadf5059374c8
2026-05-28 12:12:40 +02:00
Ricardo Wurmus 41c6878fca gnu: r-rhtslib: Update to 3.8.0.
* gnu/packages/bioconductor.scm (r-rhtslib): Update to 3.8.0.

Change-Id: I0a2b85c5db63c6583e685dafdcf1be36619dbb32
2026-05-28 12:12:40 +02:00
Ricardo Wurmus 866725e21c gnu: r-rdisop: Update to 1.72.0.
* gnu/packages/bioconductor.scm (r-rdisop): Update to 1.72.0.

Change-Id: I25e35fd09371e511acbd2cff38f65b893f625620
2026-05-28 12:12:40 +02:00
Ricardo Wurmus d303f771e7 gnu: r-rarr: Update to 2.0.0.
* gnu/packages/bioconductor.scm (r-rarr): Update to 2.0.0.
[propagated-inputs]: Remove r-biocgenerics and r-delayedarray; add r-lifecycle.

Change-Id: Ic4a8af53abeedaf083a241eae18f34c6016f6498
2026-05-28 12:12:39 +02:00
Ricardo Wurmus 9036daf90d gnu: r-raggedexperiment: Update to 1.36.0.
* gnu/packages/bioconductor.scm (r-raggedexperiment): Update to 1.36.0.

Change-Id: Ic0bf19fcc6044a9a24d6e375c4f41ffd78df4a2c
2026-05-28 12:12:39 +02:00
Ricardo Wurmus a35d14d52c gnu: r-radiogx: Update to 2.16.0.
* gnu/packages/bioconductor.scm (r-radiogx): Update to 2.16.0.

Change-Id: Ic73284307ca196c12f93a3439fec747a6aa9c1fb
2026-05-28 12:12:39 +02:00
Ricardo Wurmus 06eaa17b9e gnu: r-r4rna: Update to 1.40.0.
* gnu/packages/bioconductor.scm (r-r4rna): Update to 1.40.0.

Change-Id: I3cad9c1a26f6e1e91f8e8ca5a921455a8d00cba0
2026-05-28 12:12:39 +02:00
Ricardo Wurmus 6186597c43 gnu: r-r3cseq: Update to 1.58.0.
* gnu/packages/bioconductor.scm (r-r3cseq): Update to 1.58.0.

Change-Id: I9642abc5e49f467b9536f29cedff765094887279
2026-05-28 12:12:39 +02:00
Ricardo Wurmus 1b41aab170 gnu: r-hpar: Update to 1.54.0.
* gnu/packages/bioconductor.scm (r-hpar): Update to 1.54.0.

Change-Id: If2c2efdc9ad5213996250c15d81d7e042c833840
2026-05-28 12:12:39 +02:00
Ricardo Wurmus c54c558332 gnu: r-gypsum: Update to 1.8.0.
* gnu/packages/bioconductor.scm (r-gypsum): Update to 1.8.0.

Change-Id: Iee1ee433aaf6a51689011779f7e413ab98188d8b
2026-05-28 12:12:39 +02:00
Ricardo Wurmus 67c859f5dd gnu: r-gseabase: Update to 1.74.0.
* gnu/packages/bioconductor.scm (r-gseabase): Update to 1.74.0.

Change-Id: Ic444ad49c357a9a3054cee58e19c4b23e34f59ea
2026-05-28 12:12:39 +02:00
Ricardo Wurmus 058f495df9 gnu: r-gostats: Update to 2.78.0.
* gnu/packages/bioconductor.scm (r-gostats): Update to 2.78.0.

Change-Id: I5ee8e050dc7ee406c79bf8956b884639a78938bf
2026-05-28 12:12:38 +02:00
Ricardo Wurmus 0e4ae637f2 gnu: r-globaltest: Update to 5.66.0.
* gnu/packages/bioconductor.scm (r-globaltest): Update to 5.66.0.

Change-Id: I87b23bd9a726ce219dffd1507948c6b02ef2eb85
2026-05-28 12:12:38 +02:00
Ricardo Wurmus ebc8e28ced gnu: r-globalancova: Update to 4.30.0.
* gnu/packages/bioconductor.scm (r-globalancova): Update to 4.30.0.

Change-Id: I3c2d7785eb2ad9c1156acae5fb95bd92b14324a5
2026-05-28 12:12:38 +02:00
Ricardo Wurmus 5eef28b40a gnu: r-glad: Update to 2.76.0.
* gnu/packages/bioconductor.scm (r-glad): Update to 2.76.0.

Change-Id: I2511f56543ddb43d8303625b32887425e31b443f
2026-05-28 12:12:38 +02:00
Ricardo Wurmus d572b02b70 gnu: r-genomicranges: Update to 1.64.0.
* gnu/packages/bioconductor.scm (r-genomicranges): Update to 1.64.0.
[native-inputs]: Add r-biocstyle.

Change-Id: I9a1c6eeed71dc6174046b0429d8ea409d1fe0ed2
2026-05-28 12:12:38 +02:00
Ricardo Wurmus 98a53235ee gnu: r-genomicfiles: Update to 1.48.0.
* gnu/packages/bioconductor.scm (r-genomicfiles): Update to 1.48.0.

Change-Id: I2a7d6afbab4c5c2889efb1e45d8db4a02cf8c480
2026-05-28 12:12:38 +02:00
Ricardo Wurmus 069c6764ab gnu: r-genomicfeatures: Update to 1.64.0.
* gnu/packages/bioconductor.scm (r-genomicfeatures): Update to 1.64.0.

Change-Id: I29c63234819be55c430b2987e0deec6b25f15cc7
2026-05-28 12:12:38 +02:00
Ricardo Wurmus 09ed9e1547 gnu: r-genomicdatacommons: Update to 1.36.0.
* gnu/packages/bioconductor.scm (r-genomicdatacommons): Update to 1.36.0.

Change-Id: I39b1698bb20c8a46b8672dfa04d4324c17af2da1
2026-05-28 12:12:37 +02:00
Ricardo Wurmus 1f7c7258b7 gnu: r-genomicalignments: Update to 1.48.0.
* gnu/packages/bioconductor.scm (r-genomicalignments): Update to 1.48.0.
[native-inputs]: Add r-biocmanager and r-biocstyle.

Change-Id: Ied3ea007d47c3eec1ea2ae273c7bbe36c04f3519
2026-05-28 12:12:37 +02:00
Ricardo Wurmus e2792d00bd gnu: r-genomeinfodb: Update to 1.48.0.
* gnu/packages/bioconductor.scm (r-genomeinfodb): Update to 1.48.0.
[native-inputs]: Add r-biocstyle.

Change-Id: Idb670a003dc3f7a4a43a799bfa27f07cf9668080
2026-05-28 12:12:37 +02:00
Ricardo Wurmus 52d7835f33 gnu: r-genomation: Update to 1.44.0.
* gnu/packages/bioconductor.scm (r-genomation): Update to 1.44.0.

Change-Id: I5d820238de0a4a45228b8773ccc2b1d98114c22e
2026-05-28 12:12:37 +02:00
Ricardo Wurmus 253644cc9d gnu: r-geneoverlap: Update to 1.48.0.
* gnu/packages/bioconductor.scm (r-geneoverlap): Update to 1.48.0.

Change-Id: I1c81732524bfa0466d471020e95dae25c475e7dd
2026-05-28 12:12:37 +02:00
Ricardo Wurmus 4404ce011a gnu: r-genefilter: Update to 1.94.0.
* gnu/packages/bioconductor.scm (r-genefilter): Update to 1.94.0.
[native-inputs]: Add r-biocstyle.

Change-Id: I4b878bd22ecc24d05bd0fde89aec6309e19ec4c4
2026-05-28 12:12:37 +02:00
Ricardo Wurmus 9613e22caa gnu: r-gcptools: Update to 1.2.0.
* gnu/packages/bioconductor.scm (r-gcptools): Update to 1.2.0.

Change-Id: I3ff35f24706af1734c559c91715f94ac9a3455ba
2026-05-28 12:12:37 +02:00
Ricardo Wurmus 7cd8e44251 gnu: r-gage: Update to 2.62.0.
* gnu/packages/bioconductor.scm (r-gage): Update to 2.62.0.

Change-Id: Ibca65b38d028cd8455985b3aa510e02ef48e4b8e
2026-05-28 12:12:37 +02:00
Ricardo Wurmus b4c5ed39e4 gnu: r-fastseg: Update to 1.58.0.
* gnu/packages/bioconductor.scm (r-fastseg): Update to 1.58.0.

Change-Id: I211891d94ad0970e9eea100ae96c8d65651c4c2a
2026-05-28 12:12:36 +02:00
Ricardo Wurmus 54cfa4d161 gnu: r-epidish: Update to 2.28.0.
* gnu/packages/bioconductor.scm (r-epidish): Update to 2.28.0.
[propagated-inputs]: Add r-genefilter.

Change-Id: Icf86175abea5b24ec244a64978f4c14a8590d4fa
2026-05-28 12:12:36 +02:00
Ricardo Wurmus 66597b0ac4 gnu: r-ensembldb: Update to 2.36.0.
* gnu/packages/bioconductor.scm (r-ensembldb): Update to 2.36.0.

Change-Id: Id58a311bbfed154731dfd2ff1e6b248cbfda0147
2026-05-28 12:12:36 +02:00
Ricardo Wurmus 2651f1edfa gnu: r-enmix: Update to 1.48.0.
* gnu/packages/bioconductor.scm (r-enmix): Update to 1.48.0.

Change-Id: Ibb91b7c10c03aed0ed5c377380c8c841de7203e1
2026-05-28 12:12:36 +02:00
Ricardo Wurmus 2e12bb67ab gnu: r-enhancedvolcano: Update to 1.30.0.
* gnu/packages/bioconductor.scm (r-enhancedvolcano): Update to 1.30.0.

Change-Id: If8aaf8d567b245f734b949fb160fca12d331db22
2026-05-28 12:12:36 +02:00
Ricardo Wurmus c5491f1795 gnu: r-edger: Update to 4.10.0.
* gnu/packages/bioconductor.scm (r-edger): Update to 4.10.0.

Change-Id: Id6082776eb5c81600f396b52b4f1ea46c10ed2a9
2026-05-28 12:12:36 +02:00
Ricardo Wurmus fd68261bd3 gnu: r-edaseq: Update to 2.46.0.
* gnu/packages/bioconductor.scm (r-edaseq): Update to 2.46.0.

Change-Id: Id3a969a43019ca5b0bad356df35fcbe51e10834e
2026-05-28 12:12:36 +02:00
Ricardo Wurmus e6b676a8ba gnu: r-dittoseq: Update to 1.24.0.
* gnu/packages/bioconductor.scm (r-dittoseq): Update to 1.24.0.

Change-Id: I2ab05798ca3b5d55df854922242d19bd3881c175
2026-05-28 12:12:35 +02:00
Ricardo Wurmus 388def04d4 gnu: r-dirichletmultinomial: Update to 1.54.0.
* gnu/packages/bioconductor.scm (r-dirichletmultinomial): Update to 1.54.0.

Change-Id: If91ff92ff4733c39414d07dce8d721a7d6ef4586
2026-05-28 12:12:35 +02:00
Ricardo Wurmus badcf4065a gnu: r-diffcyt: Update to 1.32.0.
* gnu/packages/bioconductor.scm (r-diffcyt): Update to 1.32.0.

Change-Id: If067405666ead6dafa029fb9e1d5d58dbcf1f965
2026-05-28 12:12:35 +02:00
Ricardo Wurmus c8caa2e64c gnu: r-dexseq: Update to 1.58.0.
* gnu/packages/bioconductor.scm (r-dexseq): Update to 1.58.0.
[propagated-inputs]: Remove r-rcolorbrewer.

Change-Id: Id1434b90286e75c494c4da08b2a3d4c67713edff
2026-05-28 12:12:35 +02:00
Ricardo Wurmus bc8c6a3b88 gnu: r-deseq2: Update to 1.52.0.
* gnu/packages/bioconductor.scm (r-deseq2): Update to 1.52.0.

Change-Id: I0f426a081b5ff48624400dd3f517ab58000a4252
2026-05-28 12:12:35 +02:00
Ricardo Wurmus c8c95988e7 gnu: r-complexheatmap: Update to 2.28.0.
* gnu/packages/bioconductor.scm (r-complexheatmap): Update to 2.28.0.

Change-Id: If8ee31f2f7feabf42f016f7498114fce5d0a31a7
2026-05-28 12:12:35 +02:00
Ricardo Wurmus 02fdbc8cf0 gnu: r-chipseq: Update to 1.62.0.
* gnu/packages/bioconductor.scm (r-chipseq): Update to 1.62.0.

Change-Id: Ia79716cc3b6c073bcf9552e6e0ad23abf699aadf
2026-05-28 12:12:35 +02:00
Ricardo Wurmus db27abc9d7 gnu: r-chipseeker: Update to 1.48.0.
* gnu/packages/bioconductor.scm (r-chipseeker): Update to 1.48.0.

Change-Id: Ib12520c5426643ab95fa597bf8d66229f406ad47
2026-05-28 12:12:35 +02:00
Ricardo Wurmus 4e31fcde4f gnu: r-champ: Update to 2.42.0.
* gnu/packages/bioconductor.scm (r-champ): Update to 2.42.0.

Change-Id: Ia5288df56e0e03d624d7613efc543c2c8ef0075f
2026-05-28 12:12:34 +02:00
Ricardo Wurmus 957a3a38cb gnu: r-category: Update to 2.78.0.
* gnu/packages/bioconductor.scm (r-category): Update to 2.78.0.

Change-Id: I692afa9142868b187211480daf7304cb4c79c79f
2026-05-28 12:12:34 +02:00
Ricardo Wurmus 448e715da4 gnu: r-bsgenome: Update to 1.80.0.
* gnu/packages/bioconductor.scm (r-bsgenome): Update to 1.80.0.

Change-Id: I0bd7f241f5f6b3ad51217597f37ffafb24cdbd00
2026-05-28 12:12:34 +02:00
Ricardo Wurmus 8812f6fb1d gnu: r-biovizbase: Update to 1.60.0.
* gnu/packages/bioconductor.scm (r-biovizbase): Update to 1.60.0.

Change-Id: I85610bed6b86b8390ffcad9bad7d424553fdb86c
2026-05-28 12:12:34 +02:00
Ricardo Wurmus 468dbd141f gnu: r-biostrings: Update to 2.80.0.
* gnu/packages/bioconductor.scm (r-biostrings): Update to 2.80.0.

Change-Id: I4e63151f057a23b8d8fe4c5bd10fa1c63a13058b
2026-05-28 12:12:34 +02:00
Ricardo Wurmus b0433e86d8 gnu: r-biocparallel: Update to 1.45.0.
* gnu/packages/bioconductor.scm (r-biocparallel): Update to 1.45.0.

Change-Id: I92bfa27982c5d1d1a38b1b41f836ec0a5f331691
2026-05-28 12:12:34 +02:00
Ricardo Wurmus 0c3e31e005 gnu: r-biomart: Update to 2.68.0.
* gnu/packages/bioconductor.scm (r-biomart): Update to 2.68.0.
[native-inputs]: Add r-withr.

Change-Id: I7cc6912d2f3b502989ad6086ac345ac3f4e293a6
2026-05-28 12:12:34 +02:00
Ricardo Wurmus 5fb654afbe gnu: r-biobase: Update to 2.72.0.
* gnu/packages/bioconductor.scm (r-biobase): Update to 2.72.0.
[native-inputs]: Add r-biocmanager.

Change-Id: I1c2b9d7c4275dd7cbe3807d6274565cc5e159349
2026-05-28 12:12:33 +02:00
Ricardo Wurmus 00677d2bff gnu: r-bamsignals: Update to 1.43.0.
* gnu/packages/bioconductor.scm (r-bamsignals): Update to 1.43.0.

Change-Id: I580b32b67da7d06200a0c016b7f4bc928408798a
2026-05-28 12:12:33 +02:00
Ricardo Wurmus 6f6d1d4dbb gnu: r-aroma-light: Update to 3.42.0.
* gnu/packages/bioconductor.scm (r-aroma-light): Update to 3.42.0.

Change-Id: Ife7e0fe7a2e8aaf723535d39660399af88d6b656
2026-05-28 12:12:33 +02:00
Ricardo Wurmus 1b42bf2804 gnu: r-annotationhub: Update to 4.2.0.
* gnu/packages/bioconductor.scm (r-annotationhub): Update to 4.2.0.

Change-Id: I9a2283b9982f3ad77ff2e734b7a433de8bb10358
2026-05-28 12:12:33 +02:00
Ricardo Wurmus 7b23610da3 gnu: r-annotationforge: Update to 1.54.0.
* gnu/packages/bioconductor.scm (r-annotationforge): Update to 1.54.0.
[native-inputs]: Add r-biocfilecache and r-biocstyle.

Change-Id: If35cb5a1356f8ac3d501fadbf293e39806e053f6
2026-05-28 12:12:33 +02:00
Ricardo Wurmus 7b10378e32 gnu: r-annotationfilter: Update to 1.36.0.
* gnu/packages/bioconductor.scm (r-annotationfilter): Update to 1.36.0.

Change-Id: I10270e59635008a3c220683f8a8b7dab3ded3676
2026-05-28 12:12:33 +02:00
Ricardo Wurmus 46f96855cf gnu: r-annotationdbi: Update to 1.74.0.
* gnu/packages/bioconductor.scm (r-annotationdbi): Update to 1.74.0.
[native-inputs]: Add r-biocstyle.

Change-Id: If24be7c23f4efd94990e08fb4b3918bf1ca578c9
2026-05-28 12:12:33 +02:00
Ricardo Wurmus fcbc8730d1 gnu: r-annotate: Update to 1.90.0.
* gnu/packages/bioconductor.scm (r-annotate): Update to 1.90.0.

Change-Id: I061eef0d507dfaf1a026baf335ebfe24f297d609
2026-05-28 12:12:33 +02:00
Ricardo Wurmus b8edc41954 gnu: r-affxparser: Update to 1.84.0.
* gnu/packages/bioconductor.scm (r-affxparser): Update to 1.84.0.

Change-Id: Idb9b1082f546c79abea0328d4f572b29061dc9ac
2026-05-28 12:12:32 +02:00
Ricardo Wurmus b8188fd204 gnu: r-affyio: Update to 1.82.0.
* gnu/packages/bioconductor.scm (r-affyio): Update to 1.82.0.

Change-Id: I24981f23fa305af2ae3c0f1985fe2b281897fd06
2026-05-28 12:12:32 +02:00
Ricardo Wurmus 2da200b31e gnu: r-affycontam: Update to 1.70.0.
* gnu/packages/bioconductor.scm (r-affycontam): Update to 1.70.0.

Change-Id: I85a23408ee9f6e4d48fae566ae116e3b02bf1e1c
2026-05-28 12:12:32 +02:00
Ricardo Wurmus 13b5078030 gnu: r-affycomp: Update to 1.88.0.
* gnu/packages/bioconductor.scm (r-affycomp): Update to 1.88.0.

Change-Id: I2a090db8c6e63f241973eb7108cfca3e51d91577
2026-05-28 12:12:32 +02:00
Ricardo Wurmus bbfec31bec gnu: r-affy: Update to 1.90.0.
* gnu/packages/bioconductor.scm (r-affy): Update to 1.90.0.

Change-Id: Ic9bede0cd8e3de513c5b1066efd518cf82ec6ae1
2026-05-28 12:12:32 +02:00
Ricardo Wurmus fbd396072b gnu: r-nebulosa: Update to 1.22.0.
* gnu/packages/bioconductor.scm (r-nebulosa): Update to 1.22.0.

Change-Id: I7c6256e1b1d5dde17304e0e63d2c57005605a552
2026-05-28 12:12:32 +02:00
Ricardo Wurmus a3250a67a7 gnu: r-italics: Update to 2.72.0.
* gnu/packages/bioconductor.scm (r-italics): Update to 2.72.0.

Change-Id: Iefd52d7343c720400eb3a4441fcb1fc0267be2ab
2026-05-28 12:12:32 +02:00
Ricardo Wurmus 23225793d8 gnu: r-isoformswitchanalyzer: Update to 2.12.0.
* gnu/packages/bioconductor.scm (r-isoformswitchanalyzer): Update to 2.12.0.

Change-Id: I1c5e8fd57e073f2c810e13c57d9f4e3e30aaf357
2026-05-28 12:12:31 +02:00
Ricardo Wurmus 974d7148c8 gnu: r-iranges: Update to 2.46.0.
* gnu/packages/bioconductor.scm (r-iranges): Update to 2.46.0.

Change-Id: Ic4a74bd08d89738cbba63f3bc439a9c5991f4d29
2026-05-28 12:12:31 +02:00
Ricardo Wurmus f47376c6aa gnu: r-infercnv: Update to 1.28.0.
* gnu/packages/bioconductor.scm (r-infercnv): Update to 1.28.0.

Change-Id: Ie13deea245c5157a691576283060563d84ae3353
2026-05-28 12:12:31 +02:00
Ricardo Wurmus 49c56b2414 gnu: r-immreferent: Update to 1.0.0.
* gnu/packages/bioconductor.scm (r-immreferent): Update to 1.0.0.

Change-Id: Ib27515cadf7e2e6912d09a2b770e3c77ee7a39c0
2026-05-28 12:12:31 +02:00
Ricardo Wurmus a5dd3ff7f9 gnu: r-immapex: Update to 1.6.0.
* gnu/packages/bioconductor.scm (r-immapex): Update to 1.6.0.

Change-Id: I477776856c7305b941e2aea91e0f229b46d694ec
2026-05-28 12:12:31 +02:00
Ricardo Wurmus 803a7c57d9 gnu: r-ideoviz: Update to 1.48.0.
* gnu/packages/bioconductor.scm (r-ideoviz): Update to 1.48.0.

Change-Id: I0a9af1f6409484e46017ce5f86939e6e5af8602b
2026-05-28 12:12:31 +02:00
Ricardo Wurmus af138339f1 gnu: r-bluster: Update to 1.22.0.
* gnu/packages/bioconductor.scm (r-bluster): Update to 1.22.0.

Change-Id: I4507c9c518a2460d55616ac0fe4d7af3e13fce09
2026-05-28 12:12:31 +02:00
Ricardo Wurmus fe931d37ba gnu: r-escape: Update to 2.8.0.
* gnu/packages/bioconductor.scm (r-escape): Update to 2.8.0.

Change-Id: Iabc23768b6c72ee90e60b8416f28f062fe3899a6
2026-05-28 12:12:31 +02:00
Ricardo Wurmus 834fc0723a gnu: r-dyndoc: Update to 1.90.0.
* gnu/packages/bioconductor.scm (r-dyndoc): Update to 1.90.0.

Change-Id: Ieeccc39cacab5327c88d35fc4ea4b4cc45bfed17
2026-05-28 12:12:30 +02:00
Ricardo Wurmus 26799ea10d gnu: r-dss: Update to 2.60.0.
* gnu/packages/bioconductor.scm (r-dss): Update to 2.60.0.

Change-Id: Ib53717c46d13c74badb8ca911b8fe392d151bffd
2026-05-28 12:12:30 +02:00
Ricardo Wurmus 4ab649f308 gnu: r-dropletutils: Update to 1.32.0.
* gnu/packages/bioconductor.scm (r-dropletutils): Update to 1.32.0.

Change-Id: I8e4765f8a71efd1c4ef09e5117e49f7689d9b761
2026-05-28 12:12:30 +02:00
Ricardo Wurmus 554e9aa345 gnu: r-drimseq: Update to 1.40.0.
* gnu/packages/bioconductor.scm (r-drimseq): Update to 1.40.0.
[native-inputs]: Add r-biocstyle.

Change-Id: I5d310495c560de1a046b204d51d663631b9685a6
2026-05-28 12:12:30 +02:00
Ricardo Wurmus 8bc235df82 gnu: r-dmrcate: Update to 3.7.0.
* gnu/packages/bioconductor.scm (r-dmrcate): Update to 3.7.0.
[native-inputs]: Add r-biocmanager.

Change-Id: Ib4654c5dba796c42955f4fa2487e39e9c560a306
2026-05-28 12:12:30 +02:00
Ricardo Wurmus 31d20af3d8 gnu: r-derfinderhelper: Update to 1.46.0.
* gnu/packages/bioconductor.scm (r-derfinderhelper): Update to 1.46.0.

Change-Id: Ic6c985f09d8623c3da83acf1bf853652a43e0ce6
2026-05-28 12:12:30 +02:00
Ricardo Wurmus c58c34ce9f gnu: r-derfinder: Update to 1.46.0.
* gnu/packages/bioconductor.scm (r-derfinder): Update to 1.46.0.

Change-Id: Ic76dbc5eb4fa5d87d5b966c3b88cdca9cdc0bf56
2026-05-28 12:12:30 +02:00
Ricardo Wurmus 1110a2d53f gnu: r-densvis: Update to 1.22.0.
* gnu/packages/bioconductor.scm (r-densvis): Update to 1.22.0.

Change-Id: I65145d217afc6f8bb394136d2e1e3d8caa48a9d4
2026-05-28 12:12:30 +02:00
Ricardo Wurmus ecce4bbaaf gnu: r-delayedarray: Update to 0.38.0.
* gnu/packages/bioconductor.scm (r-delayedarray): Update to 0.38.0.

Change-Id: Ic600563c33ec25eeee4cc4f8fd6d61a7949f8711
2026-05-28 12:12:29 +02:00
Ricardo Wurmus 1fcbe2bd6c gnu: r-degreport: Update to 1.48.0.
* gnu/packages/bioconductor.scm (r-degreport): Update to 1.48.0.

Change-Id: I98c74e6c3e7fe16cf5e290e9f072a8a88012e5fe
2026-05-28 12:12:29 +02:00
Ricardo Wurmus b0ac0bc735 gnu: r-deepsnv: Update to 1.58.0.
* gnu/packages/bioconductor.scm (r-deepsnv): Update to 1.58.0.

Change-Id: Idd739e14f6ed6bdd2d459c0653eb3f67185093c8
2026-05-28 12:12:29 +02:00
Ricardo Wurmus 007b7c31fb gnu: r-deconvr: Update to 1.18.0.
* gnu/packages/bioconductor.scm (r-deconvr): Update to 1.18.0.

Change-Id: I93cf57f4ba7b4cb13e0a73eddd32c00896fffb89
2026-05-28 12:12:29 +02:00
Ricardo Wurmus 0566a31513 gnu: r-decontam: Update to 1.32.0.
* gnu/packages/bioconductor.scm (r-decontam): Update to 1.32.0.

Change-Id: I659f833b26f27d76a4f8db032b37ec9f10151713
2026-05-28 12:12:29 +02:00
Ricardo Wurmus 5c01d1ee2d gnu: r-decomptumor2sig: Update to 2.28.0.
* gnu/packages/bioconductor.scm (r-decomptumor2sig): Update to 2.28.0.

Change-Id: I7a117da1503bca8aedc431dfb0abe6040c357415
2026-05-28 12:12:29 +02:00
Ricardo Wurmus cfcbcb061f gnu: r-decipher: Update to 3.8.0.
* gnu/packages/bioconductor.scm (r-decipher): Update to 3.8.0.

Change-Id: If8c355190fed789a23a4caa8d968ebe4a7244b64
2026-05-28 12:12:29 +02:00
Ricardo Wurmus eee0d4b52a gnu: r-dearseq: Update to 1.24.0.
* gnu/packages/bioconductor.scm (r-dearseq): Update to 1.24.0.

Change-Id: I3b4adfb4d61df164db4a383d961c48bd322edcb0
2026-05-28 12:12:29 +02:00
Ricardo Wurmus 172038e10e gnu: r-damefinder: Update to 1.24.0.
* gnu/packages/bioconductor.scm (r-damefinder): Update to 1.24.0.

Change-Id: Ic6df599989e7652bcd4d8658648625d16bb7bd55
2026-05-28 12:12:28 +02:00
Ricardo Wurmus bf32c26813 gnu: r-dama: Update to 1.84.0.
* gnu/packages/bioconductor.scm (r-dama): Update to 1.84.0.

Change-Id: I2f2ba97de23627bf01f0a3828330325cd540f30d
2026-05-28 12:12:28 +02:00
Ricardo Wurmus 3748b81510 gnu: r-csaw: Update to 1.46.0.
* gnu/packages/bioconductor.scm (r-csaw): Update to 1.46.0.

Change-Id: I36326bda4fff82ad4599f332ac9361bcba0af3ab
2026-05-28 12:12:28 +02:00
Ricardo Wurmus 5785757160 gnu: r-coverageview: Update to 1.50.0.
* gnu/packages/bioconductor.scm (r-coverageview): Update to 1.50.0.

Change-Id: I90ce68655c23e6fe39978e40f115ecced1d8f0ca
2026-05-28 12:12:28 +02:00
Ricardo Wurmus 4dc258dc5c gnu: r-coregx: Update to 2.16.0.
* gnu/packages/bioconductor.scm (r-coregx): Update to 2.16.0.

Change-Id: I6a0f43f92c1b77cb229c06c79b0eec7ae7c82ba5
2026-05-28 12:12:28 +02:00
Ricardo Wurmus bf25bf22bb gnu: r-convert: Update to 1.88.0.
* gnu/packages/bioconductor.scm (r-convert): Update to 1.88.0.

Change-Id: I7ae2eaf2da6fef566142c77f49edab1a7f2d726b
2026-05-28 12:12:28 +02:00
Ricardo Wurmus 04e49318d0 gnu: r-cigarillo: Update to 1.2.0.
* gnu/packages/bioconductor.scm (r-cigarillo): Update to 1.2.0.

Change-Id: I1062bf18a29d3375aaca5423f712255d6f108e0b
2026-05-28 12:12:27 +02:00
Ricardo Wurmus 3b57c4c2b5 gnu: r-chihaya: Update to 1.12.0.
* gnu/packages/bioconductor.scm (r-chihaya): Update to 1.12.0.

Change-Id: I56ebb38a4a4a7cac573e88215da831f21a122efb
2026-05-28 12:12:27 +02:00
Ricardo Wurmus ddce837e3e gnu: r-cellid: Update to 1.19.0.
* gnu/packages/bioconductor.scm (r-cellid): Update to 1.19.0.

Change-Id: Ia408222e9489331f53ec496d928e87074343ea54
2026-05-28 12:12:27 +02:00
Ricardo Wurmus 88d68fba02 gnu: r-ccfindr: Update to 1.32.0.
* gnu/packages/bioconductor.scm (r-ccfindr): Update to 1.32.0.

Change-Id: Ibf3e87999a8b9544d0f792cf37a4e521eecb8bc6
2026-05-28 12:12:27 +02:00
Ricardo Wurmus cf3620ea4d gnu: r-cardelino: Update to 1.14.0.
* gnu/packages/bioconductor.scm (r-cardelino): Update to 1.14.0.

Change-Id: I73b733a3013bc24241ad79d4647c7904796ce6ba
2026-05-28 12:12:27 +02:00
Ricardo Wurmus fc58401762 gnu: r-breakpointr: Update to 1.30.0.
* gnu/packages/bioconductor.scm (r-breakpointr): Update to 1.30.0.
[native-inputs]: Add r-biocstyle.

Change-Id: Ibfb391525c6ae0c110195cd7d524b7082afa44cf
2026-05-28 12:12:27 +02:00
Ricardo Wurmus c611d83df6 gnu: r-biocgenerics: Update to 0.58.0.
* gnu/packages/bioconductor.scm (r-biocgenerics): Update to 0.58.0.

Change-Id: I41c378b898f877ed2ebdb287865b292404b9f007
2026-05-28 12:12:27 +02:00
Ricardo Wurmus 77b7707bb1 gnu: r-biocversion: Update to 3.23.1.
* gnu/packages/bioconductor.scm (r-biocversion): Update to 3.23.1.

Change-Id: Icf93c7207a9ce9139e03548caec0347dd653b16b
2026-05-28 12:12:27 +02:00
Ricardo Wurmus 2245ec7fe7 gnu: r-biocmake: Update to 1.4.0.
* gnu/packages/bioconductor.scm (r-biocmake): Update to 1.4.0.

Change-Id: Ic8c7974cd2720f5f2c7e31c594265b9b7f9b7534
2026-05-28 12:12:26 +02:00
Ricardo Wurmus a5dd8bdc78 gnu: r-banocc: Update to 1.35.0.
* gnu/packages/bioconductor.scm (r-banocc): Update to 1.35.0.

Change-Id: Id3f388ebb061fdc3c71903c770c0d5fd1abe6d5e
2026-05-28 12:12:26 +02:00
Ricardo Wurmus 44ef749bea gnu: r-bandits: Update to 1.28.0.
* gnu/packages/bioconductor.scm (r-bandits): Update to 1.28.0.

Change-Id: I14a577b40dca247b69ec71a50e92b178999d8eb1
2026-05-28 12:12:26 +02:00
Ricardo Wurmus fdeaa3f33c gnu: r-bambu: Update to 3.14.0.
* gnu/packages/bioconductor.scm (r-bambu): Update to 3.14.0.

Change-Id: I933ed11ef36f0bb4245b660f69f787bead4a492b
2026-05-28 12:12:26 +02:00
Ricardo Wurmus 785d0aa787 gnu: r-badregionfinder: Update to 1.39.0.
* gnu/packages/bioconductor.scm (r-badregionfinder): Update to 1.39.0.

Change-Id: Idb738f5ac2b2824862d45e5c00ec6a0ce84f231d
2026-05-28 12:12:26 +02:00
Ricardo Wurmus 4196fd505c gnu: r-bader: Update to 1.50.0.
* gnu/packages/bioconductor.scm (r-bader): Update to 1.50.0.

Change-Id: I358927a78dcce727c481f96ea82be783ebe638b0
2026-05-28 12:12:26 +02:00
Ricardo Wurmus 7611fcd7c2 gnu: r-basespacer: Update to 1.55.0.
* gnu/packages/bioconductor.scm (r-basespacer): Update to 1.55.0.

Change-Id: I67d58052f427ec2987e53b366833a3ad11c9f0eb
2026-05-28 12:12:26 +02:00
Ricardo Wurmus 0d7a2bd272 gnu: r-bags: Update to 2.51.0.
* gnu/packages/bioconductor.scm (r-bags): Update to 2.51.0.

Change-Id: Ia129c73b74b6ab3c20127874d32d64d1c1498c46
2026-05-28 12:12:26 +02:00
Ricardo Wurmus cb94e62717 gnu: r-baalchip: Update to 1.37.0.
* gnu/packages/bioconductor.scm (r-baalchip): Update to 1.37.0.

Change-Id: I6e519a66e440c99077bb1f725c2a31abddab71f8
2026-05-28 12:12:25 +02:00
Ricardo Wurmus 3468110c5f gnu: r-awst: Update to 1.19.0.
* gnu/packages/bioconductor.scm (r-awst): Update to 1.19.0.

Change-Id: I8585304e332760a5b8fdb17fe549cf40258f10e1
2026-05-28 12:12:25 +02:00
Ricardo Wurmus b465b1fb81 gnu: r-awfisher: Update to 1.26.0.
* gnu/packages/bioconductor.scm (r-awfisher): Update to 1.26.0.

Change-Id: I96bafcfc714bb21e00b51445072597fffadc71b9
2026-05-28 12:12:25 +02:00
Ricardo Wurmus 0a7bcafa51 gnu: r-attract: Update to 1.64.0.
* gnu/packages/bioconductor.scm (r-attract): Update to 1.64.0.

Change-Id: I9c3bca1cd85f2439a5c6586b14873a7192aa0ec0
2026-05-28 12:12:25 +02:00
Ricardo Wurmus fddb7d2727 gnu: r-atsnp: Update to 1.27.0.
* gnu/packages/bioconductor.scm (r-atsnp): Update to 1.27.0.

Change-Id: I9301f7376c5995f4098970f59aae821ef645f782
2026-05-28 12:12:25 +02:00
Ricardo Wurmus da41b1d115 gnu: r-atena: Update to 1.18.0.
* gnu/packages/bioconductor.scm (r-atena): Update to 1.18.0.

Change-Id: If4ed6374a1ab02f7978a851d893bbd2a2456109c
2026-05-28 12:12:25 +02:00
Ricardo Wurmus e445919a6c gnu: r-assorthead: Update to 1.6.0.
* gnu/packages/bioconductor.scm (r-assorthead): Update to 1.6.0.

Change-Id: I22eea70d50a53e450cc1e612b717fd3c4bfe114c
2026-05-28 12:12:25 +02:00
Ricardo Wurmus 1b7b6678b8 gnu: r-asset: Update to 2.30.0.
* gnu/packages/bioconductor.scm (r-asset): Update to 2.30.0.

Change-Id: I04158ec5902d411d6626b7399dfd38cac9cd5b43
2026-05-28 12:12:25 +02:00
Ricardo Wurmus 7f52a20ec7 gnu: r-assessorf: Update to 1.30.0.
* gnu/packages/bioconductor.scm (r-assessorf): Update to 1.30.0.

Change-Id: I415715cd6c7a549dc008ffd0fa8c5b2cc1859c8e
2026-05-28 12:12:24 +02:00
Ricardo Wurmus 43cfb5beb6 gnu: r-aspli: Update to 2.22.0.
* gnu/packages/bioconductor.scm (r-aspli): Update to 2.22.0.

Change-Id: I020c5308e90f7e799845e33bbd6a245453604557
2026-05-28 12:12:24 +02:00
Ricardo Wurmus c42616ff06 gnu: r-asics: Update to 2.28.0.
* gnu/packages/bioconductor.scm (r-asics): Update to 2.28.0.

Change-Id: If8944f947b884a424287c74f3a68fcc75d160a09
2026-05-28 12:12:24 +02:00
Ricardo Wurmus 7a400155a9 gnu: r-asgsca: Update to 1.46.0.
* gnu/packages/bioconductor.scm (r-asgsca): Update to 1.46.0.

Change-Id: Ic022a519d521bcd8c93feef9671a68800c2aa4a3
2026-05-28 12:12:24 +02:00
Ricardo Wurmus 57cba833d4 gnu: r-aseb: Update to 1.56.0.
* gnu/packages/bioconductor.scm (r-aseb): Update to 1.56.0.

Change-Id: Ia60496fb7ff0a6a88401e604777179a3b724b901
2026-05-28 12:12:24 +02:00
Ricardo Wurmus 6dd7ddeb0b gnu: r-asafe: Update to 1.38.0.
* gnu/packages/bioconductor.scm (r-asafe): Update to 1.38.0.

Change-Id: I5bea5eb7b878d4583f6a35a5e375308ace4b3550
2026-05-28 12:12:24 +02:00
Ricardo Wurmus 6b4e414a11 gnu: r-arrayquality: Update to 1.90.0.
* gnu/packages/bioconductor.scm (r-arrayquality): Update to 1.90.0.

Change-Id: I515d07fe5fb1f2317c32e5507dabba2505d7b305
2026-05-28 12:12:24 +02:00
Ricardo Wurmus 51bded5dec gnu: r-arraymvout: Update to 1.70.0.
* gnu/packages/bioconductor.scm (r-arraymvout): Update to 1.70.0.

Change-Id: I39a3b55f2dc4c3724532a199b509cecd8e820945
2026-05-28 12:12:24 +02:00
Ricardo Wurmus 3cb6b06cec gnu: r-arrayqualitymetrics: Update to 3.68.0.
* gnu/packages/bioconductor.scm (r-arrayqualitymetrics): Update to 3.68.0.
[propagated-inputs]: Add r-jsonlite.
[native-inputs]: Remove r-biocstyle.

Change-Id: I3d588dc78c091eb12cc64ed67e92d5f38141889b
2026-05-28 12:12:23 +02:00
Ricardo Wurmus e885e0459c gnu: r-arrayexpress: Update to 1.72.0.
* gnu/packages/bioconductor.scm (r-arrayexpress): Update to 1.72.0.

Change-Id: Ie9482b5ad035df6f05c925b41fc449c6ad20fd13
2026-05-28 12:12:23 +02:00
Ricardo Wurmus e30df20dc9 gnu: r-antiprofiles: Update to 1.52.0.
* gnu/packages/bioconductor.scm (r-antiprofiles): Update to 1.52.0.

Change-Id: Ic338000054a7fa2471d654c7f3e20faee2fbcf36
2026-05-28 12:12:23 +02:00
Ricardo Wurmus f1bffe6c48 gnu: r-annmap: Update to 1.54.0.
* gnu/packages/bioconductor.scm (r-annmap): Update to 1.54.0.

Change-Id: Ie4f84f6b8c617e962813a371d7bb878cc84f5f96
2026-05-28 12:12:23 +02:00
Ricardo Wurmus 040abd305f gnu: r-anf: Update to 1.34.0.
* gnu/packages/bioconductor.scm (r-anf): Update to 1.34.0.

Change-Id: I7160b1151332b9e230b03417aa01ce0d397812c9
2026-05-28 12:12:23 +02:00
Ricardo Wurmus ee4314caa3 gnu: r-altcdfenvs: Update to 2.74.0.
* gnu/packages/bioconductor.scm (r-altcdfenvs): Update to 2.74.0.

Change-Id: Ie9a2796f802a6f0a3390d6842b922e7a99fb6bf5
2026-05-28 12:12:23 +02:00
Ricardo Wurmus 60c4dfe38d gnu: r-alpsnmr: Update to 4.14.0.
* gnu/packages/bioconductor.scm (r-alpsnmr): Update to 4.14.0.

Change-Id: I0265e448562f2c962f2e90bf2907d79b1c64148e
2026-05-28 12:12:23 +02:00
Ricardo Wurmus e6d7b46888 gnu: r-alphabeta: Update to 1.26.0.
* gnu/packages/bioconductor.scm (r-alphabeta): Update to 1.26.0.

Change-Id: I316ae020dc0ab0458967bdc2bf4f6055aa62f026
2026-05-28 12:12:23 +02:00
Ricardo Wurmus b218b9faeb gnu: r-alevinqc: Update to 1.28.0.
* gnu/packages/bioconductor.scm (r-alevinqc): Update to 1.28.0.

Change-Id: Ic962718fe5b2d908872fb4e6c10ba29052ffd950
2026-05-28 12:12:22 +02:00
Ricardo Wurmus 4784a57f2a gnu: r-aldex2: Update to 1.44.0.
* gnu/packages/bioconductor.scm (r-aldex2): Update to 1.44.0.

Change-Id: I3d9e53a54564511966b437603c681091c11849e6
2026-05-28 12:12:22 +02:00
Ricardo Wurmus 569f6719ee gnu: r-anvilgcp: Update to 1.6.0.
* gnu/packages/bioconductor.scm (r-anvilgcp): Update to 1.6.0.

Change-Id: I3559a37fa9a49ede93dcff8c5d51b85cd4078412
2026-05-28 12:12:22 +02:00
Ricardo Wurmus 780d8ff2c2 gnu: r-anvilbase: Update to 1.6.0.
* gnu/packages/bioconductor.scm (r-anvilbase): Update to 1.6.0.

Change-Id: I3a821ea67b4d74f698b86182db90e37164a14a10
2026-05-28 12:12:22 +02:00
Ricardo Wurmus 1ea6a295a0 gnu: r-anvil: Update to 1.23.12.
* gnu/packages/bioconductor.scm (r-anvil): Update to 1.23.12.
[propagated-inputs]: Add r-digest and r-keyring.

Change-Id: I8e2b8dc5014ccf50c28ceb7d45eb5f0f87f49f7c
2026-05-28 12:12:22 +02:00
Ricardo Wurmus 3b582d34e4 gnu: r-annotationhubdata: Update to 1.42.0.
* gnu/packages/bioconductor.scm (r-annotationhubdata): Update to 1.42.0.

Change-Id: I801bcf2fee5e6aac8773e33387d0a32c175f7f7f
2026-05-28 12:12:22 +02:00
Ricardo Wurmus dccc67ff7a gnu: r-anndatar: Update to 1.1.3.
* gnu/packages/bioconductor.scm (r-anndatar): Update to 1.1.3.
[native-inputs]: Add r-rarr.

Change-Id: If21f49639bbd388aee0abfdb52e18a1f01a92635
2026-05-28 12:12:22 +02:00
Ricardo Wurmus 3f9cd984ef gnu: r-animalcules: Update to 1.28.0.
* gnu/packages/bioconductor.scm (r-animalcules): Update to 1.28.0.

Change-Id: Id472a096557d1c3e243bcb689e5af332cf90ddb5
2026-05-28 12:12:22 +02:00
Ricardo Wurmus aca5930213 gnu: r-ancombc: Update to 2.14.0.
* gnu/packages/bioconductor.scm (r-ancombc): Update to 2.14.0.
[propagated-inputs]: Remove r-cvxr; add r-quadprog.

Change-Id: Ibf4ac30fe71a7555238749871b749228076e3b8e
2026-05-28 12:12:21 +02:00
Ricardo Wurmus acba911f0c gnu: r-anaquin: Update to 2.36.0.
* gnu/packages/bioconductor.scm (r-anaquin): Update to 2.36.0.

Change-Id: Ie0271e3e2a03a045b98d089037c2a47309187c6e
2026-05-28 12:12:21 +02:00
Ricardo Wurmus 5dada9be6b gnu: r-amaretto: Update to 1.28.0.
* gnu/packages/bioconductor.scm (r-amaretto): Update to 1.28.0.

Change-Id: I2374172e5e0258a630d8de4087b6f1574a1967bc
2026-05-28 12:12:21 +02:00
Ricardo Wurmus 6999b3994a gnu: r-amplican: Update to 1.34.0.
* gnu/packages/bioconductor.scm (r-amplican): Update to 1.34.0.
[propagated-inputs]: Remove r-dplyr; add r-rlang.

Change-Id: I700d1893804951488c7aaaae80a0d769ca215c74
2026-05-28 12:12:21 +02:00
Ricardo Wurmus aec3dfc362 gnu: r-amountain: Update to 1.38.0.
* gnu/packages/bioconductor.scm (r-amountain): Update to 1.38.0.

Change-Id: I720609d875647d43caf46a8d9703a98c0f5d1fae
2026-05-28 12:12:21 +02:00
Ricardo Wurmus dbaaa1562c gnu: r-alabaster-se: Update to 1.12.0.
* gnu/packages/bioconductor.scm (r-alabaster-se): Update to 1.12.0.

Change-Id: If05684691b1efaf8729ce1c270be28d56f8f5b2a
2026-05-28 12:12:21 +02:00
Ricardo Wurmus d0bee36b5b gnu: r-alabaster-schemas: Update to 1.12.0.
* gnu/packages/bioconductor.scm (r-alabaster-schemas): Update to 1.12.0.

Change-Id: Ib2a5ca2a0c2a68be48ddf5da949ebc6731b23b6d
2026-05-28 12:12:21 +02:00
Ricardo Wurmus 92c9384844 gnu: r-alabaster-sce: Update to 1.12.0.
* gnu/packages/bioconductor.scm (r-alabaster-sce): Update to 1.12.0.

Change-Id: I79271590b0028bb612575cd348397c0e7a402c01
2026-05-28 12:12:21 +02:00
Ricardo Wurmus f48e11e613 gnu: r-alabaster-ranges: Update to 1.12.0.
* gnu/packages/bioconductor.scm (r-alabaster-ranges): Update to 1.12.0.

Change-Id: Iab66eb6f58541ddb1ddce6bdce2116a0df5fac48
2026-05-28 12:12:20 +02:00
Ricardo Wurmus f7c2d2a2be gnu: r-alabaster-matrix: Update to 1.12.0.
* gnu/packages/bioconductor.scm (r-alabaster-matrix): Update to 1.12.0.

Change-Id: Ic896ff156076cda83231ab05f7a27319df0387a7
2026-05-28 12:12:20 +02:00
Ricardo Wurmus b1f5bd30d7 gnu: r-alabaster-base: Update to 1.12.0.
* gnu/packages/bioconductor.scm (r-alabaster-base): Update to 1.12.0.

Change-Id: I74733c2fc292053a6dd94e88c2006ef6b43c3484
2026-05-28 12:12:20 +02:00
Ricardo Wurmus 206ea1fe40 gnu: r-airpart: Update to 1.20.0.
* gnu/packages/bioconductor.scm (r-airpart): Update to 1.20.0.

Change-Id: I1a4ad603b26ab27ff4256ceb26caecd8e61ea0c4
2026-05-28 12:12:20 +02:00
Ricardo Wurmus e1b8ed38e2 gnu: r-aims: Update to 1.44.0.
* gnu/packages/bioconductor.scm (r-aims): Update to 1.44.0.

Change-Id: I80f68c2506fed3a21475c9d091748778d077042e
2026-05-28 12:12:20 +02:00
Ricardo Wurmus 3a67b3395a gnu: r-adductomicsr: Update to 1.27.0.
* gnu/packages/bioconductor.scm (r-adductomicsr): Update to 1.27.0.

Change-Id: I452b2ab088eb733946beefec0553bad06e7d4f2d
2026-05-28 12:12:20 +02:00
Ricardo Wurmus 7fe5381522 gnu: r-agilp: Update to 3.44.0.
* gnu/packages/bioconductor.scm (r-agilp): Update to 3.44.0.

Change-Id: I32b147c03e950e9fd24c06c48a1e571496bbf02c
2026-05-28 12:12:20 +02:00
Ricardo Wurmus 4da9fb78e7 gnu: r-aggregatebiovar: Update to 1.22.0.
* gnu/packages/bioconductor.scm (r-aggregatebiovar): Update to 1.22.0.

Change-Id: I79b6e9da53beee514da1aaa7d42aced559b2669e
2026-05-28 12:12:20 +02:00
Ricardo Wurmus 5353f69525 gnu: r-agdex: Update to 1.60.0.
* gnu/packages/bioconductor.scm (r-agdex): Update to 1.60.0.

Change-Id: I6cbd998169a1dcce32358190f91f069d6735b1f6
2026-05-28 12:12:19 +02:00
Ricardo Wurmus e40851173a gnu: r-affyrnadegradation: Update to 1.58.0.
* gnu/packages/bioconductor.scm (r-affyrnadegradation): Update to 1.58.0.

Change-Id: Idb23a327c813cbd08cdc86a0ee46e4df7127b0a3
2026-05-28 12:12:19 +02:00
Ricardo Wurmus 9af9723713 gnu: r-affyplm: Update to 1.88.0.
* gnu/packages/bioconductor.scm (r-affyplm): Update to 1.88.0.

Change-Id: I2f07b8e1ae034c95d5c924fceddf4dbfeb4a605b
2026-05-28 12:12:19 +02:00
Ricardo Wurmus fcc574a108 gnu: r-affylmgui: Update to 1.86.0.
* gnu/packages/bioconductor.scm (r-affylmgui): Update to 1.86.0.

Change-Id: Ibb33c86cd77ff054ee952360ea1d56c4f07a865b
2026-05-28 12:12:19 +02:00
Ricardo Wurmus da907b8389 gnu: r-affyilm: Update to 1.64.0.
* gnu/packages/bioconductor.scm (r-affyilm): Update to 1.64.0.

Change-Id: Ie1ddcaec1139a4c625919b8c410b03b3895a1b7a
2026-05-28 12:12:19 +02:00
Ricardo Wurmus 98ec3853ce gnu: r-affixcan: Update to 1.30.0.
* gnu/packages/bioconductor.scm (r-affixcan): Update to 1.30.0.

Change-Id: I91fb7314e6e92ca395ae3b070bc698df6fbdcea0
2026-05-28 12:12:19 +02:00
Ricardo Wurmus a8133ab467 gnu: r-adsplit: Update to 1.82.0.
* gnu/packages/bioconductor.scm (r-adsplit): Update to 1.82.0.

Change-Id: I3984eff74bb6f5d6fc8193b965d7eea02f73bf34
2026-05-28 12:12:19 +02:00
Ricardo Wurmus 7c9c23761c gnu: r-adimpute: Update to 1.22.0.
* gnu/packages/bioconductor.scm (r-adimpute): Update to 1.22.0.

Change-Id: Ib5c3a7a8498d47ea5384cf1d3286d4e4f0583083
2026-05-28 12:12:19 +02:00
Ricardo Wurmus a0535206c5 gnu: r-adamgui: Update to 1.28.0.
* gnu/packages/bioconductor.scm (r-adamgui): Update to 1.28.0.

Change-Id: I74de3c4cfd03f63c804bf35f2e3c5046091bc8d3
2026-05-28 12:12:18 +02:00
Ricardo Wurmus bb46f090d8 gnu: r-adam: Update to 1.28.0.
* gnu/packages/bioconductor.scm (r-adam): Update to 1.28.0.

Change-Id: Iec734d38ce10def7ccd208fc0fc7985849c36376
2026-05-28 12:12:18 +02:00
Ricardo Wurmus a0c8b9ba91 gnu: r-adacgh2: Update to 2.52.0.
* gnu/packages/bioconductor.scm (r-adacgh2): Update to 2.52.0.

Change-Id: Ia8d4367f14613201bd41a43e7964286a36d887a3
2026-05-28 12:12:18 +02:00
Ricardo Wurmus 88e8873681 gnu: r-absseq: Update to 1.66.0.
* gnu/packages/bioconductor.scm (r-absseq): Update to 1.66.0.

Change-Id: Ibc11ec5b37ea7f05455098b97a3df629574e2596
2026-05-28 12:12:18 +02:00
Ricardo Wurmus efcfbc2ae6 gnu: r-abarray: Update to 1.80.0.
* gnu/packages/bioconductor.scm (r-abarray): Update to 1.80.0.

Change-Id: I851fa6fbbab2294799e0158e95c2b1c5991e9df9
2026-05-28 12:12:18 +02:00
Ricardo Wurmus 80b1a9b8b7 gnu: r-zebrafishrnaseq: Update to 1.31.0.
* gnu/packages/bioconductor.scm (r-zebrafishrnaseq): Update to 1.31.0.

Change-Id: I462fda4217a9af201aa7d734a9cc241e8efa5164
2026-05-28 12:12:18 +02:00
Ricardo Wurmus a6f706d2e5 gnu: r-tximportdata: Update to 1.39.0.
* gnu/packages/bioconductor.scm (r-tximportdata): Update to 1.39.0.

Change-Id: I195cffc48b625fa7d078cc5bb6cb202f083e1fc5
2026-05-28 12:12:18 +02:00
Ricardo Wurmus bae207ccb5 gnu: r-tcgabiolinksgui-data: Update to 1.31.0.
* gnu/packages/bioconductor.scm (r-tcgabiolinksgui-data): Update to 1.31.0.

Change-Id: I4d8e02e29445709e9de3ff7770a21b5972e66f19
2026-05-28 12:12:18 +02:00
Ricardo Wurmus 54fc955180 gnu: r-systempiperdata: Update to 2.15.6.
* gnu/packages/bioconductor.scm (r-systempiperdata): Update to 2.15.6.

Change-Id: Id3f9d669ef5197c8ae8ba39dd14d034180dd73fe
2026-05-28 12:12:17 +02:00
Ricardo Wurmus 260025eb7f gnu: r-sesamedata: Update to 1.29.10.
* gnu/packages/bioconductor.scm (r-sesamedata): Update to 1.29.10.

Change-Id: I548345d576455c95229563c408bd83dd6a14e863
2026-05-28 12:12:17 +02:00
Ricardo Wurmus 91193c172e gnu: r-scpdata: Update to 1.19.0.
* gnu/packages/bioconductor.scm (r-scpdata): Update to 1.19.0.

Change-Id: Iad34e7e42fabea2360208fa4357da8d8550853e9
2026-05-28 12:12:17 +02:00
Ricardo Wurmus 33fd3fdb6c gnu: r-rtcga-rnaseq: Update to 20151101.41.0.
* gnu/packages/bioconductor.scm (r-rtcga-rnaseq): Update to 20151101.41.0.

Change-Id: I8c6fd76736f7e050ea11720f42bc14eec4f639b8
2026-05-28 12:12:17 +02:00
Ricardo Wurmus dd4fe41105 gnu: r-rnbeads-hg19: Update to 1.43.0.
* gnu/packages/bioconductor.scm (r-rnbeads-hg19): Update to 1.43.0.

Change-Id: I547ec25b44745cb3f62d58e3a18dd4da7bf87a9c
2026-05-28 12:12:17 +02:00
Ricardo Wurmus 4ac3ea8cbd gnu: r-rnaseqdata-hnrnpc-bam-chr14: Update to 0.49.0.
* gnu/packages/bioconductor.scm (r-rnaseqdata-hnrnpc-bam-chr14): Update to 0.49.0.

Change-Id: I6fbed63b3a351ecef3176e63fb6b280dddc03e66
2026-05-28 12:12:17 +02:00
Ricardo Wurmus 0befd14170 gnu: r-rcistarget-hg19-motifdbs-cisbponly-500bp: Update to 1.31.0.
* gnu/packages/bioconductor.scm (r-rcistarget-hg19-motifdbs-cisbponly-500bp): Update to 1.31.0.

Change-Id: I24af780e2c7b985c162d0be60952167de17273eb
2026-05-28 12:12:17 +02:00
Ricardo Wurmus 884a699d8e gnu: r-curatedtcgadata: Update to 1.33.2.
* gnu/packages/bioconductor.scm (r-curatedtcgadata): Update to 1.33.2.

Change-Id: Ib7bf3caadc4709e775ae73dfe55d1c3365c20906
2026-05-28 12:12:17 +02:00
Ricardo Wurmus b6031296ab gnu: r-gagedata: Update to 2.49.0.
* gnu/packages/bioconductor.scm (r-gagedata): Update to 2.49.0.

Change-Id: I6f46751c349699b3ddffa1b43677bb7035645144
2026-05-28 12:12:16 +02:00
Ricardo Wurmus babcd17fbd gnu: r-affydata: Update to 1.59.0.
* gnu/packages/bioconductor.scm (r-affydata): Update to 1.59.0.

Change-Id: Ia093f97cbd29275fa939dcbea1b383c391af8b43
2026-05-28 12:12:16 +02:00
Ricardo Wurmus 227f42feaa gnu: r-all: Update to 1.53.0.
* gnu/packages/bioconductor.scm (r-all): Update to 1.53.0.

Change-Id: If1c618823ab1d1a8c054b8e9ef965aa26b3ea0ff
2026-05-28 12:12:16 +02:00
Ricardo Wurmus 2ddaa57c4f gnu: r-hsmmsinglecell: Update to 1.31.0.
* gnu/packages/bioconductor.scm (r-hsmmsinglecell): Update to 1.31.0.

Change-Id: Ic7909dd71eebbd6321e94a4ae5ce2533e2fab0e5
2026-05-28 12:12:16 +02:00
Ricardo Wurmus 65de631530 gnu: r-prolocdata: Update to 1.49.0.
* gnu/packages/bioconductor.scm (r-prolocdata): Update to 1.49.0.

Change-Id: Ibadfeddd52a35baa06e96d5c9d30c1e652ccc3d1
2026-05-28 12:12:16 +02:00
Ricardo Wurmus 8488bcf6a3 gnu: r-pasillabamsubset: Update to 0.49.0.
* gnu/packages/bioconductor.scm (r-pasillabamsubset): Update to 0.49.0.

Change-Id: I5f73363f1a2b373bf1afce0124909f401ecc2139
2026-05-28 12:12:16 +02:00
Ricardo Wurmus 51fd295a38 gnu: r-pasilla: Update to 1.39.0.
* gnu/packages/bioconductor.scm (r-pasilla): Update to 1.39.0.

Change-Id: I34e3b56b7f5fbc88e0607104fa75058b4302cb1e
2026-05-28 12:12:16 +02:00
Ricardo Wurmus 735f4a054e gnu: r-msigdb: Update to 1.19.0.
* gnu/packages/bioconductor.scm (r-msigdb): Update to 1.19.0.

Change-Id: I43c9dfc5742958890aa1447ba6e78a41dbf37154
2026-05-28 12:12:16 +02:00
Ricardo Wurmus e177419ebd gnu: r-msdata: Update to 0.51.2.
* gnu/packages/bioconductor.scm (r-msdata): Update to 0.51.2.

Change-Id: I76c3e0a18ae48dc1c8a8e1ce6d349611fa9dd718
2026-05-28 12:12:15 +02:00
Ricardo Wurmus 10871d42ec gnu: r-minionsummarydata: Update to 1.41.0.
* gnu/packages/bioconductor.scm (r-minionsummarydata): Update to 1.41.0.

Change-Id: I26187a599e9e6701ef209c9c6441d65ee0fd4237
2026-05-28 12:12:15 +02:00
Ricardo Wurmus 2f4c3e9563 gnu: r-minfidataepic: Update to 1.37.0.
* gnu/packages/bioconductor.scm (r-minfidataepic): Update to 1.37.0.

Change-Id: Ic2df799d285cfaf0948581b9d796cb5d788648fb
2026-05-28 12:12:15 +02:00
Ricardo Wurmus 47a29c06e0 gnu: r-minfidata: Update to 0.57.0.
* gnu/packages/bioconductor.scm (r-minfidata): Update to 0.57.0.

Change-Id: Iff0bac7fd93c0190166bb762d60c288e6624334d
2026-05-28 12:12:15 +02:00
Ricardo Wurmus 6668ecc7da gnu: r-mousegastrulationdata: Update to 1.25.0.
* gnu/packages/bioconductor.scm (r-mousegastrulationdata): Update to 1.25.0.

Change-Id: I4702751e18585256e0b9cfffeb747d7dba66266f
2026-05-28 12:12:15 +02:00
Ricardo Wurmus cf907ef192 gnu: r-methylclockdata: Update to 1.19.0.
* gnu/packages/bioconductor.scm (r-methylclockdata): Update to 1.19.0.

Change-Id: I38ac4026735859f75e971f0d9e9c555039370b1e
2026-05-28 12:12:15 +02:00
Ricardo Wurmus 00bd570d10 gnu: r-methylaiddata: Update to 1.43.0.
* gnu/packages/bioconductor.scm (r-methylaiddata): Update to 1.43.0.
[native-inputs]: Add r-biocstyle.

Change-Id: Ib17e05bd05dae573770ce1229757da3a10a321c7
2026-05-28 12:12:15 +02:00
Ricardo Wurmus b5006648a8 gnu: r-macrophage: Update to 1.27.0.
* gnu/packages/bioconductor.scm (r-macrophage): Update to 1.27.0.

Change-Id: Ifbeb0ad042613ac3c43fbc625650cfd9b581f935
2026-05-28 12:12:15 +02:00
Ricardo Wurmus 0141050995 gnu: r-lungcancerlines: Update to 0.49.2.
* gnu/packages/bioconductor.scm (r-lungcancerlines): Update to 0.49.2.

Change-Id: Ifd9a5bb011d3acef332624b81a42fc554cf8cdba
2026-05-28 12:12:14 +02:00
Ricardo Wurmus 4543ef6cad gnu: r-leukemiaseset: Update to 1.47.0.
* gnu/packages/bioconductor.scm (r-leukemiaseset): Update to 1.47.0.

Change-Id: I0cf23ce8363b56d6ba4af40899fc7fbcaaf2bdfc
2026-05-28 12:12:14 +02:00
Ricardo Wurmus 06d2c6709d gnu: r-jaspar2016: Update to 1.39.0.
* gnu/packages/bioconductor.scm (r-jaspar2016): Update to 1.39.0.

Change-Id: I798ff62d84b8af0de47010a581e4428384f33d26
2026-05-28 12:12:14 +02:00
Ricardo Wurmus 4c5df0fafa gnu: r-italicsdata: Update to 2.49.0.
* gnu/packages/bioconductor.scm (r-italicsdata): Update to 2.49.0.

Change-Id: I34a5ccfe7f3d47630139d073accb14f199a3b6ea
2026-05-28 12:12:14 +02:00
Ricardo Wurmus 1675bc4086 gnu: r-illuminadatatestfiles: Update to 1.49.0.
* gnu/packages/bioconductor.scm (r-illuminadatatestfiles): Update to 1.49.0.

Change-Id: I74fa338aaf36d1787810fdcc999a1bb82ebecb99
2026-05-28 12:12:14 +02:00
Ricardo Wurmus a9c7b04d5b gnu: r-illumina450probevariants-db: Update to 1.47.0.
* gnu/packages/bioconductor.scm (r-illumina450probevariants-db): Update to 1.47.0.

Change-Id: I0d7d54a4edaabbed41aaf1f86b0893b2fa49d79b
2026-05-28 12:12:14 +02:00
Ricardo Wurmus 3ad3e76f22 gnu: r-hdcytodata: Update to 1.31.0.
* gnu/packages/bioconductor.scm (r-hdcytodata): Update to 1.31.0.

Change-Id: I7b778ba51a0af146b456883129ba48fbe98511d2
2026-05-28 12:12:14 +02:00
Ricardo Wurmus 6534d1f1c3 gnu: r-hellorangesdata: Update to 1.37.0.
* gnu/packages/bioconductor.scm (r-hellorangesdata): Update to 1.37.0.

Change-Id: I0a1a85f6c5870d9ece78f13202d5ed5da000f9dc
2026-05-28 12:12:14 +02:00
Ricardo Wurmus 1597ddee80 gnu: r-gsvadata: Update to 1.47.3.
* gnu/packages/bioconductor.scm (r-gsvadata): Update to 1.47.3.
[propagated-inputs]: Remove r-hgu95a-db; add r-matrix and r-spatialexperiment.

Change-Id: I55d1fc41ef089c221e5faf88604f6f743cf6ed1d
2026-05-28 12:12:13 +02:00
Ricardo Wurmus ffc6233e93 gnu: r-golubesets: Update to 1.53.0.
* gnu/packages/bioconductor.scm (r-golubesets): Update to 1.53.0.

Change-Id: I389431bd96e38bb9f260a1d44eedbc3bf9b1826a
2026-05-28 12:12:13 +02:00
Ricardo Wurmus bc1e629e79 gnu: r-genomationdata: Update to 1.43.0.
* gnu/packages/bioconductor.scm (r-genomationdata): Update to 1.43.0.

Change-Id: Ifbce156e84ef44d808b019a95d2beafdb4381ddc
2026-05-28 12:12:13 +02:00
Ricardo Wurmus 9f25a0b080 gnu: r-genelendatabase: Update to 1.47.0.
* gnu/packages/bioconductor.scm (r-genelendatabase): Update to 1.47.0.

Change-Id: I4c51a16fd953a8ceb6ce224cf1746c5c99457cb0
2026-05-28 12:12:13 +02:00
Ricardo Wurmus 76d87665f2 gnu: r-flowworkspacedata: Update to 3.23.0.
* gnu/packages/bioconductor.scm (r-flowworkspacedata): Update to 3.23.0.

Change-Id: I39af3521685fc1093ca14d32bb2e0a32059096b3
2026-05-28 12:12:13 +02:00
Ricardo Wurmus 37913d0113 gnu: r-flowsorted-blood-epic: Update to 2.15.0.
* gnu/packages/bioconductor.scm (r-flowsorted-blood-epic): Update to 2.15.0.

Change-Id: I09290c6b795d4e6138d46ffc8d023f37e00cea35
2026-05-28 12:12:13 +02:00
Ricardo Wurmus f2755728fd gnu: r-flowsorted-blood-450k: Update to 1.49.0.
* gnu/packages/bioconductor.scm (r-flowsorted-blood-450k): Update to 1.49.0.

Change-Id: I23da9db7553695979cbb4982899c9315c258ee41
2026-05-28 12:12:13 +02:00
Ricardo Wurmus 89f9599b7e gnu: r-faahko: Update to 1.51.0.
* gnu/packages/bioconductor.scm (r-faahko): Update to 1.51.0.

Change-Id: I0a3f1ddb157b599c0eed9047c5950c81c48dd253
2026-05-28 12:12:13 +02:00
Ricardo Wurmus 5a28d642ee gnu: r-derfinderdata: Update to 2.29.0.
* gnu/packages/bioconductor.scm (r-derfinderdata): Update to 2.29.0.

Change-Id: I3350d36847c95f9b477264aad6679b7fd74729ba
2026-05-28 12:12:12 +02:00
Ricardo Wurmus cae36769e0 gnu: r-copyhelper: Update to 1.43.0.
* gnu/packages/bioconductor.scm (r-copyhelper): Update to 1.43.0.

Change-Id: I38cb03efc9f69977c37537826b17506206f1ca95
2026-05-28 12:12:12 +02:00
Ricardo Wurmus 3b155fd6d6 gnu: r-chipexoqualexample: Update to 1.35.0.
* gnu/packages/bioconductor.scm (r-chipexoqualexample): Update to 1.35.0.

Change-Id: Ifec45ee0071ca0a52dcbee4027e140ea653cfb0a
2026-05-28 12:12:12 +02:00
Ricardo Wurmus 6e1a4e5a48 gnu: r-champdata: Update to 2.43.0.
* gnu/packages/bioconductor.scm (r-champdata): Update to 2.43.0.

Change-Id: I494425b262e26d5503cab03cc3d85e7f002ca492
2026-05-28 12:12:12 +02:00
Ricardo Wurmus 324f4bd9c3 gnu: r-celldex: Update to 1.21.0.
* gnu/packages/bioconductor.scm (r-celldex): Update to 1.21.0.

Change-Id: Icaf9f2c25db279fd11c2789914a67da0a393ce3f
2026-05-28 12:12:12 +02:00
Ricardo Wurmus ea55c6d7c2 gnu: r-breastcancervdx: Update to 1.49.0.
* gnu/packages/bioconductor.scm (r-breastcancervdx): Update to 1.49.0.

Change-Id: I9d9d41ced7b9f4ee4d6a28ca2dfb300493464064
2026-05-28 12:12:12 +02:00
Ricardo Wurmus 43b18706de gnu: r-breakpointrdata: Update to 1.29.0.
* gnu/packages/bioconductor.scm (r-breakpointrdata): Update to 1.29.0.
[native-inputs]: Add r-biocstyle.

Change-Id: I3ce64ac8751f4e6545237a3af7691c8238996ba5
2026-05-28 12:12:12 +02:00
Ricardo Wurmus 524dfdfeef gnu: r-biscuiteerdata: Update to 1.25.0.
* gnu/packages/bioconductor.scm (r-biscuiteerdata): Update to 1.25.0.

Change-Id: I5ec81f26dc5ae2adad466c0de588e966cbf0fbb4
2026-05-28 12:12:12 +02:00
Ricardo Wurmus 9d1269e270 gnu: r-bodymaprat: Update to 1.27.0.
* gnu/packages/bioconductor.scm (r-bodymaprat): Update to 1.27.0.

Change-Id: I541da491e77cf2d728c8b7a54ae7f7216e75ac24
2026-05-28 12:12:11 +02:00
Ricardo Wurmus 63a96728b2 gnu: r-bladderbatch: Update to 1.49.0.
* gnu/packages/bioconductor.scm (r-bladderbatch): Update to 1.49.0.

Change-Id: Ie97c50e3bcfb150081e09f3e160e99871309463b
2026-05-28 12:12:11 +02:00
Ricardo Wurmus 0b93bba387 gnu: r-biotmledata: Update to 1.35.0.
* gnu/packages/bioconductor.scm (r-biotmledata): Update to 1.35.0.

Change-Id: I8e765bec14dcdf7b92fc83ee6e81cd47a631f8fa
2026-05-28 12:12:11 +02:00
Ricardo Wurmus f17d0eb6bd gnu: r-bcellviper: Update to 1.47.0.
* gnu/packages/bioconductor.scm (r-bcellviper): Update to 1.47.0.

Change-Id: Iaedf90390de4d27732b987f9c812bc2c9c8f7d0d
2026-05-28 12:12:11 +02:00
Ricardo Wurmus dc28a919be gnu: r-arrmdata: Update to 1.47.0.
* gnu/packages/bioconductor.scm (r-arrmdata): Update to 1.47.0.

Change-Id: Iedf65a93b75ee07647105b6a4cf0097253d6c817
2026-05-28 12:12:11 +02:00
Ricardo Wurmus af371fce63 gnu: r-airway: Update to 1.31.0.
* gnu/packages/bioconductor.scm (r-airway): Update to 1.31.0.

Change-Id: Ib399273379453427cb934a3cac40a7ff98395c6d
2026-05-28 12:12:11 +02:00
Ricardo Wurmus 446f8ef43f gnu: r-adductdata: Update to 1.27.0.
* gnu/packages/bioconductor.scm (r-adductdata): Update to 1.27.0.

Change-Id: Ic52d396eabe6a6f664baac364cdb89a081603c6b
2026-05-28 12:12:11 +02:00
Ricardo Wurmus f744a9f36a gnu: r-org-mm-eg-db: Update to 3.23.0.
* gnu/packages/bioconductor.scm (r-org-mm-eg-db): Update to 3.23.0.

Change-Id: Ibf77a8a53151a5777e2cbbd6f1d7ae2d8d02e4b4
2026-05-28 12:12:11 +02:00
Ricardo Wurmus ff2da43284 gnu: r-org-hs-eg-db: Update to 3.23.1.
* gnu/packages/bioconductor.scm (r-org-hs-eg-db): Update to 3.23.1.

Change-Id: Ic47d38bcc3b3c2fb1b6a1db8f3b96f7ce1691f9c
2026-05-28 12:12:10 +02:00
Ricardo Wurmus c128de78bd gnu: r-go-db: Update to 3.23.1.
* gnu/packages/bioconductor.scm (r-go-db): Update to 3.23.1.

Change-Id: I1a5a8a2ec8a09a42be2128a321d1a2abba62d887
2026-05-28 12:12:10 +02:00
Ricardo Wurmus 82ef75d2b9 gnu: r-reactome-db: Update to 1.96.0.
* gnu/packages/bioconductor.scm (r-reactome-db): Update to 1.96.0.

Change-Id: Ia435c43ce19a65c0fc083aa174d6ba37d1896d72
2026-05-28 12:12:10 +02:00
Ricardo Wurmus 8317ec025c gnu: r-decoupler: Update to 2.17.0.
* gnu/packages/bioconductor.scm (r-decoupler): Update to 2.17.0.
[arguments]: Disable one more test.

Change-Id: Ie21ecd3f6eebca67280f0d4307956d1f1ff08a57
2026-05-28 12:12:10 +02:00
Ricardo Wurmus 368f3e993e gnu: r-iclusterplus: Update to 1.48.0.
* gnu/packages/bioconductor.scm (r-iclusterplus): Update to 1.48.0.
[propagated-inputs]: Add r-irlba.

Change-Id: I29903a1feb10afa1da7acb40c6fb7b43b17b409b
2026-05-28 12:12:10 +02:00
Ricardo Wurmus 533a8b4607 gnu: r-gsva: Update to 2.6.0.
* gnu/packages/bioconductor.scm (r-gsva): Update to 2.6.0.
[arguments]: Disable some tests.
[propagated-inputs]: Add r-delayedmatrixstats.

Change-Id: I884be9a85704afaa6a833248d47ae6cb2809767b
2026-05-28 12:12:10 +02:00
Ricardo Wurmus 4131d52da3 gnu: r-biobtreer: Update to 1.24.0.
* gnu/packages/bioconductor.scm (r-biobtreer): Update to 1.24.0.

Change-Id: I37a0503850f6096e984eff0e13ac22a0973f510c
2026-05-28 12:12:10 +02:00
Ricardo Wurmus 334444efd8 gnu: r-xcms: Update to 4.10.0.
* gnu/packages/bioconductor.scm (r-xcms): Update to 4.10.0.
[native-inputs]: Replace r-msdata with r-msdatahub.

Change-Id: Iae399db54b0aa0c28861ed2616e4531429459faf
2026-05-28 12:12:10 +02:00
Ricardo Wurmus 82c92afcc9 gnu: r-msnbase: Update to 2.37.0.
* gnu/packages/bioconductor.scm (r-msnbase): Update to 2.37.0.
[arguments]: Disable tests.

Change-Id: I87ad4c7b087ea2d7de36f4b10105c55150b6cb9e
2026-05-28 12:12:09 +02:00
Ricardo Wurmus f80514fd66 gnu: r-msexperiment: Update to 1.14.0.
* gnu/packages/bioconductor.scm (r-msexperiment): Update to 1.14.0.
[arguments]: Disable tests.
[native-inputs]: Replace r-msdata with r-msdatahub.

Change-Id: I2ea67239a3b441a4c2099c9ced846d5d79afee1d
2026-05-28 12:12:09 +02:00
Ricardo Wurmus 4511030cfc gnu: r-msbackendsql: Update to 1.12.0.
* gnu/packages/bioconductor.scm (r-msbackendsql): Update to 1.12.0.
[arguments]: Disable tests.
[native-inputs]: Replace r-msdata with r-msdatahub.

Change-Id: Ic17b560985e16a0b36ffe8bc117515a1983adf5b
2026-05-28 12:12:09 +02:00
Ricardo Wurmus a64dee83af gnu: r-biocset: Update to 1.25.0.
* gnu/packages/bioconductor.scm (r-biocset): Update to 1.25.0.
[arguments]: Disable one more test.

Change-Id: I7db8745396ab30970ad91de50402bb5fef41290c
2026-05-28 12:12:09 +02:00
Ricardo Wurmus 518984d3a8 gnu: r-phyloseq: Update to 1.56.0.
* gnu/packages/bioconductor.scm (r-phyloseq): Update to 1.56.0.
[native-inputs]: Add r-sparsearray.

Change-Id: Iacf99f3e7285849e58f6bf4d6b2d6300b14bc86c
2026-05-28 12:12:09 +02:00
Ricardo Wurmus abf4d0dfeb gnu: r-sva: Update to 3.59.0.
* gnu/packages/bioconductor.scm (r-sva): Update to 3.59.0.
[arguments]: Disable vignettes.

Change-Id: Ib9eaee22e7d192dceac1345ce8fbceefd7b130a7
2026-05-28 12:12:09 +02:00
Ricardo Wurmus c55cc846ab gnu: r-biomformat: Update to 1.40.0.
* gnu/packages/bioconductor.scm (r-biomformat): Update to 1.40.0.
[properties]: Record updater-extra-propagated-inputs.

Change-Id: Ib5a769c142794c43a11e43c3c84c967a088195fb
2026-05-28 12:12:09 +02:00
Ricardo Wurmus d774b80f90 gnu: r-bgeecall: Update to 1.28.0.
* gnu/packages/bioconductor.scm (r-bgeecall): Update to 1.28.0.
[propagated-inputs]: Remove duplicate r-sjmisc.

Change-Id: I3b318e22f9b4873e3287d598bb18e06319c7e433
2026-05-28 12:12:09 +02:00
Ricardo Wurmus ddfc0f3d7d gnu: r-biocpkgtools: Update to 1.30.0.
* gnu/packages/bioconductor.scm (r-biocpkgtools): Update to 1.30.0.
[native-inputs]: Drop labels.

Change-Id: Ibe9d94f33773b21e2fc9c75adb978dccd748e7a9
2026-05-28 12:12:08 +02:00
Ricardo Wurmus e73974d547 gnu: r-mast: Update to 1.38.0.
* gnu/packages/bioconductor.scm (r-mast): Update to 1.38.0.
[native-inputs]: Drop labels.

Change-Id: I817434671bf10cf1ba17a7a63bcaef5ef8e03e94
2026-05-28 12:12:08 +02:00
Ricardo Wurmus 4a40a031a7 gnu: Remove r-pryr.
This package was removed from CRAN in 2023.  It fails to build with R 4.6.0.

* gnu/packages/cran.scm (r-pryr): Remove variable.

Change-Id: I966b317db519f4b78d5592c12c69b8777b2a4a05
2026-05-28 12:12:08 +02:00
Ricardo Wurmus aeb62e983b gnu: r-glimma: Update to 2.21.0.
* gnu/packages/bioconductor.scm (r-glimma): Update to 2.21.0.
[native-inputs]: Remove r-pryr.

Change-Id: I9316020faf8a453785d6791847d4a3ff6e1ece62
2026-05-28 12:12:08 +02:00
Ricardo Wurmus 1f353b3f12 gnu: Remove r-rbokeh.
This package was removed from CRAN in 2023.  It depends on pryr (also removed
in 2023), which fails to build with R 4.6.0.

* gnu/packages/cran.scm (r-rbokeh): Remove variable.

Change-Id: Idc4e38c27e43755d29aec9f842c21d7d2ec230b6
2026-05-28 12:12:08 +02:00
Ricardo Wurmus b279b550f2 gnu: r-mscoreutils: Update to 1.24.0.
* gnu/packages/bioconductor.scm (r-mscoreutils): Update to 1.24.0.
[source]: Remove patch.
[native-inputs]: Add r-rlang.
* gnu/packages/patches/r-mscoreutils-0001-fix-non-API-call-to-R-SETLENGTH-by-using-lengthgets.patch:
Remove file.
* gnu/local.mk (dist_patch_DATA): Remove it.

Change-Id: Iff65329afeea448c14ca8dd989bcf9be1af79895
2026-05-28 12:12:08 +02:00
Ricardo Wurmus 41e9f8b556 gnu: r-sparsearray: Update to 1.12.0.
* gnu/packages/bioconductor.scm (r-sparsearray): Update to 1.12.0.
[source]: Remove patch.
* gnu/packages/patches/r-sparsearray-r-4.6.0-compat.patch: Remove file.
* gnu/local.mk (dist_patch_DATA): Remove it.

Change-Id: Ief14b637fc6ee1bec96065ff41cc501a2e63f010
2026-05-28 12:12:08 +02:00
Ricardo Wurmus 7f06acf3e5 gnu: r-h5mread: Update to 1.4.0.
* gnu/packages/bioconductor.scm (r-h5mread): Update to 1.4.0.
[source]: Remove patch.
* gnu/packages/patches/r-h5mread-0001-h5mread-1.3.2-Get-rid-of-non-API-calls-to-R.patch: Remove file.
* gnu/local.mk (dist_patch_DATA): Remove it.

Change-Id: I40b81ee9b81865b780477ceeacae8b9c0b24d466
2026-05-28 12:12:08 +02:00
Ricardo Wurmus b44a7a6801 gnu: r-snpstats: Update to 1.62.0.
* gnu/packages/bioconductor.scm (r-snpstats): Update to 1.62.0.
[source]: Remove patches.
* gnu/packages/patches/r-snpstats-0001-fixed-non-API-except-for-IS_S4_OBJECT.patch,
gnu/packages/patches/r-snpstats-0002-fixed-IS_S4_OBJECT.patch:
Remove files.
* gnu/local.mk (dist_patch_DATA): Remove them.

Change-Id: If2a8e6e77899eb6a278fe7ebda0f7593c5e6a9b2
2026-05-28 12:12:07 +02:00
Ricardo Wurmus 0e007695a2 gnu: r-shortread: Update to 1.70.0.
* gnu/packages/bioconductor.scm (r-shortread): Update to 1.70.0.
[source]: Remove patch.
* gnu/packages/patches/r-shortread-0001-ShortRead-1.69.3-Get-rid-of-non-API-calls-to-R.patch:
Remove file.
* gnu/local.mk (dist_patch_DATA): Remove it.

Change-Id: I45ca6fca8edaa7dc727e86cb16fc3c61c27f286d
2026-05-28 12:12:07 +02:00
Ricardo Wurmus 9a0b04a22b gnu: r-rsamtools: Update to 2.28.0.
* gnu/packages/bioconductor.scm (r-rsamtools): Update to 2.28.0.
[source]: Remove patch.
* gnu/packages/patches/r-rsamtools-r-4.6.0-compat.patch: Remove file.
* gnu/local.mk (dist_patch_DATA): Remove it.

Change-Id: I2b6467026dedc59e43e4151c0d01d344e247aeee
2026-05-28 12:12:07 +02:00
Ricardo Wurmus 7731f955ec gnu: r-scrapper: Update to 1.6.0.
* gnu/packages/bioconductor.scm (r-scrapper): Update to 1.6.0.
[arguments]: Enable all tests; update patch to remove dependency on
Rigraphlib.
[propagated-inputs]: Add r-s4vectors and r-sparsearray.
[native-inputs]: Remove r-matrixgenerics and r-scrnaseq; add
r-singlecellexperiment and r-summarizedexperiment.

Change-Id: Idc7aacb24130028dc99c7b091dd9a773c5ecea46
2026-05-28 12:12:07 +02:00
Ricardo Wurmus 7cd74dbcde gnu: igraph-for-r-rigraphlib: Update to 1.0.1.
* gnu/packages/graph.scm (igraph-for-r-rigraphlib): Update to 1.0.1.
[source]: Adjust snippet to preserve qhull and cxsparse.
[arguments]: Inherit from igraph; remove 'patch-suitesparse phase; disable
infomap support.
[inputs]: Remove suitesparse-cxsparse.

Change-Id: I34fcb77d0cda31a8a2bb3982c7da462db6c72342
2026-05-28 12:12:07 +02:00
Ricardo Wurmus 6953181b4a gnu: Add r-aisdk.
* gnu/packages/cran.scm (r-aisdk): New variable.

Change-Id: Ie499307037d30c22cb58764d46aa8810da4a5787
2026-05-28 12:12:07 +02:00
Ricardo Wurmus 3f8c70f196 gnu: Add r-bedmatrix.
* gnu/packages/cran.scm (r-bedmatrix): New variable.

Change-Id: Ie7ca95f1e0197a2cb46147d524b308d01c9e7b51
2026-05-28 12:12:07 +02:00
Ricardo Wurmus 9fe5a1c7df gnu: Add r-prompter.
* gnu/packages/cran.scm (r-prompter): New variable.

Change-Id: I4d9f2723773d13cb9ecf15c3b8ba45a35d4b03ba
2026-05-28 12:12:06 +02:00
Ricardo Wurmus 31be212221 gnu: r-rhdf5: Update to 2.55.16.
* gnu/packages/bioconductor.scm (r-rhdf5): Update to 2.55.16.
[arguments]: Disable some tests.
[native-inputs]: Remove r-mockery; add r-withr.

Change-Id: Idb6fb3839e38cdddfd80b48559ed342c9630b412
2026-05-28 12:12:06 +02:00
Ricardo Wurmus a8929aa2d4 gnu: r-mmuphin: Update to 1.99.3.
* gnu/packages/bioconductor.scm (r-mmuphin): Update to 1.99.3.
[propagated-inputs]: Replace r-maaslin2 with r-maaslin3.

Change-Id: Icddacb6d8e444d70a12363365599232aac091ea4
2026-05-28 12:12:06 +02:00
Ricardo Wurmus c29e8350f7 gnu: Add r-maaslin3.
* gnu/packages/bioconductor.scm (r-maaslin3): New variable.

Change-Id: Ieb6a89cf42447061716e46e1818423c543ff06aa
2026-05-28 12:12:06 +02:00
Ricardo Wurmus 0601cf2509 gnu: r-biomformat: Update to 1.39.17.
* gnu/packages/bioconductor.scm (r-biomformat): Update to 1.39.17.
[native-inputs]: Add r-s4vectors, r-summarizedexperiment, and r-tibble.

Change-Id: I46968a937257f0bdcb9ba5e20a932a7792a03ab5
2026-05-28 12:12:06 +02:00
Ricardo Wurmus f3fd8326d3 gnu: r-immapex: Update to 1.5.4.
* gnu/packages/bioconductor.scm (r-immapex): Update to 1.5.4.
[arguments]: Disable tests that depend on missing datasets.
[propagated-inputs]: Remove r-hash, r-httr, and r-rvest; add r-immreferent.

Change-Id: I21b2f4c9a3a7ba280a16411cb4aded5811ecd534
2026-05-28 12:12:06 +02:00
Ricardo Wurmus 99a83615bb gnu: Add r-immreferent.
* gnu/packages/bioconductor.scm (r-immreferent): New variable.

Change-Id: Ife39138266d69e60d3c3e728d0fdb408afe27394
2026-05-28 12:12:06 +02:00
Ricardo Wurmus 0f28ceff98 gnu: r-degreport: Update to 1.47.0.
* gnu/packages/bioconductor.scm (r-degreport): Update to 1.47.0.
[arguments]: Update origin label.
[native-inputs]: Drop labels.

Change-Id: Ib2f18d2bc83ec8aebcd92e4e106c0685eef47a75
2026-05-28 12:12:06 +02:00
Ricardo Wurmus b7c88ffdb8 gnu: r-rhdf5filters: Update to 1.23.3.
* gnu/packages/bioconductor.scm (r-rhdf5filters): Update to 1.23.3.
[arguments]: Add phase 'patch-build-system.

Change-Id: Id147a122596e38f7cf5818131cbc774882c53818
2026-05-28 12:12:06 +02:00
Ricardo Wurmus 789ebad80a gnu: r-devtools: Remove another test that needs Internet access.
* gnu/packages/cran.scm (r-devtools)[arguments]: Update list of skipped tests.

Change-Id: Idc0081515528d3fa206e7c04eda5b294925c78e7
2026-05-28 12:12:05 +02:00
Ricardo Wurmus e9d6cf80bf gnu: r-rhdf5lib: Update to 2.0.0.
* gnu/packages/bioconductor.scm (r-rhdf5lib): Update to 2.0.0.
[source]: Delete "vendor" directory.
[arguments]: Skip bad tests; rewrite 'do-not-use-bundled-hdf5.
[propagated-inputs]: Replace hdf5-1.10 with hdf5.
[native-inputs]: Remove sources of hdf5-1.10.

Change-Id: I06b995259da523c843e68f491c74c792a1a8b048
2026-05-28 12:12:05 +02:00
Ricardo Wurmus 3a65b81e0f gnu: Add r-ecodive.
* gnu/packages/cran.scm (r-ecodive): New variable.

Change-Id: I435ccdd7a1d9958867bdb1c4225752040b966f84
2026-05-28 12:12:05 +02:00
Ricardo Wurmus 0838c21d3f gnu: Add r-enrichit.
* gnu/packages/cran.scm (r-enrichit): New variable.

Change-Id: I1d38fc1e6ef24d0ddcb8d12601942a86fcd5adb9
2026-05-28 12:12:05 +02:00
Ricardo Wurmus e2f18ae3ea gnu: Add r-genio.
* gnu/packages/cran.scm (r-genio): New variable.

Change-Id: Ic7323a848899cd093b54f928c538d8de6d919a4a
2026-05-28 12:12:05 +02:00
Ricardo Wurmus 4a1dfcc57d gnu: r-tinytex: Add TeX Live packages.
* gnu/packages/cran.scm (r-tinytex)[arguments]: Disable a test; add phase
'set-HOME.
[propagated-inputs]: Add ghostscript and a texlive-local-tree.

Change-Id: Ia2752d2b72978b3abfca0424ed0b5683a0067e23
2026-05-28 12:12:05 +02:00
Ricardo Wurmus e20a7dce97 gnu: r-biostrings: Update to 2.79.5.
* gnu/packages/patches/r-biostrings-r4.6.0-compat.patch: Remove file.
* gnu/local.mk (dist_patch_DATA): Remove it.
* gnu/packages/bioconductor.scm (r-biostrings): Update to 2.79.5.
[source]: Remove patch.

Change-Id: I90e0161aa311bdfa990250b056ad238380bb2439
2026-05-28 12:12:05 +02:00
Ricardo Wurmus 6a8f1b19ed gnu: Add r-ptmods.
* gnu/packages/bioconductor.scm (r-ptmods): New variable.

Change-Id: I119eaa062236368c05fc62e5658896ba7aedf9b0
2026-05-28 12:12:05 +02:00
Ricardo Wurmus 0075c0e239 guix: Update Bioconductor version to 3.23.
* guix/import/cran.scm (%bioconductor-version): Set to 3.23.

Change-Id: If6bde9a9a9ca407ea7c4aeb742c93f83c1a58ba4
2026-05-28 12:12:04 +02:00
Ricardo Wurmus 96a9ec8f11 gnu: r-lhs: Update to 1.3.0.
* gnu/packages/cran.scm (r-lhs): Update to 1.3.0.

Change-Id: Ia409ed70bb2efaa981de65ed401b2cadf5f50c9f
2026-05-28 12:12:04 +02:00
Ricardo Wurmus 759cf8e1eb gnu: r-haplo-stats: Update to 1.9.8.7.
* gnu/packages/cran.scm (r-haplo-stats): Update to 1.9.8.7.
[propagated-inputs]: Remove r-rms; add r-mass.

Change-Id: I9462a4f05b79f067cd65847749bc4f3c2418398a
2026-05-28 12:12:04 +02:00
Ricardo Wurmus 210ee30d9a gnu: r-getopt: Update to 1.21.1.
* gnu/packages/cran.scm (r-getopt): Update to 1.21.1.

Change-Id: I46686f7dff7839dc177699661166ec2b0fa6131e
2026-05-28 12:12:04 +02:00
Ricardo Wurmus 61d762c7c2 gnu: r-safetensors: Update to 0.2.1.
* gnu/packages/cran.scm (r-safetensors): Update to 0.2.1.

Change-Id: Ifb9eebfbf97ec31c02dc18f87276a8c538609750
2026-05-28 12:12:04 +02:00
Ricardo Wurmus 22e93ba64f gnu: r-tclust: Update to 2.2-0.
* gnu/packages/cran.scm (r-tclust): Update to 2.2-0.

Change-Id: I81c53f38a4fe869ccf64155262fd6199824ca6a7
2026-05-28 12:12:04 +02:00
Ricardo Wurmus 04a80af8a8 gnu: r-pak: Update to 0.9.5.
* gnu/packages/cran.scm (r-pak): Update to 0.9.5.

Change-Id: I77b182237848fdc4bbc25ba2be03f623bf71b04d
2026-05-28 12:12:04 +02:00
Ricardo Wurmus 57c264be1e gnu: r-datawizard: Update to 1.3.1.
* gnu/packages/cran.scm (r-datawizard): Update to 1.3.1.
[native-inputs]: Add r-fixest and r-openssl.

Change-Id: I13d9f71f6803ed92105491c48dd579ec6f0fc19a
2026-05-28 12:12:04 +02:00
Ricardo Wurmus 9002ccf73e gnu: r-consort: Update to 1.2.3.
* gnu/packages/cran.scm (r-consort): Update to 1.2.3.

Change-Id: I62dfd870e3c86fe504d8bad6f4a8cc1b1e1ada7d
2026-05-28 12:12:03 +02:00
Ricardo Wurmus c3108ee3d3 gnu: r-conos: Update to 1.5.4.
* gnu/packages/bioconductor.scm (r-conos): Update to 1.5.4.
[propagated-inputs]: Add r-pagoda2.
[native-inputs]: Remove r-pagoda2.

Change-Id: I35d44e60304490687848e375c57f74fe8baf9ffc
2026-05-28 12:12:03 +02:00
Ricardo Wurmus c49776a525 gnu: r-metafor: Update to 5.0-1.
* gnu/packages/cran.scm (r-metafor): Update to 5.0-1.
[arguments]: Do not skip any tests.
[native-inputs]: Remove r-lme4 and r-minqa; add r-mumin.

Change-Id: Ibe882467f3edc9b6259967b7a2f838a88e7fee68
2026-05-28 12:12:03 +02:00
Efraim Flashner 48dda47112 gnu: rust-crates: Adjust indentation.
* gnu/packages/rust-crates.scm: Adjust indentation.

Change-Id: I7c9f279dd8d6485b967342391171223d8259898c
2026-05-28 13:04:11 +03:00
Efraim Flashner 44b166c0d3 gnu: sequoia-wot-tools: Update to 0.15.2.
* gnu/packages/sequoia.scm (sequoia-wot-tools): Update to 0.15.2.
[source]: Update source URI.
[arguments]: Remove cargo-test-flags. Update bash shell completion
directory.
[native-inputs]: Add gnupg.
* gnu/packages/rust-crates.scm (lookup-cargo-inputs)
[sequoia-wot-tools]: Update entry.

Change-Id: If2b32e42e4e2a58017e69bd6d05fc9c680583cb2
2026-05-28 12:37:12 +03:00
Ricardo Wurmus f857f129f6 gnu: python-idna-ssl: Fix build with Python 3.12.
* gnu/packages/python-xyz.scm (python-idna-ssl)[arguments]: Add phase
'python3.12-compatibility.
[propagated-inputs]: Add python-urllib3.

Change-Id: Ibeac1108869602c91a4e99c82939140c63df788f
2026-05-28 08:46:59 +02:00
Ricardo Wurmus 5cf70a0c7c gnu: omins-lv2: Fix build with Python 3.12.
* gnu/packages/audio.scm (omins-lv2):[arguments]: Add phase
'python3.12-compatibility.

Change-Id: I0dd9baca5ba90074fd0c0d14e22889208cf4b026
2026-05-28 08:46:59 +02:00
Ricardo Wurmus 9f7df5e6bc gnu: python-biopython-1.73: Fix build with Python 3.12.
* gnu/packages/bioinformatics.scm (python-biopython-1.73)
[arguments]: Replace phase 'python3.11-compatibility with
'python3.12-compatibility; update to patch out use of removed symbol.

Change-Id: Ia3a641b31bcd30713a06493d8c5ffffc77e63b91
2026-05-28 08:46:59 +02:00
Ricardo Wurmus c803b2d243 gnu: ams-lv2: Fix build with Python 3.12.
* gnu/packages/music.scm (ams-lv2)[arguments]: Replace phase
'python3.11-compatibility with 'python3.12-compatibility; update to patch out
use of removed "imp" module.

Change-Id: If621e95b9f46f995887e3e4b02f5343b04ebe6f9
2026-05-28 08:46:59 +02:00
Cayetano Santos 2652c0e7e8 gnu: emacs-diff-hl: Update to 1.10.0-1.7d873b2.
* gnu/packages/emacs-xyz.scm (emacs-diff-hl): Update to 1.10.0-1.7d873b2.
[native-inputs]: Remove git-minimal; add git-minimal/pinned.

Change-Id: I08e2583b7fee53f123a3cb7ac45bbb0a4533ce24
2026-05-28 07:43:24 +02:00
Cayetano Santos 1f096c273e gnu: kicad-doc: Use pinned git-minimal.
* gnu/packages/electronics.scm (kicad-doc)[native-inputs]: Remove
git-minimal; add git-minimal/pinned.

Change-Id: I390dcc749ff952cfade49affdd27940a63326acf
2026-05-28 07:34:34 +02:00
jgart 51980d899c gnu: trealla: Update to 2.100.15.
* gnu/packages/prolog.scm (trealla): Update to 2.100.15.

Change-Id: I91abb149f3472712b7b3c008f8ba160f75037265
2026-05-27 22:55:00 -04:00
Nicolas Graves 950eef6fb5 gnu: chez, racket: Update.
* gnu/packages/chez.scm
  (chez-scheme-for-racket): Update to 10.4.0-pre-release.1-1.
  (chez-scheme): Update to 10.4.0.
  (chez-nanopass, chez-nanopass-bootstrap): Update to 1.9.4.
* gnu/packages/racket.scm
  (%racket-version, racket): Update to 9.1.
  (%racket-origin): Refresh base32 hashes and modules accordingly.

Change-Id: I7f01eb99f02814ff252f6bece1ab7f3aa722d1ba
Merges: https://codeberg.org/guix/guix/pulls/7851
Reviewed-by: Zhu Zihao <all_but_last@163.com>
Signed-off-by: Nguyễn Gia Phong <cnx@loang.net>
2026-05-28 11:15:45 +09:00
Hugo Buddelmeijer 4e345918a1 gnu: micropython: Update to 1.28.0.
Fixes: CVE-2026-1998

* gnu/packages/python.scm (micropython): Update to 1.28.0.

Change-Id: I87ad70dbeb0edba2a771d33e74e43b33af49a9c8
Signed-off-by: Andreas Enge <andreas@enge.fr>
2026-05-27 23:10:20 +02:00
gemmaro b99a013eab gnu: ruby-racc: Update to 1.8.1 and enable tests.
* gnu/packages/ruby-xyz.scm (ruby-racc): Update to 1.8.1.
[source]: Use the Git repository for tests.
[arguments]<#:tests?>: Remove the disabling of tests.
<#:phases>: Add the compile phase before the build phase to support the
optional native extension for performance improvements.
[native-inputs]: Remove ruby-hoe and add ruby-test-unit-core.

Change-Id: If3295179b6401db63cd5c1ab3beb77fe0579eaae
Signed-off-by: Andreas Enge <andreas@enge.fr>
2026-05-27 22:34:07 +02:00
Ashish SHUKLA 7e94069983 gnu: labwc: Update to 0.20.0.
* gnu/packages/wm.scm (labwc): Update to 0.20.0.
[inputs]: Replace wlroots-0.19 with wlroots-0.20.

Change-Id: Ib42fb2c37e3cdb78bddf3d8404fb4f88ca6ef38c
Signed-off-by: Andreas Enge <andreas@enge.fr>
2026-05-27 22:04:44 +02:00
Ashish SHUKLA d01a4ea610 gnu: wlroots: Update to 0.20.1.
* gnu/packages/wm.scm (wlroots): Update to 0.20.1.

Change-Id: I16734cf156a80358e94ffbe10de9ec1fc9c603ac
Signed-off-by: Andreas Enge <andreas@enge.fr>
2026-05-27 22:04:44 +02:00
luca da69abdca1 gnu: evince: Update to 48.4.
* gnu/packages/gnome.scm (evince): Update to 48.4.

Change-Id: I2638b0ce644f680a1361b2ff3e9e233eb8131fa3
Signed-off-by: Andreas Enge <andreas@enge.fr>
2026-05-27 20:27:45 +02:00
orahcio f4b0275610 gnu: sway: Update to 1.12.
* gnu/packages/wm.scm (sway): Update to 1.12.
[inputs]: Replace wlroots-0.19 with wlroots-0.20.

Change-Id: I66a9c7f4ddf6f84daf0ce239cbb44933ba9dfd3a
Signed-off-by: Andreas Enge <andreas@enge.fr>
2026-05-27 20:25:43 +02:00
Cayetano Santos 50454dab4a gnu: Add python-udapi.
* gnu/packages/python-xyz.scm (python-udapi): New variable.

Change-Id: I9e7679c0030ac1fb281f638b286182bb2736a242
2026-05-27 20:04:12 +02:00
Yappaholic 89747ea3ac gnu: mangowm: Update to 0.13.1.
* gnu/packages/wm.scm (mangowm): Update to 0.13.1.

Signed-off-by: Andreas Enge <andreas@enge.fr>
2026-05-27 19:42:06 +02:00
Zhu Zihao 41111228d5 gnu: 7zip: Update to 26.01 [security-fixes].
Contains Fixes for:
CVE-2026-48095: 7-Zip Heap Buffer Overflow Can Lead to Code Execution

* gnu/packages/compression.scm (7zip): Update to 26.01.

Change-Id: I352bb1669438acd11d68a9cabc638c6c403b169b
Signed-off-by: Andreas Enge <andreas@enge.fr>
2026-05-27 18:39:26 +02:00
Reepca Russelstein f519ddf733 daemon: Allow ADDR_NO_RANDOMIZE to be omitted if `--allow-aslr'.
Docker's default seccomp filter prevents use of the ADDR_NO_RANDOMIZE flag
with the personality system call.  It causes personality to return EPERM.  In
general, we assume that any result other than the only documented one, EINVAL,
is caused by seccomp.  If we detect that ADDR_NO_RANDOMIZE is blocked, and the
--allow-aslr option was passed, we simply don't use it.

This allows guix-daemon to continue to work even in these containers, without
any implicit weakening of reproducibility.

Since it is presumably desirable to be able to build guix itself in such an
environment, also pass --allow-aslr to guix-daemon in test-env.

* nix/libstore/globals.hh (Settings::allowASLR): new field.
* nix/nix-daemon/guix-daemon.cc (options): add --allow-aslr option.
  (parse_opt): use it to set Settings::allowASLR.
* nix/libstore/build.cc (DerivationGoal::startBuilder): detect when
  ADDR_NO_RANDOMIZE is blocked and --allow-aslr is passed and don't use it in
  that case.
* doc/guix.texi: document --allow-aslr in "Invoking guix-daemon".
* build-aux/test-env.in: always pass --allow-aslr.

Fixes: guix/guix#3917
Change-Id: I51c5899a9559e161f9e107c2e6a36df395ab3134
Signed-off-by: Ludovic Courtès <ludo@gnu.org>
Modified-by: Ludovic Courtès <ludo@gnu.org>
Merges: #4616
2026-05-27 18:25:16 +02:00
Ludovic Courtès 4ac91ee39c gnu: gdb: Update to 17.2.
* gnu/packages/gdb.scm (gdb-17): Update to 17.2.

Change-Id: Ib3e905ab04a8562a5ca9ddf0a6959e6bc30c7b6a
Signed-off-by: Ludovic Courtès <ludo@gnu.org>
Merges: #8806
2026-05-27 18:25:16 +02:00
Ludovic Courtès 752d3c0a52 gnu: lout: Update to 3.43.4.
* gnu/packages/lout.scm (lout): Update to 3.43.4.

Change-Id: I3bf469b427411706ba5b3ef1cdb056174d94a0f0
Signed-off-by: Ludovic Courtès <ludo@gnu.org>
Merges: #8805
2026-05-27 18:25:16 +02:00
Ludovic Courtès de20eed853 gnu: man-pages: Update to 6.18.
* gnu/packages/man.scm (man-pages): Update to 6.18.

Change-Id: If778879c9faed3123400b43a2d48a593283ed789
Signed-off-by: Ludovic Courtès <ludo@gnu.org>
Merges: #8808
2026-05-27 18:25:16 +02:00
Ludovic Courtès 9b755bfffd gnu: xdot: Update to 1.6.
* gnu/packages/graphviz.scm (xdot): Update to 1.6.

Change-Id: Id4eac906640421f8651b3a37e87daaf0ea7466c4
Signed-off-by: Ludovic Courtès <ludo@gnu.org>
Merges: #8807
2026-05-27 18:25:15 +02:00
Ludovic Courtès bcfe9dba35 ci: (Cross-)build the architecture-specific Linux-libre packages.
* gnu/ci.scm (core-packages): In ‘target-linux?’ case, add the
linux-libre-*-generic architecture-specific kernel packages.

Change-Id: Ie9579b5b77160e57e563542a03fdd6e563fcc193
Signed-off-by: Ludovic Courtès <ludo@gnu.org>
Merges: #8776
2026-05-27 18:25:15 +02:00
André Batista fe11a2a2e9 gnu: mullvadbrowser: Update to 15.0.14.
Fixes CVEs: 2026-8388, 2026-8391, 2026-8401, 2026-8946, 2026-8947,
2026-8949, 2026-8950, 2026-8953, 2026-8954, 2026-8955, 2026-8956,
2026-8957, 2026-8958, 2026-8959, 2026-8961, 2026-8962, 2026-8968,
2026-8970, 2026-8974 and 2026-8975.

See:
<https://www.mozilla.org/en-US/security/advisories/mfsa2026-48/> for
details.

* gnu/packages/tor-browsers.scm (%mullvadbrowser-build-date): Update to
20260518170000.
(%mullvadbrowser-version): Update to 15.0.14.
(%mullvadbrowser-firefox-version): Update to 140.11.0esr-15.0-1-build2.
(mullvadbrowser-translation-base): Update to 6749f7ce29.

Change-Id: I854d2d3db669920c67abc18c624288bc9091e979
Signed-off-by: Andreas Enge <andreas@enge.fr>
2026-05-27 17:48:54 +02:00
André Batista 79f8ab94ab gnu: torbrowser: Update to 15.0.14.
Fixes CVEs: 2026-8388, 2026-8391, 2026-8401, 2026-8946, 2026-8947,
2026-8949, 2026-8950, 2026-8953, 2026-8954, 2026-8955, 2026-8956,
2026-8957, 2026-8958, 2026-8959, 2026-8961, 2026-8962, 2026-8968,
2026-8970, 2026-8974 and 2026-8975.

See:
<https://www.mozilla.org/en-US/security/advisories/mfsa2026-48/> for
details.

* gnu/packages/tor-browsers.scm (%torbrowser-build-date): Update to
20260518170000.
(%torbrowser-version): Update to 15.0.14.
(%torbrowser-firefox-version): Update to 140.11.0esr-15.0-1-build3.
(torbrowser-translation-base): Update to 6749f7ce29.
(torbrowser-translation-specific): Update to a2e92e2c255.

Change-Id: I4737675dabde352c2f9602efe9c82d43aaf7c66c
Signed-off-by: Andreas Enge <andreas@enge.fr>
2026-05-27 17:48:34 +02:00
Andreas Enge b8d0488032 gnu: Remove packagekit-qt5.
* gnu/packages/qt.scm (packagekit-qt5): Delete variable.

Fixes: guix/guix#8056
Change-Id: I6adb8a34b6339d5be2b9e61d91865465b0e2378d
2026-05-27 17:41:34 +02:00
Andreas Enge 56d9e3e9ce gnu: packagekit-qt6: Disinherit from packagekit-qt5.
* gnu/packages/qt.scm (packagekit-qt6)[inherit]: Drop field.
(version, source, build-system, home-page, license): Copy-paste from
packagekit-qt5.
(arguments, inputs): Rewrite.

Change-Id: I89656a7a03df716d3035096675f2c689bca8b2d5
2026-05-27 17:41:29 +02:00
Andreas Enge 5a90fd6df0 gnu: Remove qcoro-qt5.
* gnu/packages/qt.scm (qcoro-qt5): Delete variable.

Change-Id: I8e35406e3291564ae85de7a87514857b0e0b0bef
2026-05-27 17:41:27 +02:00
Andreas Enge 233640eb06 gnu: qcoro-qt6: Disinherit from qcoro-qt5.
* gnu/packages/qt.scm (qcoro-qt6)[inherit]: Drop field.
[version, source, build-system, native-inputs, home-page, description,
license]: Copy-paste from qcoro-qt5.
[arguments, inputs]: Rewrite.

Change-Id: Ib2dd82f3c28600cfdbec1ff7c02f5e185c05a349
2026-05-27 17:41:24 +02:00
Andreas Enge c276bb2d89 gnu: Remove libqaccessibilityclient-qt5.
* gnu/packages/kde-frameworks.scm (libqaccessibilityclient-qt5): Delete variable.

Change-Id: I2bba01ac7b92b3381f9b37d3aa48b80f13ca5426
2026-05-27 17:41:23 +02:00
Andreas Enge c88cd7fcae gnu: Remove qxlsx-qt5.
* gnu/packages/qt.scm (qxlsx-qt5): Delete variable.

Change-Id: Id271d638c2e30bf374f801dc82e10ad6782c43ce
2026-05-27 17:41:21 +02:00
Andreas Enge d7b397aa91 gnu: Add guile-with-gmp.
This variant compiles with GMP instead of the built-in mini-gmp.

* gnu/packages/guile.scm (guile-with-gmp): New variable.

Change-Id: I82f7d52452fef3817566645cadb7df0f48465cdd
2026-05-27 17:36:52 +02:00
jgart 19da15f871 gnu: trealla: Update to 2.100.10.
* gnu/packages/prolog.scm (trealla): Update to 2.100.10.

Change-Id: I0fe95d759a16d00370d89dd2ae3b15dad97b7580
2026-05-27 09:04:10 -04:00
luca 8e871e15a5 gnu: kcachegrind: Update to 26.04.1.
* gnu/packages/kde-sdk.scm (kcachegrind): Update to 26.04.1.

Change-Id: I4cfde19a7d03d50e20231d5263d2cc7373cf7845
2026-05-27 18:01:12 +05:30
Efraim Flashner bf3c923f6d gnu: openshadinglanguage: Don't use custom check phase.
* gnu/packages/graphics.scm (openshadinglanguage)[arguments]: Add
test-exclude keyword. Remove custom 'check phase.

Change-Id: Ie53ba6e148be22ce0fe75d0d86aa839427b5624b
2026-05-27 11:52:57 +03:00
Efraim Flashner 6c7c1a4b28 gnu: Remove rust-pipewire-0.8.0.fd3d8f7.
* gnu/packages/rust-sources.scm (rust-pipewire-0.8.0.fd3d8f7): Remove
variable.

Change-Id: I1154b5d6b530d5e78855925b89aac2e51a090b8e
2026-05-27 11:52:57 +03:00
Efraim Flashner 646ade357a gnu: keepassxc: Don't use custom check phase.
* gnu/packages/password-utils.scm (keepassxc)[arguments]: Add
test-exclude keyword. Remove custom 'check phase.

Change-Id: Id05c6ae14932c79e3df39ce926da57d0f62a0ca5
2026-05-27 11:52:53 +03:00
luca 91c5e436f6 gnu: ninja: Move to build-tools.
* gnu/packages/build-tools.scm (ninja, ninja/pinned, samurai)
  (samu-as-ninja-wrapper): Move to here...
* gnu/packages/ninja.scm (ninja, ninja/pinned, samurai)
  (samu-as-ninja-wrapper): ...from here.  New deprecated variables.
* guix/build-system/cmake.scm (default-ninja):
  Switch to loading from build-tools module.
* guix/build-system/meson.scm (default-ninja): Likewise.

Change-Id: Ia32fb258159cfcc9a0f1ef91c335c71c25a6d7ef
Closes: https://codeberg.org/guix/guix/issues/3595
Merges: https://codeberg.org/guix/guix/pulls/4329
Signed-off-by: Nguyễn Gia Phong <cnx@loang.net>
2026-05-27 16:55:34 +09:00
bdunahu 47deb7a819 gnu: Add font-medieval-sharp.
* gnu/packages/fonts.scm (font-medieval-sharp): New variable.

Change-Id: Icfd91104d0f5d66d8db4fa084463c76484bb3a7f
Merges: https://codeberg.org/guix/guix/pulls/7479
Reviewed-by: moksh <mysticmoksh@riseup.net>
Reviewed-by: kestrel <kestrel.w@proton.me>
Signed-off-by: Nguyễn Gia Phong <cnx@loang.net>
2026-05-27 16:42:00 +09:00
bdunahu 3cb2f74b0d gnu: pantalaimon: Switch to python-dbus.
Since ef6d874c33 ("gnu: python-notify2: Switch to python-dbus."),
python-notify2 propagates python-dbus rather than python-dbus-1.2.
Because pantalaimon propagates python-notify2 as well as
python-dbus-1.2, we have a collision.

python-dbus-1.2 was specified as an input to pantalaimon
in commit 1f9e47518b ("gnu: python-dbus: Rename to python-dbus-1.2 "),
to adapt the reference, so there should be no compatibility reasons
to use the older version.

* gnu/packages/matrix.scm (pantalaimon)[propagated-inputs]:
  Replace python-dbus-1.2 with python-dbus.

Change-Id: I8da0bfab0d0eb25c00625ca3c1674d41a84caed9
Fixes: https://codeberg.org/guix/guix/issues/8839
Merges: https://codeberg.org/guix/guix/issues/8855
Signed-off-by: Nguyễn Gia Phong <cnx@loang.net>
2026-05-27 15:35:26 +09:00
Vagrant Cascadian c1b36b6524 gnu: linux-libre 5.10: Update to 5.10.257.
* gnu/packages/linux.scm (linux-libre-5.10-version): Update to 5.10.257.
(linux-libre-5.10-pristine-source): Update hash.
2026-05-26 20:41:41 -07:00
Vagrant Cascadian e7c2bd4d49 gnu: linux-libre 5.15: Update to 5.15.208.
* gnu/packages/linux.scm (linux-libre-5.15-version): Update to 5.15.208.
(linux-libre-5.15-pristine-source): Update hash.
2026-05-26 20:41:38 -07:00
Vagrant Cascadian 0345a20749 gnu: linux-libre 6.1: Update to 6.1.174.
* gnu/packages/linux.scm (linux-libre-6.1-version): Update to 6.1.174.
(linux-libre-6.1-pristine-source): Update hash.
2026-05-26 20:41:36 -07:00
Vagrant Cascadian 573e9a2f4d gnu: linux-libre 6.6: Update to 6.6.141.
* gnu/packages/linux.scm (linux-libre-6.6-version): Update to 6.6.141.
(linux-libre-6.6-pristine-source): Update hash.
2026-05-26 20:41:33 -07:00
Maxim Cournoyer 17960b2313 doc: Add missing menu entry for volunteer run mirrors.
* doc/guix.texi (Substitutes): Add missing menu entry.

Change-Id: Ia2e6e516ddff3f836b51c34fd8441350793c352d
2026-05-27 09:21:17 +09:00
Anderson Torres 2f6fb22400 gnu: os-prober: Update to 1.84.
* gnu/packages/bootloaders.scm (os-prober): Update to 1.84.
[source]: use git-fetch.

Change-Id: I3b994c8801616df00248858d9f7d8560be1aced6
Signed-off-by: Vagrant Cascadian <vagrant@debian.org>
Co-Authored-by: Vagrant Cascadian <vagrant@debian.org>
2026-05-26 15:57:14 -07:00
Anderson Torres 63e7c1b4ed gnu: os-prober: Cleanup.
* gnu/packages/bootloaders.scm (os-prober): Cleanup.
[arguments]: Use gexps.
[home-page]: Fix redirect.

Change-Id: I81d0112b198f2176768be58fac220e87f8921310
Signed-off-by: Vagrant Cascadian <vagrant@debian.org>
2026-05-26 15:56:32 -07:00
Ron Nazarov cf1c24736e gnu: Add ectool.
* gnu/packages/coreboot.scm (ectool): New variable.

Change-Id: I0fbde5f3c55fc7f43577a73462336859ab48b632
Signed-off-by: Vagrant Cascadian <vagrant@debian.org>
2026-05-26 15:12:59 -07:00
Denis 'GNUtoo' Carikli 87ab0daf6b gnu: Add bucts.
* gnu/packages/coreboot.scm (bucts): New variable.

Co-authored-by: Ron Nazarov <ron@noisytoot.org>
Signed-off-by: Denis 'GNUtoo' Carikli <GNUtoo@cyberdimension.org>
Change-Id: I5964f138c3947298f047afb16dd30b54c396018b
Signed-off-by: Vagrant Cascadian <vagrant@debian.org>
2026-05-26 15:12:48 -07:00
Ricardo Wurmus bfc2d9c69b gnu: python-google-pasta: Fix tests.
* gnu/packages/python-xyz.scm (python-google-pasta)[arguments]: Add phase
'fix-tests to patch procedure name.

Change-Id: Id85b61cc827269b7c38dc1159b197d2de8dd37d9
2026-05-26 20:52:52 +02:00
Sören Tempel b433486c7d gnu: mtr: Remove dependency on libcap.
This is only needed so that mtr can call setcap(8) from its Makefile,
which we don't want it to do.

See https://codeberg.org/guix/guix/issues/8614

* gnu/packages/networking.scm (mtr)[inputs]: Remove libcap.

Change-Id: I0c532cc4772ed2336bf3251aa5dc4b857b47fe7e
2026-05-26 19:44:18 +02:00
Sören Tempel 9609336829 services: web: Add system tests for gunicorn.
* gnu/tests/web.scm (%gunicorn-os): New variable.
(run-gunicorn-test): New variable.
(%test-gunicorn): New variable.

Change-Id: I1ee3fd4c29c7c44aa9c271c6775f953790ca60c3
2026-05-26 18:43:22 +02:00
Sören Tempel 056de157b2 services: gunicorn: Allow configuration of control-socket.
Since gunicorn is run in its own Linux namespace, where $HOME is
read-only, creating that control-socket fails and prevents gunicorn
from starting by default.  Therefore, this patch disables it by
default but allows supplying a custom path via a newly added
configuration field.

* gnu/services/web.scm (gunicorn-app): Add gunicorn-app-control-socket.
(gunicorn-shepherd-services): Respect gunicorn-app-control-socket.
* doc/guix.texi (gunicorn-app): Document it.

Change-Id: I648079b630293a47801713425728a4d602c8088c
2026-05-26 18:43:22 +02:00
Sören Tempel 5b4c715e2a services: gunicorn: Fix usage with non-uri listening addresses.
If the provided unix-socket? parameter is not an URI uri->string returns
to be raised.  For example, on inputs such as "0.0.0.0:8080".  This is
fixed in this commit by first checking if the input parameter is a valid
URI, before calling uri-scheme.

* gnu/tests/web.scm (unix-socket?): Check URI before calling uri-scheme.

Change-Id: Icd9cb1e215a09b1f5dcbec4630e7df3256cde4aa
2026-05-26 18:43:16 +02:00
Nicolas Goaziou 04eaafe0dc gnu: texlive-neoschool: Update to 2026.1-79141.
* gnu/packages/tex.scm (texlive-neoschool): Update to 2026.1-79141.

Change-Id: Iaeb2ad32d983ad49ab2470bdbcfa88eac2dab5dd
2026-05-26 18:36:00 +02:00
jgart 72ad38a46f gnu: trealla: Update to 2.100.9.
* gnu/packages/prolog.scm (trealla): Update to 2.100.9.

Change-Id: Id312720718da7db981122662793384bae95091a6
2026-05-26 12:19:37 -04:00
Anderson Torres 3116440b9a gnu: Remove emacs-4clojure.
Since 2025-12-30 the repository is archived.  Further, the 4clojure site
itself is down for good.

* gnu/packages/emacs-xyz.scm (emacs-4clojure): Delete variable.

Closes guix/guix#7841
Fixes guix/guix!8583

Change-Id: Idd3c12f8a2bf328ff5a35cb63039176d80274fe5
Signed-off-by: Cayetano Santos <csantosb@inventati.org>
2026-05-26 18:15:05 +02:00
Nguyễn Gia Phong d12594eb54 Revert "gnu: qtile: Update to 0.36.0."
This reverts commit 8709675a51.
2026-05-27 00:09:10 +09:00
Cayetano Santos 47dffdc2f6 gnu: nvc: Update to 1.21.0.
* gnu/packages/electronics.scm (nvc): Update to 1.21.0.

Change-Id: I05d41216badd2369722be1ce3ba4b3d8e3138589
2026-05-26 15:13:22 +02:00
Roman Scherer 567d2bc7ea gnu: gtk: Disable svg suite on aarch64.
* gnu/packages/gtk.scm (gtk)[#:configure-flags]: If target-aarch64?,
add “--no-suite=svg”.

Change-Id: Ife603e82bcdacc7034e25e4831dc39a4ad793d3b
Signed-off-by: Liliana Marie Prikler <liliana.prikler@gmail.com>
2026-05-26 15:03:07 +02:00
bdunahu 3a264df1ee gnu: Add angband-sdl2.
* gnu/packages/games.scm (angband-sdl2): New variable.

Change-Id: I855fe78d1157dedf1aa80475f016eced0582883c
Signed-off-by: Liliana Marie Prikler <liliana.prikler@gmail.com>
2026-05-26 15:03:07 +02:00
bdunahu 895f880ac7 gnu: angband: Only delete nonfree assets from checkout.
These changes allow for future graphical versions of this package.

* gnu/packages/patches/angband-remove-nonfree-tile-options.patch: New file.
* gnu/local.mk: (dist_patch_DATA): Register it.
* gnu/packages/games.scm (angband)[source]: Apply it.  Selectively snip out nonfree tilesets.  Do not delete makefiles which enable graphics…
[#:phases]<disable-graphics-and-sounds>: …but do delete them here.
[#:configure-flags]: Add ‘--disable-x11’.

Change-Id: I5cdfcf63747b13ba7763e43fbbf56bfe126a440b
Signed-off-by: Liliana Marie Prikler <liliana.prikler@gmail.com>
2026-05-26 15:03:06 +02:00
Nguyễn Gia Phong 948bac0f46 guix: packages: origin-actual-file-name: Support Fossil.
This fixes the file-name false positive in guix lint.
If an origin-file-name is not specified, fossil-fetch computes one
from the repository's URI and check-in hash.

* guix/fossil-download.scm: Export <fossil-reference> record name.
* guix/packages.scm (origin-actual-file-name): Add support for Fossil.

Change-Id: I740af495c8e624caa947c667c6cbe379ddf033c8
2026-05-26 21:37:17 +09:00
Patrick Norton 8c95d6364a gnu: Add git-quick-stats.
* gnu/packages/version-control.scm (git-quick-stats): New variable.

Merges guix/guix!8748

Change-Id: Icfd4c133491a4faa4e234dd962571b5a4dde8f33
Signed-off-by: Cayetano Santos <csantosb@inventati.org>
2026-05-26 11:28:02 +02:00
Maxim Cournoyer 21898c0a1a Revert "gnu: openresolv: Update to 3.17.4."
This reverts commit 094e50ffc5.  It broke
NetworkManager's name resolution.

Fixes: #8813
2026-05-26 16:07:53 +09:00
Maxim Cournoyer dc4db2273a service: dnsmasq: Expose new options for authoritative operation.
* gnu/services/dns.scm (<dnsmasq-configuration>)
[authoritative-servers, authoritative-zones, host-records]: New fields.
(dnsmasq-shepherd-service): Use them.
* doc/guix.texi (DNS Services): Add a new example and document the new fields.

Change-Id: Ib26c3f59e90b2a9997ecdac03c5564ae02b6754e
Reviewed-by: Nguyễn Gia Phong <cnx@loang.net>
2026-05-26 16:07:53 +09:00
Maxim Cournoyer 7d9b4b7bb7 service: dnsmasq: Add 'locals' configuration option.
* gnu/services/dns.scm (<dnsmasq-configuration>)
[locals]: New field.
(dnsmasq-shepherd-service): Use it.
* doc/guix.texi (DNS Services): Document it.

Change-Id: I1c2bc86c1636aa82451d1a38959380c3791fd8d4
2026-05-26 16:07:53 +09:00
Maxim Cournoyer 185b9f4f19 service: dnsmasq: Add ipv4? and ipv6? configuration options.
* gnu/services/dns.scm (<dnsmasq-configuration>) [ipv4?, ipv6?]: New fields.
(dnsmasq-shepherd-service): Use them.
* doc/guix.texi (DNS Services): Document them.

Change-Id: I50a4e407cea9e55295c9cfff081b7678ab7e061c
2026-05-26 16:07:53 +09:00
Nguyễn Gia Phong 663293331b teams: Nguyễn Gia Phong: Add to the Lua team.
* etc/teams.scm ("Nguyễn Gia Phong"): Add lua to the team list.

Change-Id: I9fe8ce6ac20bb327228473f1217a86905104778a
Merges: https://codeberg.org/guix/guix/pulls/8819
Reviewed-by: Maxim Cournoyer <maxim@guixotic.coop>
Reviewed-by: Carlo Zancanaro <carlo@zancanaro.id.au>
2026-05-26 16:02:18 +09:00
Nguyễn Gia Phong 9b8833ea6e gnu: libfossil: Remove explicit source file name.
* gnu/packages/version-control.scm (libfossil)[source]:
  Remove explicit file-name, which is the same as the default one.

Change-Id: I763d9c4553108e10aa0e4fad18cf5a22a6cbe3ea
2026-05-26 15:59:58 +09:00
luca 664f30f290 gnu: btop: Update to 1.4.7.
* gnu/packages/admin.scm (btop): Update to 1.4.7.

Change-Id: I836386740842fe2127db210b3a55d73d5e1eb2d5
Reviewed-by: Sughosha <sughosha@disroot.org>
Signed-off-by: Nguyễn Gia Phong <cnx@loang.net>
2026-05-26 13:13:46 +09:00
Spencer King 3375afec60 gnu: Add python-islenska.
* gnu/packages/language.scm (arnastofnun-dim)
  (python-islenska-bootstrap, python-islenska): New variables.

Change-Id: I2ccb8cdfa02dc419dffbff4a5b1af81c6af107ce
Merges: https://codeberg.org/guix/guix/pulls/7237
Modified-by: Nguyễn Gia Phong <cnx@loang.net>
Signed-off-by: Nguyễn Gia Phong <cnx@loang.net>
2026-05-26 11:42:50 +09:00
Vagrant Cascadian 74180388ea gnu: linux-libre 6.12: Update to 6.12.91.
* gnu/packages/linux.scm (linux-libre-6.12-version): Update to 6.12.91.
(linux-libre-6.12-pristine-source): Update hash.
2026-05-25 17:05:01 -07:00
Vagrant Cascadian d401b80857 gnu: linux-libre 6.18: Update to 6.18.33.
* gnu/packages/linux.scm (linux-libre-6.18-version): Update to 6.18.33.
(linux-libre-6.18-pristine-source): Update hash.
2026-05-25 17:04:45 -07:00
Vagrant Cascadian 1fb10e0469 gnu: linux-libre 7.0: Update to 7.0.10.
* gnu/packages/linux.scm (linux-libre-7.0-version): Update to 7.0.10.
(linux-libre-7.0-pristine-source): Update hash.
2026-05-25 17:04:42 -07:00
Sharlatan Hellseher d40667e9d9 gnu: packages/python-science: Sort python-[am] variables.
* gnu/packages/python-science.scm (9python-dvc-data, python-dvc-objects,
python-einops, python-fbpca): Sort variables alphabetically.

Change-Id: I19e296bfcc2360e81ceaa81fd44688645113c1a4
2026-05-25 23:57:00 +01:00
Spencer King 5b5ed99030 gnu: Add python-autoray.
* gnu/packages/python-science.scm (python-autoray): New variable.

Merges: guix/guix!8810
Change-Id: I1393870b5e3881cb1e28154361b8c7f7853514eb
Modified-by: Sharlatan Hellseher <sharlatanus@gmail.com>
Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
2026-05-25 23:47:07 +01:00
Sharlatan Hellseher 18a2f2a0ab gnu: go-github-com-sigstore-rekor: Enable more tests.
* gnu/packages/golang-web.scm (go-github-com-sigstore-rekor):
[arguments] <embed-files>: Embed JSON files.
<test-subdirs>: Activate more.
[propagated-inputs]: Add go-github-com-google-rpmpack.

Change-Id: Iaa9b1a367b516af9b37b52f3888ee9b4873cfbbd
2026-05-25 23:37:19 +01:00
Sharlatan Hellseher 5331378604 gnu: Add nfpm.
* gnu/packages/golang-xyz.scm (nfpm): New variable.

Change-Id: I30d402d707048fbb560fa92737940c344331e19e
2026-05-25 23:37:19 +01:00
Sharlatan Hellseher 2126ca5961 gnu: Add chglog.
* gnu/packages/golang-xyz.scm (chglog): New variable.

Change-Id: Ifec35d44fff2eaab6b845fb6e5323db1060480f8
2026-05-25 23:37:14 +01:00
Sharlatan Hellseher 7afcbac09f gnu: Add kubernetes-crd-ref-docs.
* gnu/packages/kubernetes.scm (kubernetes-crd-ref-docs): New variable.

Change-Id: I6fe2b3330fd17a028d855eb78655cdacacc02c38
2026-05-25 23:37:14 +01:00
Sharlatan Hellseher 565f4e8743 gnu: Add kubernetes-controller-tools.
* gnu/packages/kubernetes.scm (kubernetes-controller-tools): New variable.

Change-Id: I91a40a9d0cfed25ecfb262a96739e6b18a5bc77b
2026-05-25 23:37:14 +01:00
Patrick Norton f3e194d6eb gnu: Add go-github-com-goreleaser-nfpm-v2.
* gnu/packages/golang-xyz.scm (go-github-com-goreleaser-nfpm-v2): New
variable.

Change-Id: Ic286a05ce6f67f48e826210d8717ca203706b899
Relates-to: guix/guix!5417
Reviewed-by: Arthur Rodrigues <arthurhdrodrigues@proton.me>
Modified-by: Arthur Rodrigues <arthurhdrodrigues@proton.me>
Modified-by: Sharlatan Hellseher <sharlatanus@gmail.com>
Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>

Change-Id: If2f29158facd446048c5ebb8b808da901d33bfdc
2026-05-25 23:36:57 +01:00
Arthur Rodrigues 2cdc7e23c1 gnu: Add go-github-com-sassoftware-go-rpmutils.
* gnu/packages/golang-compression.scm (go-github-com-sassoftware-go-rpmutils): New variable.

Change-Id: I2ea6bf9f1a288dff3bdaa0749e914d172e3eda06
Relates-to: guix/guix!5417
Modified-by: Sharlatan Hellseher <sharlatanus@gmail.com>
Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
2026-05-25 23:11:16 +01:00
Arthur Rodrigues d21ee40ae8 gnu: Add go-github-com-muesli-mango-cobra.
* gnu/packages/golang-xyz.scm (go-github-com-muesli-mango-cobra): New variable.

Change-Id: I540ab25006c6f798a4c593af7ac4d90293fc6df0
Relates-to: #5417
Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
2026-05-25 23:08:29 +01:00
Arthur Rodrigues de8efe86b3 gnu: Add go-github-com-muesli-mango-pflag.
* gnu/packages/golang-xyz.scm (go-github-com-muesli-mango-pflag): New variable.

Change-Id: I450410eb6a38e9659672a7cd7258f317f372c702
Relates-to: guix/guix!5417
Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
2026-05-25 23:08:29 +01:00
Arthur Rodrigues a30abf4690 gnu: Add go-github-com-muesli-mango.
* gnu/packages/golang-xyz.scm (go-github-com-muesli-mango): New variable.

Change-Id: I76a4cf2583ef083b7cc83c498cd4cb7307ea7cf8
Relates-to: guix/guix!5417
Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
2026-05-25 23:08:29 +01:00
Arthur Rodrigues b7e563cffe gnu: Add go-github-com-muesli-roff.
* gnu/packages/golang-xyz.scm (go-github-com-muesli-roff): New variable.

Change-Id: Id1be530cc9bbcf0422aa6330fd625297c841e489
Relates-to: guix/guix!5417
Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
2026-05-25 23:08:29 +01:00
Arthur Rodrigues 1dfc621cde gnu: Add go-github-com-caarlos0-go-version.
* gnu/packages/golang-xyz.scm (go-github-com-caarlos0-go-version): New variable.

Change-Id: I2ff3528e6ee2d23f093996c25d00c3b5d2b6fee8
Relates-to: guix/guix!5417
Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
2026-05-25 23:08:29 +01:00
Arthur Rodrigues a9db71dae5 gnu: Add go-github-com-invopop-jsonschema.
* gnu/packages/golang-web.scm (go-github-com-invopop-jsonschema): New variable.

Change-Id: Ie1f596c1f9e7e82518cd3697b947306942571d4b
Relates-to: guix/guix!5417
Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
2026-05-25 23:08:28 +01:00
Arthur Rodrigues f8c27ee084 gnu: Add go-github-com-pb33f-ordered-map-v2.
* gnu/packages/golang-xyz.scm (go-github-com-pb33f-ordered-map-v2): New variable.

Change-Id: I1e1124f9b39a4159caad01e2cb2ddeb09dd16e51
Relates-to: guix/guix!5417
Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
2026-05-25 23:08:28 +01:00
Patrick Norton c95418302e gnu: Add go-github-com-goreleaser-chglog.
* gnu/packages/golang-xyz.scm (go-github-com-goreleaser-chglog): New
variable.

Change-Id: Iba81e76b9897fcf90c3ef2434f14034a5db461f8
Relates-to: #5417
Reviewed-by: Arthur Rodrigues <arthurhdrodrigues@proton.me>
Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>

Change-Id: Ib3f02cfa70c89c4763c867405385c11e2706678c
2026-05-25 23:08:28 +01:00
Patrick Norton 79243efc4a gnu: Add go-gitlab-com-digitalxero-go-conventional-commit.
* gnu/packages/golang-vcs.scm
(go-gitlab-com-digitalxero-go-conventional-commit): New variable.

Change-Id: Ia366ebed43a75ee741f2355106f4e7555e3f9375
Relates-to: guix/guix!5417
Reviewed-by: Arthur Rodrigues <arthurhdrodrigues@proton.me>
Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
2026-05-25 23:08:28 +01:00
Patrick Norton 2908ff30dd gnu: Add go-github-com-google-rpmpack.
* gnu/packages/golang-compression.scm (go-github-com-google-rpmpack): New
variable.

Change-Id: I2a7ebd61aaa2e8384c5a9a64f7feefe75dddc57b
Relates-to: guix/guix!5417
Reviewed-by: Arthur Rodrigues <arthurhdrodrigues@proton.me>
Modified-by: Sharlatan Hellseher <sharlatanus@gmail.com>
Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
2026-05-25 23:08:28 +01:00
Patrick Norton 5ae5ced182 gnu: Add go-github-com-cavaliergopher-cpio.
* gnu/packages/golang-compression.scm (go-github-com-cavaliergopher-cpio): New
variable.

Change-Id: I55faf4a19bd29ca16e73540517570518dc3bbf88
Relates-to: guix/guix!5417
Reviewed-by: Arthur Rodrigues <arthurhdrodrigues@proton.me>
Modified-by: Sharlatan Hellseher <sharlatanus@gmail.com>
Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
2026-05-25 23:08:28 +01:00
Patrick Norton dc192b2c3c gnu: Add go-github-com-ccojocar-zxcvbn-go.
* gnu/packages/golang-xyz.scm (go-github-com-ccojocar-zxcvbn-go): New
variable.

Change-Id: I50f943a27db405b04eff54a4485f41b4cc0f5453
Relates-to: guix/guix!5417
Reviewed-by: Arthur Rodrigues <arthurhdrodrigues@proton.me>
Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
2026-05-25 23:08:28 +01:00
Patrick Norton b5c159c14d gnu: Add go-github-com-blakesmith-ar.
* gnu/packages/golang-compression.scm (go-github-com-blakesmith-ar): New
variable.

Change-Id: I0ba5b6617100ae919687193c1ca4c9e97aeadfe5
Relates-to: guix/guix!5417
Reviewed-by: Arthur Rodrigues <arthurhdrodrigues@proton.me>
Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
2026-05-25 23:08:28 +01:00
Patrick Norton b634112df9 gnu: Add go-github-com-aleksi-pointer.
* gnu/packages/golang-xyz.scm (go-github-com-aleksi-pointer): New
variable.

Change-Id: I05e3fdbade711af55fd51ae9f37c8180ba14f44e
Relates-to: guix/guix!5417
Reviewed-by: Arthur Rodrigues <arthurhdrodrigues@proton.me>
Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
2026-05-25 23:08:28 +01:00
Patrick Norton eaafc8f38d gnu: Add go-github-com-elastic-crd-ref-docs.
* gnu/packages/kubernetes.scm (go-github-com-elastic-crd-ref-docs): New variable.

Change-Id: I1d1caae7803946550d0009bb1e207dcb73ee1090
Relates-to: guix/guix!5417
Reviewed-by: Arthur Rodrigues <arthurhdrodrigues@proton.me>
Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>

Change-Id: I7cc15ba804ac36fefd3e3f59a480e6e7cf33bc98
2026-05-25 23:08:27 +01:00
Patrick Norton 01cbcb4ee4 gnu: Add go-github-com-tcnksm-go-httpstat.
* gnu/packages/golang-web.scm (go-github-com-tcnksm-go-httpstat): New
variable.

Change-Id: I408ca9bd82cf5f525459108a563457d5f8417e2b
Relates-to: guix/guix!5417
Reviewed-by: Arthur Rodrigues <arthurhdrodrigues@proton.me>
Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
2026-05-25 23:08:27 +01:00
Patrick Norton c61cab0077 gnu: Add go-github-com-toqueteos-webbrowser.
* gnu/packages/golang-web.scm (go-github-com-toqueteos-webbrowser): New variable.

Change-Id: I7a9ae128062dcb3015eed65ac4bdc3fb9e7b40c1
Relates-to: guix/guix!5417
Reviewed-by: Arthur Rodrigues <arthurhdrodrigues@proton.me>
Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
2026-05-25 23:08:27 +01:00
Patrick Norton 4a28c0c638 gnu: Add go-sigs-k8s-io-controller-tools.
* gnu/packages/kubernetes.scm (go-sigs-k8s-io-controller-tools): New
variable.

Change-Id: Iea8c614f484076374a7cf6b9a730bb494d303c03
Relates-to: guix/guix!5417
Reviewed-by: Arthur Rodrigues <arthurhdrodrigues@proton.me>
Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
2026-05-25 23:08:27 +01:00
Arthur Rodrigues ba62c285a3 gnu: Add go-github-com-gobuffalo-flect.
* gnu/packages/golang-xyz.scm (go-github-com-gobuffalo-flect): New variable.

Change-Id: I80a9882d9441e758fd9793c08a27965b88935ddc
Relates-to: guix/guix!5417
Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
2026-05-25 23:08:24 +01:00
Sharlatan Hellseher d1b4f8e8ad gnu: go-jsonnet: Update to 0.22.0.
* gnu/packages/golang-apps.scm (go-jsonnet): Update to 0.22.0.

Change-Id: Ic7bf26e20846644ddd653e612541b3c631f338e1
2026-05-25 21:47:16 +01:00
Sharlatan Hellseher eccf44b2d1 gnu: go-fxlint: Update to 1.24.0.
* gnu/packages/golang-apps.scm (go-fxlint): Update to 1.24.0.

Change-Id: Ib5e1ffbad1de673e55edd7660e04ff7ebf7064ae
2026-05-25 21:46:35 +01:00
Sharlatan Hellseher 616ef76552 gnu: go-chroma: Update to 2.24.1.
* gnu/packages/golang-apps.scm (go-chroma): Update to 2.24.1.

Change-Id: Ic4cccd700c5241319ea931b3b76b7e3d9f3acede
2026-05-25 21:43:59 +01:00
Ankit Gadiya 8b0bee2a97 gnu: gopls: Update to 0.22.0.
* gnu/packages/golang-apps.scm (gopls): Update to 0.22.0.
[arguments]: Use go-1.26.
[native-inputs]: Remove go-golang-org-x-sys; add
go-github-com-fsnotify-fsnotify, go-github.com-google-jsonschema-go,
go-github-com-modelcontextprotocol-go-sdk.

Merges: guix/guix!8825
Change-Id: I28049d4faf92f54dc382abb64d2a2ff0570caccf
Modified-by: Sharlatan Hellseher <sharlatanus@gmail.com>
Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
2026-05-25 21:43:59 +01:00
Cayetano Santos 37592835c4 doc: Add agitjo under the ’perfect setup’ section.
This is a complement to the AGit workflow included in "Submitting
Patches".

* doc/guix.texi: Mention ‘emacs-agitjo’ in the ’Emacs’ subsection.

Merges guix/guix!8445

Change-Id: Ia49a0da71e8b08e252ff4dd996c414173920ecac
2026-05-25 19:57:33 +02:00
Hugo Buddelmeijer 6f6dc2286c gnu: valgrind/interactive: Fix shebangs by adding python as input.
* gnu/packages/valgrind.scm (valgrind/interactive): Fix shebangs.
  [inputs]: Add python.

Change-Id: Idc8590bfe5ed529046cb41f365de759c1c07effd
Merges: https://codeberg.org/guix/guix/pulls/8611
Signed-off-by: Nguyễn Gia Phong <cnx@loang.net>
2026-05-26 00:43:54 +09:00
Ashish SHUKLA b48412b52f gnu: got: Update to 0.125
* gnu/packages/version-control.scm (got): Update to 0.125.

Change-Id: I08867461d0c70cbceadcb82defc191fe1e45e7e7
Merges: https://codeberg.org/guix/guix/pulls/8677
Signed-off-by: Nguyễn Gia Phong <cnx@loang.net>
2026-05-26 00:38:12 +09:00
Foster Hangdaan 8709675a51 gnu: qtile: Update to 0.36.0.
* gnu/packages/wm.scm (qtile): Update to 0.36.0.

Change-Id: I6d91026ed7462a76f8c4fa87885ed591f6bdbac7
Merges: https://codeberg.org/guix/guix/pulls/8817
Signed-off-by: Nguyễn Gia Phong <cnx@loang.net>
2026-05-26 00:32:45 +09:00
Zhu Zihao 59e74d19f3 time-machine: Use accurate word for time travel in command help.
Time travel works in both directions, as mentioned in
info "(guix) Invoking guix time-machine".

* guix/scripts/time-machine.scm (show-help): Amend 'in an older version'
  with 'in a different version'.

Change-Id: I5da267e58e64381de86d6711dcd104592c30ef6c
Merges: https://codeberg.org/guix/guix/pulls/1163
Reviewed-by: Andreas Enge <andreas@enge.fr>
Signed-off-by: Nguyễn Gia Phong <cnx@loang.net>
2026-05-26 00:23:01 +09:00
Nemin 31566995dc doc: Mention the volunteer run mirrors.
* doc/guix.texi (Volunteer Run Mirrors): New subsection.
* doc/guix.texi (Official Substitution Servers):
  Rephrase due to new subsection.

Change-Id: I6e0861b632a78b705ce7ed8615a423c6d370f4c9
Merges: https://codeberg.org/guix/guix/pulls/6272
Reviewed-by: Maxim Cournoyer <maxim@guixotic.coop>
Signed-off-by: Nguyễn Gia Phong <cnx@loang.net>
2026-05-26 00:20:52 +09:00
Yappaholic 4d65795173 gnu: Add lua-5.5.
* gnu/packages/lua.scm (lua-5.5): New variable.

Merges: https://codeberg.org/guix/guix/pulls/8515
Reviewed-by: Carlo Zancanaro <carlo@zancanaro.id.au>
Signed-off-by: Nguyễn Gia Phong <cnx@loang.net>
2026-05-26 00:13:16 +09:00
Phillip Davis 781c25ada9 tests: import: gem: Add test for mixed valid and gibberish licenses.
Verifies that when only one of multiple license strings is recognized,
the resulting list has the correct license followed by one instance
of the symbol 'unknown-license!

* tests/import/gem.scm (test-mixed-licenses-json): New fixture.
  ("gem->guix-package with mixed valid and gibberish licenses"):
  New test.

Change-Id: I33a003d50ba20d30360b52c448ae28ad9d37233b
Merges: https://codeberg.org/guix/guix/pulls/8276
Reviewed-by: Carlo Zancanaro <carlo@zancanaro.id.au>
Signed-off-by: Nguyễn Gia Phong <cnx@loang.net>
2026-05-26 00:09:55 +09:00
Phillip Davis 514b17c58a tests: import: gem: Add test for unrecognized license identifiers.
Exercises the map in 4f78d33f0 where every license
string is unrecognized, so the resulting package should have
(license (list unknown-license! unknown-license!)).

* tests/import/gem.scm (test-gibberish-licenses-json): New fixture.
  ("gem->guix-package with gibberish license identifiers"): New test.

Change-Id: I85cbb0574f9393749a84f4cf5818d4c1083a8476
Reviewed-by: Carlo Zancanaro <carlo@zancanaro.id.au>
Signed-off-by: Nguyễn Gia Phong <cnx@loang.net>
2026-05-26 00:09:43 +09:00
Phillip Davis 3df17cb25a import: gem: Use spdx-string->license for license lookup.
Similar to what was done for the crate importer in 263a267b75.

* guix/import/gem.scm (string->license): Try spdx-string->license first,
  returning symbols instead of license objects.  Fall back
  to the existing hardcoded table for non-SPDX strings.
  (make-gem-sexp): Remove license->symbol calls;
  licenses are now symbols directly.
* tests/import/gem.scm (test-spdx-json): New fixture.
  ("gem->guix-package with SPDX license identifiers"): New test.

Change-Id: I5fa0ebdfd3a3393eab5ef0554ed09887a89bc107
Reviewed-by: Carlo Zancanaro <carlo@zancanaro.id.au>
Signed-off-by: Nguyễn Gia Phong <cnx@loang.net>
2026-05-26 00:09:12 +09:00
Phillip Davis abbf03a2ef import: gem: Fix null at home-page.
The RubyGems API returns "homepage_uri": null for gems with no homepage.
guile-json parses JSON null as the Guile symbol 'null', which passes
through into the generated package sexp as (home-page null)—an unbound
variable error at evaluation time.

* tests/import/gem.scm (test-no-homepage-json): New fixture.
  ("gem->guix-package, bald homepage_uri"): New test.
* guix/import/gem.scm (non-empty-string-or-false): New procedure.
  (<gem>)[home-page]: Use it.
* guix/import/utils.scm (non-empty-string-or-false):
  New exported procedure, moved to here...
* guix/import/gem.scm (non-empty-string-or-false): ...from here...
* guix/import/pypi.scm (non-empty-string-or-false): ...and here.

Change-Id: If8f2ca32834d762c753797067ef87937503ff9f9
Reviewed-by: Carlo Zancanaro <carlo@zancanaro.id.au>
Signed-off-by: Nguyễn Gia Phong <cnx@loang.net>
2026-05-26 00:08:11 +09:00
Roman Scherer 5bad9d084c gnu: inkscape: Disable geom-pathstroke-test on non-x68.
* gnu/packages/inkscape.scm (inkscape)[arguments]<#:phases>:
  Add disable-geom-pathstroke-test on non-x68.

Change-Id: Ifbd4429d55fd3a66796b7f0219c1b4f1bb00be14
Merges: https://codeberg.org/guix/guix/pulls/8812
Signed-off-by: Nguyễn Gia Phong <cnx@loang.net>
2026-05-26 00:04:28 +09:00
Roman Scherer a066241c22 gnu: lib2geom: Disable failing polynomial-test on non-x68.
* gnu/packages/graphics.scm (lib2geom)[arguments]<#:phases>:
  Add disable-polynomial-test on non-x86.

Change-Id: If8fea8381d9ad4e31719463aa6a78efc8ef24efb
Signed-off-by: Nguyễn Gia Phong <cnx@loang.net>
2026-05-26 00:04:28 +09:00
Nguyễn Gia Phong a12284aeba teams: Nguyễn Gia Phong: Remove from the Python team.
* etc/teams.scm ("Nguyễn Gia Phong"): Remove python from the team list.

Change-Id: Ia0b43321b756ec45c8d8b215da57c824c5670dc8
Merges: https://codeberg.org/guix/guix/pulls/8792
2026-05-25 23:40:29 +09:00
Sughosha 1ebc547b5a gnu: Add skcms.
* gnu/packages/graphics.scm (skcms): New variable.

Change-Id: I9aba6db9a09f22d91f9b45ef3ac9913c701c6ff5
Merges: https://codeberg.org/guix/guix/pulls/8719
Signed-off-by: Nguyễn Gia Phong <cnx@loang.net>
2026-05-25 22:54:42 +09:00
Sughosha 192806899f gnu: Add sjpeg.
* gnu/packages/image.scm (sjpeg): New variable.

Change-Id: I4eaba610e73848116ab0f5f106dc92e126b0209e
Signed-off-by: Nguyễn Gia Phong <cnx@loang.net>
2026-05-25 22:54:42 +09:00
Sughosha 7c23908791 gnu: Add openjph.
* gnu/packages/image.scm (openjph): New variable.

Change-Id: Id1f082e887672e854d23191efd3cfe47630d0c49
Signed-off-by: Nguyễn Gia Phong <cnx@loang.net>
2026-05-25 22:54:42 +09:00
226 changed files with 9350 additions and 6201 deletions
+5 -6
View File
@@ -42,12 +42,11 @@
;; For use with 'bug-reference-prog-mode'. Extra bug-reference
;; configuration should be done in your Emacs user configuration file;
;; refer to (info (guix) The Perfect Setup).
(eval . (setq-local
;; #8545, guix/guix#8545, guix/guix!8545, but not !8545
bug-reference-bug-regexp
(rx (group (or (seq (zero-or-more "guix/guix") "#")
(seq (one-or-more "guix/guix") "!"))
(group (one-or-more digit))))))
(eval . (setq-local bug-reference-bug-regexp
;; #8545 (issues), !8545 (PRs), guix/guix#8545 and
;; guix/guix!8545
(rx (group (seq (? "guix/guix") (or "#" "!"))
(group (one-or-more digit))))))
(bug-reference-url-format . "https://codeberg.org/guix/guix/issues/%s")
(eval . (add-to-list 'completion-ignored-extensions ".go"))
+6 -6
View File
@@ -292,12 +292,12 @@ guix/build-system/julia\.scm @guix/julia
gnu/packages/(kde)(-.+|)\.scm$ @guix/kde
gnu/build/linux-modules\.scm @guix/kernel
gnu/packages/aux-files/linux-libre.*$ @guix/kernel
gnu/packages/linux\.scm @guix/kernel
gnu/tests/linux-modules\.scm @guix/kernel
guix/build/linux-module-build-system\.scm @guix/kernel
guix/build-system/linux-module\.scm @guix/kernel
gnu/build/linux-modules\.scm @guix/linux-libre
gnu/packages/aux-files/linux-libre.*$ @guix/linux-libre
gnu/packages/linux\.scm @guix/linux-libre
gnu/tests/linux-modules\.scm @guix/linux-libre
guix/build/linux-module-build-system\.scm @guix/linux-libre
guix/build-system/linux-module\.scm @guix/linux-libre
gnu/packages/lisp(-.+|)\.scm$ @guix/lisp
guix/build/asdf-build-system\.scm @guix/lisp
+8
View File
@@ -1281,6 +1281,14 @@ $(GIT_HOOKS_DIR):
$(GIT_HOOKS_DIR)/%: etc/git/% | $(GIT_HOOKS_DIR)/
if [ -n "$(GIT_HOOKS_DIR)" ]; then cp "$<" "$@"; fi
# Special-case the pre-push hook installation, to ensure it is always
# up-to-date with its source.
.PHONY: $(GIT_HOOKS_DIR)/pre-push
$(GIT_HOOKS_DIR)/pre-push: etc/git/pre-push | $(GIT_HOOKS_DIR)
@if [ -n "$(GIT_HOOKS_DIR)" ]; then \
cmp "--silent" "$<" "$@" || cp "$<" "$@"; \
fi
$(GIT_CONFIG_FILE): etc/git/gitconfig
if [ -n "$(GIT_CONFIG_FILE)" ]; then \
git config --fixed-value --replace-all include.path \
+1
View File
@@ -120,6 +120,7 @@ running 'guix-daemon $extra_options'" >&2
"@abs_top_builddir@/pre-inst-env" \
"@abs_top_builddir@/guix-daemon" \
$extra_options \
--allow-aslr \
--substitute-urls="$GUIX_BINARY_SUBSTITUTE_URL" &
daemon_pid=$!
+27
View File
@@ -618,6 +618,33 @@ enhance @code{scheme-mode} and Geiser. @xref{Introduction,,,
emacs-guix, Emacs-Guix Reference Manual}, to make sure you don't miss
out!
@unnumberedsubsubsec Submitting Pull Requests Following the AGit Workflow
@cindex AGit workflow, for pull requests (Emacs).
@url{https://codeberg.org/halvin/agitjo, Agitjo} is a helper to ease
AGit workflow based patch submission (@pxref{Submitting Patches}).
Install it with:
@example
guix install emacs-agitjo
@end example
Assuming your local checkout is on the branch containing the changes you
would like to submit for inclusion in the @code{master} branch, use
@command{M-x agitjo-push} then:
@itemize
@item
Set options like the title @option{-t} and the session identifier
@option{-s}.
@item
Invoke one of the push commands to execute a @command{git push} operation.
@end itemize
When creating a new pull request, a dedicated buffer will open for
drafting a description. The force-push option @option{-f} is enabled to
push changes to the existing pull request.
@unnumberedsubsubsec Taming Boilerplate with Templates
@cindex code snippets
+146 -14
View File
@@ -53,7 +53,7 @@ Copyright @copyright{} 2017, 2019--2026 Maxim Cournoyer@*
Copyright @copyright{} 20172022 Tobias Geerinckx-Rice@*
Copyright @copyright{} 2017 George Clemmer@*
Copyright @copyright{} 2017 Andy Wingo@*
Copyright @copyright{} 2017, 2018, 2019, 2020, 2023, 2024, 2025 Arun Isaac@*
Copyright @copyright{} 2017, 2018, 2019, 2020, 2023, 2024, 2025, 2026 Arun Isaac@*
Copyright @copyright{} 2017 nee@*
Copyright @copyright{} 2018 Rutger Helling@*
Copyright @copyright{} 2018, 2021, 2023, 2025, 2026 Oleg Pykhalov@*
@@ -124,7 +124,7 @@ Copyright @copyright{} 2023 Thomas Ieong@*
Copyright @copyright{} 2023 Saku Laesvuori@*
Copyright @copyright{} 2023 Graham James Addis@*
Copyright @copyright{} 2023-2025 Tomas Volf@*
Copyright @copyright{} 2024, 2025 Herman Rimm@*
Copyright @copyright{} 2024-2026 Herman Rimm@*
Copyright @copyright{} 2024 Matthew Trzcinski@*
Copyright @copyright{} 2024 Richard Sent@*
Copyright @copyright{} 2024 Dariqq@*
@@ -152,6 +152,7 @@ Copyright @copyright{} 2026 David Elsing@*
Copyright @copyright{} 2026 Nguyễn Gia Phong@*
Copyright @copyright{} 2026 Yarl Baudig@*
Copyright @copyright{} 2026 Joan Vilardaga Castro@*
Copyright @copyright{} 2026 Nemin@*
Permission is granted to copy, distribute and/or modify this document
under the terms of the GNU Free Documentation License, Version 1.3 or
@@ -305,6 +306,7 @@ Package Management
Substitutes
* Official Substitute Servers:: One particular source of substitutes.
* Volunteer Run Mirrors:: Additional, regional sources of substitutes.
* Substitute Server Authorization:: How to enable or disable substitutes.
* Getting Substitutes from Other Servers:: Substitute diversity.
* Substitute Authentication:: How Guix verifies substitutes.
@@ -1779,6 +1781,21 @@ user namespaces is missing (@pxref{Build Environment Setup}). Use at
your own risk!
@end quotation
@cindex ASLR (address space layout randomization), for builds
@cindex address space layout randomization (ASLR), for builds
@cindex Docker, running @command{guix-daemon}
@cindex @command{guix-daemon}, running under Docker
@item --allow-aslr
Allow builds to start even if @acronym{ASLR, Address Space Layout
Randomization} cannot be disabled on Linux systems. This is normally
done so as to increase reproducibility, but some environments, such as
those affected by Docker's default seccomp policy, don't permit
disabling ASLR. Passing this option will allow builds to start with
reduced reproducibility regardless.
Note that passing this option doesn't ensure that ASLR is enabled, it
only allows builds to start even when disabling it is blocked.
@item --isolate-host-loopback
Prevent fixed-output chroot builds from accessing the host loopback.
When this is used, fixed-output builds will have their own loopback
@@ -3936,6 +3953,7 @@ also result from derivation builds, can be available as substitutes.
@menu
* Official Substitute Servers:: One particular source of substitutes.
* Volunteer Run Mirrors:: Additional, regional sources of substitutes.
* Substitute Server Authorization:: How to enable or disable substitutes.
* Getting Substitutes from Other Servers:: Substitute diversity.
* Substitute Authentication:: How Guix verifies substitutes.
@@ -3966,13 +3984,54 @@ could use the information gathered to determine, for instance, whether
your system has unpatched security vulnerabilities.
Substitutes from the official build farms are enabled by default when
using Guix System (@pxref{GNU Distribution}). However,
they are disabled by default when using Guix on a foreign distribution,
unless you have explicitly enabled them via one of the recommended
installation steps (@pxref{Installation}). The following paragraphs
describe how to enable or disable substitutes for the official build
farm; the same procedure can also be used to enable substitutes for any
other substitute server.
using Guix System (@pxref{GNU Distribution}). However, they are
disabled by default when using Guix on a foreign distribution, unless
you have explicitly enabled them via one of the recommended installation
steps (@pxref{Installation}). Please @pxref{Substitute Server
Authorization} on how to enable or disable substitutes for the official
build farm; the same procedure can also be used to enable substitutes
for any other substitute server.
@node Volunteer Run Mirrors
@subsection Volunteer Run Mirrors
@cindex substitutes
@cindex mirrors
Beyond the two official substitute servers, there are additionally
volunteer run mirrors. These mirrors do not build their own
substitutes, but rather copy them from the official build farm and
distribute them to users. Enabling a mirror may be beneficial in case
the official servers are temporarily unavailable or provide inadequate
bandwidth at the user's location.
@quotation Note
Mirrored substitutes are signed by the original builder, not the mirror.
This means that mirror operators @strong{cannot} add or modify binaries,
as long as you trust only the official substitute servers,
@pxref{Substitute Server Authorization}.
@end quotation
List of volunteer run mirrors, grouped by location (with the build farm
they mirror in parentheses):
@table @asis
@item Germany
@itemize
@item @code{https://hydra-guix-129.guix.gnu.org} (bordeaux.guix.gnu.org)
@end itemize
@item People's Republic of China
@itemize
@item @code{https://mirrors.sjtug.sjtu.edu.cn/guix} (ci.guix.gnu.org)
@item @code{https://mirrors.sjtug.sjtu.edu.cn/guix-bordeaux} (bordeaux.guix.gnu.org)
@end itemize
@item Russia
@itemize
@item @code{https://mirror.yandex.ru/mirrors/guix/} (bordeaux.guix.gnu.org)
@end itemize
@end table
To enable receiving substitutions from these mirrors, please @pxref{Getting
Substitutes from Other Servers}.
@node Substitute Server Authorization
@subsection Substitute Server Authorization
@@ -16065,6 +16124,10 @@ the tag name for separating the numbers of the version.
pre-releases; to make it also look for pre-releases, set the this
property to @code{#t}.
@item @code{stable-version-regexp}: a regular expression for matching the
version string, if specified the updater will pick the latest version from
matching ones when the @option{--target-version} option is omitted.
@end itemize
@lisp
@@ -16651,6 +16714,12 @@ guix lint @var{options} @var{package}@dots{}
@end example
If no package is given on the command line, then all packages are checked.
To check packages in particular source files, the syntax is:
@example
guix lint @var{options} --whole-file @var{file}@dots{}
@end example
The @var{options} may be zero or more of the following:
@table @code
@@ -16688,9 +16757,23 @@ Only enable the checkers that do not depend on Internet access.
Add @var{directory} to the front of the package module search path
(@pxref{Package Modules}).
This allows users to define their own packages and make them visible to
the command-line tools.
@item --whole-file
@itemx -f
Check the top-level package definitions in the given files; subsequent
arguments are treated as file names rather than package names. This
option also enables a special checker which checks if a package
alphabetically succeeds the one above it.
For example, to check if the packages in @file{gnu/packages/matrix.scm}
are sorted alphabetically, and if the package names therein follow
established conventions, run:
@example
guix lint -c name -f gnu/packages/matrix.scm
@end example
The previous two options allow users to define their own packages and
make them visible to the command-line tools.
@end table
@node Invoking guix size
@@ -36234,6 +36317,10 @@ Launch the app as this group (it must be an existing group).
A list of sockets (as path strings) which gunicorn will be listening
on. This list must contain at least one socket.
@item @code{control-socket} (default: #f) (type: string)
If set, creates a gunicorn control-socket at the given path. Note that,
the control socket should refer to a path listed in @code{mappings}.
@item @code{socket-user} (default: @code{user}) (type: string)
Owner of the directory containing the socket (must be an existing user).
@@ -36678,13 +36765,16 @@ The Mumi package to use.
Data directory to store Debbugs data from upstream Debbugs instance.
@item @code{rsync-remote}
Remote rsync path from which to download Debbugs data. The remote is
polled every 5 minutes, unless a previous instance of rsync is already
running.
Remote rsync path from which to download Debbugs data.
@item @code{rsync-flags} (default: @code{'()})
Additional flags to pass to @command{rsync}.
@item @code{rsync-and-index-event} (default: @code{#~(calendar-event #:minutes '#$(iota 12 0 5))})
Shepherd calendar event to run the rsync and indexing timer at. By
default, this is once every 5 minutes. The timer job is not run if an
earlier instance of it is still running.
@item @code{mailer?} (default: @code{#true})
Whether to enable or disable the mailer component.
@@ -38069,6 +38159,21 @@ This is the type of the dnsmasq service, whose value should be a
(servers '("192.168.1.1"))))
@end lisp
The following example shows a slightly more complex configuration that
defines an authoritative DNS server on a given subdomain.
@lisp
(service dnsmasq-service-type
(dnsmasq-configuration
(listen-addresses '("10.1.1.1"))
(no-resolv? #t)
(no-hosts? #t)
(authoritative-servers '("vpn.example.com")) ;self
(authoritative-zones '("vpn.example.com"))
(host-records '("some-service.vpn.example.com,10.1.1.1"))))
@end lisp
For more examples, refer to @samp{man 8 dnsmasq.}
@code{dnsmasq-service-type} provides two actions:
@table @code
@@ -38158,12 +38263,33 @@ ie a subnet for which an interface exists on the server.
@item @code{listen-addresses} (default: @code{'()})
Listen on the given IP addresses.
@item @code{ipv4?} (default: @code{#t})
Whether to include A records in answers.
@item @code{ipv6?} (default: @code{#t})
Whether to include AAAA records in answers.
@item @code{resolv-file} (default: @code{"/etc/resolv.conf"})
The file to read the IP address of the upstream nameservers from.
@item @code{no-resolv?} (default: @code{#f})
When true, don't read @var{resolv-file}.
@item @code{authoritative-servers} (default: @code{'()})
A list of strings corresponding to valid @option{--auth-server} values,
such as a domain name. This is useful to make @command{dnsmasq}
authoritative for a given domain name or interface.
@item @code{authoritative-zones} (default: @code{'()})
A list of strings corresponding to valid @option{--auth-zone} values,
such as a domain name. This is useful to make @command{dnsmasq}
authoritative for a given domain name. Note that this must be used in
conjunction with the @code{authoritative-servers} option.
@item @code{host-records} (default: @code{'()})
A list of strings corresponding to valid @option{--host-record} values,
for example @code{'("some-service.example.com,10.1.1.1")}.
@item @code{forward-private-reverse-lookup?} (default: @code{#t})
When false, all reverse lookups for private IP ranges are answered with
"no such domain" rather than being forwarded upstream.
@@ -38172,6 +38298,12 @@ When false, all reverse lookups for private IP ranges are answered with
When true, dnsmasq queries the servers in the same order as they appear
in @var{servers}.
@item @code{locals} (default: @code{'()})
Specify domain name @emph{patterns} which should be treated as local,
that is, for which there should be no delegation to upstream servers.
Provided pattern values should be of the form
@code{'("/vpn.example.com/")}.
@item @code{servers} (default: @code{'()})
Specify IP address of upstream servers directly.
+6 -5
View File
@@ -1,5 +1,4 @@
#!/bin/sh
# From Gerrit Code Review 3.11.1.
#
# Part of Gerrit Code Review (https://www.gerritcodereview.com/)
#
@@ -70,9 +69,9 @@ dest="$1.tmp.${random}"
trap 'rm -f "$dest" "$dest-2"' EXIT
if ! cat "$1" | sed -e '/>8/q' | git stripspace --strip-comments > "${dest}" ; then
echo "cannot strip comments from $1"
exit 1
if ! sed -e '/>8/q' "$1" | git stripspace --strip-comments > "${dest}" ; then
echo "cannot strip comments from $1"
exit 1
fi
if test ! -s "${dest}" ; then
@@ -91,7 +90,7 @@ else
pattern=".*"
fi
if git interpret-trailers --parse < "$1" | grep -q "^$token: $pattern$" ; then
if git interpret-trailers --no-divider --parse < "$1" | grep -q "^$token: $pattern$" ; then
exit 0
fi
@@ -99,6 +98,7 @@ fi
# sentinel at the end to make sure there is one.
# Avoid the --in-place option which only appeared in Git 2.8
if ! git interpret-trailers \
--no-divider \
--trailer "Signed-off-by: SENTINEL" < "$1" > "$dest-2" ; then
echo "cannot insert Signed-off-by sentinel line in $1"
exit 1
@@ -110,6 +110,7 @@ fi
# Avoid the --in-place option which only appeared in Git 2.8
# Avoid the --where option which only appeared in Git 2.15
if ! git -c trailer.where=before interpret-trailers \
--no-divider \
--trailer "Signed-off-by: $token: $value" < "$dest-2" |
sed -e "s/^Signed-off-by: \($token: \)/\1/" \
-e "/^Signed-off-by: SENTINEL/d" > "$dest" ; then
+7 -7
View File
@@ -876,8 +876,8 @@ and the maven-build-system."
"The plasma desktop environment, and KDE Applications."
#:scope (list (make-regexp* "^gnu/packages/(kde)(-.+|)\\.scm$"))))
(define-team kernel
(team 'kernel
(define-team linux-libre
(team 'linux-libre
#:name "Linux-libre kernel team"
#:scope (list "gnu/build/linux-modules.scm"
(make-regexp* "^gnu/packages/aux-files/linux-libre.*$")
@@ -1298,7 +1298,7 @@ the \"texlive\" importer."
(define-member (person "Leo Famulari"
"leo@famulari.name"
"lfam")
kernel)
linux-libre)
(define-member (person "Efraim Flashner"
"efraim@flashner.co.il"
@@ -1383,7 +1383,7 @@ the \"texlive\" importer."
(define-member (person "Vagrant Cascadian"
"vagrant@debian.org"
"vagrantc")
debian embedded kernel)
debian embedded linux-libre)
(define-member (person "Vagrant Cascadian" ;XXX: duplicate
"vagrant@reproducible-builds.org"
@@ -1537,7 +1537,7 @@ the \"texlive\" importer."
(define-member (person "Rodion Goritskov"
"rodion@goritskov.com"
"rodion-goritskov")
games java kde kernel release)
games java kde linux-libre release)
(define-member (person "Jason Conroy"
"jconroy@tscripta.net"
@@ -1577,7 +1577,7 @@ the \"texlive\" importer."
(define-member (person "Nguyễn Gia Phong"
"cnx@loang.net"
"cnx")
build-tools python qa-packages sysadmin vcs)
build-tools lua qa-packages sysadmin vcs)
(define-member (person "Lilah Tascheter"
"lilah@lunabee.space"
@@ -1622,7 +1622,7 @@ the \"texlive\" importer."
(define-member (person "Wilko Meyer"
"w@wmeyer.eu"
"theesm")
kernel perl)
linux-libre perl)
(define-member (person "Untrusem"
"mysticmoksh@riseup.net"
+10 -1
View File
@@ -173,7 +173,16 @@ SYSTEM."
(define (core-packages system)
"Return the 'core' package set suitable for SYSTEM, which might be a system
type or a GNU triplet."
(cond ((target-linux? system) (append %core-packages %linux-packages))
(cond ((target-linux? system)
(append %core-packages
%linux-packages
(cond ((target-arm32? system)
(list linux-libre-arm-generic))
((target-aarch64? system)
(list linux-libre-arm64-generic))
((target-riscv64? system)
(list linux-libre-riscv64-generic))
(else '()))))
((target-hurd? system) (append %core-packages %hurd-packages))
((target-mingw? system) %core-packages-for-mingw)
(else '())))
+7 -10
View File
@@ -1006,6 +1006,7 @@ dist_patch_DATA = \
%D%/packages/patches/alure-dumb-2.patch \
%D%/packages/patches/amd-smi-newer-libdrm.patch \
%D%/packages/patches/amd-smi-python.patch \
%D%/packages/patches/angband-remove-nonfree-tile-options.patch \
%D%/packages/patches/ibus-anthy-fix-tests.patch \
%D%/packages/patches/ibus-table-paths.patch \
%D%/packages/patches/antiword-CVE-2014-8123.patch \
@@ -1880,6 +1881,7 @@ dist_patch_DATA = \
%D%/packages/patches/lua-5.4-pkgconfig.patch \
%D%/packages/patches/lua-5.4-liblua-so.patch \
%D%/packages/patches/lua-5.4-search-paths.patch \
%D%/packages/patches/lua-5.5-search-paths.patch \
%D%/packages/patches/lua-5.x-search-path-helpers.patch \
%D%/packages/patches/lua-lgi-fix-pango.patch \
%D%/packages/patches/lua-lgi-fix-ref.patch \
@@ -1965,7 +1967,7 @@ dist_patch_DATA = \
%D%/packages/patches/mswebrtc-cmake.patch \
%D%/packages/patches/mtools-mformat-uninitialized.patch \
%D%/packages/patches/mupen64plus-ui-console-notice.patch \
%D%/packages/patches/musl-cross-locale.patch \
%D%/packages/patches/musl-CVE-2026-40200.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 \
@@ -1991,6 +1993,7 @@ dist_patch_DATA = \
%D%/packages/patches/nhc98-c-update.patch \
%D%/packages/patches/nheko-0-12-1-fix-rendering-replies.patch \
%D%/packages/patches/nix-dont-build-html-doc.diff \
%D%/packages/patches/nlohmann_json_fix_char8_t.patch \
%D%/packages/patches/nfs4-acl-tools-0.3.7-fixpaths.patch \
%D%/packages/patches/neovim-tree-sitter-grammar-path.patch \
%D%/packages/patches/network-manager-plugin-ownership.patch \
@@ -2021,7 +2024,6 @@ dist_patch_DATA = \
%D%/packages/patches/ocaml-4.07-dynamically-allocate-signal-stack.patch \
%D%/packages/patches/ocaml-4.09-dynamically-allocate-signal-stack.patch \
%D%/packages/patches/ocaml-4.09-multiple-definitions.patch \
%D%/packages/patches/ogs-6.5.7-netcdfconverter.patch \
%D%/packages/patches/omake-fix-non-determinism.patch \
%D%/packages/patches/oneko-remove-nonfree-characters.patch \
%D%/packages/patches/onetbb-other-arches.patch \
@@ -2366,16 +2368,8 @@ dist_patch_DATA = \
%D%/packages/patches/renpy-fix-integer-slots.patch \
%D%/packages/patches/reposurgeon-add-missing-docbook-files.patch \
%D%/packages/patches/rdkit-unbundle-external-dependencies.patch \
%D%/packages/patches/r-biostrings-r4.6.0-compat.patch \
%D%/packages/patches/r-h5mread-0001-h5mread-1.3.2-Get-rid-of-non-API-calls-to-R.patch \
%D%/packages/patches/r-httpuv-1.6.6-unvendor-libuv.patch \
%D%/packages/patches/r-mscoreutils-0001-fix-non-API-call-to-R-SETLENGTH-by-using-lengthgets.patch \
%D%/packages/patches/r-rsamtools-r-4.6.0-compat.patch \
%D%/packages/patches/r-snpstats-0001-fixed-non-API-except-for-IS_S4_OBJECT.patch \
%D%/packages/patches/r-snpstats-0002-fixed-IS_S4_OBJECT.patch \
%D%/packages/patches/r-sapa-lapack.patch \
%D%/packages/patches/r-shortread-0001-ShortRead-1.69.3-Get-rid-of-non-API-calls-to-R.patch \
%D%/packages/patches/r-sparsearray-r-4.6.0-compat.patch \
%D%/packages/patches/ripperx-missing-file.patch \
%D%/packages/patches/rpcbind-CVE-2017-8779.patch \
%D%/packages/patches/rtosc-0.3.1-fix-invalid-comparison-operator.patch \
@@ -2460,6 +2454,7 @@ dist_patch_DATA = \
%D%/packages/patches/shared-mime-info-xdgmime-path.patch \
%D%/packages/patches/sharutils-CVE-2018-1000097.patch \
%D%/packages/patches/showtime-python-3.11-compat.patch \
%D%/packages/patches/simpleitk-r-4.6.0.patch \
%D%/packages/patches/sipwitch-fix-build-with-exosip5.patch \
%D%/packages/patches/slim-config.patch \
%D%/packages/patches/slim-gcc-14.patch \
@@ -2494,6 +2489,7 @@ dist_patch_DATA = \
%D%/packages/patches/swift-corelibs-libdispatch-5.7.3-modulemap.patch \
%D%/packages/patches/swift-llvm-5.7.3-linux.patch \
%D%/packages/patches/swig-support-gcc-12.patch \
%D%/packages/patches/swig-support-r-4.6.0.patch \
%D%/packages/patches/swish-e-search.patch \
%D%/packages/patches/swish-e-format-security.patch \
%D%/packages/patches/t1lib-CVE-2010-2642.patch \
@@ -2632,6 +2628,7 @@ dist_patch_DATA = \
%D%/packages/patches/x265-arm-flags.patch \
%D%/packages/patches/x265-4-arm-flags.patch \
%D%/packages/patches/xdg-desktop-portal-wlr-harcoded-length.patch\
%D%/packages/patches/xdmf-3.0.0-hdf5.patch \
%D%/packages/patches/xf86-video-siliconmotion-fix-ftbfs.patch \
%D%/packages/patches/xfig-Enable-error-message-for-missing-libraries.patch \
%D%/packages/patches/xfig-Fix-double-free-when-requesting-MediaBox.patch \
+42 -9
View File
@@ -144,7 +144,7 @@
#:use-module (gnu packages elf)
#:use-module (gnu packages file)
#:use-module (gnu packages file-systems)
#:use-module (gnu packages flex)
#:use-module (gnu packages compiler-tools)
#:use-module (gnu packages fonts)
#:use-module (gnu packages freedesktop)
#:use-module (gnu packages gawk)
@@ -1084,7 +1084,7 @@ console.")
(define-public btop
(package
(name "btop")
(version "1.4.6")
(version "1.4.7")
(source (origin
(method git-fetch)
(uri (git-reference
@@ -1093,7 +1093,7 @@ console.")
(file-name (git-file-name name version))
(sha256
(base32
"1nj58dbv3c0rj8fngldkyrmdmacmjnbg8ch1c07ik97kqnnzd3l7"))))
"0d3cr5l6gpcwhxgnrizny5b5kg6fys2hy9a58bc68w4n2hc040fy"))))
(build-system gnu-build-system)
(native-inputs (list lowdown))
(arguments
@@ -2979,7 +2979,7 @@ system is under heavy load.")
(define-public stress-ng
(package
(name "stress-ng")
(version "0.20.01")
(version "0.21.01")
(source
(origin
(method git-fetch)
@@ -2988,7 +2988,7 @@ system is under heavy load.")
(commit (string-append "V" version))))
(file-name (git-file-name name version))
(sha256
(base32 "1jkinrxh9ppv7xfii9xlisnd2679wnj4ljq12h8y0nvwrm8fkm0b"))))
(base32 "11w8xjm53lgnxfvg286lavqjh0il3bfr1fsgyk915167r4vlabqq"))))
(build-system gnu-build-system)
(arguments
;; XXX The test suite seems to cause instability on the VisionFive 2
@@ -4434,7 +4434,7 @@ buffers.")
(define-public igt-gpu-tools
(package
(name "igt-gpu-tools")
(version "2.3")
(version "2.4")
(source
(origin
(method git-fetch)
@@ -4443,7 +4443,7 @@ buffers.")
(commit (string-append "v" version))))
(file-name (git-file-name name version))
(sha256
(base32 "1vyqrsvxraib98r4i6cjmxq7nis480s2ns95v78dscygcci42i8a"))))
(base32 "0ijvfa5wamihzbl8l29sc27ml0kmgzlld83jm5mln6bb4bvny4gs"))))
(build-system meson-build-system)
(arguments
`(#:tests? #f ; many of the tests try to load kernel modules
@@ -4461,6 +4461,7 @@ buffers.")
libdrm
libpciaccess
libunwind
pciutils
procps
python))
(native-inputs
@@ -7071,7 +7072,7 @@ network, which causes enabled computers to power on.")
(define-public witr
(package
(name "witr")
(version "0.3.1")
(version "0.3.2")
(source
(origin
(method git-fetch)
@@ -7080,7 +7081,7 @@ network, which causes enabled computers to power on.")
(commit (string-append "v" version))))
(file-name (git-file-name name version))
(sha256
(base32 "03v9n4mdvqm0knqjl4s64321i5clqpmlrlkkdb87glzb9p28sg00"))))
(base32 "06vxrgd0j2v6s4snmyviwpp66hm5zai7xca9318inhyg4jw3ngg5"))))
(build-system go-build-system)
(arguments
(list
@@ -7227,6 +7228,38 @@ has a focus on performance. It can be used as a greeter by starting
it from @file{~/.bashrc} for example.")
(license license:agpl3+)))
(define-public zeptofetch
(package
(name "zeptofetch")
(version "1.21")
(source
(origin
(method git-fetch)
(uri (git-reference
(url "https://gitlab.archlinux.org/gurov/zeptofetch")
(commit (string-append "v" version))))
(file-name (git-file-name name version))
(sha256
(base32 "1f1dm9nrp0z0prqy90csrkbk98ixp0jx76ax473qb0qsbb7ys4g7"))))
(build-system gnu-build-system)
(arguments
(list
#:tests? #f ; No tests available.
#:make-flags
#~(list (string-append "PREFIX="
#$output))
#:phases
#~(modify-phases %standard-phases
(delete 'configure)))) ; No configure script.
(home-page "https://gitlab.archlinux.org/gurov/zeptofetch")
(synopsis
"Fast, minimal system information tool for Linux.")
(description
"This package provides a system fetch tool, similar to
@command{neofetch}, @command{fastfetch}, etc. It is lightweight and
has a focus on performance.")
(license license:gpl3+)))
(define-public zzz
(package
(name "zzz")
+1 -1
View File
@@ -52,7 +52,7 @@
#:use-module (gnu packages cpp)
#:use-module (gnu packages curl)
#:use-module (gnu packages documentation)
#:use-module (gnu packages flex)
#:use-module (gnu packages compiler-tools)
#:use-module (gnu packages fltk)
#:use-module (gnu packages fontutils)
#:use-module (gnu packages gcc)
+1 -1
View File
@@ -22,7 +22,7 @@
#:use-module (gnu packages base)
#:use-module (gnu packages bison)
#:use-module (gnu packages dejagnu)
#:use-module (gnu packages flex)
#:use-module (gnu packages compiler-tools)
#:use-module (gnu packages gawk)
#:use-module (gnu packages gettext)
#:use-module (gnu packages linux)
+1 -1
View File
@@ -50,7 +50,7 @@
#:use-module (gnu packages base)
#:use-module (gnu packages bison)
#:use-module (gnu packages compression)
#:use-module (gnu packages flex)
#:use-module (gnu packages compiler-tools)
#:use-module (gnu packages gettext)
#:use-module (gnu packages image)
#:use-module (gnu packages linux)
+1 -1
View File
@@ -66,7 +66,7 @@
#:use-module (gnu packages curl)
#:use-module (gnu packages databases)
#:use-module (gnu packages documentation)
#:use-module (gnu packages flex)
#:use-module (gnu packages compiler-tools)
#:use-module (gnu packages fontutils)
#:use-module (gnu packages fortran-xyz)
#:use-module (gnu packages freedesktop)
+12 -3
View File
@@ -103,7 +103,7 @@
#:use-module (gnu packages elf)
#:use-module (gnu packages emacs)
#:use-module (gnu packages file)
#:use-module (gnu packages flex)
#:use-module (gnu packages compiler-tools)
#:use-module (gnu packages fltk)
#:use-module (gnu packages fontutils)
#:use-module (gnu packages freedesktop)
@@ -137,7 +137,6 @@
#:use-module (gnu packages music)
#:use-module (gnu packages ncurses)
#:use-module (gnu packages networking)
#:use-module (gnu packages ninja)
#:use-module (gnu packages onc-rpc)
#:use-module (gnu packages oneapi)
#:use-module (gnu packages perl)
@@ -2136,7 +2135,17 @@ envelope follower, distortion effects, tape effects and more.")
(base32
"01hnx4hhbz3ap3bw15s42q4q1mw1mhdjwygq4550wvjfg6k4ga8w"))))
(build-system waf-build-system)
(arguments (list #:tests? #false)) ;There are no tests.
(arguments
(list
#:tests? #false ;There are no tests.
#:phases
'(modify-phases %standard-phases
(add-after 'unpack 'python3.12-compatibility
(lambda _
(substitute* "waflib/Context.py"
(("imp.new_module") "types.ModuleType")
(("import os, re, imp, sys")
"import os, re, types, sys")))))))
(inputs (list lv2))
(native-inputs (list pkg-config))
(home-page "https://git.drobilla.net/cgit.cgi/omins.lv2.git/")
+1704 -1599
View File
File diff suppressed because it is too large Load Diff
File diff suppressed because it is too large Load Diff
+1 -1
View File
@@ -28,7 +28,7 @@
#:use-module (guix build-system gnu)
#:use-module (gnu packages m4)
#:use-module (gnu packages perl)
#:use-module (gnu packages flex)
#:use-module (gnu packages compiler-tools)
#:use-module (srfi srfi-1))
(define-public bison
+57 -52
View File
@@ -48,13 +48,14 @@
#:use-module (gnu packages base)
#:use-module (gnu packages disk)
#:use-module (gnu packages bison)
#:use-module (gnu packages build-tools)
#:use-module (gnu packages cdrom)
#:use-module (gnu packages check)
#:use-module (gnu packages compression)
#:use-module (gnu packages cross-base)
#:use-module (gnu packages disk)
#:use-module (gnu packages firmware)
#:use-module (gnu packages flex)
#:use-module (gnu packages compiler-tools)
#:use-module (gnu packages fontutils)
#:use-module (gnu packages gcc)
#:use-module (gnu packages gettext)
@@ -65,7 +66,6 @@
#:use-module (gnu packages man)
#:use-module (gnu packages mtools)
#:use-module (gnu packages ncurses)
#:use-module (gnu packages ninja)
#:use-module (gnu packages package-management)
#:use-module (gnu packages perl)
#:use-module (gnu packages pkg-config)
@@ -1815,63 +1815,68 @@ For more information, refer to
(define-public os-prober
(package
(name "os-prober")
(version "1.81")
(version "1.84")
(source
(origin
(method url-fetch)
(uri (string-append "mirror://debian/pool/main/o/os-prober/os-prober_"
version ".tar.xz"))
(method git-fetch)
(uri (git-reference
(url "https://salsa.debian.org/installer-team/os-prober.git")
(commit version)))
(file-name (git-file-name name version))
(sha256
(base32 "10w8jz6mqhp0skdcam9mpgv79vx1sv7lkpra3rqjg0jkhvn2in9g"))))
(base32 "1bji3w6nbqaz8zqrbmy8b1j5dph9xn7bdh1cd2z8ia1q125i6mgp"))))
(build-system gnu-build-system)
(arguments
`(#:modules ((guix build gnu-build-system)
(list
#:tests? #f ; No tests.
#:modules '((guix build gnu-build-system)
(guix build utils)
(ice-9 regex) ; for string-match
(srfi srfi-26)) ; for cut
#:make-flags
(list ,(string-append "CC=" (cc-for-target)))
#:tests? #f ; no tests
#:phases
(modify-phases %standard-phases
(replace 'configure
(lambda* (#:key outputs #:allow-other-keys)
(substitute* (find-files ".")
(("/usr") (assoc-ref outputs "out")))
(substitute* (find-files "." "50mounted-tests$")
(("mkdir") "mkdir -p"))))
(replace 'install
(lambda* (#:key outputs #:allow-other-keys)
(define (find-files-non-recursive directory)
(find-files directory
(lambda (file stat)
(string-match (string-append "^" directory "/[^/]*$")
file))
#:directories? #t))
(ice-9 regex) ; string-match
(srfi srfi-26)) ; cut
#:make-flags
#~(list (string-append "CC=" #$(cc-for-target)))
#:phases
#~(modify-phases %standard-phases
(replace 'configure
(lambda _
(substitute* (find-files ".")
(("/usr") #$output))
(substitute* (find-files "." "50mounted-tests$")
(("mkdir") "mkdir -p -v"))))
(replace 'install
(lambda _
(define (find-files-non-recursive directory)
(find-files directory
(lambda (file stat)
(string-match (string-append "^" directory "/[^/]*$")
file))
#:directories? #t))
(let* ((out (assoc-ref outputs "out"))
(bin (string-append out "/bin"))
(lib (string-append out "/lib"))
(share (string-append out "/share")))
(for-each (cut install-file <> bin)
(list "linux-boot-prober" "os-prober"))
(install-file "newns" (string-append lib "/os-prober"))
(install-file "common.sh" (string-append share "/os-prober"))
(install-file "os-probes/mounted/powerpc/20macosx"
(string-append lib "/os-probes/mounted"))
(for-each
(lambda (directory)
(for-each
(lambda (file)
(let ((destination (string-append lib "/" directory
"/" (basename file))))
(mkdir-p (dirname destination))
(copy-recursively file destination)))
(append (find-files-non-recursive (string-append directory "/common"))
(find-files-non-recursive (string-append directory "/x86")))))
(list "os-probes" "os-probes/mounted" "os-probes/init"
"linux-boot-probes" "linux-boot-probes/mounted"))))))))
(home-page "https://joeyh.name/code/os-prober")
(let ((bin (string-append #$output "/bin"))
(lib (string-append #$output "/lib"))
(share (string-append #$output "/share")))
(for-each (cut install-file <> bin)
(list "linux-boot-prober" "os-prober"))
(install-file "newns" (string-append lib "/os-prober"))
(install-file "common.sh" (string-append share "/os-prober"))
(install-file "os-probes/mounted/powerpc/20macosx"
(string-append lib "/os-probes/mounted"))
(for-each
(lambda (directory)
(for-each
(lambda (file)
(let ((destination (string-append lib "/" directory
"/" (basename file))))
(mkdir-p (dirname destination))
(copy-recursively file destination)))
(append (find-files-non-recursive (string-append directory "/common"))
(find-files-non-recursive (string-append directory "/x86")))))
(list "linux-boot-probes"
"linux-boot-probes/mounted"
"os-probes"
"os-probes/init"
"os-probes/mounted"))))))))
(home-page "https://joeyh.name/code/os-prober/")
(synopsis "Detect other operating systems")
(description "os-prober probes disks on the system for other operating
systems so that they can be added to the bootloader. It also works out how to
+114 -2
View File
@@ -64,7 +64,6 @@
#:use-module (gnu packages logging)
#:use-module (gnu packages lua)
#:use-module (gnu packages man)
#:use-module (gnu packages ninja)
#:use-module (gnu packages package-management)
#:use-module (gnu packages pcre)
#:use-module (gnu packages perl)
@@ -77,6 +76,7 @@
#:use-module (gnu packages python-crypto)
#:use-module (gnu packages python-web)
#:use-module (gnu packages python-xyz)
#:use-module (gnu packages compiler-tools)
#:use-module (gnu packages regex)
#:use-module (gnu packages rpc)
#:use-module (gnu packages serialization)
@@ -104,7 +104,8 @@
#:use-module (guix packages)
#:use-module (guix search-paths)
#:use-module (guix utils)
#:use-module (ice-9 optargs))
#:use-module (ice-9 optargs)
#:use-module (srfi srfi-1))
(define-public acr
(package
@@ -1483,3 +1484,114 @@ Features:
@item Support for languages outside C/C++ (e.g. Go, Rust, Zig).
@end itemize")
(license license:asl2.0)))
(define-public ninja/pinned
(hidden-package
(package
(name "ninja")
(version "1.13.2")
(source (origin
(method git-fetch)
(uri (git-reference
(url "https://github.com/ninja-build/ninja")
(commit (string-append "v" version))))
(file-name (git-file-name name version))
(sha256
(base32
"0lp9dmxbjyjwv089i8mgq3nvnhpbnsn01ifm05m9s47w7cifrl8g"))))
(build-system gnu-build-system)
(inputs (list python-wrapper re2c))
(arguments
'(; Tests now require googletest, which is a circular dependency.
#:tests? #f
#:phases
(modify-phases %standard-phases
(replace 'configure
(lambda _
(substitute* "src/subprocess-posix.cc"
(("/bin/sh") (which "sh")))
(substitute* "src/subprocess_test.cc"
(("/bin/echo") (which "echo")))))
(replace 'build
(lambda _
(invoke "./configure.py" "--bootstrap")))
(replace 'check
(lambda* (#:key tests? #:allow-other-keys)
(when tests?
(invoke "./configure.py")
(invoke "./ninja" "ninja_test")
(invoke "./ninja_test"))))
(replace 'install
(lambda* (#:key outputs #:allow-other-keys)
(let* ((out (assoc-ref outputs "out"))
(bin (string-append out "/bin"))
(doc (string-append out "/share/doc/ninja")))
(install-file "ninja" bin)
(install-file "doc/manual.asciidoc" doc)))))))
(home-page "https://ninja-build.org/")
(synopsis "Small build system")
(description
"Ninja is a small build system with a focus on speed. It differs from
other build systems in two major respects: it is designed to have its input
files generated by a higher-level build system, and it is designed to run
builds as fast as possible.")
(license license:asl2.0))))
(define-public ninja
(package/inherit ninja/pinned
(properties (alist-delete 'hidden? (package-properties ninja/pinned)))))
(define-public samurai
(package
(name "samurai")
(version "1.2")
(source (origin
(method git-fetch)
(uri (git-reference
(url "https://github.com/michaelforney/samurai")
(commit version)))
(file-name (git-file-name name version))
(sha256
(base32
"04iw18hgkm72yrl83a2xh1jc47w9rilpb95kwick0j37b4q3gxj4"))))
(build-system gnu-build-system)
(arguments
(list #:tests? #f ;no test suite
#:make-flags #~(list (string-append "CC=" #$(cc-for-target))
(string-append "PREFIX=" #$output))
#:phases #~(modify-phases %standard-phases
(add-after 'unpack 'patch-/bin/sh
(lambda* (#:key inputs #:allow-other-keys)
(substitute* "build.c"
(("/bin/sh")
(search-input-file inputs "bin/sh")))))
(delete 'configure))))
(inputs (list bash-minimal))
(home-page "https://github.com/michaelforney/samurai")
(synopsis "Ninja-compatible build tool written in C")
(description "@code{samurai} is a ninja-compatible build tool written in
C99 with a focus on simplicity, speed, and portability. It is
feature-complete and supports most of the same options as ninja. This package
provides the command @command{samu}. For a @command{ninja} command
replacement, use the @code{samu-as-ninja-wrapper} package.")
(license (list license:asl2.0 ;for the most part
license:expat)))) ;htab.h, htab.c and tree.c
(define-public samu-as-ninja-wrapper
(package/inherit samurai
(name "samu-as-ninja-wrapper")
(build-system trivial-build-system)
(arguments
(list #:builder
(with-imported-modules '((guix build utils))
#~(begin
(use-modules (guix build utils))
(let ((bindir (string-append #$output "/bin"))
(samu (string-append #$(this-package-input "samurai")
"/bin/samu")))
(mkdir-p bindir)
(symlink samu (string-append bindir "/ninja")))))))
(inputs (list samurai))
(description "This package provides the @command{ninja} command,
implemented as a symbolic link to the @command{samu} command of @code{samurai}
package.")))
-1
View File
@@ -63,7 +63,6 @@
#:use-module (gnu packages bison)
#:use-module (gnu packages check)
#:use-module (gnu packages compiler-tools)
#:use-module (gnu packages flex)
#:use-module (gnu packages gawk)
#:use-module (gnu packages gcc)
#:use-module (gnu packages perl)
+1 -1
View File
@@ -52,7 +52,7 @@
#:use-module (gnu packages bash)
#:use-module (gnu packages bison)
#:use-module (gnu packages compression)
#:use-module (gnu packages flex)
#:use-module (gnu packages compiler-tools)
#:use-module (gnu packages fontutils)
#:use-module (gnu packages gettext)
#:use-module (gnu packages docbook)
+1 -1
View File
@@ -46,7 +46,7 @@
#:use-module (gnu packages compression)
#:use-module (gnu packages cpp)
#:use-module (gnu packages documentation)
#:use-module (gnu packages flex)
#:use-module (gnu packages compiler-tools)
#:use-module (gnu packages fonts)
#:use-module (gnu packages fontutils)
#:use-module (gnu packages fortran-xyz)
+11 -12
View File
@@ -302,7 +302,7 @@ will name the threaded machine type unless THREADS? is provided as #f."
(name "chez-scheme-for-racket")
;; The version should match `(scheme-version #t)`.
;; See s/cmacros.ss c. line 360.
(version "10.3.0-pre-release.2") ; expect a chez-nanopass-bootstrap update
(version "10.4.0-pre-release.1-1") ; expect a chez-nanopass-bootstrap update
(source #f)
(build-system gnu-build-system)
(inputs `(,@(if (nix-system->native-chez-machine-type)
@@ -507,7 +507,7 @@ version of Chez Scheme.")
(name "chez-scheme")
;; The version should match `(scheme-version-number #t)`.
;; See s/cmacros.ss c. line 360.
(version "10.2.0") ; expect a chez-nanopass-bootstrap update
(version "10.4.0") ; expect a chez-nanopass-bootstrap update
(source (origin
(method git-fetch)
(uri (git-reference
@@ -515,7 +515,7 @@ version of Chez Scheme.")
(commit (string-append "v" version))))
(sha256
(base32
"14iv4kfkyvrkigr1n2prf71n2l3vs0sf0549rvh6y4x2faa2l329"))
"079vlkl27qdvsg1rsynmd828m42n98c2dnldkhsxf2slfsqd9kv5"))
(file-name (git-file-name name version))
(patches (search-patches "chez-scheme-bin-sh.patch"))
(snippet #~(begin
@@ -840,9 +840,9 @@ User's Guix}, among other documents.")
(define-public chez-nanopass-bootstrap
(hidden-package
(package
(name "chez-nanopass")
(version "1.9.2")
(properties `((chez-nanopass-release-date . "October 18, 2020")))
(name "chez-nanopass-bootstrap")
(version "1.9.4")
(properties '((chez-nanopass-release-date . "December 29, 2025")))
(source
(origin
(method git-fetch)
@@ -850,7 +850,7 @@ User's Guix}, among other documents.")
(url "https://github.com/nanopass/nanopass-framework-scheme")
(commit (string-append "v" version))))
(sha256
(base32 "16vjsik9rrzbabbhbxbaha51ppi3f9n8rk59pc6zdyffs0vziy4i"))
(base32 "1qq0vnbrvcialgjgnblfq3qp1ilqg94h0kg896ksd9v4g7ipj9v0"))
(file-name (git-file-name "nanopass-framework-scheme" version))
(snippet
#~(begin
@@ -929,10 +929,9 @@ create compilers, making them easier to understand and maintain.")
(define-public chez-nanopass
(package
(inherit chez-nanopass-bootstrap)
;; This release has a significant bug fix. Expect the next releases of
;; chez-scheme{,-for-racket} to want this for chez-nanopass-bootstrap.
(version "1.9.3")
(properties '((chez-nanopass-release-date . "August 24, 2025")))
(name "chez-nanopass")
(version "1.9.4")
(properties '((chez-nanopass-release-date . "December 29, 2025")))
(source
(let ((bootstrap-origin (package-source chez-nanopass-bootstrap)))
(origin
@@ -941,7 +940,7 @@ create compilers, making them easier to understand and maintain.")
(url (git-reference-url (origin-uri bootstrap-origin)))
(commit (string-append "v" version))))
(sha256
(base32 "0757x3a3b4kcd3jk52h4ikqzv7cc1mvphlw592f0r5pz99bkxiin"))
(base32 "1qq0vnbrvcialgjgnblfq3qp1ilqg94h0kg896ksd9v4g7ipj9v0"))
(file-name (git-file-name "nanopass-framework-scheme" version)))))
(native-inputs (list chez-scheme stex))))
+95 -47
View File
@@ -20,65 +20,113 @@
(define-module (gnu packages chicken)
#:use-module (gnu packages)
#:use-module (gnu packages bash)
#:use-module (guix gexp)
#:use-module (guix packages)
#:use-module (guix utils)
#:use-module (guix build-system chicken)
#:use-module (guix build-system gnu)
#:use-module (guix download)
#:use-module (guix git-download)
#:use-module (guix svn-download)
#:use-module ((guix licenses)
#:prefix license:))
#:prefix license:)
#:use-module (srfi srfi-1))
;; This package is build from pre-built C source code, provided in the CHICKEN
;; release tarball. Based on this bootstrap compiler, we build CHICKEN from
;; the Scheme source, thus enabling us to (at least) patch it.
;;
;; See <https://issues.guix.gnu.org/22366>.
(define-public chicken-bootstrap
(hidden-package
(package
(name "chicken-bootstrap")
(version "5.4.0")
(source (origin
(method url-fetch)
(uri (string-append "https://code.call-cc.org/releases/"
version "/chicken-" version ".tar.gz"))
(sha256
(base32
"0pzcrnzkjw2sa44vy59wbygvlc3nva8zisprkdnvyrqi3jk4lp9w"))))
(build-system gnu-build-system)
(arguments
`(#:modules ((guix build gnu-build-system)
(guix build utils)
(srfi srfi-1))
;; No `configure' script; run "make check" after "make install" as
;; prescribed by README.
#:phases
(modify-phases %standard-phases
(delete 'configure)
(delete 'check)
(add-after 'install 'check
(assoc-ref %standard-phases 'check)))
#:make-flags (let ((out (assoc-ref %outputs "out")))
(list "PLATFORM=linux"
(string-append "PREFIX=" out)
(string-append "VARDIR=" out "/var/lib")))
;; Parallel builds are not supported, as noted in README.
#:parallel-build? #f))
(native-search-paths
(list (search-path-specification
(variable "CHICKEN_REPOSITORY_PATH")
;; TODO extract binary version into a module level definition.
(files (list "var/lib/chicken/11")))))
;; Reference gcc-toolchain lazily to avoid circular module dependency
;; problems.
(propagated-inputs (list (module-ref (resolve-interface
'(gnu packages commencement))
'gcc-toolchain)))
(home-page "https://www.call-cc.org/")
(synopsis "R5RS Scheme implementation that compiles native code via C")
(description
"CHICKEN is a compiler for the Scheme programming language. CHICKEN
pr oduces portable and efficient C, supports almost all of the R5RS Scheme
la nguage standard, and includes many enhancements and extensions.")
(license license:bsd-3))))
;; The CHICKEN compiler is itself written in CHICKEN, the CHICKEN release
;; tarballs includes auto-generated C code to mitigate the compiler
;; bootstrapping problem. To be able to patch the original Scheme source,
;; we compile from this Scheme source here using the chicken-bootstrap
;; compiler obtained from the autogenerated C code.
;;
;; See <https://issues.guix.gnu.org/22366>.
(define-public chicken
(package
(inherit chicken-bootstrap)
(name "chicken")
(version "5.4.0")
(source (origin
(method url-fetch)
(uri (string-append "https://code.call-cc.org/releases/"
version "/chicken-" version ".tar.gz"))
(sha256
(base32
"0pzcrnzkjw2sa44vy59wbygvlc3nva8zisprkdnvyrqi3jk4lp9w"))))
(build-system gnu-build-system)
(arguments
`(#:modules ((guix build gnu-build-system)
(guix build utils)
(srfi srfi-1))
;; No `configure' script; run "make check" after "make install" as
;; prescribed by README.
#:phases
(modify-phases %standard-phases
(delete 'configure)
(delete 'check)
(add-after 'install 'check
(assoc-ref %standard-phases 'check)))
#:make-flags (let ((out (assoc-ref %outputs "out")))
(list "PLATFORM=linux"
(string-append "PREFIX=" out)
(string-append "VARDIR=" out "/var/lib")))
;; Parallel builds are not supported, as noted in README.
#:parallel-build? #f))
(native-search-paths
(list (search-path-specification
(variable "CHICKEN_REPOSITORY_PATH")
;; TODO extract binary version into a module level definition.
(files (list "var/lib/chicken/11")))))
;; Reference gcc-toolchain lazily to avoid circular module dependency
;; problems.
(propagated-inputs (list (module-ref (resolve-interface
'(gnu packages commencement))
'gcc-toolchain)))
(home-page "https://www.call-cc.org/")
(synopsis "R5RS Scheme implementation that compiles native code via C")
(description
"CHICKEN is a compiler for the Scheme programming language. CHICKEN
produces portable and efficient C, supports almost all of the R5RS Scheme
language standard, and includes many enhancements and extensions.")
(license license:bsd-3)))
(substitute-keyword-arguments (package-arguments chicken-bootstrap)
((#:phases phases)
#~(modify-phases #$phases
;; CHICKEN contains auto-generated C code, remove it and
;; compile from the Scheme source using chicken-bootstrap.
(add-after 'unpack 'remove-auto-generated-code
(lambda _
(invoke "make" "spotless")))
;; Invoke commands by name, not by path.
;;
;; See <https://codeberg.org/guix/guix/issues/8471>.
(add-after 'unpack 'fix-paths
(lambda* (#:key inputs #:allow-other-keys)
(let ((sh (search-input-file inputs "/bin/sh"))
(cp (search-input-file inputs "/bin/cp")))
(substitute* "egg-compile.scm"
(("/bin/sh") sh)
(("\"cp\"") (string-append "\"" cp "\"")))
(substitute* "posixunix.scm"
(("/bin/sh") sh))
(substitute* "chicken-install.scm"
(("\"sh \"") (string-append "\"" sh " \""))))))))))
(inputs (list chicken-bootstrap))
(properties
(alist-delete 'hidden? (package-properties chicken-bootstrap)))))
(define-public chicken-compile-file
(package
-1
View File
@@ -53,7 +53,6 @@
#:use-module (gnu packages llvm)
#:use-module (gnu packages kerberos)
#:use-module (gnu packages maths)
#:use-module (gnu packages ninja)
#:use-module (gnu packages node)
#:use-module (gnu packages nss)
#:use-module (gnu packages pciutils)
+53 -7
View File
@@ -23,19 +23,24 @@
;;; along with GNU Guix. If not, see <http://www.gnu.org/licenses/>.
(define-module (gnu packages clojure)
#:use-module (gnu packages)
#:use-module (gnu packages base)
#:use-module (gnu packages golang-build)
#:use-module (gnu packages golang-check)
#:use-module (gnu packages golang-xyz)
#:use-module (gnu packages golang)
#:use-module (gnu packages guile)
#:use-module (gnu packages java)
#:use-module (gnu packages maven)
#:use-module (guix gexp)
#:use-module ((guix licenses) #:prefix license:)
#:use-module (guix packages)
#:use-module (guix download)
#:use-module (guix git-download)
#:use-module (gnu packages)
#:use-module (guix build-system ant)
#:use-module (guix build-system clojure)
#:use-module (guix build-system copy)
#:use-module (guix build-system clojure))
#:use-module (guix build-system go)
#:use-module (guix download)
#:use-module (guix gexp)
#:use-module (guix git-download)
#:use-module ((guix licenses) #:prefix license:)
#:use-module (guix packages))
(define-public clojure-spec-alpha
(package
@@ -1253,3 +1258,44 @@ an operation on the service. invoke takes a map and returns a map, and works
the same way for every operation on every service.")
(home-page "https://github.com/cognitect-labs/aws-api")
(license license:asl2.0)))
(define-public let-go
(package
(name "let-go")
(version "1.7.4")
(source
(origin
(method git-fetch)
(uri (git-reference
(url "https://github.com/nooga/let-go")
(commit (string-append "v" version))))
(file-name (git-file-name name version))
(sha256
(base32 "139a129fw3w9a4bcfgms60ll90vy2vmqinbmjn44zmgx4fr2adif"))))
(build-system go-build-system)
(arguments
(list
#:go go-1.26
#:install-source? #f
#:import-path "github.com/nooga/let-go"))
(native-inputs
(list go-github-com-davecgh-go-spew
go-github-com-alimpfard-line
go-github-com-hashicorp-go-uuid
go-github-com-kr-pretty
go-github-com-pmezard-go-difflib
go-github-com-stretchr-testify
go-github-com-zeebo-bencode
go-golang-org-x-sys
go-gopkg-in-check-v1
go-gopkg-in-yaml-v3))
(home-page "https://nooga.github.io/let-go")
(synopsis "Clojure dialect written in Go")
(description
"let-go is a Clojure dialect with a bytecode compiler and a stack virtual
machine, written in the Go programming language.
It is not a drop-in replacement for Clojure JVM. It does not load JARs and
does not aim to. Most idiomatic Clojure code runs unmodified, but a real
project with library dependencies will need adjustments.")
(license license:expat)))
+1 -1
View File
@@ -32,7 +32,7 @@
#:use-module (gnu packages check)
#:use-module (gnu packages compression)
#:use-module (gnu packages docbook)
#:use-module (gnu packages flex)
#:use-module (gnu packages compiler-tools)
#:use-module (gnu packages gettext)
#:use-module (gnu packages libevent)
#:use-module (gnu packages linux)
+1 -1
View File
@@ -25,7 +25,7 @@
#:use-module (guix gexp)
#:use-module (gnu packages bison)
#:use-module (gnu packages dbm)
#:use-module (gnu packages flex)
#:use-module (gnu packages compiler-tools)
#:use-module (gnu packages multiprecision)
#:use-module (gnu packages ncurses)
#:use-module (gnu packages perl)
+1 -1
View File
@@ -66,7 +66,7 @@
#:use-module (gnu packages curl)
#:use-module (gnu packages elf)
#:use-module (gnu packages emacs)
#:use-module (gnu packages flex)
#:use-module (gnu packages compiler-tools)
#:use-module (gnu packages gcc)
#:use-module (gnu packages gettext)
#:use-module (gnu packages golang-build)
+1 -1
View File
@@ -42,7 +42,7 @@
#:use-module (gnu packages m4)
#:use-module (gnu packages gawk)
#:use-module (gnu packages bison)
#:use-module (gnu packages flex)
#:use-module (gnu packages compiler-tools)
#:use-module (gnu packages guile)
#:use-module (gnu packages gettext)
#:use-module (gnu packages multiprecision)
+106 -4
View File
@@ -1,8 +1,11 @@
;;; GNU Guix --- Functional package management for GNU
;;; Copyright © 2012-2014, 2019, 2022 Ludovic Courtès <ludo@gnu.org>
;;; Copyright © 2016, 2024-2025 Efraim Flashner <efraim@flashner.co.il>
;;; Copyright © 2017, 2020, 2021 Sergei Trofimovich <slyfox@inbox.ru>
;;; Copyright © 2018, 2022 Tobias Geerinckx-Rice <me@tobias.gr>
;;; Copyright © 2021 Foo Chuan Wei <chuanwei.foo@hotmail.com>
;;; Copyright © 2022 Ludovic Courtès <ludo@gnu.org>
;;; Copyright © 2022 Tobias Geerinckx-Rice <me@tobias.gr>
;;; Copyright © 2024-2025 Efraim Flashner <efraim@flashner.co.il>
;;; Copyright © 2024 Janneke Nieuwenhuizen <janneke@gnu.org>
;;; Copyright © 2025 Alexey Abramov <levenson@mmer.org>
;;; Copyright © 2025 Anderson Torres <anderson.torres.8519@gmail.com>
;;;
;;; This file is part of GNU Guix.
@@ -22,14 +25,21 @@
(define-module (gnu packages compiler-tools)
#:use-module (gnu packages autotools)
#:use-module (gnu packages bison)
#:use-module (gnu packages gawk)
#:use-module (gnu packages m4)
#:use-module (gnu packages man)
#:use-module (gnu packages python)
#:use-module (gnu packages)
#:use-module (guix build-system gnu)
#:use-module (guix build-system trivial)
#:use-module (guix download)
#:use-module (guix gexp)
#:use-module (guix git-download)
#:use-module ((guix licenses) #:prefix license:)
#:use-module (guix packages))
#:use-module (guix packages)
#:use-module (guix utils)
#:use-module (srfi srfi-1))
(define-public byacc
(package
@@ -65,6 +75,59 @@ consist of a set of LALR(1) parsing tables and a driver routine written in the
C programming language.")
(license license:public-domain)))
(define-public flex
(package
(name "flex")
(version "2.6.4")
(source
(origin
(method url-fetch)
(uri (string-append
"https://github.com/westes/flex"
"/releases/download/v" version "/"
"flex-" version ".tar.gz"))
(sha256
(base32
"15g9bv236nzi665p9ggqjlfn4dwck5835vf0bbw2cz7h5c1swyp8"))))
(build-system gnu-build-system)
(arguments
(if (%current-target-system)
(list #:configure-flags
#~'("ac_cv_func_malloc_0_nonnull=yes"
"ac_cv_func_realloc_0_nonnull=yes"))
'()))
(native-inputs
(list help2man
;; m4 is not present in PATH when cross-building
m4))
(inputs
(list
(package
(inherit bison)
(arguments
;; Disable tests, since they require flex.
(substitute-keyword-arguments arguments
((#:tests? _ #f) #f)))
(inputs (modify-inputs inputs
(delete "flex"))))))
(propagated-inputs (list m4))
(home-page "https://github.com/westes/flex")
(synopsis "Fast lexical analyser generator")
(description
"Flex is a tool for generating scanners. A scanner, sometimes
called a tokenizer, is a program which recognizes lexical patterns in
text. The flex program reads user-specified input files, or its standard
input if no file names are given, for a description of a scanner to
generate. The description is in the form of pairs of regular expressions
and C code, called rules. Flex generates a C source file named,
\"lex.yy.c\", which defines the function yylex(). The file \"lex.yy.c\"
can be compiled and linked to produce an executable. When the executable
is run, it analyzes its input for occurrences of text matching the
regular expressions for each rule. Whenever it finds a match, it
executes the corresponding C code.")
(license (license:non-copyleft "file://COPYING"
"See COPYING in the distribution."))))
(define-public oyacc
(package
(name "oyacc")
@@ -112,3 +175,42 @@ besides libc.")
(description
"This package provides the @command{yacc} command, implemented as a
symbolic link to the @command{oyacc} command from the same-named package.")))
(define-public re2c
(package
(name "re2c")
(version "4.2")
(source
(origin
(method url-fetch)
(uri (string-append "https://github.com/skvadrik/" name
"/releases/download/" version "/"
name "-" version ".tar.xz"))
(sha256
(base32
"07ysqgdm0h566a8lwnpdgycp93vz7zskzihsgah3bla0ycj2pp69"))))
(build-system gnu-build-system)
(arguments
(list
#:tests?
(not (or (%current-target-system)
;; TODO: run_tests.py hangs
(system-hurd?)))
#:phases
(if (target-arm32?)
#~(modify-phases %standard-phases
(add-after 'unpack 'patch-sources
(lambda _
(invoke "patch" "-p1" "--force" "--input"
#$(local-file (search-patch
"re2c-Use-maximum-alignment.patch"))))))
#~%standard-phases)))
(native-inputs
(list python)) ; for the test driver
(home-page "https://re2c.org/")
(synopsis "Lexer generator")
(description
"@code{re2c, Regular Expressions to Code} is a flexible lexical analyser.
Instead of using traditional table-driven approaches, it encodes a finite
state machine directly in the code in the form of jumps and comparisons.")
(license license:public-domain)))
+33 -2
View File
@@ -42,6 +42,7 @@
;;; Copyright © 2024 David Elsing <david.elsing@posteo.net>
;;; Copyright © 2024 Artyom V. Poptsov <poptsov.artyom@gmail.com>
;;; Copyright © 2024, 2025 Zheng Junjie <873216071@qq.com>
;;; Copyright © 2026 Jake Forster <jakecameron.forster@gmail.com>
;;;
;;; This file is part of GNU Guix.
;;;
@@ -1475,7 +1476,7 @@ for most inputs, but the resulting compressed files are anywhere from 20% to
(define-public 7zip
(package
(name "7zip")
(version "26.00")
(version "26.01")
(source
(origin
(method git-fetch)
@@ -1483,7 +1484,7 @@ for most inputs, but the resulting compressed files are anywhere from 20% to
(url "https://github.com/ip7z/7zip")
(commit version)))
(sha256
(base32 "1fvgl9qp2pl5c0jmvgbdx6qig3qd80mhxvml42yby8y412x65sh7"))
(base32 "0qwzn9pz1m6f8q20cqgmfqp1qx6s7959xnyikpr60n1v8c1mj98q"))
(file-name (git-file-name name version))
(modules '((guix build utils)
(ice-9 regex)))
@@ -3191,3 +3192,33 @@ exported by the zlib library.")
ratio at the cost of high CPU/memory usage.")
(home-page "https://github.com/byronknoll/cmix")
(license license:gpl3)))
(define-public zlib-ng
(package
(name "zlib-ng")
(version "2.3.3")
(source (origin
(method git-fetch)
(uri (git-reference
(url "https://github.com/zlib-ng/zlib-ng")
(commit version)))
(file-name (git-file-name name version))
(sha256
(base32
"0g4pxy7gc1slw9n6j583hzps32mml30f08gmmg1adsq4y3dl2cny"))))
(build-system cmake-build-system)
(native-inputs (list googletest))
(home-page "https://github.com/zlib-ng/zlib-ng")
(synopsis "Fork of the zlib data compression library")
(description
"zlib-ng is a @code{zlib} replacement with optimizations for next
generation systems.")
(license license:zlib)))
(define-public zlib-ng-compat
(package/inherit zlib-ng
(name "zlib-ng-compat")
(arguments
(substitute-keyword-arguments arguments
((#:configure-flags flags #~(list))
#~(cons "-DZLIB_COMPAT=ON" #$flags))))))
+1 -1
View File
@@ -35,7 +35,7 @@
#:use-module (gnu packages boost)
#:use-module (gnu packages compression)
#:use-module (gnu packages emacs)
#:use-module (gnu packages flex)
#:use-module (gnu packages compiler-tools)
#:use-module (gnu packages gawk)
#:use-module (gnu packages multiprecision)
#:use-module (gnu packages ocaml)
+71 -1
View File
@@ -23,7 +23,7 @@
(define-module (gnu packages coreboot)
#:use-module (gnu packages bison)
#:use-module (gnu packages compression)
#:use-module (gnu packages flex)
#:use-module (gnu packages compiler-tools)
#:use-module (gnu packages pciutils)
#:use-module ((guix licenses) #:prefix license:)
#:use-module (guix build-system cargo)
@@ -127,6 +127,76 @@ formats:
It also comes with example files generated by bincfg.")
(license license:gpl3+)))
(define-public bucts
(package
(name "bucts")
(version %coreboot-version)
(source %coreboot-origin)
(build-system gnu-build-system)
(arguments
(list
#:tests? #f ;no tests
#:make-flags #~(list (string-append "CC=" #$(cc-for-target)))
#:phases #~(modify-phases %standard-phases
(delete 'configure) ;no configure script
(add-after 'unpack 'enter-source
(lambda _
(chdir "util/bucts")))
(add-after 'enter-source 'set-version
(lambda _
(substitute* "Makefile"
(("^VERSION:=*")
#$(string-append "VERSION:=" version)))))
;; no install target
(replace 'install
(lambda _
(let ((bin (string-append #$output "/bin"))
(doc (string-append #$output "/share/doc/bucts/"))
(licenses (string-append #$output
"/share/licenses/bucts/")))
(install-file "bucts" bin)
(install-file "readme.md" doc)
(install-file "../../COPYING" licenses)))))))
(inputs (list pciutils))
(home-page "https://coreboot.org")
(synopsis "Tool to swap the BIOS bootblock and backup bootblock on the
Intel I945 chipsets")
(description
"The @command{bucts} command can flip a bit in the BUC.TS register of the
Intel I945 chipsets and show the register status. When the bit is set, it
swaps the bootblock location. Because the bootblock region is often set
read-only by the default BIOS, this enables to bypass that restriction and is
used as part of a procedure to replace the nonfree BIOS with free software on
various computers (Lenovo X60, X60s, X60T, T60, probably more).")
(license license:gpl2)))
(define-public ectool
(package
(name "ectool")
(version %coreboot-version)
(source %coreboot-origin)
(build-system gnu-build-system)
(arguments
(list
#:tests? #f ; no test suite
#:make-flags
#~(list (string-append "CC=" #$(cc-for-target))
"INSTALL=install"
(string-append "PREFIX=" #$output))
#:phases
#~(modify-phases %standard-phases
(add-after 'unpack 'chdir
(lambda _
(chdir "util/ectool")))
(delete 'configure)))) ; no configure script
(home-page "https://doc.coreboot.org/util.html")
(synopsis "Tool to dump and modify @acronym{EC, Embedded Controller} RAM
on computers such as laptops")
(description "This package provides @command{ectool}, a program to dump
and modify the contents of @acronym{EC, Embedded Controller} RAM
on mobile computers.")
(license license:gpl2)))
(define-public ifdtool
(package
(name "ifdtool")
+67
View File
@@ -53,6 +53,7 @@
;;; Copyright © 2025 Murilo <murilo@disroot.org>
;;; Copyright © 2026 Justin Veilleux <terramorpha@cock.li>
;;; Copyright © 2026 Daniel Littlewood <dan@danielittlewood.xyz>
;;; Copyright © 2026 bdunahu <bdunahu@operationnull.com>
;;;
;;; This file is part of GNU Guix.
;;;
@@ -1433,6 +1434,9 @@ data transfer object.")
(define-public nlohmann-json
(package
(name "nlohmann-json")
;; XXX: Merge related package `nlohmann-json-no-char8-t' back into here when
;; updating from 3.12.0, as the unique patch it applies will already be
;; incorporated in.
(version "3.12.0")
(home-page "https://github.com/nlohmann/json")
(source
@@ -1506,6 +1510,46 @@ intuitive syntax and trivial integration.")
(define-deprecated-package json-modern-cxx
nlohmann-json)
(define-public nlohmann-json-no-char8-t
(package
;; XXX: Version 3.12.0 does not work without char8_t support.
;; OpenRCT2 compiles with -fno-char8_t, and thus requires this patch.
;; See https://github.com/nlohmann/json/pull/4736
(inherit nlohmann-json)
(name "nlohmann-json-no-char8-t")
(version "3.12.0")
(source
(origin
(method git-fetch)
(uri (git-reference (url "https://github.com/nlohmann/json")
(commit (string-append "v" version))))
(sha256
(base32 "09nqq56ighr3lghhn3fs399lkllghz717j0xyp87x0giw86ayh3h"))
(file-name (git-file-name name version))
(modules '((guix build utils)))
(snippet
#~(begin
;; Delete bundled software. Preserve doctest_compatibility.h, which
;; is a wrapper library added by this package.
(install-file "./tests/thirdparty/doctest/doctest_compatibility.h"
"/tmp")
(delete-file-recursively "./tests/thirdparty")
(install-file "/tmp/doctest_compatibility.h"
"./tests/thirdparty/doctest")
;; Adjust for the unbundled fifo_map and doctest.
(substitute* (find-files "./tests/" "\\.h(pp)?")
(("#include \"doctest\\.h\"") "#include <doctest/doctest.h>")
(("#include <doctest\\.h>") "#include <doctest/doctest.h>"))
(with-directory-excursion "tests/src"
(let ((files (find-files "." "\\.cpp$")))
(substitute* files
(("#include ?\"(fifo_map.hpp)\"" all fifo-map-hpp)
(string-append
"#include <fifo_map/" fifo-map-hpp ">")))))))
(patches
(search-patches "nlohmann_json_fix_char8_t.patch"))))))
(define-public jthread
(let ((commit "0fa8d394254886c555d6faccd0a3de819b7d47f8")
(revision "0"))
@@ -4480,6 +4524,29 @@ file name and location, as well as filters with friendly names (such as
"This package provides a simple S-Expression parser for C++.")
(license license:gpl3+))))
(define-public sfl-library
(package
(name "sfl-library")
(version "2.2.0")
(source
(origin
(method git-fetch)
(uri (git-reference
(url "https://github.com/slavenf/sfl-library")
(commit version)))
(file-name (git-file-name name version))
(sha256
(base32 "1ngy86b9y1b8a4j37c14m1jrg0q5b12jj8b0gdnpl5sjb1r2fljk"))))
(build-system cmake-build-system)
(arguments (list #:tests? #f)) ;no tests
(home-page "https://github.com/slavenf/sfl-library")
(synopsis "Header-only C++11/20 container library")
(description "sfl-library provides many STL-like (Standard Template Library)
containers including vectors, associative containers, and unordered containers
based on hash tables. These containers are designed for C++11 and C++20
constant expression usage.")
(license license:zlib)))
(define-public string-view-lite
(package
(name "string-view-lite")
+953 -537
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+104 -82
View File
@@ -32,7 +32,7 @@
;;; Copyright © 2017 Kristofer Buffington <kristoferbuffington@gmail.com>
;;; Copyright © 2018 Amirouche Boubekki <amirouche@hypermove.net>
;;; Copyright © 2018 Joshua Sierles, Nextjournal <joshua@nextjournal.com>
;;; Copyright © 2018, 2021, 2022, 2023 Maxim Cournoyer <maxim@guixotic.coop>
;;; Copyright © 2018, 2021-2023, 2026 Maxim Cournoyer <maxim@guixotic.coop>
;;; Copyright © 2019 Jack Hill <jackhill@jackhill.us>
;;; Copyright © 2019 Alex Griffin <a@ajgrf.com>
;;; Copyright © 2019 Gábor Boskovits <boskovits@gmail.com>
@@ -109,7 +109,7 @@
#:use-module (gnu packages dbm)
#:use-module (gnu packages docbook)
#:use-module (gnu packages emacs)
#:use-module (gnu packages flex)
#:use-module (gnu packages compiler-tools)
#:use-module (gnu packages freedesktop)
#:use-module (gnu packages gawk)
#:use-module (gnu packages gcc)
@@ -131,6 +131,7 @@
#:use-module (gnu packages guile-xyz)
#:use-module (gnu packages icu4c)
#:use-module (gnu packages jemalloc)
#:use-module (gnu packages kerberos)
#:use-module (gnu packages language)
#:use-module (gnu packages libedit)
#:use-module (gnu packages libevent)
@@ -147,6 +148,7 @@
#:use-module (gnu packages networking)
#:use-module (gnu packages node)
#:use-module (gnu packages onc-rpc)
#:use-module (gnu packages openldap)
#:use-module (gnu packages openstack)
#:use-module (gnu packages pantheon)
#:use-module (gnu packages parallel)
@@ -175,6 +177,7 @@
#:use-module (gnu packages ruby)
#:use-module (gnu packages ruby-check)
#:use-module (gnu packages ruby-xyz)
#:use-module (gnu packages security-token)
#:use-module (gnu packages serialization)
#:use-module (gnu packages sphinx)
#:use-module (gnu packages ssh)
@@ -1183,50 +1186,81 @@ autocompletion and syntax highlighting.")
auto-completion and syntax highlighting.")
(license license:bsd-3)))
;; XXX When updating, check whether boost-for-mysql is still needed.
;; It might suffice to patch cmake/boost.cmake as done in the past.
(define-public mysql
(package
(name "mysql")
(version "5.7.33")
(version "9.7.0")
(source (origin
(method url-fetch)
(uri (list (string-append
"https://dev.mysql.com/get/Downloads/MySQL-"
"https://cdn.mysql.com/Downloads/MySQL-"
(version-major+minor version) "/"
name "-" version ".tar.gz")
(string-append
"https://downloads.mysql.com/archives/get/file/"
name "-" version ".tar.gz")))
(sha256
(base32
"1bb343mf7n0qg2qz497gxjsqprygrjz1q1pbz76hgqxnsy08sfxd"))))
"0v9hc8yzp0f5pwl4kr1a8k7lwyf62g95klxb6avfrc2npjx79dbl"))
(modules '((guix build utils)
(ice-9 ftw)
(srfi srfi-26)))
(snippet
#~(begin
(define (delete-all-but directory . preserve)
(with-directory-excursion directory
(let* ((pred (negate (cut member <>
(cons* "." ".." preserve))))
(items (scandir "." pred)))
(for-each (cut delete-file-recursively <>) items))))
;; Delete bundled source libraries.
(delete-all-but "extra"
;; XXX: The build system doesn't currently
;; support unbundling these.
"json" ;used by bundled opentelemetry
"libbacktrace"
"libcno"
"opentelemetry-cpp"
"opentelemetry-proto"
"rapidjson"
"unordered_dense"
"xxhash")))))
(build-system cmake-build-system)
(arguments
(list
#:tests? #f ;FIXME: teach build system to use system googletest
#:configure-flags
#~(list "-DBUILD_CONFIG=mysql_release"
"-DWITH_SSL=system"
"-DWITH_ZLIB=system"
"-DDEFAULT_CHARSET=utf8"
"-DDEFAULT_COLLATION=utf8_general_ci"
"-DWITH_AUTHENTICATION_LDAP=ON"
"-DWITH_AUTHENTICATION_WEBAUTHN=ON"
"-DWITH_BENCHMARK=OFF"
;; XXX: BUILD_ID is disabled so that the INFO_BIN target is not
;; run; this target relies on running mysqld before it is
;; installed, which fails in our case.
"-DWITH_BUILD_ID=OFF"
"-DWITH_FIDO=system"
"-DWITH_SYSTEM_LIBS=ON"
"-DWITH_UNIT_TESTS=OFF" ;avoid bundled googletest
"-DREPRODUCIBLE_BUILD=ON"
"-DMYSQL_DATADIR=/var/lib/mysql"
"-DMYSQL_UNIX_ADDR=/run/mysqld/mysqld.sock"
"-DINSTALL_INFODIR=share/mysql/docs"
"-DINSTALL_INFODIR=share/info"
"-DINSTALL_MANDIR=share/man"
"-DINSTALL_PLUGINDIR=lib/mysql/plugin"
"-DINSTALL_SCRIPTDIR=bin"
"-DINSTALL_INCLUDEDIR=include/mysql"
"-DINSTALL_DOCREADMEDIR=share/mysql/docs"
"-DINSTALL_SUPPORTFILESDIR=share/mysql"
"-DINSTALL_MYSQLSHAREDIR=share/mysql"
"-DINSTALL_MYSQLTESTDIR=OFF"
"-DINSTALL_DOCDIR=share/mysql/docs"
"-DINSTALL_SHAREDIR=share/mysql"
;; Get rid of test data.
"-DINSTALL_MYSQLTESTDIR="
"-DINSTALL_SQLBENCHDIR=")
"-DINSTALL_SHAREDIR=share/mysql")
#:phases
#~(modify-phases %standard-phases
(add-before 'configure 'disable-broken-abi-check
(lambda _
;; The ABI check started failing with MySQL 9.7.0 for unknown
;; reasons.
(substitute* "cmake/abi_check.cmake"
(("RUN_ABI_CHECK 1")
"RUN_ABI_CHECK 0"))))
(add-after 'install 'remove-extra-binaries
(lambda _
;; Remove the 3 *_embedded files, which weigh in at
@@ -1253,35 +1287,51 @@ auto-completion and syntax highlighting.")
(dirname coreutils)
(dirname grep)
(dirname ps)
(dirname sed))))))))))
(dirname sed)))))))
(add-after 'install 'fix-permissions
;; XXX: Otherwise, the guix daemon reports: "suspicious ownership
;; or permission on `/gnu/store/...-mysql-9.7.0'; rejecting this
;; build output".
(lambda _
(chmod #$output #o755))))))
(native-inputs
(list bison perl pkg-config))
(inputs
(list bash-minimal
boost-for-mysql
boost
coreutils
curl
cyrus-sasl
gawk
grep
icu4c
libaio
libedit
libfido2
libtirpc
lz4
mit-krb5
ncurses
openssl-1.1
openldap
openssl
protobuf
procps
rpcsvc-proto ; rpcgen
sed
zlib))
zlib
`(,zstd "lib")))
(home-page "https://www.mysql.com/")
(synopsis "Fast, easy to use, and popular database")
(description
"MySQL is a fast, reliable, and easy to use relational database
management system that supports the standardized Structured Query
Language.")
(license license:gpl2)))
(license license:gpl2))) ;v2 only -- see 'Election of GPLv2' in LICENSE
(define-public mysql-connector-python
(package
(name "mysql-connector-python")
(version "8.3.0")
(version "9.7.0")
(source
(origin
(method git-fetch)
@@ -1290,66 +1340,23 @@ Language.")
(commit version)))
(file-name (git-file-name name version))
(sha256
(base32 "18jvpnnwmfrn961rvqmsygp7dw3spf3swhxhal4hhj5hqddckj5f"))))
(base32 "0zdm35apj1cfraxwlqfmr04pm87qpw73ilb8p88cn08zsa8q11hg"))))
(build-system pyproject-build-system)
(arguments
(list
;; tests: 1371 passed
#:phases
#~(modify-phases %standard-phases
(add-after 'unpack 'compatibility
(lambda _
(substitute* "src/mysql_capi.c"
(("res = mysql_options\\(&self->session, MYSQL_OPT_LOAD_DATA_LOCAL_DIR.*")
"res = 0;")
(("mysql_options\\(&self->session, MYSQL_OPT_LOAD_DATA_LOCAL_DIR.*")
"")
(("mysql_options\\(&self->session, MYSQL_OPT_TLS_CIPHERSUITES.*")
"")
;; The C API does not have mysql_bind_param, so we produce an
;; error here.
(("status = mysql_bind_param.*") "status = 1;")
(("#include \"mysql_capi_conversion\\.h\"" all)
(string-append all "\n" "#include <stdbool.h>")))))
(add-after 'unpack 'chdir
(lambda _
;; Our protobuf is too old for the mysqlx dev API, so use the
;; classic one without the C modules.
(chdir "mysql-connector-python")))
(add-before 'build 'prepare-build
(lambda _
(setenv "MYSQL_CAPI" #$(this-package-input "mysql"))))
(replace 'check
(lambda* (#:key tests? #:allow-other-keys)
(when tests?
;; Some of these tests might be failing due to the build
;; container's restrictions, others are due to the version
;; mismatch.
(substitute* "tests/cext/test_cext_api.py"
(("def test_change_user") "def _do_not_test_change_user")
(("def test_get_character_set_info")
"def _do_not_test_get_character_set_info"))
(substitute* "tests/test_bugs.py"
(("def test_change_user") "def _do_not_test_change_user")
(("def test_lost_connection") "def _do_not_test_lost_connection")
(("def test_kill_query") "def _do_not_test_kill_query")
;; These all fail because of expired certificates.
(("def test_cext_verify_server_certificate")
"def _do_not_test_cext_verify_server_certificate")
(("def test_pure_verify_server_certificate")
"def _do_not_test_pure_verify_server_certificate")
(("def test_verify_server_name_cext_cnx")
"def _do_not_test_verify_server_name_cext_cnx")
(("def test_verify_server_name_pure_cnx")
"def _do_not_test_verify_server_name_pure_cnx"))
(substitute* '("tests/test_connection.py"
"tests/test_aio_connection.py")
(("def test_allow_local_infile_in_path")
"def _do_not_test_allow_local_infile_in_path")
;; This fails because of expired certificates.
(("def test_connect_with_unix_socket")
"def _do_not_test_connect_with_unix_socket"))
(substitute* "tests/test_constants.py"
(("def test_deprecated")
"def _do_not_test_deprecated"))
(mkdir-p "/tmp/datadir")
(invoke "python3" "unittests.py"
"--verbosity=3"
@@ -1357,9 +1364,8 @@ Language.")
"--keep"
"--mysql-topdir=/tmp/datadir"
"--unix-socket=/tmp/datadir")))))))
(propagated-inputs (list python-protobuf))
(inputs (list mysql protobuf-3.20 openssl-1.1 zlib))
(native-inputs (list python-setuptools))
(inputs (list mysql openssl zlib `(,zstd "lib")))
(home-page "https://dev.mysql.com/doc/connector-python/en/index.html")
(synopsis "MySQL driver written in Python")
(description "MySQL Connector/Python enables Python programs to access
@@ -1666,14 +1672,14 @@ and high-availability (HA).")
(define-public postgresql-17
(package
(name "postgresql")
(version "17.7")
(version "17.10")
(source (origin
(method url-fetch)
(uri (string-append "https://ftp.postgresql.org/pub/source/v"
version "/postgresql-" version ".tar.bz2"))
(sha256
(base32
"1dg9labqgph2idaypb8khdvbag29pr3h4bqv5w8k7kgc08rk97pg"))
"144cb40gn1lasvz0jvz4i72mda8k7pm1bx6azq2vggfddm8h72h7"))
(patches (search-patches
"postgresql-disable-normalize_exec_path.patch"))))
(build-system gnu-build-system)
@@ -1736,14 +1742,14 @@ pictures, sounds, or video.")
(package
(inherit postgresql-17)
(name "postgresql")
(version "16.10")
(version "16.14")
(source (origin
(method url-fetch)
(uri (string-append "https://ftp.postgresql.org/pub/source/v"
version "/postgresql-" version ".tar.bz2"))
(sha256
(base32
"0hib575m9x3z8c71gkcv9jsyq77d3qk7q2zgzvfy6clwrvs8b16y"))
"0w9lgsn03m4k0v3m622v7fk3gqbfbjvwv34mrrc0i4ip4wa7gl7n"))
(patches (search-patches
"postgresql-disable-normalize_exec_path.patch"))))
(arguments
@@ -1767,14 +1773,14 @@ pictures, sounds, or video.")
(package
(inherit postgresql-16)
(name "postgresql")
(version "15.15")
(version "15.18")
(source (origin
(method url-fetch)
(uri (string-append "https://ftp.postgresql.org/pub/source/v"
version "/postgresql-" version ".tar.bz2"))
(sha256
(base32
"1ais46b2ij38y75i1w336as03pybyndsd2pp2q8gdjq9igmsllsp"))
"1d13qckpslfqamdmp23q3rbzxlp1rqwszylilyllpsp3gzwhvpqi"))
(patches (search-patches
"postgresql-disable-resolve_symlinks.patch"))))
(native-inputs (modify-inputs native-inputs
@@ -1787,6 +1793,7 @@ pictures, sounds, or video.")
(inherit postgresql-15)
(name "postgresql")
(version "14.20")
(replacement postgresql-14.23)
(source (origin
(inherit (package-source postgresql-15))
(uri (string-append "https://ftp.postgresql.org/pub/source/v"
@@ -1795,6 +1802,19 @@ pictures, sounds, or video.")
(base32
"0sv45dsmyplfys6dfdjdwmrczl46s82x35xdh311nxj02q7z29vm"))))))
(define-public postgresql-14.23
(package
(inherit postgresql-14)
(name "postgresql")
(version "14.23")
(source (origin
(inherit (package-source postgresql-14))
(uri (string-append "https://ftp.postgresql.org/pub/source/v"
version "/postgresql-" version ".tar.bz2"))
(sha256
(base32
"19clihp73ak2p5di90jhg50lqjkkr0iy349gkki30qsl5f11cwnc"))))))
(define-deprecated/public postgresql-13 #f
(package
(inherit postgresql-14)
@@ -5645,7 +5665,7 @@ with integrated support for finding required rows quickly.")
(define-public apache-arrow
(package
(name "apache-arrow")
(version "23.0.1")
(version "24.0.0")
(source
(origin
(method git-fetch)
@@ -5655,7 +5675,7 @@ with integrated support for finding required rows quickly.")
(file-name (git-file-name name version))
(sha256
(base32
"1qn7wgavi3kiz4d6w1naqj5631bg87fnj6gbhaxmpmynm5hi9wm7"))))
"1j3gs5ffa9gx2y2nggmi2zn5rj0bsnjnxrzfnipx6050jz6n8dx9"))))
(build-system cmake-build-system)
(arguments
(list
@@ -5823,6 +5843,8 @@ __version_tuple__ = version_tuple = (~a)~%" version version-tuple))))))
pkg-config
python-cython
python-pytest
python-pytest-runner
python-scikit-build-core
python-setuptools-scm
python-setuptools))
(outputs '("out"))
+1 -1
View File
@@ -20,7 +20,7 @@
#:use-module (gnu packages bison)
#:use-module (gnu packages compression)
#:use-module (gnu packages cpp)
#:use-module (gnu packages flex)
#:use-module (gnu packages compiler-tools)
#:use-module (gnu packages libffi)
#:use-module (gnu packages ncurses)
#:use-module (gnu packages python)
+1 -2
View File
@@ -58,7 +58,7 @@
#:use-module (gnu packages code)
#:use-module (gnu packages compression)
#:use-module (gnu packages digest)
#:use-module (gnu packages flex)
#:use-module (gnu packages compiler-tools)
#:use-module (gnu packages fontutils)
#:use-module (gnu packages gcc)
#:use-module (gnu packages gdb)
@@ -77,7 +77,6 @@
#:use-module (gnu packages mail)
#:use-module (gnu packages multiprecision)
#:use-module (gnu packages ncurses)
#:use-module (gnu packages ninja)
#:use-module (gnu packages perl)
#:use-module (gnu packages pkg-config)
#:use-module (gnu packages pretty-print)
+1 -1
View File
@@ -56,7 +56,7 @@
#:use-module (gnu packages curl)
#:use-module (gnu packages education)
#:use-module (gnu packages emacs)
#:use-module (gnu packages flex)
#:use-module (gnu packages compiler-tools)
#:use-module (gnu packages fribidi)
#:use-module (gnu packages gettext)
#:use-module (gnu packages glib)
-1
View File
@@ -105,7 +105,6 @@
#:use-module (gnu packages libbsd)
#:use-module (gnu packages linux)
#:use-module (gnu packages ncurses)
#:use-module (gnu packages ninja)
#:use-module (gnu packages nss)
#:use-module (gnu packages perl)
#:use-module (gnu packages perl-web)
+1 -1
View File
@@ -41,6 +41,7 @@
#:use-module (gnu packages)
#:use-module (gnu packages base)
#:use-module (gnu packages bash)
#:use-module (gnu packages build-tools)
#:use-module (gnu packages check)
#:use-module (gnu packages compression)
#:use-module (gnu packages curl)
@@ -48,7 +49,6 @@
#:use-module (gnu packages gdb)
#:use-module (gnu packages libedit)
#:use-module (gnu packages llvm)
#:use-module (gnu packages ninja)
#:use-module (gnu packages perl)
#:use-module (gnu packages pkg-config)
#:use-module (gnu packages python)
+3 -3
View File
@@ -56,7 +56,7 @@
#:use-module (gnu packages datastructures)
#:use-module (gnu packages documentation)
#:use-module (gnu packages elf)
#:use-module (gnu packages flex)
#:use-module (gnu packages compiler-tools)
#:use-module (gnu packages freedesktop)
#:use-module (gnu packages gcc)
#:use-module (gnu packages glib)
@@ -1425,7 +1425,7 @@ and TCP-capable recursive DNS server for finding domains on the internet.")
(define-public openresolv
(package
(name "openresolv")
(version "3.17.4")
(version "3.13.2")
(source
(origin
(method git-fetch)
@@ -1435,7 +1435,7 @@ and TCP-capable recursive DNS server for finding domains on the internet.")
(file-name (git-file-name name version))
(sha256
(base32
"1lawj50qhr2yj7fy3p8x4m3kqz4lbvghnjc4jlqnxp484hg83ki3"))
"03m8n0j0kxxm5kpl66gz4lxr1qqgrp8zlkaq9j8fz27fih0g75xf"))
(patches
(search-patches "openresolv-restartcmd-guix.patch"))))
(build-system gnu-build-system)
+1 -1
View File
@@ -57,7 +57,7 @@
#:use-module (gnu packages bison)
#:use-module (gnu packages kde-frameworks)
#:use-module (gnu packages docbook)
#:use-module (gnu packages flex)
#:use-module (gnu packages compiler-tools)
#:use-module (gnu packages ghostscript)
#:use-module (gnu packages graphviz)
#:use-module (gnu packages gettext)
+1 -1
View File
@@ -29,7 +29,7 @@
#:use-module (gnu packages compression)
#:use-module (gnu packages curl)
#:use-module (gnu packages databases)
#:use-module (gnu packages flex)
#:use-module (gnu packages compiler-tools)
#:use-module (gnu packages gettext)
#:use-module (gnu packages pkg-config)
#:use-module (gnu packages base)
+1 -1
View File
@@ -42,7 +42,7 @@
#:use-module (gnu packages curl)
#:use-module (gnu packages databases)
#:use-module (gnu packages django)
#:use-module (gnu packages flex)
#:use-module (gnu packages compiler-tools)
#:use-module (gnu packages fonts)
#:use-module (gnu packages fontutils)
#:use-module (gnu packages freedesktop)
+12 -12
View File
@@ -90,7 +90,7 @@
#:use-module (gnu packages elf)
#:use-module (gnu packages embedded)
#:use-module (gnu packages engineering)
#:use-module (gnu packages flex)
#:use-module (gnu packages compiler-tools)
#:use-module (gnu packages fontutils)
#:use-module (gnu packages freedesktop)
#:use-module (gnu packages gawk)
@@ -1021,7 +1021,7 @@ files.")
(define-public klayout
(package
(name "klayout")
(version "0.30.8")
(version "0.30.9")
(source
(origin (method git-fetch)
(uri (git-reference
@@ -1030,7 +1030,7 @@ files.")
(file-name (git-file-name name version))
(sha256
(base32
"0aw0y5k27pslql9pir6nplapj6ml6fkhzd815s13rlnw3bm0fcs6"))))
"1v5ddw7xixvdc3qshd0lkrc3ayk2q5wkk1zbhvsidq0kzlqbr2z5"))))
(build-system copy-build-system)
(arguments
(list
@@ -1314,7 +1314,7 @@ package.")
#:tests? #f)) ;no test suite
(native-inputs (list asciidoc
gettext-minimal
git-minimal
git-minimal/pinned
perl
perl-unicode-linebreak
perl-yaml-tiny
@@ -2207,7 +2207,7 @@ which allows one to install the M8 firmware on any Teensy.")
(define-public magic
(package
(name "magic")
(version "8.3.644")
(version "8.3.652")
(source
(origin
(method git-fetch)
@@ -2216,7 +2216,7 @@ which allows one to install the M8 firmware on any Teensy.")
(commit version)))
(file-name (git-file-name name version))
(sha256
(base32 "0qp1alm4pczfm77r8lxwgzrwh02ihvfmk9sbwjlfbrixg1dn85xb"))))
(base32 "07q2lldcq6zb1apa5d3paciha92r6jlp7xny8pc31f56k5s9jnmz"))))
(build-system gnu-build-system)
(arguments
(list
@@ -2312,7 +2312,7 @@ coverage.")
(define-public netgen
(package
(name "netgen")
(version "1.5.319")
(version "1.5.320")
(source
(origin
(method git-fetch)
@@ -2321,7 +2321,7 @@ coverage.")
(commit version)))
(file-name (git-file-name name version))
(sha256
(base32 "16xd2xcsny1bb6yk4lz34jfpwfb5xi2i9izxjymmalnzhg32i9cz"))))
(base32 "11mvf0nrsfc1lxbgqhmczi0maw4n10lib2xqnhpkyy73ci489147"))))
(build-system gnu-build-system)
(arguments
(list
@@ -2521,7 +2521,7 @@ Automation}, portable and vendor neutral FPGA place and route tool.")
(define-public nvc
(package
(name "nvc")
(version "1.20.1")
(version "1.21.0")
(source (origin
(method git-fetch)
(uri (git-reference
@@ -2530,7 +2530,7 @@ Automation}, portable and vendor neutral FPGA place and route tool.")
(file-name (git-file-name name version))
(sha256
(base32
"1b38x2ch468s4p6mrq6c8s0d95vb84p6w4v8in79l4w7sfy8jnr0"))))
"00hnrzk9dw88srfmjxxb9xkgnd5n26pmqlcw1bff1y0bckblsr38"))))
(build-system gnu-build-system)
(arguments
(list #:out-of-source? #t
@@ -4376,7 +4376,7 @@ input and outputs an XML dataset.")
(define-public qucs-s
(package
(name "qucs-s")
(version "26.1.0") ;update qucsator-rf accordingly
(version "26.1.1") ;update qucsator-rf accordingly
(source
(origin
(method git-fetch)
@@ -4386,7 +4386,7 @@ input and outputs an XML dataset.")
(file-name (git-file-name name version))
(sha256
(base32
"0aiyrcrxln4v6qm2dmigb54wl0mj499q3g18pz87m1s2lfgicpb1"))))
"009siqmn76r2l17hnjqmr6ap8nw969hd5fyqigb4p3i8cvjq7gmx"))))
(build-system qt-build-system)
(arguments
(list
+84 -71
View File
@@ -4547,43 +4547,6 @@ boilerplate code from defining new Flymake backend functions.")
(description "This package adds Clojure syntax checker clj-kondo.")
(license license:gpl3+)))
(define-public emacs-flymake-shellcheck
;; No tag, version grabbed from source .el file.
(let ((commit "ac534e9ef15c82ac86ae65fe5004d29dbc8c92c7")
(revision "1"))
(package
(name "emacs-flymake-shellcheck")
(version (git-version "0.1" revision commit))
(source
(origin
(method git-fetch)
(uri (git-reference
(url "https://github.com/federicotdn/flymake-shellcheck")
(commit commit)))
(file-name (git-file-name name version))
(sha256
(base32 "04yfb4sy41spjzk9mhm4gy0h8vnjx09p2g6nm1yzgd9a5ph9sqgl"))))
(build-system emacs-build-system)
(arguments
'(#:phases
(modify-phases %standard-phases
(add-after 'unpack 'substitute-shellcheck-path
(lambda* (#:key inputs #:allow-other-keys)
(make-file-writable "flymake-shellcheck.el")
(emacs-substitute-sexps "flymake-shellcheck.el"
("defcustom flymake-shellcheck-path"
`(or (executable-find "shellcheck")
,(search-input-file inputs "bin/shellcheck")))))))))
(inputs
(list shellcheck))
(home-page "https://github.com/federicotdn/flymake-shellcheck")
(synopsis "Flymake backend for Bash/Sh powered by ShellCheck")
(description
"This package provides a backend for Flymake to use the
tool ShellCheck for static analyzing @command{bash} and @command{sh}
scripts.")
(license license:gpl3+))))
(define-public emacs-a
(package
(name "emacs-a")
@@ -5303,6 +5266,39 @@ to prevent advertisers from tracking you when you open URLs (or listen to
podcasts) in Emacs.")
(license (list license:gpl3+)))))
(define-public emacs-emcp
(let ((commit "a91016452ef73813ea4a7e84cde233176d87a97f")
(revision "0"))
(package
(name "emacs-emcp")
(version (git-version "0.1.0" revision commit))
(source
(origin
(method git-fetch)
(uri (git-reference
(url "https://codeberg.org/martenlienen/emcp")
(commit commit)))
(file-name (git-file-name name version))
(sha256
(base32
"08wbpj95l38fsdihxhgryb74psl11agw5n9swnpf1j3qyhwa13cn"))))
(build-system emacs-build-system)
(arguments
(list
#:test-command
#~(list "emacs" "-Q" "-batch"
"-l" "emcp-tests.el"
"-f"
"ert-run-tests-batch-and-exit")))
(propagated-inputs
(list emacs-elisp-refs emacs-magit emacs-http-server))
(home-page "https://codeberg.org/martenlienen/emcp")
(synopsis "Emacs MCP client")
(description
"@code{emacs-emcp} is an Emacs client for the @acronym{Model Context
Protocol, MCP}, designed to connect LLM agents directly to Emacs.")
(license license:gpl3+))))
(define emacs-emms-print-metadata
(package
(name "emacs-emms-print-metadata")
@@ -15526,34 +15522,6 @@ underlying library functionality for performing various activities related to
the game of chess.")
(license license:gpl3+)))
(define-public emacs-4clojure
;; There is no release. Base version is extracted from Version keyword in
;; the main file.
(let ((commit "4eccf8c7d4341a36c269451838114b27836699f9")
(revision "1"))
(package
(name "emacs-4clojure")
(version (git-version "0.2.1" revision commit))
(source
(origin
(method git-fetch)
(uri (git-reference
(url "https://github.com/emacsorphanage/4clojure")
(commit commit)))
(file-name (git-file-name name version))
(sha256
(base32 "19x653lzc1dxil4ix257hciidbdmbhaxhs6qhlkwi9ygjrlrgvnk"))))
(build-system emacs-build-system)
(propagated-inputs
(list emacs-request))
(home-page "https://github.com/emacsorphanage/4clojure/")
(synopsis "Open and evaluate 4clojure questions in Emacs")
(description "Emacs 4clojure interacts with
@url{http://www.4clojure.com, 4clojure} problems. You can open a specific
question and move to the next or previous one. You can also verify your
answers.")
(license license:gpl3+))))
(define-public emacs-base16-theme
(package
(name "emacs-base16-theme")
@@ -16822,6 +16790,51 @@ line program.")
requests library that uses the url library.")
(license license:gpl2+))))
(define-public emacs-http-server
(let ((commit "00e746baf4a622a7545b4af5c5237a55d51f801b")
(revision "0"))
(package
(name "emacs-http-server")
(version (git-version "0.1.0" revision commit))
(source
(origin
(method git-fetch)
(uri (git-reference
(url "https://codeberg.org/martenlienen/http-server.el")
(commit commit)))
(file-name (git-file-name name version))
(sha256
(base32
"0j7ls15ljk22qxy6hs2qzcjnbdfvrq4qwly8s6kfbczi74mw5iji"))))
(build-system emacs-build-system)
(arguments
(list
#:test-command
#~(list "emacs" "-Q" "-batch"
"-l" "http-server.el"
"-l" "http-server-ws.el"
"-l" "http-server-tests.el"
"-l" "http-server-ws-tests.el"
"--eval"
(string-append
"(ert-run-tests-batch-and-exit "
"'(and (not http-server-accepts-extra-methods)
(not http-server-rejects-unsupported-methods)))"))
#:phases
#~(modify-phases %standard-phases
(add-after 'unpack 'build-info-manual
(lambda _
(invoke "makeinfo" "--no-split"
"-o" "http-server.info" "docs/http-server.texi"))))))
(native-inputs
(list emacs-package-lint emacs-plz emacs-websocket texinfo))
(home-page "https://codeberg.org/martenlienen/http-server.el")
(synopsis "Emacs HTTP server")
(description
"This library implements an HTTP server inside of Emacs to communicate
with the user or other external programs.")
(license license:gpl3+))))
(define-public emacs-rtfm-mode
(package
(name "emacs-rtfm-mode")
@@ -23859,8 +23872,8 @@ actually changing the buffer's text.")
(define-public emacs-diff-hl
;; No new tags or releases since 2024.
(let ((commit "e79aa49ad3cbbe85379cf6646db3aaacd3b04708")
(revision "0"))
(let ((commit "7d873b2f58908de1ea2f499da9bf993e088953d7")
(revision "1"))
(package
(name "emacs-diff-hl")
(version (git-version "1.10.0" revision commit))
@@ -23872,7 +23885,7 @@ actually changing the buffer's text.")
(commit commit)))
(file-name (git-file-name name version))
(sha256
(base32 "0fvxngcbx36vqj72fllfp5iqwihcqd1dfhmqr3m1284191q83na3"))))
(base32 "15a9cjlpjsfcb2hxqbb123389qhiqs06mn01pas2l0jqhc2p86v9"))))
(build-system emacs-build-system)
(arguments
(list
@@ -23895,7 +23908,7 @@ actually changing the buffer's text.")
(invoke "git" "init")
(invoke "git" "add" ".")
(invoke "git" "commit" "-m" "Commit all."))))))
(native-inputs (list git-minimal))
(native-inputs (list git-minimal/pinned))
(home-page "https://github.com/dgutov/diff-hl")
(synopsis "Highlight uncommitted changes using VC")
(description
@@ -42107,7 +42120,7 @@ add popup descriptions to existing keymaps
(define-public emacs-forgejo
(package
(name "emacs-forgejo")
(version "0.2.2")
(version "0.2.3")
(source (origin
(method git-fetch)
(uri (git-reference
@@ -42116,7 +42129,7 @@ add popup descriptions to existing keymaps
(file-name (git-file-name name version))
(sha256
(base32
"0hf4sckxdygxa84g3pi3m2qy16ngx76jsrf192q5l4fppsyirnws"))))
"1c8s8a0hwb44jddxsrd74bh8rwaz8z5mn9ga8jmwxy7w045xfln1"))))
(build-system emacs-build-system)
(arguments
(list #:lisp-directory "lisp"
+1 -1
View File
@@ -57,7 +57,7 @@
#:use-module (gnu packages compression)
#:use-module (gnu packages cross-base)
#:use-module (gnu packages dejagnu)
#:use-module (gnu packages flex)
#:use-module (gnu packages compiler-tools)
#:use-module (gnu packages gcc)
#:use-module (gnu packages gdb)
#:use-module (gnu packages guile)
+2 -2
View File
@@ -68,6 +68,7 @@
#:use-module (gnu packages bash)
#:use-module (gnu packages bison)
#:use-module (gnu packages boost)
#:use-module (gnu packages build-tools)
#:use-module (gnu packages cdrom)
#:use-module (gnu packages check)
#:use-module (gnu packages cmake)
@@ -80,7 +81,7 @@
#:use-module (gnu packages engineering)
#:use-module (gnu packages elf)
#:use-module (gnu packages file-systems)
#:use-module (gnu packages flex)
#:use-module (gnu packages compiler-tools)
#:use-module (gnu packages fltk)
#:use-module (gnu packages fonts)
#:use-module (gnu packages fontutils)
@@ -107,7 +108,6 @@
#:use-module (gnu packages music)
#:use-module (gnu packages ncurses)
#:use-module (gnu packages networking)
#:use-module (gnu packages ninja)
#:use-module (gnu packages parallel)
#:use-module (gnu packages pkg-config)
#:use-module (gnu packages pretty-print)
+1 -1
View File
@@ -113,7 +113,7 @@
#:use-module (gnu packages emacs-build)
#:use-module (gnu packages emacs-xyz)
#:use-module (gnu packages file)
#:use-module (gnu packages flex)
#:use-module (gnu packages compiler-tools)
#:use-module (gnu packages fontutils)
#:use-module (gnu packages freedesktop)
#:use-module (gnu packages gawk)
+1 -1
View File
@@ -24,7 +24,7 @@
(define-module (gnu packages esolangs)
#:use-module (gnu packages)
#:use-module (gnu packages bison)
#:use-module (gnu packages flex)
#:use-module (gnu packages compiler-tools)
#:use-module (gnu packages ncurses)
#:use-module (gnu packages python)
#:use-module (gnu packages python-build)
+1 -1
View File
@@ -30,7 +30,7 @@
#:use-module (gnu packages)
#:use-module (gnu packages autotools)
#:use-module (gnu packages bison)
#:use-module (gnu packages flex)
#:use-module (gnu packages compiler-tools)
#:use-module (gnu packages glib)
#:use-module (gnu packages graphviz)
#:use-module (gnu packages linux)
+1 -1
View File
@@ -78,7 +78,7 @@
#:use-module (gnu packages docbook)
#:use-module (gnu packages elf)
#:use-module (gnu packages file)
#:use-module (gnu packages flex)
#:use-module (gnu packages compiler-tools)
#:use-module (gnu packages freedesktop)
#:use-module (gnu packages gawk)
#:use-module (gnu packages gettext)
+1 -2
View File
@@ -99,7 +99,7 @@
#:use-module (gnu packages emacs)
#:use-module (gnu packages emacs-xyz)
#:use-module (gnu packages dbm)
#:use-module (gnu packages flex)
#:use-module (gnu packages compiler-tools)
#:use-module (gnu packages freedesktop)
#:use-module (gnu packages gettext)
#:use-module (gnu packages glib)
@@ -129,7 +129,6 @@
#:use-module (gnu packages multiprecision)
#:use-module (gnu packages ncurses)
#:use-module (gnu packages networking)
#:use-module (gnu packages ninja)
#:use-module (gnu packages nss)
#:use-module (gnu packages perl)
#:use-module (gnu packages pdf)
+1 -1
View File
@@ -68,7 +68,7 @@
#:use-module (gnu packages elf)
#:use-module (gnu packages embedded)
#:use-module (gnu packages flashing-tools)
#:use-module (gnu packages flex)
#:use-module (gnu packages compiler-tools)
#:use-module (gnu packages fontutils)
#:use-module (gnu packages freedesktop)
#:use-module (gnu packages gawk)
+1 -1
View File
@@ -72,7 +72,7 @@
#:use-module (gnu packages electronics)
#:use-module (gnu packages elf)
#:use-module (gnu packages embedded)
#:use-module (gnu packages flex)
#:use-module (gnu packages compiler-tools)
#:use-module (gnu packages ghostscript)
#:use-module (gnu packages gnupg)
#:use-module (gnu packages golang-xyz)
+6 -64
View File
@@ -1,7 +1,5 @@
;;; GNU Guix --- Functional package management for GNU
;;; Copyright © 2012, 2013, 2014, 2019 Ludovic Courtès <ludo@gnu.org>
;;; Copyright © 2016 Efraim Flashner <efraim@flashner.co.il>
;;; Copyright © 2024 Janneke Nieuwenhuizen <janneke@gnu.org>
;;; Copyright © 2026 Anderson Torres <anderson.torres.8519@gmail.com>
;;;
;;; This file is part of GNU Guix.
;;;
@@ -19,65 +17,9 @@
;;; along with GNU Guix. If not, see <http://www.gnu.org/licenses/>.
(define-module (gnu packages flex)
#:use-module (guix licenses)
#:use-module (guix packages)
#:use-module (guix download)
#:use-module (guix build-system gnu)
#:use-module (guix gexp)
#:use-module (guix utils)
#:use-module (gnu packages)
#:use-module (gnu packages m4)
#:use-module (gnu packages man)
#:use-module (gnu packages bison)
#:use-module (srfi srfi-1))
#:use-module (gnu packages compiler-tools)
#:use-module (guix deprecation))
(define-public flex
(package
(name "flex")
(version "2.6.4")
(source (origin
(method url-fetch)
(uri (string-append
"https://github.com/westes/flex"
"/releases/download/v" version "/"
"flex-" version ".tar.gz"))
(sha256
(base32
"15g9bv236nzi665p9ggqjlfn4dwck5835vf0bbw2cz7h5c1swyp8"))))
(build-system gnu-build-system)
(inputs
(let ((bison-for-tests
(package
(inherit bison)
(arguments
;; Disable tests, since they require flex.
(substitute-keyword-arguments arguments
((#:tests? _ #f) #f)))
(inputs (alist-delete "flex" (package-inputs bison))))))
`(("bison" ,bison-for-tests))))
(arguments
(if (%current-target-system)
(list #:configure-flags
#~'("ac_cv_func_malloc_0_nonnull=yes"
"ac_cv_func_realloc_0_nonnull=yes"))
'()))
;; m4 is not present in PATH when cross-building
(native-inputs
(list help2man m4))
(propagated-inputs (list m4))
(home-page "https://github.com/westes/flex")
(synopsis "Fast lexical analyser generator")
(description
"Flex is a tool for generating scanners. A scanner, sometimes
called a tokenizer, is a program which recognizes lexical patterns in
text. The flex program reads user-specified input files, or its standard
input if no file names are given, for a description of a scanner to
generate. The description is in the form of pairs of regular expressions
and C code, called rules. Flex generates a C source file named,
\"lex.yy.c\", which defines the function yylex(). The file \"lex.yy.c\"
can be compiled and linked to produce an executable. When the executable
is run, it analyzes its input for occurrences of text matching the
regular expressions for each rule. Whenever it finds a match, it
executes the corresponding C code.")
(license (non-copyleft "file://COPYING"
"See COPYING in the distribution."))))
;; XXX: Deprecated on 2026-05-28.
(define-deprecated/public-alias flex
(@ (gnu packages compiler-tools) flex))
+59 -8
View File
@@ -74,6 +74,7 @@
;;; Copyright © 2026 Carlos Durán Domínguez <wurt@wurt.eu>
;;; Copyright © 2026 Joan Vilardaga Castro <codeberg-hn80@joanvc.cat>
;;; Copyright © 2026 Sughosha <sughosha@disroot.org>
;;; Copyright © 2026 bdunahu <bdunahu@operationnull.com>
;;;
;;; This file is part of GNU Guix.
;;;
@@ -334,14 +335,14 @@ mediums.")
(version "4.1")
(source
(origin
(method git-fetch)
(uri (git-reference
(url "https://github.com/rsms/inter")
(commit (string-append "v" version))))
(file-name (git-file-name name version))
(method url-fetch)
(uri (string-append
"https://github.com/rsms/inter/releases/download/"
"v" version "/Inter-" version ".zip"))
(sha256
(base32 "1g54vl3jkpan0s1mzrb1s8zjqzy9787ffjg9sfy6yjy4k3qg8xhx"))))
(base32 "07miarbl5ain7pg7sxlrb2j4m9prbriacyqpv1mvckwxlkagv0wq"))))
(build-system font-build-system)
(outputs '("out" "ttf" "woff"))
(home-page "https://rsms.me/inter")
(synopsis "Variable font family optimized for screen readability")
(description
@@ -399,6 +400,30 @@ Lisnoti is available in regular, italic, bold and bold-italic
variants.")
(license license:silofl1.1))))
(define-public font-literata
(package
(name "font-literata")
(version "3.103")
(source (origin
(method git-fetch)
(uri (git-reference
(url "https://github.com/googlefonts/literata")
(commit version)))
(file-name (git-file-name name version))
(sha256
(base32
"1nnr5y6fz7da06ihinmna2a1g79q8l41bgr62l6jpl43p1dw93dn"))))
(build-system font-build-system)
(outputs (list "out" "woff"))
(home-page "https://github.com/googlefonts/literata")
(synopsis "Contemporary serif typeface for long-form reading")
(description
"Literata is a serif screen font family. It was conceived for intensive
editorial use, especially on screens of all sorts. Its main potential is in
digital publishing, whether on the web, electronic press, or mobile
applications.")
(license license:silofl1.1)))
(define-public font-inconsolata
(package
(name "font-inconsolata")
@@ -2817,6 +2842,32 @@ family.")
(define-deprecated-package font-adobe-source-serif-pro
font-adobe-source-serif)
(define-public font-medieval-sharp
;; No releases, use newest commit.
(let ((commit "ee7510b6b13854fd340e7d2e44c218780f672cd1")
(revision "1"))
(package
(name "font-medieval-sharp")
;; From FONTLOG.txt.
(version (git-version "3.1.0" revision commit))
(source
(origin
(method git-fetch)
(uri (git-reference
(url "https://github.com/wmk69/Medieval-Sharp")
(commit commit)))
(file-name (git-file-name name version))
(sha256
(base32
"1r300591pra4nxpm5kppl5q3ihsp01wk2zh24f9pvv0jgf1ik87x"))))
(build-system font-build-system)
(home-page "https://github.com/wmk69/Medieval-Sharp")
(synopsis "Font based on gothic letters")
(description
"Medieval Sharp is a font created for inscriptions on stone, based on
gothic letters.")
(license license:silofl1.1))))
(define-public font-microsoft-cascadia
(package
(name "font-microsoft-cascadia")
@@ -4260,7 +4311,7 @@ typographical palette.")
(define-public font-mona-sans
(package
(name "font-mona-sans")
(version "2.0.26")
(version "2.0.27")
(source
(origin
(method git-fetch)
@@ -4270,7 +4321,7 @@ typographical palette.")
(file-name (git-file-name name version))
(sha256
(base32
"09b6apxq659y4dkkm5swy683q6hviibv1cd48ragm5rd1376hsaz"))))
"10xbs857d21zrfx0cpzcsyyk76j921qq68qpz5r2kl4jr3gz541z"))))
(build-system font-build-system)
(outputs '("out" "ttf" "woff"))
(home-page "https://github.com/mona-sans")
+2 -2
View File
@@ -47,11 +47,12 @@
#:use-module (gnu packages autotools)
#:use-module (gnu packages bash)
#:use-module (gnu packages bison)
#:use-module (gnu packages build-tools)
#:use-module (gnu packages check)
#:use-module (gnu packages compression)
#:use-module (gnu packages datastructures)
#:use-module (gnu packages docbook)
#:use-module (gnu packages flex)
#:use-module (gnu packages compiler-tools)
#:use-module (gnu packages fonts)
#:use-module (gnu packages freedesktop)
#:use-module (gnu packages fribidi)
@@ -69,7 +70,6 @@
#:use-module (gnu packages linux)
#:use-module (gnu packages man)
#:use-module (gnu packages mc)
#:use-module (gnu packages ninja)
#:use-module (gnu packages perl)
#:use-module (gnu packages pkg-config)
#:use-module (gnu packages python)
+174 -120
View File
@@ -98,6 +98,7 @@
;;; Copyright © 2026 Cayetano Santos <csantosb@inventati.org>
;;; Copyright © 2026 Carlos Durán Domínguez <wurt@wurt.eu>
;;; Copyright © 2026 Nikita Alkhovik <forgoty13@gmail.com>
;;; Copyright © 2026 bdunahu <bdunahu@operationnull.com>
;;;
;;; This file is part of GNU Guix.
;;;
@@ -143,7 +144,7 @@
#:use-module (gnu packages documentation)
#:use-module (gnu packages emacs)
#:use-module (gnu packages emulators)
#:use-module (gnu packages flex)
#:use-module (gnu packages compiler-tools)
#:use-module (gnu packages fltk)
#:use-module (gnu packages fonts)
#:use-module (gnu packages fontutils)
@@ -200,7 +201,6 @@
#:use-module (gnu packages ncurses)
#:use-module (gnu packages netpbm)
#:use-module (gnu packages networking)
#:use-module (gnu packages ninja)
#:use-module (gnu packages ocaml)
#:use-module (gnu packages oneapi)
#:use-module (gnu packages opencl)
@@ -3988,27 +3988,26 @@ that beneath its ruins lay buried an ancient evil.")
(base32 "0hgzdvlh0j42w4q9kch9xvhnbvcrypac01xhpksw35gj9my887cp"))
(modules '((guix build utils)))
(snippet
;; So, some of the sounds/graphics/tilesets are under different
;; licenses... some of them even nonfree! This is a console-only
;; version of this package so we just remove them.
;; In the future, if someone tries to make a graphical variant of
;; this package, they can deal with that mess themselves. :)
'(begin
(for-each (lambda (subdir)
(let ((lib-subdir (string-append "lib/" subdir)))
(delete-file-recursively lib-subdir)))
'("fonts" "icons" "sounds" "tiles"))
(substitute* "lib/Makefile"
;; And don't try to invoke makefiles in the directories we removed.
(("gamedata customize help screens fonts tiles sounds icons user")
"gamedata customize help screens user"))
;; Remove nonfree .dll files too.
(delete-file-recursively "src/win")))))
(for-each delete-file-recursively
'("lib/tiles/shockbolt" ;nonfree
"src/win")) ;contains .dlls!
;; Don't build the shockbolt directory either.
(substitute* "lib/tiles/Makefile"
(("shockbolt") ""))))
(patches (search-patches "angband-remove-nonfree-tile-options.patch"))))
(build-system gnu-build-system)
(arguments
`(#:configure-flags (list (string-append "--bindir=" %output "/bin"))
`(#:configure-flags (list (string-append "--bindir=" %output "/bin")
"--disable-x11")
#:phases
(modify-phases %standard-phases
(add-after 'unpack 'disable-graphics-and-sounds
(lambda _
(substitute* "lib/Makefile"
;; Do not build any graphics for this version.
(("gamedata customize help screens fonts tiles sounds icons user")
"gamedata customize help screens user"))))
(add-before 'build 'fix-infinite-loop-on-sighup
;; XXX Release 4.2.6 has a major bug where sending the process a
;; SIGHUP when closing the terminal causes it to infinite loop
@@ -4058,6 +4057,59 @@ the depths below Angband, seeking riches, fighting monsters, and preparing to
fight Morgoth, the Lord of Darkness.")
(license license:gpl2)))
(define-public angband-sdl2
(package
(inherit angband)
(name "angband-sdl2")
(arguments
(substitute-keyword-arguments
(package-arguments angband)
((#:configure-flags flags)
#~(cons* "--enable-sdl2" #$flags))
((#:phases phases)
#~(modify-phases #$phases
(delete 'disable-graphics-and-sounds)
(add-after 'unpack 'patch-sdl-wrapper-headers
(lambda _
(with-directory-excursion "src"
(substitute* '("snd-sdl.c"
"main-sdl2.c"
"sdl2/pui-win.h")
(("\"SDL_image.h\"") "\"SDL2/SDL_image.h\"")
(("\"SDL_mixer.h\"") "\"SDL2/SDL_mixer.h\"")
(("\"SDL_ttf.h\"") "\"SDL2/SDL_ttf.h\"")))))
(add-after 'unpack 'patch-desktop-file
(lambda* (#:key outputs #:allow-other-keys)
(let ((out (assoc-ref outputs "out")))
(substitute* "lib/icons/angband-sdl2.desktop"
(("Exec=angband" _)
(string-append "Exec=" #$output "/bin/angband-sdl2"))))))
(add-after 'install 'rename-binary
(lambda _
(with-directory-excursion #$output
;; allows parallel installation with angband
(rename-file "bin/angband"
"bin/angband-sdl2"))))))))
(inputs
(modify-inputs inputs
(prepend sdl2
sdl2-image
sdl2-mixer
sdl2-ttf)))
(description "Angband is a Classic dungeon exploration roguelike. Explore
the depths below Angband, seeking riches, fighting monsters, and preparing to
fight Morgoth, the Lord of Darkness.
This version includes the SDL2 frontend, providing tilesets and sounds which
can be enabled through in-game options.")
;; XXX: fonts and adam bolt tileset are free but being clarified:
;; https://github.com/angband/angband/issues/6608
;; For the rest, see:
;; https://github.com/angband/angband/blob/master/docs/copying.rst
(license (list license:gpl2 ;code, nomad+old tilesets
license:cc-by-sa3.0 ;david gervais tileset
license:cc-by-sa4.0)))) ;sounds
(define-public pingus
;; Latest release is from 2021-12-24.
(let ((commit "7d65221e1cd1026053c8a5a08ad911fbdd13d3ed")
@@ -6096,39 +6148,22 @@ have a steep learning curve.")))
(define-public openrct2-title-sequences
(package
(name "openrct2-title-sequences")
(version "0.1.2")
(version "0.4.26")
(source
(origin
(method url-fetch)
(uri (string-append "https://github.com/OpenRCT2/title-sequences/releases/download/v"
version "/title-sequence-v" version ".zip"))
(uri (string-append "https://github.com/OpenRCT2/title-sequences"
"/releases/download/v" version
"/title-sequences.zip"))
(file-name (string-append name "-" version ".zip"))
(sha256
(base32
"0qbyxrsw8hlgaq0r5d7lx7an3idy4qbfv7yiw9byhldk763n9cfw"))))
(build-system trivial-build-system)
(native-inputs
`(("bash" ,bash)
("coreutils" ,coreutils)
("unzip" ,unzip)))
"0n680llpcyzl22bbphp9diz4m86gz2rn97yxlky44qspn63rgfys"))))
(build-system copy-build-system)
(arguments
`(#:modules ((guix build utils))
#:builder
(begin
(use-modules (guix build utils))
(let* ((out (assoc-ref %outputs "out"))
(openrct2-title-sequences (string-append out
"/share/openrct2/title-sequences"))
(source (assoc-ref %build-inputs "source"))
(unzip (search-input-file %build-inputs "/bin/unzip")))
(copy-file source (string-append ,name "-" ,version ".zip"))
(invoke unzip (string-append ,name "-" ,version ".zip"))
(delete-file (string-append ,name "-" ,version ".zip"))
(mkdir-p openrct2-title-sequences)
(copy-recursively "."
openrct2-title-sequences)
#t))))
(home-page "https://github.com/OpenRCT2/OpenRCT2")
(list #:install-plan #~'(("." "/share/openrct2/title-sequences"))))
(native-inputs (list unzip))
(home-page "https://openrct2.io")
(synopsis "Title sequences for OpenRCT2")
(description
"openrct2-title-sequences is a set of title sequences for OpenRCT2.")
@@ -6138,38 +6173,22 @@ have a steep learning curve.")))
(define-public openrct2-objects
(package
(name "openrct2-objects")
(version "1.0.20")
(version "1.7.9")
(source
(origin
(method url-fetch)
(uri (string-append "https://github.com/OpenRCT2/objects/releases/download/v"
version "/objects.zip"))
(uri (string-append "https://github.com/OpenRCT2/objects"
"/releases/download/v" version "/objects.zip"))
(file-name (string-append name "-" version ".zip"))
(sha256
(base32 "1q7a38kcwrfijav6app1gf253yfv8b0rljbkah8040y6i7snw9mw"))))
(build-system trivial-build-system)
(native-inputs
`(("bash" ,bash)
("coreutils" ,coreutils)
("unzip" ,unzip)))
(base32 "1mpa4vpgs4m9izak8h5rkfcn80jbcm2di717k97g30kf1k91wijm"))))
(build-system copy-build-system)
(arguments
`(#:modules ((guix build utils))
#:builder
(begin
(use-modules (guix build utils))
(let* ((out (assoc-ref %outputs "out"))
(openrct2-objects (string-append out
"/share/openrct2/objects"))
(source (assoc-ref %build-inputs "source"))
(unzip (search-input-file %build-inputs "/bin/unzip")))
(copy-file source (string-append ,name "-" ,version ".zip"))
(invoke unzip (string-append ,name "-" ,version ".zip"))
(delete-file (string-append ,name "-" ,version ".zip"))
(mkdir-p openrct2-objects)
(copy-recursively "."
openrct2-objects)
#t))))
(home-page "https://github.com/OpenRCT2/OpenRCT2")
;; zip has multiple top-level directories to install.
(list #:install-plan #~'((".." "/share/openrct2/objects"
#:exclude ("environment-variables")))))
(native-inputs (list unzip))
(home-page "https://openrct2.io")
(synopsis "Objects for OpenRCT2")
(description
"openrct2-objects is a set of objects for OpenRCT2.")
@@ -6265,7 +6284,7 @@ that follows two aliens who come to Earth in search of a stolen artifact.")
(define-public openrct2
(package
(name "openrct2")
(version "0.3.3")
(version "0.5.0")
(source
(origin
(method git-fetch)
@@ -6274,53 +6293,88 @@ that follows two aliens who come to Earth in search of a stolen artifact.")
(commit (string-append "v" version))))
(file-name (git-file-name name version))
(sha256
(base32 "01nanpbz5ycdhkyd46fjfvj18sw729l4vk7xg12600f9rjngjk76"))))
(base32 "0pxlk3a8akl0ghcbqqq5xw8chmxss7kwbvi52ixfqri68n46srxh"))
(modules '((guix build utils)))
(snippet
#~(begin
(with-directory-excursion "src/thirdparty"
(for-each delete-file-recursively
'("quickjs-ng" "sfl")))
(substitute* "src/openrct2/CMakeLists.txt"
;; use sys quickjs for scripting features
(("if \\(ENABLE_SCRIPTING\\)") "if (false)")
(("add_library\\(OpenRCT2[^\n]+" all)
(string-join
`(,all
"find_library(QJS_L NAMES qjs REQUIRED)"
"find_path(QJS_I NAMES quickjs.h REQUIRED)"
"target_link_libraries(libopenrct2 ${QJS_L})"
"target_include_directories(libopenrct2 SYSTEM PRIVATE ${QJS_I})")
"\n")))))))
(build-system cmake-build-system)
(arguments
`(#:configure-flags (list "-DDOWNLOAD_OBJECTS=OFF"
"-DDOWNLOAD_TITLE_SEQUENCES=OFF")
#:tests? #f ; tests require network access
#:phases
(modify-phases %standard-phases
(add-after 'unpack 'fix-usr-share-paths&add-data
(lambda* (#:key inputs outputs #:allow-other-keys)
(let ((titles (assoc-ref inputs "openrct2-title-sequences"))
(objects (assoc-ref inputs "openrct2-objects")))
;; Fix some references to /usr/share.
(substitute* "src/openrct2/platform/Platform.Linux.cpp"
(("/usr/share")
(string-append (assoc-ref %outputs "out") "/share")))
(copy-recursively
(string-append titles "/share/openrct2/title-sequences")
"data/title")
(copy-recursively
(string-append objects "/share/openrct2/objects")
"data/object"))))
(add-before 'configure 'get-rid-of-errors
(lambda _
;; Don't treat warnings as errors.
(substitute* "CMakeLists.txt"
(("-Werror") ""))
#t)))))
(inputs `(("curl" ,curl)
("duktape" ,duktape)
("fontconfig" ,fontconfig)
("freetype" ,freetype)
("icu4c" ,icu4c)
("jansson" ,jansson)
("nlohmann-json" ,nlohmann-json)
("libpng" ,libpng)
("libzip" ,libzip)
("mesa" ,mesa)
("openrct2-objects" ,openrct2-objects)
("openrct2-title-sequences" ,openrct2-title-sequences)
("openssl" ,openssl)
("sdl2" ,sdl2)
("speexdsp" ,speexdsp)
("zlib" ,zlib)))
(native-inputs
(list pkg-config))
(home-page "https://github.com/OpenRCT2/OpenRCT2")
(list
#:configure-flags #~(list "-DDOWNLOAD_OBJECTS=OFF"
"-DDOWNLOAD_TITLE_SEQUENCES=OFF"
"-DDOWNLOAD_OPENSFX=OFF"
"-DDOWNLOAD_OPENMUSIC=OFF"
"-DDISABLE_DISCORD_RPC=ON"
"-DDISABLE_VERSION_CHECKER=ON")
;; many issues such as https://github.com/OpenRCT2/OpenRCT2/issues/12719
#:tests? #f
#:phases
#~(modify-phases %standard-phases
(add-after 'unpack 'fix-usr-share-paths&add-data
;; TODO: OpenRCT2 can optionally use free music and sounds!
;; https://github.com/OpenRCT2/OpenMusic
;; https://github.com/OpenRCT2/OpenSoundEffects
;; ideally we package these instead of the ones the user is supposed
;; to supply.
(lambda* (#:key inputs #:allow-other-keys)
(let ((titles (assoc-ref inputs "openrct2-title-sequences"))
(objects (assoc-ref inputs "openrct2-objects"))
(sfl (assoc-ref inputs "sfl-library")))
;; Fix some references to /usr/share.
(substitute* "src/openrct2/platform/Platform.Linux.cpp"
(("/usr/share")
(string-append #$output "/share")))
(copy-recursively
(string-append titles "/share/openrct2/title-sequences")
"data/title")
(copy-recursively
(string-append objects "/share/openrct2/objects")
"data/object")
(copy-recursively
(string-append sfl "/include")
"src/thirdparty"))))
(add-before 'configure 'get-rid-of-errors
(lambda _
;; Don't treat warnings as errors.
(substitute* "CMakeLists.txt"
(("-Werror") "")))))))
(inputs
(list curl
flac
fontconfig
freetype
icu4c
jansson
libpng
libvorbis
libzip
mesa
nlohmann-json-no-char8-t
openrct2-objects
openrct2-title-sequences
openssl
quickjs-ng
sdl2
sfl-library
speexdsp
zlib
(list zstd "lib")))
(native-inputs (list pkg-config))
(home-page "https://openrct2.io")
(synopsis "Free software re-implementation of RollerCoaster Tycoon 2")
(description "OpenRCT2 is a free software re-implementation of
RollerCoaster Tycoon 2 (RCT2). The gameplay revolves around building and
@@ -6328,8 +6382,8 @@ maintaining an amusement park containing attractions, shops and facilities.
Note that this package does @emph{not} provide the game assets (sounds,
images, etc.)")
;; See <https://github.com/OpenRCT2/OpenRCT2/wiki/Required-RCT2-files>
;; regarding assets.
;; See bottom of:
;; https://github.com/OpenRCT2/OpenRCT2/blob/develop/distribution/readme.txt
(license license:gpl3+)))
(define-public openriichi
@@ -6907,7 +6961,7 @@ tactics.")
(define-public widelands
(package
(name "widelands")
(version "1.3")
(version "1.3.1")
(source
(origin
(method git-fetch)
@@ -6916,7 +6970,7 @@ tactics.")
(commit (string-append "v" version))))
(file-name (git-file-name name version))
(sha256
(base32 "1j288rkflqmzxbacrrx35y8qm4mvbvd30c03cmkvh8b29jkgz3gp"))
(base32 "0ab9s1imqdq1krfwlba1ipx3pwnvy91aqqzr15ssfzixy4wj5mww"))
(modules '((guix build utils)))
(snippet
#~(delete-file-recursively "src/third_party/minizip"))))
+1 -1
View File
@@ -51,7 +51,7 @@
#:use-module (gnu packages docbook)
#:use-module (gnu packages graphviz)
#:use-module (gnu packages elf)
#:use-module (gnu packages flex)
#:use-module (gnu packages compiler-tools)
#:use-module (gnu packages perl)
#:use-module (guix packages)
#:use-module (guix download)
+3 -3
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@@ -31,7 +31,7 @@
#:use-module (gnu packages bison)
#:use-module (gnu packages cross-base)
#:use-module (gnu packages dejagnu)
#:use-module (gnu packages flex)
#:use-module (gnu packages compiler-tools)
#:use-module (gnu packages guile)
#:use-module (gnu packages hurd)
#:use-module (gnu packages llvm)
@@ -80,14 +80,14 @@
(define-public gdb-17
(package
(name "gdb")
(version "17.1")
(version "17.2")
(source (origin
(method url-fetch)
(uri (string-append "mirror://gnu/gdb/gdb-"
version ".tar.xz"))
(sha256
(base32
"0xnqqv3j463r5rnfmblj3zwhf0l0lyy4bp1zaid8zxn9fignz68l"))))
"1312lccryan1jfkjwkbw9mpxgyfnmlr8dj4lbkxx3cz4f86nq0qw"))))
(build-system gnu-build-system)
(outputs '("out" "debug"))
(arguments
+4 -6
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@@ -91,7 +91,7 @@
#:use-module (gnu packages docbook)
#:use-module (gnu packages documentation)
#:use-module (gnu packages elf)
#:use-module (gnu packages flex)
#:use-module (gnu packages compiler-tools)
#:use-module (gnu packages fonts)
#:use-module (gnu packages fontutils)
#:use-module (gnu packages freedesktop)
@@ -128,7 +128,6 @@
#:use-module (gnu packages mpi)
#:use-module (gnu packages multiprecision)
#:use-module (gnu packages ncurses)
#:use-module (gnu packages ninja)
#:use-module (gnu packages pcre)
#:use-module (gnu packages pdf)
#:use-module (gnu packages perl)
@@ -808,7 +807,7 @@ OpenGeoSys")
(define-public ogs-serial
(package
(name "ogs-serial")
(version "6.5.7")
(version "6.5.8")
(source
(origin
(method git-fetch)
@@ -817,9 +816,7 @@ OpenGeoSys")
(commit version)))
(file-name (git-file-name name version))
(sha256
(base32 "1wflgkbcsa4sr8g63img0ld6h4jm1b7hjzsa2m4gsbzc6j7kd41w"))
;; Remove patch on next release, likely 6.5.8
(patches (search-patches "ogs-6.5.7-netcdfconverter.patch"))))
(base32 "037il6jw2j1g7bvrwvbp20yf0cnz7c7f3wmszxfv5ay7l54sffqg"))))
(build-system cmake-build-system)
(arguments
(list
@@ -874,6 +871,7 @@ OpenGeoSys")
tclap
tfel
vtk
xdmf
xmlpatch
zlib))
(propagated-inputs
+1 -1
View File
@@ -50,7 +50,7 @@
#:use-module (gnu packages compression)
#:use-module (gnu packages documentation)
#:use-module (gnu packages elf)
#:use-module (gnu packages flex)
#:use-module (gnu packages compiler-tools)
#:use-module (gnu packages fontutils)
#:use-module (gnu packages freedesktop)
#:use-module (gnu packages gettext)
+1 -1
View File
@@ -56,7 +56,7 @@
#:use-module (gnu packages elf)
#:use-module (gnu packages enlightenment)
#:use-module (gnu packages file)
#:use-module (gnu packages flex)
#:use-module (gnu packages compiler-tools)
#:use-module (gnu packages freedesktop)
#:use-module (gnu packages gettext)
#:use-module (gnu packages gnome)
+3 -3
View File
@@ -136,7 +136,7 @@
#:use-module (gnu packages documentation)
#:use-module (gnu packages elf)
#:use-module (gnu packages enchant)
#:use-module (gnu packages flex)
#:use-module (gnu packages compiler-tools)
#:use-module (gnu packages fonts)
#:use-module (gnu packages file-systems)
#:use-module (gnu packages firmware)
@@ -2529,7 +2529,7 @@ forgotten when the session ends.")
(define-public evince
(package
(name "evince")
(version "48.1")
(version "48.4")
(source
(origin
(method url-fetch)
@@ -2537,7 +2537,7 @@ forgotten when the session ends.")
(version-major version) "/"
"evince-" version ".tar.xz"))
(sha256
(base32 "047s8d4qh9jijk1kp4kfzy4afwwcd0kr11a8j1dkypd0ldprm2vx"))))
(base32 "0s46prlb55ghnz136ra8whmrirydmz08lzjrrpa3arl8cb3cb5pj"))))
(build-system meson-build-system)
(arguments
`(#:glib-or-gtk? #t
+2 -2
View File
@@ -324,7 +324,7 @@ applications and libraries. It is used by AqBanking.")
(define-public aqbanking
(package
(name "aqbanking")
(version "6.8.5")
(version "6.9.2")
(source
(origin
(method git-fetch)
@@ -333,7 +333,7 @@ applications and libraries. It is used by AqBanking.")
(commit version)))
(sha256
(base32
"1xqhhxhr1azqvdn47389h469d3srl5l3n1nx82jx2djbx9sdzdq9"))
"1n1867vdml71p9dbcx70rmf10b12l7l0vq847bbizrkq7b0ha8w0"))
(file-name (git-file-name name version))))
(build-system gnu-build-system)
(arguments
+65 -65
View File
@@ -693,14 +693,14 @@ and signature functionality from Python programs.")
(define-public perl-gnupg-interface
(package
(name "perl-gnupg-interface")
(version "1.05")
(version "1.06")
(source (origin
(method url-fetch)
(uri (string-append "mirror://cpan/authors/id/B/BP/BPS/"
"GnuPG-Interface-" version ".tar.gz"))
(sha256
(base32
"0ig0ra2s1v2rw2ikm1hd0iwf2phhcr8kbc90jhr8kdpvlkymshsl"))))
"07946rsmz0ibasd53l4qiwg0dl1h65p8byja4d7fiflxsklxccs4"))))
(build-system perl-build-system)
(inputs
(list gnupg))
@@ -764,7 +764,7 @@ parties.")
(define-public signing-party
(package
(name "signing-party")
(version "2.11")
(version "2.12")
(home-page "https://salsa.debian.org/signing-party-team/signing-party")
(source (origin
(method git-fetch)
@@ -774,7 +774,7 @@ parties.")
(file-name (git-file-name name version))
(sha256
(base32
"1aig5ssabzbk4mih7xd04vgr931bw0flbi8dz902wlr610gyv5s5"))))
"1a4x02rcs5ryvfnhb6naiwc5jsil5k1fh8b01fkijkbzbh54qjc5"))))
(build-system gnu-build-system)
(native-inputs
;; autoconf-wrapper is required due to the non-standard
@@ -788,56 +788,57 @@ parties.")
perl-net-idn-encode
libmd))
(arguments
`(#:tests? #f ; no test suite
#:phases
(modify-phases %standard-phases
(replace 'configure
(lambda* (#:key outputs #:allow-other-keys)
(let ((out (assoc-ref outputs "out")))
(substitute* "keyanalyze/Makefile"
(("LDLIBS") (string-append "CC=" (which "gcc") "\nLDLIBS")))
(substitute* "keyanalyze/Makefile"
(("\\./configure") (string-append "./configure --prefix=" out)))
(substitute* "gpgwrap/Makefile"
(("\\} clean")
(string-append "} clean\ninstall:\n\tinstall -D bin/gpgwrap "
out "/bin/gpgwrap\n")))
(substitute* '("gpgsigs/Makefile" "keyanalyze/Makefile"
"keylookup/Makefile" "sig2dot/Makefile"
"springgraph/Makefile")
(("/usr") out))
(setenv "CONFIG_SHELL" (which "sh")))))
(replace 'install
(lambda* (#:key outputs #:allow-other-keys #:rest args)
(let ((out (assoc-ref outputs "out"))
(install (assoc-ref %standard-phases 'install)))
(apply install args)
(for-each
(lambda (dir file)
(copy-file (string-append dir "/" file)
(string-append out "/bin/" file)))
'("caff" "caff" "caff" "gpgdir" "gpg-key2ps"
"gpglist" "gpg-mailkeys" "gpgparticipants")
'("caff" "pgp-clean" "pgp-fixkey" "gpgdir" "gpg-key2ps"
"gpglist" "gpg-mailkeys" "gpgparticipants"))
(for-each
(lambda (dir file)
(copy-file (string-append dir "/" file)
(string-append out "/share/man/man1/" file)))
'("caff" "caff" "caff" "gpgdir"
"gpg-key2ps" "gpglist" "gpg-mailkeys"
"gpgparticipants" "gpgsigs" "gpgwrap/doc"
"keyanalyze" "keyanalyze/pgpring" "keyanalyze")
'("caff.1" "pgp-clean.1" "pgp-fixkey.1" "gpgdir.1"
"gpg-key2ps.1" "gpglist.1" "gpg-mailkeys.1"
"gpgparticipants.1" "gpgsigs.1" "gpgwrap.1"
"process_keys.1" "pgpring.1" "keyanalyze.1")))))
(add-after 'install 'wrap-programs
(lambda* (#:key outputs #:allow-other-keys)
(let* ((out (assoc-ref outputs "out")))
(wrap-program
(string-append out "/bin/caff")
`("PERL5LIB" ":" prefix (,(getenv "PERL5LIB"))))))))))
(list #:tests? #f ; no test suite
#:phases
#~(modify-phases %standard-phases
(replace 'configure
(lambda _
(substitute* "keyanalyze/Makefile"
(("LDLIBS")
(string-append "CC=" (which "gcc") "\nLDLIBS")))
(substitute* "keyanalyze/Makefile"
(("\\./configure")
(string-append "./configure --prefix=" #$output)))
(substitute* "gpgwrap/Makefile"
(("\\} clean")
(string-append
"} clean\ninstall:\n\tinstall -D bin/gpgwrap "
#$output "/bin/gpgwrap\n")))
(substitute* '("gpgsigs/Makefile" "keyanalyze/Makefile"
"keylookup/Makefile" "sig2dot/Makefile"
"springgraph/Makefile")
(("/usr") #$output))
(setenv "CONFIG_SHELL" (which "sh"))))
(replace 'install
(lambda* (#:key #:allow-other-keys #:rest args)
(let ((install (assoc-ref %standard-phases 'install)))
(apply install args)
(for-each
(lambda (dir file)
(copy-file (string-append dir "/" file)
(string-append #$output "/bin/" file)))
'("caff" "caff" "caff" "gpgdir" "gpg-key2ps"
"gpglist" "gpg-mailkeys" "gpgparticipants")
'("caff" "pgp-clean" "pgp-fixkey" "gpgdir" "gpg-key2ps"
"gpglist" "gpg-mailkeys" "gpgparticipants"))
(for-each
(lambda (dir file)
(copy-file
(string-append dir "/" file)
(string-append #$output "/share/man/man1/" file)))
'("caff" "caff" "caff" "gpgdir"
"gpg-key2ps" "gpglist" "gpg-mailkeys"
"gpgparticipants" "gpgsigs" "gpgwrap/doc"
"keyanalyze" "keyanalyze/pgpring" "keyanalyze")
'("caff.1" "pgp-clean.1" "pgp-fixkey.1" "gpgdir.1"
"gpg-key2ps.1" "gpglist.1" "gpg-mailkeys.1"
"gpgparticipants.1" "gpgsigs.1" "gpgwrap.1"
"process_keys.1" "pgpring.1" "keyanalyze.1")))))
(add-after 'install 'wrap-programs
(lambda _
(wrap-program
(string-append #$output "/bin/caff")
`("PERL5LIB" ":" prefix (,(getenv "PERL5LIB")))))))))
(synopsis "Collection of scripts for simplifying gnupg key signing")
(description
"Signing-party is a collection for all kinds of PGP/GnuPG related things,
@@ -1149,25 +1150,24 @@ however, pgpdump produces more detailed and easier to understand output.")
(define-public gpa
(package
(name "gpa")
(version "0.11.0")
(version "0.11.1")
(source (origin
(method url-fetch)
(uri (string-append "mirror://gnupg/gpa/"
name "-" version ".tar.bz2"))
(sha256
(base32
"1k1kvxffyb4nm83yp3mnx9bfmcciwb7vfw8c3xscnh85yxdzma16"))))
"02sx9my3s4yjxzxzs8pfif8wvpjrjsh75wwa5mxd0h867v6v5i8b"))))
(build-system gnu-build-system)
(arguments
`(#:make-flags '("CFLAGS=-Wno-implicit-function-declaration")
#:phases
(modify-phases %standard-phases
(add-after 'install 'wrap-program
(lambda* (#:key inputs outputs #:allow-other-keys)
(let ((out (assoc-ref outputs "out"))
(gnupg (assoc-ref inputs "gnupg")))
(wrap-program (string-append out "/bin/gpa")
`("PATH" ":" prefix (,(string-append gnupg "/bin"))))))))))
(list #:make-flags #~(list "CFLAGS=-Wno-implicit-function-declaration")
#:phases
#~(modify-phases %standard-phases
(add-after 'install 'wrap-program
(lambda* (#:key inputs #:allow-other-keys)
(let ((gnupg (assoc-ref inputs "gnupg")))
(wrap-program (string-append #$output "/bin/gpa")
`("PATH" ":" prefix (,(string-append gnupg "/bin"))))))))))
(native-inputs (list pkg-config))
(inputs
(list bash-minimal
+17 -14
View File
@@ -2,8 +2,9 @@
;;; Copyright © 2023 JOULAUD François <Francois.JOULAUD@radiofrance.com>
;;; Copyright © 2025 Maxim Cournoyer <maxim@guixotic.coop>
;;; Copyright © 2025 Tomas Volf <~@wolfsden.cz>
;;; Copyright © 2025 Sharlatan Hellseher <sharlatanus@gmail.com>
;;; Copyright © 2025-2026 Sharlatan Hellseher <sharlatanus@gmail.com>
;;; Copyright © 2025 jgart <jgart@dismail.de>
;;; Copyright © 2026 Ankit Gadiya <git@argp.in>
;;;
;;; This file is part of GNU Guix.
;;;
@@ -48,7 +49,7 @@
(define-public go-chroma
(package
(name "go-chroma")
(version "2.20.0")
(version "2.24.1")
(source
(origin
(method git-fetch)
@@ -57,7 +58,7 @@
(commit (string-append "v" version ))))
(file-name (git-file-name name version))
(sha256
(base32 "05w4hnfcxqdlsz7mkc0m3jbp1aj67wzyhq5jh8ldfgnyjnlafia3"))))
(base32 "0kww0yhwqzzgl8n3alislf0136rk7kh507bbvr32a30wmk5dzi81"))))
(build-system go-build-system)
(arguments
(list
@@ -83,17 +84,16 @@ translators for Pygments lexers and styles.")
(define-public go-fxlint
(package
(name "go-fxlint")
(version "0.0.0-20251227140935-d5da5b04ac90")
(version "1.24.0")
(source
(origin
(method git-fetch)
(uri (git-reference
(url "https://github.com/uber-go/fx")
(commit (go-version->git-ref version
#:subdir "tools"))))
(commit (string-append "v" version ))))
(file-name (git-file-name name version))
(sha256
(base32 "0yw9x95v82dcxh0zf13inz8c3q7p2hmzqzgja360b1yifi01rvrc"))))
(base32 "0iifq4gjd873l444qh32x2zzsz2yinrvpjsdfphxsfk1h0cyk4q9"))))
(build-system go-build-system)
(arguments
(list
@@ -115,7 +115,7 @@ that handle none of the event types.")
(define-public go-jsonnet
(package
(name "go-jsonnet")
(version "0.21.0")
(version "0.22.0")
(source
(origin
(method git-fetch)
@@ -124,7 +124,7 @@ that handle none of the event types.")
(commit (string-append "v" version))))
(file-name (git-file-name name version))
(sha256
(base32 "0d05f16qxabfhaj0l3da3x7zl5g8jbvkcyn39bidd2a278sb3p97"))))
(base32 "1c7h14rvavgadvbsyfa9j4rchsgxb5j363f53rhcvghvmblzddiv"))))
(build-system go-build-system)
(arguments
(list
@@ -276,19 +276,20 @@ import of a 3rd party package at runtime).")
(name "gopls")
;; XXX: Starting from 0.14.0 gppls needs golang.org/x/telemetry, which
;; needs to be discussed if it may be included in Guix.
(version "0.19.1")
(version "0.22.0")
(source
(origin
(method git-fetch)
(uri (git-reference
(url "https://go.googlesource.com/tools")
(commit (go-version->git-ref version #:subdir "gopls"))))
(url "https://go.googlesource.com/tools")
(commit (go-version->git-ref version #:subdir "gopls"))))
(file-name (git-file-name name version))
(sha256
(base32 "1dihdw4nzp21hlbwxf6qyhyfgavi1a55lmlyk36czd85v0jcp6a0"))))
(base32 "0n5ixvk6c8hww5z9lvf74dx6p4j573bq3ssvp77n6033l0fcbv94"))))
(build-system go-build-system)
(arguments
(list
#:go go-1.26
#:install-source? #f
#:import-path "golang.org/x/tools/gopls"
#:unpack-path "golang.org/x/tools"
@@ -311,11 +312,13 @@ import of a 3rd party package at runtime).")
(setenv "GODEBUG" "gotypesalias=1"))))))
(native-inputs
(list go-github-com-fatih-gomodifytags
go-github-com-fsnotify-fsnotify
go-github-com-google-go-cmp
go-github-com-google-jsonschema-go
go-github-com-jba-templatecheck
go-github-com-modelcontextprotocol-go-sdk
go-golang-org-x-mod
go-golang-org-x-sync
go-golang-org-x-sys
go-golang-org-x-telemetry
go-golang-org-x-text
go-golang-org-x-tools
+261
View File
@@ -2151,6 +2151,57 @@ testing and improve the efficiency of unit test writing.")
testing of time-sensitive code.")
(license license:expat)))
(define-public go-github-com-josharian-mapfs
(package
(name "go-github-com-josharian-mapfs")
(version "0.0.0-20210615234106-095c008854e6")
(source
(origin
(method git-fetch)
(uri (git-reference
(url "https://github.com/josharian/mapfs")
(commit (go-version->git-ref version))))
(file-name (git-file-name name version))
(sha256
(base32 "09i6shqwacx8nm6jfyhc1zvry8fcb3ddd98m96skzybv9lckq7h4"))))
(build-system go-build-system)
(arguments
(list
#:import-path "github.com/josharian/mapfs"))
(home-page "https://github.com/josharian/mapfs")
(synopsis "Fork of Go std's testing/fstest.MapFS")
(description
"This is a fork of the @code{MapFS} component of the Go standard
library's testing/fstest package.")
(license license:bsd-3)))
(define-public go-github-com-josharian-txtarfs
(package
(name "go-github-com-josharian-txtarfs")
(version "0.0.0-20240408113805-5dc76b8fe6bf")
(source
(origin
(method git-fetch)
(uri (git-reference
(url "https://github.com/josharian/txtarfs")
(commit (go-version->git-ref version))))
(file-name (git-file-name name version))
(sha256
(base32 "129rf6hviw46rxcnnkc8jb1k579798rrhnh1k3nn7npi260ia44m"))))
(build-system go-build-system)
(arguments
(list
#:import-path "github.com/josharian/txtarfs"))
(propagated-inputs
(list go-github-com-josharian-mapfs
go-golang-org-x-tools))
(home-page "https://github.com/josharian/txtarfs")
(synopsis "Convert a txtar to an io.FS")
(description
"This package turns a @url{https://pkg.go.dev/golang.org/x/tools/txtar,
txtar} into an @url{https://pkg.go.dev/io/fs, fs.FS}.")
(license license:expat)))
(define-public go-github-com-joshdk-go-junit
(package
(name "go-github-com-joshdk-go-junit")
@@ -2662,6 +2713,56 @@ error messages, preserving the order of @code{have} (actual result) before
@code{want} (expected result) to minimize confusion.")
(license license:asl2.0)))
(define-public go-github-com-newmo-oss-go-caller
(package
(name "go-github-com-newmo-oss-go-caller")
(version "0.1.0")
(source
(origin
(method git-fetch)
(uri (git-reference
(url "https://github.com/newmo-oss/go-caller")
(commit (string-append "v" version))))
(file-name (git-file-name name version))
(sha256
(base32 "1hn0wj2v6yvn83lpilbcb9xpa36fmcbv83rk6fhr2rwckp2dxy8p"))))
(build-system go-build-system)
(arguments
(list
#:import-path "github.com/newmo-oss/go-caller"))
(native-inputs
(list go-github-com-google-go-cmp))
(home-page "https://github.com/newmo-oss/go-caller")
(synopsis "Collect stack traces at runtime")
(description
"This package provides a library for collecting stack traces at runtime.")
(license license:expat)))
(define-public go-github-com-newmo-oss-gotestingmock
(package
(name "go-github-com-newmo-oss-gotestingmock")
(version "0.2.0")
(source
(origin
(method git-fetch)
(uri (git-reference
(url "https://github.com/newmo-oss/gotestingmock")
(commit (string-append "v" version))))
(file-name (git-file-name name version))
(sha256
(base32 "1flgmarj961k4vl6d7i2740snrdfjiv4aigb87v5aznvi8bwa5d3"))))
(build-system go-build-system)
(arguments
(list
#:import-path "github.com/newmo-oss/gotestingmock"))
(propagated-inputs
(list go-github-com-newmo-oss-go-caller))
(home-page "https://github.com/newmo-oss/gotestingmock")
(synopsis "Mocking utilities for Go")
(description
"This package provides mocking utilities for unit tests in Go.")
(license license:expat)))
(define-public go-github-com-onsi-ginkgo
(package
(name "go-github-com-onsi-ginkgo")
@@ -3267,6 +3368,84 @@ and CLI tool.")
such as readers and writers that fail after N consecutive reads/writes.")
(license license:expat)))
(define-public go-github-com-tenntenn-golden
(package
(name "go-github-com-tenntenn-golden")
(version "0.5.5")
(source
(origin
(method git-fetch)
(uri (git-reference
(url "https://github.com/tenntenn/golden")
(commit (string-append "v" version))))
(file-name (git-file-name name version))
(sha256
(base32 "09w3h7c4z930z91dg7bfs9m680pw9zgqyyikw88gisv1z86y3qlz"))))
(build-system go-build-system)
(arguments
(list
#:import-path "github.com/tenntenn/golden"))
(native-inputs
(list go-github-com-google-go-cmp))
(propagated-inputs
(list go-github-com-josharian-txtarfs
go-golang-org-x-tools))
(home-page "https://github.com/tenntenn/golden")
(synopsis "Utilities for golden file tests")
(description "This package provides utilities for golden file tests.")
(license license:expat)))
(define-public go-github-com-tenntenn-modver
(package
(name "go-github-com-tenntenn-modver")
(version "1.0.1")
(source
(origin
(method git-fetch)
(uri (git-reference
(url "https://github.com/tenntenn/modver")
(commit (string-append "v" version))))
(file-name (git-file-name name version))
(sha256
(base32 "1p4402lizz5ny0l49yxa65ryhx09wm8g13lx4pw0nw0s4r06rw3g"))))
(build-system go-build-system)
(arguments
(list
#:import-path "github.com/tenntenn/modver"))
(native-inputs
(list go-github-com-google-go-cmp))
(propagated-inputs
(list go-github-com-hashicorp-go-version))
(home-page "https://github.com/tenntenn/modver")
(synopsis "Utility for Go modules")
(description "This package provides utilities for Go modules.")
(license license:expat)))
(define-public go-github-com-tenntenn-text-transform
(package
(name "go-github-com-tenntenn-text-transform")
(version "0.0.0-20250402111347-ba836492e880")
(source
(origin
(method git-fetch)
(uri (git-reference
(url "https://github.com/tenntenn/text")
(commit (go-version->git-ref version))))
(file-name (git-file-name name version))
(sha256
(base32 "19f302js8pxyqnl189992zp6pl169b4gpgn6wywpdir77vm56pih"))))
(build-system go-build-system)
(arguments
(list
#:import-path "github.com/tenntenn/text/transform"
#:unpack-path "github.com/tenntenn/text"))
(propagated-inputs
(list go-golang-org-x-text))
(home-page "https://github.com/tenntenn/text")
(synopsis "Text transformation utilities")
(description "This package provides text transformation utilities in Go.")
(license license:expat)))
(define-public go-github-com-tj-assert
(package
(name "go-github-com-tj-assert")
@@ -3549,6 +3728,34 @@ goroutine leaks and understanding goroutine lifecycles.")
based on Go @code{testing} library procedures.")
(license license:cc0)))
(define-public go-gitlab-com-bosi-decorder
(package
(name "go-gitlab-com-bosi-decorder")
(version "0.4.2")
(source
(origin
(method git-fetch)
(uri (git-reference
(url "https://gitlab.com/bosi/decorder")
(commit (string-append "v" version))))
(file-name (git-file-name name version))
(sha256
(base32 "0g9x5f7mhvdzwki57902qgb4ih2gipkg255nf9hjv30flfnl2294"))))
(build-system go-build-system)
(arguments
(list
#:import-path "gitlab.com/bosi/decorder"
#:test-flags #~(list "-vet=off")))
(propagated-inputs
(list go-golang-org-x-tools))
(home-page "https://gitlab.com/bosi/decorder")
(synopsis "Declaration order and number linter for golang")
(description
"This package provides a declaration order linter for Go. In case of
this tool declarations are @code{type}, @code{const}, @code{var} and
@code{func}.")
(license license:expat)))
(define-public go-go-abhg-dev-requiredfield
(package
(name "go-go-abhg-dev-requiredfield")
@@ -3657,6 +3864,60 @@ and restore them afterwards.")
of @url{https://github.com/wadey/gocovmerge}.")
(license license:bsd-2)))
(define-public go-go-simpler-org-assert
(package
(name "go-go-simpler-org-assert")
(version "0.9.0")
(source
(origin
(method git-fetch)
(uri (git-reference
(url "https://github.com/go-simpler/assert")
(commit (string-append "v" version))))
(file-name (git-file-name name version))
(sha256
(base32 "0pg3yhicggby978n8war9n5zzigr95mvnsipnk6zgsjn6gyvjdm5"))))
(build-system go-build-system)
(arguments
(list
#:import-path "go-simpler.org/assert"))
(home-page "https://go-simpler.org/assert")
(synopsis "Assertions for the standard testing package")
(description
"This package implements assertions for the standard @code{testing}
package, and is a minimalistic replacement for the @code{stretchr/testify}
package.")
(license license:mpl2.0)))
(define-public go-go-simpler-org-musttag
(package
(name "go-go-simpler-org-musttag")
(version "0.14.0")
(source
(origin
(method git-fetch)
(uri (git-reference
(url "https://github.com/go-simpler/musttag")
(commit (string-append "v" version))))
(file-name (git-file-name name version))
(sha256
(base32 "15kvnppc2q8ay1m8lhag0bmdx08kc68lzv78699qkyi6bcw68ajf"))))
(build-system go-build-system)
(arguments
(list
#:import-path "go-simpler.org/musttag"
#:test-flags #~(list "-skip" "TestAnalyzer")))
(native-inputs
(list go-go-simpler-org-assert))
(propagated-inputs
(list go-golang-org-x-tools))
(home-page "https://go-simpler.org/musttag")
(synopsis "Enforce field tags in (un)marshaled structs")
(description
"This package checks that exported fields of a struct passed to a
@code{Marshal}-like function are annotated with the relevant tag.")
(license license:mpl2.0)))
(define-public go-go-simpler-org-sloglint
(package
(name "go-go-simpler-org-sloglint")
+115
View File
@@ -150,6 +150,31 @@ the @code{c2go} tool at
@url{https://github.com/andybalholm/c2go,https://github.com/andybalholm/c2go}.")
(license license:expat)))
(define-public go-github-com-blakesmith-ar
(package
(name "go-github-com-blakesmith-ar")
(version "0.0.0-20190502131153-809d4375e1fb")
(source
(origin
(method git-fetch)
(uri (git-reference
(url "https://github.com/blakesmith/ar")
(commit (go-version->git-ref version))))
(file-name (git-file-name name version))
(sha256
(base32 "00fxkc04b9cb53xxzw5gdqqpwlqv9n5kk0yn2lb5w4rgj5gm8ph1"))))
(build-system go-build-system)
(arguments
(list
#:import-path "github.com/blakesmith/ar"
#:test-flags #~(list "-vet=off")))
(home-page "https://github.com/blakesmith/ar")
(synopsis "Golang archive file reader")
(description
"This package provides a Golang file reader for archive files generated
with @code{ar}.")
(license license:expat)))
(define-public go-github-com-bodgit-sevenzip
(package
(name "go-github-com-bodgit-sevenzip")
@@ -221,6 +246,31 @@ blocks allowing it to only read the compressed blocks required.")
(license (list license:bsd-3
license:expat))))
(define-public go-github-com-cavaliergopher-cpio
(package
(name "go-github-com-cavaliergopher-cpio")
(version "1.0.1")
(source
(origin
(method git-fetch)
(uri (git-reference
(url "https://github.com/cavaliergopher/cpio")
(commit (string-append "v" version))))
(file-name (git-file-name name version))
(sha256
(base32 "0b1ix8z9kwfpwqi0q08ivcfcimlqk781jbzbfw7qbqavh702w3m2"))))
(build-system go-build-system)
(arguments
(list
#:import-path "github.com/cavaliergopher/cpio"))
(home-page "https://github.com/cavaliergopher/cpio")
(synopsis "Readers and writers for CPIO archives")
(description
"This package provides readers and writers for CPIO archives. Currently,
only the SVR4 (New ASCII) format is supported, both with and without
checksums.")
(license license:bsd-3)))
(define-public go-github-com-containerd-stargz-snapshotter-estargz
(package
(name "go-github-com-containerd-stargz-snapshotter-estargz")
@@ -385,6 +435,37 @@ Implements the XFLATE format, an random-access extension to DEFLATE.
compression format.")
(license license:bsd-3)))
(define-public go-github-com-google-rpmpack
(package
(name "go-github-com-google-rpmpack")
(version "0.7.1")
(source
(origin
(method git-fetch)
(uri (git-reference
(url "https://github.com/google/rpmpack")
(commit (string-append "v" version))))
(file-name (git-file-name name version))
(sha256
(base32 "17h2s1g191cvbs16fnclkpb42d9mx6mdmhd04kxzv8bss7m59pr4"))))
(build-system go-build-system)
(arguments
(list
#:import-path "github.com/google/rpmpack"))
(native-inputs
(list go-github-com-google-go-cmp))
(propagated-inputs
(list go-github-com-cavaliergopher-cpio
go-github-com-klauspost-compress
go-github-com-klauspost-pgzip
go-github-com-ulikunitz-xz))
(home-page "https://github.com/google/rpmpack")
(synopsis "Pack files to rpm files")
(description
"Package rpmpack packs files to rpm files. It is designed to be simple
to use and deploy, not requiring any filesystem access to create rpm files.")
(license license:asl2.0)))
(define-public go-github-com-hhrutter-lzw
(package
(name "go-github-com-hhrutter-lzw")
@@ -884,6 +965,40 @@ format's \"Extra Fields\". The intention is to eventually support and provide
a low-level API for the majority of PKWARE's and Info-ZIP's extra fields.")
(license license:expat)))
(define-public go-github-com-sassoftware-go-rpmutils
(package
(name "go-github-com-sassoftware-go-rpmutils")
(version "0.4.0")
(source
(origin
(method git-fetch)
(uri (git-reference
(url "https://github.com/sassoftware/go-rpmutils")
(commit (string-append "v" version))))
(file-name (git-file-name name version))
(sha256
(base32 "06ymwjn6xvc4cpxcsh5achwgma4i075ikbzq8jm143m0pck4pmfi"))))
(build-system go-build-system)
(arguments
(list
#:import-path "github.com/sassoftware/go-rpmutils"))
(native-inputs
(list go-github-com-stretchr-testify
go-go-uber-org-goleak))
(propagated-inputs
(list go-github-com-datadog-zstd
go-github-com-klauspost-compress
go-github-com-protonmail-go-crypto
go-github-com-ulikunitz-xz
go-github-com-xi2-xz
go-golang-org-x-sys))
(home-page "https://github.com/sassoftware/go-rpmutils")
(synopsis "Parse RPM packages in Golang")
(description
"This package provides some Golang interfaces for handling RPM packages,
such extracting RPM header and CPIO content.")
(license license:asl2.0)))
(define-public go-github-com-sorairolake-lzip-go
(package
(name "go-github-com-sorairolake-lzip-go")
+2 -2
View File
@@ -4293,7 +4293,7 @@ purpose of improving obfs4proxy's meek_lite transport.")
(define-public go-go-mau-fi-libsignal
(package
(name "go-go-mau-fi-libsignal")
(version "0.1.2")
(version "0.2.1")
(source
(origin
(method git-fetch)
@@ -4309,7 +4309,7 @@ purpose of improving obfs4proxy's meek_lite transport.")
(commit (string-append "v" version))))
(file-name (git-file-name name version))
(sha256
(base32 "1pd2kijza7dr5nbgfw176ca1r3rmgpx8h22gqjp557awxqhw9lzr"))))
(base32 "0jwqhaaqjf5fb322karppisbg5s1la459a0cwvhbii899nzyd59k"))))
(build-system go-build-system)
(arguments
(list
+86
View File
@@ -1,5 +1,6 @@
;;; GNU Guix --- Functional package management for GNU
;;; Copyright © 2026 Sughosha <sughosha@disroot.org>
;;; Copyright © 2026 orahcio <orahcio@gmail.com>
;;;
;;; This file is part of GNU Guix.
;;;
@@ -249,3 +250,88 @@ multiple return values, Go's native multiple return values are used instead.
Whenever a native GTK call could return an unexpected NULL pointer, an
additional error is returned in the Go binding.")
(license license:isc)))
(define-public go-github-com-jackmordaunt-icns-v3
(package
(name "go-github-com-jackmordaunt-icns-v3")
(version "3.0.1")
(source
(origin
(method git-fetch)
(uri (git-reference
(url "https://github.com/JackMordaunt/icns")
(commit (string-append "v" version))))
(file-name (git-file-name name version))
(sha256
(base32 "04wnxv79b1xbca16kgz98zc929q60lwcgcc6q784lkz2a1clh2z2"))
(modules '((guix build utils)))
(snippet
#~(begin
;; Submodules with their own go.mod files and packaged separately:
(delete-file-recursively "cmd")))))
(build-system go-build-system)
(arguments
(list
#:import-path "github.com/jackmordaunt/icns/v3"
#:test-flags #~(list "-vet=off")))
(propagated-inputs
(list go-github-com-nfnt-resize))
(home-page "https://github.com/jackmordaunt/icns")
(synopsis "Easily create .icns files")
(description
"This package provides Go library to easily convert @code{.jpg} and
@code{.png} to @code{.icns}, or to convert from any @code{image.Image} to
@code{.icns}.")
(license license:expat)))
(define-public go-github-com-sergeymakinen-go-bmp
(package
(name "go-github-com-sergeymakinen-go-bmp")
(version "1.0.0")
(source
(origin
(method git-fetch)
(uri (git-reference
(url "https://github.com/sergeymakinen/go-bmp")
(commit (string-append "v" version))))
(file-name (git-file-name name version))
(sha256
(base32 "0bglvxqmjvgclcfjpkznxyifj5r0bh837c2iw6x1vylc7lqcq07h"))))
(build-system go-build-system)
(arguments
(list
#:import-path "github.com/sergeymakinen/go-bmp"))
(home-page "https://github.com/sergeymakinen/go-bmp")
(synopsis "BMP image decoder and encoder")
(description "Package bmp implements a BMP image decoder and encoder.")
(license license:bsd-3)))
(define-public go-github-com-sergeymakinen-go-ico
(package
(name "go-github-com-sergeymakinen-go-ico")
(version "1.0.0-beta.0")
(source
(origin
(method git-fetch)
(uri (git-reference
(url "https://github.com/sergeymakinen/go-ico")
(commit (string-append "v" version))))
(file-name (git-file-name name version))
(sha256
(base32 "115fgnhn1j91zvkigl1x03jkc2dn6vx7qvfmm6l59d24qkfv6cwn"))))
(build-system go-build-system)
(arguments
(list
#:import-path "github.com/sergeymakinen/go-ico"))
(propagated-inputs
(list go-github-com-sergeymakinen-go-bmp))
(home-page "https://github.com/sergeymakinen/go-ico")
(synopsis "ICO and CUR file decoders and encoders")
(description "Package ico implements an ICO file decoder and encoder.")
(license license:bsd-3)))
;;;
;;; Avoid adding new packages to the end of this file. To reduce the chances
;;; of a merge conflict, place them above in alphabetic order:
;;; guix import --insert=gnu/packages/golang-graphics.scm pypi <package-name>.
;;;
+24
View File
@@ -607,6 +607,30 @@ Actions} locally.")
It's a static checker for GitHub Actions workflow files.")
(license license:expat)))
(define-public go-gitlab-com-digitalxero-go-conventional-commit
(package
(name "go-gitlab-com-digitalxero-go-conventional-commit")
(version "1.0.7")
(source
(origin
(method git-fetch)
(uri (git-reference
(url "https://gitlab.com/digitalxero/go-conventional-commit.git")
(commit (string-append "v" version))))
(file-name (git-file-name name version))
(sha256
(base32 "1191j3k9ma5sv8w2zsw8gb1407561zll0ca8hwy0dja6s0b3z0xy"))))
(build-system go-build-system)
(arguments
(list
#:import-path "gitlab.com/digitalxero/go-conventional-commit"))
(home-page "https://gitlab.com/digitalxero/go-conventional-commit")
(synopsis "Go parser for conventional commits")
(description
"This package provides a Go parser for conventional-commit messages
@url{https://www.conventionalcommits.org/}.")
(license license:expat)))
(define-public go-github-com-xanzy-go-gitlab
(package
(name "go-github-com-xanzy-go-gitlab")
+168 -33
View File
@@ -3724,6 +3724,51 @@ lookups. It implements looking up the following records:
Storage}.")
(license license:asl2.0)))
(define-public go-github-com-beeper-argo-go
(package
(name "go-github-com-beeper-argo-go")
(version "1.1.2")
(source
(origin
(method git-fetch)
(uri (git-reference
(url "https://github.com/beeper/argo-go")
(commit (string-append "v" version))))
(file-name (git-file-name name version))
(sha256
(base32 "1c11aqbap9yxpnc8bvzjiy5cg53brhc47hw2q24xjvbw5d90r2ff"))))
(build-system go-build-system)
(arguments
(list
#:import-path "github.com/beeper/argo-go"
#:embed-files #~(list "prelude.graphql")
#:test-flags
#~(list "-vet=off"
"-skip" (string-join
;; These test groups fail with panic by similar error:
;; UnsignedDecode failed for 10000000000000000000000:
;; varint: varint too large for 64-bit. Encoded:
;; 80808092abb7b2f099bc08.
(list "TestUnsignedRoundTrip"
"TestQueriesEquivalence"
"TestStarWarsEquivalence"
"TestZigZagRoundTrip"
;; UnsignedDecode error mismatch for too long
;; varint.
"TestUnsignedDecodeTooLong")
"|"))))
(native-inputs
(list go-github-com-stretchr-testify))
(propagated-inputs
(list go-github-com-elliotchance-orderedmap-v3
go-github-com-vektah-gqlparser-v2))
(home-page "https://github.com/beeper/argo-go")
(synopsis "Go implementation of Argo for GraphQL")
(description
"Go implementation of Argo, a compact and compressible binary
serialization format for GraphQL.")
(license license:expat)))
(define-public go-github-com-beevik-ntp
(package
(name "go-github-com-beevik-ntp")
@@ -10796,6 +10841,33 @@ dhcpv6 and dhcpv4
@end itemize")
(license license:bsd-3)))
(define-public go-github-com-invopop-jsonschema
(package
(name "go-github-com-invopop-jsonschema")
(version "0.14.0")
(source
(origin
(method git-fetch)
(uri (git-reference
(url "https://github.com/invopop/jsonschema")
(commit (string-append "v" version))))
(file-name (git-file-name name version))
(sha256
(base32 "0y881agfaycn5l5qn2y2jmiskchi0cvn5v602hna4ljy9rv5jxw2"))))
(build-system go-build-system)
(arguments
(list
#:import-path "github.com/invopop/jsonschema"))
(native-inputs
(list go-github-com-stretchr-testify))
(propagated-inputs
(list go-github-com-pb33f-ordered-map-v2))
(home-page "https://github.com/invopop/jsonschema")
(synopsis "Go JSON Schema Reflection")
(description
"Package jsonschema uses reflection to generate JSON Schemas from Go types.")
(license license:expat)))
(define-public go-github-com-ipfs-go-cid
(package
(name "go-github-com-ipfs-go-cid")
@@ -16985,9 +17057,11 @@ kinds of referrer URLs (search, social, ...).")
(list
#:skip-build? #t
#:import-path "github.com/sigstore/rekor"
;; XXX: Remove when all inputs are packaged.
#:embed-files #~(list ".*\\.json")
;; ;; XXX: Remove when all inputs are packaged.
#:test-subdirs
#~(list "pkg/events/newentry"
#~(list "pkg/client"
"pkg/events/newentry"
"pkg/indexstorage/mysql"
"pkg/pki/minisign"
"pkg/pki/pgp"
@@ -16995,7 +17069,10 @@ kinds of referrer URLs (search, social, ...).")
"pkg/pki/tuf"
"pkg/pki/x509"
"pkg/pubsub/gcp"
"pkg/util")))
"pkg/tle"
"pkg/types"
"pkg/util"
"pkg/verify")))
(native-inputs
(list go-github-com-asaskevich-govalidator
go-github-com-data-dog-go-sqlmock
@@ -17023,6 +17100,7 @@ kinds of referrer URLs (search, social, ...).")
go-github-com-go-openapi-validate
go-github-com-go-sql-driver-mysql
go-github-com-go-viper-mapstructure-v2
go-github-com-google-rpmpack
go-github-com-google-trillian
go-github-com-grpc-ecosystem-go-grpc-middleware
go-github-com-hashicorp-go-cleanhttp
@@ -17066,7 +17144,6 @@ kinds of referrer URLs (search, social, ...).")
;; go-github-com-adamkorcz-go-fuzz-headers-1
;; go-github-com-cavaliercoder-go-rpm
;; go-github-com-go-redis-redismock-v9
;; go-github-com-google-rpmpack
;; go-github-com-sassoftware-relic
;; go-github-com-sassoftware-relic-v7
;; go-go-step-sm-crypto
@@ -18549,6 +18626,31 @@ Tailscale for access control.")
Tailscale.")
(license license:bsd-3)))
(define-public go-github-com-tcnksm-go-httpstat
(package
(name "go-github-com-tcnksm-go-httpstat")
(version "0.2.0")
(source
(origin
(method git-fetch)
(uri (git-reference
(url "https://github.com/tcnksm/go-httpstat")
(commit (string-append "v" version))))
(file-name (git-file-name name version))
(sha256
(base32 "18jn40ra97waxx1mf23pkh6rq46y0nqd7vi3zcx9cwc39zqaf9bc"))))
(build-system go-build-system)
(arguments
(list
#:tests? #f ;Tests require network connection
#:import-path "github.com/tcnksm/go-httpstat"))
(home-page "https://github.com/tcnksm/go-httpstat")
(synopsis "Trace HTTP latency information in Go")
(description
"Package httpstat traces HTTP latency infomation, such as DNSLookup and
TCP Connection, on any Golang HTTP request with no big code modification.")
(license license:expat)))
(define-public go-github-com-tdewolff-minify-v2
(package
(name "go-github-com-tdewolff-minify-v2")
@@ -19080,6 +19182,30 @@ caching protocol. It provides support to programmatically store and retrieve
build caches, instead of relying on the standard actions/cache YAML step.")
(license license:expat)))
(define-public go-github-com-toqueteos-webbrowser
(package
(name "go-github-com-toqueteos-webbrowser")
(version "1.2.1")
(source
(origin
(method git-fetch)
(uri (git-reference
(url "https://github.com/toqueteos/webbrowser")
(commit (string-append "v" version))))
(file-name (git-file-name name version))
(sha256
(base32 "0bnn02zcfc9xkxc2qvv4q6wy5sipcwc0hwmx7hdhvv3lsw177flw"))))
(build-system go-build-system)
(arguments
(list
#:import-path "github.com/toqueteos/webbrowser"))
(home-page "https://github.com/toqueteos/webbrowser")
(synopsis "Simple API for opening web pages")
(description
"This package provides a simple API for opening web pages on your default
browser.")
(license license:expat)))
(define-public go-github-com-transparency-dev-tessera
(package
(name "go-github-com-transparency-dev-tessera")
@@ -20791,28 +20917,30 @@ state machine. See @url{https://raft.github.io/raft.pdf} for more info.")
(define-public go-go-mau-fi-whatsmeow
(package
(name "go-go-mau-fi-whatsmeow")
(version "0.0.0-20241215104421-68b0856cce22")
(version "0.0.0-20260529101937-a7ea56383ec4")
(source
(origin
(method git-fetch)
(uri (git-reference
(url "https://github.com/tulir/whatsmeow")
(commit (go-version->git-ref version))))
(url "https://github.com/tulir/whatsmeow")
(commit (go-version->git-ref version))))
(file-name (git-file-name name version))
(sha256
(base32 "1y3h132g3w6ihc8jn587wvyha9xm3sinjlr0znqq7krvynz3z8id"))))
(base32 "0i6vcn6l5sf0wsyr3k856xiz5pq3ivl9a7xd1bzqzlq74jmivivc"))))
(build-system go-build-system)
(arguments
(list
#:import-path "go.mau.fi/whatsmeow"))
(propagated-inputs
(list go-github-com-google-uuid
go-github-com-gorilla-websocket
(list go-github-com-beeper-argo-go
go-github-com-coder-websocket
go-github-com-google-uuid
go-github-com-rs-zerolog
go-go-mau-fi-libsignal
go-go-mau-fi-util
go-golang-org-x-crypto
go-golang-org-x-net
go-golang-org-x-sync
go-google-golang-org-protobuf))
(home-page "https://go.mau.fi/whatsmeow")
(synopsis "Go library for the WhatsApp web multidevice API")
@@ -23262,16 +23390,16 @@ the code or routes.")
(define-public go-maunium-net-go-mautrix
(package
(name "go-maunium-net-go-mautrix")
(version "0.22.1")
(version "0.28.0")
(source
(origin
(method git-fetch)
(uri (git-reference
(url "https://github.com/mautrix/go")
(commit (string-append "v" version))))
(url "https://github.com/mautrix/go")
(commit (string-append "v" version))))
(file-name (git-file-name name version))
(sha256
(base32 "0msqbs3qc9ljckj41hgvp16p0sbfzm25wzldb68av9svimscwnmm"))))
(base32 "09isb4q876mkcwm2yk7vgzwhd3yw1n0s78qvdb7wpmab6vvxjnlf"))))
(build-system go-build-system)
(arguments
(list
@@ -23287,27 +23415,32 @@ the code or routes.")
;; golang.org/x/net/publicsuffix/table.go:33:12: pattern data/text:
;; cannot embed irregular file data/text
"text")
#:test-flags
#~(list "-skip" (string-join
;; Network access is required for the tets.
(list "TestClient_Version"
"TestResolveServerName/RM_Step_3B"
"TestResolveServerName/RM_Step_3C"
"TestResolveServerName/RM_Step_3C_MSC4040"
"TestResolveServerName/RM_Step_3D"
"TestResolveServerName/RM_Step_4"
"TestResolveServerName/RM_Step_4_MSC4040"
"TestResolveServerName/maunium")
"|")
"-vet=off")))
;; XXX: The final application needs a "libolm" package.
(native-inputs
(list olm))
#:test-flags
#~(list "-skip" (string-join
;; Network access is required for the tets.
(list "TestCrossSignVerification_ScanQRAndConfirmScan"
"TestSelfVerification_Accept_QRContents"
"TestSelfVerification_ScanQRAndConfirmScan"
"TestSelfVerification_ScanQRTransactionIDCorrup"
"TestSelfVerification_ScanQRKeyCorrupted"
"TestVerification_SAS"
"TestVerification_SAS_BothCallStart"
"TestVerification_Start"
"TestVerification_StartThenCancel"
"TestVerification_Accept_NoSupportedMethods"
"TestVerification_Accept_CorrectMethodsPresented"
"TestVerification_Accept_CancelOnNonParticipati"
"TestVerification_ErrorOnDoubleAccept"
"TestVerification_CancelOnDoubleStart"
"TestClient_Version"
"TestResolveServerName"
"TestServerKeyResponse_VerifySelfSignature"
"TestServerKeyResponse_FailWithFilter")
"|"))))
(propagated-inputs
(list go-filippo-io-edwards25519
go-github-com-chzyer-readline
go-github-com-gorilla-mux
go-github-com-gorilla-websocket
go-github-com-coder-websocket
go-github-com-lib-pq
go-github-com-mattn-go-sqlite3
go-github-com-rs-xid
@@ -23324,7 +23457,9 @@ the code or routes.")
go-golang-org-x-net
go-golang-org-x-sync
go-gopkg-in-yaml-v3
go-maunium-net-go-mauflag))
go-maunium-net-go-mauflag
;; XXX: The final application needs a "libolm" package.
olm))
(home-page "https://maunium.net/go/mautrix")
(synopsis "Golang Matrix framework")
(description
+574 -4
View File
@@ -78,6 +78,7 @@
;;; Copyright © 2026 Vinicius Monego <monego@posteo.net>
;;; Copyright © 2026 Daniel Littlewood <dan@danielittlewood.xyz>
;;; Copyright © 2026 Sughosha <sughosha@disroot.org>
;;; Copyright © 2026 orahcio <orahcio@gmail.com>
;;;
;;; This file is part of GNU Guix.
;;;
@@ -113,7 +114,9 @@
#:use-module (gnu packages golang-check)
#:use-module (gnu packages golang-compression)
#:use-module (gnu packages golang-crypto)
#:use-module (gnu packages golang-graphics)
#:use-module (gnu packages golang-maths)
#:use-module (gnu packages golang-vcs)
#:use-module (gnu packages golang-web)
#:use-module (gnu packages graph)
#:use-module (gnu packages imagemagick)
@@ -442,6 +445,33 @@ a human-readable byte format.")
time dependencies in tests.")
(license license:asl2.0)))
(define-public go-code-rocketnine-space-tslocum-cbind
(package
(name "go-code-rocketnine-space-tslocum-cbind")
(version "0.1.5")
(source
(origin
(method git-fetch)
(uri (git-reference
(url "https://codeberg.org/tslocum/cbind.git")
(commit (string-append "v" version))))
(file-name (git-file-name name version))
(sha256
(base32 "0a0gpzapm3jsivdf5h6lvlxhzngrmyj7xp5fdk20l8r4yba7yqsy"))))
(build-system go-build-system)
(arguments
(list
#:import-path "code.rocketnine.space/tslocum/cbind"
#:test-flags #~(list "--skip" "TestConfiguration")))
(propagated-inputs
(list go-github-com-gdamore-tcell-v2))
(home-page "https://codeberg.org/tslocum/cbind")
(synopsis "Key event handling library for tcell")
(description
"Package cbind provides a tcell key event encoding, decoding and handling
as human-readable strings.")
(license license:expat)))
(define-public go-codeberg-org-anaseto-gruid
(package
(name "go-codeberg-org-anaseto-gruid")
@@ -1761,6 +1791,30 @@ strings for a safe use as command line arguments in the most common POSIX
shells.")
(license license:expat)))
(define-public go-github-com-aleksi-pointer
(package
(name "go-github-com-aleksi-pointer")
(version "1.2.0")
(source
(origin
(method git-fetch)
(uri (git-reference
(url "https://github.com/AlekSi/pointer")
(commit (string-append "v" version))))
(file-name (git-file-name name version))
(sha256
(base32 "0rncmanv62wwy7ihvjhvb695mkvy4kdzhgnn90zygs9yrfzzk0wk"))))
(build-system go-build-system)
(arguments
(list
#:import-path "github.com/AlekSi/pointer"))
(home-page "https://github.com/AlekSi/pointer")
(synopsis "Helper Go library to convert between pointers and values")
(description
"This package provides helpers to convert between pointers and values of
built-in and, with generics, of any types.")
(license license:expat)))
(define-public go-github-com-alexflint-go-filemutex
(package
(name "go-github-com-alexflint-go-filemutex")
@@ -1815,6 +1869,33 @@ software (based on Python's
@uref{https://github.com/pycontribs/tendo, tendo}).")
(license license:expat)))
(define-public go-github-com-alimpfard-line
(package
(name "go-github-com-alimpfard-line")
(version "0.0.0-20230131232016-03b4e7dee324")
(source
(origin
(method git-fetch)
(uri (git-reference
(url "https://github.com/alimpfard/line")
(commit (go-version->git-ref version))))
(file-name (git-file-name name version))
(sha256
(base32 "0swjy1z7hqy4xgq2hfa457rs7p9d7fw5lmdh0zaf3n25rqv10ds1"))))
(build-system go-build-system)
(arguments
(list
#:import-path "github.com/alimpfard/line"))
(propagated-inputs
(list go-golang-org-x-sys))
(home-page "https://github.com/alimpfard/line")
(synopsis "Terminal line editor")
(description
"This package provides a full reimplementation of SerenityOS's LibLine in
Go language. It supports flexible autocompletion, live prompt, buffer update
and stylisation, multiline editing and more.")
(license license:bsd-2)))
(define-public go-github-com-alsm-ioprogress
(package
(name "go-github-com-alsm-ioprogress")
@@ -4409,6 +4490,29 @@ information for Golang.")
variables into structs.")
(license license:expat)))
(define-public go-github-com-caarlos0-go-version
(package
(name "go-github-com-caarlos0-go-version")
(version "0.2.2")
(source
(origin
(method git-fetch)
(uri (git-reference
(url "https://github.com/caarlos0/go-version")
(commit (string-append "v" version))))
(file-name (git-file-name name version))
(sha256
(base32 "0kp78am3yzffz8r70f1skq0m2vms0wk37f76hqbfg1r29hay1ban"))))
(build-system go-build-system)
(arguments
(list
#:import-path "github.com/caarlos0/go-version"))
(home-page "https://github.com/caarlos0/go-version")
(synopsis "Fetch Go module version")
(description
"Package goversion provides utilities to get the Go module version information.")
(license license:expat)))
(define-public go-github-com-calebcase-tmpfile
(package
(name "go-github-com-calebcase-tmpfile")
@@ -4461,6 +4565,36 @@ color palette} for Go applications. Catppuccin is a community-driven pastel
theme with four flavors: Latte, Frappe, Macchiato, and Mocha.")
(license license:expat)))
(define-public go-github-com-ccojocar-zxcvbn-go
(package
(name "go-github-com-ccojocar-zxcvbn-go")
(version "1.0.4")
(source
(origin
(method git-fetch)
(uri (git-reference
(url "https://github.com/ccojocar/zxcvbn-go")
(commit (string-append "v" version))))
(file-name (git-file-name name version))
(sha256
(base32 "0dlrd6afpfwnpj6cbbvjhwbf33ldr0nzffl8p43jrmn62mwf7cn7"))))
(build-system go-build-system)
(arguments
(list
#:import-path "github.com/ccojocar/zxcvbn-go"))
(native-inputs
(list go-github-com-stretchr-testify))
(home-page "https://github.com/ccojocar/zxcvbn-go")
(synopsis "Password-strength generator in Go")
(description
"This package provides a password strength generators written in Golang.
It attempts to give sound password advice through pattern matching and
conservative entropy calculations. It finds 10k common passwords, common
American names and surnames, common English words, and common patterns like
dates, repeats (aaa), sequences (abcd), and QWERTY patterns. It's an active
fork of @url{https://github.com/nbutton23/zxcvbn-go}.")
(license license:expat)))
(define-public go-github-com-cention-sany-utf7
(package
(name "go-github-com-cention-sany-utf7")
@@ -4605,7 +4739,7 @@ contexts (e.g. testing).")
(define-public go-github-com-charlievieth-fastwalk
(package
(name "go-github-com-charlievieth-fastwalk")
(version "1.0.8")
(version "1.0.14")
(source
(origin
(method git-fetch)
@@ -4614,7 +4748,7 @@ contexts (e.g. testing).")
(commit (string-append "v" version))))
(file-name (git-file-name name version))
(sha256
(base32 "17zy17q31p8b93bf703rr0xqafp02bb0slkrgpxb8r0aaxz3zg4y"))))
(base32 "0ab90pdqgnd0a6ylmq35zca0imj2pp4pxz2bcmg2zx0szv3910im"))))
(build-system go-build-system)
(arguments
(list
@@ -9692,6 +9826,37 @@ O(1) for @code{Set}, @code{Get}, @code{Delete} and @code{Len}.")
#~(modify-phases %standard-phases
(delete 'remove-submodule)))))))
(define-public go-github-com-elliotchance-orderedmap-v3
(package
(name "go-github-com-elliotchance-orderedmap-v3")
(version "3.1.0")
(source
(origin
(method git-fetch)
(uri (git-reference
(url "https://github.com/elliotchance/orderedmap")
(commit (string-append "v" version))))
(file-name (git-file-name name version))
(sha256
(base32 "1w681qsybcf34g0wn9hm6nnzc9jcdv59ahjiqdq9hs22xq0qgnjj"))))
(build-system go-build-system)
(arguments
(list
;; Projects includes v1, v2 and v3 in the same source tree.
#:import-path "github.com/elliotchance/orderedmap/v3"
#:unpack-path "github.com/elliotchance/orderedmap"))
(native-inputs
(list go-github-com-stretchr-testify))
(home-page "https://github.com/elliotchance/orderedmap")
(synopsis "Ordered map in with amortized O(1) for Set, Get, Delete and Len")
(description
"An @code{*OrderedMap} is a high performance ordered map that maintains
amortized O(1) for @code{Set}, @code{Get}, @code{Delete} and @code{Len}.
Internally an @code{*OrderedMap} uses the composite type
@url{https://go.dev/blog/maps, map} combined with a trimmed down linked list
to maintain the order.")
(license license:expat)))
(define-public go-github-com-elliotwutingfeng-asciiset
(package
(name "go-github-com-elliotwutingfeng-asciiset")
@@ -10024,6 +10189,36 @@ and @code{io.ReadCloser}) with overwrites
" This package is a fork of dlclark/regexp2 providing a
more similar API to regexp."))))
(define-public go-github-com-esiqveland-notify
(package
(name "go-github-com-esiqveland-notify")
(version "0.13.3")
(source
(origin
(method git-fetch)
(uri (git-reference
(url "https://github.com/esiqveland/notify")
(commit (string-append "v" version))))
(file-name (git-file-name name version))
(sha256
(base32 "03d27a8rl55j6dqclg3233dj3j7v0i0p9cda06f9c4a21djamrfb"))))
(build-system go-build-system)
(arguments
(list
#:import-path "github.com/esiqveland/notify"))
(native-inputs
(list go-github-com-stretchr-testify))
(propagated-inputs
(list go-github-com-godbus-dbus-v5))
(home-page "https://github.com/esiqveland/notify")
(synopsis "Delivering desktop notifications over DBus")
(description
"Notify is a Go library for interacting with the DBus notification
service defined by freedesktop.org at
@url{https://developer.gnome.org/notification-spec/}. Notify can deliver
desktop notifications over DBus, ala how @code{libnotify} does it.")
(license license:bsd-3)))
(define-public go-github-com-ettle-strcase
(package
(name "go-github-com-ettle-strcase")
@@ -10815,6 +11010,37 @@ library in go standard library.")
"Go library that pluralizes and singularizes English nouns.")
(license license:bsd-2)))
(define-public go-github-com-gen2brain-beeep
(package
(name "go-github-com-gen2brain-beeep")
(version "0.11.2")
(source
(origin
(method git-fetch)
(uri (git-reference
(url "https://github.com/gen2brain/beeep")
(commit (string-append "v" version))))
(file-name (git-file-name name version))
(sha256
(base32 "0jvfspz941r93djf83gsjqw8w9v34fa9dys1465iwbq769ayizmw"))))
(build-system go-build-system)
(arguments
(list
#:import-path "github.com/gen2brain/beeep"
#:test-flags #~(list "--skip" "TestAlert|TestNotify")))
(propagated-inputs
(list go-github-com-esiqveland-notify
go-github-com-godbus-dbus-v5
go-github-com-jackmordaunt-icns-v3
go-github-com-sergeymakinen-go-ico
go-golang-org-x-sys))
(home-page "https://github.com/gen2brain/beeep")
(synopsis "Sending desktop notifications, alerts and beeps")
(description
"Package beeep provides a cross-platform library for sending desktop
notifications and beeps.")
(license license:bsd-2)))
(define-public go-github-com-ghemawat-stream
(package
(name "go-github-com-ghemawat-stream")
@@ -11726,6 +11952,33 @@ native Go structure.")
(description "Package yaml implements YAML support for the Go language.")
(license license:asl2.0)))
(define-public go-github-com-gobuffalo-flect
(package
(name "go-github-com-gobuffalo-flect")
(version "1.0.3")
(source
(origin
(method git-fetch)
(uri (git-reference
(url "https://github.com/gobuffalo/flect")
(commit (string-append "v" version))))
(file-name (git-file-name name version))
(sha256
(base32 "0lyb1876byv9q52y6dlq17aahwl108mhp67cmxykckjpxxykb442"))))
(build-system go-build-system)
(arguments
(list
#:import-path "github.com/gobuffalo/flect"))
(native-inputs
(list go-github-com-stretchr-testify))
(home-page "https://github.com/gobuffalo/flect")
(synopsis "Inflection engine for Golang")
(description
"This package provides a new inflection engine to replace
@url{https://github.com/markbates/inflect,} designed to be more modular,
readable, and easier to fix issues on than the original.")
(license license:expat)))
(define-public go-github-com-gobwas-glob
(package
(name "go-github-com-gobwas-glob")
@@ -12569,6 +12822,41 @@ color (24-bit, RGB)
@end itemize")
(license license:expat)))
(define-public go-github-com-goreleaser-chglog
(package
(name "go-github-com-goreleaser-chglog")
(version "0.7.4")
(source
(origin
(method git-fetch)
(uri (git-reference
(url "https://github.com/goreleaser/chglog")
(commit (string-append "v" version))))
(file-name (git-file-name name version))
(sha256
(base32 "09ni4y644zhp3bf9nwy9qc9wkxrn2hla6nczg3zpn0ls8qaxjd40"))))
(build-system go-build-system)
(arguments
(list
#:import-path "github.com/goreleaser/chglog"))
(native-inputs
(list go-github-com-go-git-go-billy-v5
go-github-com-google-go-cmp
go-github-com-smartystreets-goconvey
go-github-com-spf13-cobra
go-github-com-spf13-viper))
(propagated-inputs
(list go-github-com-go-git-go-git-v5
go-github-com-masterminds-semver-v3
go-github-com-masterminds-sprig-v3
go-gitlab-com-digitalxero-go-conventional-commit
go-go-yaml-in-yaml-v3))
(home-page "https://github.com/goreleaser/chglog")
(synopsis "Changelog management Go library")
(description
"This package provides Go functions to manage changelogs.")
(license license:expat)))
(define-public go-github-com-goreleaser-fileglob
(package
(name "go-github-com-goreleaser-fileglob")
@@ -12599,6 +12887,66 @@ underneath and returns only matching files or directories, depending on the
configuration.")
(license license:expat)))
(define-public go-github-com-goreleaser-nfpm-v2
(package
(name "go-github-com-goreleaser-nfpm-v2")
(version "2.44.0")
(source
(origin
(method git-fetch)
(uri (git-reference
(url "https://github.com/goreleaser/nfpm")
(commit (string-append "v" version))))
(file-name (git-file-name name version))
(sha256
(base32 "17dmzkvy3ihjjaxi10l9xc1mcg9vmlr2v1xc4a361fa22aqigz0v"))))
(build-system go-build-system)
(arguments
(list
#:go go-1.25
#:import-path "github.com/goreleaser/nfpm/v2"
#:unpack-path "github.com/goreleaser/nfpm/v2"
;; Tests fail due to read-only filesystem when trying to manipulate mode
;; of the files.
#:test-flags
#~(list "-skip" "TestPrepareForPackager|TestDeepPathsWithGlobAndUmask")
#:phases
#~(modify-phases %standard-phases
(add-after 'unpack 'fix-tests
(lambda* (#:key unpack-path #:allow-other-keys)
(with-directory-excursion (string-append "src/" unpack-path)
(substitute* "rpm/rpm_test.go"
(("/bin/bash") (which "bash")))))))))
(native-inputs
(list go-github-com-caarlos0-go-version
go-github-com-invopop-jsonschema
go-github-com-muesli-mango-cobra
go-github-com-muesli-roff
go-github-com-sassoftware-go-rpmutils
go-github-com-stretchr-testify))
(propagated-inputs
(list go-dario-cat-mergo
go-github-com-aleksi-pointer
go-github-com-blakesmith-ar
go-github-com-google-rpmpack
go-github-com-goreleaser-chglog
go-github-com-goreleaser-fileglob
go-github-com-klauspost-compress
go-github-com-klauspost-pgzip
go-github-com-masterminds-semver-v3
go-github-com-protonmail-go-crypto
go-github-com-protonmail-gopenpgp-v2
go-github-com-spf13-cobra
go-github-com-ulikunitz-xz
go-gopkg-in-yaml-v3))
(home-page "https://github.com/goreleaser/nfpm")
(synopsis "Go library to package programs in various Linux formats")
(description
"nFPM is Not FPM -- provides ways to package programs in popular Linux
packaging formats, such as @code{deb}, @code{rpm}, @code{apk}, @code{ipk} and
Arch.")
(license license:expat)))
(define-public go-github-com-gorhill-cronexpr
(package
(name "go-github-com-gorhill-cronexpr")
@@ -20520,6 +20868,90 @@ for any given struct and a set of its potential member values. This can be
used to generate extensive test matrixes among other things.")
(license license:expat)))
(define-public go-github-com-muesli-mango
(package
(name "go-github-com-muesli-mango")
(version "0.2.0")
(source
(origin
(method git-fetch)
(uri (git-reference
(url "https://github.com/muesli/mango")
(commit (string-append "v" version))))
(file-name (git-file-name name version))
(sha256
(base32 "16d0sga6cbdxzlqkibcgw0civkw11fpkcjpgv21i0q5j9mjbsjw4"))))
(build-system go-build-system)
(arguments
(list
#:import-path "github.com/muesli/mango"))
(propagated-inputs
(list go-github-com-muesli-roff))
(home-page "https://github.com/muesli/mango")
(synopsis "Golang man-page generator")
(description
"This package provides a man-page generator for the Go flag, pflag, cobra, coral,
and kong packages. It extracts commands, flags, and arguments from the target
program and enables it to self-document.")
(license license:expat)))
(define-public go-github-com-muesli-mango-cobra
(package
(name "go-github-com-muesli-mango-cobra")
(version "1.3.0")
(source
(origin
(method git-fetch)
(uri (git-reference
(url "https://github.com/muesli/mango-cobra")
(commit (string-append "v" version))))
(file-name (git-file-name name version))
(sha256
(base32 "11vvm3f2mq8yaqbfrjbzdcyvkn9f75rp4kygxyvqwc5jsw1kdwal"))))
(build-system go-build-system)
(arguments
(list
#:import-path "github.com/muesli/mango-cobra"))
(propagated-inputs
(list go-github-com-muesli-mango
go-github-com-muesli-mango-pflag
go-github-com-muesli-roff
go-github-com-spf13-cobra))
(home-page "https://github.com/muesli/mango-cobra")
(synopsis "Cobra adapter for mango")
(description
"This package provides a cobra adapter for the
@url{https://github.com/muesli/mango,mango} man-page generator.")
(license license:expat)))
(define-public go-github-com-muesli-mango-pflag
(package
(name "go-github-com-muesli-mango-pflag")
(version "0.2.0")
(source
(origin
(method git-fetch)
(uri (git-reference
(url "https://github.com/muesli/mango-pflag")
(commit (string-append "v" version))))
(file-name (git-file-name name version))
(sha256
(base32 "1k4m88i9shs36a8n86k3a1vlxmdf5vwavkih2f2j3xj718hnhpw0"))))
(build-system go-build-system)
(arguments
(list
#:import-path "github.com/muesli/mango-pflag"))
(propagated-inputs
(list go-github-com-muesli-mango
go-github-com-muesli-roff
go-github-com-spf13-pflag))
(home-page "https://github.com/muesli/mango-pflag")
(synopsis "Pflag adapter for mango")
(description
"This package provides a pflag adapter for the
@url{https://github.com/muesli/mango, mango} man-page generator.")
(license license:expat)))
(define-public go-github-com-muesli-reflow
(package
(name "go-github-com-muesli-reflow")
@@ -20547,6 +20979,32 @@ used to generate extensive test matrixes among other things.")
helping you to transform blocks of text.")
(license license:expat)))
(define-public go-github-com-muesli-roff
(package
(name "go-github-com-muesli-roff")
(version "0.1.0")
(source
(origin
(method git-fetch)
(uri (git-reference
(url "https://github.com/muesli/roff")
(commit (string-append "v" version))))
(file-name (git-file-name name version))
(sha256
(base32 "0l263rqwq2ccr1lpamsvs48dddsr70xim8mv6rsj2x9y3prcq3yh"))))
(build-system go-build-system)
(arguments
(list
#:import-path "github.com/muesli/roff"
;; Expected title heading, got:
;; .TH TITLE 1 "2026-05-22" "Title" "A short description"
#:test-flags #~(list "-skip" "TestTitleHeading")))
(home-page "https://github.com/muesli/roff")
(synopsis "Write roff documents in Go")
(description "This package provides tools to write @code{roff}
documents in Golang.")
(license license:expat)))
(define-public go-github-com-muesli-termenv
(package
(name "go-github-com-muesli-termenv")
@@ -22506,6 +22964,36 @@ expiration times, it doesn't need to serialize or transmit its contents over
the network.")
(license license:expat)))
(define-public go-github-com-pb33f-ordered-map-v2
(package
(name "go-github-com-pb33f-ordered-map-v2")
(version "2.3.1")
(source
(origin
(method git-fetch)
(uri (git-reference
(url "https://github.com/pb33f/ordered-map")
(commit (string-append "v" version))))
(file-name (git-file-name name version))
(sha256
(base32 "1k4r1rvlziddaszm1jvgz27nkrk1jfka0zik16f4b3gmhdnmd9vc"))))
(build-system go-build-system)
(arguments
(list
#:import-path "github.com/pb33f/ordered-map/v2"))
(native-inputs
(list go-github-com-stretchr-testify))
(propagated-inputs
(list go-github-com-bahlo-generic-list-go
go-github-com-buger-jsonparser
go-go-yaml-in-yaml-v4))
(home-page "https://github.com/pb33f/ordered-map")
(synopsis "Ordered maps in Golang")
(description
"This package provides a Golang implementation of an ordered map, which
is a map that also keeps track of the order in which keys were inserted.")
(license license:asl2.0)))
(define-public go-github-com-pbnjay-memory
(let ((commit "7b4eea64cf580186c0eceb10dc94ba3a098af46c")
(revision "2"))
@@ -29425,6 +29913,31 @@ utilities for cty Golang module.")
"Package yaml can marshal and unmarshal cty values in YAML format.")
(license license:asl2.0)))
(define-public go-github-com-zeebo-bencode
(package
(name "go-github-com-zeebo-bencode")
(version "1.0.0")
(source
(origin
(method git-fetch)
(uri (git-reference
(url "https://github.com/zeebo/bencode")
(commit (string-append "v" version))))
(file-name (git-file-name name version))
(sha256
(base32 "0c6bw1if1vbcr9l4684a4jdri8z31m8msjpp7z6y2p9s1jqjhkrp"))))
(build-system go-build-system)
(arguments
(list
#:import-path "github.com/zeebo/bencode"))
(home-page "https://github.com/zeebo/bencode")
(synopsis "Bencode marshal and unmarshal library")
(description
"This library implements encoding and decoding of
@url{https://wiki.theory.org/BitTorrentSpecification#Bencoding, bencoded}
objects.")
(license license:expat)))
(define-public go-github-com-zeebo-errs
(package
(name "go-github-com-zeebo-errs")
@@ -29738,6 +30251,31 @@ connections.")
"This package provides a pretty printing library for Golang values.")
(license license:expat)))
(define-public go-github-com-zyedidia-clipboard
(package
(name "go-github-com-zyedidia-clipboard")
(version "1.0.4")
(source
(origin
(method git-fetch)
(uri (git-reference
(url "https://github.com/zyedidia/clipboard")
(commit (string-append "v" version))))
(file-name (git-file-name name version))
(sha256
(base32 "1nrs2ll6dh31wyzxh2zbykwvpavhlpzysfk6qgfj5s4rz6ck8glz"))))
(build-system go-build-system)
(arguments
(list
#:tests? #f ;requires clipboard (xclip or xsel)
#:import-path "github.com/zyedidia/clipboard"))
(home-page "https://github.com/zyedidia/clipboard")
(synopsis "Clipboard for Golang")
(description
"Package clipboard read/write on clipboard. It's an alternative fork of
@url{https://github.com/atotto/clipboard}.")
(license license:bsd-3)))
(define-public go-github-com-zyedidia-clipper
(package
(name "go-github-com-zyedidia-clipper")
@@ -30246,7 +30784,7 @@ Identifier (RFC3986) specification in Go.")
(define-public go-go-mau-fi-util
(package
(name "go-go-mau-fi-util")
(version "0.8.4")
(version "0.9.9")
(source
(origin
(method git-fetch)
@@ -30255,7 +30793,7 @@ Identifier (RFC3986) specification in Go.")
(commit (string-append "v" version))))
(file-name (git-file-name name version))
(sha256
(base32 "0zzkrbwgbxfppsxjck8qgj4xxzpiq25sx4p3zwjh6s1yz3kfb97p"))))
(base32 "1d6365n4j5hx172mi5f9rk49l7cgcbf8qvi721b0l34j2m036rsy"))))
(build-system go-build-system)
(arguments
(list
@@ -33637,6 +34175,22 @@ library.")
;;; Executables:
;;;
(define-public chglog
(package/inherit go-github-com-goreleaser-chglog
(name "chglog")
(arguments
(substitute-keyword-arguments arguments
((#:tests? _ #t) #f)
((#:install-source? _ #t) #f)
((#:import-path _) "github.com/goreleaser/chglog/cmd/chglog")
((#:unpack-path _ "") "github.com/goreleaser/chglog")))
(native-inputs
(append
(package-native-inputs go-github-com-goreleaser-chglog)
(package-propagated-inputs go-github-com-goreleaser-chglog)))
(inputs '())
(propagated-inputs '())))
(define-public containers-storage
(package/inherit go-github-com-containers-storage
(name "containers-storage")
@@ -34177,6 +34731,22 @@ various modes for analyzing and transforming YAML data.")))
(propagated-inputs '())
(inputs '())))
(define-public nfpm
(package/inherit go-github-com-goreleaser-nfpm-v2
(name "nfpm")
(arguments
(substitute-keyword-arguments arguments
((#:import-path _) "github.com/goreleaser/nfpm/v2/cmd/nfpm")
((#:install-source? _ #t) #f)
((#:tests? _ #t) #f)
((#:unpack-path _ "") "github.com/goreleaser/nfpm/v2")))
(native-inputs
(append
(package-native-inputs go-github-com-goreleaser-nfpm-v2)
(package-propagated-inputs go-github-com-goreleaser-nfpm-v2)))
(inputs '())
(propagated-inputs '())))
(define-public oci-runtime-tool
(package/inherit go-github-com-opencontainers-runtime-tools
(name "oci-runtime-tool")
+36 -4
View File
@@ -1,5 +1,5 @@
;;; GNU Guix --- Functional package management for GNU
;;; Copyright © 2017-2025 Ricardo Wurmus <rekado@elephly.net>
;;; Copyright © 2017-2026 Ricardo Wurmus <rekado@elephly.net>
;;; Copyright © 2018 Joshua Sierles, Nextjournal <joshua@nextjournal.com>
;;; Copyright © 2018, 2020, 2022 Tobias Geerinckx-Rice <me@tobias.gr>
;;; Copyright © 2019, 2021, 2022, 2024 Efraim Flashner <efraim@flashner.co.il>
@@ -55,7 +55,7 @@
#:use-module (gnu packages cran)
#:use-module (gnu packages datastructures)
#:use-module (gnu packages docbook)
#:use-module (gnu packages flex)
#:use-module (gnu packages compiler-tools)
#:use-module (gnu packages fontutils)
#:use-module (gnu packages gd)
#:use-module (gnu packages graphics)
@@ -227,7 +227,7 @@ more.")
(package
(inherit igraph)
(name "igraph")
(version "0.10.15")
(version "1.0.1")
(source
(origin
(inherit (package-source igraph))
@@ -239,7 +239,39 @@ more.")
(file-name (git-file-name name version))
(sha256
(base32
"0z9jqvl65j4z6brrjlfyykba2bs10az6dx6m8g41snlfnx21a82d")))))))
"01mynhbl2ph0gkc0zr5klwqvczwcimfs2kdn6didwg4k8gsrcxlr"))
(modules '((guix build utils)
(ice-9 ftw)
(srfi srfi-26)))
;; We need the vendored versions of qhull and cxsparse.
(snippet '(begin
(delete-file-recursively "src/isomorphism/bliss")
(substitute* '("src/CMakeLists.txt"
"etc/cmake/benchmark_helpers.cmake")
;; Remove extraneous bundling related variables.
((".*_IS_VENDORED.*") "")
((".*add_sub.*isomorphism/bliss.*") "")
(("(.*TARGETS.*)bliss(.*)pcg(.*)"
_ part1 part2 part3)
(string-append part1 part2 part3))
((" pcg ") " pcg_random "))))))
(arguments
(substitute-keyword-arguments (package-arguments igraph)
((#:phases phases '%standard-phases)
#~(modify-phases #$phases
;; We have to use the bundled version because it has been
;; modified from upstream.
(delete 'patch-suitesparse)))
((#:configure-flags flags)
#~(list "-DBUILD_SHARED_LIBS=ON"
"-DIGRAPH_INFOMAP_SUPPORT=OFF"
"-DCMAKE_C_FLAGS=-Wno-error=incompatible-pointer-types"
;; Use the same integer width as suitesparse-cxsparse, which
;; uses int64_t in SuiteSparse v6.0.0 and later.
"-DIGRAPH_INTEGER_SIZE=64"))))
(inputs
(modify-inputs (package-inputs igraph)
(delete "suitesparse-cxsparse"))))))
(define-public python-igraph
(package
+90 -20
View File
@@ -78,7 +78,7 @@
#:use-module (gnu packages crypto)
#:use-module (gnu packages datastructures)
#:use-module (gnu packages documentation)
#:use-module (gnu packages flex)
#:use-module (gnu packages compiler-tools)
#:use-module (gnu packages fonts)
#:use-module (gnu packages fontutils)
#:use-module (gnu packages freedesktop)
@@ -111,7 +111,6 @@
#:use-module (gnu packages maths)
#:use-module (gnu packages mp3)
#:use-module (gnu packages multiprecision)
#:use-module (gnu packages ninja)
#:use-module (gnu packages opencl)
#:use-module (gnu packages oneapi)
#:use-module (gnu packages pciutils)
@@ -998,24 +997,17 @@ baking tools to produce normal maps.")
(string-append "-DLLVM_BC_GENERATOR="
#$(this-package-native-input "clang")
"/bin/clang++"))
#:phases
#~(modify-phases %standard-phases
(replace 'check
(lambda* (#:key tests? #:allow-other-keys)
(when tests?
(invoke
"ctest" "--exclude-regex"
(string-join
(list
"osl-imageio" ; file does not exist
"osl-imageio.opt" ; file does not exist
"osl-imageio.opt.rs_bitcode" ; file does not exist
"texture-udim" ; file does not exist
"texture-udim.opt" ; file does not exist
"texture-udim.opt.rs_bitcode" ; file does not exist
"example-deformer" ; could not find OSLConfig
"python-oslquery") ; no module oslquery
"|"))))))))
#:test-exclude (string-join
(list
"osl-imageio" ; file does not exist
"osl-imageio.opt" ; file does not exist
"osl-imageio.opt.rs_bitcode" ; file does not exist
"texture-udim" ; file does not exist
"texture-udim.opt" ; file does not exist
"texture-udim.opt.rs_bitcode" ; file does not exist
"example-deformer" ; could not find OSLConfig
"python-oslquery") ; no module oslquery
"|")))
(native-inputs
(list bison
clang
@@ -1347,6 +1339,19 @@ basic geometries.")
(file-name (git-file-name name version))
(sha256
(base32 "0gfgzwm5s50caj5s6l7irgmlifpmypd0fnm6ckzli1fdziwjgdwi"))))
(arguments
;; https://gitlab.com/inkscape/lib2geom/-/work_items/82
(if (or (target-aarch64?)
(target-riscv64?)
(target-ppc64le?))
(substitute-keyword-arguments arguments
((#:phases phases #~%standard-phases)
#~(modify-phases #$phases
(add-after 'unpack 'disable-polynomial-test
(lambda _
(substitute* "tests/CMakeLists.txt"
(("polynomial-test") "")))))))
arguments))
(properties '((hidden? . #f)))))
(define-public pstoedit
@@ -2392,6 +2397,71 @@ and engineering community.")
(define-deprecated coin3D-4 coin3d)
(export coin3D-4)
(define-public skcms
;; No tags are available.
(let ((commit "a7a3b15f06355692d86a3b8373c579a521598f4c")
(revision "0"))
(package
(name "skcms")
(version (git-version "0" revision commit))
(source
(origin
(method git-fetch)
(uri (git-reference
(url "https://skia.googlesource.com/skcms")
(commit commit)))
(file-name (git-file-name name version))
(sha256
(base32 "0ylrsm7cinw59ilgbffazbgifax81kkya5cxq8q8wybnxx6z6ps6"))))
(build-system gnu-build-system)
(arguments
(list
#:phases
#~(modify-phases %standard-phases
(add-after 'unpack 'patch-includes
(lambda _
(substitute* "skcms.h"
(("src\\/skcms_public\\.h") "skcms/skcms_public.h"))))
(delete 'configure)
(replace 'build
(lambda _
;; Some CPUs may not support these features.
(let ((cflags (append '("-DSKCMS_DISABLE_HSW=1"
"-DSKCMS_DISABLE_SKX=1")
(if #$(target-mingw?)
'("-DSKCMS_HAS_MUSTTAIL=0")
'())))
(ldflags '("-lstdc++")))
(apply invoke #$(cc-for-target)
`("-O2" "-g" "-fPIC" ,@cflags
"skcms.cc"
"src/skcms_TransformBaseline.cc"
"src/skcms_TransformHsw.cc"
"src/skcms_TransformSkx.cc"
"-shared" ,@ldflags
"-o" "libskcms.so"))
(apply invoke #$(cc-for-target)
`(,@cflags
"tests.c" "test_only.c"
"-Wl,-rpath=." "-L." "-lskcms" ,@ldflags
"-o" "tests")))))
(replace 'check
(lambda* (#:key tests? #:allow-other-keys)
(when tests?
(invoke "./tests"))))
(replace 'install
(lambda _
(install-file "libskcms.so" (string-append #$output "/lib"))
(install-file "skcms.h" (string-append #$output "/include"))
(install-file "src/skcms_public.h"
(string-append #$output "/include/skcms")))))))
(native-inputs (list ninja))
(home-page "https://skia.org/")
(synopsis "Color management engine")
(description
"skcms is the color management engine. It is a part of @code{skia}.")
(license license:bsd-3))))
(define-public skia
;; Releases follow those of Chromium, about every 6 weeks. The release
;; version can be found on this page:
+2 -2
View File
@@ -341,7 +341,7 @@ $(AM_CPPFLAGS) $(CPPFLAGS) $(AM_CFLAGS) $(CFLAGS) $(srcdir)/predicates_init.c \
(define-public xdot
(package
(name "xdot")
(version "1.4")
(version "1.6")
(source
(origin
;; PyPI tarball is missing some test files.
@@ -351,7 +351,7 @@ $(AM_CPPFLAGS) $(CPPFLAGS) $(AM_CFLAGS) $(CFLAGS) $(srcdir)/predicates_init.c \
(commit version)))
(file-name (git-file-name name version))
(sha256
(base32 "1l34ahvcz90j3j7aspp9wqvxpq10mzgq7l0sanrj142ihdnbahvy"))))
(base32 "0gg54k6zhdviz17aa3harc82f7bx4mpwnj292q066dzamvr87svq"))))
(build-system pyproject-build-system)
(arguments
(list
+1 -1
View File
@@ -37,7 +37,7 @@
#:use-module (gnu packages bash)
#:use-module (gnu packages ruby-xyz)
#:use-module (gnu packages bison)
#:use-module (gnu packages flex)
#:use-module (gnu packages compiler-tools)
#:use-module (gnu packages ghostscript)
#:use-module (gnu packages netpbm)
#:use-module (gnu packages perl)
+1 -1
View File
@@ -56,7 +56,7 @@
#:use-module (gnu packages compression)
#:use-module (gnu packages documentation)
#:use-module (gnu packages elf)
#:use-module (gnu packages flex)
#:use-module (gnu packages compiler-tools)
#:use-module (gnu packages freedesktop)
#:use-module (gnu packages gettext)
#:use-module (gnu packages ghostscript)
+2 -1
View File
@@ -1173,7 +1173,8 @@ application suites.")
'("--no-suite=gsk-compare-gl"
"--no-suite=gsk-compare-cairo"
"--no-suite=gsk-compare-ngl"
"--no-suite=gsk-compare-vulkan")
"--no-suite=gsk-compare-vulkan"
"--no-suite=svg")
'()))
#:phases
#~(modify-phases %standard-phases
+35 -3
View File
@@ -4019,6 +4019,38 @@ with documentation.
;; details.
(license license:gpl3+)))
(define-public guile-scriba
(package
(name "guile-scriba")
(version "0.1.2")
(source
(origin
(method git-fetch)
(uri (git-reference
(url "https://codeberg.org/jjba23/scriba.git")
(commit (string-append "v" version))))
(file-name (git-file-name name version))
(sha256
(base32 "1chhbhy21g6zghc3alpqhvb6nizylmzzapjariykv41f47ynhljs"))))
(build-system guile-build-system)
(arguments
(list
#:source-directory "src"))
(propagated-inputs (list guile-json-4))
(inputs (list guile-3.0))
(synopsis "Structured logging framework for Guile Scheme")
(description
"Scriba is a structured logging library for GNU Guile that prioritizes
flexibility and observability. It provides modular log routing, formatting,
and filtering, allowing developers to generate human-readable console logs
during development and machine-readable JSON logs for production environments.
Key features include an auto-logger configured via environment variables,
dynamically scoped log contexts using Scheme parameters, ahead-of-time log
level filtering, and minimal runtime overhead achieved through memoization
and compile-time macros.")
(home-page "https://codeberg.org/jjba23/scriba")
(license license:lgpl3+)))
(define-public guile-simple-iterators
(let ((commit "50f16a2b2aa57e657e52e19fb3c35bdc182cfa36")
(revision "0"))
@@ -7526,7 +7558,7 @@ in a large number of randomly generated test cases.")
(define-public guile-veritas
(package
(name "guile-veritas")
(version "0.1.6")
(version "0.3.0")
(source
(origin
(method git-fetch)
@@ -7535,13 +7567,13 @@ in a large number of randomly generated test cases.")
(commit (string-append "v" version))))
(file-name (git-file-name name version))
(sha256
(base32 "1h4si2p8gj4wfhvn4cshga2kjxf59vd4nwvxkc2i3g5gv3kxhm3k"))))
(base32 "1i64pd5pcx37i25hnks7zj8pbwf1fdy0s5y9ic2sgn800zqq1dxy"))))
(build-system guile-build-system)
(arguments
(list
#:source-directory "src"))
(native-inputs (list guile-3.0))
(propagated-inputs (list guile-fibers))
(propagated-inputs (list guile-fibers guile-json-4))
(home-page "https://codeberg.org/jjba23/veritas")
(synopsis "Testing framework for Guile")
(description
+12 -1
View File
@@ -44,7 +44,7 @@
#:use-module (gnu packages compression)
#:use-module (gnu packages crypto)
#:use-module (gnu packages dbm)
#:use-module (gnu packages flex)
#:use-module (gnu packages compiler-tools)
#:use-module (gnu packages gawk)
#:use-module (gnu packages gettext)
#:use-module (gnu packages gperf)
@@ -529,6 +529,17 @@ without requiring the source code to be rewritten.")
;;; (security or else) and this deprecation could be removed.
(define-deprecated/public-alias guile-3.0/fixed guile-3.0/pinned)
(define-public guile-with-gmp
(package/inherit guile-3.0-latest
(name "guile-with-gmp")
(propagated-inputs
(modify-inputs propagated-inputs
(append gmp)))
(arguments
(substitute-keyword-arguments arguments
((#:configure-flags flags #~'())
#~(delete "--enable-mini-gmp" #$flags))))))
(define-public guile-3.0/pinned
;; A package of Guile that's rarely changed. It is the one used in the
;; `base' module, and thus changing it entails a full rebuild.
+1 -1
View File
@@ -61,7 +61,7 @@
#:use-module (gnu packages debian)
#:use-module (gnu packages disk)
#:use-module (gnu packages documentation)
#:use-module (gnu packages flex)
#:use-module (gnu packages compiler-tools)
#:use-module (gnu packages freedesktop)
#:use-module (gnu packages gcc)
#:use-module (gnu packages gettext)
+1 -1
View File
@@ -52,7 +52,7 @@
#:use-module (gnu packages compression)
#:use-module (gnu packages elf)
#:use-module (gnu packages file)
#:use-module (gnu packages flex)
#:use-module (gnu packages compiler-tools)
#:use-module (gnu packages gawk)
#:use-module (gnu packages gcc)
#:use-module (gnu packages ghostscript)
+1 -1
View File
@@ -33,7 +33,7 @@
#:use-module (gnu packages base)
#:use-module (gnu packages bash)
#:use-module (gnu packages compression)
#:use-module (gnu packages flex)
#:use-module (gnu packages compiler-tools)
#:use-module (gnu packages bison)
#:use-module (gnu packages elf)
#:use-module (gnu packages m4)
+1 -1
View File
@@ -38,7 +38,7 @@
#:use-module (gnu packages cross-base)
#:use-module (gnu packages crypto)
#:use-module (gnu packages disk)
#:use-module (gnu packages flex)
#:use-module (gnu packages compiler-tools)
#:use-module (gnu packages gawk)
#:use-module (gnu packages gnupg)
#:use-module (gnu packages bison)
+33 -24
View File
@@ -36,6 +36,7 @@
#:use-module (guix licenses)
#:use-module (guix packages)
#:use-module (guix gexp)
#:use-module (guix deprecation)
#:use-module (guix download)
#:use-module (guix git-download)
#:use-module (guix build-system cmake)
@@ -946,37 +947,42 @@ traditional Chinese output.")
hanja dictionary and small hangul character classification.")
(license lgpl2.1+)))
(define-public ibus-libhangul
(define-public ibus-hangul
(package
(name "ibus-libhangul")
(version "1.5.3")
(name "ibus-hangul")
(version "1.5.5")
(source
(origin
(method url-fetch)
(uri (string-append "https://github.com/libhangul/ibus-hangul/"
"releases/download/" version
"/ibus-hangul-" version ".tar.gz"))
(method git-fetch)
(uri (git-reference
(url "https://github.com/libhangul/ibus-hangul")
(commit version)))
(file-name (git-file-name name version))
(sha256
(base32
"1400ba2p34vr9q285lqvjm73f6m677cgfdymmjpiwyrjgbbiqrjy"))))
(base32 "0wsbh6ii223wdai2qwcwy6sj5jr9zzma7511fhkfq4m2qxdhwsn7"))))
(build-system gnu-build-system)
(arguments
`(#:phases
(modify-phases %standard-phases
(add-after 'install 'wrap
(lambda* (#:key inputs outputs #:allow-other-keys)
(wrap-program (string-append (assoc-ref outputs "out")
"/libexec/ibus-setup-hangul")
`("GUIX_PYTHONPATH" ":" prefix (,(getenv "GUIX_PYTHONPATH")))
`("LD_LIBRARY_PATH" ":" prefix
(,(string-append (assoc-ref inputs "libhangul") "/lib")))
`("GI_TYPELIB_PATH" ":" prefix
(,(getenv "GI_TYPELIB_PATH"))))
#t)))))
(list
#:make-flags
#~'("DISABLE_GUI_TESTS=ibus-hangul")
#:phases
#~(modify-phases %standard-phases
(add-after 'install 'wrap
(lambda* (#:key inputs #:allow-other-keys)
(wrap-program (string-append #$output
"/libexec/ibus-setup-hangul")
`("GUIX_PYTHONPATH" ":" prefix (,(getenv "GUIX_PYTHONPATH")))
`("LD_LIBRARY_PATH" ":" prefix
(,(dirname (search-input-file inputs "lib/libhangul.so"))))
`("GI_TYPELIB_PATH" ":" prefix
(,(getenv "GI_TYPELIB_PATH")))))))))
(native-inputs
`(("pkg-config" ,pkg-config)
("gettext" ,gettext-minimal)
("glib:bin" ,glib "bin")))
(list autoconf
automake
gettext-minimal
`(,glib "bin")
libtool
pkg-config))
(inputs
(list bash-minimal
ibus
@@ -991,6 +997,9 @@ hanja dictionary and small hangul character classification.")
"ibus-hangul is a Korean input method engine for IBus.")
(license gpl2+)))
;; XXX: Deprecated on 2026-05-26.
(define-deprecated-package ibus-libhangul ibus-hangul)
(define-public ibus-table
(package
(name "ibus-table")
+7 -5
View File
@@ -72,7 +72,7 @@
#:use-module (gnu packages docbook)
#:use-module (gnu packages documentation)
#:use-module (gnu packages engineering)
#:use-module (gnu packages flex)
#:use-module (gnu packages compiler-tools)
#:use-module (gnu packages fontutils)
#:use-module (gnu packages game-development)
#:use-module (gnu packages gcc)
@@ -1521,7 +1521,7 @@ libraries designed for computer vision research and implementation.")
python
onetbb
vxl-1
zlib))
zlib-ng-compat))
(native-inputs
(list castxml
git-minimal
@@ -1923,7 +1923,7 @@ and Scan Tailor Enhanced versions as well as including many more bug fixes.")
(define-public simpleitk
(package
(name "simpleitk")
(version "2.5.3")
(version "2.5.4")
(source
(origin
(method git-fetch)
@@ -1932,7 +1932,9 @@ and Scan Tailor Enhanced versions as well as including many more bug fixes.")
(commit (string-append "v" version))))
(file-name (git-file-name name version))
(sha256
(base32 "0fvacjfq0p8v7r2cmzwwh7bxb6ayavznhj0m81dah463x472qkd2"))))
(base32 "1bzj5naqbgv2b31iqgz7qqk9rixsvjqycjz6l7w3gm7v1aj14jpb"))
(patches
(search-patches "simpleitk-r-4.6.0.patch"))))
(build-system cmake-build-system)
(outputs '("out" "python" "r"))
(arguments
@@ -2032,7 +2034,7 @@ and Scan Tailor Enhanced versions as well as including many more bug fixes.")
version "/SimpleITKData-" version ".tar.gz"))
(sha256
(base32
"0i4f87g1rh6xxisw06gwwyi8f216qqs6ih3gghi3k49vsl0h4g5d")))))
"0hryvi9fgqac00ng1bfhw3lm0al1dh0ka6jglba2q368nls428nx")))))
(synopsis "Simplified interface to @acronym{ITK, Insight Toolkit}")
(description
"SimpleITK is an image analysis toolkit built on top of @acronym{ITK,
+85
View File
@@ -39,6 +39,7 @@
;;; Copyright © 2025 Vinicius Monego <monego@posteo.net>
;;; Copyright © 2025 Igorj Gorjaĉev <igor@goryachev.org>
;;; Copyright © 2026 Daniel Littlewood <dan@danielittlewood.xyz>
;;; Copyright © 2026 Luis Guilherme Coelho <lgcoelho@disroot.org>
;;;
;;; This file is part of GNU Guix.
;;;
@@ -94,13 +95,16 @@
#:use-module (gnu packages gnome)
#:use-module (gnu packages golang-build)
#:use-module (gnu packages golang-xyz)
#:use-module (gnu packages gstreamer)
#:use-module (gnu packages gtk)
#:use-module (gnu packages graphics)
#:use-module (gnu packages haskell-xyz)
#:use-module (gnu packages image)
#:use-module (gnu packages image-processing)
#:use-module (gnu packages imagemagick)
#:use-module (gnu packages kde-frameworks)
#:use-module (gnu packages linux)
#:use-module (gnu packages logging)
#:use-module (gnu packages maths)
#:use-module (gnu packages ncurses)
#:use-module (gnu packages pdf)
@@ -108,6 +112,7 @@
#:use-module (gnu packages perl-check)
#:use-module (gnu packages photo)
#:use-module (gnu packages pkg-config)
#:use-module (gnu packages pretty-print)
#:use-module (gnu packages profiling)
#:use-module (gnu packages python)
#:use-module (gnu packages python-build)
@@ -120,6 +125,8 @@
#:use-module (gnu packages sqlite)
#:use-module (gnu packages suckless)
#:use-module (gnu packages stb)
#:use-module (gnu packages tbb)
#:use-module (gnu packages tls)
#:use-module (gnu packages terminals)
#:use-module (gnu packages upnp)
#:use-module (gnu packages version-control)
@@ -1286,6 +1293,84 @@ workspaces.
(define-deprecated-package python-ueberzug
ueberzug)
(define-public ueberzugpp
(package
(name "ueberzugpp")
(version "2.9.10")
(source
(origin
(method git-fetch)
(uri (git-reference
(url "https://github.com/jstkdng/ueberzugpp")
(commit (string-append "v" version))))
(file-name (git-file-name name version))
(sha256
(base32 "1jac2sca4pmcxp8xcvaxhf6j15phyc85gb5n9ymajbahnd4hbcv2"))))
(build-system cmake-build-system)
(arguments
(list #:tests? #f ; no tests
#:configure-flags
#~(list "-DENABLE_OPENCV=ON"
"-DENABLE_X11=ON"
"-DENABLE_WAYLAND=ON")))
(native-inputs
(list extra-cmake-modules
gobject-introspection
pkg-config))
(inputs
(list cairo
chafa
cli11
expat
fftw
fmt
imagemagick
imath
lcms
libexif
libgsf
librsvg
libsixel
libwebp
libxcb
matio
nlohmann-json
opencv
openexr
openssl
orc
pango
poppler
range-v3
spdlog
tbb
vips
wayland
wayland-protocols
xcb-util-image))
(home-page "https://github.com/jstkdng/ueberzugpp")
(synopsis "Drop in replacement for ueberzug written in C++")
(description "Überzug++ is a command line utility written in C++ which
allows to draw images on terminals by using X11/Wayland child windows, sixels,
kitty and iterm2.
Advantages over @command{w3mimgdisplay}:
@itemize
@item Support for Wayland: Sway, Hyprland, niri and Wayfire
@item No race conditions as a new window is created to display images
@item Expose events will be processed, so images will be redrawn on switch
workspaces
@item Tmux support on X11, Sway and Hyprland
@item Terminals without the @env{WINDOWID} environment variable are supported
@item Chars are used as position - and size unit
@item No memory leak (usage of smart pointers)
@item A lot of image formats supported (through OpenCV and libvips).
@item GIF and animated WEBP support on X11, Sixel, Sway and hyprland
@item Fast image downscaling (through OpenCV and OpenCL)
@item Cache resized images for faster viewing
@end itemize")
(license license:gpl3)))
(define-public vv
(package
(name "vv")
+105
View File
@@ -45,6 +45,7 @@
;;; Copyright © 2025 Junker <dk@junkeria.club>
;;; Copyright © 2025 Hugo Buddelmeijer <hugo@buddelmeijer.nl>
;;; Copyright © 2026 Carlos Durán Domínguez <wurt@wurt.eu>
;;; Copyright © 2026 Sughosha <sughosha@disroot.org>
;;;
;;; This file is part of GNU Guix.
;;;
@@ -1104,6 +1105,53 @@ images of initially unknown height.")
(license (list license:isc ; pbmtools/p?m.5
license:gpl2+)))) ; the rest
(define-public sjpeg
;; No tags available.
(let ((commit "46da5aec5fce05faabf1facf0066e36e6b1c4dff")
(revision "0"))
(package
(name "sjpeg")
(version (git-version "0" revision commit))
(source
(origin
(method git-fetch)
(uri (git-reference
(url "https://github.com/webmproject/sjpeg")
(commit commit)))
(file-name (git-file-name name version))
(sha256
(base32 "0r496mp2ylisspwxl4883pzbl0l8qpscd1x9l7sb5nnmknawr868"))))
(build-system cmake-build-system)
(arguments
(list
#:phases
#~(modify-phases %standard-phases
(add-after 'unpack 'patch-cmake
(lambda _
;; Enable building shared libraries.
(substitute* "CMakeLists.txt"
(("add_library\\(sjpeg " all)
(string-append all "SHARED ")))))
(add-before 'check 'patch-tests
(lambda _
(with-directory-excursion "../source/tests"
(substitute* '("test_cmd.sh" "test_png_jpg.sh")
(("\\.\\./examples") "../../build")))))
(replace 'check
(lambda* (#:key tests? #:allow-other-keys)
(when tests?
(with-directory-excursion "../source/tests"
(invoke "./test_cmd.sh")
(invoke "./test_png_jpg.sh"))))))))
(inputs (list freeglut libjpeg-turbo libpng zlib))
(home-page "https://github.com/webmproject/sjpeg")
(synopsis "Simple JPEG encoder")
(description
"sjpeg is a simple encoding library for encoding baseline JPEG files.
It is also a command-line tool that takes PNG or JPEG images as input to
produce JPEG files.")
(license license:asl2.0))))
(define-public openjpeg-data
(package
(name "openjpeg-data")
@@ -1180,6 +1228,63 @@ JPEG 2000 Reference Software.")
(home-page "https://github.com/uclouvain/openjpeg")
(license license:bsd-2)))
(define jp2k-test-codestreams
(origin
(method git-fetch)
(uri (git-reference
(url "https://github.com/aous72/jp2k_test_codestreams")
(commit "eda0844b9f3be47d9b64194bcea5eb1ac2285e39")))
(sha256
(base32 "1sci4a4dvgrgmrf942zdf0hqhcx30a5lffwfy6r3hya35l3q8q8f"))))
(define-public openjph
(package
(name "openjph")
(version "0.27.3")
(source
(origin
(method git-fetch)
(uri (git-reference
(url "https://github.com/aous72/OpenJPH")
(commit version)))
(file-name (git-file-name name version))
(sha256
(base32 "1knygwn4bf6n53qr12w05yava7464x3c70rf5r20sz8adjcfccvx"))))
(build-system cmake-build-system)
(arguments
(list
#:configure-flags
#~(if #$(%current-target-system)
'()
'("-DOJPH_BUILD_TESTS=ON"))
#:phases
#~(modify-phases %standard-phases
(add-after 'unpack 'patch-cmake
(lambda _
(substitute* "tests/CMakeLists.txt"
(("^FetchContent_MakeAvailable\\(googletest\\)")
#$(if (%current-target-system)
""
"find_package(GTest REQUIRED)"))
(("^FetchContent_MakeAvailable\\(jp2k_test_codestreams\\).*")
""))))
#$@(if (%current-target-system)
#~()
#~((add-before 'check 'unpack-jp2k-test-codestreams
(lambda _
(copy-recursively #$jp2k-test-codestreams
"tests/jp2k_test_codestreams"))))))))
(native-inputs (if (%current-target-system)
'()
(list googletest)))
(inputs (list libtiff))
(home-page "https://github.com/aous72/OpenJPH")
(synopsis "JPEG2000 Part-15 (or JPH or HTJ2K) implementation")
(description
"OpenJPH is an implementation of @acronym{HTJ2K, High-throughput JPEG2000},
also known as JPH, JPEG2000 Part 15, ISO/IEC 15444-15, and ITU-T T.814.")
(license license:bsd-2)))
(define-public openslide
(package
(name "openslide")
+9
View File
@@ -379,6 +379,15 @@ as the native format.")
;; Re-instate the tests disabled in inkscape/pinned, now that
;; their ImageMagick requirement is satisfied.
#~((replace 'check (assoc-ref gnu:%standard-phases 'check))))
#$@(if (or (target-aarch64?)
(target-ppc64le?)
(target-riscv64?))
'((add-after 'unpack 'disable-geom-pathstroke-test
(lambda _
;; https://gitlab.com/inkscape/lib2geom/-/work_items/80
(substitute* "testfiles/CMakeLists.txt"
((" geom-pathstroke-test") "")))))
'())
(replace 'wrap-program
;; Ensure Python is available at runtime.
(lambda _
+1 -1
View File
@@ -34,7 +34,7 @@
#:use-module (gnu packages elf)
#:use-module (gnu packages engineering)
#:use-module (gnu packages file)
#:use-module (gnu packages flex)
#:use-module (gnu packages compiler-tools)
#:use-module (gnu packages gawk)
#:use-module (gnu packages gcc)
#:use-module (gnu packages glib)
+1 -8
View File
@@ -58,7 +58,7 @@
#:use-module (gnu packages databases)
#:use-module (gnu packages docbook)
#:use-module (gnu packages ebook)
#:use-module (gnu packages flex)
#:use-module (gnu packages compiler-tools)
#:use-module (gnu packages freedesktop)
#:use-module (gnu packages gettext)
#:use-module (gnu packages gl)
@@ -326,13 +326,6 @@ surveys")
accessibility clients such as screen readers.")
(license license:lgpl2.1+)))
(define-public libqaccessibilityclient-qt5
(package
(inherit libqaccessibilityclient)
(name "libqaccessibilityclient-qt5")
(inputs (modify-inputs inputs
(replace "qtbase" qtbase-5)))))
(define-public qca
(package
(name "qca")
+1 -1
View File
@@ -57,7 +57,7 @@
#:use-module (gnu packages djvu)
#:use-module (gnu packages documentation)
#:use-module (gnu packages ebook)
#:use-module (gnu packages flex)
#:use-module (gnu packages compiler-tools)
#:use-module (gnu packages fontutils)
#:use-module (gnu packages freedesktop)
#:use-module (gnu packages fribidi)
+1 -1
View File
@@ -46,7 +46,7 @@
#:use-module (gnu packages cyrus-sasl)
#:use-module (gnu packages databases)
#:use-module (gnu packages documentation)
#:use-module (gnu packages flex)
#:use-module (gnu packages compiler-tools)
#:use-module (gnu packages freedesktop)
#:use-module (gnu packages geo)
#:use-module (gnu packages glib)

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