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Author SHA1 Message Date
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