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140998 commits

Author SHA1 Message Date
guix-patches--- via
bcdd77177b
gnu: Add zydis.
* gnu/packages/engineering.scm (zydis): New variable.

Change-Id: I6e0b04e1d957f8c172e81177f6669415beeaf20a
Signed-off-by: Zheng Junjie <zhengjunjie@iscas.ac.cn>
2024-08-19 13:36:55 +08:00
guix-patches--- via
724960a264
gnu: Add zycore.
* gnu/packages/engineering.scm (zycore): New variable.

Change-Id: Ia38413f43bc667a9a12916d3f0e786e06f6d358f
Signed-off-by: Zheng Junjie <zhengjunjie@iscas.ac.cn>
2024-08-19 13:36:55 +08:00
Zheng Junjie
734e83d4fa
gnu: chrony: Fix cross-compilation.
* gnu/packages/ntp.scm (chrony)[arguments]<#:phases>: Add set-CC phase.

Change-Id: I0bc7c271875c5ba68743583fb3932e238b3b37c0
2024-08-19 13:36:55 +08:00
Artyom V. Poptsov
77c4c02d41
gnu: chrony: Update to 4.5.
* gnu/packages/ntp.scm (chrony): Update to 4.5.
  [source]: Download from GitLab as the original site is not accessible
  anymore.
  [native-inputs]: Add "bison" and "ruby-asciidoctor".
  [synopsis]: Fix a typo.
  [description]: Improve formatting.
  [home-page]: Change to "https://chrony-project.org/".

Change-Id: I33b053fff0aced37cefab9f3c5df44fe2b9abb0c
Signed-off-by: Zheng Junjie <zhengjunjie@iscas.ac.cn>
2024-08-19 13:36:52 +08:00
Nikola
58a839273d
gnu: at-spi2-core: Remove unnecessary test timeout.
Guix provides its own superior-quality time-outs.

* gnu/packages/gtk.scm (at-spi2-core)[arguments]: Remove the
‘timeout’ argument from the test invocation.

Change-Id: Ic324c5992d48cafa4b6b9856b381d461083d8de2
Signed-off-by: Tobias Geerinckx-Rice <me@tobias.gr>
2024-08-18 02:00:00 +02:00
Jonathan Brielmaier
b1b3724996
gnu: icedove-minimal: Add StartupWMClass.
Fixes https://issues.guix.gnu.org/69267

* gnu/packages/gnuzilla.scm (icedove-minimal)[arguments]: Set
MOZ_APP_REMOTINGNAME and StartupWMClass.

Change-Id: Ibf334c2d840a49aa7ec84da44eceecd85cb3bcd2
2024-08-18 22:18:18 +02:00
Jonathan Brielmaier
25c3534f54
gnu: icedove. Update to 115.14.0.
* gnu/packages/gnuzilla.scm (%icedove-version): Update to 115.14.0.

Change-Id: I7564b525059f6c26beeee4bf9514fa38cc2aaa58
2024-08-18 22:18:18 +02:00
Jonathan Brielmaier
e20abffb2b
gnu: icedove-wayland: Use icedove-minimal instead of icedove.
`icedove` does currently not built.

* gnu/packages/gnuzilla.scm (icedove-wayland): Use `icedove-minimal` instead of
`icedove`.

Change-Id: Idc01d6a93071cff11ef139e6738aff1c7687d975
2024-08-18 22:18:18 +02:00
Jonathan Brielmaier
fa5929cd3f
gnu: icedove: Update to 115.10.1.
* gnu/packages/gnuzilla.scm (all-mozilla-102-locales,
%icecat-102-base-version, %icecat-102-version, icecat-102-source):
Remove variables.
(%icedove-build-id, %icedove-version, thunderbird-comm-source): Update for 115.10.1.
(thunderbird-comm-l10n): Switch to provided tarball.
(icedove-source)[origin]: Add `zstd` package. Use `icecat-source`.
Provide l10n folder from tarball.
(icedove-minimal)[arguments]: Use MACH_BUILD_PYTHON_NATIVE_PACKAGE_SOURCE instead
of deprecated MACH_USE_SYSTEM_PYTHON. Use GUIX_PYTHONPATH and bundled
NSS library.
[inputs]: Use `icu4c-73`. Add `nspr`. Remove `nss` for now.
[native-inputs]: Update clang and llvm to version 15. Use newer
`node-lts`.
(make-l10n-package)[arguments]: Set GUIX_PYTHONPATH.

Change-Id: Ie6d9eb00f609c9872ac985adec72da92ee4be336
2024-08-18 22:18:18 +02:00
Jonathan Brielmaier
15a96bd6e9
gnu: icu4c: Add patch for VTIMEZONE bug.
Icedove@115 does not properly work without this patch. See:
https://bugzilla.mozilla.org/show_bug.cgi?id=1843007

* gnu/packages/icu4c.scm (icu4c-73)[source]: Use patch.
* gnu/packages/patches/icu4c-icu-22132-fix-vtimezone.patch: New file.
* gnu/local.mk (dist_patch_DATA): Register patch.
Change-Id: Ie64d1e33afedbaedbaafaeb607a201eb671ac7bd

Change-Id: I6d753eacc7daac5663128b20a550044d0fd0ddb7
2024-08-18 22:18:18 +02:00
Ricardo Wurmus
41c44ffd56
gnu: r-dmrseq: Update to 1.24.1.
* gnu/packages/bioconductor.scm (r-dmrseq): Update to 1.24.1.

Change-Id: I22fb49eee056e0dd5306fec4575fcb38cbe916aa
2024-08-17 21:54:22 +02:00
Ricardo Wurmus
8bb976d4d6
gnu: r-bgeecall: Update to 1.20.1.
* gnu/packages/bioconductor.scm (r-bgeecall): Update to 1.20.1.
[propagated-inputs]: Add r-txdbmaker.

Change-Id: Ia51c1ccdb0e49d8dc74a61f605f00c86718bc1f8
2024-08-17 21:54:22 +02:00
Ricardo Wurmus
2e65b4811e
gnu: r-mscoreutils: Update to 1.16.1.
* gnu/packages/bioconductor.scm (r-mscoreutils): Update to 1.16.1.

Change-Id: I233a01625f223c571dae863c977825d4a2909ee7
2024-08-17 21:54:22 +02:00
Ricardo Wurmus
775ba94a50
gnu: r-scater: Update to 1.32.1.
* gnu/packages/bioconductor.scm (r-scater): Update to 1.32.1.

Change-Id: I0232d463f243505a9b3706d64e6666eb245ceb1c
2024-08-17 21:54:22 +02:00
Ricardo Wurmus
aa08111f38
gnu: r-hdf5array: Update to 1.32.1.
* gnu/packages/bioconductor.scm (r-hdf5array): Update to 1.32.1.

Change-Id: Iebab45185f6f1fe3e6919a1e70e45127d9f1124f
2024-08-17 21:54:22 +02:00
Ricardo Wurmus
7e83109d92
gnu: r-s4vectors: Update to 0.42.1.
* gnu/packages/bioconductor.scm (r-s4vectors): Update to 0.42.1.

Change-Id: I58dc50344c5eb477da9d4ddd4447bcb41f456037
2024-08-17 21:54:22 +02:00
Ricardo Wurmus
1d475e94d4
gnu: r-multiassayexperiment: Update to 1.30.3.
* gnu/packages/bioconductor.scm (r-multiassayexperiment): Update to 1.30.3.

Change-Id: Iabbd0c74d7515f8f166827b8b99b2ac49b271c13
2024-08-17 21:54:21 +02:00
Ricardo Wurmus
2a88a148fc
gnu: r-universalmotif: Update to 1.22.1.
* gnu/packages/bioconductor.scm (r-universalmotif): Update to 1.22.1.

Change-Id: I60a617d120e5da046decb491b7641f1e10aac0cb
2024-08-17 21:54:21 +02:00
Ricardo Wurmus
32a3206b4b
gnu: r-clusterprofiler: Update to 4.12.2.
* gnu/packages/bioconductor.scm (r-clusterprofiler): Update to 4.12.2.

Change-Id: I17d837fb314c26fcb26c13240a01c91bc2da9797
2024-08-17 21:54:21 +02:00
Ricardo Wurmus
91a56bc013
gnu: r-enrichplot: Update to 1.24.2.
* gnu/packages/bioconductor.scm (r-enrichplot): Update to 1.24.2.

Change-Id: I188e7e908a09337d4bacf4802b1557ddd31048f3
2024-08-17 21:54:21 +02:00
Ricardo Wurmus
ad1acb8114
gnu: r-dose: Update to 3.30.2.
* gnu/packages/bioconductor.scm (r-dose): Update to 3.30.2.

Change-Id: Ic07fab82efcbda004d6c7ff21d4ed7b49cc426fb
2024-08-17 21:54:21 +02:00
Ricardo Wurmus
7079d13d04
gnu: r-chippeakanno: Update to 3.38.1.
* gnu/packages/bioconductor.scm (r-chippeakanno): Update to 3.38.1.

Change-Id: Ia4c89074674f3473e11f3b9e1f9ed828701591f6
2024-08-17 21:54:21 +02:00
Ricardo Wurmus
efb25a259a
gnu: r-qfeatures: Update to 1.14.2.
* gnu/packages/bioconductor.scm (r-qfeatures): Update to 1.14.2.

Change-Id: I93c4fc00d19b18a1e0981f21dd0950d1e1a81f37
2024-08-17 21:54:21 +02:00
Ricardo Wurmus
20134ae2e4
gnu: r-seqarray: Update to 1.44.1.
* gnu/packages/bioconductor.scm (r-seqarray): Update to 1.44.1.

Change-Id: I06bb0b45d1a4299e835f7a18c7ed70d847bdb565
2024-08-17 21:54:21 +02:00
Ricardo Wurmus
f74e27f072
gnu: r-msa: Update to 1.36.1.
* gnu/packages/bioconductor.scm (r-msa): Update to 1.36.1.

Change-Id: I91665d8ff4cd7570b5bcad27ff132611a09b8ecc
2024-08-17 21:54:21 +02:00
Ricardo Wurmus
2a1a1738dd
gnu: r-limma: Update to 3.60.4.
* gnu/packages/bioconductor.scm (r-limma): Update to 3.60.4.

Change-Id: Iaaf9317ab3921070f5b8e06a7948b42575bbe00b
2024-08-17 21:54:21 +02:00
Ricardo Wurmus
0e0b349f6b
gnu: r-raggedexperiment: Update to 1.28.1.
* gnu/packages/bioconductor.scm (r-raggedexperiment): Update to 1.28.1.

Change-Id: If7e8b60435413acda999f055bf9f104929e7f50f
2024-08-17 21:54:21 +02:00
Ricardo Wurmus
43b84eeb84
gnu: r-edger: Update to 4.2.1.
* gnu/packages/bioconductor.scm (r-edger): Update to 4.2.1.

Change-Id: Ia8cb57ada3f036f7fe45972ad1d3a8ff2e53c27b
2024-08-17 21:54:21 +02:00
Ricardo Wurmus
e00e778eee
gnu: r-iranges: Update to 2.38.1.
* gnu/packages/bioconductor.scm (r-iranges): Update to 2.38.1.

Change-Id: I95d34fb3f339590c1980b7a77093835baa0e0136
2024-08-17 21:54:21 +02:00
Ricardo Wurmus
defb0e7676
gnu: r-dmrcate: Update to 3.0.5.
* gnu/packages/bioconductor.scm (r-dmrcate): Update to 3.0.5.

Change-Id: I88768682f65b821e188f29c4dfee94927040cbbd
2024-08-17 21:54:21 +02:00
Ricardo Wurmus
2dff160f09
gnu: r-degreport: Update to 1.40.1.
* gnu/packages/bioconductor.scm (r-degreport): Update to 1.40.1.

Change-Id: I35e7284270c81cd10178e7d848dfa5872645405d
2024-08-17 21:54:21 +02:00
Ricardo Wurmus
8d988b6bea
gnu: r-anvil: Update to 1.16.1.
* gnu/packages/bioconductor.scm (r-anvil): Update to 1.16.1.

Change-Id: Ief1b321d44a3bd534c6107c4434957c0de2dd977
2024-08-17 21:54:21 +02:00
Ricardo Wurmus
ef08d1330d
gnu: r-desctools: Update to 0.99.55.
* gnu/packages/statistics.scm (r-desctools): Update to 0.99.55.

Change-Id: Ic6b6222e1702db59786ad2ab73645425645575a1
2024-08-17 21:54:21 +02:00
Ricardo Wurmus
ea717b12d3
gnu: r-exact: Update to 3.3.
* gnu/packages/statistics.scm (r-exact): Update to 3.3.

Change-Id: If388135e98d31308d6d6170f30038ea9b44c994f
2024-08-17 21:54:21 +02:00
Ricardo Wurmus
8c0709893b
gnu: r-lme4: Update to 1.1-35.5.
* gnu/packages/statistics.scm (r-lme4): Update to 1.1-35.5.

Change-Id: I886898d0158ba4a6d29e61e8a19a280ce387ee2e
2024-08-17 21:54:21 +02:00
Ricardo Wurmus
811ba5c0de
gnu: r-rcppeigen: Update to 0.3.4.0.1.
* gnu/packages/statistics.scm (r-rcppeigen): Update to 0.3.4.0.1.

Change-Id: I4b7b3569c414d57a1af788fedcdaaf1e59e42fe7
2024-08-17 21:54:21 +02:00
Ricardo Wurmus
92e07c893e
gnu: r-pcapp: Update to 2.0-4-1.
* gnu/packages/statistics.scm (r-pcapp): Update to 2.0-4-1.

Change-Id: I7a08f67e636843e36bc80af0d94778f6d2b202d6
2024-08-17 21:54:21 +02:00
Ricardo Wurmus
595667be4d
gnu: r-sparsem: Update to 1.84-2.
* gnu/packages/statistics.scm (r-sparsem): Update to 1.84-2.

Change-Id: Id2123705c08bab173a4c8da3029e9bbda4db3ceb
2024-08-17 21:54:21 +02:00
Ricardo Wurmus
864e9d4e03
gnu: r-segmented: Update to 2.1-1.
* gnu/packages/statistics.scm (r-segmented): Update to 2.1-1.

Change-Id: I754caaac1fca6903103b3c36f3d4894350c9a63d
2024-08-17 21:54:21 +02:00
Ricardo Wurmus
30b84babc9
gnu: r-rcurl: Update to 1.98-1.16.
* gnu/packages/statistics.scm (r-rcurl): Update to 1.98-1.16.

Change-Id: I7c1570708479711e32a98e586cf51ddf7958e4b6
2024-08-17 21:54:20 +02:00
Ricardo Wurmus
bb4b4782d7
gnu: r-bitops: Update to 1.0-8.
* gnu/packages/statistics.scm (r-bitops): Update to 1.0-8.

Change-Id: I0f5e97d07097a0ec13cce1b1d61e4633cdb9cd70
2024-08-17 21:54:20 +02:00
Ricardo Wurmus
df62a81202
gnu: r-rcpparmadillo: Update to 14.0.0-1.
* gnu/packages/statistics.scm (r-rcpparmadillo): Update to 14.0.0-1.

Change-Id: I9594cab48497f4767b2f5435828057704efdb01f
2024-08-17 21:54:20 +02:00
Ricardo Wurmus
dc2c1bd1d9
gnu: r-withr: Update to 3.0.1.
* gnu/packages/statistics.scm (r-withr): Update to 3.0.1.

Change-Id: Ic9302091cacb203a3d6e45183c871ba12276e3ba
2024-08-17 21:54:20 +02:00
Ricardo Wurmus
e4bc7819d6
gnu: r-openssl: Update to 2.2.1.
* gnu/packages/statistics.scm (r-openssl): Update to 2.2.1.

Change-Id: Id279140de607eb0f8324ab2e38ce248398110979
2024-08-17 21:54:20 +02:00
Ricardo Wurmus
56e6495adc
gnu: r-checkmate: Update to 2.3.2.
* gnu/packages/statistics.scm (r-checkmate): Update to 2.3.2.

Change-Id: I8dbd8ed86a5cc652da180c1bac951abc7ba82fb5
2024-08-17 21:54:20 +02:00
Ricardo Wurmus
4524ade9d5
gnu: r-knitr: Update to 1.48.
* gnu/packages/statistics.scm (r-knitr): Update to 1.48.

Change-Id: I87ec28f830230f8fd51f7a2701a6bc83c14bd3b6
2024-08-17 21:54:20 +02:00
Ricardo Wurmus
fbbf69f501
gnu: r-yaml: Update to 2.3.10.
* gnu/packages/statistics.scm (r-yaml): Update to 2.3.10.

Change-Id: I64802f3c68be2498ea48755608ddf55dc3adae3e
2024-08-17 21:54:20 +02:00
Ricardo Wurmus
bb8bab522a
gnu: r-nlme: Update to 3.1-166.
* gnu/packages/statistics.scm (r-nlme): Update to 3.1-166.

Change-Id: I7df0e68f3e685acb145d3c07f9de14ee1ab141a6
2024-08-17 21:54:20 +02:00
Ricardo Wurmus
5520c9e8d1
gnu: r-webmockr: Update to 1.0.0.
* gnu/packages/cran.scm (r-webmockr): Update to 1.0.0.

Change-Id: I732b25faa1d2cc6cf17fb8c9dfb9dbc7f194c0d9
2024-08-17 21:54:20 +02:00
Ricardo Wurmus
d9064cd6f6
gnu: r-crul: Update to 1.5.0.
* gnu/packages/cran.scm (r-crul): Update to 1.5.0.

Change-Id: Ic25ca2096424aa624eca983b68f622240e212b0a
2024-08-17 21:54:20 +02:00