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Commit Graph

133829 Commits

Author SHA1 Message Date
Ricardo Wurmus
d97a67d41d gnu: homer: Install config.txt.
* gnu/packages/bioinformatics.scm (homer)[native-inputs]: Add config.txt.
[arguments]: Update 'configure phase to place config.txt in expected location;
patch configuration code to optionally load a user's configuration file.

Change-Id: Ib05c828e751c6568524bbef45997a42fade4545a
2024-12-02 13:41:08 +01:00
Ricardo Wurmus
af774e2780 gnu: homer: Install homer executable.
* gnu/packages/bioinformatics.scm (homer)[arguments]: Update 'install phase to
also install "homer" to the bin directory.

Change-Id: Ia2d23fce493f9c10cc43ac126cd83956b4b9bb05
2024-12-02 13:41:08 +01:00
Efraim Flashner
541abedc0a Merge remote-tracking branch 'origin/rust-team'
Change-Id: I6d5c28252f060eeb69eb02fd281e7268bb885b29
2024-12-02 14:13:39 +02:00
Efraim Flashner
b764dbc319 gnu: zstd: Fix cross-building to mingw32.
* gnu/packages/compression.scm (zstd)[arguments]: Adjust the custom
'adjust-library-locations phase to have separate logic for targeting
mingw32.  Adjust the make-flags to add some extra flags when targeting
mingw32.

Change-Id: Ifd32a6bd9157af93c7338dacc96467e2756b9314
2024-12-02 13:54:08 +02:00
Efraim Flashner
767bfcb45c gnu: redis: Add comment about upcoming license change.
* gnu/packages/databases.scm (redis): Add a note with the package to be
aware of the upcoming non-free license change.

Change-Id: I60ef9bce81b6650d88f567e98c5bcf543a13082e
2024-12-02 13:54:04 +02:00
Ricardo Wurmus
2756c660fb gnu: python-pairtools: Update to 1.1.0-fix.
* gnu/packages/bioinformatics.scm (python-pairtools): Update to 1.1.0-fix.
[build-system]: Use pyproject-build-system.
[arguments]: Add phase 'patch-setup.py.
[native-inputs]: Add python-pytest-cov, python-setuptools, and python-wheel.

Change-Id: Ifa3c12de228420d8fdd7b0053bb9da80b9b3efe4
2024-12-02 10:49:06 +01:00
Ricardo Wurmus
207c69e40d gnu: Add macs-3.
* gnu/packages/bioinformatics.scm (macs-3): New variable.

Change-Id: I4bc417e90a1e9d6d28226ea4f66ddc035826c2c4
2024-12-02 10:28:59 +01:00
Ricardo Wurmus
1f047996b8 gnu: python-hmmlearn: Update to 0.3.3.
* gnu/packages/machine-learning.scm (python-hmmlearn): Update to 0.3.3.
[build-system]: Use pyproject-build-system.
[arguments]: Remove custom 'check phase; add phases 'set-core-count and
'build-extensions.
[propagated-inputs]: Remove pybind11 and python-setuptools-scm.
[native-inputs]: Add pybind11, python-setuptools-scm, and util-linux.
[properties]: Add hints for the updater.

Change-Id: I1acb69c74ae9c4a508fe28cdaf834d258e7778ff
2024-12-02 10:28:59 +01:00
Ricardo Wurmus
30c2403a85 gnu: Add python-cykhash.
* gnu/packages/python-xyz.scm (python-cykhash): New variable.

Change-Id: I7f46da1f53b10957c102ca21e74f144955676730
2024-12-02 10:28:59 +01:00
Thanos Apollo
ca3a79ccee gnu: emacs-gnosis: Update to 0.4.8.
* gnu/packages/emacs-xyz.scm (emacs-gnosis): Update to 0.4.8.
[home-page]: Add ending slash.
[synopsis]: Remove ending period.
[description]: Use two spaces after sentence.

Change-Id: Ie80016fc190e66695b7a8ea8e3fded7854ebc872
Signed-off-by: Hilton Chain <hako@ultrarare.space>
2024-12-02 07:49:50 +08:00
Ian Eure
41fd9cfc65 gnu: librewolf: Update to 133.0-1 [security fixes].
New upstream version.  Fixes CVEs:

CVE-2024-11691: Out-of-bounds write in Apple GPU drivers via WebGL
CVE-2024-11700: Potential Tapjacking Exploit for Intent Confirmation
                on Android
CVE-2024-11692: Select list elements could be shown over another site
CVE-2024-11701: Misleading Address Bar State During Navigation
                Interruption
CVE-2024-11702: Inadequate Clipboard Protection in Private Browsing
                Mode on Android
CVE-2024-11693: Download Protections were bypassed by .library-ms
                files on Windows
CVE-2024-11694: CSP Bypass and XSS Exposure via Web Compatibility
                Shims
CVE-2024-11695: URL Bar Spoofing via Manipulated Punycode and
                Whitespace Characters
CVE-2024-11703: Password access without authentication via PIN bypass
                on Android
CVE-2024-11696: Unhandled Exception in Add-on Signature Verification
CVE-2024-11697: Improper Keypress Handling in Executable File
                Confirmation Dialog
CVE-2024-11704: Potential Double-Free Vulnerability in PKCS#7
                Decryption Handling
CVE-2024-11698: Fullscreen Lock-Up When Modal Dialog Interrupts
                Transition on macOS
CVE-2024-11705: Null Pointer Dereference in NSC_DeriveKey
CVE-2024-11706: Null Pointer Dereference in PKCS#12 Utility
CVE-2024-11708: Data race with PlaybackParams
CVE-2024-11699: Memory safety bugs fixed in Firefox 133, Firefox ESR
                128.5, and Thunderbird 128.5

* gnu/packages/librewolf.scm (librewolf): Update to 133.0-1.

Change-Id: I611505daf4d4f0940405190471f443d99102c2b9
Signed-off-by: Hilton Chain <hako@ultrarare.space>
2024-12-02 07:42:22 +08:00
Ian Eure
395abb86a6 gnu: nss-rapid: Update to 3.107.
* gnu/packages/nss.scm (nss-rapid): Update to 3.107.

Change-Id: I05c6e9c6633ed222d26b76ae5def35179f31f317
Signed-off-by: Hilton Chain <hako@ultrarare.space>
2024-12-02 07:42:22 +08:00
Hilton Chain
b91b992ed0 gnu: redis: Update to 7.2.6.
* gnu/packages/databases.scm (redis): Update to 7.2.6.
[arguments]<#:phases>: Update failing tests.

Change-Id: Ife107541697fda4f0928497560871f8ffb07d445
2024-12-02 07:42:20 +08:00
Ludovic Courtès
db59509931 gnu: git-minimal: Add ‘upstream-name’ property.
* gnu/packages/version-control.scm (git-minimal)[properties]: Add
‘upstream-name’.

Change-Id: I2d2516003b7f686852a3531859d06ca7f4e4820d
2024-12-01 20:14:16 +01:00
Ludovic Courtès
79be44fb51 gnu: gnutls: Change release monitoring URL.
* gnu/packages/tls.scm (gnutls)[properties]: Change release monitoring
URL.  Add ‘upstream-name’.

Change-Id: If6ee941246b130914ddf7ca11c074a9547b9d739
2024-12-01 20:14:16 +01:00
Ludovic Courtès
2227a6b084 gnu: Update updater properties for GnuPG-related packages.
* gnu/packages/gnupg.scm (libgpg-error)[properties]: Remove.
(libgcrypt)[properties]: Remove.
(libassuan)[properties]: Remove.
(libksba)[properties]: Remove.
(npth)[properties]: Remove.
(gnupg)[properties]: Remove.
(gpgme)[properties]: Remove.
(pinentry-tty)[properties]: Change for ‘generic-html’.
(gpa)[properties]: Remove.

Change-Id: I1eb9d6ad5bb3ecbfbef3d44dbae281a3de7ebac7
2024-12-01 20:14:15 +01:00
Ludovic Courtès
4b5dae8def packages: Factorize ‘all-packages’.
* gnu/packages.scm (all-packages): New procedure.
* etc/source-manifest.scm (all-packages): Remove.
* guix/scripts/graph.scm (all-packages): Remove.
* guix/scripts/refresh.scm (all-packages): Remove.
* guix/scripts/weather.scm (all-packages): Remove.

Change-Id: I6072952c4b877b541037ce86402cfb7744eeb0a0
2024-12-01 20:14:15 +01:00
Efraim Flashner
85743578bc gnu: ucx: Enable building on riscv64-linux.
* gnu/packages/fabric-management.scm (ucx)[supported-systems]: Add
riscv64-linux.

Change-Id: I84d506c3ebfd8d4d237a6545ba125f4a037fa821
2024-12-01 19:58:10 +02:00
Efraim Flashner
d767459ba3 gnu: ucx: Fix building on powerpc64le-linux.
* gnu/packages/fabric-management.scm (ucx)[source]: Add snippet to add
missing include file.

Change-Id: I65a0d6e57a2728013030f3f344305744fa913390
2024-12-01 19:57:10 +02:00
Herman Rimm
2348283dab bootloader: u-boot: Add procedure to share installer code.
* gnu/bootloader/u-boot.scm (make-u-boot-installer): Add procedure.
(install-u-boot-ts7970-q-2g-1000mhz-c-u-boot,
install-qemu-riscv64-u-boot): Remove variables.
(install-starfive-visionfive2-uEnv.txt,
u-boot-ts7970-q-2g-1000mhz-c-bootloader,
u-boot-qemu-riscv64-bootloader): Use make-u-boot-installer.

Change-Id: I0b0b507925a7c8ca608f7307d442d9588862ae91
Signed-off-by: Ludovic Courtès <ludo@gnu.org>
2024-12-01 17:56:00 +01:00
Herman Rimm
ca748392ce bootloader: grub: Add procedure to share EFI installer code.
* gnu/bootloader/grub.scm (make-grub-efi-bootloader): Add procedure.
(install-grub-efi, install-grub-efi32): Remove variables.
(install-grub-efi-removable): Deprecate variable.

Change-Id: Ie10b506bb1088179d459ddafe3229fd730ac45aa
Signed-off-by: Ludovic Courtès <ludo@gnu.org>
2024-12-01 17:55:56 +01:00
Ludovic Courtès
15647355e5 gnu: openmpi@5: Update to 5.0.6.
* gnu/packages/mpi.scm (openmpi-5): Update to 5.0.6.

Change-Id: I1aed5f0e76d64a215c4a13f445628ec206e31acf
2024-12-01 17:48:20 +01:00
Ludovic Courtès
db1d75b9fd gnu: rdma-core: Update to 54.0.
* gnu/packages/linux.scm (rdma-core): Update to 54.0.

Change-Id: I7f10ec57a1cad585abb08bdc30bd9e2aaafe7624
2024-12-01 17:48:15 +01:00
Ludovic Courtès
8ba6651d39 gnu: ucx: Update to 1.17.0.
* gnu/packages/fabric-management.scm (ucx): Update to 1.17.0.
* gnu/packages/patches/ucx-tcp-iface-ioctl.patch: Rebase.

Change-Id: I2089de93da88f4f81c4b233eb03abae1f41dfe7f
2024-12-01 17:48:11 +01:00
Ludovic Courtès
c25fd8eeb1 Revert "gnu: ucx: Update to 1.17.0."
This reverts commit 7c36577cde, which
broke unit tests running in the chroot build environment.

For instance, tests of ‘hdf5-parallel-openmpi’ would fail with:

  Testing ../../src/h5diff/ph5diff -c 1_vds.h5 2_vds.h5                 *FAILED*
  ====Expected result (expect_sorted) differs from actual result (actual_sorted)
      *** expect_sorted	2024-12-01 16:41:03.795879595 +0000
      --- actual_sorted	2024-12-01 16:41:03.791879542 +0000
      ***************
      *** 1,3 ****
      --- 1,15 ----
	Not comparable: </vds_dset> has rank 3, dimensions [5x18x8], max dimensions [18446744073709551615x18x8]
	Warning: </vds_dset> or </vds_dset> is a virtual dataset
      + [1733071262.437780] [localhost:33263:0]       tcp_iface.c:893  UCX  ERROR scandir(/sys/class/net) failed: No such file or directory
      + [1733071262.468994] [localhost:33247:0]       tcp_iface.c:893  UCX  ERROR scandir(/sys/class/net) failed: No such file or directory
      + [1733071262.479911] [localhost:33242:0]       tcp_iface.c:893  UCX  ERROR scandir(/sys/class/net) failed: No such file or directory

Change-Id: I9c08d3c5375a2abd7d78344dfbef9b407828d1e0
2024-12-01 17:46:43 +01:00
Jonathan Brielmaier
4f6e9c7de1 gnu: icedove: Update to 115.16.3.
* gnu/packages/gnuzilla.scm (icedove): Update to 115.16.3.

Change-Id: I076e670a5442a910ac6d5aeb7ed8f64236442062
2024-12-01 14:12:33 +01:00
Efraim Flashner
1bcf1a0146 gnu: openmpi-5: Don't force building with ucx.
* gnu/packages/mpi.scm (openmpi-5)[inputs]: Use inherited inputs to only
add ucx when it is supported.
[arguments]: Only add configure-flag for ucx when it is included as an
input.

Change-Id: I4a5fc86999ffbafdb99bd68c170fc7a1fa6a33a5
2024-12-01 14:55:08 +02:00
Efraim Flashner
7c36577cde gnu: ucx: Update to 1.17.0.
* gnu/packages/mpi.scm (ucx): Update to 1.17.0.
[source]: Remove patch.  Add snippet to add missing header.
[supported-systems]: Add riscv64-linux.
* gnu/packages/patches/ucx-tcp-iface-ioctl.patch: Remove file.
* gnu/local.mk (dist_patch_DATA): Remove it.

Change-Id: I56db18f32ec0baa8439a31a1781763f318e8726e
2024-12-01 14:55:08 +02:00
Efraim Flashner
0aae7c333d gnu: libfabric: Check for transitive supported packages.
* gnu/packages/linux.scm (libfabric)[inputs]: Adjust if-supported
function to check the package-transitive-supported-systems.

Change-Id: I47d14b08906753d20f6f2a7ab4068a9e84319350
2024-12-01 14:55:08 +02:00
Efraim Flashner
2790f7b437 gnu: cassini-headers: Limit supported systems.
* gnu/packages/linux.scm (cassini-headers)[supported-systems]: New field.

Change-Id: I44efa95de527099774abb57da78410c627fdc968
2024-12-01 14:55:04 +02:00
Josep Bigorra
d08c219b4a gnu: Add scenefx.
* gnu/packages/wm.scm (scenefx): New variable.

Signed-off-by: Zheng Junjie <zhengjunjie@iscas.ac.cn>
Change-Id: Ia91747cbec59226a83a020b5fedbfd99886c35df
2024-12-01 19:04:50 +08:00
Lynn Leichtle
af13915b28 gnu: cataclysm-dda: Update to 0-H.
* gnu/packages/games.scm (cataclysm-dda): Update to 0.H.

Signed-off-by: Zheng Junjie <zhengjunjie@iscas.ac.cn>
Change-Id: I8f3776b1bbb4ead2d409b2e1a3c4c98537126f12
2024-12-01 19:04:26 +08:00
Zheng Junjie
ff3c9fd5e3 gnu: plasma-nm: Add missing inputs.
* gnu/packages/kde-plasma.scm (plasma-nm)[inputs]: Add
mobile-broadband-provider-info.
[arguments]: Stop replace 'check phase.

Change-Id: I82b220694e26b48f190c1c5d6609da39e955cc30
2024-12-01 18:15:07 +08:00
Sergey Trofimov
e5c1a708f5 gnu: geoclue: Update to 2.7.2.
* gnu/packages/gnome.scm (geoclue): Update to 2.7.2.
* gnu/packages/patches/geoclue-config.patch: Adjust.

Reviewed-by: Maxim Cournoyer <maxim.cournoyer@gmail.com>
Signed-off-by: Liliana Marie Prikler <liliana.prikler@gmail.com>
2024-12-01 10:55:53 +01:00
Liliana Marie Prikler
d1dd176af5 gnu: gimp-next: Update to 3.0.0-RC1.
* gnu/packages/gimp.scm (gimp-next): Update to 3.0.0-RC1.
[inputs]: Add python-pygobject.

Reviewed-by: Maxim Cournoyer <maxim.cournoyer@gmail.com>
2024-12-01 10:55:53 +01:00
Liliana Marie Prikler
70caf73108 gnu: gegl: Update to 0.4.50.
* gnu/packages/gimp.scm (gegl): Update to 0.4.50.

Reviewed-by: Maxim Cournoyer <maxim.cournoyer@gmail.com>
2024-12-01 10:55:53 +01:00
Liliana Marie Prikler
011dbaedb5 gnu: babl: Update to 0.1.110.
* gnu/packages/gimp.scm (babl): Update to 0.1.110.

Reviewed-by: Maxim Cournoyer <maxim.cournoyer@gmail.com>
2024-12-01 10:55:52 +01:00
Ricardo Wurmus
c5b16964bb gnu: r-voltron: Add Python inputs.
* gnu/packages/bioinformatics.scm (r-voltron)[inputs]: Add python,
python-numpy, python-pandas, python-anndata, python-h5py, python-natsort,
python-numcodecs, python-packaging, python-scipy, python-tifffile, and
python-zarr.

Change-Id: Iab137936550b51d6839d9beaa47f6102a8f3c355
2024-12-01 10:41:35 +01:00
Ricardo Wurmus
c7e412e775 gnu: r-voltron: Update to 0.2.0-1.9f9415c.
* gnu/packages/bioinformatics.scm (r-voltron): Update to 0.2.0-1.9f9415c.
[inputs]: Remove tbb.
[propagated-inputs]: Remove r-anndata, r-fastdummies, r-fnn, r-ggforce,
r-hdf5r, r-htmltools, r-interp, r-morpho, r-raster, r-s4vectors, r-scales,
r-terra, r-umap, and r-xml; add r-basilisk, r-ids, r-rann, r-rcdt,
r-rcppannoy, r-rcpparmadillo, r-reticulate, r-s4arrays, and r-sp.
[native-inputs]: Add r-testthat.
[description]: Update.

Change-Id: I8051ade560e03f8e3760560ec7b78d9941c00e08
2024-12-01 10:26:38 +01:00
Ricardo Wurmus
5531485c5d gnu: Add r-rcdt.
* gnu/packages/cran.scm (r-rcdt): New variable.

Change-Id: I83b00c95f2c3c6f82e9e9cf8f173ba087e1c29e0
2024-12-01 10:26:38 +01:00
Ricardo Wurmus
f228b01738 gnu: Add r-colorsgen.
* gnu/packages/cran.scm (r-colorsgen): New variable.

Change-Id: I1acb2b0dd2661a5abdb59451522da6dffa85f470
2024-12-01 10:26:38 +01:00
Sharlatan Hellseher
5725688923 gnu: imppg: Disable tests on non x86_64 architectures.
Tests regretion after update to the latest version as seen in CI log
<https://ci.guix.gnu.org/build/6720267/log/raw>.

* gnu/packages/astronomy.scm (imppg) [arguments]<test-flags>: Silent
tests on non x86_64 architectures, report upstream as well.

Change-Id: I875350ac60dc2f6a72eb1216a614d8943d41f9ed
2024-12-01 08:58:22 +00:00
Zheng Junjie
f4831760a9 gnu: weechat: Switch to git source.
* gnu/packages/irc.scm (weechat)[source]: Use git-fetch.

Change-Id: I031d494db1b7c273bc87d0bdb21ee51c2c3ae10b
2024-12-01 16:03:57 +08:00
Zheng Junjie
f9c3a6dd2a gnu: weechat: Improve style.
* gnu/packages/irc.scm (weechat)[native-inputs]: Remove label.
[arguments]: Use G-expressions.

Change-Id: I08e2f4135760e61acbae915f045fb3838d965b25
2024-12-01 16:03:57 +08:00
Ashish SHUKLA
0cd8edf926 gnu: weechat: Update to 4.4.4.
* gnu/packages/irc.scm (weechat): Update to 4.4.4.

Change-Id: I08c120df160c3ff7095f2418fe9f9553df3abe3c
Signed-off-by: Zheng Junjie <zhengjunjie@iscas.ac.cn>
2024-12-01 16:03:57 +08:00
Zheng Junjie
db2b0d7df0 gnu: lftp: Use G-expressions.
* gnu/packages/ftp.scm (lftp)[arguments]: Use G-expressions.

Change-Id: I504465e7604d9638442b063753a8cf8abf3616a9
2024-12-01 16:03:57 +08:00
Ashish SHUKLA
f45aae2287 gnu: lftp: Update to 4.9.3.
The updated information is sourced from the upstream repository at
GitHub: https://github.com/lavv17/lftp

* gnu/packages/ftp.scm (lftp): Update to 4.9.3.
[source]<origin>: Switch to git upstream.
[native-inputs]: Add autoconf, automake, gettext-minimal, bison, gnulib,
gperf, and libtool.
[arguments]<#:phases>: Add unpack-gnulib phase. Delete existing bootstrap
phase. Add new bootstrap phase to invoke it after patch-source-shebangs.
[home-page]: Update it.

Change-Id: I73771ed7e577da4bc82a8e74550eca83413dc8de
Signed-off-by: Zheng Junjie <zhengjunjie@iscas.ac.cn>
2024-12-01 16:03:57 +08:00
Nicolas Graves
2dc38e493b gnu: b4: Fix git binary access.
* gnu/packages/version-control.scm (b4)[arguments]<#:phases>: Fix
phase 'hardcode-git-bin.

Signed-off-by: Zheng Junjie <zhengjunjie@iscas.ac.cn>
2024-12-01 16:03:57 +08:00
Zheng Junjie
db8a0b480a gnu: wget2: Use G-expressions.
* gnu/packages/wget.scm (wget2): Use G-expressions.

Change-Id: I8fbb5bab0746c5c98d2513fb31936ba56a8b7049
2024-12-01 16:03:54 +08:00
Ricardo Wurmus
adfda4a075 gnu: pigx-scrnaseq: Update to 1.1.10.
* gnu/packages/bioinformatics.scm (pigx-scrnaseq): Update to 1.1.10.
[arguments]: Remove quasiquote.

Change-Id: I6cab358addfb376a878929bfb5041edc00cd336a
2024-12-01 08:52:51 +01:00