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Author SHA1 Message Date
Ricardo Wurmus 63e9dc40c9
gnu: r-seurat: Update to 5.1.0.
* gnu/packages/cran.scm (r-seurat): Update to 5.1.0.

Change-Id: I070c848853e26c3b8c031e92ef24f39b08962348
2024-05-13 22:27:37 +02:00
Ricardo Wurmus 336e3ad957
gnu: r-imager: Update to 1.0.2.
* gnu/packages/cran.scm (r-imager): Update to 1.0.2.

Change-Id: I678a384037c4c265d2a2b06f2b3b8013abb6d017
2024-05-13 22:27:37 +02:00
Ricardo Wurmus 6d7d9513e3
gnu: r-farver: Update to 2.1.2.
* gnu/packages/cran.scm (r-farver): Update to 2.1.2.

Change-Id: Ic73015b3cd86c9cbaceedf6a721db8d6fe825c6c
2024-05-13 22:27:37 +02:00
Ricardo Wurmus ec14825484
gnu: r-options: Update to 0.2.0.
* gnu/packages/cran.scm (r-options): Update to 0.2.0.

Change-Id: Ia011d3fb5295a58ea49396b090186beae2bab575
2024-05-13 22:27:37 +02:00
Ricardo Wurmus c590b6f1cc
gnu: r-polspline: Update to 1.1.25.
* gnu/packages/cran.scm (r-polspline): Update to 1.1.25.

Change-Id: I0fb7c7912036cff5fd56d577cf29a464e34a2775
2024-05-13 22:27:37 +02:00
Ricardo Wurmus f8bf75b1c9
gnu: r-qlcmatrix: Update to 0.9.8.
* gnu/packages/cran.scm (r-qlcmatrix): Update to 0.9.8.
[native-inputs]: Add r-knitr and r-rmarkdown.

Change-Id: I08e55b72ffacf17b41c895801d6cbdad52658e6b
2024-05-13 22:27:37 +02:00
Ricardo Wurmus adf2088ca5
gnu: r-effectsize: Update to 0.8.8.
* gnu/packages/cran.scm (r-effectsize): Update to 0.8.8.

Change-Id: I51270018adaf62fdbcb3e5ad73b99f618b346b9a
2024-05-13 22:27:37 +02:00
Ricardo Wurmus 7744aaf2b0
gnu: r-insight: Update to 0.19.11.
* gnu/packages/cran.scm (r-insight): Update to 0.19.11.

Change-Id: I3cb8ef7e28309d542cb30d993264cc79811b8d59
2024-05-13 22:27:37 +02:00
Tomas Volf b8c0bdea4e
gnu: cgit: Update to 1.2.3-3.dbadd85.
* gnu/packages/version-control.scm (cgit): Update to 1.2.3-3.dbadd85.

Change-Id: I41827d1d97f28be71af5532b554d6b7a5e1123cc
Signed-off-by: Christopher Baines <mail@cbaines.net>
2024-05-13 19:31:20 +01:00
Zheng Junjie a5455ed672
gnu: fcitx5-configtool: Remove inputs label.
* gnu/packages/fcitx5.scm (fcitx5-configtool)
[inputs]: Remove label.

Change-Id: Ib45fbf71d5f2ffbac3285e388629b6cf0ca004fe
Signed-off-by: Christopher Baines <mail@cbaines.net>
2024-05-13 19:31:20 +01:00
Zheng Junjie 86c1f3857c
gnu: fcitx5-configtool: Enable kcm support.
* gnu/packages/fcitx5.scm (fcitx5-configtool)
[arguments]: Remove it.
[inputs]: Add qtdeclarative, qtquickcontrols2, ki18n, kpackage, kdeclarative,
kiconthemes, kcoreaddons, plasma-framework, kwindowsystem, kirigami, libxkbcommon.

Change-Id: I43a43458232a5ad3c1d156c779359e356cbf98b8
Signed-off-by: Christopher Baines <mail@cbaines.net>
2024-05-13 19:31:20 +01:00
Alexey Abramov 7d6d54202a
gnu: isc-dhcp: Add debianutils as an input.
dhclient provides a hook mechanism for users.  In order to run these hooks,
dhclient-script uses run-parts to run all the executable files found in
requested directory. run-parts is part of debianutils packages.

* gnu/packages/admin.scm (isc-dhcp)[inputs]: Add "debianutils" to provide
access to run-parts.

Signed-off-by: Christopher Baines <mail@cbaines.net>
Change-Id: I2057881da57a6065d65d1de95e51ed1c8b19e15f
2024-05-13 19:31:20 +01:00
Fabio Natali b1de64812a
gnu: notmuch: Add sfsexp input.
sfsexp is a C/C++ library for the manipulation (read, parse, modify, and
create) of symbolic expressions.  In an environment where sfsexp is available,
Notmuch will compile with support for a S-expression-based query format.  This
commit is to add sfsexp as a Notmuch dependency and therefore to add S-exp
support.

* gnu/packages/mail.scm (notmuch)[native-inputs]: Add git-minimal/pinned.
[inputs]: Add sfsexp.

Change-Id: Ic3b4a30b2672ad690d66b283e9bdc8e2197f97a7
Signed-off-by: Christopher Baines <mail@cbaines.net>
2024-05-13 19:31:20 +01:00
Fabio Natali 99181ad981
gnu: Add sfsexp.
* gnu/packages/c.scm (sfsexp): New variable.

Change-Id: Iabfbe10b4ad6134ae886a3d26487f881107b559c
Signed-off-by: Christopher Baines <mail@cbaines.net>
2024-05-13 19:31:20 +01:00
Christopher Baines 3db1a8341c
store: Add with-store/non-blocking.
For some applications, it's important to establish a non-blocking connection
rather than just making the socket non-blocking after the connection is
established. This is because there is I/O on the socket that will block during
the handshake.

I've noticed this blocking during the handshake causing issues in the build
coordinator for example.

This commit adds a new with-store variant to avoid changing the behaviour of
with-store/open-connection to ensure that this change can't break anything
that depends on the blocking nature of the socket.

* guix/store.scm (open-unix-domain-socket, open-inet-socket): Take
 #:non-blocking? and use SOCK_NONBLOCK when calling socket if appropriate.
(connect-to-daemon, open-connection, call-with-store): Take #:non-blocking?
and pass it on.
(with-store/non-blocking): New syntax rule.
* .dir-locals.el (scheme-mode): Add entry for with-store/non-blocking.

Change-Id: I8225762b78448bc1f7b698c8de5d736e13f577bf
2024-05-13 19:31:17 +01:00
Efraim Flashner 1632fd0f1b
gnu: evdi: Update to 1.14.4.
* gnu/packages/linux.scm (evdi): Update to 1.14.4.
(libevdi)[native-inputs]: Add pkg-config.

Change-Id: I5e25a2a4a10608af927b2315dbd56b568ef56a1a
2024-05-13 20:00:54 +03:00
Karl Hallsby b23aa4c1d6
gnu: Add tree-sitter-erlang.
* gnu/packages/tree-sitter.scm (tree-sitter-erlang): New variable.

Change-Id: Ib1449549249816736bf30a1d419a23fd7a45570e

Change-Id: I99cdde6418e04d4898f0f6509d2e7d849e2a4f22
Signed-off-by: Zheng Junjie <zhengjunjie@iscas.ac.cn>
2024-05-14 00:24:12 +08:00
Karl Hallsby 6b6ad68559
gnu: Add tree-sitter-vhdl.
* gnu/packages/tree-sitter.scm (tree-sitter-vhdl): New variable.

Change-Id: Ia26e33f9898573e70c9afdd4025e3770d042dbd6

Change-Id: I07b2b89f878957af1544344122cdfe8970efc9f7
Signed-off-by: Zheng Junjie <zhengjunjie@iscas.ac.cn>
2024-05-14 00:24:12 +08:00
Karl Hallsby 65186deae4
gnu: Add tree-sitter-verilog.
* gnu/packages/tree-sitter.scm (tree-sitter-verilog): New variable.

Change-Id: I2066aff3cf39cebda956125cdac71236502a7ac5

Change-Id: If4acb8c10cd3942f46dcb05b8009760a6452b67a
Signed-off-by: Zheng Junjie <zhengjunjie@iscas.ac.cn>
2024-05-14 00:24:12 +08:00
Zheng Junjie 40af021e28
gnu: foot: Fix cross-compilation.
* gnu/packages/terminals.scm (foot): Fix cross-compilation.
[arguments]<#:configure-flags>: When cross-compilation, Remove -Db_lto=true.
[native-inputs]: When cross-compilation, Add wayland, pkg-config-for-build.
[inputs]: Add wayland-protocols.

Change-Id: Ia56d2583254bd9ab463e5b39859eae8eb5092c9b
2024-05-14 00:24:12 +08:00
Zheng Junjie 38598c693f
gnu: utf8proc: fix cross-compilation.
* gnu/packages/textutils.scm (utf8proc): fix cross-compilation.
[arguments]<#:make-flags>: Use CC-FOR-TARGET.
<#:phases>: When cross-compilation, Get test data from native-inputs.

Change-Id: I42699e62f28585cc215a8843b5daad9c52af44c9
2024-05-14 00:24:12 +08:00
Zheng Junjie ecfd88cbe3
gnu: cairo: Fix cross-compilation.
* gnu/packages/gtk.scm (cairo)[arguments]: Add ‘fix-cross-compilation’ phase
when cross-compiling.

Change-Id: I3579bb1249c749ee5f164bb4dd47f585b181c2bc
Signed-off-by: Zheng Junjie <zhengjunjie@iscas.ac.cn>
2024-05-14 00:24:12 +08:00
Ludovic Courtès 58be9a79e2
gnu: guix: Update to 7ca9809.
This is a followup to 7757fdd491.

* gnu/packages/package-management.scm (guix): Update to 7ca9809.

Change-Id: Ic1e6d75223eb7e1371805f51b9f230ef846c536c
2024-05-13 18:22:53 +02:00
Ludovic Courtès 7ca9809cdb
tests: Skip ‘terminal-string-width’ test on encodings other than UTF-8.
* tests/syscalls.scm ("terminal-string-width Japanese"): Skip when the
encoding of (current-output-port) is not UTF-8.

Reported-by: Ashvith Shetty <ashvithshetty10@gmail.com>
Change-Id: Ic284dd088d6b148d6fcb457290a28fdb0838b83d
2024-05-13 16:31:35 +02:00
Ludovic Courtès 723d45866f
tests: Remove interference from the user’s Git config.
* tests/guix-download.sh: Set ‘GIT_CONFIG_GLOBAL’ and
‘GIT_CONFIG_SYSTEM’.

Reported-by: Ashvith Shetty <ashvithshetty10@gmail.com>
Change-Id: Ibe14d23db2e8af58b85c78248997c6dde78e11e0
2024-05-13 16:31:35 +02:00
Massimo Zaniboni efbdfe1900
file-systems: Add "virtiofs" to the list of pseudo file system types.
* gnu/system/file-systems.scm (%pseudo-file-system-types): Add "virtiofs"
to the list of pseudo file system types.

Change-Id: Ib1d99127e65f6543c592faec1c54bd0c5eae3ad7
Signed-off-by: Ludovic Courtès <ludo@gnu.org>
2024-05-13 16:31:34 +02:00
Tomas Volf 9dce86b1cb
.dir-locals: Configure indentation for swap-space.
* .dir-locals.el (scheme-mode): Indent swap-space same as file-system.

Change-Id: Id9f2cbd3c81343b479ab1e4df29c65f8b5bd739f
Signed-off-by: Ludovic Courtès <ludo@gnu.org>
2024-05-13 16:31:34 +02:00
Tomas Volf dc4c6ab4cb
doc: Fix bug in hg-reference documentation.
The field is called changeset, not revision.  And the string does not have to
be a number.

* doc/guix.texi (origin Reference): Fix documentation for hg-reference.

Change-Id: Ic622dfc7b44caf42d070cdab8e42808dd96e6d63
Signed-off-by: Ludovic Courtès <ludo@gnu.org>
2024-05-13 16:31:34 +02:00
Tomas Volf 408c4511a6
doc: Document cvs-fetch and cvs-reference.
For some reason, they were missing from the documentation.  This commit adds
them including an example of usage.

* doc/guix.texi (origin Reference): Add cvs-fetch and cvs-reference.

Change-Id: I6622a9f70e6d71ed31fbb3d2689df4a6946f8868
Signed-off-by: Ludovic Courtès <ludo@gnu.org>
2024-05-13 16:31:34 +02:00
Ludovic Courtès 7757fdd491
daemon: Loop over ‘copy_file_range’ upon short writes.
Fixes <https://issues.guix.gnu.org/70877>.

* nix/libutil/util.cc (copyFile): Loop over ‘copy_file_range’ instead of
throwing upon short write.

Reported-by: Ricardo Wurmus <rekado@elephly.net>
Change-Id: Id7b8a65ea59006c2d91bc23732309a68665b9ca0
2024-05-13 16:31:34 +02:00
Ricardo Wurmus be235a3092
gnu: Add r-anndatar.
* gnu/packages/bioinformatics.scm (r-anndatar): New variable.

Change-Id: I6060c5c15a46c064aa03ec2431a72ea88f925706
2024-05-13 16:12:12 +02:00
Christopher Baines 7b0f145802
Use po4a-minimal for guix.
As this avoids the indirect dependency on nss, which has a testsuite that
takes a long time to run.

* gnu/packages/package-management.scm (guix)[native-inputs]: Use po4a-minimal.
* guix/self.scm (%packages, translate-texi-manuals): Use po4a-minimal.

Change-Id: Iac7555cc850c1618d3d54f1b290faa4f9cfb4f8a
2024-05-13 12:01:49 +01:00
Christopher Baines 8fb98fe33b
gnu: Add po4a-minimal.
The main reason is to avoid the texlive-updmap.cfg input indirectly pulling in
nss, which has a very time consuming testsuite.

* gnu/packages/gettext.scm (po4a-minimal): New variable.

Change-Id: If8d46a18a02e57d5427852e8e122de01f970ded4
2024-05-13 12:01:49 +01:00
Christopher Baines 31d1cc82b3
gnu: nss/fixed: Tweak performance test.
As I'm seeing this test fail with results of 5 to 7 seconds.

* gnu/packages/nss.scm (nss/fixed)[arguments]: Tweak a test to have a higher
time threshold.

Change-Id: Icb0551cd986acf67b2ba17dc8772a67b9747d31a
2024-05-13 12:01:46 +01:00
Efraim Flashner 08360a2cd0
gnu: atril: Expand package description.
* gnu/packages/mate.scm (atril)[description]: Expand with the upstream
description.

Change-Id: Ibd142094a5fbb4028613a03da0bd6de75cc9f6fe
2024-05-13 12:38:07 +03:00
Efraim Flashner ca892fc9ef
gnu: atril: Remove input labels.
* gnu/packages/mate.scm (atril)[native-inputs]: Remove package labels.
[inputs]: Same.

Change-Id: I9bdb69426d4b3285b09310642b881ac9bcee0d47
2024-05-13 12:37:02 +03:00
Tomas Volf d86b6233d5
gnu: slirp4netns: Update to 1.3.0.
* gnu/packages/containers.scm (slirp4netns): Update to 1.3.0.

Change-Id: I1f9c75a6e3dab996465879cf6734799a8b9e9d53
Signed-off-by: Christopher Baines <mail@cbaines.net>
2024-05-13 09:11:06 +01:00
Jonathan Brielmaier 173420d73c
gnu: gnome-maps: Update to 46.10.
* gnu/packages/geo.scm (gnome-maps): Update to 46.10.
[arguments]: Add phase to setup time zones for a new test.
[native-inputs]: Add libportal and tzdata-for-tests.

Change-Id: Ife9b17eda68662d2adb289acfeacf1dc8f179a46
Signed-off-by: Christopher Baines <mail@cbaines.net>
2024-05-13 09:11:06 +01:00
Jonathan Brielmaier 7db57257d5
gnu: libshumate: Update to 1.2.1.
* gnu/packages/gnome.scm (libshumate): Update to 1.2.1.
[arguments]: Drop `-Dlibsoup3=true` configure flag as it got removed
upstream.  It only supports libsoup3 now.
[native-inputs]: Add gperf.
[propagated-inputs]: Add json-glib and protobuf-c.

Change-Id: Ibe63b6f2060f6684f8f68f44c2221ba9d6ad5a45
Signed-off-by: Christopher Baines <mail@cbaines.net>
2024-05-13 09:11:06 +01:00
kiasoc5 43cd76fa58
gnu: mg: Update to 20230501.
* gnu/packages/text-editors.scm (mg): Update to 20230501.

Change-Id: Ie72901207562488f392d5877e1b41a41067893f4
Signed-off-by: Christopher Baines <mail@cbaines.net>
2024-05-13 09:11:06 +01:00
antlers 0309080ffc
gnu: zfs: Update to 2.2.3.
* gnu/packages/file-systems.scm (zfs): Update to 2.2.3.

Signed-off-by: Christopher Baines <mail@cbaines.net>
Change-Id: If77ba25fe98603d79fd08623ce12a9fa916bae43
2024-05-13 09:11:06 +01:00
Andy Tai 0b3f2f28c6
gnu: llama-cpp: Update to 0.0.0-2.fed0108.
As last update was in February and new changes for new models and memory leaks
fixes since then.

* gnu/packages/machine-learning.scm (llama-cpp): Update to 0.0.0-2.fed0108.
[arguments]<#:phases>: Add 'disable-unrunable-tests' phase.  Change
replacement of 'install to be a post-install 'install-main' phase so libraries
and header files are normally installed.

Change-Id: Ia6532945f588747c4d58fdb7611d6a9c3c596705
Signed-off-by: Christopher Baines <mail@cbaines.net>
2024-05-13 09:11:06 +01:00
Andy Tai cc212af83e
gnu: opensycl: Rename to adaptivecpp and update to 24.02.0.
* gnu/packages/sycl.scm (adaptivecpp): New variable.
(opensync): Redefine using DEPRECATED-PACKAGE.

Change-Id: I7ac3f49409d539962de34510ed9255021b795724
Signed-off-by: Christopher Baines <mail@cbaines.net>
2024-05-13 09:11:06 +01:00
Rostislav Svoboda e5fa18b628
guix: channels: Handle single case with authenticating message.
* guix/channels.scm (authenticate-channel): Handle single case with
authenticating message.

Change-Id: I7759607f37405e6d3bd4b7f5958fd11d908db204
Reviewed-by: Dale Mellor <guix-devel-0brg6a@rdmp.org>
Signed-off-by: Christopher Baines <mail@cbaines.net>
2024-05-13 09:11:05 +01:00
Christopher Baines 63dfce508a
gnu: guix-data-service: Update to 0.0.1-49.f4be647.
* gnu/packages/web.scm (guix-data-service): Update to 0.0.1-49.f4be647.

Change-Id: I874df868fed2d22dd1bb8c696a55d8396581b9a6
2024-05-13 09:11:05 +01:00
Christopher Baines 034306b3b7
gnu: nar-herder: Update to 0-31.0e89dbb.
* gnu/packages/package-management.scm (nar-herder): Update to 0-31.0e89dbb.

Change-Id: Ia238baa6bd835d3fa8ea81d1f0a12c3fee333973
2024-05-13 09:11:05 +01:00
Christopher Baines 4f45bf4e94
gnu: guix-build-coordinator: Update to 0-103.ff81428.
* gnu/packages/package-management.scm (guix-build-coordinator): Update to
0-103.ff81428.

Change-Id: I91cb97a69c2650efa35291cfab724b4e80007e06
2024-05-13 09:11:05 +01:00
Efraim Flashner 109679cdfa
Revert "gnu: python-xcffib: Update to 1.4.0."
This reverts commit 56980ea500.

This package includes files which need to be bootstrapped, to produce
the bindings matching our version of libxcb.
2024-05-13 11:00:00 +03:00
Efraim Flashner ed3f818b15
gnu: alfa: Reuse 'check phase.
* gnu/packages/astronomy.scm (alfa)[arguments]: Set test-target. Replace
custom 'post-install-check phase with the standard 'check phase.

Change-Id: Ic5f77ac3a3a6ef62ce36ad5fa8892db6d0894d04
2024-05-13 10:52:54 +03:00
Efraim Flashner a0221c3424
gnu: alfa: Skip tests when cross compiling.
* gnu/packages/astronomy.scm (alfa)[arguments]: Also skip tests when
cross compiling.

Change-Id: Ie96b418a652feff6b4dfc79ffcac9d0f1900fce5
2024-05-13 10:50:12 +03:00