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140715 commits

Author SHA1 Message Date
Ludovic Courtès
2cccf2f11c
services: Truly mark ‘setuid-program-service-type’ as deprecated.
* gnu/services.scm (setuid-program-service-type): Define with
‘define-deprecated/alias’.

Change-Id: Ibafe333e7f261185b5a70b38cfb4845abf2f643b
2024-08-19 16:36:04 +02:00
Ludovic Courtès
52ac2db924
services: privileged-program: No libcap when cross-compiling to the Hurd.
* gnu/services.scm (privileged-program->activation-gexp): Add
‘let-system’ form to define staged ‘libcap’ variable.  Use
‘supported-package?’ only when not cross-compiling.

Change-Id: Ifa9bd97b5dc8c3a162d8427533b41d3c30bac18d
2024-08-19 16:34:07 +02:00
Romain GARBAGE
4dc1442cc1
gnu: openmpi: Set default version to 4.x.
* gnu/packages/mpi.scm (openmpi-4): New variable.
(openmpi): Redefine variable.

Change-Id: If5bb4429c935982ddaa1a5acbd728367ebbfd6fd
Signed-off-by: Ludovic Courtès <ludo@gnu.org>
2024-08-19 16:15:05 +02:00
Romain GARBAGE
208c296f96
gnu: Add openmpi-5.
* gnu/packages/mpi.scm (openmpi-5): New variable.

Change-Id: I048692b2e928077c9cfa9fb8076ceb356251e1db
Signed-off-by: Ludovic Courtès <ludo@gnu.org>
2024-08-19 16:15:05 +02:00
Romain GARBAGE
13278a2a46
gnu: slurm: Add PMIx support.
* gnu/packages/parallel.scm (slurm) [inputs]: Add dependency.
[arguments]: Update configure flags.
(slurm-21.08)[inputs]: New field.

Change-Id: I6544be5eb44980191d0788738ab960263c56c0ba
Signed-off-by: Ludovic Courtès <ludo@gnu.org>
2024-08-19 16:15:05 +02:00
Ludovic Courtès
1150b443c1
gnu: slurm: Always inherit from the immediately newer version.
* gnu/packages/parallel.scm (slurm-21.08): Change ‘inherit’ to refer to
the immediately newer version.
(slurm-20.11, slurm-20.02, slurm-19.05, slurm-18.08): Likewise.

Change-Id: I327eaa3535bc273c8744583b966da22381c8a576
2024-08-19 16:15:05 +02:00
Romain GARBAGE
aa66072496
gnu: Add prrte.
* gnu/packages/parallel.scm (prrte): New variable.

Change-Id: I4427eec1a5c7d94ed5f9cbceb55f9372834a8971
Signed-off-by: Ludovic Courtès <ludo@gnu.org>
2024-08-19 16:15:05 +02:00
Romain GARBAGE
06e6a161aa
gnu: Add openpmix.
* gnu/packages/parallel.scm (openpmix): New variable.

Change-Id: Id23bc710c9b61ede0aebf7e2a18863fbe5fb8304
Signed-off-by: Ludovic Courtès <ludo@gnu.org>
2024-08-19 16:15:05 +02:00
fanquake
9aa38f98cb
gnu: gcc@12: Update to 12.4.0.
* gnu/packages/gcc.scm (gcc-12): Update to 12.4.0.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
Change-Id: Ibdd003d5b61eb4b9e6a1b56428d01d51cca97b44
2024-08-19 16:15:01 +02:00
Ashish SHUKLA
d3832de763
gnu: libgit2-1.8: Update to 1.8.1.
* gnu/packages/version-control.scm (libgit2-1.8): Update to 1.8.1.
  [source]: deps/http-parser does not exist so update the list
  [arguments]: semantics of -DUSE_HTTP_PARSER has changed, so
  update configure-flags to reflect the same

Change-Id: Ifd9694a93326f7c3d368bd354a5fadf4e4b93119
Signed-off-by: Ludovic Courtès <ludo@gnu.org>
2024-08-19 12:30:26 +02:00
Romain GARBAGE
07adb7e26a
gnu: Add mpich-ofi.
* gnu/packages/mpi.scm (mpich-ofi): New variable.

Change-Id: I577fa8fc15ffe7df82d737721ca5a2e034c1e43a
Signed-off-by: Ludovic Courtès <ludo@gnu.org>
2024-08-19 12:02:35 +02:00
Romain GARBAGE
2a6ea3895b
gnu: libfabric: Add support for extra providers.
* gnu/packages/linux.scm (libfabric) [arguments]: Add configure flags.

Change-Id: I57e43ffd92e8268112e48928af38b0fecc256a67
Signed-off-by: Ludovic Courtès <ludo@gnu.org>
2024-08-19 12:02:34 +02:00
Luca Cirrottola
84c62cf166
gnu: hdf5-parallel-openmpi: Update to 1.14.x.
Fixes <https://issues.guix.gnu.org/68313>.

HDF5 1.14.3 contains the fix for <https://github.com/HDFGroup/hdf5/pull/3421>.

* gnu/packages/maths.scm (hdf5-parallel-openmpi): Inherit from HDF5-1.14.
[arguments]: Take arguments from HDF5-1.14.  Use gexps.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
Change-Id: I99222a1085dcd75c3c9ac83a0e88495e86a8cf59
2024-08-19 12:02:05 +02:00
Luca Cirrottola
832f2bcb92
gnu: hdf5@1.14: Update to 1.14.3.
* gnu/packages/maths.scm (hdf5-1.14): Update to 1.14.3.
[arguments]: New field.

Co-authored-by: Ludovic Courtès <ludovic.courtes@inria.fr>
Change-Id: If413ec4d00de0de86020d8f56f2e3f9ec52ed0a9
2024-08-19 12:01:46 +02:00
Tobias Geerinckx-Rice
26080c6b53
Revert "gnu: at-spi2-core: Remove unnecessary test timeout."
This reverts commit 58a839273d.
Hello I am new here:

  <cbaines>nckx, 58a839273d leads to
  nearly 4000 rebuilds
2024-08-18 02:00:00 +02:00
Andy Tai
f30509e165
gnu: direvent: Update to 5.4.
* gnu/packages/admin.scm (direvent): update to 5.4.

Change-Id: I955abd8e3d75ff2fa7afa99c8d6b2eed2328b20a
Signed-off-by: Zheng Junjie <zhengjunjie@iscas.ac.cn>
2024-08-19 13:38:34 +08:00
Evgeny Pisemsky
edb54d378d
gnu: gitile: Replace outdated dependency.
* gnu/packages/version-control.scm (gitile): Replace outdated dependency.
* gnu/packages/guile-xyz.scm (guile-syntax-highlight-for-gitile): Remove.

Change-Id: I24295a24d0dfef08d5161c206757996ccdd881fd
2024-08-19 13:36:56 +08:00
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
Tobias Geerinckx-Rice
71f0676a29
privilege: Add POSIX capabilities(7) support.
* gnu/system/privilege.scm (<privileged-program>): Add a field
representing the program's POSIX capabilities.
(privileged-program-capabilities): New public procedure.
* doc/guix.texi (Privileged Programs): Document it.
* gnu/build/activation.scm (activate-privileged-programs): Take a LIBCAP
package argument providing setcap(8) to apply said capabilities.
* gnu/services.scm (privileged-program->activation-gexp): Pass said
package argument where supported.  Include privileged-program-capabilities
in the compatibility hack.
2024-08-11 02:00:00 +02:00
Tobias Geerinckx-Rice
4e58dfee6c
system: Add privileged-programs to <operating-system>.
* gnu/system.scm (<operating-system>): Add new privileged-programs
field, that defaults to…
(%default-privileged-programs): …this new variable, renamed from…
(%setuid-programs): …this, which is now defined as the empty list.
* doc/guix.texi (Setuid Programs): Rename this…
(Privileged Programs): …to this.  Adjust all refs.  Update all mentions
of ‘setuid’ (whether in prose, variable names, or code samples) to use
the new ‘privilege[d]’ terminology instead.
(operating-system Reference, X Window, Invoking guix system)
(Service Reference): Adjust likewise.
2024-08-11 02:00:00 +02:00
Tobias Geerinckx-Rice
beb37ea4ad
system: Use privileged-program-service-type by default.
* gnu/system.scm (operating-system-default-essential-services)
(hurd-default-essential-services): Substitute
privileged-program-service-type for setuid-program-service-type.
2024-08-11 02:00:00 +02:00
Tobias Geerinckx-Rice
d73ca7ecb6
services: Rename setuid-program-service-type.
* gnu/services.scm (setuid-program->activation-gexp): Rename this…
(privileged-program->activation-gexp): …to this.
Operate on a list of <privileged-program> records.
(privileged-program-service-type): New variable, renamed from
setuid-program-service-type.  Rename the service-type accordingly.
(setuid-program-service-type): Redefine as an alias for the above.
2024-08-11 02:00:00 +02:00
Tobias Geerinckx-Rice
f3b84be52d
build: Rename activate-setuid-programs.
* gnu/build/activation.scm (activate-setuid-programs): Rename this…
(activate-privileged-programs): …to this.
Operate on a list of <privileged-program> records.
* gnu/services.scm (setuid-program->activation-gexp): Adjust caller.
2024-08-11 02:00:00 +02:00
Tobias Geerinckx-Rice
9099f8bdcc
system: (gnu system setuid) wraps (gnu system privilege).
* gnu/system/setuid.scm (setuid-program): Rewrite as syntax to create a
<privileged-program> record that is setuid by default.
(setuid-program?, setuid-program-program, setuid-program-setuid?)
(setuid-program-setgid?, setuid-program-user, setuid-program-group):
Alias their privileged-program equivalent.
2024-08-11 02:00:00 +02:00
Tobias Geerinckx-Rice
39471f2627
system: Add (gnu system privilege).
* gnu/system/privilege.scm: New file.
* gnu/local.mk (GNU_SYSTEM_MODULES): Add it.
2024-08-11 02:00:00 +02:00
Tobias Geerinckx-Rice
902b15b24d
gnu: Replace (almost) all uses of /run/setuid-programs.
…those good for master, anyway.

* gnu/packages/admin.scm (ktsuss, opendoas, hosts)
[arguments]: Replace /run/setuid-programs with /run/privileged/bin.
* gnu/packages/containers.scm (slirp4netns)[arguments]: Likewise.
* gnu/packages/debian.scm (pbuilder)[arguments]: Likewise.
* gnu/packages/disk.scm (udevil)[arguments]: Likewise.
* gnu/packages/enlightenment.scm (efl, enlightenment)
[arguments]: Likewise.
* gnu/packages/gnome.scm (gdm, gnome-control-center)
[arguments]: Likewise.
* gnu/packages/linux.scm (singularity)[arguments]: Likewise.
* gnu/packages/lxde.scm (spacefm)[arguments]: Likewise.
* gnu/packages/monitoring.scm (zabbix-agentd)[arguments]: Likewise.
* gnu/packages/virtualization.scm (ganeti)[arguments]: Likewise.
* gnu/packages/xdisorg.scm (xsecurelock)[arguments]: Likewise.
* gnu/services/dbus.scm (dbus-configuration-directory): Likewise.
* gnu/services/ganeti.scm (%default-ganeti-environment-variables):
Likewise.
* gnu/services/monitoring.scm (zabbix-agent-shepherd-service): Likewise.
* gnu/tests/ldap.scm (marionette): Likewise.
* gnu/tests/monitoring.scm (os): Likewise.
2024-08-11 02:00:00 +02:00
Tobias Geerinckx-Rice
e364d1a494
system: Use /run/privileged/bin in search paths.
* gnu/system.scm (operating-system-etc-service):
Substitute /run/privileged/bin for deprecated /run/setuid-programs.
2024-08-11 02:00:00 +02:00
Tobias Geerinckx-Rice
d6c9754c56
services: setuid-program: Populate /run/privileged/bin.
Create /run/setuid-programs compatibility symlinks so that we can
migrate all users (both package and human) piecemeal at our leisure.

Apart from being symlinks, this should be a user-invisible change.

* gnu/build/activation.scm (%privileged-program-directory): New variable.
[activate-setuid-programs]: Put privileged copies in
%PRIVILEGED-PROGRAM-DIRECTORY, with compatibility symlinks to each in
%SETUID-DIRECTORY.
* gnu/services.scm (setuid-program-service-type): Update docstring.
* doc/guix.texi (Setuid Programs): Update @file{} name accordingly.
2024-08-11 02:00:00 +02:00
Tobias Geerinckx-Rice
0dffb851e0
system: Disallow file-like setuid-programs.
It has been a warning for well over a year now.  Now, with
privileged-programs coming, don't let's support nested deprecation
hacks.

* gnu/system.scm (<operating-system>):
Don't ‘sanitize’ the setuid-programs field.
(ensure-setuid-program-list): Delete syntax.
(%ensure-setuid-program-list): Delete variable.
2024-08-11 02:00:00 +02:00
Andrew Tropin
6c045f2c9e
gnu: kmonad: Update to 0.4.2-1.07cd1cb.
* gnu/packages/haskell-apps.scm (kmonad): Update to 0.4.2-1.07cd1cb.

Change-Id: I8a8d36577804d2221b39b430d26e9fd17204c0de
2024-08-18 08:36:35 +04:00
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