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2024-08-19gnu: Add mpich-ofi.Romain GARBAGE
* gnu/packages/mpi.scm (mpich-ofi): New variable. Change-Id: I577fa8fc15ffe7df82d737721ca5a2e034c1e43a Signed-off-by: Ludovic Courtès <ludo@gnu.org>
2024-08-19gnu: libfabric: Add support for extra providers.Romain GARBAGE
* gnu/packages/linux.scm (libfabric) [arguments]: Add configure flags. Change-Id: I57e43ffd92e8268112e48928af38b0fecc256a67 Signed-off-by: Ludovic Courtès <ludo@gnu.org>
2024-08-19gnu: hdf5-parallel-openmpi: Update to 1.14.x.Luca Cirrottola
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
2024-08-19gnu: hdf5@1.14: Update to 1.14.3.Luca Cirrottola
* 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
2024-08-18Revert "gnu: at-spi2-core: Remove unnecessary test timeout."Tobias Geerinckx-Rice
This reverts commit 58a839273d1e4fac2b3a0ec456aabdf82deaa124. Hello I am new here: <cbaines>nckx, 58a839273d1e4fac2b3a0ec456aabdf82deaa124 leads to nearly 4000 rebuilds
2024-08-19gnu: direvent: Update to 5.4.Andy Tai
* gnu/packages/admin.scm (direvent): update to 5.4. Change-Id: I955abd8e3d75ff2fa7afa99c8d6b2eed2328b20a Signed-off-by: Zheng Junjie <zhengjunjie@iscas.ac.cn>
2024-08-19gnu: gitile: Replace outdated dependency.Evgeny Pisemsky
* gnu/packages/version-control.scm (gitile): Replace outdated dependency. * gnu/packages/guile-xyz.scm (guile-syntax-highlight-for-gitile): Remove. Change-Id: I24295a24d0dfef08d5161c206757996ccdd881fd
2024-08-19gnu: Add zydis.guix-patches--- via
* gnu/packages/engineering.scm (zydis): New variable. Change-Id: I6e0b04e1d957f8c172e81177f6669415beeaf20a Signed-off-by: Zheng Junjie <zhengjunjie@iscas.ac.cn>
2024-08-19gnu: Add zycore.guix-patches--- via
* gnu/packages/engineering.scm (zycore): New variable. Change-Id: Ia38413f43bc667a9a12916d3f0e786e06f6d358f Signed-off-by: Zheng Junjie <zhengjunjie@iscas.ac.cn>
2024-08-19gnu: chrony: Fix cross-compilation.Zheng Junjie
* gnu/packages/ntp.scm (chrony)[arguments]<#:phases>: Add set-CC phase. Change-Id: I0bc7c271875c5ba68743583fb3932e238b3b37c0
2024-08-19gnu: chrony: Update to 4.5.Artyom V. Poptsov
* 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>
2024-08-18gnu: at-spi2-core: Remove unnecessary test timeout.Nikola
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>
2024-08-18gnu: icedove-minimal: Add StartupWMClass.Jonathan Brielmaier
Fixes https://issues.guix.gnu.org/69267 * gnu/packages/gnuzilla.scm (icedove-minimal)[arguments]: Set MOZ_APP_REMOTINGNAME and StartupWMClass. Change-Id: Ibf334c2d840a49aa7ec84da44eceecd85cb3bcd2
2024-08-18gnu: icedove. Update to 115.14.0.Jonathan Brielmaier
* gnu/packages/gnuzilla.scm (%icedove-version): Update to 115.14.0. Change-Id: I7564b525059f6c26beeee4bf9514fa38cc2aaa58
2024-08-18gnu: icedove-wayland: Use icedove-minimal instead of icedove.Jonathan Brielmaier
`icedove` does currently not built. * gnu/packages/gnuzilla.scm (icedove-wayland): Use `icedove-minimal` instead of `icedove`. Change-Id: Idc01d6a93071cff11ef139e6738aff1c7687d975
2024-08-18gnu: icedove: Update to 115.10.1.Jonathan Brielmaier
* 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
2024-08-18gnu: icu4c: Add patch for VTIMEZONE bug.Jonathan Brielmaier
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
2024-08-11privilege: Add POSIX capabilities(7) support.Tobias Geerinckx-Rice
* 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.
2024-08-11system: Add privileged-programs to <operating-system>.Tobias Geerinckx-Rice
* 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.
2024-08-11system: Use privileged-program-service-type by default.Tobias Geerinckx-Rice
* gnu/system.scm (operating-system-default-essential-services) (hurd-default-essential-services): Substitute privileged-program-service-type for setuid-program-service-type.
2024-08-11services: Rename setuid-program-service-type.Tobias Geerinckx-Rice
* 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.
2024-08-11build: Rename activate-setuid-programs.Tobias Geerinckx-Rice
* 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.
2024-08-11system: (gnu system setuid) wraps (gnu system privilege).Tobias Geerinckx-Rice
* 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.
2024-08-11system: Add (gnu system privilege).Tobias Geerinckx-Rice
* gnu/system/privilege.scm: New file. * gnu/local.mk (GNU_SYSTEM_MODULES): Add it.
2024-08-11gnu: Replace (almost) all uses of /run/setuid-programs.Tobias Geerinckx-Rice
…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.
2024-08-11system: Use /run/privileged/bin in search paths.Tobias Geerinckx-Rice
* gnu/system.scm (operating-system-etc-service): Substitute /run/privileged/bin for deprecated /run/setuid-programs.
2024-08-11services: setuid-program: Populate /run/privileged/bin.Tobias Geerinckx-Rice
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.
2024-08-11system: Disallow file-like setuid-programs.Tobias Geerinckx-Rice
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.
2024-08-18gnu: kmonad: Update to 0.4.2-1.07cd1cb.Andrew Tropin
* gnu/packages/haskell-apps.scm (kmonad): Update to 0.4.2-1.07cd1cb. Change-Id: I8a8d36577804d2221b39b430d26e9fd17204c0de
2024-08-17gnu: r-dmrseq: Update to 1.24.1.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-dmrseq): Update to 1.24.1. Change-Id: I22fb49eee056e0dd5306fec4575fcb38cbe916aa
2024-08-17gnu: r-bgeecall: Update to 1.20.1.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-bgeecall): Update to 1.20.1. [propagated-inputs]: Add r-txdbmaker. Change-Id: Ia51c1ccdb0e49d8dc74a61f605f00c86718bc1f8
2024-08-17gnu: r-mscoreutils: Update to 1.16.1.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-mscoreutils): Update to 1.16.1. Change-Id: I233a01625f223c571dae863c977825d4a2909ee7
2024-08-17gnu: r-scater: Update to 1.32.1.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-scater): Update to 1.32.1. Change-Id: I0232d463f243505a9b3706d64e6666eb245ceb1c
2024-08-17gnu: r-hdf5array: Update to 1.32.1.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-hdf5array): Update to 1.32.1. Change-Id: Iebab45185f6f1fe3e6919a1e70e45127d9f1124f
2024-08-17gnu: r-s4vectors: Update to 0.42.1.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-s4vectors): Update to 0.42.1. Change-Id: I58dc50344c5eb477da9d4ddd4447bcb41f456037
2024-08-17gnu: r-multiassayexperiment: Update to 1.30.3.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-multiassayexperiment): Update to 1.30.3. Change-Id: Iabbd0c74d7515f8f166827b8b99b2ac49b271c13
2024-08-17gnu: r-universalmotif: Update to 1.22.1.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-universalmotif): Update to 1.22.1. Change-Id: I60a617d120e5da046decb491b7641f1e10aac0cb
2024-08-17gnu: r-clusterprofiler: Update to 4.12.2.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-clusterprofiler): Update to 4.12.2. Change-Id: I17d837fb314c26fcb26c13240a01c91bc2da9797
2024-08-17gnu: r-enrichplot: Update to 1.24.2.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-enrichplot): Update to 1.24.2. Change-Id: I188e7e908a09337d4bacf4802b1557ddd31048f3
2024-08-17gnu: r-dose: Update to 3.30.2.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-dose): Update to 3.30.2. Change-Id: Ic07fab82efcbda004d6c7ff21d4ed7b49cc426fb
2024-08-17gnu: r-chippeakanno: Update to 3.38.1.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-chippeakanno): Update to 3.38.1. Change-Id: Ia4c89074674f3473e11f3b9e1f9ed828701591f6
2024-08-17gnu: r-qfeatures: Update to 1.14.2.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-qfeatures): Update to 1.14.2. Change-Id: I93c4fc00d19b18a1e0981f21dd0950d1e1a81f37
2024-08-17gnu: r-seqarray: Update to 1.44.1.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-seqarray): Update to 1.44.1. Change-Id: I06bb0b45d1a4299e835f7a18c7ed70d847bdb565
2024-08-17gnu: r-msa: Update to 1.36.1.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-msa): Update to 1.36.1. Change-Id: I91665d8ff4cd7570b5bcad27ff132611a09b8ecc
2024-08-17gnu: r-limma: Update to 3.60.4.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-limma): Update to 3.60.4. Change-Id: Iaaf9317ab3921070f5b8e06a7948b42575bbe00b
2024-08-17gnu: r-raggedexperiment: Update to 1.28.1.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-raggedexperiment): Update to 1.28.1. Change-Id: If7e8b60435413acda999f055bf9f104929e7f50f
2024-08-17gnu: r-edger: Update to 4.2.1.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-edger): Update to 4.2.1. Change-Id: Ia8cb57ada3f036f7fe45972ad1d3a8ff2e53c27b
2024-08-17gnu: r-iranges: Update to 2.38.1.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-iranges): Update to 2.38.1. Change-Id: I95d34fb3f339590c1980b7a77093835baa0e0136
2024-08-17gnu: r-dmrcate: Update to 3.0.5.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-dmrcate): Update to 3.0.5. Change-Id: I88768682f65b821e188f29c4dfee94927040cbbd
2024-08-17gnu: r-degreport: Update to 1.40.1.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-degreport): Update to 1.40.1. Change-Id: I35e7284270c81cd10178e7d848dfa5872645405d
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