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2021-07-31gnu: gnutls: Patch the Guile bindings for EINTR/EAGAIN handling.Ludovic Courtès
* gnu/packages/patches/gnutls-guile-eintr-eagain.patch: New file. * gnu/local.mk (dist_patch_DATA): Add it. * gnu/packages/tls.scm (gnutls)[source]: Use it.
2021-07-31gnu: mesa: Update to 21.1.6.John Kehayias
* gnu/packages/gl.scm (mesa): Update to 21.1.6. * gnu/packages/patches/mesa-skip-tests.patch: Remove cache_test.c as it is no longer needed (test passes). Signed-off-by: Ludovic Courtès <ludo@gnu.org>
2021-07-31gnu: libdrm: Update to 2.4.107.Kaelyn Takata
* gnu/packages/xdisorg.scm (libdrm): Update to 2.4.107, and change libpciaccess to a propagated input as the pkg-config for libdrm_intel now includes it in the libs. [arguments]: Add conditional testing support to the replacement for the standard check phase. Signed-off-by: Ludovic Courtès <ludo@gnu.org>
2021-07-30build-system/python: Handle missing metadata on Python 2.Marius Bakke
* gnu/packages/aux-files/python/sanity-check.py: Catch the less specific EnvironmentError rather than FileNotFoundError as the latter is Python 3 only.
2021-07-29Merge branch 'master' into core-updates-frozenMarius Bakke
Conflicts: gnu/packages/bioinformatics.scm gnu/packages/cmake.scm gnu/packages/curl.scm gnu/packages/emacs-xyz.scm gnu/packages/gpodder.scm gnu/packages/music.scm gnu/packages/patches/glibc-bootstrap-system.patch gnu/packages/python-xyz.scm gnu/packages/shells.scm gnu/packages/statistics.scm
2021-07-29gnu: r-xcms: Update to 3.14.1.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-xcms): Update to 3.14.1.
2021-07-29gnu: r-reportingtools: Update to 2.32.1.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-reportingtools): Update to 2.32.1.
2021-07-29gnu: php: Update to 7.4.22 [security fixes].Tobias Geerinckx-Rice
* gnu/packages/php.scm (php): Update to 7.4.22.
2021-07-29system: Add (gnu system setuid).Christopher Lemmer Webber
I flubbed and somehow when including the patch series, this got dropped. Oops... should fix things again. * gnu/system/setuid.scm: New file.
2021-07-29services: Migrate to <setuid-program>.Brice Waegeneire
* gnu/services/dbus.scm (dbus-setuid-programs, polkit-setuid-programs): Return setuid-programs. * gnu/services/desktop.scm (enlightenment-setuid-programs): Return setuid-programs. (%desktop-services)[mount-setuid-helpers]: Use setuid-programs. * gnu/services/docker.scm (singularity-setuid-programs): Return setuid-programs. * gnu/services/xorg.scm(screen-locker-setuid-programs): Return setuid-programs. * gnu/system.scm (%setuid-programs): Return setuid-programs. * doc/guix.texi (Setuid Programs, operating-system Reference): Replace 'list of G-expressions' with 'list of <setuid-program>'.
2021-07-29services: setuid: More configurable setuid support.Chris Lemmer-Webber
New record <setuid-program> with fields for setting the specific user and group, as well as specifically selecting the setuid and setgid bits, for a program within the setuid-program-service. * gnu/services.scm (setuid-program-file-like-deprecated): New function. (setuid-program-service-type): Make use of setuid-program->activation-gexp. Adjust the extend property to handle <setuid-program>. * gnu/build/activation.scm (activate-setuid-programs): Update to expect a <setuid-record> list for each program entry. * gnu/system.scm: (operating-system-setuid-programs): Renamed to %operating-system-setuid-programs and replace it with new procedure. (operating-system-default-essential-services, hurd-default-essential-services): Replace operating-system-setuid-programs with %operating-system-setuid-programs. * gnu/system/setuid.scm: New file. * doc/guix.texi (Setuid Programs): Document <setuid-program>. Co-authored-by: Brice Waegeneire <brice@waegenei.re>
2021-07-29gnu: r-matrixstats: Update to 0.60.0.Ricardo Wurmus
* gnu/packages/statistics.scm (r-matrixstats): Update to 0.60.0.
2021-07-29gnu: r-e1071: Update to 1.7-8.Ricardo Wurmus
* gnu/packages/statistics.scm (r-e1071): Update to 1.7-8.
2021-07-29gnu: r-protolite: Update to 2.1.1.Ricardo Wurmus
* gnu/packages/cran.scm (r-protolite): Update to 2.1.1.
2021-07-29gnu: r-lwgeom: Update to 0.2-7.Ricardo Wurmus
* gnu/packages/cran.scm (r-lwgeom): Update to 0.2-7.
2021-07-29gnu: r-mgsub: Update to 1.7.3.Ricardo Wurmus
* gnu/packages/cran.scm (r-mgsub): Update to 1.7.3.
2021-07-29gnu: r-matrixcalc: Update to 1.0-5.Ricardo Wurmus
* gnu/packages/cran.scm (r-matrixcalc): Update to 1.0-5.
2021-07-29gnu: r-leiden: Update to 0.3.9.Ricardo Wurmus
* gnu/packages/cran.scm (r-leiden): Update to 0.3.9.
2021-07-29gnu: r-dalex: Update to 2.3.0.Ricardo Wurmus
* gnu/packages/cran.scm (r-dalex): Update to 2.3.0.
2021-07-29gnu: r-sf: Update to 1.0-2.Ricardo Wurmus
* gnu/packages/cran.scm (r-sf): Update to 1.0-2.
2021-07-29gnu: r-summarytools: Update to 1.0.0.Ricardo Wurmus
* gnu/packages/cran.scm (r-summarytools): Update to 1.0.0.
2021-07-29gnu: r-ggeffects: Update to 1.1.1.Ricardo Wurmus
* gnu/packages/cran.scm (r-ggeffects): Update to 1.1.1.
2021-07-29gnu: r-pillar: Update to 1.6.2.Ricardo Wurmus
* gnu/packages/cran.scm (r-pillar): Update to 1.6.2.
2021-07-29gnu: r-vioplot: Update to 0.3.7.Ricardo Wurmus
* gnu/packages/cran.scm (r-vioplot): Update to 0.3.7.
2021-07-29gnu: r-stringdist: Update to 0.9.7.Ricardo Wurmus
* gnu/packages/cran.scm (r-stringdist): Update to 0.9.7.
2021-07-29gnu: r-broom: Update to 0.7.9.Ricardo Wurmus
* gnu/packages/cran.scm (r-broom): Update to 0.7.9.
2021-07-29gnu: r-rpostgresql: Update to 0.7.Ricardo Wurmus
* gnu/packages/cran.scm (r-rpostgresql): Update to 0.7.
2021-07-29gnu: r-arrow: Update to 5.0.0.Ricardo Wurmus
* gnu/packages/cran.scm (r-arrow): Update to 5.0.0.
2021-07-29gnu: apache-arrow: Update to 5.0.0.Ricardo Wurmus
* gnu/packages/databases.scm (apache-arrow): Update to 5.0.0.
2021-07-29gnu: util-linux: Explicitly depend on 'file'.Marius Bakke
...instead of using the variant that happens to be in %FINAL-INPUTS. * gnu/packages/linux.scm (util-linux)[inputs]: Add FILE. While at it, remove labels. [native-inputs]: Remove labels.
2021-07-29gnu: util-linux: Remove cross-compilation workaround.Marius Bakke
* gnu/packages/linux.scm (util-linux)[arguments]: Look for /etc/services in both NATIVE-INPUTS and INPUTS, instead of by input label. Remove unused variable. [inputs]: When cross-compiling, don't add NET-BASE.
2021-07-29gnu: util-linux: Update to 2.37.1.Marius Bakke
This fixes an infinite loop in 'mkswap'; see <https://bugzilla.redhat.com/show_bug.cgi?id=1971877>. * gnu/packages/linux.scm (util-linux): Update to 2.37.1.
2021-07-29gnu: r-with-tests: Add missing TeX Live packages.Ricardo Wurmus
* gnu/packages/statistics.scm (r-with-tests)[native-inputs]: Add texlive-grfext and texlive-latex-l3backend to the texlive union.
2021-07-29gnu: Add texlive-grfext.Ricardo Wurmus
* gnu/packages/tex.scm (texlive-grfext): New variable.
2021-07-29gnu: vim-guix-vim: Update to 0.3.0.Efraim Flashner
* gnu/packages/vim.scm (vim-guix-vim): Update to 0.3.0. [source]: Update source uri.
2021-07-29gnu: julia-weakrefstrings: Update to 1.1.0.Efraim Flashner
* gnu/packages/julia-xyz.scm (julia-weakrefstrings): Update to 1.1.0.
2021-07-29gnu: julia-typedtables: Update to 1.4.0.Efraim Flashner
* gnu/packages/julia-xyz.scm (julia-typedtables): Update to 1.4.0.
2021-07-29gnu: julia-staticarrays: Update to 1.2.9.Efraim Flashner
* gnu/packages/julia-xyz.scm (julia-staticarrays): Update to 1.2.9.
2021-07-29gnu: julia-static: Update to 0.3.0.Efraim Flashner
* gnu/packages/julia-xyz.scm (julia-static): Update to 0.3.0.
2021-07-29gnu: julia-sortingalgorithms: Update to 1.0.1.Efraim Flashner
* gnu/packages/julia-xyz.scm (julia-sortingalgorithms): Update to 1.0.1.
2021-07-29gnu: julia-simpletraits: Update to 0.9.4.Efraim Flashner
* gnu/packages/julia-xyz.scm (julia-simpletraits): Update to 0.9.4.
2021-07-29gnu: julia-recipespipeline: Update to 0.3.4.Efraim Flashner
* gnu/packages/julia-xyz.scm (julia-recipespipeline): Update to 0.3.4.
2021-07-29gnu: julia-plotutils: Update to 1.0.11.Efraim Flashner
* gnu/packages/julia-xyz.scm (julia-plotutils): Update to 1.0.11.
2021-07-29gnu: julia-offsetarrays: Update to 1.10.3.Efraim Flashner
* gnu/packages/julia-xyz.scm (julia-offsetarrays): Update to 1.10.3.
2021-07-29gnu: julia-mutablearithmetics: Update to 0.2.20.Efraim Flashner
* gnu/packages/julia-xyz.scm (julia-mutablearithmetics): Update to 0.2.20.
2021-07-29gnu: julia-matrixfactorizations: Update to 0.8.4.Efraim Flashner
* gnu/packages/julia-xyz.scm (julia-matrixfactorizations): Update to 0.8.4.
2021-07-29gnu: julia-lazyarrays: Update to 0.21.11.Efraim Flashner
* gnu/packages/julia-xyz.scm (julia-lazyarrays): Update to 0.21.11.
2021-07-29gnu: julia-json3: Update to 1.9.0.Efraim Flashner
* gnu/packages/julia-xyz.scm (julia-json3): Update to 1.9.0.
2021-07-29gnu: julia-irtools: Update to 0.4.3.Efraim Flashner
* gnu/packages/julia-xyz.scm (julia-irtools): Update to 0.4.3.
2021-07-29gnu: julia-imagecore: Update to 0.9.1.Efraim Flashner
* gnu/packages/julia-xyz.scm (julia-imagecore): Update to 0.9.1.
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