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2020-03-08gnu: Add jack-select.Ricardo Wurmus
* gnu/packages/music.scm (jack-select): New variable.
2020-03-08gnu: taxtastic: Update to 0.8.11.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (taxtastic): Update to 0.8.11. [source]: Fetch from Github. [arguments]: Build with default Python; add phases 'prepare-directory, 'python37-compatibility, and update 'check phase. [propagated-inputs]: Replace Python 2 variants with Python 3 variants.
2020-03-08gnu: guile-next: Revert to 3.0.0.Ludovic Courtès
Guile 3.0.1 segfaults while building guix-system-tests.drv on and "guile3.0-guix" on x86_64-linux. * gnu/packages/guile.scm (guile-next): Revert to 3.0.0. (guile-3.0):
2020-03-08gnu: Add perl-config-inifiles.Roel Janssen
* gnu/packages/perl.scm (perl-config-inifiles): New variable.
2020-03-08gnu: Add perl-attribute-util.Roel Janssen
* gnu/packages/perl.scm (perl-attribute-util): New variable.
2020-03-08gnu: Add font-opendyslexic.Efraim Flashner
* gnu/packages/fonts.scm (font-opendyslexic): New variable. (font-open-dyslexic): Mark as deprecated package.
2020-03-08gnu: beep: Remove dependency on GCC 8.Ludovic Courtès
* gnu/packages/terminals.scm (beep)[native-inputs]: Remove.
2020-03-08gnu: beep: Update to 1.4.9.Vincent Legoll
* gnu/packages/terminals.scm (beep): Update to 1.4.9. Signed-off-by: Ludovic Courtès <ludo@gnu.org>
2020-03-08services: certbot: Add server option.Jack Hill
* gnu/services/certbot.scm (certbot-configuration): Add server option. (certbot-command): Use server option. (certbot-actication): Use server option. (certbot-nginx-server-configurations): Use server option. * doc/guix.texi (Certificate Services): Document server option. Co-authored-by: Tobias Geerinckx-Rice <me@tobias.gr> Signed-off-by: Ludovic Courtès <ludo@gnu.org>
2020-03-08system: Export 'operating-system' missing fields.Brice Waegeneire
* gnu/system.scm: Export 'operating-system-firmware', 'operating-system-keyboard-layout', 'operating-system-name-service-switch', 'operating-system-pam-services', 'operating-system-setuid-programs', 'operating-system-skeletons', 'operating-system-sudoers-file', 'operating-system-swap-devices'. Signed-off-by: Ludovic Courtès <ludo@gnu.org>
2020-03-08gnu: guile-next: Update to 3.0.1.Ludovic Courtès
* gnu/packages/guile.scm (guile-3.0): Update to 3.0.1. Use "mirror://" URL.
2020-03-08gnu: r-robust: Update to 0.5-0.0.Ricardo Wurmus
* gnu/packages/statistics.scm (r-robust): Update to 0.5-0.0.
2020-03-08gnu: r-rapidjsonr: Update to 1.2.0.Ricardo Wurmus
* gnu/packages/cran.scm (r-rapidjsonr): Update to 1.2.0.
2020-03-08gnu: r-atacseqqc: Update to 1.10.3.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-atacseqqc): Update to 1.10.3. [native-inputs]: Add r-knitr.
2020-03-08gnu: Reword and extend descriptions for some KDE packages.Hartmut Goebel
* gnu/packages/kde-multimedia.scm (libkcompatdisc)[description]: Extend. * gnu/packages/kde-pim.scm (akonadi-search, kalarmcal, kdemailimporter, kdepim-apps-libs, kidentitymanagement, kldap, kmailtransport, kmbox, kmime, kontactinterface, kpimtextedit)[description]: Reword and extend. (ktnef, kpimcommon, libkdepim)[synopsis, description]: Reword and extend. (kmailtransport)[synopsis]: Fix space. * gnu/packages/kde-systemtools.scm (khelpcenter)[description]: Extend.
2020-03-08gnu: Add emacs-org-journal.Martin Becze
* gnu/packages/emacs-xyz.scm (emacs-org-journal): New Variable.
2020-03-08gnu: python-umap-learn: Fix build.Roel Janssen
* gnu/packages/machine-learning.scm (python-umap-learn): Add python-joblib to run the test suite.
2020-03-08services: nfs: Run rpc.mountd in foreground.Maxim Cournoyer
Fixes <https://bugs.gnu.org/39708>. Shepherd doesn't keep track of processes that fork themselves and would disable the process after restarting it a couple times. * gnu/services/nfs.scm (nfs-shepherd-services): Invoke rpc.mountd with the '--foreground' option.
2020-03-07gnu: QEMU: Fix CVE-2020-8608.Leo Famulari
* gnu/packages/patches/qemu-CVE-2020-8608.patch: New file. * gnu/local.mk (dist_patch_DATA): Add it. * gnu/packages/virtualization.scm (qemu)[source]: Use it.
2020-03-07gnu: brotli: Remove packageLars-Dominik Braun
Same package is provided by google-brotli. * gnu/packages/compression.scm (brotli): Redefine as a deprecated alias for "google-brotli". Co-authored-by: Ludovic Courtès <ludo@gnu.org>
2020-03-07gnu: woff2: Update to 1.0.2Lars-Dominik Braun
* gnu/packages/fontutils.scm (woff2): Update to 1.0.2 and switch to cmake * gnu/packages/patches/woff2-libbrotli.patch: Remove * gnu/local.mk (dist_patch_DATA): Remove patch Signed-off-by: Ludovic Courtès <ludo@gnu.org>
2020-03-07gnu: ccache: Fix indentationVincent Legoll
* gnu/packages/ccache.scm (ccache): Fix indentation Signed-off-by: Ludovic Courtès <ludo@gnu.org>
2020-03-07gnu: ccache: Update to 3.7.7.Vincent Legoll
gnu/packages/ccache.scm (ccache): Update to 3.7.7, update homepage to ccache.dev, get source code from github, remove fortran 77 from description. Signed-off-by: Ludovic Courtès <ludo@gnu.org>
2020-03-07gnu: eudev: Add variant with corrected Btrfs rules.Ludovic Courtès
Discussed at <https://bugs.gnu.org/39926>. * gnu/packages/linux.scm (eudev/btrfs-fix): New variable. * gnu/services/base.scm (<udev-configuration>)[udev]: Default to it. (udev-service): Likewise for #:udev.
2020-03-07gnu: guile: Add 2.2.7.Ludovic Courtès
* gnu/packages/guile.scm (guile-2.2.7): New variable. (guile-2.2/bug-fix): Redefine as a deprecated alias for GUILE-2.2.7. * gnu/packages/admin.scm (shepherd)[native-inputs, inputs]: Use GUILE-2.2.7. * gnu/packages/patches/guile-finalization-crash.patch: Remove. * gnu/local.mk (dist_patch_DATA): Remove it.
2020-03-07gnu: emacs-xr: Update to 1.17.Nicolas Goaziou
* gnu/packages/emacs-xyz.scm (emacs-xr): Update to 1.17.
2020-03-07gnu: emacs-relint: Update to 1.15.Nicolas Goaziou
* gnu/packages/emacs-xyz.scm (emacs-relint): Update to 1.15.
2020-03-07gnu: r-dplyr: Update to 0.8.5.Ricardo Wurmus
* gnu/packages/statistics.scm (r-dplyr): Update to 0.8.5. [native-inputs]: Add r-knitr.
2020-03-07gnu: r-survival: Update to 3.1-11.Ricardo Wurmus
* gnu/packages/statistics.scm (r-survival): Update to 3.1-11.
2020-03-07gnu: r-lifecycle: Update to 0.2.0.Ricardo Wurmus
* gnu/packages/cran.scm (r-lifecycle): Update to 0.2.0. [native-inputs]: Add r-knitr.
2020-03-07gnu: r-covr: Update to 3.5.0.Ricardo Wurmus
* gnu/packages/cran.scm (r-covr): Update to 3.5.0. [native-inputs]: Add r-knitr.
2020-03-07gnu: r-pscl: Update to 1.5.5.Ricardo Wurmus
* gnu/packages/cran.scm (r-pscl): Update to 1.5.5.
2020-03-07gnu: r-mosaic: Add r-knitr.Ricardo Wurmus
* gnu/packages/cran.scm (r-mosaic)[native-inputs]: Add r-knitr.
2020-03-07gnu: r-insight: Update to 0.8.2.Ricardo Wurmus
* gnu/packages/cran.scm (r-insight): Update to 0.8.2. [native-inputs]: Add r-knitr.
2020-03-07gnu: r-heatmaply: Add r-knitr.Ricardo Wurmus
* gnu/packages/cran.scm (r-heatmaply)[native-inputs]: Add r-knitr.
2020-03-07gnu: r-methylkit: Add r-knitr.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-methylkit)[native-inputs]: Add r-knitr.
2020-03-07gnu: r-ggrepel: Add r-knitr.Ricardo Wurmus
* gnu/packages/cran.scm (r-ggrepel)[native-inputs]: Add r-knitr.
2020-03-07gnu: r-multiassayexperiment: Update to 1.12.4.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-multiassayexperiment): Update to 1.12.4.
2020-03-07gnu: r-depecher: Update to 1.2.2.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-depecher): Update to 1.2.2. [native-inputs]: Add r-knitr.
2020-03-07gnu: r-xcms: Update to 3.8.2.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-xcms): Update to 3.8.2.
2020-03-07gnu: r-yamss: Update to 1.12.1.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-yamss): Update to 1.12.1.
2020-03-07gnu: r-viridis: Add r-knitr.Ricardo Wurmus
* gnu/packages/statistics.scm (r-viridis)[native-inputs]: Add r-knitr.
2020-03-07gnu: r-vsn: Add r-knitr.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-vsn)[native-inputs]: Add r-knitr.
2020-03-07fd: Install bash completion properly.Michael Rohleder
* gnu/packages/rust-apps.scm (fd)[arguments]: Replace the dash in "bash-completion.d" with an underscore. Signed-off-by: Jakub Kądziołka <kuba@kadziolka.net>
2020-03-07gnu: anki: Fix mpv audio playbackRobert Smith
* gnu/packages/patches/anki-mpv-args.patch: New file. * gnu/local.mk (dist_patch_DATA): Adjust accordingly. * gnu/packages/education.scm (anki): Adjust accordingly, wrap anki's PATH to include mpv executable. Signed-off-by: Jakub Kądziołka <kuba@kadziolka.net>
2020-03-07gnu: next: Fix build with SBCL 2.0.2.Pierre Neidhardt
* gnu/packages/web-browsers.scm (next)[arguments]: Fix lambda-list type error on SBCL 2.0.2.
2020-03-07gnu: s6-rc: Update to 0.5.1.2.Tobias Geerinckx-Rice
* gnu/packages/skarnet.scm (s6-rc): Update to 0.5.1.2.
2020-03-07gnu: s6-portable-utils: Update to 2.2.2.2.Tobias Geerinckx-Rice
* gnu/packages/skarnet.scm (s6-portable-utils): Update to 2.2.2.2.
2020-03-07gnu: s6-networking: Update to 2.3.1.2.Tobias Geerinckx-Rice
* gnu/packages/skarnet.scm (s6-networking): Update to 2.3.1.2.
2020-03-07gnu: s6-linux-utils: Update to 2.5.1.2.Tobias Geerinckx-Rice
* gnu/packages/skarnet.scm (s6-linux-utils): Update to 2.5.1.2.
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