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2020-03-09gnu: r-rcppannoy: Update to 0.0.16.Ricardo Wurmus
* gnu/packages/cran.scm (r-rcppannoy): Update to 0.0.16. [native-inputs]: Remove r-knitr.
2020-03-09gnu: r-quantmod: Update to 0.4-16.Ricardo Wurmus
* gnu/packages/cran.scm (r-quantmod): Update to 0.4-16.
2020-03-09gnu: r-vcd: Update to 1.4-6.Ricardo Wurmus
* gnu/packages/cran.scm (r-vcd): Update to 1.4-6.
2020-03-09gnu: r-ggrepel: Update to 0.8.2.Ricardo Wurmus
* gnu/packages/cran.scm (r-ggrepel): Update to 0.8.2.
2020-03-08services: cuirass: Allow passing extra command line options.Christopher Baines
This is so that the options supported by the service configuration don't have to always be changed. Generally though all options should be explicitly supported and documented, so this is mostly to facilitate experimentation. * gnu/services/cuirass.scm (<cuirass-configuration>): Add an extra-options field. (cuirass-shepherd-service): Pass the extra options to the shepherd servvices. * doc/guix.texi (Continuous Integration): Document it.
2020-03-08services: guix-data-service: Allow passing extra options.Christopher Baines
This is so that the options supported by the service configuration don't have to always be changed. Generally though all options should be explicitly supported and documented, so this is mostly to facilitate experimentation. * gnu/services/guix.scm (<guix-data-service-configuration>): Add extra-options and extra-process-jobs-options to the record type. (guix-data-service-shepherd-services): Handle these new configuration record fields. * doc/guix.texi (Guix Data Service): Document these new options.
2020-03-08gnu: guix-data-service: Update to 0.0.1-18.18eb9df.Christopher Baines
* gnu/packages/web.scm (guix-data-service): Update to 0.0.1-18.18eb9df. (inputs, native-inputs): Switch to using the Guile 3 package variants where applicable.
2020-03-09gnu: python-virtualenv: Update to 20.0.8.Jakub Kądziołka
* gnu/packages/python-xyz.scm (python-virtualenv): Update to 20.0.8. [arguments]: Remove the now-redundant 'disable-failing-test phase. [native-inputs]: Add python-setuptools and python-setuptools-scm. [inputs]: Add python-{appdirs, distlib, filelock, six, importlib-metadata}.
2020-03-09gnu: python-xyz: Add python-filelock.Jakub Kądziołka
* gnu/packages/python-xyz.scm (python-filelock): New variable.
2020-03-09gnu: python-xyz: Add python-distlib.Jakub Kądziołka
* gnu/packages/python-xyz.scm (python-distlib): New variable.
2020-03-08gnu: ngless: Update to 1.1.0.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (ngless): Update to 1.1.0.
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.
2020-03-08gexp: Default to current target.Mathieu Othacehe
* guix/gexp.scm (lower-object): Set target argument to 'current by default and look for the current target system at bind time if needed, (gexp->file): ditto, (gexp->script): ditto, (lower-gexp): make sure lowered extensions are not cross-compiled. * tests/gexp.scm: Add cross-compilation test-cases for gexp->script and gexp->file with a target passed explicitely and with a default target.
2020-03-08store: Add set-current-target procedure.Mathieu Othacehe
* guix/store.scm (set-current-target): New exported procedure.
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.
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