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* services: cuirass: Allow passing extra command line options.Christopher Baines2020-03-08
| | | | | | | | | | | 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.
* services: guix-data-service: Allow passing extra options.Christopher Baines2020-03-08
| | | | | | | | | | | | 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.
* gnu: guix-data-service: Update to 0.0.1-18.18eb9df.Christopher Baines2020-03-08
| | | | | | * 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.
* gnu: python-virtualenv: Update to 20.0.8.Jakub Kądziołka2020-03-09
| | | | | | | | * 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}.
* gnu: python-xyz: Add python-filelock.Jakub Kądziołka2020-03-09
| | | | * gnu/packages/python-xyz.scm (python-filelock): New variable.
* gnu: python-xyz: Add python-distlib.Jakub Kądziołka2020-03-09
| | | | * gnu/packages/python-xyz.scm (python-distlib): New variable.
* gnu: ngless: Update to 1.1.0.Ricardo Wurmus2020-03-08
| | | | * gnu/packages/bioinformatics.scm (ngless): Update to 1.1.0.
* gnu: Add jack-select.Ricardo Wurmus2020-03-08
| | | | * gnu/packages/music.scm (jack-select): New variable.
* gnu: taxtastic: Update to 0.8.11.Ricardo Wurmus2020-03-08
| | | | | | | | * 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.
* gnu: guile-next: Revert to 3.0.0.Ludovic Courtès2020-03-08
| | | | | | | | 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):
* gnu: Add perl-config-inifiles.Roel Janssen2020-03-08
| | | | * gnu/packages/perl.scm (perl-config-inifiles): New variable.
* gnu: Add perl-attribute-util.Roel Janssen2020-03-08
| | | | * gnu/packages/perl.scm (perl-attribute-util): New variable.
* gnu: Add font-opendyslexic.Efraim Flashner2020-03-08
| | | | | * gnu/packages/fonts.scm (font-opendyslexic): New variable. (font-open-dyslexic): Mark as deprecated package.
* gnu: beep: Remove dependency on GCC 8.Ludovic Courtès2020-03-08
| | | | * gnu/packages/terminals.scm (beep)[native-inputs]: Remove.
* gnu: beep: Update to 1.4.9.Vincent Legoll2020-03-08
| | | | | | * gnu/packages/terminals.scm (beep): Update to 1.4.9. Signed-off-by: Ludovic Courtès <ludo@gnu.org>
* services: certbot: Add server option.Jack Hill2020-03-08
| | | | | | | | | | | * 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>
* system: Export 'operating-system' missing fields.Brice Waegeneire2020-03-08
| | | | | | | | | | * 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>
* gnu: guile-next: Update to 3.0.1.Ludovic Courtès2020-03-08
| | | | * gnu/packages/guile.scm (guile-3.0): Update to 3.0.1. Use "mirror://" URL.
* gexp: Default to current target.base-for-series-3111Mathieu Othacehe2020-03-08
| | | | | | | | | | | * 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.
* store: Add set-current-target procedure.Mathieu Othacehe2020-03-08
| | | | * guix/store.scm (set-current-target): New exported procedure.
* gnu: r-robust: Update to 0.5-0.0.base-for-series-3110Ricardo Wurmus2020-03-08
| | | | * gnu/packages/statistics.scm (r-robust): Update to 0.5-0.0.
* gnu: r-rapidjsonr: Update to 1.2.0.Ricardo Wurmus2020-03-08
| | | | * gnu/packages/cran.scm (r-rapidjsonr): Update to 1.2.0.
* gnu: r-atacseqqc: Update to 1.10.3.Ricardo Wurmus2020-03-08
| | | | | * gnu/packages/bioconductor.scm (r-atacseqqc): Update to 1.10.3. [native-inputs]: Add r-knitr.
* gnu: Reword and extend descriptions for some KDE packages.Hartmut Goebel2020-03-08
| | | | | | | | | | * 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.
* gnu: Add emacs-org-journal.Martin Becze2020-03-08
| | | | * gnu/packages/emacs-xyz.scm (emacs-org-journal): New Variable.
* gnu: python-umap-learn: Fix build.Roel Janssen2020-03-08
| | | | | * gnu/packages/machine-learning.scm (python-umap-learn): Add python-joblib to run the test suite.
* services: nfs: Run rpc.mountd in foreground.Maxim Cournoyer2020-03-08
| | | | | | | | | | 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.
* gnu: QEMU: Fix CVE-2020-8608.Leo Famulari2020-03-07
| | | | | | * 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.
* gnu: brotli: Remove packageLars-Dominik Braun2020-03-07
| | | | | | | | | 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>
* gnu: woff2: Update to 1.0.2Lars-Dominik Braun2020-03-07
| | | | | | | | * 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>
* gnu: ccache: Fix indentationVincent Legoll2020-03-07
| | | | | | * gnu/packages/ccache.scm (ccache): Fix indentation Signed-off-by: Ludovic Courtès <ludo@gnu.org>
* gnu: ccache: Update to 3.7.7.Vincent Legoll2020-03-07
| | | | | | | | 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>
* gnu: eudev: Add variant with corrected Btrfs rules.Ludovic Courtès2020-03-07
| | | | | | | | 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.
* gnu: guile: Add 2.2.7.Ludovic Courtès2020-03-07
| | | | | | | | * 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.
* gnu: emacs-xr: Update to 1.17.Nicolas Goaziou2020-03-07
| | | | * gnu/packages/emacs-xyz.scm (emacs-xr): Update to 1.17.
* gnu: emacs-relint: Update to 1.15.Nicolas Goaziou2020-03-07
| | | | * gnu/packages/emacs-xyz.scm (emacs-relint): Update to 1.15.
* gnu: r-dplyr: Update to 0.8.5.Ricardo Wurmus2020-03-07
| | | | | * gnu/packages/statistics.scm (r-dplyr): Update to 0.8.5. [native-inputs]: Add r-knitr.
* gnu: r-survival: Update to 3.1-11.Ricardo Wurmus2020-03-07
| | | | * gnu/packages/statistics.scm (r-survival): Update to 3.1-11.
* gnu: r-lifecycle: Update to 0.2.0.Ricardo Wurmus2020-03-07
| | | | | * gnu/packages/cran.scm (r-lifecycle): Update to 0.2.0. [native-inputs]: Add r-knitr.
* gnu: r-covr: Update to 3.5.0.Ricardo Wurmus2020-03-07
| | | | | * gnu/packages/cran.scm (r-covr): Update to 3.5.0. [native-inputs]: Add r-knitr.
* gnu: r-pscl: Update to 1.5.5.Ricardo Wurmus2020-03-07
| | | | * gnu/packages/cran.scm (r-pscl): Update to 1.5.5.
* gnu: r-mosaic: Add r-knitr.Ricardo Wurmus2020-03-07
| | | | * gnu/packages/cran.scm (r-mosaic)[native-inputs]: Add r-knitr.
* gnu: r-insight: Update to 0.8.2.Ricardo Wurmus2020-03-07
| | | | | * gnu/packages/cran.scm (r-insight): Update to 0.8.2. [native-inputs]: Add r-knitr.
* gnu: r-heatmaply: Add r-knitr.Ricardo Wurmus2020-03-07
| | | | * gnu/packages/cran.scm (r-heatmaply)[native-inputs]: Add r-knitr.
* gnu: r-methylkit: Add r-knitr.Ricardo Wurmus2020-03-07
| | | | * gnu/packages/bioinformatics.scm (r-methylkit)[native-inputs]: Add r-knitr.
* gnu: r-ggrepel: Add r-knitr.Ricardo Wurmus2020-03-07
| | | | * gnu/packages/cran.scm (r-ggrepel)[native-inputs]: Add r-knitr.
* import/cran: Add vignette builder to native inputs.Ricardo Wurmus2020-03-07
| | | | | * guix/import/cran.scm (needs-knitr?): New procedure. (description->package): Use it.
* gnu: r-multiassayexperiment: Update to 1.12.4.Ricardo Wurmus2020-03-07
| | | | * gnu/packages/bioconductor.scm (r-multiassayexperiment): Update to 1.12.4.
* gnu: r-depecher: Update to 1.2.2.Ricardo Wurmus2020-03-07
| | | | | * gnu/packages/bioconductor.scm (r-depecher): Update to 1.2.2. [native-inputs]: Add r-knitr.
* gnu: r-xcms: Update to 3.8.2.Ricardo Wurmus2020-03-07
| | | | * gnu/packages/bioconductor.scm (r-xcms): Update to 3.8.2.
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