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2017-08-09Merge branch 'master' into core-updatesMark H Weaver
2017-08-09gnu: python-nbformat: Update to 4.3.0.Leo Famulari
* gnu/packages/python.scm (python-nbformat, python2-nbformat): Update to 4.3.0.
2017-08-09gnu: gnupg: Update to 2.1.23.Leo Famulari
* gnu/packages/gnupg.scm (gnupg): Update to 2.1.23. [arguments]: Remove 'enable-gpg2-is-gpg' from #:configure-flags, since it is now the default.
2017-08-09gnu: r-wgcna: Update to 1.61.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-wgcna): Update to 1.61. [propagated-inputs]: Add r-rcpp, r-robust, r-survival.
2017-08-09gnu: Add r-robust.Ricardo Wurmus
* gnu/packages/statistics.scm (r-robust): New variable.
2017-08-09gnu: Add r-fit-models.Ricardo Wurmus
* gnu/packages/statistics.scm (r-fit-models): New variable.
2017-08-09gnu: Add r-rrcov.Ricardo Wurmus
* gnu/packages/statistics.scm (r-rrcov): New variable.
2017-08-09gnu: Add r-pcapp.Ricardo Wurmus
* gnu/packages/statistics.scm (r-pcapp): New variable.
2017-08-09gnu: r-gdtools: Update to 0.1.5.Ricardo Wurmus
* gnu/packages/statistics.scm (r-gdtools): Update to 0.1.5.
2017-08-09gnu: r-ggbeeswarm: Update to 0.6.0.Ricardo Wurmus
* gnu/packages/statistics.scm (r-ggbeeswarm): Update to 0.6.0.
2017-08-09gnu: icecat: Add more fixes from upstream mozilla-esr52.Mark H Weaver
* gnu/packages/gnuzilla.scm (icecat)[source]: Add fixes for CVE-2017-7802, CVE-2017-7803, CVE-2017-7807, and the remaining 6 out of 23 changesets for CVE-2017-7779.
2017-08-09gnu: icecat: Rename patches to reflect CVE assignments.Mark H Weaver
Document that our existing patches include fixes for CVE-2017-7753, CVE-2017-7784, CVE-2017-7786, CVE-2017-7787, CVE-2017-7791, CVE-2017-7792, CVE-2017-7798, CVE-2017-7798, CVE-2017-7800, CVE-2017-7801, and 17 out of 23 changesets for CVE-2017-7779. * gnu/packages/gnuzilla.scm (icecat)[source]: Rename patches to reflect CVE assignments.
2017-08-09gnu: gnurl: Update to 7.55.0.ng0
* gnu/packages/gnunet.scm (gnurl): Update to 7.55.0. Signed-off-by: Tobias Geerinckx-Rice <me@tobias.gr>
2017-08-09gnu: virt-manager: Update to 1.4.2.Tobias Geerinckx-Rice
* gnu/packages/virtualization.scm (virt-manager): Update to 1.4.2.
2017-08-09gnu: libgdata: Disable failing tests.Tobias Geerinckx-Rice
* gnu/packages/gnome.scm (libgdata)[arguments]: Add ‘disable-failing-tests’ phase.
2017-08-09gnu: Add reference to (gnu packages graph).Ricardo Wurmus
This is a follow-up to 1738138cb3a48ed2f55c59c8d7c6ce12a4c4dcb3.
2017-08-09gnu: r-igraph: Move to (gnu packages graph).Ricardo Wurmus
* gnu/packages/statistics.scm (r-igraph): Move from here... * gnu/packages/graph.scm (r-igraph): ...to here.
2017-08-09gnu: Add python-igraph.Ricardo Wurmus
* gnu/packages/graph.scm (python-igraph): New variable.
2017-08-09gnu: Add igraph.Ricardo Wurmus
* gnu/packages/graph.scm: New file. * gnu/local.mk (GNU_SYSTEM_MODULES): Add it.
2017-08-09gnu: viewnior: Don't build icon-theme.cache.Efraim Flashner
* gnu/packages/image-viewers.scm (viewnior)[arguments]: Add phase to disable building the icon-theme.cache.
2017-08-09gnu: googletest: Build shared libraries.Manolis Ragkousis
* gnu/packages/check.scm (googletest)[arguments]: Pass "-DBUILD_SHARED_LIBS=ON" in #:configure-flags.
2017-08-09gnu: Add ois.Manolis Ragkousis
* gnu/packages/game-development.scm (ois): New variable.
2017-08-09gnu: dealii: Update to 8.5.0.Eric Bavier
* gnu/packages/maths.scm (dealii): Update to 8.5.0. [arguments]: Delete 'hint-example-prefix phase, which would need adjusting for this version. Users can use e.g. 'export DEAL_II_DIR=$GUIX_ENVIRONMENT'. Adjust configuration flags.
2017-08-09gnu: stress-make: Patch default shell.Eric Bavier
* gnu/packages/debug.scm (stress-make)[arguments]: Add 'set-default-shell phase.
2017-08-09gnu: suitesparse: Update to 4.5.5.Eric Bavier
* gnu/packages/maths.scm (suitesparse): Update to 4.5.5. [source]: Add 'modules' and 'snippet' field to remove bundled source. [arguments]: Remove 'prepare-out' phase. Adjust #:make-flags for metis. Make build parallel, since it now appears to be safe. [inputs]: Add metis.
2017-08-09gnu: suitesparse: Use modify-phases.Eric Bavier
* gnu/packages/maths.scm (suitesparse)[arguments]: Use modify-phases.
2017-08-09gnu: petsc, slepc: Use 'parallel-job-count'.Eric Bavier
* gnu/packages/maths.scm (petsc, slepc)[arguments]: Set #:make-flags to override default unlimited '-j'. (petsc)[arguments]: Scrub build machine cores from installed files in 'clean-local-references' phase.
2017-08-09gnu: slepc: Update to 3.7.4.Eric Bavier
* gnu/packages/maths.scm (slepc): Update to 3.7.4. [source]: Use direct source link. Remove 'file-name' field.
2017-08-09gnu: petsc: Update to 3.7.6.Eric Bavier
* gnu/packages/maths.scm (petsc): Update to 3.7.6.
2017-08-09gnu: epiphany: Update to 3.24.3.Tobias Geerinckx-Rice
* gnu/packages/gnome.scm (epiphany): Update to 3.24.3.
2017-08-09gnu: tracker: Update to 1.12.2.Tobias Geerinckx-Rice
* gnu/packages/gnome.scm (tracker): Update to 1.12.2.
2017-08-09gnu: gnome-online-accounts: Update to 3.24.2.Tobias Geerinckx-Rice
* gnu/packages/gnome.scm (gnome-online-accounts): Update to 3.24.2.
2017-08-09gnu: mutter: Update to 3.24.4.Tobias Geerinckx-Rice
* gnu/packages/gnome.scm (mutter): Update to 3.24.4.
2017-08-09gnu: gedit: Support gspell.Tobias Geerinckx-Rice
* gnu/packages/gnome.scm (gedit)[arguments]: Remove #:configure-flags. [inputs]: Add gspell.
2017-08-09gnu: gedit: Update to 3.22.1.Tobias Geerinckx-Rice
* gnu/packages/gnome.scm (gedit): Update to 3.22.1.
2017-08-09gnu: gspell: Propagate enchant dependency.Tobias Geerinckx-Rice
* gnu/packages/gnome.scm (gspell)[inputs]: Move enchant from here... [propagated-inputs]: ...to here.
2017-08-09gnu: gspell: Order inputs alphabetically.Tobias Geerinckx-Rice
* gnu/packages/gnome.scm (gspell)[inputs, native-inputs]: Re-order.
2017-08-09gnu: gnumeric: Update to 1.12.35.Tobias Geerinckx-Rice
* gnu/packages/gnome.scm (gnumeric): Update to 1.12.35.
2017-08-09gnu: brasero: Update to 3.12.2.Tobias Geerinckx-Rice
* gnu/packages/gnome.scm (brasero): Update to 3.12.2.
2017-08-09gnu: Use HTTPS for gnome.org and subdomains.Tobias Geerinckx-Rice
* gnu/packages/fonts.scm (font-bitstream-vera)[home-page]: Use HTTPS. * gnu/packages/glib.scm (glib)[home-page]: Likewise. * gnu/packages/gnome.scm (gcr, libgnome-keyring, gnome-keyring, evince) (gnome-icon-theme, libgsf, gnome-mime-data, vala, vte, python2-rsvg) (glib-networking, gnome-settings-daemon, libchamplain, grilo, grilo-plugins) (gjs, zenity, mutter, network-manager, network-manager-applet, gdm) [home-page]: Likewise. * gnu/packages/gtk.scm (gtk-engines, murrine)[home-page]: Likewise.
2017-08-08gnu: 0ad: Update to 0.0.22-alpha.Christopher Baines
* gnu/packages/games.scm (0ad-data, 0ad): Update to 0.0.22-alpha.
2017-08-08services: herd: Add a stop-service procedure.Christopher Baines
* gnu/services/herd.scm (stop-service): New procedure.
2017-08-08services: herd: Fix matching ok responses from shepherd service.Christopher Baines
Previously the match expression case for a successful response (where error is #f) required that the result component contained a list with a single element. As far as I see when looking at the responses from the shepherd, this is not normally the case. Therefore, to avoid treating successful responses as errors, make the match requirement more permissive, accepting any value. * gnu/services/herd.scm (invoke-action): Change match condition for ok responses.
2017-08-08gnu: babl: Update to 0.1.28.Efraim Flashner
* gnu/packages/gimp.scm (babl): Update to 0.1.28.
2017-08-08gnu: gegl: Use 'modify-phases' syntax.Efraim Flashner
* gnu/packages/gimp.scm (gegl)[arguments]: Use the 'modify-phases' syntax.
2017-08-08gnu: gegl: Fix building on aarch64.Efraim Flashner
* gnu/packages/gimp.scm (gegl)[arguments]: Add '-lm' configure-flag.
2017-08-08gnu: ruby-activesupport: Update to 5.1.3.Ben Woodcroft
* gnu/packages/ruby.scm (ruby-activesupport): Update to 5.1.3.
2017-08-08gnu: pciutils: Update to 3.5.5.Tobias Geerinckx-Rice
* gnu/packages/pciutils.scm (pciutils): Update to 3.5.5.
2017-08-08gnu: hunspell: Update to 1.6.1.Tobias Geerinckx-Rice
* gnu/packages/libreoffice.scm (hunspell): Update to 1.6.1. [native-inputs]: Add autoconf, automake, and libtool. [arguments]: Add ‘bootstrap’ phase.
2017-08-08gnu: hunspell: Update home page.Tobias Geerinckx-Rice
* gnu/packages/libreoffice.scm (hunspell)[home-page]: Update it.
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