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2018-07-05gnu: r-getopt: Move from bioinformatics to cran.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-getopt): Move from here... * gnu/packages/cran.scm (r-getopt): ...to here.
2018-07-05gnu: Add r-goplot.Ricardo Wurmus
* gnu/packages/cran.scm (r-goplot): New variable.
2018-07-05gnu: Add r-biasedurn.Ricardo Wurmus
* gnu/packages/cran.scm (r-biasedurn): New variable.
2018-07-05doc: Improve UEFI/BIOS bootloader documentation.Ludovic Courtès
Partly fixes <https://bugs.gnu.org/30312>. * doc/guix.texi (Preparing for Installation): Add note on how to choose between UEFI and BIOS. (Using the Configuration System)[Bootloader]: New subsubsection. (Bootloader Configuration): Expound on the bootloader type and target. * gnu/system/examples/desktop.tmpl: Switch to UEFI. * gnu/system/examples/bare-bones.tmpl: Explicitly mention "legacy" and "BIOS" in the comments.
2018-07-05gnu: qtox: Update to 1.16.1.Rutger Helling
* gnu/packages/messaging.scm (qtox): Update to 1.16.1.
2018-07-05gnu: emacs-async: Update to 1.9.3.Tobias Geerinckx-Rice
* gnu/packages/emacs.scm (emacs-async): Update to 1.9.3. [source]: Update URI.
2018-07-05gnu: nml: Update to 0.4.5.Tobias Geerinckx-Rice
* gnu/packages/game-development.scm (nml): Update to 0.4.5.
2018-07-05gnu: nml: Use HTTPS home page.Tobias Geerinckx-Rice
* gnu/packages/game-development.scm (nml)[home-page]: Use HTTPS.
2018-07-05gnu: r-lava: Update to 1.6.2.Tobias Geerinckx-Rice
* gnu/packages/cran.scm (r-lava): Update to 1.6.2.
2018-07-05gnu: r-broom: Update to 0.4.5.Tobias Geerinckx-Rice
* gnu/packages/cran.scm (r-broom): Update to 0.4.5.
2018-07-05gnu: r-broom: Use HTTPS home page.Tobias Geerinckx-Rice
* gnu/packages/cran.scm (r-broom)[home-page]: Use HTTPS.
2018-07-05Don't force colour in aliases.Tobias Geerinckx-Rice
* gnu/system/shadow.scm (default-skeletons): Substitute ‘--color=auto’ for ‘--color’ (which implies ‘=always’) in aliases. * doc/guix.texi (G-Expressions): Also adjust examples as that makes more sense.
2018-07-05gnu: gtkwave: Mark up description.Tobias Geerinckx-Rice
* gnu/packages/fpga.scm (gtkwave)[description]: Use @dfn.
2018-07-05gnu: exempi: Mark up description.Tobias Geerinckx-Rice
* gnu/packages/freedesktop.scm (exempi)[description]: Use @dfn.
2018-07-05gnu: keepalived: Update to 2.0.5.Tobias Geerinckx-Rice
* gnu/packages/cluster.scm (keepalived): Update to 2.0.5.
2018-07-05gnu: inxi: Update to 3.0.14-1.Tobias Geerinckx-Rice
* gnu/packages/admin.scm (inxi-minimal): Update to 3.0.14-1.
2018-07-04gnu: linux-libre: Update to 4.17.4.Mark H Weaver
* gnu/packages/linux.scm (%linux-libre-version): Update to 4.17.4. (%linux-libre-hash): Update hash.
2018-07-04gnu: linux-libre@4.14: Update to 4.14.53.Mark H Weaver
* gnu/packages/linux.scm (%linux-libre-4.14-version): Update to 4.14.53. (%linux-libre-4.14-hash): Update hash.
2018-07-04gnu: linux-libre@4.9: Update to 4.9.111.Mark H Weaver
* gnu/packages/linux.scm (linux-libre-4.9): Update to 4.9.111.
2018-07-04gnu: linux-libre@4.4: Update to 4.4.139.Mark H Weaver
* gnu/packages/linux.scm (linux-libre-4.4): Update to 4.4.139.
2018-07-04gnu: Remove linux-libre@4.1.Mark H Weaver
* gnu/packages/linux.scm (linux-libre-4.1): Remove variable. * gnu/packages/aux-files/linux-libre/4.1-i686.conf, gnu/packages/aux-files/linux-libre/4.1-x86_64.conf: Delete files. * Makefile.am (AUX_FILES): Remove them.
2018-07-05gnu: pigx-scrnaseq: Update to 0.0.6.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (pigx-scrnaseq): Update to 0.0.6. [arguments]: Remove "wrap-executable" phase.
2018-07-05services: mingetty: Use '--nohangup'.Ludovic Courtès
See the discussion at <https://lists.gnu.org/archive/html/guix-devel/2018-07/msg00049.html>. * gnu/services/base.scm (mingetty-shepherd-service): Pass "--nohangup" to mingetty.
2018-07-04system: Default .bashrc uses '--color=auto' for grep and ls.Ludovic Courtès
Reported by Tobias Geerinckx-Rice <me@tobias.gr> and Björn Höfling <bjoern.hoefling@bjoernhoefling.de>. * gnu/system/shadow.scm (default-skeletons)["bashrc"]: Use '--color=auto' instead of '--color'.
2018-07-04gnu: maven: Fix maven crash when compiling java8 code.Julien Lepiller
* gnu/packages/maven.scm (maven)[arguments]: Configure classloading properly instead of adding jars to maven's classpath.
2018-07-04gnu: maven-compat: Fix test failure.Julien Lepiller
* gnu/packages/maven.scm (maven-compat)[arguments]: Add recreate-removed-jar phase.
2018-07-04gnu: maven-artifact: Update to 3.5.4.Julien Lepiller
* gnu/packages/maven.scm (maven-artifact): Update to 3.5.4. (maven-core)[arguments]: Use new version.
2018-07-04gnu: maven-wagon-provider-api: Update to 3.1.0.Julien Lepiller
* gnu/packages/maven.scm (maven-wagon-provider-api): Update to 3.1.0.
2018-07-04gnu: java-plexus-compiler-api: Update to 2.8.4.Julien Lepiller
* gnu/packages/java.scm (java-plexus-compiler-api): Update to 2.8.4.
2018-07-04vm: Disable KVM on i386.Ludovic Courtès
* gnu/build/vm.scm (load-in-linux-vm): Disable KVM on i386.
2018-07-04gnu: ledger: Use HTTPS home page URI.Arun Isaac
* gnu/packages/finance.scm (ledger)[home-page]: Use HTTPS URI.
2018-07-04gnu: ledger: Use invoke and fix #t return.Arun Isaac
* gnu/packages/finance.scm (ledger)[arguments]: Replace system* with invoke in build-doc phase. Remove #t return from relocate-elisp phase since emacs-generate-autoloads already returns #t.
2018-07-04gnu: ledger: Skip failing test.Arun Isaac
* gnu/packages/finance.scm (ledger)[arguments]: Set #:make-flags to skip failing test BaselineTest_cmd-org. Replace check phase with the check phase from gnu-build-system.
2018-07-04gnu: qtox: Update to 1.16.0.Rutger Helling
* gnu/packages/messaging.scm (qtox): Update to 1.16.0.
2018-07-04gnu: clutter-gtk: Update to 1.8.4.Tobias Geerinckx-Rice
* gnu/packages/gnome.scm (clutter-gtk): Update to 1.8.4.
2018-07-04gnu: totem: Update to 3.26.1.Tobias Geerinckx-Rice
I did not re-enable #:parallel-build? because I was unable to reproduce the original failure in the first place. * gnu/packages/gnome.scm (totem): Update to 3.26.1.
2018-07-04gnu: exempi: Update to 2.4.5.Tobias Geerinckx-Rice
* gnu/packages/freedesktop.scm (exempi): Update to 2.4.5.
2018-07-04gnu: gtkwave: Update to 3.3.91.Tobias Geerinckx-Rice
* gnu/packages/fpga.scm (gtkwave): Update to 3.3.91.
2018-07-04gnu: kicad-library: Update to 4.0.7.Tobias Geerinckx-Rice
* gnu/packages/engineering.scm (kicad-library): Update to 4.0.7.
2018-07-04gnu: kicad-library: Return #t from phases.Tobias Geerinckx-Rice
* gnu/packages/engineering.scm (kicad-library)[arguments]: Substitute INVOKE for SYSTEM*.
2018-07-04gnu: r-learnr: Update to 0.9.2.1.Tobias Geerinckx-Rice
* gnu/packages/cran.scm (r-learnr): Update to 0.9.2.1.
2018-07-03gnu: Add r-loomr.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-loomr): New variable.
2018-07-03gnu: Add r-itertools.Ricardo Wurmus
* gnu/packages/cran.scm (r-itertools): New variable.
2018-07-03gnu: Update stellarium to 0.18.0.Björn Höfling
[[PGP Signed Part:Good signature from BF286CB6593E5FFD Björn Höfling <bjoern.hoefling@bjoernhoefling.de> (trust undefined) created at 2018-06-29T20:39:51+0200 using DSA]] * gnu/packages/astronomy.scm (stellarium): Update to 0.18.0. [home-page]: Update URL. Signed-off-by: Ludovic Courtès <ludo@gnu.org>
2018-07-03gnu: emacs-helm-system-packages: Update to 1.10.0.Pierre Neidhardt
* gnu/packages/emacs.scm (emacs-helm-system-packages): Update to 1.10.0. Signed-off-by: Ludovic Courtès <ludo@gnu.org>
2018-07-03gnu: Add pocl.Fis Trivial
* gnu/packages/opencl.scm (pocl): New variable. Signed-off-by: Ludovic Courtès <ludo@gnu.org>
2018-07-03tests: basic: Wait for /var/run/shepherd/socket to be ready.Ludovic Courtès
* gnu/tests/base.scm (run-basic-test)["shepherd socket ready"]: New test.
2018-07-03gnu: pigx-bsseq: Update to 0.0.10.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (pigx-bsseq): Update to 0.0.10. [arguments]: Remove "wrap-executable" phase.
2018-07-03gnu: pigx-rnaseq: Update to 0.0.4.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (pigx-rnaseq): Update to 0.0.4. [arguments]: Remove "wrap-executable" phase.
2018-07-03gnu: pigx-chipseq: Update to 0.0.20.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (pigx-chipseq): Update to 0.0.20.
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