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* gnu: Add python-bx-python.Ricardo Wurmus2018-10-21
| | | | | * gnu/packages/bioinformatics.scm (python-bx-python): New variable. (python2-bx-python): Define in terms of python-bx-python.
* gnu: python2-bx-python: Update to 0.8.2.Ricardo Wurmus2018-10-21
| | | | | | | | | * gnu/packages/bioinformatics.scm (python2-bx-python): Update to 0.8.2. [source]: Remove obsolete snippet. [inputs]: Move python2-numpy from here... [propagated-inputs]: ...to here; add python2-six. [native-inputs]: Add python2-lzo and python2-cython. [home-page]: Update to new home at Github.
* gnu: bwa-pssm: Fetch from git.Ricardo Wurmus2018-10-21
| | | | * gnu/packages/bioinformatics.scm (bwa-pssm)[source]: Fetch from git.
* gnu: tophat: Update to 2.1.1.Ricardo Wurmus2018-10-21
| | | | | | * gnu/packages/bioinformatics.scm (tophat): Update to 2.1.1. * gnu/packages/patches/tophat-build-with-later-seqan.patch: Delete file. * gnu/local.mk (dist_patch_DATA): Remove patch.
* gnu: linux-libre: Update to 4.18.16.Mark H Weaver2018-10-21
| | | | | * gnu/packages/linux.scm (%linux-libre-version): Update to 4.18.16. (%linux-libre-hash): Update hash.
* gnu: linux-libre@4.14: Update to 4.14.78.Mark H Weaver2018-10-21
| | | | | * gnu/packages/linux.scm (%linux-libre-4.14-version): Update to 4.14.78. (%linux-libre-4.14-hash): Update hash.
* gnu: linux-libre@4.9: Update to 4.9.135.Mark H Weaver2018-10-21
| | | | * gnu/packages/linux.scm (linux-libre-4.9): Update to 4.9.135.
* gnu: linux-libre@4.4: Update to 4.4.162.Mark H Weaver2018-10-21
| | | | * gnu/packages/linux.scm (linux-libre-4.4): Update to 4.4.162.
* gnu: Add emacs-slime-repl-ansi-color.Pierre Neidhardt2018-10-21
| | | | * gnu/packages/emacs.scm (emacs-slime-repl-ansi-color): New variable.
* gnu: rng-tools: Update to 6.6.Marius Bakke2018-10-21
| | | | * gnu/packages/linux.scm (rng-tools): Update to 6.6.
* gnu: fluidsynth: Update to 2.0.1.Marius Bakke2018-10-21
| | | | | | | * gnu/packages/audio.scm (fluidsynth): Update to 2.0.1. (fluidsynth-1): New public variable. * gnu/packages/games.scm (gzdoom)[inputs]: Change FLUIDSYNTH to FLUIDSYNTH-1. * gnu/packages/music.scm (lmms)[inputs]: Likewise.
* gnu: libgxps: Update to 0.3.0.Marius Bakke2018-10-21
| | | | | | | | | * gnu/packages/gnome.scm (libgxps): Update to 0.3.0. [source](patches): Remove. [build-system]: Switch to MESON-BUILD-SYSTEM. [inputs]: Change LIBJPEG to LIBJPEG-TURBO. * gnu/packages/patches/libgxps-CVE-2017-11590.patch: Delete file. * gnu/local.mk (dist_patch_DATA): Adjust accordingly.
* gnu: libgxps: Propagate required inputs.Marius Bakke2018-10-21
| | | | | * gnu/packages/gnome.scm (libgxps)[inputs]: Move CAIRO, GLIB and LIBARCHIVE ... [propagated-inputs]: ... here. New field.
* gnu: re2: Update to 2018-10-01.Marius Bakke2018-10-21
| | | | * gnu/packages/regex.scm (re2): Update to 2018-10-01.
* gnu: libgphoto2: Update to 2.5.19.Marius Bakke2018-10-21
| | | | * gnu/packages/photo.scm (libgphoto2): Update to 2.5.19.
* gnu: appstream-glib: Update to 0.7.14.Marius Bakke2018-10-21
| | | | * gnu/packages/glib.scm (appstream-glib): Update to 0.7.14.
* gnu: openal: Update to 1.19.1.Marius Bakke2018-10-21
| | | | * gnu/packages/audio.scm (openal): Update to 1.19.1.
* gnu: kodi: Disable version checker.Efraim Flashner2018-10-21
| | | | | | | Fixes bug#32997. * gnu/packages/kodi.scm (kodi)[arguments]: Add substitution to remove the version checking configuration option.
* gnu: python2-dendropy: Disable failing test.Ben Woodcroft2018-10-21
| | | | | * gnu/packages/bioinformatics.scm (python2-dendropy)[arguments]: Disable failing test.
* gnu: bowtie: Update to 2.3.4.3.Ricardo Wurmus2018-10-20
| | | | | | | | | * gnu/packages/bioinformatics.scm (bowtie): Update to 2.3.4.3. [source]: Fetch from git. [inputs]: Replace python-2 with python-wrapper; move perl, perl-clone, perl-test-deep, and perl-test-simple from here... [native-inputs]: ...to here. [arguments]: Simplify check phase.
* gnu: blast+: Use INVOKE and return #T unconditionally.Ricardo Wurmus2018-10-20
| | | | | * gnu/packages/bioinformatics.scm (blast+)[arguments]: Use INVOKE and return #T unconditionally.
* gnu: bedops: Update to 2.4.35.Ricardo Wurmus2018-10-20
| | | | | * gnu/packages/bioinformatics.scm (bedops): Update to 2.4.35. [source]: Fetch from git.
* gnu: bedops: Use INVOKE.Ricardo Wurmus2018-10-20
| | | | * gnu/packages/bioinformatics.scm (bedops)[arguments]: Use INVOKE.
* gnu: bamm: Fetch from git and use INVOKE.Ricardo Wurmus2018-10-20
| | | | | * gnu/packages/bioinformatics.scm (bamm)[source]: Fetch from git. [arguments]: Use INVOKE and return #T unconditionally.
* gnu: aragorn: Use invoke and simplify.Ricardo Wurmus2018-10-20
| | | | | * gnu/packages/bioinformatics.scm (aragorn)[arguments]: Use INVOKE in build phase; simplify install phase.
* gnu: clipper: Update to 1.2.1.Ricardo Wurmus2018-10-20
| | | | | | * gnu/packages/bioinformatics.scm (clipper): Update to 1.2.1. [source]: Fetch from git. [arguments]: Add fix-typo phase.
* gnu: python-pybedtools: Update to 0.7.10.Ricardo Wurmus2018-10-20
| | | | | | | | | | * gnu/packages/bioinformatics.scm (python2-pybedtools): Update to 0.7.10. [arguments]: Disable broken tests. [propagated-inputs]: Replace bedtools with bedtools-2.26; add python-matplotlib, python-pysam, and python-pyyaml. [native-inputs]: Remove python-pyyaml; add kentutils, python-numpy, python-pandas, and python-six. (python-pybedtools): New variable.
* gnu: Add bedtools-2.26.Ricardo Wurmus2018-10-20
| | | | * gnu/packages/bioinformatics.scm (bedtools-2.26): New variable.
* gnu: cataclysm-dda: Update snapshot.Kei Kebreau2018-10-20
| | | | * gnu/packages/games.scm (cataclysm-dda): Update snapshot to 0b2c194e5.
* gnu: maxima: Update to 5.42.0.Kei Kebreau2018-10-20
| | | | * gnu/packages/maths.scm (maxima): Update to 5.42.0.
* gnu: python-glances: Update to 3.0.2.Oleg Pykhalov2018-10-20
| | | | * gnu/packages/python.scm (python-glances): Update to 3.0.2.
* gnu: emacs-hy-mode: Update to 1.0.3.Oleg Pykhalov2018-10-20
| | | | * gnu/packages/emacs.scm (emacs-hy-mode): Update to 1.0.3.
* gnu: emacs-erc-hl-nicks: Update to 1.3.3.Oleg Pykhalov2018-10-20
| | | | * gnu/packages/emacs.scm (emacs-erc-hl-nicks): Update to 1.3.3.
* gnu: emacs-yasnippet: Update to 0.13.0.Oleg Pykhalov2018-10-20
| | | | * gnu/packages/emacs.scm (emacs-yasnippet): Update to 0.13.0.
* gnu: emacs-nginx-mode: Update to 1.1.9.Oleg Pykhalov2018-10-20
| | | | * gnu/packages/emacs.scm (emacs-nginx-mode): Update to 1.1.9.
* gnu: emacs-rainbow-mode: Update to 1.0.1.Oleg Pykhalov2018-10-20
| | | | * gnu/packages/emacs.scm (emacs-rainbow-mode): Update to 1.0.1.
* gnu: emacs-smart-mode-line: Update to 2.12.0.Oleg Pykhalov2018-10-20
| | | | * gnu/packages/emacs.scm (emacs-smart-mode-line): Update to 2.12.0.
* gnu: emacs-fill-column-indicator: Update to 1.89.Oleg Pykhalov2018-10-20
| | | | * gnu/packages/emacs.scm (emacs-fill-column-indicator): Update to 1.89.
* gnu: emacs-ggtags: Update to 0.8.13.Oleg Pykhalov2018-10-20
| | | | * gnu/packages/emacs.scm (emacs-ggtags): Update to 0.8.13.
* gnu: emacs-which-key: Update to 3.3.0.Oleg Pykhalov2018-10-20
| | | | * gnu/packages/emacs.scm (emacs-which-key): Update to 3.3.0.
* gnu: Add soundconverter.Christopher Baines2018-10-20
| | | | | | * gnu/packages/gnome.scm (soundconverter): New variable. * gnu/packages/patches/soundconverter-remove-gconf-dependency.patch: New file. * gnu/local.mk (dist_patch_DATA): Add it.
* gnu: Add enchive.nixo2018-10-19
| | | | | | * gnu/packages/crypto.scm (enchive): New variable. Signed-off-by: Ludovic Courtès <ludo@gnu.org>
* services: ntp: Document 'ntp-service-type' and 'ntp-configuration'.Ludovic Courtès2018-10-19
| | | | | | | | | | | * gnu/services/networking.scm (<ntp-configuration>)[servers]: Add default value. (ntp-service-type)[default-value]: New field. (ntp-service): Mark as deprecated. * gnu/services/desktop.scm (%desktop-services): Use (service ntp-service-type) instead of calling 'ntp-service'. * doc/guix.texi (Networking Services): Document 'ntp-service-type' and 'ntp-configuration'.
* gnu: Add i3blocks.Meiyo Peng2018-10-19
| | | | | | * gnu/packages/wm.scm (i3blocks): New variable. Signed-off-by: Ludovic Courtès <ludo@gnu.org>
* gnu: qsynth: Update to 0.5.3.Ricardo Wurmus2018-10-19
| | | | * gnu/packages/audio.scm (qsynth): Update to 0.5.3.
* gnu: sbcl-slime-swank: Remove reference to unbound variable.Ludovic Courtès2018-10-19
| | | | | | | Fixes a regression introduced in commit c4d4ae1e16254a96caaeb5ccb4486f301ae4f1b7. * gnu/packages/lisp.scm (sbcl-slime-swank)[license]: Remove extra 'license'.
* gnu: guile-wiredtiger: Update to 0.7.0.Amirouche2018-10-19
| | | | | | | | | * gnu/packages/databases.scm (guile-wiredtiger): Update to 0.7.0. [inputs]: Replace wiredtiger with wiredtiger-3 [propagated-inputs]: Remove guile-lib, add guile-bytestructures [description]: Update it. Signed-off-by: Ludovic Courtès <ludo@gnu.org>
* gnu: Add wiredtiger 3.1.0Amirouche2018-10-19
| | | | | | | * gnu/packages/databases.scm (wiredtiger-3): New variable that inherits from wiredtiger Signed-off-by: Ludovic Courtès <ludo@gnu.org>
* tests: Run 'guix pack' tests using the external store.Ludovic Courtès2018-10-19
| | | | | | | | | | | | | Fixes <https://bugs.gnu.org/32184>. * guix/tests.scm (call-with-external-store): New procedure. (with-external-store): New macro. * tests/pack.scm (%store): Remove. (test-assertm): Add 'store' parameter. ("self-contained-tarball"): Wrap in 'with-external-store'. * tests/guix-pack.sh: Connect to the external store, if possible, by setting NIX_STORE_DIR and GUIX_DAEMON_SOCKET. Remove most uses of '--bootstrap'.
* pack: Fix "-C none -f tarball".Ludovic Courtès2018-10-19
| | | | | | | | | | | | | Fixes a regression introduced in 48b444304e206c35cf2c8e0d87a4711f1aac4fd4 whereby "guix pack -C none hello" would fail with: ERROR: In procedure string-join: In procedure string-join: Wrong type argument in position 1: #f builder for `/gnu/store/…-tarball-pack.tar.drv' failed with exit code 1 * guix/scripts/pack.scm (self-contained-tarball): Adjust for when 'compressor-command' returns #f.
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