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2018-10-21gnu: delly: Update to 0.7.9....* gnu/packages/bioinformatics.scm (delly): Update to 0.7.9. [source]: Fetch from git. [arguments]: Add phase install-templates; use default install phase. [native-inputs]: Remove python-2. [home-page]: Use new home page. * gnu/packages/patches/delly-use-system-libraries.patch: Delete file. * gnu/local.mk (dist_patch_DATA): Remove patch. Ricardo Wurmus
2018-10-21gnu: deeptools: Update to 3.1.3....* gnu/packages/bioinformatics.scm (deeptools): Update to 3.1.3. Ricardo Wurmus
2018-10-21gnu: eolie: Update to 0.9.45....* gnu/packages/gnome.scm (eolie): Update to 0.9.45. Ricardo Wurmus
2018-10-21gnu: python-dendropy: Fetch from git....* gnu/packages/bioinformatics.scm (python-dendropy)[source]: Fetch from git. Ricardo Wurmus
2018-10-21gnu: python-py2bit: Update to 0.3.0....* gnu/packages/bioinformatics.scm (python-py2bit): Update to 0.3.0. Ricardo Wurmus
2018-10-21gnu: cutadapt: Update to 1.18....* gnu/packages/bioinformatics.scm (cutadapt): Update to 1.18. [inputs]: Add python-dnaio. Ricardo Wurmus
2018-10-21gnu: Add python-dnaio....* gnu/packages/bioinformatics.scm (python-dnaio): New variable. Ricardo Wurmus
2018-10-21gnu: crossmap: Update to 0.2.9....* gnu/packages/bioinformatics.scm (crossmap): Update to 0.2.9. * gnu/packages/patches/crossmap-allow-system-pysam.patch: Delete file. * gnu/local.mk (dist_patch_DATA): Remove patch. Ricardo Wurmus
2018-10-21gnu: python-twobitreader: Update to 3.1.6....* gnu/packages/bioinformatics.scm (python-twobitreader): Update to 3.1.6. [source]: Fetch from git. Ricardo Wurmus
2018-10-21gnu: Add python-bx-python....* gnu/packages/bioinformatics.scm (python-bx-python): New variable. (python2-bx-python): Define in terms of python-bx-python. Ricardo Wurmus
2018-10-21gnu: python2-bx-python: Update to 0.8.2....* 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. Ricardo Wurmus
2018-10-21gnu: bwa-pssm: Fetch from git....* gnu/packages/bioinformatics.scm (bwa-pssm)[source]: Fetch from git. Ricardo Wurmus
2018-10-21gnu: tophat: Update to 2.1.1....* 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. Ricardo Wurmus
2018-10-21gnu: linux-libre: Update to 4.18.16....* gnu/packages/linux.scm (%linux-libre-version): Update to 4.18.16. (%linux-libre-hash): Update hash. Mark H Weaver
2018-10-21gnu: linux-libre@4.14: Update to 4.14.78....* gnu/packages/linux.scm (%linux-libre-4.14-version): Update to 4.14.78. (%linux-libre-4.14-hash): Update hash. Mark H Weaver
2018-10-21gnu: linux-libre@4.9: Update to 4.9.135....* gnu/packages/linux.scm (linux-libre-4.9): Update to 4.9.135. Mark H Weaver
2018-10-21gnu: linux-libre@4.4: Update to 4.4.162....* gnu/packages/linux.scm (linux-libre-4.4): Update to 4.4.162. Mark H Weaver
2018-10-21gnu: Add emacs-slime-repl-ansi-color....* gnu/packages/emacs.scm (emacs-slime-repl-ansi-color): New variable. Pierre Neidhardt
2018-10-21gnu: rng-tools: Update to 6.6....* gnu/packages/linux.scm (rng-tools): Update to 6.6. Marius Bakke
2018-10-21gnu: fluidsynth: Update to 2.0.1....* 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. Marius Bakke
2018-10-21gnu: libgxps: Update to 0.3.0....* 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. Marius Bakke
2018-10-21gnu: libgxps: Propagate required inputs....* gnu/packages/gnome.scm (libgxps)[inputs]: Move CAIRO, GLIB and LIBARCHIVE ... [propagated-inputs]: ... here. New field. Marius Bakke
2018-10-21gnu: re2: Update to 2018-10-01....* gnu/packages/regex.scm (re2): Update to 2018-10-01. Marius Bakke
2018-10-21gnu: libgphoto2: Update to 2.5.19....* gnu/packages/photo.scm (libgphoto2): Update to 2.5.19. Marius Bakke
2018-10-21gnu: appstream-glib: Update to 0.7.14....* gnu/packages/glib.scm (appstream-glib): Update to 0.7.14. Marius Bakke
2018-10-21gnu: openal: Update to 1.19.1....* gnu/packages/audio.scm (openal): Update to 1.19.1. Marius Bakke
2018-10-21gnu: kodi: Disable version checker....Fixes bug#32997. * gnu/packages/kodi.scm (kodi)[arguments]: Add substitution to remove the version checking configuration option. Efraim Flashner
2018-10-21gnu: python2-dendropy: Disable failing test....* gnu/packages/bioinformatics.scm (python2-dendropy)[arguments]: Disable failing test. Ben Woodcroft
2018-10-20gnu: bowtie: Update to 2.3.4.3....* 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. Ricardo Wurmus
2018-10-20gnu: blast+: Use INVOKE and return #T unconditionally....* gnu/packages/bioinformatics.scm (blast+)[arguments]: Use INVOKE and return #T unconditionally. Ricardo Wurmus
2018-10-20gnu: bedops: Update to 2.4.35....* gnu/packages/bioinformatics.scm (bedops): Update to 2.4.35. [source]: Fetch from git. Ricardo Wurmus
2018-10-20gnu: bedops: Use INVOKE....* gnu/packages/bioinformatics.scm (bedops)[arguments]: Use INVOKE. Ricardo Wurmus
2018-10-20gnu: bamm: Fetch from git and use INVOKE....* gnu/packages/bioinformatics.scm (bamm)[source]: Fetch from git. [arguments]: Use INVOKE and return #T unconditionally. Ricardo Wurmus
2018-10-20gnu: aragorn: Use invoke and simplify....* gnu/packages/bioinformatics.scm (aragorn)[arguments]: Use INVOKE in build phase; simplify install phase. Ricardo Wurmus
2018-10-20gnu: clipper: Update to 1.2.1....* gnu/packages/bioinformatics.scm (clipper): Update to 1.2.1. [source]: Fetch from git. [arguments]: Add fix-typo phase. Ricardo Wurmus
2018-10-20gnu: python-pybedtools: Update to 0.7.10....* 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. Ricardo Wurmus
2018-10-20gnu: Add bedtools-2.26....* gnu/packages/bioinformatics.scm (bedtools-2.26): New variable. Ricardo Wurmus
2018-10-20gnu: cataclysm-dda: Update snapshot....* gnu/packages/games.scm (cataclysm-dda): Update snapshot to 0b2c194e5. Kei Kebreau
2018-10-20gnu: maxima: Update to 5.42.0....* gnu/packages/maths.scm (maxima): Update to 5.42.0. Kei Kebreau
2018-10-20gnu: python-glances: Update to 3.0.2....* gnu/packages/python.scm (python-glances): Update to 3.0.2. Oleg Pykhalov
2018-10-20gnu: emacs-hy-mode: Update to 1.0.3....* gnu/packages/emacs.scm (emacs-hy-mode): Update to 1.0.3. Oleg Pykhalov
2018-10-20gnu: emacs-erc-hl-nicks: Update to 1.3.3....* gnu/packages/emacs.scm (emacs-erc-hl-nicks): Update to 1.3.3. Oleg Pykhalov
2018-10-20gnu: emacs-yasnippet: Update to 0.13.0....* gnu/packages/emacs.scm (emacs-yasnippet): Update to 0.13.0. Oleg Pykhalov
2018-10-20gnu: emacs-nginx-mode: Update to 1.1.9....* gnu/packages/emacs.scm (emacs-nginx-mode): Update to 1.1.9. Oleg Pykhalov
2018-10-20gnu: emacs-rainbow-mode: Update to 1.0.1....* gnu/packages/emacs.scm (emacs-rainbow-mode): Update to 1.0.1. Oleg Pykhalov
2018-10-20gnu: emacs-smart-mode-line: Update to 2.12.0....* gnu/packages/emacs.scm (emacs-smart-mode-line): Update to 2.12.0. Oleg Pykhalov
2018-10-20gnu: emacs-fill-column-indicator: Update to 1.89....* gnu/packages/emacs.scm (emacs-fill-column-indicator): Update to 1.89. Oleg Pykhalov
2018-10-20gnu: emacs-ggtags: Update to 0.8.13....* gnu/packages/emacs.scm (emacs-ggtags): Update to 0.8.13. Oleg Pykhalov
2018-10-20gnu: emacs-which-key: Update to 3.3.0....* gnu/packages/emacs.scm (emacs-which-key): Update to 3.3.0. Oleg Pykhalov
2018-10-20gnu: Add soundconverter....* 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. Christopher Baines
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