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* gnu: snap: Update to 4.2.2.2.Nicolas Goaziou2018-10-22
| | | | * gnu/packages/education.scm (snap): Update to 4.2.2.2. Update source URL.
* gnu: Add r-ruvseq.Ricardo Wurmus2018-10-22
| | | | * gnu/packages/bioconductor.scm (r-ruvseq): New variable.
* gnu: livemedia-utils: Update to 2018.10.17 [fixes CVE-2018-4013].Leo Famulari2018-10-22
| | | | * gnu/packages/video.scm (livemedia-utils): Update to 2018.10.17.
* gnu: libmpdclient: Update to 2.16.Leo Famulari2018-10-21
| | | | * gnu/packages/mpd.scm (libmpdclient): Update to 2.16.
* gnu: knot: Update to 2.7.3.Tobias Geerinckx-Rice2018-10-22
| | | | * gnu/packages/dns.scm (knot): Update to 2.7.3.
* gnu: OpenSSH: Update to 7.9p1.Leo Famulari2018-10-21
| | | | * gnu/packages/ssh.scm (openssh): Update to 7.9p1.
* gnu: light: Update to 1.2.Pierre Langlois2018-10-21
| | | | | | | | | * gnu/packages/linux.scm (light): Update to 1.2. [source]: Switch to url-fetch. [arguments]: Remove. [native-inputs]: Remove help2man. Add autoconf and automake. Signed-off-by: Ludovic Courtès <ludo@gnu.org>
* gnu: Add python-ilinkedlist.Luther Thompson2018-10-21
| | | | * gnu/packages/python.scm (python-ilinkedlist): New variable.
* install: Make /var/guix/…/guix-profile a relative symlink.Ludovic Courtès2018-10-21
| | | | | * gnu/build/install.scm (populate-single-profile-directory): Make /var/guix/profiles/per-user/root/guix-profile a relative symlink.
* gnu: flexbar: Update to 3.4.0.Ricardo Wurmus2018-10-21
| | | | | | | | * gnu/packages/bioinformatics.scm (flexbar): Update to 3.4.0. [source]: Fetch from git. [arguments]: Adjust check and install phases. [home-page]: Update to new home at Github. [license]: Change to bsd-3.
* gnu: seqan: Update to 2.4.0.Ricardo Wurmus2018-10-21
| | | | | | | * gnu/packages/bioinformatics.scm (seqan): Update to 2.4.0. [native-inputs]: Replace bzip2 with xz. (seqan-1): New variable. (tophat)[inputs]: Use seqan-1.
* gnu: khmer: Update to 2.1.2.Ricardo Wurmus2018-10-21
| | | | | | | | | | * gnu/packages/bioinformatics.scm (khmer): Update to 2.1.2. [source]: Fetch from git; remove bundled libraries in snippet. [arguments]: Remove "set-paths" phase; remove "post-install-check" phase; remove "reset-gzip-timestamps" phase. [native-inputs]: Remove seqan and python-nose; add python-cython, python-pytest, and python-pytest-runner. [inputs]: Remove gcc-4.9.
* gnu: python-screed: Update to 1.0.Ricardo Wurmus2018-10-21
| | | | | | | * gnu/packages/bioinformatics.scm (python-screed): Update to 1.0. [arguments]: Run tests after installation. [native-inputs]: Add python-pytest, python-pytest-cov, and python-pytest-runner; remove python-nose.
* gnu: fasttree: Use INVOKE.Ricardo Wurmus2018-10-21
| | | | | * gnu/packages/bioinformatics.scm (fasttree)[arguments]: Use INVOKE; simplify install phase.
* gnu: express-beta-diversity: Update to 1.0.8.Ricardo Wurmus2018-10-21
| | | | | | * gnu/packages/bioinformatics.scm (express-beta-diversity): Update to 1.0.8. [source]: Fetch from git. [arguments]: Use INVOKE; remove "exit-source" build phase; simplify.
* gnu: edirect: Update to 10.2.20181018.Ricardo Wurmus2018-10-21
| | | | | | * gnu/packages/bioinformatics.scm (edirect): Update to 10.2.20181018. [arguments]: Add simple check phase; simplify other phases. [inputs]: Add perl-xml-simple.
* gnu: eigensoft: Update to 7.2.1.Ricardo Wurmus2018-10-21
| | | | | * gnu/packages/bioinformatics.scm (eigensoft): Update to 7.2.1. [arguments]: Remove Makefile modification.
* gnu: discrover: Fetch from git.Ricardo Wurmus2018-10-21
| | | | * gnu/packages/bioinformatics.scm (discrover)[source]: Fetch from git.
* gnu: Add texlive-latex-examplep.Ricardo Wurmus2018-10-21
| | | | * gnu/packages/tex.scm (texlive-latex-examplep): New variable.
* gnu: Add texlive-latex-verbatimbox.Ricardo Wurmus2018-10-21
| | | | * gnu/packages/tex.scm (texlive-latex-verbatimbox): New variable.
* gnu: Add texlive-latex-readarray.Ricardo Wurmus2018-10-21
| | | | * gnu/packages/tex.scm (texlive-latex-readarray): New variable.
* gnu: Add texlive-generic-listofitems.Ricardo Wurmus2018-10-21
| | | | * gnu/packages/tex.scm (texlive-generic-listofitems): New variable.
* gnu: Add texlive-latex-doi.Ricardo Wurmus2018-10-21
| | | | * gnu/packages/tex.scm (texlive-latex-doi): New variable.
* gnu: diamond: Fetch from git.Ricardo Wurmus2018-10-21
| | | | * gnu/packages/bioinformatics.scm (diamond)[source]: Fetch from git.
* gnu: delly: Update to 0.7.9.Ricardo Wurmus2018-10-21
| | | | | | | | | | * 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.
* gnu: deeptools: Update to 3.1.3.Ricardo Wurmus2018-10-21
| | | | * gnu/packages/bioinformatics.scm (deeptools): Update to 3.1.3.
* gnu: eolie: Update to 0.9.45.Ricardo Wurmus2018-10-21
| | | | * gnu/packages/gnome.scm (eolie): Update to 0.9.45.
* gnu: python-dendropy: Fetch from git.Ricardo Wurmus2018-10-21
| | | | * gnu/packages/bioinformatics.scm (python-dendropy)[source]: Fetch from git.
* gnu: python-py2bit: Update to 0.3.0.Ricardo Wurmus2018-10-21
| | | | * gnu/packages/bioinformatics.scm (python-py2bit): Update to 0.3.0.
* gnu: cutadapt: Update to 1.18.Ricardo Wurmus2018-10-21
| | | | | * gnu/packages/bioinformatics.scm (cutadapt): Update to 1.18. [inputs]: Add python-dnaio.
* gnu: Add python-dnaio.Ricardo Wurmus2018-10-21
| | | | * gnu/packages/bioinformatics.scm (python-dnaio): New variable.
* gnu: crossmap: Update to 0.2.9.Ricardo Wurmus2018-10-21
| | | | | | * 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.
* gnu: python-twobitreader: Update to 3.1.6.Ricardo Wurmus2018-10-21
| | | | | * gnu/packages/bioinformatics.scm (python-twobitreader): Update to 3.1.6. [source]: Fetch from git.
* 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.
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