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2018-10-22gnu: python-markdown: Update home page.Marius Bakke
* gnu/packages/python.scm (python-markdown)[home-page]: Change to current.
2018-10-22gnu: python-m2crypto: Update to 0.30.1.Marius Bakke
* gnu/packages/python-crypto.scm (python-m2crypto): Update to 0.30.1.
2018-10-22gnu: python-m2crypto: python-typing is only needed for python2.Marius Bakke
* gnu/packages/python-crypto.scm (python-m2crypto)[propagated-inputs]: Remove. [properties]: New field. (python2-m2crypto)[propagated-inputs]: Add PYTHON2-TYPING.
2018-10-22gnu: xorg-server: Update to 1.20.2.Marius Bakke
* gnu/packages/xorg.scm (xorg-server): Update to 1.20.2.
2018-10-22gnu: xf86-input-libinput: Update to 0.28.1.Marius Bakke
* gnu/packages/xorg.scm (xf86-input-libinput): Update to 0.28.1.
2018-10-22gnu: libmd: Update to 1.0.1.Marius Bakke
* gnu/packages/crypto.scm (libmd): Update to 1.0.1.
2018-10-22gnu: samba: Update to 4.8.6.Marius Bakke
* gnu/packages/samba.scm (samba): Update to 4.8.6.
2018-10-22gnu: Add GN.Marius Bakke
* gnu/packages/build-tools.scm (gn): New public variable.
2018-10-22gnu: python-lazy-object-proxy: Update to 1.3.1.Marius Bakke
* gnu/packages/python.scm (python-lazy-object-proxy): Update to 1.3.1.
2018-10-22gnu: python-mistune: Update to 0.8.4.Marius Bakke
* gnu/packages/python.scm (python-mistune): Update to 0.8.4.
2018-10-22gnu: liblxqt: Update to 0.13.0.Meiyo Peng
* gnu/packages/lxqt.scm (liblxqt): Update to 0.13.0. [source]: Remove patches. [home-page]: Use HTTPS. * gnu/packages/patches/liblxqt-include.patch: Remove file. * gnu/local.mk (dist_patch_DATA): Remove it. Signed-off-by: 宋文武 <iyzsong@member.fsf.org>
2018-10-22gnu: libqtxdg: Update to 3.2.0.Meiyo Peng
* gnu/packages/lxqt.scm (libqtxdg): Update to 3.2.0. Signed-off-by: 宋文武 <iyzsong@member.fsf.org>
2018-10-22gnu: Add emacs-scribble-mode.Christopher Lemmer Webber
* gnu/packages/emacs.scm (emacs-scribble-mode): New variable.
2018-10-22gnu: snap: Update to 4.2.2.2.Nicolas Goaziou
* gnu/packages/education.scm (snap): Update to 4.2.2.2. Update source URL.
2018-10-22gnu: Add r-ruvseq.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-ruvseq): New variable.
2018-10-22gnu: livemedia-utils: Update to 2018.10.17 [fixes CVE-2018-4013].Leo Famulari
* gnu/packages/video.scm (livemedia-utils): Update to 2018.10.17.
2018-10-21gnu: libmpdclient: Update to 2.16.Leo Famulari
* gnu/packages/mpd.scm (libmpdclient): Update to 2.16.
2018-10-22gnu: knot: Update to 2.7.3.Tobias Geerinckx-Rice
* gnu/packages/dns.scm (knot): Update to 2.7.3.
2018-10-21gnu: OpenSSH: Update to 7.9p1.Leo Famulari
* gnu/packages/ssh.scm (openssh): Update to 7.9p1.
2018-10-21gnu: light: Update to 1.2.Pierre Langlois
* 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>
2018-10-21gnu: Add python-ilinkedlist.Luther Thompson
* gnu/packages/python.scm (python-ilinkedlist): New variable.
2018-10-21install: Make /var/guix/…/guix-profile a relative symlink.Ludovic Courtès
* gnu/build/install.scm (populate-single-profile-directory): Make /var/guix/profiles/per-user/root/guix-profile a relative symlink.
2018-10-21gnu: flexbar: Update to 3.4.0.Ricardo Wurmus
* 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.
2018-10-21gnu: seqan: Update to 2.4.0.Ricardo Wurmus
* 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.
2018-10-21gnu: khmer: Update to 2.1.2.Ricardo Wurmus
* 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.
2018-10-21gnu: python-screed: Update to 1.0.Ricardo Wurmus
* 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.
2018-10-21gnu: fasttree: Use INVOKE.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (fasttree)[arguments]: Use INVOKE; simplify install phase.
2018-10-21gnu: express-beta-diversity: Update to 1.0.8.Ricardo Wurmus
* 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.
2018-10-21gnu: edirect: Update to 10.2.20181018.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (edirect): Update to 10.2.20181018. [arguments]: Add simple check phase; simplify other phases. [inputs]: Add perl-xml-simple.
2018-10-21gnu: eigensoft: Update to 7.2.1.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (eigensoft): Update to 7.2.1. [arguments]: Remove Makefile modification.
2018-10-21gnu: discrover: Fetch from git.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (discrover)[source]: Fetch from git.
2018-10-21gnu: Add texlive-latex-examplep.Ricardo Wurmus
* gnu/packages/tex.scm (texlive-latex-examplep): New variable.
2018-10-21gnu: Add texlive-latex-verbatimbox.Ricardo Wurmus
* gnu/packages/tex.scm (texlive-latex-verbatimbox): New variable.
2018-10-21gnu: Add texlive-latex-readarray.Ricardo Wurmus
* gnu/packages/tex.scm (texlive-latex-readarray): New variable.
2018-10-21gnu: Add texlive-generic-listofitems.Ricardo Wurmus
* gnu/packages/tex.scm (texlive-generic-listofitems): New variable.
2018-10-21gnu: Add texlive-latex-doi.Ricardo Wurmus
* gnu/packages/tex.scm (texlive-latex-doi): New variable.
2018-10-21gnu: diamond: Fetch from git.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (diamond)[source]: Fetch from git.
2018-10-21gnu: delly: Update to 0.7.9.Ricardo Wurmus
* 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.
2018-10-21gnu: deeptools: Update to 3.1.3.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (deeptools): Update to 3.1.3.
2018-10-21gnu: eolie: Update to 0.9.45.Ricardo Wurmus
* gnu/packages/gnome.scm (eolie): Update to 0.9.45.
2018-10-21gnu: python-dendropy: Fetch from git.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (python-dendropy)[source]: Fetch from git.
2018-10-21gnu: python-py2bit: Update to 0.3.0.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (python-py2bit): Update to 0.3.0.
2018-10-21gnu: cutadapt: Update to 1.18.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (cutadapt): Update to 1.18. [inputs]: Add python-dnaio.
2018-10-21gnu: Add python-dnaio.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (python-dnaio): New variable.
2018-10-21gnu: crossmap: Update to 0.2.9.Ricardo Wurmus
* 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.
2018-10-21gnu: python-twobitreader: Update to 3.1.6.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (python-twobitreader): Update to 3.1.6. [source]: Fetch from git.
2018-10-21gnu: Add python-bx-python.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (python-bx-python): New variable. (python2-bx-python): Define in terms of python-bx-python.
2018-10-21gnu: python2-bx-python: Update to 0.8.2.Ricardo Wurmus
* 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.
2018-10-21gnu: bwa-pssm: Fetch from git.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (bwa-pssm)[source]: Fetch from git.
2018-10-21gnu: tophat: Update to 2.1.1.Ricardo Wurmus
* 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.
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