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* gnu: r-lattice: Move to other recommended R packages.•••* gnu/packages/statistics.scm (r-lattice): Move to the set of recommended R packages. Ricardo Wurmus2017-03-171-20/+20
* gnu: Add r-kernsmooth.•••* gnu/packages/statistics.scm (r-kernsmooth): New variable. Ricardo Wurmus2017-03-171-0/+22
* gnu: Add r-foreign.•••* gnu/packages/statistics.scm (r-foreign): New variable. Ricardo Wurmus2017-03-171-0/+20
* gnu: Add r-codetools.•••* gnu/packages/statistics.scm (r-codetools): New variable. Ricardo Wurmus2017-03-171-0/+18
* gnu: Add r-cluster.•••* gnu/packages/statistics.scm (r-cluster): New variable. Ricardo Wurmus2017-03-171-0/+20
* gnu: Add r-class.•••* gnu/packages/statistics.scm (r-class): New variable. Ricardo Wurmus2017-03-171-0/+22
* gnu: Add r-mass.•••* gnu/packages/statistics.scm (r-mass): New variable. Ricardo Wurmus2017-03-171-0/+21
* gnu: Add r-boot.•••* gnu/packages/statistics.scm (r-boot): New variable. Ricardo Wurmus2017-03-171-0/+21
* gnu: youtube-dl: Update to 2017.03.16.•••* gnu/packages/video.scm (youtube-dl): Update to 2017.03.16. Tobias Geerinckx-Rice2017-03-171-2/+2
* gnu: asciidoc: Use local docbook-xml package.•••* gnu/packages/documentation.scm (asciidoc)[inputs]: Add docbook-xml. [arguments]: Add 'make-local-docbook-xml' phase. Kei Kebreau2017-03-161-0/+9
* gnu: Add knot.•••* gnu/packages/dns.scm (knot): New variable. Tobias Geerinckx-Rice2017-03-171-1/+80
* gnu: Add liburcu.•••* gnu/packages/datastructures.scm (liburcu): New variable. Tobias Geerinckx-Rice2017-03-171-1/+25
* gnu: dns: Fix typo and use @dfn in descriptions.•••* gnu/packages/dns.scm (bind)[description]: Use @dfn to expand acronyms. (yadifa)[description]: Likewise, and fix a typo. Tobias Geerinckx-Rice2017-03-171-6/+6
* gnu: linux-libre: Update to 4.10.3.•••* gnu/packages/linux.scm (%linux-libre-version): Update to 4.10.3. (%linux-libre-hash): Update hash. Leo Famulari2017-03-161-2/+2
* gnu: linux-libre@4.4: Update to 4.4.54.•••* gnu/packages/linux.scm (linux-libre-4.4): Update to 4.4.54. Leo Famulari2017-03-161-2/+2
* gnu: linux-libre@4.9: Update to 4.9.15.•••* gnu/packages/linux.scm (linux-libre-4.9): Update to 4.9.15. Leo Famulari2017-03-161-2/+2
* gnu: qemu: Fix CVE-2017-{2620,2630}.•••* gnu/packages/patches/qemu-CVE-2017-2620.patch, gnu/packages/patches/qemu-CVE-2017-2630.patch: New files. * gnu/local.mk (dist_patch_DATA): Add them. * gnu/packages/qemu.scm (qemu)[source]: Use them. Leo Famulari2017-03-164-0/+185
* gnu: virglrenderer: Fix CVE-2017-6386.•••* gnu/packages/patches/virglrenderer-CVE-2017-6386.patch: New file. * gnu/local.mk (dist_patch_DATA): Add it. * gnu/packages/spice.scm (virglrenderer)[source]: Use it. Leo Famulari2017-03-163-0/+56
* services: connman: Rework service.•••* gnu/services/networking.scm (connman-service): Remove. (<connman-configuration>): New record specifying the package to be used (connman) and whether vpn plugin shall be disabled (disable-vpn?). (connman-configuration): New exported variable. (connman-configuration?): New exported variable. (connman-service-type): Export it. * doc/guix.texi (Networking Services): Adjust accordingly. Signed-off-by: Ludovic Courtès <ludo@gnu.org> Mathieu Othacehe2017-03-161-37/+49
* gnu: password-store: Fix compatibility with GnuPG 2.1.19.•••* gnu/packages/patches/password-store-gnupg-compat.patch: New file. * gnu/local.mk (dist_patch_DATA): Add it. * gnu/packages/password-utils.scm (password-store)[source]: Use it. Signed-off-by: Clément Lassieur <clement@lassieur.org> Clément Lassieur2017-03-163-1/+58
* gnu: Add r-seurat.•••* gnu/packages/bioinformatics.scm (r-seurat): New variable. Co-authored-by: Ricardo Wurmus <rekado@elephly.net> Raoul Jean Pierre Bonnal2017-03-161-0/+79
* gnu: sra-tools: Update to 2.8.2-1.•••* gnu/packages/bioinformatics.scm (sra-tools): Update to 2.8.2-1. [arguments]: Add DEFAULT_CRT and DEFAULT_KFG to make flags. Ricardo Wurmus2017-03-161-3/+9
* gnu: ncbi-vdb: Install configuration files.•••* gnu/packages/bioinformatics.scm (ncbi-vdb)[arguments]: Add phase "install-configuration-files". Ricardo Wurmus2017-03-161-0/+8
* gnu: ncbi-vdb: Override search path for java-ngs.•••* gnu/packages/bioinformatics.scm (ncbi-vdb)[arguments]: Patch "package.prl" to ensure that java-ngs is found by the configure script; remove configure flag "--with-ngs-java-prefix". Ricardo Wurmus2017-03-161-2/+5
* gnu: ncbi-vdb: Use modify-phases syntax.•••* gnu/packages/bioinformatics.scm (ncbi-vdb)[arguments]: Use modify-phases syntax. Ricardo Wurmus2017-03-161-55/+54
* gnu: ncbi-vdb: Update to 2.8.2.•••* gnu/packages/bioinformatics.scm (ncbi-vdb): Update to 2.8.2. Ricardo Wurmus2017-03-161-2/+2
* gnu: ngs-sdk: Update to 1.3.0.•••* gnu/packages/bioinformatics.scm (ngs-sdk): Update to 1.3.0. Ricardo Wurmus2017-03-161-2/+2
* gnu: Add pzstd.•••* gnu/packages/compression.scm (pzstd): New variable. Tobias Geerinckx-Rice2017-03-161-0/+41
* gnu: Add zstd.•••* gnu/packages/compression.scm (zstd): New variable. Tobias Geerinckx-Rice2017-03-161-0/+44
* gnu: python-publicsuffix2: Update to 2.20160818.•••* gnu/packages/python.scm (python-publicsuffix2): Update to 2.20160818. Tobias Geerinckx-Rice2017-03-161-2/+2
* gnu: awscli: Update to 1.11.63.•••* gnu/packages/python.scm (awscli): Update to 1.11.63. Tobias Geerinckx-Rice2017-03-161-2/+2
* gnu: python-botocore: Update to 1.5.26.•••* gnu/packages/python.scm (python-botocore): Update to 1.5.26. Tobias Geerinckx-Rice2017-03-161-2/+2
* gnu: python-ptyprocess: Update to 0.5.1.•••* gnu/packages/python.scm (python-ptyprocess): Update to 0.5.1. Tobias Geerinckx-Rice2017-03-161-2/+2
* gnu: Add prboom-plus.•••* gnu/packages/games.scm (prboom-plus): New variable. Kei Kebreau2017-03-151-1/+46
* gnu: Add tftp-hpa.•••* gnu/packages/networking.scm (tftp-hpa): New variable. Signed-off-by: Leo Famulari <leo@famulari.name> Gábor Boskovits2017-03-151-0/+25
* gnu: guile-next: Update to 2.2.0.•••* gnu/packages/guile.scm (guile-next): Update to 2.2.0. Andy Wingo2017-03-151-4/+4
* gnu: profanity: Make the source URL version-agnostic.•••* gnu/packages/messaging.scm (profanity)[source]: Use (version) in the source URL. Leo Famulari2017-03-151-1/+2
* gnu: units: Update to 2.14.•••* gnu/packages/maths.scm (units): Update to 2.14. Tobias Geerinckx-Rice2017-03-151-2/+2
* gnu: no-more-secrets: Update to 0.3.2.•••* gnu/packages/games.scm (no-more-secrets): Update to 0.3.2. Tobias Geerinckx-Rice2017-03-151-2/+2
* gnu: mailutils: Update to 3.2.•••* gnu/packages/mail.scm (mailutils): Update to 3.2. Tobias Geerinckx-Rice2017-03-151-2/+2
* gnu: Use INSTALL-FILE where appropriate.•••* gnu/packages/admin.scm (wpa-supplicant-minimal): Substitute the simpler INSTALL-FILE for COPY-FILE when invoked with redundant arguments. * gnu/packages/bioinformatics.scm (couger, aragorn, express-beta-diversity, edirect, fasttree, rsem, samtools-0.1): Likewise. * gnu/packages/code.scm (withershins): Likewise. * gnu/packages/conky.scm (conky): Likewise. * gnu/packages/debug.scm (delta, american-fuzzy-lop): Likewise. * gnu/packages/emacs.scm (emacs-mit-scheme-doc): Likewise. * gnu/packages/engineering.scm (librecad): Likewise. Tobias Geerinckx-Rice2017-03-157-49/+38
* gnu: cryptsetup: Update to 1.7.4.•••* gnu/packages/cryptsetup.scm (cryptsetup): Update to 1.7.4. Tobias Geerinckx-Rice2017-03-151-2/+2
* gnu: man-pages: Update to 4.10.•••* gnu/packages/man.scm (man-pages): Update to 4.10. [home-page]: Use HTTPS. Tobias Geerinckx-Rice2017-03-151-3/+3
* gnu: Add profanity.•••* gnu/packages/messaging.scm (profanity): New variable. Signed-off-by: Leo Famulari <leo@famulari.name> Mekeor Melire2017-03-151-0/+35
* gnu: Add libstrophe.•••* gnu/packages/messaging.scm (libstrophe): New variable. Signed-off-by: Leo Famulari <leo@famulari.name> Mekeor Melire2017-03-151-0/+35
* gnu: Add libmesode.•••* gnu/packages/messaging.scm (libmesode): New variable. Signed-off-by: Leo Famulari <leo@famulari.name> Mekeor Melire2017-03-151-0/+36
* gnu: bitcoin-core: Update to 0.14.0.•••* gnu/packages/finance.scm (bitcoin-core): Update to 0.14.0. Leo Famulari2017-03-151-2/+2
* gnu: mariadb: Update to 10.1.22 [fixes CVE-2017-3302 and CVE-2017-3313].•••* gnu/packages/databases.scm (mariadb): Update to 10.1.22. Marius Bakke2017-03-151-2/+2
* gnu: python-waf: Update to 1.9.8.•••* gnu/packages/python.scm (python-waf, python2-waf): Update to 1.9.8. [home-page]: Use https. Efraim Flashner2017-03-151-3/+3
* gnu: direnv: Update to 2.11.3.•••* gnu/packages/shellutils.scm (direnv): Update to 2.11.3. Tobias Geerinckx-Rice2017-03-151-2/+2