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* gnu: Add AnnotationDbi.•••* gnu/packages/bioinformatics.scm (r-annotationdbi): New variable. Ricardo Wurmus2016-01-071-0/+27
* gnu: Add Biobase.•••* gnu/packages/bioinformatics.scm (r-biobase): New variable. Ricardo Wurmus2016-01-071-0/+22
* gnu: Add snow.•••* gnu/packages/statistics.scm (r-snow): New variable. Ricardo Wurmus2016-01-071-0/+21
* gnu: Add futile.logger.•••* gnu/packages/statistics.scm (r-futile-logger): New variable. Ricardo Wurmus2016-01-071-0/+24
* gnu: Add futile.options.•••* gnu/packages/statistics.scm (r-futile-options): New variable. Ricardo Wurmus2016-01-071-0/+22
* gnu: Add lambda.r.•••* gnu/packages/statistics.scm (r-lambda-r): New variable. Ricardo Wurmus2016-01-071-0/+21
* gnu: Add r-xml.•••* gnu/packages/statistics.scm (r-xml): New variable. Ricardo Wurmus2016-01-071-0/+25
* gnu: Add RCurl.•••* gnu/packages/statistics.scm (r-rcurl): New variable. Ricardo Wurmus2016-01-071-0/+32
* gnu: Add RSQLite.•••* gnu/packages/statistics.scm (r-rsqlite): New variable. Ricardo Wurmus2016-01-071-0/+22
* gnu: Add xmlstarlet.•••* gnu/packages/xml.scm (xmlstarlet): New variable. Raimon Grau2016-01-071-0/+25
* gnu: zita-convolver: Drop the '-march=native' optimization.•••* gnu/packages/audio.scm (zita-convolver)[source]: Add snippet. 宋文武2016-01-071-0/+5
* gnu: zita-resampler: Drop the '-march=native' optimization.•••* gnu/packages/audio.scm (zita-resampler)[source]: Add snippet. 宋文武2016-01-071-0/+5
* gnu: Add ruby-ansi.•••* gnu/packages/ruby.scm (ruby-ansi): New variable. Ben Woodcroft2016-01-071-0/+36
* gnu: edirect: Update to 3.50.•••* gnu/packages/bioinformatics.scm (edirect): Update to 3.50. [native-inputs]: Remove "unzip". Ricardo Wurmus2016-01-071-5/+3
* gnu: w3m: Enable SSL, disable broken protocols and ciphers.•••Fixes <http://bugs.gnu.org/16791>. * gnu/packages/patches/w3m-force-ssl_verify_server-on.patch: New file. * gnu/packages/patches/w3m-disable-sslv2-and-sslv3.patch: New file. * gnu/packages/patches/w3m-disable-weak-ciphers.patch: New file. * gnu/packages/w3m.scm (w3m)[source]: Add patches. * gnu-system.am (dist_patch_DATA): Add the new files. Leo Famulari2016-01-074-1/+76
* gnu: w3m: Update patch to use '-p1'.•••* gnu/packages/patches/w3m-fix-compile.patch: Rename this file... * gnu/packages/patches/w3m-libgc.patch: ...to this, and adjust patch prefix level to '-p1'. * gnu-system.am (dist_patch_DATA): Update patch name. * gnu/packages/w3m.scm (w3m)[source]: Update patch name. [source]: Drop patch flag -p0. Leo Famulari2016-01-073-17/+30
* build-system/gnu: Make 'package-with-explicit-inputs' idempotent.•••* guix/build-system/gnu.scm (package-with-explicit-inputs): Use 'ensure-keyword-arguments' instead of appending to ARGS. * gnu/packages/commencement.scm (static-bash-for-glibc): Add missing #:guile argument. Ludovic Courtès2016-01-061-2/+3
* gnu: guix: Update development snapshot to f888c0b.•••* gnu/packages/package-management.scm (guix-devel): Update to f888c0b. Ludovic Courtès2016-01-061-4/+4
* gnu: gmsh: Update to 2.11.0.•••* gnu/packages/maths.scm (gmsh): Update to 2.11.0. [arguments]: Replace 'check phase. Eric Bavier2016-01-061-3/+11
* gnu: sudo: Use /var/run/sudo instead of /run/sudo.•••* gnu/packages/admin.scm (sudo)[arguments]: Pass --with-rundir=/var/run/sudo since /var/run is cleaned up at boot time on GuixSD whereas /run is not. Ludovic Courtès2016-01-061-2/+2
* gnu: ldc: Fix license.•••* gnu/packages/ldc.scm (ldc)[license]: Replace invalid use of 'license:x11-style' by LICENSE:BOOST1.0. Ludovic Courtès2016-01-061-1/+1
* gnu: icedtea7: Rename to icedtea-7.•••* gnu/packages/java.scm (icedtea7): Rename variable to... (icedtea-7): ...this. (icedtea): Refer to "icedtea-7". Ricardo Wurmus2016-01-061-2/+2
* gnu: icedtea6: Rename to icedtea-6.•••* gnu/packages/java.scm (icedtea6): Rename variable to... (icedtea-6): ...this. Ricardo Wurmus2016-01-061-4/+4
* gnu: icedtea6, icedtea7: Rename package to "icedtea".•••* gnu/packages/java.scm (icedtea6): Change package name to "icedtea". (icedtea7): Inherit package name. Ricardo Wurmus2016-01-061-3/+3
* gnu: Add and use default IcedTea.•••* gnu/packages/java.scm (icedtea): New variable. (swt)[native-inputs]: Replace "icedtea6" with "icedtea". * gnu/packages/bioinformatics.scm (htsjdk)[native-inputs]: Likewise. (ngs-java)[inputs]: Likewise. * gnu/packages/kodi.scm (kodi)[native-inputs]: Replace "icedtea7" with "icedtea". * gnu/packages/ruby.scm (ruby-rjb)[native-inputs]: Replace "icedtea7" with "icedtea". Ricardo Wurmus2016-01-064-6/+8
* gnu: icedtea6, icedtea7: Unpack to "openjdk.src".•••* gnu/packages/java.scm (icedtea6)[arguments]: Unpack OpenJDK sources to "openjdk.src". (icedtea7)[arguments]: Inherit "--with-openjdk-src-dir" flag; refer to "openjdk.src" in build phases; simplify "unpack" phase. [native-inputs]: Rename "openjdk-drop" to "openjdk-src". Ricardo Wurmus2016-01-061-56/+47
* gnu: Add Jellyfish.•••* gnu/packages/bioinformatics.scm (jellyfish): New variable. Ricardo Wurmus2016-01-061-0/+50
* gnu: calibre: Update to 2.48.0.•••* gnu/packages/ebook.scm (calibre): Update to 2.48.0. Andreas Enge2016-01-051-3/+3
* gnu: Add LDC.•••* gnu/packages/ldc.scm: New file. * gnu/packages/patches/ldc-disable-tests.patch: New file. * gnu-system.am (GNU_SYSTEM_MODULES): Add ldc.scm. (dist_patch_DATA): Add patch file. Roel Janssen2016-01-052-0/+208
* gnu: Add emacs-undo-tree.••• * gnu/packages/emacs.scm (emacs-undo-tree): New variable. Signed-off-by: Ludovic Courtès <ludo@gnu.org> Dmitry Bogatov2016-01-051-0/+21
* gnu: emacs: Remove 'info.info'.•••* gnu/packages/emacs.scm (emacs)[arguments]: Use 'modify-phases'. Add 'remove-info.info' phase. Ludovic Courtès2016-01-051-9/+15
* gnu: gtk+: Add patch to support GUIX_GTK3_PATH.•••* gnu/packages/patches/gtk3-respect-GUIX_GTK3_PATH: New file. * gnu-system.am (dist_patch_DATA): Add it. * gnu/packages/gtk.scm (gtk+) [source]: Add patch. [native-search-paths]: Add search path for GUIX_GTK3_PATH. Ricardo Wurmus2016-01-042-2/+45
* gnu: gtk+-2: Add patch to support GUIX_GTK2_PATH.•••* gnu/packages/patches/gtk2-respect-GUIX_GTK2_PATH: New file. * gnu-system.am (dist_patch_DATA): Add it. * gnu/packages/gtk.scm (gtk+-2) [source]: Add patch. [native-search-paths]: Add search path for GUIX_GTK2_PATH. Ricardo Wurmus2016-01-042-2/+53
* gnu: julia: Update to 0.4.2.•••* gnu/packages/patches/julia-0.3.10-fix-empty-array.patch: Remove file. * gnu-system.am (dist_patch_DATA): Remove it. * gnu/packages/julia.scm (julia): Update to 0.4.2. [arguments]: Remove phase "fix-building-with-mcjit-llvm"; replace phase "patch-include-path" with "fix-include-and-link-paths"; add phase "hardcode-paths"; add missing make-flags. [inputs]: Replace "pcre" with "pcre2"; replace "git" with "libgit2"; add "coreutils"; add "libuv-julia"; add "wget"; add "which". [native-inputs]: Remove "which". Ricardo Wurmus2016-01-042-45/+69
* gnu: Add libuv-julia.•••* gnu/packages/julia.scm (libuv-julia): New variable. Ricardo Wurmus2016-01-041-0/+26
* gnu: utf8proc: Update to 1.3.1.•••* gnu/packages/textutils.scm (utf8proc): Update to 1.3.1. [arguments]: Remove custom "install" phase. Ricardo Wurmus2016-01-041-14/+6
* gnu: samba: Update to 4.3.3.•••Fixes CVE-2015-{3223,5252,5299,5296,8467,5330}. * gnu/packages/samba.scm (samba): Update to 4.3.3. Leo Famulari2016-01-031-2/+2
* gnu: ldb: Update to 1.1.24.•••Required for samba-4.3.3 in order to fix CVE-2015-5330 and CVE-2015-3223. * gnu/packages/samba.scm (ldb): Update to 1.2.24. Leo Famulari2016-01-031-2/+2
* gnu: Add Asymptote.•••* gnu/packages/bdw-gc.scm (libgc-for-c++): New variable. * gnu/packages/plotutils.scm (asymptote): New variable. * gnu/packages/patches/asymptote-gsl2.patch: New file. * gnu-system.am (dist_patch_DATA): Add it. Eric Bavier2016-01-023-0/+109
* gnu: Add python-markdown.•••* gnu/packages/python.scm (python-markdown, python2-markdown): New variables. Signed-off-by: Leo Famulari <leo@famulari.name> Erik Edrosa2016-01-021-1/+34
* gnu: love: Update to 0.10.0.•••* gnu/packages/game-development.scm (love): Update to 0.10.0. 宋文武2016-01-021-2/+3
* gnu: guile-ssh: Update to 0.9.0.•••* gnu/packages/ssh.scm (guile-ssh): Update to 0.9.0. Ludovic Courtès2016-01-011-2/+2
* gnu: Add xaos.•••* gnu/packages/maths.scm (xaos): New variable. Signed-off-by: Alex Kost <alezost@gmail.com> Fabian Harfert2015-12-311-0/+31
* gnu: Move cursynth to (gnu packages music).•••* gnu/packages/cursynth.scm: Remove. * gnu/packages/music.scm (cursynth): New variable, from cursynth.scm. * gnu-system.am (GNU_SYSTEM_MODULES): Remove cursynth.scm. Leo Famulari2015-12-302-53/+27
* gnu: libcue: Update source URL.•••* gnu/packages/cdrom.scm (libcue)[source]: Update URL. Leo Famulari2015-12-301-2/+3
* gnu: python-mox3: Update to 0.13.0.•••* gnu/packages/openstack.scm (python-mox3): Update to 0.13.0. Efraim Flashner2015-12-301-2/+2
* gnu: python-fixtures: Update to 1.4.0.•••* gnu/packages/python.scm (python-fixtures): Update to 1.4.0. Efraim Flashner2015-12-301-5/+3
* gnu: python-pyld: Update to 0.6.8.•••* gnu/packages/python.scm (python-pyld): Update to 0.6.8. Efraim Flashner2015-12-301-6/+3
* gnu: python-virtualenv: Update to 13.1.2.•••* gnu/packages/python.scm (python-virtualenv): Update to 13.1.2. [arguments]: Custom test command. [inputs]: Remove python-nose, add python-pytest. Efraim Flashner2015-12-301-6/+9
* gnu: python-oslosphinx: Update to 4.2.0.•••* gnu/packages/openstack.scm (python-oslosphinx): Update to 4.2.0. Efraim Flashner2015-12-301-2/+2
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