jackhill/guix/guix.git
8 years agognu-maintenance: Move FTP directory info to 'properties' fields.
Ludovic Courtès [Thu, 14 Apr 2016 20:18:56 +0000 (22:18 +0200)]
gnu-maintenance: Move FTP directory info to 'properties' fields.

* guix/gnu-maintenance.scm (ftp-server/directory): Rewrite to honor
PACKAGE's properties.  Remove list of quirks.
(releases): Add #:server and #:directory parameters.  Remove call
to 'ftp-server/directory'.
(latest-release): Likewise.
(latest-release*): Add call to 'ftp-server/directory'.  Honor
'upstream-name' property of PACKAGE.
* gnu/packages/fonts.scm (font-gnu-freefont-ttf): Add 'properties'
field.
* gnu/packages/gnupg.scm (libgpg-error, libgcrypt, libassuan):
(libksba, gnupg): Likewise.
* gnu/packages/gnuzilla.scm (icecat): Likewise.
* gnu/packages/package-management.scm (guix-0.10.0): Likewise.
* gnu/packages/pretty-print.scm (source-highlight): Likewise.
* gnu/packages/scheme.scm (mit-scheme): Likewise.
* gnu/packages/telephony.scm (ucommon): Likewise.
* gnu/packages/tls.scm (gnutls): Likewise.

8 years agognu-maintenance: Recognize source tarball with "-src" in their name.
Ludovic Courtès [Thu, 14 Apr 2016 19:48:05 +0000 (21:48 +0200)]
gnu-maintenance: Recognize source tarball with "-src" in their name.

* guix/gnu-maintenance.scm (tarball->version): Add special case for
tarball names containing "-src".

8 years agoupstream: Pass a package object to updaters.
Ludovic Courtès [Thu, 14 Apr 2016 19:40:20 +0000 (21:40 +0200)]
upstream: Pass a package object to updaters.

* guix/upstream.scm (package-update-path): Pass PACKAGE to
'latest-release'.
* guix/gnu-maintenance.scm (latest-release*)
(latest-gnome-release, latest-xorg-release): Adjust accordingly.
* guix/import/cran.scm (latest-cran-release):
(latest-bioconductor-release): Likewise.
* guix/import/elpa.scm (latest-release): Likewise.
* guix/import/gem.scm (latest-release): Likewise.
* guix/import/github.scm (latest-release): Likewise.
* guix/import/hackage.scm (latest-release): Likewise.
* guix/import/pypi.scm (latest-release): Likewise.

8 years agoRevert "gnu: util-linux: Add "static" output."
David Thompson [Thu, 14 Apr 2016 17:24:10 +0000 (13:24 -0400)]
Revert "gnu: util-linux: Add "static" output."

This reverts commit df887432be25e1534b9ecdccf39c98857b1d0786.

8 years agognu: r-htmltools: Update to 0.3.5.
Ricardo Wurmus [Wed, 13 Apr 2016 14:08:08 +0000 (16:08 +0200)]
gnu: r-htmltools: Update to 0.3.5.

* gnu/packages/web.scm (r-htmltools): Update to 0.3.5.
[propagated-inputs]: Add r-rcpp.

8 years agognu: Add r-nnet.
Ricardo Wurmus [Thu, 31 Mar 2016 15:05:27 +0000 (17:05 +0200)]
gnu: Add r-nnet.

* gnu/packages/machine-learning.scm (r-nnet): New variable.

8 years agognu: Add r-igraph.
Ricardo Wurmus [Thu, 31 Mar 2016 13:43:48 +0000 (15:43 +0200)]
gnu: Add r-igraph.

* gnu/packages/statistics.scm (r-igraph): New variable.

8 years agognu: Add r-nmf.
Ricardo Wurmus [Thu, 31 Mar 2016 13:43:12 +0000 (15:43 +0200)]
gnu: Add r-nmf.

* gnu/packages/statistics.scm (r-nmf): New variable.

8 years agognu: Add r-rngtools.
Ricardo Wurmus [Thu, 31 Mar 2016 13:42:49 +0000 (15:42 +0200)]
gnu: Add r-rngtools.

* gnu/packages/statistics.scm (r-rngtools): New variable.

8 years agognu: Add r-registry.
Ricardo Wurmus [Thu, 31 Mar 2016 13:42:30 +0000 (15:42 +0200)]
gnu: Add r-registry.

* gnu/packages/statistics.scm (r-registry): New variable.

8 years agognu: Add r-pkgmaker.
Ricardo Wurmus [Thu, 31 Mar 2016 13:42:08 +0000 (15:42 +0200)]
gnu: Add r-pkgmaker.

* gnu/packages/statistics.scm (r-pkgmaker): New variable.

8 years agognu: Add r-irlba.
Ricardo Wurmus [Thu, 31 Mar 2016 13:41:41 +0000 (15:41 +0200)]
gnu: Add r-irlba.

* gnu/packages/statistics.scm (r-irlba): New variable.

8 years agognu: Add r-latticeextra.
Ricardo Wurmus [Thu, 31 Mar 2016 13:40:49 +0000 (15:40 +0200)]
gnu: Add r-latticeextra.

* gnu/packages/statistics.scm (r-latticeextra): New variable.

8 years agognu: Add r-xtable.
Ricardo Wurmus [Thu, 31 Mar 2016 13:40:10 +0000 (15:40 +0200)]
gnu: Add r-xtable.

* gnu/packages/statistics.scm (r-xtable): New variable.

8 years agognu: Add r-locfit.
Ricardo Wurmus [Thu, 31 Mar 2016 13:39:44 +0000 (15:39 +0200)]
gnu: Add r-locfit.

* gnu/packages/statistics.scm (r-locfit): New variable.

8 years agognu: Add r-formula.
Ricardo Wurmus [Thu, 31 Mar 2016 13:39:16 +0000 (15:39 +0200)]
gnu: Add r-formula.

* gnu/packages/statistics.scm (r-formula): New variable.

8 years agognu: Add r-foreign.
Ricardo Wurmus [Thu, 31 Mar 2016 13:38:27 +0000 (15:38 +0200)]
gnu: Add r-foreign.

* gnu/packages/statistics.scm (r-foreign): New variable.

8 years agognu: Add r-cluster.
Ricardo Wurmus [Thu, 31 Mar 2016 13:37:52 +0000 (15:37 +0200)]
gnu: Add r-cluster.

* gnu/packages/statistics.scm (r-cluster): New variable.

8 years agognu: Add r-acepack.
Ricardo Wurmus [Thu, 31 Mar 2016 13:36:42 +0000 (15:36 +0200)]
gnu: Add r-acepack.

* gnu/packages/statistics.scm (r-acepack): New variable.

8 years agognu: hwloc: Update to 1.11.2.
Ludovic Courtès [Thu, 14 Apr 2016 08:19:40 +0000 (10:19 +0200)]
gnu: hwloc: Update to 1.11.2.

* gnu/packages/mpi.scm (hwloc): Update to 1.11.2.  Change URLs to https.

8 years agolint: Emit an ANSI erase-in-line sequence.
Danny Milosavljevic [Fri, 8 Apr 2016 15:59:12 +0000 (17:59 +0200)]
lint: Emit an ANSI erase-in-line sequence.

* guix/scripts/lint.scm (run-checkers): Add '\x1b[K' to progress
messages and after 'for-each'.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
8 years agognu: packages: Use 'search-patches' everywhere.
Alex Kost [Fri, 8 Apr 2016 12:18:13 +0000 (15:18 +0300)]
gnu: packages: Use 'search-patches' everywhere.

* gnu/packages/abiword.scm: Use 'search-patches' for 'patches' field.
* gnu/packages/acl.scm: Likewise.
* gnu/packages/admin.scm: Likewise.
* gnu/packages/algebra.scm: Likewise.
* gnu/packages/animation.scm: Likewise.
* gnu/packages/apr.scm: Likewise.
* gnu/packages/audacity.scm: Likewise.
* gnu/packages/audio.scm: Likewise.
* gnu/packages/autotools.scm: Likewise.
* gnu/packages/avahi.scm: Likewise.
* gnu/packages/backup.scm: Likewise.
* gnu/packages/base.scm: Likewise.
* gnu/packages/bash.scm: Likewise.
* gnu/packages/bioinformatics.scm: Likewise.
* gnu/packages/cdrom.scm: Likewise.
* gnu/packages/ci.scm: Likewise.
* gnu/packages/cmake.scm: Likewise.
* gnu/packages/cpio.scm: Likewise.
* gnu/packages/cross-base.scm: Likewise.
* gnu/packages/dico.scm: Likewise.
* gnu/packages/doxygen.scm: Likewise.
* gnu/packages/ebook.scm: Likewise.
* gnu/packages/elf.scm: Likewise.
* gnu/packages/emacs.scm: Likewise.
* gnu/packages/engineering.scm: Likewise.
* gnu/packages/firmware.scm: Likewise.
* gnu/packages/flashing-tools.scm: Likewise.
* gnu/packages/fltk.scm: Likewise.
* gnu/packages/ftp.scm: Likewise.
* gnu/packages/games.scm: Likewise.
* gnu/packages/gawk.scm: Likewise.
* gnu/packages/gcc.scm: Likewise.
* gnu/packages/gd.scm: Likewise.
* gnu/packages/ghostscript.scm: Likewise.
* gnu/packages/glib.scm: Likewise.
* gnu/packages/gnome.scm: Likewise.
* gnu/packages/gnucash.scm: Likewise.
* gnu/packages/gnunet.scm: Likewise.
* gnu/packages/gnupg.scm: Likewise.
* gnu/packages/gnuzilla.scm: Likewise.
* gnu/packages/graphics.scm: Likewise.
* gnu/packages/grub.scm: Likewise.
* gnu/packages/gtk.scm: Likewise.
* gnu/packages/guile.scm: Likewise.
* gnu/packages/icu4c.scm: Likewise.
* gnu/packages/idutils.scm: Likewise.
* gnu/packages/image.scm: Likewise.
* gnu/packages/imagemagick.scm: Likewise.
* gnu/packages/irc.scm: Likewise.
* gnu/packages/ldc.scm: Likewise.
* gnu/packages/libcanberra.scm: Likewise.
* gnu/packages/libevent.scm: Likewise.
* gnu/packages/libreoffice.scm: Likewise.
* gnu/packages/libunwind.scm: Likewise.
* gnu/packages/libusb.scm: Likewise.
* gnu/packages/linux.scm: Likewise.
* gnu/packages/lirc.scm: Likewise.
* gnu/packages/llvm.scm: Likewise.
* gnu/packages/lsh.scm: Likewise.
* gnu/packages/lua.scm: Likewise.
* gnu/packages/lxqt.scm: Likewise.
* gnu/packages/mail.scm: Likewise.
* gnu/packages/maths.scm: Likewise.
* gnu/packages/mcrypt.scm: Likewise.
* gnu/packages/messaging.scm: Likewise.
* gnu/packages/mit-krb5.scm: Likewise.
* gnu/packages/mp3.scm: Likewise.
* gnu/packages/multiprecision.scm: Likewise.
* gnu/packages/music.scm: Likewise.
* gnu/packages/ninja.scm: Likewise.
* gnu/packages/nvi.scm: Likewise.
* gnu/packages/ocaml.scm: Likewise.
* gnu/packages/orpheus.scm: Likewise.
* gnu/packages/ots.scm: Likewise.
* gnu/packages/parallel.scm: Likewise.
* gnu/packages/patchutils.scm: Likewise.
* gnu/packages/pcre.scm: Likewise.
* gnu/packages/pdf.scm: Likewise.
* gnu/packages/perl.scm: Likewise.
* gnu/packages/plotutils.scm: Likewise.
* gnu/packages/polkit.scm: Likewise.
* gnu/packages/pulseaudio.scm: Likewise.
* gnu/packages/python.scm: Likewise.
* gnu/packages/qemu.scm: Likewise.
* gnu/packages/qt.scm: Likewise.
* gnu/packages/ratpoison.scm: Likewise.
* gnu/packages/rdf.scm: Likewise.
* gnu/packages/readline.scm: Likewise.
* gnu/packages/rush.scm: Likewise.
* gnu/packages/scheme.scm: Likewise.
* gnu/packages/screen.scm: Likewise.
* gnu/packages/sdl.scm: Likewise.
* gnu/packages/slim.scm: Likewise.
* gnu/packages/ssh.scm: Likewise.
* gnu/packages/tcl.scm: Likewise.
* gnu/packages/tcsh.scm: Likewise.
* gnu/packages/texinfo.scm: Likewise.
* gnu/packages/tls.scm: Likewise.
* gnu/packages/tor.scm: Likewise.
* gnu/packages/tv.scm: Likewise.
* gnu/packages/valgrind.scm: Likewise.
* gnu/packages/version-control.scm: Likewise.
* gnu/packages/video.scm: Likewise.
* gnu/packages/vpn.scm: Likewise.
* gnu/packages/vtk.scm: Likewise.
* gnu/packages/w3m.scm: Likewise.
* gnu/packages/web.scm: Likewise.
* gnu/packages/wicd.scm: Likewise.
* gnu/packages/wm.scm: Likewise.
* gnu/packages/xdisorg.scm: Likewise.
* gnu/packages/xfce.scm: Likewise.
* gnu/packages/xiph.scm: Likewise.
* gnu/packages/xml.scm: Likewise.
* gnu/packages/xorg.scm: Likewise.
* gnu/packages/zip.scm: Likewise.

8 years agopackages: Add 'search-patches'.
Alex Kost [Fri, 8 Apr 2016 08:28:40 +0000 (11:28 +0300)]
packages: Add 'search-patches'.

* gnu/packages.scm (search-patches): New macro.

8 years agodownload: Follow HTTP 307 "Temporary Redirection".
Alex Kost [Tue, 12 Apr 2016 08:14:59 +0000 (11:14 +0300)]
download: Follow HTTP 307 "Temporary Redirection".

Fixes <http://bugs.gnu.org/23275>.
Reported by Albin Söderqvist <albin@fripost.org>.

* guix/build/download.scm (http-fetch): Follow redirections upon 307.
  This is what 'binaries.openttd.org' does.

8 years agognu: Add maim.
Alex Kost [Mon, 4 Apr 2016 16:53:37 +0000 (19:53 +0300)]
gnu: Add maim.

* gnu/packages/xdisorg.scm (maim): New variable.

8 years agognu: Add slop.
Alex Kost [Sun, 3 Apr 2016 11:36:33 +0000 (14:36 +0300)]
gnu: Add slop.

* gnu/packages/xdisorg.scm (slop): New variable.

8 years agognu: linux-libre-4.4: Update to 4.4.7.
Mark H Weaver [Wed, 13 Apr 2016 22:08:31 +0000 (18:08 -0400)]
gnu: linux-libre-4.4: Update to 4.4.7.

* gnu/packages/linux.scm (linux-libre-4.4): Update to 4.4.7.

8 years agognu: linux-libre: Update to 4.5.1.
Mark H Weaver [Wed, 13 Apr 2016 22:04:49 +0000 (18:04 -0400)]
gnu: linux-libre: Update to 4.5.1.

* gnu/packages/linux.scm (linux-libre): Update to 4.5.1.

8 years agognu: pcmanfm, libfm: Update to 1.2.4.
Raymond Nicholson [Thu, 7 Apr 2016 20:07:59 +0000 (21:07 +0100)]
gnu: pcmanfm, libfm: Update to 1.2.4.

* gnu/packages/lxde.scm (pcmanfm): Update to 1.2.4.
* gnu/packages/lxde.scm (libfm): Update to 1.2.4.

Signed-off-by: Leo Famulari <leo@famulari.name>
8 years agognu: qsynth: Update to 0.4.1.
Ricardo Wurmus [Tue, 12 Apr 2016 17:29:12 +0000 (19:29 +0200)]
gnu: qsynth: Update to 0.4.1.

* gnu/packages/audio.scm (qsynth): Update to 0.4.1.

8 years agognu: Add giac-xcas.
Nicolas Goaziou [Thu, 7 Apr 2016 12:43:15 +0000 (14:43 +0200)]
gnu: Add giac-xcas.

* gnu/packages/algebra.scm (giac-xcas): New variable.

Signed-off-by: Mathieu Lirzin <mthl@gnu.org>
8 years agognu: Add mpfi.
Nicolas Goaziou [Sun, 10 Apr 2016 11:53:42 +0000 (13:53 +0200)]
gnu: Add mpfi.

* gnu/packages/multiprecision.scm (mpfi): New variable.

Signed-off-by: Mathieu Lirzin <mthl@gnu.org>
8 years agohydra: Add 'hydra-jobs.scm' target to compute the Hydra jobs.
Ludovic Courtès [Wed, 13 Apr 2016 17:18:03 +0000 (19:18 +0200)]
hydra: Add 'hydra-jobs.scm' target to compute the Hydra jobs.

* build-aux/hydra/evaluate.scm: New file.
* Makefile.am (EXTRA_DIST): Add it.

8 years agohydra: Really completely disable grafting.
Ludovic Courtès [Wed, 13 Apr 2016 17:08:41 +0000 (19:08 +0200)]
hydra: Really completely disable grafting.

This is a followup to 49c4fd2a.

* build-aux/hydra/gnu-system.scm (package->alist): Parameterize %graft?.
(qemu-jobs)[->job]: Likewise.
(tarball-jobs)[->job]: Likewise.

8 years agognu: geda-gaf: Make gsch2pcb work out-of-the-box.
David Thompson [Wed, 13 Apr 2016 14:41:57 +0000 (10:41 -0400)]
gnu: geda-gaf: Make gsch2pcb work out-of-the-box.

* gnu/packages/engineering.scm (geda-gaf)[inputs]: Add m4 and pcb.
[arguments]: Add configure flags that point to PCB data files.

8 years agognu: Add GMP-ECM.
Andreas Enge [Wed, 13 Apr 2016 11:32:05 +0000 (13:32 +0200)]
gnu: Add GMP-ECM.

* gnu/packages/algebra.scm (gmp-ecm): New variable.

8 years agognu: Add gnome-sudoku.
Kei Yamashita [Tue, 12 Apr 2016 16:47:57 +0000 (12:47 -0400)]
gnu: Add gnome-sudoku.

* gnu/packages/gnome.scm (gnome-sudoku): New variable.

Signed-off-by: 宋文武 <iyzsong@gmail.com>
8 years agognu: Add qqwing.
Kei Yamashita [Tue, 12 Apr 2016 16:47:26 +0000 (12:47 -0400)]
gnu: Add qqwing.

* gnu/packages/game-development.scm (qqwing): New variable.

Signed-off-by: 宋文武 <iyzsong@gmail.com>
8 years agognu-maintenance: update-package-source: Only update the desired package.
宋文武 [Wed, 6 Apr 2016 10:32:20 +0000 (18:32 +0800)]
gnu-maintenance: update-package-source: Only update the desired package.

Fixes <http://bugs.gnu.org/22693>.
Suggested by Andy Wingo.

* guix/upstream.scm (update-package-source): Rewrite in terms of 'edit-expression'.

8 years agoutils: Add 'location->source-properties'.
宋文武 [Wed, 6 Apr 2016 10:31:12 +0000 (18:31 +0800)]
utils: Add 'location->source-properties'.

* guix/utils (location-source->properties): New procedure.

8 years agoutils: Add 'edit-expression'.
宋文武 [Wed, 6 Apr 2016 09:35:13 +0000 (17:35 +0800)]
utils: Add 'edit-expression'.

* guix/utils.scm (edit-expression): New procedure.
* tests/utils.scm (edit-expression): New test.

8 years agognu: samba: Update to 4.3.8.
Leo Famulari [Tue, 12 Apr 2016 23:38:21 +0000 (19:38 -0400)]
gnu: samba: Update to 4.3.8.

Fixes CVE-2015-5730, CVE-2016-2110, CVE-2016-2111, CVE-2016-2112,
CVE-2016-2113, CVE-2016-2114, CVE-2016-2115, CVE-2016-2118.

* gnu/packages/samba.scm (samba): Update to 4.3.8.

8 years agognu: Add r-pracma.
Roel Janssen [Fri, 8 Apr 2016 08:48:58 +0000 (10:48 +0200)]
gnu: Add r-pracma.

* gnu/packages/maths.scm (r-pracma): New variable.

Signed-off-by: Leo Famulari <leo@famulari.name>
8 years agognu: Add xscreensaver.
Christopher Allan Webber [Fri, 8 Apr 2016 15:36:05 +0000 (10:36 -0500)]
gnu: Add xscreensaver.

* gnu/packages/xdisorg.scm (xscreensaver): New variable.

8 years agognu: fontforge: Update to 20160404.
alírio eyng [Thu, 7 Apr 2016 19:04:07 +0000 (19:04 +0000)]
gnu: fontforge: Update to 20160404.

* gnu/packages/fontutils.scm (fontforge): Update to 20160404.
  [source](snippet): Remove tottf.c modification.  Update date strings.

Co-authored-by: Eric Bavier <bavier@member.fsf.org>
8 years agognu: abduco: Update to 0.6.
Leo Famulari [Tue, 12 Apr 2016 08:48:47 +0000 (04:48 -0400)]
gnu: abduco: Update to 0.6.

* gnu/packages/abduco.scm (abduco): Update to 0.6.

8 years agognu: btrfs-progs: Add "static" output.
Tobias Geerinckx-Rice [Sun, 3 Apr 2016 19:36:29 +0000 (21:36 +0200)]
gnu: btrfs-progs: Add "static" output.

* gnu/packages/linux.scm (btrfs-progs)[outputs]: New field.
[inputs]: Add "static" outputs of util-linux for libuuid and libblkid.
[arguments]: Add 'build-static' and 'install-static' phases.

Signed-off-by: Leo Famulari <leo@famulari.name>
8 years agognu: util-linux: Add "static" output.
Tobias Geerinckx-Rice [Sun, 3 Apr 2016 19:36:28 +0000 (21:36 +0200)]
gnu: util-linux: Add "static" output.

* gnu/packages/linux.scm: (util-linux)[outputs]: New field.
[arguments]: Remove "--disable-static" from #:configure-flags.
Add 'move-static-libraries' phase.

Signed-off-by: Leo Famulari <leo@famulari.name>
8 years agognu: btrfs-progs: Update to 4.5.1.
Tobias Geerinckx-Rice [Sat, 2 Apr 2016 13:29:32 +0000 (15:29 +0200)]
gnu: btrfs-progs: Update to 4.5.1.

* gnu/packages/linux.scm (btrfs-progs): Update to 4.5.1.

Signed-off-by: Leo Famulari <leo@famulari.name>
8 years agognu: e2fsprogs: Fix misleading comment.
Leo Famulari [Mon, 11 Apr 2016 22:59:53 +0000 (18:59 -0400)]
gnu: e2fsprogs: Fix misleading comment.

* gnu/packages/linux.scm (e2fsprogs): Fix misleading comment.

8 years agognu: letsencrypt, python-acme: Update to 0.5.0
Leo Famulari [Sun, 10 Apr 2016 01:13:31 +0000 (21:13 -0400)]
gnu: letsencrypt, python-acme: Update to 0.5.0

These packages should be updated together.

* gnu/packages/tls.scm (letsencrypt): Update to 0.5.0.
(python-acme, python2-acme): Update to 0.5.0.

8 years agognu: Add r-bsgenome-dmelanogaster-ucsc-dm3.
Ricardo Wurmus [Wed, 30 Mar 2016 10:24:44 +0000 (12:24 +0200)]
gnu: Add r-bsgenome-dmelanogaster-ucsc-dm3.

* gnu/packages/bioinformatics.scm (r-bsgenome-dmelanogaster-ucsc-dm3):
  New variable.

8 years agognu: Add r-bsgenome-celegans-ucsc-ce6.
Ricardo Wurmus [Wed, 30 Mar 2016 10:24:16 +0000 (12:24 +0200)]
gnu: Add r-bsgenome-celegans-ucsc-ce6.

* gnu/packages/bioinformatics.scm (r-bsgenome-celegans-ucsc-ce6): New
  variable.

8 years agognu: Add r-bsgenome-mmusculus-ucsc-mm9.
Ricardo Wurmus [Wed, 30 Mar 2016 10:23:51 +0000 (12:23 +0200)]
gnu: Add r-bsgenome-mmusculus-ucsc-mm9.

* gnu/packages/bioinformatics.scm (r-bsgenome-mmusculus-ucsc-mm9): New
  variable.

8 years agognu: Add r-motifrg.
Ricardo Wurmus [Fri, 18 Mar 2016 11:16:17 +0000 (12:16 +0100)]
gnu: Add r-motifrg.

* gnu/packages/bioinformatics.scm (r-motifrg): New variable.

8 years agognu: Add r-bsgenome-hsapiens-ucsc-hg19.
Ricardo Wurmus [Fri, 18 Mar 2016 11:15:50 +0000 (12:15 +0100)]
gnu: Add r-bsgenome-hsapiens-ucsc-hg19.

* gnu/packages/bioinformatics.scm (r-bsgenome-hsapiens-ucsc-hg19): New
  variable.

8 years agognu: Add r-seqlogo.
Ricardo Wurmus [Fri, 18 Mar 2016 11:15:24 +0000 (12:15 +0100)]
gnu: Add r-seqlogo.

* gnu/packages/bioinformatics.scm (r-seqlogo): New variable.

8 years agognu: borg: Update to 1.0.1.
Leo Famulari [Sun, 10 Apr 2016 03:43:54 +0000 (23:43 -0400)]
gnu: borg: Update to 1.0.1.

* gnu/packages/backup.scm (borg): Update to 1.0.1.

8 years agognu: vdirsyncer: Update to 0.9.3.
Leo Famulari [Mon, 11 Apr 2016 02:28:29 +0000 (22:28 -0400)]
gnu: vdirsyncer: Update to 0.9.3.

* gnu/packages/dav.scm (vdirsyncer): Update to 0.9.3.

8 years agognu: python-werkzeug: Update to 0.11.5.
Efraim Flashner [Sun, 10 Apr 2016 20:36:58 +0000 (23:36 +0300)]
gnu: python-werkzeug: Update to 0.11.5.

* gnu/packages/python.scm (python-werkzeug): Update to 0.11.5.

8 years agognu: python-pytest-localserver: Change inputs.
Efraim Flashner [Sun, 10 Apr 2016 19:45:53 +0000 (22:45 +0300)]
gnu: python-pytest-localserver: Change inputs.

* gnu/packages/python.scm (python-pytest-localserver)[native-inputs]:
Remove zip.
[proapgated-inputs]: Move python-werkzeug ...
[inputs]: ... to here.
[propagated-inputs]: Move python-pytest, python-requests, python-six ...
[native-inputs]: ... to here.

8 years agognu: python-pytest-cache: Change inputs.
Efraim Flashner [Sun, 10 Apr 2016 19:38:44 +0000 (22:38 +0300)]
gnu: python-pytest-cache: Change inputs.

* gnu/packages/python.scm (python-pytest-cache)[propagated-inputs]: Move
python-execnet ...
[inputs]: ... to here. Add python-apipkg, python-py, python-pytest.

8 years agognu: python-execnet: Change inputs.
Efraim Flashner [Sun, 10 Apr 2016 19:32:39 +0000 (22:32 +0300)]
gnu: python-execnet: Change inputs.

* gnu/packages/python.scm (python-execnet)[propagated-inputs]: Move
python-apipkg ...
[inputs]: ... to here.

8 years agognu: python-apipkg: Change inputs.
Efraim Flashner [Sun, 10 Apr 2016 19:30:19 +0000 (22:30 +0300)]
gnu: python-apipkg: Change inputs.

* gnu/packages/python.scm (python-apipkg)[native-inputs]: Move
python-pytest.
[inputs]: ... to here.

8 years agognu: python-pytest-xdist: Change inputs.
Efraim Flashner [Sun, 10 Apr 2016 19:07:28 +0000 (22:07 +0300)]
gnu: python-pytest-xdist: Change inputs.

* gnu/packages/python.scm (python-pytest-xdist)[native-inputs]: Remove
python-setuptools.
[propagated-inputs]: Move python-execnet, python-py, python-pytest ...
[inputs]: ... to here. Add python-apipkg.
[properties]: Define python2-pytest-xdist.
(python2-pytest-xdist): Build with 'strip-python2-variant'.
[native-inputs]: Add python2-setuptools.

8 years agognu: python-pytest-runner: Define python2-pytest-runner.
Efraim Flashner [Sun, 10 Apr 2016 18:17:10 +0000 (21:17 +0300)]
gnu: python-pytest-runner: Define python2-pytest-runner.

* gnu/packages/python.scm (python-pytest-runner)[properties]: Define
python2-pytest-runner.
[native-inputs]: Remove python-setuptools.
[home-page]: Project has moved to Github.
(python2-pytest-runner)[native-inputs]: Add python2-setuptools.

8 years agognu: python-pytest-cov: Update to 2.2.1.
Efraim Flashner [Sun, 10 Apr 2016 18:00:42 +0000 (21:00 +0300)]
gnu: python-pytest-cov: Update to 2.2.1.

* gnu/packages/python.scm (python-pytest-cov): Update to 2.2.1.
[native-inputs]: Remove python-setuptools. Move python-coverage,
python-pytest ...
[inputs]: ... to here.
[properties]: Define python2-pytest-cov.
(python-pytest-cov): Build with 'strip-python2-variant'.
[inputs]: Add python2-setuptools.

8 years agognu: python-parse: Update to 1.6.6.
Efraim Flashner [Sun, 10 Apr 2016 17:52:04 +0000 (20:52 +0300)]
gnu: python-parse: Update to 1.6.6.

* gnu/packages/python.scm (python-parse): Update to 1.6.6.

8 years agognu: python-tzlocal: Update to 1.2.2.
Efraim Flashner [Sun, 10 Apr 2016 17:45:49 +0000 (20:45 +0300)]
gnu: python-tzlocal: Update to 1.2.2.

* gnu/packages/python.scm (python-tzlocal): Update to 1.2.2.
[native-inputs]: Move python-pytz ...
[inputs]: ... to here.

8 years agognu: python-parsedatetime: Update to 2.1.
Efraim Flashner [Sun, 10 Apr 2016 17:07:57 +0000 (20:07 +0300)]
gnu: python-parsedatetime: Update to 2.1.

* gnu/packages/python.scm (parsedatetime): Update to 2.1.
[native-inputs]: Remove python-setuptools, add python-nose, python-pyicu.
[properties]: Define python2-variant.
(python2-parsedatetime): Build with 'strip-python2-variant'.
[native-inputs]: Add python2-setuptools.

8 years agognu: python-dateutil-2: Update to 2.5.2.
Efraim Flashner [Sun, 10 Apr 2016 15:56:05 +0000 (18:56 +0300)]
gnu: python-dateutil-2: Update to 2.5.2.

* gnu/packages/python.scm (python-dateutil-2): Update to 2.5.2.
[inputs]: Remove python-setuptools.
[properties]: Define python2-dateutil-2.
(python2-dateutil-2): Build with 'strip-python2-variant'.
[inputs]: Add python2-setuptools.

8 years agognu: python-keyring: Update to 8.7.
Efraim Flashner [Sun, 10 Apr 2016 15:02:32 +0000 (18:02 +0300)]
gnu: python-keyring: Update to 8.7.

* gnu/packages/python.scm (python-keyring): Update to 8.7.
[native-inputs]: Remove python-setuptools, python-mock.
[properties]: Define python2-keyring.
(python2-keyring): Build with 'strip-python2-variant'.
[native-inputs]: Add python2-setuptools.

8 years agognu: python-h5py: Update to 2.6.0.
Efraim Flashner [Sun, 10 Apr 2016 14:12:31 +0000 (17:12 +0300)]
gnu: python-h5py: Update to 2.6.0.

* gnu/packages/python.scm (python-h5py): Update to 2.6.0.
[inputs]: Add python-six.
[native-inputs]: Add python-pkgconfig.
[properties]: Define python2-h5py.

8 years agognu: python-pytz: Update to 2016.3.
Efraim Flashner [Sun, 10 Apr 2016 09:27:42 +0000 (12:27 +0300)]
gnu: python-pytz: Update to 2016.3.

* gnu/packages/python.scm (python-pytz): Update to 2016.3.

8 years agognu: python-babel: Update to 2.3.2.
Efraim Flashner [Sun, 10 Apr 2016 09:21:51 +0000 (12:21 +0300)]
gnu: python-babel: Update to 2.3.2.

* gnu/packages/python.scm (python-babel): Update to 2.3.2.

8 years agognu: python-ccm: Update to 2.1.6.
Efraim Flashner [Sun, 10 Apr 2016 09:16:44 +0000 (12:16 +0300)]
gnu: python-ccm: Update to 2.1.6.

* gnu/packages/python.scm (python-ccm): Update to 2.1.6.

8 years agognu: python-httplib2: Update to 0.9.2.
Efraim Flashner [Sun, 10 Apr 2016 09:13:02 +0000 (12:13 +0300)]
gnu: python-httplib2: Update to 0.9.2.

* gnu/packages/python.scm (python-httplib2): Update to 0.9.2.

8 years agognu: python-paramiko: Update to 1.16.0.
Efraim Flashner [Sun, 10 Apr 2016 08:57:11 +0000 (11:57 +0300)]
gnu: python-paramiko: Update to 1.16.0.

* gnu/packages/python.scm (python-paramiko): Update to 1.16.0.

8 years agognu: youtube-dl: Update to 2016.04.06.
Efraim Flashner [Sun, 10 Apr 2016 08:17:55 +0000 (11:17 +0300)]
gnu: youtube-dl: Update to 2016.04.06.

* gnu/packages/video.scm (youtube-dl): Update to 2016.04.06.
[native-inputs]: Remove python-setuptools.

8 years agognu: python-requests: Rearrange inputs.
Efraim Flashner [Sun, 10 Apr 2016 07:55:28 +0000 (10:55 +0300)]
gnu: python-requests: Rearrange inputs.

* gnu/packages/python.scm (python-requests)[propagated-inputs]: Move
python-py, python-pytest, python-pytest-cov, python-wheel from here...
[native-inputs]: ... to here.

8 years agognu: livestreamer: Remove extra inputs.
Efraim Flashner [Sun, 10 Apr 2016 07:33:59 +0000 (10:33 +0300)]
gnu: livestreamer: Remove extra inputs.

* gnu/packages/video.scm (livestreamer)[native-inputs]: Remove
python-setuptools.
[propagated-inputs]: Remove python-singledispatch.

8 years agognu: offlineimap: Add sqlite support.
Efraim Flashner [Thu, 7 Apr 2016 06:51:21 +0000 (09:51 +0300)]
gnu: offlineimap: Add sqlite support.

* gnu/packages/mail.scm (offlineimap)[inputs]: Add python2-pysqlite.
[arguments]: Wrap binary with python2-pysqlite's path.

8 years agognu: icecat: Update to 38.7.1-gnu1.
Efraim Flashner [Sun, 10 Apr 2016 05:40:31 +0000 (08:40 +0300)]
gnu: icecat: Update to 38.7.1-gnu1.

* gnu/packages/gnuzilla.scm (icecat): Update to 38.7.1-gnu1.
[sources]: Remove numerous patches.
* gnu/packages/patches/icecat-CVE-2015-4477.patch,
gnu/packages/patches/icecat-CVE-2015-7207.patch,
gnu/packages/patches/icecat-CVE-2016-1952-pt01.patch,
gnu/packages/patches/icecat-CVE-2016-1952-pt02.patch,
gnu/packages/patches/icecat-CVE-2016-1952-pt03.patch,
gnu/packages/patches/icecat-CVE-2016-1952-pt04.patch,
gnu/packages/patches/icecat-CVE-2016-1952-pt05.patch,
gnu/packages/patches/icecat-CVE-2016-1952-pt06.patch,
gnu/packages/patches/icecat-CVE-2016-1954.patch,
gnu/packages/patches/icecat-CVE-2016-1960.patch,
gnu/packages/patches/icecat-CVE-2016-1961.patch,
gnu/packages/patches/icecat-CVE-2016-1962.patch,
gnu/packages/patches/icecat-CVE-2016-1964.patch,
gnu/packages/patches/icecat-CVE-2016-1965.patch,
gnu/packages/patches/icecat-CVE-2016-1966.patch,
gnu/packages/patches/icecat-CVE-2016-1974.patch,
gnu/packages/patches/icecat-icecatbug-1248851.patch,
gnu/packages/patches/icecat-update-graphite2.patch,
gnu/packages/patches/icecat-update-graphite2-pt2.patch: Remove files.
* gnu-system.am (dist_patch_DATA): Remove them.

8 years agognu: Add c-graph.
John Darrington [Fri, 8 Apr 2016 19:33:59 +0000 (21:33 +0200)]
gnu: Add c-graph.

* gnu/packages/maths.scm (c-graph): New variable.

8 years agognu: Add ibus-anthy.
Chris Marusich [Sun, 3 Apr 2016 23:31:08 +0000 (16:31 -0700)]
gnu: Add ibus-anthy.

* gnu/packages/ibus.scm (ibus-anthy): New variable.

Co-authored-by: 宋文武 <iyzsong@gmail.com>.
8 years agognu: Add anthy.
Chris Marusich [Sun, 3 Apr 2016 23:29:56 +0000 (16:29 -0700)]
gnu: Add anthy.

* gnu/packages/anthy.scm: New file.
* gnu-system.am: Add it.

Signed-off-by: 宋文武 <iyzsong@gmail.com>
8 years agognu: Add wmclock.
Kei Yamashita [Fri, 8 Apr 2016 13:34:02 +0000 (09:34 -0400)]
gnu: Add wmclock.

* gnu/packages/gnustep.scm (wmclock): New variable.

Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
8 years agognu: pcre2: Update to 10.21.
McKinley Olsen [Thu, 7 Apr 2016 22:12:24 +0000 (16:12 -0600)]
gnu: pcre2: Update to 10.21.

gnu/packages/pcre.scm (pcre2): Update to 10.21.

Signed-off-by: 宋文武 <iyzsong@gmail.com>
8 years agognu: singular: Update hash.
Andreas Enge [Fri, 8 Apr 2016 09:17:46 +0000 (11:17 +0200)]
gnu: singular: Update hash.

* gnu/packages/algebra.scm (singular)[source]: Update upstream hash. See
  http://www.singular.uni-kl.de:8002/trac/ticket/754 .

8 years agognu: linux-libre-4.1: Update to 4.1.21.
Mark H Weaver [Fri, 8 Apr 2016 01:13:40 +0000 (21:13 -0400)]
gnu: linux-libre-4.1: Update to 4.1.21.

* gnu/packages/linux.scm (linux-libre-4.1): Update to 4.1.21.

8 years agognu: redis: Update to 3.0.7.
David Thompson [Thu, 7 Apr 2016 20:43:44 +0000 (16:43 -0400)]
gnu: redis: Update to 3.0.7.

* gnu/packages/databases.scm (redis): Update to 3.0.7.

8 years agognu: python-pkgconfig: Add license prefix.
Mathieu Lirzin [Thu, 7 Apr 2016 18:12:14 +0000 (20:12 +0200)]
gnu: python-pkgconfig: Add license prefix.

* gnu/packages/python.scm (python-pkgconfig)[license]: Fix prefix.

8 years agognu: Add macchanger.
John Darrington [Thu, 7 Apr 2016 10:59:35 +0000 (12:59 +0200)]
gnu: Add macchanger.

* gnu/packages/networking.scm (macchanger): New variable.

8 years agognu: node: Update to 5.10.0.
David Thompson [Tue, 5 Apr 2016 16:11:49 +0000 (12:11 -0400)]
gnu: node: Update to 5.10.0.

* gnu/packages/node.scm (node): Update to 5.10.0.

8 years agognu: libuv: Update to 1.8.0.
David Thompson [Tue, 5 Apr 2016 16:11:23 +0000 (12:11 -0400)]
gnu: libuv: Update to 1.8.0.

* gnu/packages/libevent.scm (libuv): Update to 1.8.0.

8 years agoenvironment: container: Work around read-only /etc/resolv.conf issue.
David Thompson [Thu, 31 Mar 2016 19:43:18 +0000 (15:43 -0400)]
environment: container: Work around read-only /etc/resolv.conf issue.

* guix/scripts/environment.scm (launch-environment/container): Mount
/etc/resolv.conf as a writable file.

8 years agognu: abiword: Add epub, goffice support.
Efraim Flashner [Thu, 7 Apr 2016 08:02:52 +0000 (11:02 +0300)]
gnu: abiword: Add epub, goffice support.

* gnu/packages/abiword.scm (abiword.scm)[arguments]: Add "epub" and
"goffice" to "enable-plugins" configure flag.
[inputs]: Add goffice, libchamplain, telepathy-glib.

8 years agognu: python-cython: Update to 0.24.
Andreas Enge [Wed, 6 Apr 2016 22:44:35 +0000 (00:44 +0200)]
gnu: python-cython: Update to 0.24.

* gnu/packages/python.scm (python-cython): Update to 0.24.

8 years agognu: Add python-cysignals.
Andreas Enge [Wed, 6 Apr 2016 18:49:40 +0000 (20:49 +0200)]
gnu: Add python-cysignals.

* gnu/packages/python.scm (python-cysignals, python2-cysignals): New
  variables.

8 years agognu: Add r-zlibbioc.
Roel Janssen [Wed, 30 Mar 2016 13:05:31 +0000 (15:05 +0200)]
gnu: Add r-zlibbioc.

* gnu/packages/bioinformatics.scm (r-zlibbioc): New variable.

Signed-off-by: Leo Famulari <leo@famulari.name>