jackhill/guix/guix.git
7 years agognu: Add dovecot-trees.
ng0 [Tue, 28 Feb 2017 11:11:46 +0000 (11:11 +0000)]
gnu: Add dovecot-trees.

* gnu/packages/mail.scm (dovecot-trees): New variable.

Co-authored-by: Ludovic Courtès <ludo@gnu.org>
7 years agobuild: On 2.2, build package files with almost no optimizations.
Ludovic Courtès [Tue, 14 Mar 2017 08:57:21 +0000 (09:57 +0100)]
build: On 2.2, build package files with almost no optimizations.

* build-aux/compile-all.scm (%default-optimizations)
(%lightweight-optimizations): New variables.
(optimization-options): New procedure.
(compile-file*): Use it.

7 years agognu: wireless-regdb: Update to 2017.03.07.
Leo Famulari [Tue, 14 Mar 2017 05:54:17 +0000 (01:54 -0400)]
gnu: wireless-regdb: Update to 2017.03.07.

* gnu/packages/linux.scm (wireless-regdb): Update to 2017.03.07.

7 years agognu: guile-cairo: Honor the Guile effective version.
Ludovic Courtès [Mon, 13 Mar 2017 21:26:54 +0000 (22:26 +0100)]
gnu: guile-cairo: Honor the Guile effective version.

* gnu/packages/gtk.scm (guile-cairo)[arguments]: Add #:modules.
Get the effective version of Guile and use that in installation
directory names.

7 years agognu: guile-cairo: Use 'modify-phases'.
Ludovic Courtès [Mon, 13 Mar 2017 21:18:13 +0000 (22:18 +0100)]
gnu: guile-cairo: Use 'modify-phases'.

* gnu/packages/gtk.scm (guile-cairo)[arguments]: Use 'modify-phases'.

7 years agodownload: Export '%x509-certificate-directory'.
Ludovic Courtès [Mon, 13 Mar 2017 20:51:27 +0000 (21:51 +0100)]
download: Export '%x509-certificate-directory'.

* guix/build/download.scm (%x509-certificate-directory): Export, as
expected by (guix scripts pull) since commit
7e81d699de7a2c924a048175516fe1ac3820d8e6.

7 years agognu: Add guile2.2-lib.
Ludovic Courtès [Mon, 13 Mar 2017 20:50:39 +0000 (21:50 +0100)]
gnu: Add guile2.2-lib.

* gnu/packages/guile.scm (guile2.2-lib): New variable.

7 years agognu: Add python-flask-login.
humanitiesNerd [Sun, 12 Mar 2017 20:02:08 +0000 (21:02 +0100)]
gnu: Add python-flask-login.

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

Signed-off-by: Marius Bakke <mbakke@fastmail.com>
7 years agognu: Add python-flask-htmlmin.
humanitiesNerd [Sun, 12 Mar 2017 19:46:38 +0000 (20:46 +0100)]
gnu: Add python-flask-htmlmin.

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

Signed-off-by: Marius Bakke <mbakke@fastmail.com>
7 years agognu: Add python-htmlmin.
humanitiesNerd [Sun, 12 Mar 2017 19:44:47 +0000 (20:44 +0100)]
gnu: Add python-htmlmin.

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

Signed-off-by: Marius Bakke <mbakke@fastmail.com>
7 years agognu: diffoscope: Update to 78.
Marius Bakke [Mon, 13 Mar 2017 18:10:41 +0000 (19:10 +0100)]
gnu: diffoscope: Update to 78.

* gnu/packages/package-management.scm (diffoscope): Update to 78.

7 years agognu: Add minizip.
Marius Bakke [Thu, 13 Oct 2016 11:35:30 +0000 (12:35 +0100)]
gnu: Add minizip.

* gnu/packages/compression.scm (minizip): New variable.

7 years agognu: notmuch: Update to 0.24.
Marius Bakke [Mon, 13 Mar 2017 17:14:13 +0000 (18:14 +0100)]
gnu: notmuch: Update to 0.24.

* gnu/packages/mail.scm (notmuch, python-notmuch, python2-notmuch): Update to
0.24.

7 years agognu: xf86-video-intel: Update to 2.99.917-4-7e9e92c.
Marius Bakke [Mon, 13 Mar 2017 16:09:01 +0000 (17:09 +0100)]
gnu: xf86-video-intel: Update to 2.99.917-4-7e9e92c.

* gnu/packages/xorg.scm (xf86-video-intel): Update to 2.99.917-4-7e9e92c.

7 years agognu: xf86-video-nouveau: Update to 1.0.14.
Marius Bakke [Mon, 13 Mar 2017 16:02:50 +0000 (17:02 +0100)]
gnu: xf86-video-nouveau: Update to 1.0.14.

* gnu/packages/xorg.scm (xf86-video-nouveau): Update to 1.0.14.

7 years agognu: nss, nss-certs: Update to 3.29.3.
Marius Bakke [Mon, 13 Mar 2017 15:53:27 +0000 (16:53 +0100)]
gnu: nss, nss-certs: Update to 3.29.3.

* gnu/packages/gnuzilla.scm (nss): Update to 3.29.3.
* gnu/packages/certs.scm (nss-certs): Update to 3.29.3.

7 years agognu: nss: Use 'modify-phases' syntax.
Marius Bakke [Sun, 5 Mar 2017 14:13:46 +0000 (15:13 +0100)]
gnu: nss: Use 'modify-phases' syntax.

* gnu/packages/gnuzilla.scm (nss)[arguments]: Use 'modify-phases'.

7 years agognu: manaplus: Update to 1.7.3.4.
Alex Kost [Sat, 11 Mar 2017 16:58:30 +0000 (19:58 +0300)]
gnu: manaplus: Update to 1.7.3.4.

* gnu/packages/games.scm (manaplus): Update to 1.7.3.4.

7 years agognu: git-modes: Update to 1.2.4.
Alex Kost [Sat, 11 Mar 2017 16:55:00 +0000 (19:55 +0300)]
gnu: git-modes: Update to 1.2.4.

* gnu/packages/emacs.scm (git-modes): Update to 1.2.4.

7 years agognu: magit: Update to 2.10.3.
Alex Kost [Sat, 11 Mar 2017 16:54:34 +0000 (19:54 +0300)]
gnu: magit: Update to 2.10.3.

* gnu/packages/emacs.scm (magit): Update to 2.10.3.

7 years agognu: guile-next: Update to 2.1.8.
Andy Wingo [Mon, 13 Mar 2017 11:21:35 +0000 (12:21 +0100)]
gnu: guile-next: Update to 2.1.8.

* gnu/packages/guile.scm (guile-next): Update to 2.1.8.

7 years agognu: r-hexbin: Update to 1.27.1-1.
pjotrp [Tue, 28 Feb 2017 16:42:25 +0000 (16:42 +0000)]
gnu: r-hexbin: Update to 1.27.1-1.

The package tarball was updated in place, resulting in a change in the hash
value.  We decided to bump the version to 1.27.1-1 instead of keeping the
version at upstream's 1.27.1.

* gnu/packages/statistics.scm (r-hexbin): Update to 1.27.1-1.

7 years agognu: guile-next: Increase max-silent-time.
Ludovic Courtès [Mon, 13 Mar 2017 09:28:20 +0000 (10:28 +0100)]
gnu: guile-next: Increase max-silent-time.

* gnu/packages/guile.scm (guile-next)[properties]: Add 'max-silent-time'.

7 years agognu: linux-libre@4.4: Update to 4.4.53.
Leo Famulari [Mon, 13 Mar 2017 04:55:41 +0000 (00:55 -0400)]
gnu: linux-libre@4.4: Update to 4.4.53.

* gnu/packages/linux.scm (linux-libre-4.4): Update to 4.4.53.

7 years agognu: linux-libre@4.9: Update to 4.9.14.
Leo Famulari [Mon, 13 Mar 2017 04:53:03 +0000 (00:53 -0400)]
gnu: linux-libre@4.9: Update to 4.9.14.

* gnu/packages/linux.scm (linux-libre-4.9): Update to 4.9.14.

7 years agognu: linux-libre: Update to 4.10.2.
Leo Famulari [Mon, 13 Mar 2017 04:54:30 +0000 (00:54 -0400)]
gnu: linux-libre: Update to 4.10.2.

* gnu/packages/linux.scm (%linux-libre-version): Update to 4.10.2.
(%linux-libre-hash): Update hash.

7 years agognu: ecl: Update to 16.1.3.
Andy Patterson [Sun, 12 Mar 2017 00:10:56 +0000 (19:10 -0500)]
gnu: ecl: Update to 16.1.3.

* gnu/packages/lisp.scm (ecl): Update to 16.1.3.
[arguments]: Use a different method to set the binary used for tests.

Signed-off-by: Leo Famulari <leo@famulari.name>
7 years agognu: irssi: Update to 1.0.2.
Marius Bakke [Sun, 12 Mar 2017 18:58:52 +0000 (19:58 +0100)]
gnu: irssi: Update to 1.0.2.

* gnu/packages/irc.scm (irssi): Update to 1.0.2.

7 years agopull: Default to HTTPS.
Marius Bakke [Wed, 1 Mar 2017 21:11:02 +0000 (22:11 +0100)]
pull: Default to HTTPS.

* guix/scripts/pull.scm (%snapshot-url): Use HTTPS.
(guix-pull): Authenticate against LE-CERTS when URL is from Savannah.

7 years agoservices: Move configuration functions that shouldn't be factorized.
Clément Lassieur [Tue, 28 Feb 2017 00:44:03 +0000 (01:44 +0100)]
services: Move configuration functions that shouldn't be factorized.

* gnu/services/configuration.scm (serialize-field, serialize-string)
(serialize-space-separated-string-list, space-separated-string-list?)
(serialize-file-name, file-name?, serialize-boolean): Move these functions...
* gnu/services/cups.scm: ...to this file.
* gnu/services/kerberos.scm: ...to this file.

Configuration syntaxes are very specific to services.  Some services may have
the same configuration syntax, but none of them is common enough to be
abstracted in configuration.scm.

Signed-off-by: Clément Lassieur <clement@lassieur.org>
7 years agoservices: dovecot: Reimplement proper configuration functions.
Clément Lassieur [Tue, 28 Feb 2017 22:02:14 +0000 (23:02 +0100)]
services: dovecot: Reimplement proper configuration functions.

* gnu/services/mail.scm (uglify-field-name, serialize-field, serialize-string)
(space-separated-string-list?, serialize-space-separated-string-list)
(file-name?, serialize-file-name, serialize-boolean): Add them.

These functions were inadvertently changed while being factorized in
gnu/service/configuration.scm.

Signed-off-by: Clément Lassieur <clement@lassieur.org>
7 years agosyscalls: Adjust 'define-bits' to macro literal semantics of 2.2.
Ludovic Courtès [Sun, 12 Mar 2017 16:35:32 +0000 (17:35 +0100)]
syscalls: Adjust 'define-bits' to macro literal semantics of 2.2.

* guix/build/syscalls.scm (define-bits): Do not define NAMES... as
top-level variables since that prevents literal matches in 2.2.
Instead, determine constant values at expansion time.

7 years agoAdd 'guix pack'.
Ludovic Courtès [Sun, 12 Mar 2017 15:48:40 +0000 (16:48 +0100)]
Add 'guix pack'.

* gnu/system/install.scm (self-contained-tarball): Move to...
* guix/scripts/pack.scm: ... here.  New file.
* doc/guix.texi (Binary Installation): Mention 'guix pack'.
(Invoking guix pack): New node.
* build-aux/make-binary-tarball.scm: Remove.
* Makefile.am (MODULES): Add guix/scripts/pack.scm.
(EXTRA_DIST): Remove build-aux/make-binary-tarball.scm.
(guix-binary.%.tar.xz): Rewrite using 'guix pack'.
* build-aux/hydra/gnu-system.scm (tarball-jobs): Adjust accordingly.

7 years agognu: tintin++: Use a mirror:// URI.
Ludovic Courtès [Sun, 12 Mar 2017 14:45:21 +0000 (15:45 +0100)]
gnu: tintin++: Use a mirror:// URI.

* gnu/packages/games.scm (tintin++)[source]: Use mirror://sourceforge.

7 years agognu: offlineimap: Update to 7.0.14.
Tobias Geerinckx-Rice [Sun, 12 Mar 2017 14:44:37 +0000 (15:44 +0100)]
gnu: offlineimap: Update to 7.0.14.

* gnu/packages/mail.scm (offlineimap): Update to 7.0.14.

7 years agognu: Add le-certs.
Leo Famulari [Wed, 1 Mar 2017 01:21:10 +0000 (20:21 -0500)]
gnu: Add le-certs.

* gnu/packages/certs.scm (le-certs): New variable.

7 years agoservices: dovecot: Fix unix_listeners and fifo_listeners path types.
Clément Lassieur [Sun, 26 Feb 2017 18:54:52 +0000 (19:54 +0100)]
services: dovecot: Fix unix_listeners and fifo_listeners path types.

* gnu/services/mail.scm (unix-listener-configuration)[path]
(fifo-listener-configuration)[path]: Change type from 'file-name' to 'string'.
* doc/guix.texi (Mail Services): Document it.

Signed-off-by: Clément Lassieur <clement@lassieur.org>
7 years agognu: Add r-tsne.
Raoul Jean Pierre Bonnal [Sat, 11 Mar 2017 12:36:10 +0000 (22:36 +1000)]
gnu: Add r-tsne.

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

Signed-off-by: Ben Woodcroft <donttrustben@gmail.com>
7 years agognu: Add r-ranger.
Raoul Jean Pierre Bonnal [Sat, 11 Mar 2017 12:14:22 +0000 (22:14 +1000)]
gnu: Add r-ranger.

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

Signed-off-by: Ben Woodcroft <donttrustben@gmail.com>
7 years agognu: Add r-tclust.
Raoul Jean Pierre Bonnal [Sat, 11 Mar 2017 11:50:35 +0000 (21:50 +1000)]
gnu: Add r-tclust.

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

Signed-off-by: Ben Woodcroft <donttrustben@gmail.com>
7 years agognu: Add r-sn.
Raoul Jean Pierre Bonnal [Sat, 11 Mar 2017 11:45:53 +0000 (21:45 +1000)]
gnu: Add r-sn.

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

Co-authored-by: Ben Woodcroft <donttrustben@gmail.com>
7 years agognu: Add r-numderiv.
Raoul Jean Pierre Bonnal [Sat, 11 Mar 2017 11:39:29 +0000 (21:39 +1000)]
gnu: Add r-numderiv.

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

Signed-off-by: Ben Woodcroft <donttrustben@gmail.com>
7 years agognu: Add r-mnormt.
Raoul Jean Pierre Bonnal [Thu, 19 Jan 2017 18:55:25 +0000 (19:55 +0100)]
gnu: Add r-mnormt.

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

Signed-off-by: Ben Woodcroft <donttrustben@gmail.com>
7 years agognu: Add r-rcppprogress.
Raoul Jean Pierre Bonnal [Sat, 11 Mar 2017 06:18:44 +0000 (16:18 +1000)]
gnu: Add r-rcppprogress.

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

Signed-off-by: Ben Woodcroft <donttrustben@gmail.com>
7 years agognu: Add r-caret.
Raoul Jean Pierre Bonnal [Sat, 11 Mar 2017 06:11:24 +0000 (16:11 +1000)]
gnu: Add r-caret.

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

Signed-off-by: Ben Woodcroft <donttrustben@gmail.com>
7 years agognu: Add r-car.
Raoul Jean Pierre Bonnal [Sat, 11 Mar 2017 05:57:26 +0000 (15:57 +1000)]
gnu: Add r-car.

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

Signed-off-by: Ben Woodcroft <donttrustben@gmail.com>
7 years agognu: Add r-pbkrtest.
Raoul Jean Pierre Bonnal [Sat, 11 Mar 2017 05:48:44 +0000 (15:48 +1000)]
gnu: Add r-pbkrtest.

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

Signed-off-by: Ben Woodcroft <donttrustben@gmail.com>
7 years agognu: Add r-lme4.
Raoul Jean Pierre Bonnal [Sat, 11 Mar 2017 05:46:28 +0000 (15:46 +1000)]
gnu: Add r-lme4.

* gnu/packages/statistics.scm (r-lme4): New variable.

Signed-off-by: Ben Woodcroft <donttrustben@gmail.com>
7 years agognu: Add r-nloptr.
Raoul Jean Pierre Bonnal [Sat, 11 Mar 2017 05:19:47 +0000 (15:19 +1000)]
gnu: Add r-nloptr.

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

Signed-off-by: Ben Woodcroft <donttrustben@gmail.com>
7 years agognu: Add r-quantreg.
Raoul Jean Pierre Bonnal [Sat, 11 Mar 2017 05:03:07 +0000 (15:03 +1000)]
gnu: Add r-quantreg.

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

Signed-off-by: Ben Woodcroft <donttrustben@gmail.com>
7 years agognu: Add r-matrixmodels.
Raoul Jean Pierre Bonnal [Sat, 11 Mar 2017 05:00:50 +0000 (15:00 +1000)]
gnu: Add r-matrixmodels.

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

Signed-off-by: Ben Woodcroft <donttrustben@gmail.com>
7 years agognu: Add r-modelmetrics.
Raoul Jean Pierre Bonnal [Sat, 11 Mar 2017 04:51:50 +0000 (14:51 +1000)]
gnu: Add r-modelmetrics.

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

Signed-off-by: Ben Woodcroft <donttrustben@gmail.com>
7 years agognu: Add r-rcppeigen.
Raoul Jean Pierre Bonnal [Sat, 11 Mar 2017 04:41:37 +0000 (14:41 +1000)]
gnu: Add r-rcppeigen.

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

Signed-off-by: Ben Woodcroft <donttrustben@gmail.com>
7 years agognu: Add r-minqa.
Raoul Jean Pierre Bonnal [Sat, 11 Mar 2017 04:13:29 +0000 (14:13 +1000)]
gnu: Add r-minqa.

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

Signed-off-by: Ben Woodcroft <donttrustben@gmail.com>
7 years agobuild: GnuTLS is now a hard dependency.
Ludovic Courtès [Sat, 11 Mar 2017 23:37:33 +0000 (00:37 +0100)]
build: GnuTLS is now a hard dependency.

Discussed as part of <https://bugs.gnu.org/25975>.

* configure.ac: Check for (gnutls) and error out if it's missing.
* doc/guix.texi (Requirements): Move GnuTLS from optional to required.
(Substitutes): Remove footnote about the need for GnuTLS.

7 years agognu: wine: Update to 2.3.
Danny Milosavljevic [Fri, 10 Mar 2017 08:41:15 +0000 (09:41 +0100)]
gnu: wine: Update to 2.3.

* gnu/packages/wine.scm (wine): Update to 2.3.

7 years agognu: Add phonon-backend-gstreamer.
Thomas Danckaert [Thu, 2 Mar 2017 10:20:53 +0000 (11:20 +0100)]
gnu: Add phonon-backend-gstreamer.

* gnu/packages/kde-frameworks.scm (phonon-backend-gstreamer): New variable.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
7 years agognu: phonon: Install Qt extensions.
Thomas Danckaert [Thu, 2 Mar 2017 08:33:43 +0000 (09:33 +0100)]
gnu: phonon: Install Qt extensions.

* gnu/packages/kde-frameworks.scm (phonon)[arguments]: Add
-DPHONON-INSTALL_QT_EXTENSIONS_INTO_SYSTEM_QT configure flag, and patch the
installation directory.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
7 years agognu: re2: Set CXX for cross-compilation.
Sergei Trofimovich [Mon, 6 Mar 2017 21:54:19 +0000 (21:54 +0000)]
gnu: re2: Set CXX for cross-compilation.

* gnu/packages/regex.scm (re2)[arguments]: Specify CXX in #:make-flags.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
7 years agognu: cuirass: Update to 0.0.1 revision 5.
Mathieu Othacehe [Thu, 9 Mar 2017 12:55:18 +0000 (13:55 +0100)]
gnu: cuirass: Update to 0.0.1 revision 5.

* gnu/packages/ci.scm (cuirass): Update to 0.0.1 revision 5.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
7 years agognu: imagemagick: Update to 6.9.7-10.
Leo Famulari [Sat, 11 Mar 2017 17:26:57 +0000 (12:26 -0500)]
gnu: imagemagick: Update to 6.9.7-10.

* gnu/packages/imagemagick.scm (imagemagick): Update to 6.9.7-10.

7 years agognu: Add ghc-unexceptionalio.
rsiddharth [Fri, 24 Feb 2017 06:29:31 +0000 (06:29 +0000)]
gnu: Add ghc-unexceptionalio.

* gnu/packages/haskell.scm (ghc-unexceptionalio): New variable.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
7 years agognu: Add emacs-memoize.
Arun Isaac [Fri, 10 Mar 2017 05:30:16 +0000 (11:00 +0530)]
gnu: Add emacs-memoize.

* gnu/packages/emacs.scm (emacs-memoize): New variable.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
7 years agolinux-initrd: Add a raw-initrd and use it to define base-initrd.
Mathieu Othacehe [Thu, 9 Mar 2017 18:39:23 +0000 (19:39 +0100)]
linux-initrd: Add a raw-initrd and use it to define base-initrd.

* gnu/system/linux-initrd.scm (raw-initrd): New exported variable.
(base-initrd): Use raw-initrd to build the initrd.
* doc/guix.texi (Initial RAM Disk): Document it.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
7 years agodoc: Update the package count.
John Darrington [Fri, 10 Mar 2017 05:43:08 +0000 (06:43 +0100)]
doc: Update the package count.

* doc/guix.texi: Update the number of packages available.

7 years agognu: wget: Fix CVE-2017-6508.
Leo Famulari [Sat, 11 Mar 2017 03:35:50 +0000 (22:35 -0500)]
gnu: wget: Fix CVE-2017-6508.

* gnu/packages/patches/wget-CVE-2017-6508.patch: New file.
* gnu/local.mk (dist_patch_DATA): Add it.
* gnu/packages/wget.scm (wget)[source]: Use it.

7 years agognu: Add r-fnn.
Raoul Jean Pierre Bonnal [Sat, 11 Mar 2017 01:55:28 +0000 (11:55 +1000)]
gnu: Add r-fnn.

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

Signed-off-by: Ben Woodcroft <donttrustben@gmail.com>
7 years agognu: Add r-pbapply.
Raoul Jean Pierre Bonnal [Sat, 11 Mar 2017 01:50:25 +0000 (11:50 +1000)]
gnu: Add r-pbapply.

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

Co-authored-by: Ben Woodcroft <donttrustben@gmail.com>
7 years agognu: Add r-vgam.
Raoul Jean Pierre Bonnal [Sat, 11 Mar 2017 01:47:02 +0000 (11:47 +1000)]
gnu: Add r-vgam.

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

Signed-off-by: Ben Woodcroft <donttrustben@gmail.com>
7 years agognu: vsearch: Update to 2.4.2.
Ben Woodcroft [Sat, 11 Mar 2017 01:37:15 +0000 (11:37 +1000)]
gnu: vsearch: Update to 2.4.2.

* gnu/packages/bioinformatics.scm (vsearch): Update to 2.4.2.

7 years agognu: Add r-ape.
Raoul Jean Pierre Bonnal [Sat, 11 Mar 2017 00:32:14 +0000 (10:32 +1000)]
gnu: Add r-ape.

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

Co-authored-by: Ben Woodcroft <donttrustben@gmail.com>
7 years agognu: Add r-fpc.
Raoul Jean Pierre Bonnal [Sat, 11 Mar 2017 00:10:36 +0000 (10:10 +1000)]
gnu: Add r-fpc.

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

Signed-off-by: Ben Woodcroft <donttrustben@gmail.com>
7 years agognu: Add r-trimcluster.
Raoul Jean Pierre Bonnal [Sat, 11 Mar 2017 00:04:33 +0000 (10:04 +1000)]
gnu: Add r-trimcluster.

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

Signed-off-by: Ben Woodcroft <donttrustben@gmail.com>
7 years agognu: Add r-robustbase.
Raoul Jean Pierre Bonnal [Fri, 10 Mar 2017 23:56:57 +0000 (09:56 +1000)]
gnu: Add r-robustbase.

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

Signed-off-by: Ben Woodcroft <donttrustben@gmail.com>
7 years agognu: Add r-deoptimr.
Raoul Jean Pierre Bonnal [Fri, 10 Mar 2017 23:45:34 +0000 (09:45 +1000)]
gnu: Add r-deoptimr.

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

Signed-off-by: Ben Woodcroft <donttrustben@gmail.com>
7 years agognu: Add r-prabclus.
Raoul Jean Pierre Bonnal [Fri, 10 Mar 2017 23:36:49 +0000 (09:36 +1000)]
gnu: Add r-prabclus.

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

Signed-off-by: Ben Woodcroft <donttrustben@gmail.com>
7 years agognu: Add r-mclust.
Raoul Jean Pierre Bonnal [Thu, 19 Jan 2017 18:55:04 +0000 (19:55 +0100)]
gnu: Add r-mclust.

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

Co-authored-by: Ben Woodcroft <donttrustben@gmail.com>
7 years agognu: Add r-flexmix.
Raoul Jean Pierre Bonnal [Thu, 19 Jan 2017 18:55:03 +0000 (19:55 +0100)]
gnu: Add r-flexmix.

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

Signed-off-by: Ben Woodcroft <donttrustben@gmail.com>
7 years agognu: Add r-modeltools.
Raoul Jean Pierre Bonnal [Fri, 10 Mar 2017 23:06:55 +0000 (09:06 +1000)]
gnu: Add r-modeltools.

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

Signed-off-by: Ben Woodcroft <donttrustben@gmail.com>
7 years agognu: Add r-diptest.
Raoul Jean Pierre Bonnal [Fri, 10 Mar 2017 21:34:57 +0000 (07:34 +1000)]
gnu: Add r-diptest.

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

Signed-off-by: Ben Woodcroft <donttrustben@gmail.com>
7 years agognu: Add obnam.
Arun Isaac [Thu, 9 Mar 2017 17:27:42 +0000 (22:57 +0530)]
gnu: Add obnam.

* gnu/packages/backup.scm (obnam): New variable.

Signed-off-by: Marius Bakke <mbakke@fastmail.com>
7 years agognu: icestorm: Replace reference in icebox_vlog.
Theodoros Foradis [Sat, 14 Jan 2017 18:31:34 +0000 (20:31 +0200)]
gnu: icestorm: Replace reference in icebox_vlog.

* gnu/packages/fpga.scm (icestorm)[arguments]: Add phase
"fix-usr-local" to replace reference to /usr/local/share.

7 years agognu: dub: Update to 1.2.2.
Danny Milosavljevic [Fri, 10 Mar 2017 18:39:52 +0000 (19:39 +0100)]
gnu: dub: Update to 1.2.2.

* gnu/packages/ldc.scm (dub): Update to 1.2.2.

7 years agoservices: openssh: Fix 'PrintLastLog' default behaviour.
Clément Lassieur [Thu, 2 Mar 2017 21:06:29 +0000 (22:06 +0100)]
services: openssh: Fix 'PrintLastLog' default behaviour.

* gnu/services/ssh.scm (openssh-config-file): Add 'print-last-log?' option.
(<openssh-configuration>)[print-last-log?]: Add it.
(openssh-activation): Touch /var/log/lastlog.
* doc/guix.texi (Networking Services): Document 'print-last-log?'.

Before that, the service did not work as expected because /var/log/lastlog did
not exist.

Signed-off-by: Danny Milosavljevic <dannym@scratchpost.org>
7 years agoservices: openssh: Remove deprecated options.
Clément Lassieur [Thu, 2 Mar 2017 21:06:28 +0000 (22:06 +0100)]
services: openssh: Remove deprecated options.

* gnu/services/ssh.scm (openssh-config-file): Remove them.
(<openssh-configuration>)[rsa-authentication?]: Remove it.
(<openssh-configuration>)[protocol-number]: Remove it.
* doc/guix.texi (Networking Services): Remove them.

Signed-off-by: Danny Milosavljevic <dannym@scratchpost.org>
7 years agoservices: openssh: Enable PAM.
Clément Lassieur [Thu, 2 Mar 2017 21:06:27 +0000 (22:06 +0100)]
services: openssh: Enable PAM.

* gnu/services/ssh.scm: (openssh-pam-services): New procedure.
(openssh-service-type): Use it to extend PAM-ROOT-SERVICE-TYPE.
(<openssh-configuration>)[challenge-response-authentication?]: New field.
(<openssh-configuration>)[use-pam?]: New field.
(openssh-config-file): Add them.
* doc/guix.texi (Networking Services): Document them.

Signed-off-by: Danny Milosavljevic <dannym@scratchpost.org>
7 years agosystem: Avoid '_' as a pattern variable in 'match'.
Ludovic Courtès [Fri, 10 Mar 2017 13:41:00 +0000 (14:41 +0100)]
system: Avoid '_' as a pattern variable in 'match'.

* gnu/system.scm (operating-system-root-file-system): Don't use '_' as a
wildcard in 'match', to cope with literal semantics in 2.2.

7 years agoservices: Create /var/log upon activation.
Christopher Baines [Thu, 23 Feb 2017 08:20:57 +0000 (08:20 +0000)]
services: Create /var/log upon activation.

When launching a container created with guix system container, the
attempt to create /var/log/wtmp would fail, as /var/log did not exist.

* gnu/services.scm (activation-script): Create /var/log

Co-authored-by: Ludovic Courtès <ludo@gnu.org>
7 years agoservices: Add exim-service-type.
Carlo Zancanaro [Sat, 18 Feb 2017 23:32:58 +0000 (10:32 +1100)]
services: Add exim-service-type.

* gnu/services/mail.scm (<exim-configuration>): New record type.
(exim-computed-config-file, exim-shepherd-service, exim-activation, exim-etc,
exim-profile): New procedures.
(exim-service-type, %exim-accounts): New variables.
* doc/guix.text (Mail Services): Document it.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
7 years agognu: hmmer: Build reproducibly.
Ben J. Woodcroft [Fri, 10 Mar 2017 10:25:00 +0000 (20:25 +1000)]
gnu: hmmer: Build reproducibly.

* gnu/packages/patches/hmmer-remove-cpu-specificity.patch: New file.
* gnu/packages/bioinformatics.scm (hmmer): Use it.

7 years agognu: Add sambamba.
Ricardo Wurmus [Mon, 6 Mar 2017 11:17:49 +0000 (12:17 +0100)]
gnu: Add sambamba.

* gnu/packages/bioinformatics.scm (htslib-for-sambamba, sambamba): New
variables.

7 years agognu: pidgin: Update to 2.12.0 [fixes CVE-2017-2640].
Leo Famulari [Fri, 10 Mar 2017 06:44:08 +0000 (01:44 -0500)]
gnu: pidgin: Update to 2.12.0 [fixes CVE-2017-2640].

* gnu/packages/messaging.scm (pidgin): Update to 2.12.0.

7 years agognu: neomutt: Configure with 'lmdb' and 'kyotocabinet'.
ng0 [Tue, 7 Mar 2017 00:58:03 +0000 (00:58 +0000)]
gnu: neomutt: Configure with 'lmdb' and 'kyotocabinet'.

* gnu/packages/mail.scm (neomutt)[configure]: Add '--with-kyotocabinet'
and '--with-lmdb'.
[inputs]: Add 'lmdb' and 'kyotocabinet'.

Signed-off-by: Kei Kebreau <kei@openmailbox.org>
7 years agognu: neomutt: Update to 20170306.
ng0 [Tue, 7 Mar 2017 00:58:02 +0000 (00:58 +0000)]
gnu: neomutt: Update to 20170306.

* gnu/packages/mail.scm (neomutt): Update to 20170306.

Signed-off-by: Kei Kebreau <kei@openmailbox.org>
7 years agoRevert "gnu: neomutt: Configure with 'lmdb' and 'tokyocabinet'."
ng0 [Tue, 7 Mar 2017 00:58:01 +0000 (00:58 +0000)]
Revert "gnu: neomutt: Configure with 'lmdb' and 'tokyocabinet'."

'kyotocabinet' is more current than tokyocabinet in development
and supported in neomutt aswell.

This reverts commit ef91e2b964ec0952698dd1bf7daf76624fed2145.

Signed-off-by: Kei Kebreau <kei@openmailbox.org>
7 years agognu: hiawatha: Adjust description.
ng0 [Thu, 9 Mar 2017 21:46:13 +0000 (21:46 +0000)]
gnu: hiawatha: Adjust description.

* gnu/packages/web.scm (hiawatha)[description]: Adjust it.

Signed-off-by: Kei Kebreau <kei@openmailbox.org>
7 years agognu: Add font-tamzen.
ng0 [Tue, 21 Feb 2017 11:39:45 +0000 (11:39 +0000)]
gnu: Add font-tamzen.

* gnu/packages/fonts.scm (font-tamzen): New variable.

Signed-off-by: Kei Kebreau <kei@openmailbox.org>
7 years agognu: btrfs-progs/static: Correct description.
Tobias Geerinckx-Rice [Thu, 9 Mar 2017 21:33:10 +0000 (22:33 +0100)]
gnu: btrfs-progs/static: Correct description.

* gnu/packages/linux.scm (btrfs-progs/static)[description]: Use the correct
name of the btrfs-progs package and @command{} mark-up.

7 years agognu: btrfs-progs: Update to 4.10.
Tobias Geerinckx-Rice [Thu, 9 Mar 2017 21:28:41 +0000 (22:28 +0100)]
gnu: btrfs-progs: Update to 4.10.

* gnu/packages/linux.scm (btrfs-progs): Update to 4.10.

7 years agognu: ibus-anthy: Update to 1.5.9.
Tobias Geerinckx-Rice [Tue, 7 Mar 2017 18:35:08 +0000 (19:35 +0100)]
gnu: ibus-anthy: Update to 1.5.9.

* gnu/packages/ibus.scm (ibus-anthy): Update to 1.5.9.