jackhill/guix/guix.git
6 years agognu: antlr3-3.3: Fix java8 issue.
Gábor Boskovits [Sun, 4 Mar 2018 13:16:37 +0000 (14:16 +0100)]
gnu: antlr3-3.3: Fix java8 issue.

* gnu/packages/java.scm (antlr3-3.3)[source]: Add patch.
* gnu/packages/patches/antlr3-3_3-fix-java8-compilation.patch: New file.
* gnu/local.mk (dist_patch_DATA): Add it.

Signed-off-by: Danny Milosavljevic <dannym@scratchpost.org>
6 years agognu: antlr3-3.1: Fix java8 issue.
Gábor Boskovits [Sun, 4 Mar 2018 13:13:47 +0000 (14:13 +0100)]
gnu: antlr3-3.1: Fix java8 issue.

* gnu/packages/java.scm (antlr3-3.1)[source]: Add patch.
* gnu/packages/patches/antlr3-3_1-fix-java8-compilation.patch: New file.
* gnu/local.mk (dist_patch_DATA): Add it.

Signed-off-by: Danny Milosavljevic <dannym@scratchpost.org>
6 years agognu: go-github-com-aki237-nscjar: Declare a source file-name.
Efraim Flashner [Sun, 4 Mar 2018 10:37:33 +0000 (12:37 +0200)]
gnu: go-github-com-aki237-nscjar: Declare a source file-name.

* gnu/packages/golang.scm (go-github-com-aki237-nscjar)[source]: Declare
a source file-name.

6 years agognu: go-github-com-davidjpeacock-cli: Declare a source file-name.
Efraim Flashner [Sun, 4 Mar 2018 10:36:34 +0000 (12:36 +0200)]
gnu: go-github-com-davidjpeacock-cli: Declare a source file-name.

* gnu/packages/golang.scm (go-github-com-davidjpeacock-cli)[source]:
Declare a source file-name.

6 years agognu: go-github-com-alsm-ioprogress: Declare a source file-name.
Efraim Flashner [Sun, 4 Mar 2018 10:35:31 +0000 (12:35 +0200)]
gnu: go-github-com-alsm-ioprogress: Declare a source file-name.

* gnu/packages/golang.scm (go-github-com-alsm-ioprogress)[source]:
Declare a source file-name.

6 years agognu: freegish: Declare a source file-name.
Efraim Flashner [Sun, 4 Mar 2018 10:33:55 +0000 (12:33 +0200)]
gnu: freegish: Declare a source file-name.

* gnu/packages/games.scm (freegish)[source]: Declare a source file-name.

6 years agognu: disorderfs: Declare a source file-name.
Efraim Flashner [Sun, 4 Mar 2018 10:32:39 +0000 (12:32 +0200)]
gnu: disorderfs: Declare a source file-name.

* gnu/packages/file-systems.scm (disorderfs)[source]: Declare a source
file-name.

6 years agognu: emacs-sly: Declare a source file-name.
Efraim Flashner [Sun, 4 Mar 2018 10:30:53 +0000 (12:30 +0200)]
gnu: emacs-sly: Declare a source file-name.

* gnu/packages/emacs.scm (emacs-sly)[source]: Declare a source
file-name.

6 years agognu: emacs-epl: Declare a source file-name.
Efraim Flashner [Sun, 4 Mar 2018 10:30:08 +0000 (12:30 +0200)]
gnu: emacs-epl: Declare a source file-name.

* gnu/packages/emacs.scm (emacs-epl)[source]: Declare a source
file-name.

6 years agognu: python-apsw: Use invoke.
Efraim Flashner [Sun, 4 Mar 2018 10:03:27 +0000 (12:03 +0200)]
gnu: python-apsw: Use invoke.

* gnu/packages/databases.scm (python-apsw)[arguments]: Use invoke.

6 years agognu: python-apsw: Declare a source file-name.
Efraim Flashner [Sun, 4 Mar 2018 09:55:37 +0000 (11:55 +0200)]
gnu: python-apsw: Declare a source file-name.

* gnu/packages/databases.scm (python-apsw)[source]: Declare a source
file-name.

6 years agognu: kurly: Declare a source file-name.
Efraim Flashner [Sun, 4 Mar 2018 09:55:08 +0000 (11:55 +0200)]
gnu: kurly: Declare a source file-name.

* gnu/packages/curl.scm (kurly)[source]: Declare a source file-name.

6 years agognu: unshield: Declare a source file-name.
Efraim Flashner [Sun, 4 Mar 2018 09:51:08 +0000 (11:51 +0200)]
gnu: unshield: Declare a source file-name.

* gnu/packages/compression.scm (unshield)[source]: Declare a source
file-name.

6 years agognu: sfarkxtc: Declare a source file-name.
Efraim Flashner [Sun, 4 Mar 2018 09:50:16 +0000 (11:50 +0200)]
gnu: sfarkxtc: Declare a source file-name.

* gnu/packages/compression.scm (sfarkxtc)[source]: Declare a source
file-name.

6 years agognu: piranha: Declare a source file-name.
Efraim Flashner [Sun, 4 Mar 2018 09:48:40 +0000 (11:48 +0200)]
gnu: piranha: Declare a source file-name.

* gnu/packages/bioinformatics.scm (piranha)[source]: Declare a source
file-name.

6 years agognu: libdivsufsort: Declare a source file-name.
Efraim Flashner [Sun, 4 Mar 2018 09:47:42 +0000 (11:47 +0200)]
gnu: libdivsufsort: Declare a source file-name.

* gnu/packages/bioinformatics.scm (libdivsufsort)[source]: Declare a
source file-name.

6 years agognu: seek: Declare a source file-name.
Efraim Flashner [Sun, 4 Mar 2018 09:46:43 +0000 (11:46 +0200)]
gnu: seek: Declare a source file-name.

* gnu/packages/bioinformatics.scm (seek)[source]: Declare a source
file-name.

6 years agognu: r-dropbead: Declare a source file-name.
Efraim Flashner [Sun, 4 Mar 2018 09:45:40 +0000 (11:45 +0200)]
gnu: r-dropbead: Declare a source file-name.

* gnu/packages/bioinformatics.scm (r-dropbead)[source]: Declare a source
file-name.

6 years agognu: faust@2: Declare a source file-name.
Efraim Flashner [Sun, 4 Mar 2018 07:58:23 +0000 (09:58 +0200)]
gnu: faust@2: Declare a source file-name.

* gnu/packages/audio.scm (faust@2)[source]: Declare a source file-name.

6 years agognu: rubberband: Declare a source file-name.
Efraim Flashner [Sun, 4 Mar 2018 07:57:24 +0000 (09:57 +0200)]
gnu: rubberband: Declare a source file-name.

* gnu/packages/audio.scm (rubberband)[source]: Declare a source
file-name.

6 years agognu: qjackrcd: Declare a source file-name.
Efraim Flashner [Sun, 4 Mar 2018 07:55:46 +0000 (09:55 +0200)]
gnu: qjackrcd: Declare a source file-name.

* gnu/packages/audio.scm (qjackrcd)[source]: Declare a source file-name.

6 years agognu: lv2-devel: Declare a source file-name.
Efraim Flashner [Sun, 4 Mar 2018 07:54:51 +0000 (09:54 +0200)]
gnu: lv2-devel: Declare a source file-name.

* gnu/packages/audio.scm (lv2-devel)[source]: Declare a source file-name.

6 years agognu: lv2-mda-piano: Declare a source file-name.
Efraim Flashner [Sun, 4 Mar 2018 07:53:55 +0000 (09:53 +0200)]
gnu: lv2-mda-piano: Declare a source file-name.

* gnu/packages/audio.scm (lv2-mda-piano)[source]: Declare a source
file-name.

6 years agognu: papagayo: Declare a source file-name.
Efraim Flashner [Sun, 4 Mar 2018 07:52:08 +0000 (09:52 +0200)]
gnu: papagayo: Declare a source file-name.

* gnu/packages/animation.scm (papagayo)[source]: Declare a source
file-name.

6 years agognu: masscan: Declare a source file-name.
Efraim Flashner [Sun, 4 Mar 2018 07:48:46 +0000 (09:48 +0200)]
gnu: masscan: Declare a source file-name.

* gnu/packages/admin.scm (masscan)[source]: Declare a source file-name.

6 years agoservices: redis: Add a default-value to the redis-service-type.
Christopher Baines [Thu, 18 Jan 2018 22:45:40 +0000 (22:45 +0000)]
services: redis: Add a default-value to the redis-service-type.

* gnu/packages/databases.scm (redis-service-type)[default-value]: Set
  to (redis-configuration).

6 years agoservices: mysql: Add a default-value to the mysql-service-type.
Christopher Baines [Thu, 18 Jan 2018 22:45:35 +0000 (22:45 +0000)]
services: mysql: Add a default-value to the mysql-service-type.

* gnu/services/databases.scm (mysql-service-type)[default-value]: Set
  to (mysql-configuration).

6 years agoservices: postgresql: Add a default-value to the postgresql-service-type.
Christopher Baines [Thu, 18 Jan 2018 22:45:26 +0000 (22:45 +0000)]
services: postgresql: Add a default-value to the postgresql-service-type.

* gnu/packages/databases.scm (<postgresql-configuration>)
  [config-file,data-directory]: Add default.
  (postgresql-service-type)[default-value]:
  Set to (postgresql-configuration).

6 years agolinux-modules: Add module-aliases.
Danny Milosavljevic [Sat, 3 Mar 2018 13:55:27 +0000 (14:55 +0100)]
linux-modules: Add module-aliases.

* gnu/build/linux-modules.scm (module-aliases): New variable.

6 years agognu: tor: Update to 0.3.2.10 [security fixes].
Tobias Geerinckx-Rice [Sat, 3 Mar 2018 20:01:20 +0000 (21:01 +0100)]
gnu: tor: Update to 0.3.2.10 [security fixes].

This release fixes TROVE-2018-001 (also tracked as CVE-2018-0490),
TROVE-2018-002 (CVE-2018-049), and TROVEs-2018-00{3,4} as well.

* gnu/packages/tor.scm (tor): Update to 0.3.2.10.

6 years agognu: Add dropseq-tools.
Ricardo Wurmus [Thu, 1 Mar 2018 18:41:49 +0000 (19:41 +0100)]
gnu: Add dropseq-tools.

* gnu/packages/bioinformatics.scm (dropseq-tools): New variable.

6 years agognu: Add java-picard-2.10.3.
Ricardo Wurmus [Thu, 1 Mar 2018 18:41:48 +0000 (19:41 +0100)]
gnu: Add java-picard-2.10.3.

* gnu/packages/bioinformatics.scm (java-picard-2.10.3): New variable.

6 years agognu: Add java-htsjdk-2.10.1.
Ricardo Wurmus [Thu, 1 Mar 2018 18:41:47 +0000 (19:41 +0100)]
gnu: Add java-htsjdk-2.10.1.

* gnu/packages/bioinformatics.scm (java-htsjdk-2.10.1): New variable.

6 years agognu: Add java-htsjdk-latest.
Ricardo Wurmus [Thu, 1 Mar 2018 18:41:46 +0000 (19:41 +0100)]
gnu: Add java-htsjdk-latest.

* gnu/packages/bioinformatics.scm (java-htsjdk-latest): New variable.

6 years agognu: Add java-biojava-alignment-4.0.
Ricardo Wurmus [Thu, 1 Mar 2018 18:41:45 +0000 (19:41 +0100)]
gnu: Add java-biojava-alignment-4.0.

* gnu/packages/bioinformatics.scm (java-biojava-alignment-4.0): New variable.

6 years agognu: Add java-biojava-phylo-4.0.
Ricardo Wurmus [Thu, 1 Mar 2018 18:41:44 +0000 (19:41 +0100)]
gnu: Add java-biojava-phylo-4.0.

* gnu/packages/bioinformatics.scm (java-biojava-phylo-4.0): New variable.

6 years agognu: Add java-biojava-core-4.0.
Ricardo Wurmus [Thu, 1 Mar 2018 18:41:43 +0000 (19:41 +0100)]
gnu: Add java-biojava-core-4.0.

* gnu/packages/bioinformatics.scm (java-biojava-core-4.0): New variable.

6 years agognu: Add java-biojava-alignment.
Ricardo Wurmus [Thu, 1 Mar 2018 18:41:42 +0000 (19:41 +0100)]
gnu: Add java-biojava-alignment.

* gnu/packages/bioinformatics.scm (java-biojava-alignment): New variable.

6 years agognu: Add java-biojava-phylo.
Ricardo Wurmus [Thu, 1 Mar 2018 18:41:41 +0000 (19:41 +0100)]
gnu: Add java-biojava-phylo.

* gnu/packages/bioinformatics.scm (java-biojava-phylo): New variable.

6 years agognu: Add java-forester-1.005.
Ricardo Wurmus [Thu, 1 Mar 2018 18:41:40 +0000 (19:41 +0100)]
gnu: Add java-forester-1.005.

* gnu/packages/bioinformatics.scm (java-forester-1.005): New variable.

6 years agognu: Add java-forester.
Ricardo Wurmus [Thu, 1 Mar 2018 18:41:39 +0000 (19:41 +0100)]
gnu: Add java-forester.

* gnu/packages/bioinformatics.scm (java-forester): New variable.

6 years agognu: Add java-openchart2.
Ricardo Wurmus [Thu, 1 Mar 2018 18:41:38 +0000 (19:41 +0100)]
gnu: Add java-openchart2.

* gnu/packages/java.scm (java-openchart2): New variable.

6 years agognu: Add java-biojava-core.
Ricardo Wurmus [Thu, 1 Mar 2018 18:41:37 +0000 (19:41 +0100)]
gnu: Add java-biojava-core.

* gnu/packages/bioinformatics.scm (java-biojava-core): New variable.

6 years agognu: Add java-jdistlib.
Ricardo Wurmus [Thu, 1 Mar 2018 18:41:36 +0000 (19:41 +0100)]
gnu: Add java-jdistlib.

* gnu/packages/statistics.scm (java-jdistlib): New variable.

6 years agognu: Add java-jtransforms.
Ricardo Wurmus [Thu, 1 Mar 2018 18:41:35 +0000 (19:41 +0100)]
gnu: Add java-jtransforms.

* gnu/packages/algebra.scm (java-jtransforms): New variable.

6 years agognu: Add java-jlargearrays.
Ricardo Wurmus [Thu, 1 Mar 2018 18:41:34 +0000 (19:41 +0100)]
gnu: Add java-jlargearrays.

* gnu/packages/algebra.scm (java-jlargearrays): New variable.

6 years agognu: Add java-la4j.
Ricardo Wurmus [Thu, 1 Mar 2018 18:41:33 +0000 (19:41 +0100)]
gnu: Add java-la4j.

* gnu/packages/algebra.scm (java-la4j): New variable.

6 years agognu: Add fastqc.
Ricardo Wurmus [Fri, 23 Feb 2018 09:56:49 +0000 (10:56 +0100)]
gnu: Add fastqc.

* gnu/packages/bioinformatics.scm (fastqc): New variable.

6 years agognu: Add java-cisd-jhdf5.
Ricardo Wurmus [Fri, 23 Feb 2018 09:10:12 +0000 (10:10 +0100)]
gnu: Add java-cisd-jhdf5.

* gnu/packages/java.scm (java-cisd-jhdf5): New variable.

6 years agognu: Add java-cisd-args4j.
Ricardo Wurmus [Fri, 23 Feb 2018 09:09:50 +0000 (10:09 +0100)]
gnu: Add java-cisd-args4j.

* gnu/packages/java.scm (java-cisd-args4j): New variable.

6 years agognu: Add java-cisd-base.
Ricardo Wurmus [Wed, 22 Nov 2017 18:25:34 +0000 (19:25 +0100)]
gnu: Add java-cisd-base.

* gnu/packages/java.scm (java-cisd-base): New variable.

6 years agognu: Add texlive-fonts-iwona.
Ricardo Wurmus [Sun, 10 Dec 2017 21:26:47 +0000 (22:26 +0100)]
gnu: Add texlive-fonts-iwona.

* gnu/packages/tex.scm (texlive-fonts-iwona): New variable.

6 years agoservices: messaging: Prosody config supports file-like objects.
Clément Lassieur [Mon, 26 Feb 2018 00:12:24 +0000 (01:12 +0100)]
services: messaging: Prosody config supports file-like objects.

* doc/guix.texi (Messaging Services): Update accordingly.
* gnu/services/configuration.scm (serialize-configuration,
serialize-maybe-stem, serialize-package): Return strings or string-valued
gexps (these procedures were only used for their side-effects).
* gnu/services/messaging.scm (serialize-field, serialize-field-list,
enclose-quotes, serialize-raw-content, serialize-ssl-configuration,
serialize-virtualhost-configuration-list,
serialize-int-component-configuration-list,
serialize-ext-component-configuration-list,
serialize-virtualhost-configuration, serialize-int-component-configuration,
serialize-ext-component-configuration, serialize-prosody-configuration):
Return strings or string-valued gexps and stop printing.
(prosody-activation): Use SERIALIZE-PROSODY-CONFIGURATION's return value with
MIXED-TEXT-FILE instead of using its output with PLAIN-FILE.
(serialize-non-negative-integer, serialize-non-negative-integer-list): Convert
numbers to strings.
(file-object?, serialize-file-object, file-object-list?,
serialize-file-object-list): New procedures.
(ssl-configuration)[capath, cafile], (prosody-configuration)[plugin-paths,
groups-file]: Replace FILE-NAME with FILE-OBJECT.
* guix/gexp.scm (file-like?): New exported procedure.

6 years agognu: dictionaries: Add copyright line.
Nicolas Goaziou [Sat, 3 Mar 2018 13:23:17 +0000 (14:23 +0100)]
gnu: dictionaries: Add copyright line.

* gnu/packages/dictionaries.scm: Add copyright line.

6 years agognu: wireshark: Update to 2.4.5.
Nicolas Goaziou [Sat, 3 Mar 2018 13:21:20 +0000 (14:21 +0100)]
gnu: wireshark: Update to 2.4.5.

* gnu/packages/networking.scm (wireshark): Update to 2.4.5.

6 years agognu: grammalecte: Update to 0.6.2.
Nicolas Goaziou [Sat, 3 Mar 2018 13:06:43 +0000 (14:06 +0100)]
gnu: grammalecte: Update to 0.6.2.

* gnu/packages/dictionaries.scm (grammalecte): Update to 0.6.2.
[arguments]: Remove.

6 years agognu: Add ruby-iruby.
Christopher Baines [Tue, 10 Oct 2017 19:07:20 +0000 (20:07 +0100)]
gnu: Add ruby-iruby.

* gnu/packages/ruby.scm (ruby-iruby): New variable.

6 years agognu: Add ruby-mimemagic.
Christopher Baines [Tue, 10 Oct 2017 19:09:45 +0000 (20:09 +0100)]
gnu: Add ruby-mimemagic.

* gnu/packages/ruby.scm (ruby-mimemagic): New variable.

6 years agognu: Add ruby-data_uri.
Christopher Baines [Tue, 10 Oct 2017 19:09:18 +0000 (20:09 +0100)]
gnu: Add ruby-data_uri.

* gnu/packages/ruby.scm (ruby-data_uri): New variable.

6 years agognu: Add ruby-cztop.
Christopher Baines [Tue, 10 Oct 2017 19:08:09 +0000 (20:08 +0100)]
gnu: Add ruby-cztop.

* gnu/packages/ruby.scm (ruby-cztop): New variable.

6 years agognu: Add ruby-czmq-ffi-gen.
Christopher Baines [Tue, 10 Oct 2017 19:07:45 +0000 (20:07 +0100)]
gnu: Add ruby-czmq-ffi-gen.

* gnu/packages/ruby.scm (ruby-czmq-ffi-gen): New variable.

6 years agognu: Add ruby-bond.
Christopher Baines [Tue, 10 Oct 2017 19:02:19 +0000 (20:02 +0100)]
gnu: Add ruby-bond.

* gnu/packages/ruby.scm (ruby-bond): New variable.

6 years agognu: Add ruby-bacon-bits.
Christopher Baines [Tue, 10 Oct 2017 19:00:21 +0000 (20:00 +0100)]
gnu: Add ruby-bacon-bits.

* gnu/packages/ruby.scm (ruby-bacon-bits): New variable.

6 years agognu: Add ruby-mocha-on-bacon.
Christopher Baines [Tue, 10 Oct 2017 19:00:49 +0000 (20:00 +0100)]
gnu: Add ruby-mocha-on-bacon.

* gnu/packages/ruby.scm (ruby-mocha-on-bacon): New variable.

6 years agognu: networking: Add czmq.
Christopher Baines [Mon, 9 Oct 2017 05:57:26 +0000 (06:57 +0100)]
gnu: networking: Add czmq.

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

6 years agognu: ghc-refact: Fix typo in description.
Tobias Geerinckx-Rice [Sat, 3 Mar 2018 10:56:23 +0000 (11:56 +0100)]
gnu: ghc-refact: Fix typo in description.

* gnu/packages/haskell.scm (ghc-refact)[description]: Fix typo.

6 years agognu: quagga: Update to 1.2.4.
Tobias Geerinckx-Rice [Sat, 3 Mar 2018 01:50:09 +0000 (02:50 +0100)]
gnu: quagga: Update to 1.2.4.

* gnu/packages/networking.scm (quagga): Update to 1.2.4.

6 years agognu: conky: Remove redundant MKDIR-P.
Tobias Geerinckx-Rice [Fri, 2 Mar 2018 16:38:28 +0000 (17:38 +0100)]
gnu: conky: Remove redundant MKDIR-P.

* gnu/packages/conky.scm (conky)[arguments]: Remove redundant MKDIR-P.

6 years agognu: sslh: Update to 1.19c.
Tobias Geerinckx-Rice [Fri, 2 Mar 2018 21:39:35 +0000 (22:39 +0100)]
gnu: sslh: Update to 1.19c.

* gnu/packages/networking.scm (sslh): Update to 1.19c.

6 years agognu: wv: Edit description.
Tobias Geerinckx-Rice [Thu, 8 Feb 2018 23:02:45 +0000 (00:02 +0100)]
gnu: wv: Edit description.

Wv is still unmaintained – this just makes it more obvious.

* gnu/packages/wv.scm (wv)[description]: Mention the product versions in
addition to internal file format ones.  Align more closely with the
upstream description.

6 years agognu: libseccomp: Update to 2.3.3.
Tobias Geerinckx-Rice [Fri, 2 Mar 2018 21:40:45 +0000 (22:40 +0100)]
gnu: libseccomp: Update to 2.3.3.

* gnu/packages/linux.scm (libseccomp): Update to 2.3.3.

6 years agognu: hdparm: Update to 9.54.
Tobias Geerinckx-Rice [Fri, 2 Mar 2018 21:36:23 +0000 (22:36 +0100)]
gnu: hdparm: Update to 9.54.

* gnu/packages/linux.scm (hdparm): Update to 9.54.

6 years agognu: sdl2: Update to 2.0.8.
Tobias Geerinckx-Rice [Fri, 2 Mar 2018 21:19:08 +0000 (22:19 +0100)]
gnu: sdl2: Update to 2.0.8.

* gnu/packages/sdl.scm (sdl2): Update to 2.0.8.

6 years agognu: r-httpuv: Update to 1.3.6.2.
Ricardo Wurmus [Sat, 3 Mar 2018 09:40:05 +0000 (10:40 +0100)]
gnu: r-httpuv: Update to 1.3.6.2.

* gnu/packages/web.scm (r-httpuv): Update to 1.3.6.2.

6 years agognu: r-dbi: Update to 0.8.
Ricardo Wurmus [Sat, 3 Mar 2018 09:39:55 +0000 (10:39 +0100)]
gnu: r-dbi: Update to 0.8.

* gnu/packages/statistics.scm (r-dbi): Update to 0.8.

6 years agognu: r-performanceanalytics: Update to 1.5.2.
Ricardo Wurmus [Sat, 3 Mar 2018 09:39:17 +0000 (10:39 +0100)]
gnu: r-performanceanalytics: Update to 1.5.2.

* gnu/packages/cran.scm (r-performanceanalytics): Update to 1.5.2.
[propagated-inputs]: Add r-quadprog.
[native-inputs]: Remove gfortran.

6 years agolinux-initrd: Add virtio modules to '%base-initrd-modules'.
Ludovic Courtès [Sat, 3 Mar 2018 08:33:34 +0000 (09:33 +0100)]
linux-initrd: Add virtio modules to '%base-initrd-modules'.

Fixes a regression in installation tests, whereby 'guix system init'
would report that virtio modules are missing for the target devices.
In practice virtio modules were always available since 'base-initrd' was
always called with #:virtio? #t.  This commit simply moves them to
'%base-initrd-modules' so that 'guix system' knows they're available.

Reported by Danny Milosavljevic <dannym@scratchpost.org> at
<https://debbugs.gnu.org/cgi/bugreport.cgi?bug=30629#112>.

* gnu/system/linux-initrd.scm (default-initrd-modules): Add virtio
modules.
(base-initrd): Remove #:virtio? and 'virtio-modules'.
* gnu/system/vm.scm (expression->derivation-in-linux-vm)
(system-qemu-image, virtualized-operating-system): Remove uses of
 #:virtio?.
* doc/guix.texi (Initial RAM Disk): Update 'base-initrd' doc.

6 years agosystem: beaglebone-black: Use 'initrd-modules'.
Ludovic Courtès [Sat, 3 Mar 2018 00:29:18 +0000 (01:29 +0100)]
system: beaglebone-black: Use 'initrd-modules'.

* gnu/system/examples/beaglebone-black.tmpl: Use 'initrd-modules'
instead of 'initrd'.

6 years agovm: Add missing modules to the 'expression->derivation-in-linux-vm' initrd.
Ludovic Courtès [Sat, 3 Mar 2018 00:25:15 +0000 (01:25 +0100)]
vm: Add missing modules to the 'expression->derivation-in-linux-vm' initrd.

Fixes a regression introduced in
bc499b113a598c0e7863da9887a4133472985713, whereby the default initrd
used by 'expression->derivation-in-linux-vm' would lack all the usual
modules: virtio, nls_iso8859-1, etc.

* gnu/system/vm.scm (expression->derivation-in-linux-vm): Pass
 #:linux-modules to 'base-initrd'.

6 years agolinux-initrd: 'file-system-modules' returns the right module list.
Ludovic Courtès [Fri, 2 Mar 2018 23:04:17 +0000 (00:04 +0100)]
linux-initrd: 'file-system-modules' returns the right module list.

Fixes a bug whereby, for an "iso9660" file system, it would return
'("iso9660" "isofs"), i.e., both the key and the value.

Reported by Danny Milosavljevic <dannym@scratchpost.org>
at <https://debbugs.gnu.org/cgi/bugreport.cgi?bug=30629#115>.

* gnu/system/linux-initrd.scm (lookup-procedure): 'vhash-assoc' returns
a key/value pair; match it.

6 years agognu: cutadapt: Update to 1.16.
Ricardo Wurmus [Fri, 2 Mar 2018 22:44:16 +0000 (23:44 +0100)]
gnu: cutadapt: Update to 1.16.

* gnu/packages/bioinformatics.scm (cutadapt): Update to 1.16.
[source]: Fetch via git.
[arguments]: Remove.
[native-inputs]: Replace python-nose with python-pytest.

6 years agognu: python-xopen: Update to 0.3.2.
Ricardo Wurmus [Fri, 2 Mar 2018 22:43:55 +0000 (23:43 +0100)]
gnu: python-xopen: Update to 0.3.2.

* gnu/packages/python.scm (python-xopen): Update to 0.3.2.

6 years agognu: Add r-hpar.
Ricardo Wurmus [Fri, 2 Mar 2018 22:24:57 +0000 (23:24 +0100)]
gnu: Add r-hpar.

* gnu/packages/bioconductor.scm: New file.
* gnu/local.mk (GNU_SYSTEM_MODULES): Add it.

6 years agognu: Add r-powerplus.
Ricardo Wurmus [Fri, 2 Mar 2018 22:07:26 +0000 (23:07 +0100)]
gnu: Add r-powerplus.

* gnu/packages/cran.scm (r-powerplus): New variable.

6 years agognu: Add r-np.
Ricardo Wurmus [Fri, 2 Mar 2018 22:07:20 +0000 (23:07 +0100)]
gnu: Add r-np.

* gnu/packages/cran.scm (r-np): New variable.

6 years agognu: Add r-phontools.
Ricardo Wurmus [Fri, 2 Mar 2018 22:07:12 +0000 (23:07 +0100)]
gnu: Add r-phontools.

* gnu/packages/cran.scm (r-phontools): New variable.

6 years agognu: Add r-complexplus.
Ricardo Wurmus [Fri, 2 Mar 2018 22:07:04 +0000 (23:07 +0100)]
gnu: Add r-complexplus.

* gnu/packages/cran.scm (r-complexplus): New variable.

6 years agognu: Add r-expm.
Ricardo Wurmus [Fri, 2 Mar 2018 22:06:57 +0000 (23:06 +0100)]
gnu: Add r-expm.

* gnu/packages/cran.scm (r-expm): New variable.

6 years agognu: Add r-trend.
Ricardo Wurmus [Fri, 2 Mar 2018 22:06:50 +0000 (23:06 +0100)]
gnu: Add r-trend.

* gnu/packages/cran.scm (r-trend): New variable.

6 years agognu: Add r-cubature.
Ricardo Wurmus [Fri, 2 Mar 2018 22:06:41 +0000 (23:06 +0100)]
gnu: Add r-cubature.

* gnu/packages/cran.scm (r-cubature): New variable.

6 years agognu: Add r-urca.
Ricardo Wurmus [Fri, 2 Mar 2018 22:06:33 +0000 (23:06 +0100)]
gnu: Add r-urca.

* gnu/packages/cran.scm (r-urca): New variable.

6 years agognu: Add r-fractal.
Ricardo Wurmus [Fri, 2 Mar 2018 22:06:26 +0000 (23:06 +0100)]
gnu: Add r-fractal.

* gnu/packages/cran.scm (r-fractal): New variable.

6 years agognu: Add r-extradistr.
Ricardo Wurmus [Fri, 2 Mar 2018 22:06:17 +0000 (23:06 +0100)]
gnu: Add r-extradistr.

* gnu/packages/cran.scm (r-extradistr): New variable.

6 years agognu: Add r-tsa.
Ricardo Wurmus [Fri, 2 Mar 2018 22:06:10 +0000 (23:06 +0100)]
gnu: Add r-tsa.

* gnu/packages/cran.scm (r-tsa): New variable.

6 years agognu: Add r-wmtsa.
Ricardo Wurmus [Fri, 2 Mar 2018 22:06:00 +0000 (23:06 +0100)]
gnu: Add r-wmtsa.

* gnu/packages/cran.scm (r-wmtsa): New variable.

6 years agognu: Add r-tseries.
Ricardo Wurmus [Fri, 2 Mar 2018 22:05:52 +0000 (23:05 +0100)]
gnu: Add r-tseries.

* gnu/packages/cran.scm (r-tseries): New variable.

6 years agognu: Add r-quantmod.
Ricardo Wurmus [Fri, 2 Mar 2018 22:05:43 +0000 (23:05 +0100)]
gnu: Add r-quantmod.

* gnu/packages/cran.scm (r-quantmod): New variable.

6 years agognu: Add r-sapa.
Ricardo Wurmus [Fri, 2 Mar 2018 22:05:35 +0000 (23:05 +0100)]
gnu: Add r-sapa.

* gnu/packages/cran.scm (r-sapa): New variable.

6 years agognu: Add r-ifultools.
Ricardo Wurmus [Fri, 2 Mar 2018 22:05:14 +0000 (23:05 +0100)]
gnu: Add r-ifultools.

* gnu/packages/cran.scm (r-ifultools): New variable.

6 years agognu: Add r-splus2r.
Ricardo Wurmus [Fri, 2 Mar 2018 22:05:02 +0000 (23:05 +0100)]
gnu: Add r-splus2r.

* gnu/packages/cran.scm (r-splus2r): New variable.