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Author SHA1 Message Date
Ricardo Wurmus 08ddb98aef
gnu: r-gtools: Make output deterministic. 
* gnu/packages/statistics.scm (r-gtools)[arguments]: Add build phase to avoid
running tempdir at build time.
 2018-03-06 16:03:04 +01:00
Oleg Pykhalov 5ad13e6cdf
gnu: emacs-transmission: Update to 0.12.1. 
* gnu/packages/emacs.scm (emacs-transmission): Update to 0.12.1.
 2018-03-06 12:09:02 +03:00
Oleg Pykhalov 69611d3eac
gnu: haskell-mode: Fix find emacs-stream elisp directory. 
* gnu/packages/emacs.scm (haskell-mode)[arguments]: Find only directories with
"\\.el$" in ‘el-dir’.
 2018-03-06 10:34:59 +03:00
Rutger Helling cee03b267c
gnu: ovmf: Fix build and add FIXME. 
* gnu/packages/firmware.scm (ovmf): Replace 'invoke' with 'system*'. Add FIXME
about failing script.
 2018-03-06 08:27:07 +01:00
Gábor Boskovits 0f2778029a
gnu: java-ops4j-pax-tinybundles: Use distribution bndlib version. 
* gnu/packages/java.scm (java-ops4j-pax-tinybundles)[arguments]<#:phases>:
Modify fix-version to use the distibution version of java-aqute-bndlib.
 2018-03-05 20:42:48 +01:00
Tobias Geerinckx-Rice c8213ffc52
gnu: perl-email-address: Update to 1.909. 
* gnu/packages/perl.scm (perl-email-address): Update to 1.909.
 2018-03-05 17:32:11 +01:00
Tobias Geerinckx-Rice 1c3de94cff
gnu: perl-sub-quote: Update to 2.005000. 
* gnu/packages/xml.scm (perl-sub-quote): Update to 2.005000.
 2018-03-05 17:32:11 +01:00
Tobias Geerinckx-Rice 503a00597b
gnu: perl-xml-compile-cache: Update to 1.06. 
* gnu/packages/xml.scm (perl-xml-compile-cache): Update to 1.06.
 2018-03-05 17:32:11 +01:00
Tobias Geerinckx-Rice b5de208e84
gnu: perl-xml-rss: Update to 1.60. 
* gnu/packages/xml.scm (perl-xml-rss): Update to 1.60.
 2018-03-05 17:32:11 +01:00
Tobias Geerinckx-Rice 437e5fae13
gnu: editres: Update to 1.0.7. 
* gnu/packages/xorg.scm (editres): Update to 1.0.7.
 2018-03-05 17:32:10 +01:00
Tobias Geerinckx-Rice cc7a4bbd27
gnu: tocc, libtocc: Use HTTPS home page. 
* gnu/packages/search.scm (libtocc, tocc)[home-page]: Use HTTPS.
 2018-03-05 17:32:10 +01:00
Tobias Geerinckx-Rice 55b7cd10c2
gnu: perl-io-socket-ip: Update to 0.39. 
* gnu/packages/web.scm (perl-io-socket-ip): Update to 0.39.
 2018-03-05 17:32:10 +01:00
Tobias Geerinckx-Rice 530df311ac
gnu: perl-www-mechanize: Update to 1.87. 
* gnu/packages/web.scm (perl-www-mechanize): Update to 1.87.
 2018-03-05 17:32:09 +01:00
Tobias Geerinckx-Rice 9599339c59
gnu: openvpn: Mark up description. 
* gnu/packages/vpn.scm (openvpn)[description]: Use @dfn.
 2018-03-05 17:32:09 +01:00
Tobias Geerinckx-Rice 0d34993a65
gnu: openvpn: Update to 2.4.5. 
* gnu/packages/vpn.scm (openvpn): Update to 2.4.5.
 2018-03-05 17:32:09 +01:00
Tobias Geerinckx-Rice 211748d475
gnu: papi: Use HTTPS home page. 
* gnu/packages/profiling.scm (papi)[home-page]: Use HTTPS.
 2018-03-05 17:32:08 +01:00
Tobias Geerinckx-Rice f7c870f78a
gnu: papi: Fix documentation location. 
* gnu/packages/profiling.scm (papi)[arguments]: Install ‘documentation’
to a customary subdirectory of /share/doc.
 2018-03-05 17:32:08 +01:00
Rutger Helling 0ebc1b934d
gnu: xpra: Update to 2.2.5. 
* gnu/packages/xorg.scm (xpra): Update to 2.2.5.
 2018-03-05 12:29:37 +01:00
Mark H Weaver 6a4eaafee0
gnu: linux-libre@4.14: Update to 4.14.24. 
* gnu/packages/linux.scm (%linux-libre-4.14-version): Update to 4.14.24.
(%linux-libre-4.14-hash): Update hash.
 2018-03-05 03:43:45 -05:00
Mark H Weaver ee483a5626
gnu: linux-libre@4.9: Update to 4.9.86. 
* gnu/packages/linux.scm (linux-libre-4.9): Update to 4.9.86.
 2018-03-05 03:43:02 -05:00
Mark H Weaver 88b1a38e26
gnu: linux-libre@4.4: Update to 4.4.120. 
* gnu/packages/linux.scm (linux-libre-4.4): Update to 4.4.120.
 2018-03-05 03:42:07 -05:00
Christopher Baines 68d70f6ae3
gnu: Add emacs-terraform-mode. 
* gnu/packages/emacs.scm (emacs-terraform-mode): New variable.
 2018-03-05 07:48:49 +00:00
Christopher Baines dc97f7e20e
gnu: Add emacs-hcl-mode. 
* gnu/packages/emacs.scm (emacs-hcl-mode): New variable.
 2018-03-05 07:48:48 +00:00
Efraim Flashner 16718b6776
services: Add openntpd service. 
* gnu/packages/ntp.scm (openntpd)[arguments]: Add 'configure-flags to
set openntpd daemon's user and localstatedir. Add a custom phase to not
try to create said directory at install time.
* gnu/services/networking.scm (<openntpd-configuration>): New record type.
(openntpd-shepherd-service, openntpd-service-activation): New procedures.
(openntpd-service-type): New variable.
* doc/guix.texi (Networking Services): Add openntpd documentation.
 2018-03-05 08:46:28 +02:00
Tobias Geerinckx-Rice ac1a9ce8b0
gnu: papi: Update phase style. 
* gnu/packages/profiling.scm (papi)[arguments]: Substitute INVOKE for
SYSTEM*, end phases with #t, and don't explicitly install LICENSE.txt.
 2018-03-04 18:03:46 +01:00
Tobias Geerinckx-Rice 635dd0cc96
gnu: tomb: Update phase style. 
* gnu/packages/crypto.scm (tomb)[arguments]: Substitute INVOKE for
SYSTEM* and end phases with #t.
 2018-03-04 18:03:45 +01:00
Tobias Geerinckx-Rice 9539016e3a
gnu: tomb: Use HTTPS home page. 
* gnu/packages/crypto.scm (tomb)[home-page]: Use HTTPS.
 2018-03-04 18:03:45 +01:00
Tobias Geerinckx-Rice ed36949a9d
gnu: footswitch: Update to 0.1-2.deedd87. 
* gnu/packages/accessibility.scm (footswitch): Update to 0.1-2.deedd87.
 2018-03-04 18:03:45 +01:00
Tobias Geerinckx-Rice bd128d5e88
gnu: footswitch: Remove redundant MKDIR-P. 
* gnu/packages/accessibility.scm (footswitch)[arguments]: Remove MKDIR-P
before INSTALL-FILE.
 2018-03-04 18:03:45 +01:00
Tobias Geerinckx-Rice 92793c7b02
gnu: gitolite: Update phase style. 
* gnu/packages/version-control.scm (gitolite): Substitute INVOKE for
SYSTEM* and end phases with #t.
 2018-03-04 18:03:44 +01:00
Tobias Geerinckx-Rice 7730b7179c
gnu: gitolite: Update to 3.6.7. 
* gnu/packages/version-control.scm (gitolite): Update to 3.6.7.
 2018-03-04 18:03:44 +01:00
Tobias Geerinckx-Rice d035eaa304
gnu: ii, sic: Use HTTPS home pages. 
* gnu/packages/irc.scm (ii, sic)[home-page]: Use HTTPS.
 2018-03-04 18:03:44 +01:00
Tobias Geerinckx-Rice e0dbead5a7
gnu: ii: Update to 1.8. 
* gnu/packages/irc.scm (ii): Update to 1.8.
 2018-03-04 18:03:44 +01:00
Tobias Geerinckx-Rice 53244d1ffa
gnu: cloc: Update phase style. 
* gnu/packages/code.scm (cloc)[arguments]: Substitute INVOKE for SYSTEM*
and end phases with #t.
 2018-03-04 18:03:44 +01:00
Tobias Geerinckx-Rice 95943ed7dc
gnu: cloc: Update to 1.76. 
* gnu/packages/code.scm (cloc): Update to 1.76.
[source]: Update origin URI scheme.
[inputs]: Add perl-parallel-forkmanager.
 2018-03-04 18:03:43 +01:00
Tobias Geerinckx-Rice 03b7195794
gnu: liblo: Mark up description. 
* gnu/packages/audio.scm (liblo)[description]: Use @dfn.
 2018-03-04 18:03:43 +01:00
Marius Bakke 3e57b7d99b
gnu: multipath-tools: Update to 0.7.4. 
* gnu/packages/linux.scm (multipath-tools): Update to 0.7.4.
[source]: Download using HTTPS.
 2018-03-04 17:54:40 +01:00
Marius Bakke 5275f69e6e
gnu: freexl: Update to 1.0.5 [security fixes]. 
Fixes CVE-2018-7435, CVE-2018-7436, CVE-2018-7437, CVE-2018-7438 and
CVE-2018-7439.

* gnu/packages/xml.scm (freexl): Update to 1.0.5.
 2018-03-04 17:54:40 +01:00
Marius Bakke 5b0b520e22
gnu: ceph: Update to 12.2.4. 
* gnu/packages/patches/ceph-disable-cpu-optimizations.patch: Adjust to
upstream changes.
* gnu/packages/patches/ceph-disable-unittest-throttle.patch: Delete file.
* gnu/packages/patches/ceph-rocksdb-compat.patch: New file.
* gnu/local.mk (dist_patch_DATA): Adjust accordingly.
* gnu/packages/storage.scm (ceph): Update to 12.2.4.
[source](patches): Adjust.
[arguments]: Add "-DWITH_BABELTRACE=OFF" in #:configure-flags.  Build with
CMAKE-3.11.  Adjust file substitutions.  Wrap 'ceph' executable.
[native-inputs]: Add GPERF.
[inputs]: Replace BOOST with BOOST-1.66.  Add PYTHON2-PRETTYTABLE.
 2018-03-04 17:54:40 +01:00
Marius Bakke 1568cc14fa
gnu: Add cmake@3.11. 
* gnu/packages/cmake.scm (cmake-3.11): New public variable.
 2018-03-04 17:54:40 +01:00
Marius Bakke bbce53c4b3
gnu: Add boost@1.66.0. 
* gnu/packages/boost.scm (boost-1.66): New public variable.
 2018-03-04 17:54:40 +01:00
Marius Bakke 8293d21c66
gnu: java-snappy: Update to 1.1.7. 
* gnu/packages/compression.scm (java-snappy): Update to 1.1.7.
[arguments]: Use INVOKE instead of SYSTEM*.  Avoid CMAKE dependency.  Delete
Hadoop test.  Enable fixed test.
[native-inputs]: Add JAVA-COMMONS-LANG and JAVA-COMMONS-IO.
 2018-03-04 17:54:40 +01:00
Marius Bakke 5a43735722
gnu: snappy: Update to 1.1.7. 
* gnu/packages/compression.scm (snappy): Update to 1.1.7.
[source]: Change to git archive.  Set file-name.
[build-system]: Change to CMAKE-BUILD-SYSTEM.
[arguments]: Add #:configure-flags.
[description]: Fix infractions.
 2018-03-04 17:54:39 +01:00
Marius Bakke 7fa9cca84a
gnu: rocksdb: Update to 5.10.4. 
* gnu/packages/databases.scm (rocksdb): Update to 5.10.4.
[source]: Substitute the unbundled copy of GNU Parallel.
[arguments]: Add "V=1" "USE_RTTI=1" and
"ROCKSDBTESTS_END=db_tailing_iter_test" to #:make-flags.  Set #:test-target to
"check_some".  Respect parallel jobs in 'build-release-libraries' phase and
rename to 'build'.
[license]: Update for changes in 5.5.4.
 2018-03-04 17:54:39 +01:00
Danny Milosavljevic 81ed306dee
gnu: inkscape: Disable duplicate icon cache generation. 
* gnu/packages/inkscape.scm (inkscape): Disable duplicate icon cache
generation.
 2018-03-04 15:44:34 +01:00
Danny Milosavljevic 692f6e457e
gnu: abiword: Disable duplicate icon cache generation. 
* gnu/packages/abiword.scm (abiword): Disable duplicate icon cache generation.
 2018-03-04 15:43:46 +01:00
Danny Milosavljevic 64cdd73c22
gnu: python-funcy: Fix tests. 
* gnu/packages/python.scm (python-funcy)[native-inputs]: Delete python-pytest-warnings.
 2018-03-04 15:42:41 +01:00
Gábor Boskovits 48c8622010
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>
 2018-03-04 14:16:37 +01:00
Gábor Boskovits 4c763b4d67
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>
 2018-03-04 14:13:47 +01:00
Efraim Flashner 82f09c0e8e
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.
 2018-03-04 12:38:51 +02:00
Efraim Flashner 6de107b0c9
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.
 2018-03-04 12:38:50 +02:00
Efraim Flashner fdbece74aa
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.
 2018-03-04 12:38:50 +02:00
Efraim Flashner 661ad6f0c2
gnu: freegish: Declare a source file-name. 
* gnu/packages/games.scm (freegish)[source]: Declare a source file-name.
 2018-03-04 12:38:50 +02:00
Efraim Flashner a1dc853ef4
gnu: disorderfs: Declare a source file-name. 
* gnu/packages/file-systems.scm (disorderfs)[source]: Declare a source
file-name.
 2018-03-04 12:38:50 +02:00
Efraim Flashner aeb95f1f97
gnu: emacs-sly: Declare a source file-name. 
* gnu/packages/emacs.scm (emacs-sly)[source]: Declare a source
file-name.
 2018-03-04 12:38:50 +02:00
Efraim Flashner 5a6f7a6805
gnu: emacs-epl: Declare a source file-name. 
* gnu/packages/emacs.scm (emacs-epl)[source]: Declare a source
file-name.
 2018-03-04 12:38:47 +02:00
Efraim Flashner c553b08b49
gnu: python-apsw: Use invoke. 
* gnu/packages/databases.scm (python-apsw)[arguments]: Use invoke.
 2018-03-04 12:05:14 +02:00
Efraim Flashner f5c847ebd0
gnu: python-apsw: Declare a source file-name. 
* gnu/packages/databases.scm (python-apsw)[source]: Declare a source
file-name.
 2018-03-04 12:05:14 +02:00
Efraim Flashner c2c04cde9b
gnu: kurly: Declare a source file-name. 
* gnu/packages/curl.scm (kurly)[source]: Declare a source file-name.
 2018-03-04 12:05:14 +02:00
Efraim Flashner 277be74fa7
gnu: unshield: Declare a source file-name. 
* gnu/packages/compression.scm (unshield)[source]: Declare a source
file-name.
 2018-03-04 12:05:14 +02:00
Efraim Flashner eafe96ea9e
gnu: sfarkxtc: Declare a source file-name. 
* gnu/packages/compression.scm (sfarkxtc)[source]: Declare a source
file-name.
 2018-03-04 12:05:14 +02:00
Efraim Flashner da49d13710
gnu: piranha: Declare a source file-name. 
* gnu/packages/bioinformatics.scm (piranha)[source]: Declare a source
file-name.
 2018-03-04 12:05:13 +02:00
Efraim Flashner d9a069c2d9
gnu: libdivsufsort: Declare a source file-name. 
* gnu/packages/bioinformatics.scm (libdivsufsort)[source]: Declare a
source file-name.
 2018-03-04 12:05:13 +02:00
Efraim Flashner 5110672474
gnu: seek: Declare a source file-name. 
* gnu/packages/bioinformatics.scm (seek)[source]: Declare a source
file-name.
 2018-03-04 12:05:13 +02:00
Efraim Flashner b1d4026dfb
gnu: r-dropbead: Declare a source file-name. 
* gnu/packages/bioinformatics.scm (r-dropbead)[source]: Declare a source
file-name.
 2018-03-04 12:05:10 +02:00
Efraim Flashner a1eb506cf3
gnu: faust@2: Declare a source file-name. 
* gnu/packages/audio.scm (faust@2)[source]: Declare a source file-name.
 2018-03-04 11:01:40 +02:00
Efraim Flashner fdf359f82b
gnu: rubberband: Declare a source file-name. 
* gnu/packages/audio.scm (rubberband)[source]: Declare a source
file-name.
 2018-03-04 11:01:40 +02:00
Efraim Flashner 70aa07d296
gnu: qjackrcd: Declare a source file-name. 
* gnu/packages/audio.scm (qjackrcd)[source]: Declare a source file-name.
 2018-03-04 11:01:40 +02:00
Efraim Flashner 6677c99a8b
gnu: lv2-devel: Declare a source file-name. 
* gnu/packages/audio.scm (lv2-devel)[source]: Declare a source file-name.
 2018-03-04 11:01:40 +02:00
Efraim Flashner 35a01e67c8
gnu: lv2-mda-piano: Declare a source file-name. 
* gnu/packages/audio.scm (lv2-mda-piano)[source]: Declare a source
file-name.
 2018-03-04 11:01:39 +02:00
Efraim Flashner a18ee793d7
gnu: papagayo: Declare a source file-name. 
* gnu/packages/animation.scm (papagayo)[source]: Declare a source
file-name.
 2018-03-04 11:01:39 +02:00
Efraim Flashner 7fc944273d
gnu: masscan: Declare a source file-name. 
* gnu/packages/admin.scm (masscan)[source]: Declare a source file-name.
 2018-03-04 11:01:36 +02:00
Christopher Baines bc037c1bd1
services: redis: Add a default-value to the redis-service-type. 
* gnu/packages/databases.scm (redis-service-type)[default-value]: Set
  to (redis-configuration).
 2018-03-03 23:52:26 +00:00
Christopher Baines e903738f86
services: mysql: Add a default-value to the mysql-service-type. 
* gnu/services/databases.scm (mysql-service-type)[default-value]: Set
  to (mysql-configuration).
 2018-03-03 23:52:25 +00:00
Christopher Baines 1e6b9c6e16
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).
 2018-03-03 23:52:23 +00:00
Danny Milosavljevic 8b2219d847
linux-modules: Add module-aliases. 
* gnu/build/linux-modules.scm (module-aliases): New variable.
 2018-03-03 23:40:02 +01:00
Tobias Geerinckx-Rice c94752ad22
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.
 2018-03-03 21:31:08 +01:00
Ricardo Wurmus 1adeef3194
gnu: Add dropseq-tools. 
* gnu/packages/bioinformatics.scm (dropseq-tools): New variable.
 2018-03-03 21:28:05 +01:00
Ricardo Wurmus 72299db9fe
gnu: Add java-picard-2.10.3. 
* gnu/packages/bioinformatics.scm (java-picard-2.10.3): New variable.
 2018-03-03 21:28:02 +01:00
Ricardo Wurmus 719fa958f3
gnu: Add java-htsjdk-2.10.1. 
* gnu/packages/bioinformatics.scm (java-htsjdk-2.10.1): New variable.
 2018-03-03 21:27:59 +01:00
Ricardo Wurmus 9a599c17b7
gnu: Add java-htsjdk-latest. 
* gnu/packages/bioinformatics.scm (java-htsjdk-latest): New variable.
 2018-03-03 21:27:57 +01:00
Ricardo Wurmus 9ac7db1830
gnu: Add java-biojava-alignment-4.0. 
* gnu/packages/bioinformatics.scm (java-biojava-alignment-4.0): New variable.
 2018-03-03 21:27:56 +01:00
Ricardo Wurmus 5528f9e8f0
gnu: Add java-biojava-phylo-4.0. 
* gnu/packages/bioinformatics.scm (java-biojava-phylo-4.0): New variable.
 2018-03-03 21:27:53 +01:00
Ricardo Wurmus e44da58c16
gnu: Add java-biojava-core-4.0. 
* gnu/packages/bioinformatics.scm (java-biojava-core-4.0): New variable.
 2018-03-03 21:27:51 +01:00
Ricardo Wurmus 22c09c335b
gnu: Add java-biojava-alignment. 
* gnu/packages/bioinformatics.scm (java-biojava-alignment): New variable.
 2018-03-03 21:27:48 +01:00
Ricardo Wurmus b28c803708
gnu: Add java-biojava-phylo. 
* gnu/packages/bioinformatics.scm (java-biojava-phylo): New variable.
 2018-03-03 21:27:46 +01:00
Ricardo Wurmus 10645b9212
gnu: Add java-forester-1.005. 
* gnu/packages/bioinformatics.scm (java-forester-1.005): New variable.
 2018-03-03 21:27:44 +01:00
Ricardo Wurmus f09d16e594
gnu: Add java-forester. 
* gnu/packages/bioinformatics.scm (java-forester): New variable.
 2018-03-03 21:27:41 +01:00
Ricardo Wurmus 93abc975fe
gnu: Add java-openchart2. 
* gnu/packages/java.scm (java-openchart2): New variable.
 2018-03-03 21:27:39 +01:00
Ricardo Wurmus 5fef15e506
gnu: Add java-biojava-core. 
* gnu/packages/bioinformatics.scm (java-biojava-core): New variable.
 2018-03-03 21:27:36 +01:00
Ricardo Wurmus dbb3581383
gnu: Add java-jdistlib. 
* gnu/packages/statistics.scm (java-jdistlib): New variable.
 2018-03-03 21:27:33 +01:00
Ricardo Wurmus 4e92911c82
gnu: Add java-jtransforms. 
* gnu/packages/algebra.scm (java-jtransforms): New variable.
 2018-03-03 21:27:30 +01:00
Ricardo Wurmus 24074b0bdd
gnu: Add java-jlargearrays. 
* gnu/packages/algebra.scm (java-jlargearrays): New variable.
 2018-03-03 21:27:27 +01:00
Ricardo Wurmus c8d996080e
gnu: Add java-la4j. 
* gnu/packages/algebra.scm (java-la4j): New variable.
 2018-03-03 21:27:21 +01:00
Ricardo Wurmus bd975831c6
gnu: Add fastqc. 
* gnu/packages/bioinformatics.scm (fastqc): New variable.
 2018-03-03 21:21:48 +01:00
Ricardo Wurmus 2f0d041816
gnu: Add java-cisd-jhdf5. 
* gnu/packages/java.scm (java-cisd-jhdf5): New variable.
 2018-03-03 21:21:48 +01:00
Ricardo Wurmus 04ddca26e6
gnu: Add java-cisd-args4j. 
* gnu/packages/java.scm (java-cisd-args4j): New variable.
 2018-03-03 21:21:47 +01:00
Ricardo Wurmus 30d554732a
gnu: Add java-cisd-base. 
* gnu/packages/java.scm (java-cisd-base): New variable.
 2018-03-03 21:21:47 +01:00
Ricardo Wurmus f9e0fcb28f
gnu: Add texlive-fonts-iwona. 
* gnu/packages/tex.scm (texlive-fonts-iwona): New variable.
 2018-03-03 21:21:47 +01:00
Clément Lassieur bdcf0e6fd4
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.
 2018-03-03 18:21:52 +01:00
Nicolas Goaziou fb547c3429
gnu: dictionaries: Add copyright line. 
* gnu/packages/dictionaries.scm: Add copyright line.
 2018-03-03 14:23:17 +01:00
Nicolas Goaziou 5e332c57d1
gnu: wireshark: Update to 2.4.5. 
* gnu/packages/networking.scm (wireshark): Update to 2.4.5.
 2018-03-03 14:21:20 +01:00
Nicolas Goaziou 0645da3fe3
gnu: grammalecte: Update to 0.6.2. 
* gnu/packages/dictionaries.scm (grammalecte): Update to 0.6.2.
[arguments]: Remove.
 2018-03-03 14:06:43 +01:00
Christopher Baines 62b138caf5
gnu: Add ruby-iruby. 
* gnu/packages/ruby.scm (ruby-iruby): New variable.
 2018-03-03 12:51:27 +00:00
Christopher Baines 8279b1d3b1
gnu: Add ruby-mimemagic. 
* gnu/packages/ruby.scm (ruby-mimemagic): New variable.
 2018-03-03 12:51:26 +00:00
Christopher Baines b03eb6acb4
gnu: Add ruby-data_uri. 
* gnu/packages/ruby.scm (ruby-data_uri): New variable.
 2018-03-03 12:51:26 +00:00
Christopher Baines d0afff263c
gnu: Add ruby-cztop. 
* gnu/packages/ruby.scm (ruby-cztop): New variable.
 2018-03-03 12:51:26 +00:00
Christopher Baines fe5dd5f446
gnu: Add ruby-czmq-ffi-gen. 
* gnu/packages/ruby.scm (ruby-czmq-ffi-gen): New variable.
 2018-03-03 12:51:26 +00:00
Christopher Baines afdb437c82
gnu: Add ruby-bond. 
* gnu/packages/ruby.scm (ruby-bond): New variable.
 2018-03-03 12:51:26 +00:00
Christopher Baines a8d2bf3cab
gnu: Add ruby-bacon-bits. 
* gnu/packages/ruby.scm (ruby-bacon-bits): New variable.
 2018-03-03 12:51:26 +00:00
Christopher Baines cf646acf96
gnu: Add ruby-mocha-on-bacon. 
* gnu/packages/ruby.scm (ruby-mocha-on-bacon): New variable.
 2018-03-03 12:51:25 +00:00
Christopher Baines 433dc74611
gnu: networking: Add czmq. 
* gnu/packages/networking.scm (czmq): New variable.
 2018-03-03 12:51:23 +00:00
Tobias Geerinckx-Rice add928d35f
gnu: ghc-refact: Fix typo in description. 
* gnu/packages/haskell.scm (ghc-refact)[description]: Fix typo.
 2018-03-03 13:28:22 +01:00
Tobias Geerinckx-Rice 75377c6c48
gnu: quagga: Update to 1.2.4. 
* gnu/packages/networking.scm (quagga): Update to 1.2.4.
 2018-03-03 13:28:22 +01:00
Tobias Geerinckx-Rice e6d30cf755
gnu: conky: Remove redundant MKDIR-P. 
* gnu/packages/conky.scm (conky)[arguments]: Remove redundant MKDIR-P.
 2018-03-03 13:27:17 +01:00
Tobias Geerinckx-Rice 9d13f82da8
gnu: sslh: Update to 1.19c. 
* gnu/packages/networking.scm (sslh): Update to 1.19c.
 2018-03-03 13:27:16 +01:00
Tobias Geerinckx-Rice dbefd3ff72
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.
 2018-03-03 13:27:16 +01:00
Tobias Geerinckx-Rice 83a9003c5d
gnu: libseccomp: Update to 2.3.3. 
* gnu/packages/linux.scm (libseccomp): Update to 2.3.3.
 2018-03-03 13:27:16 +01:00
Tobias Geerinckx-Rice 74a2f8ff1f
gnu: hdparm: Update to 9.54. 
* gnu/packages/linux.scm (hdparm): Update to 9.54.
 2018-03-03 13:27:16 +01:00
Tobias Geerinckx-Rice f4009ade25
gnu: sdl2: Update to 2.0.8. 
* gnu/packages/sdl.scm (sdl2): Update to 2.0.8.
 2018-03-03 13:27:15 +01:00
Ricardo Wurmus ec8b3d48ff
gnu: r-httpuv: Update to 1.3.6.2. 
* gnu/packages/web.scm (r-httpuv): Update to 1.3.6.2.
 2018-03-03 10:46:35 +01:00
Ricardo Wurmus fac40f38fe
gnu: r-dbi: Update to 0.8. 
* gnu/packages/statistics.scm (r-dbi): Update to 0.8.
 2018-03-03 10:46:35 +01:00
Ricardo Wurmus 081d143d3b
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.
 2018-03-03 10:46:35 +01:00
Ludovic Courtès eac026e5c8
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.
 2018-03-03 09:41:21 +01:00
Ludovic Courtès f850e0da8e
system: beaglebone-black: Use 'initrd-modules'. 
* gnu/system/examples/beaglebone-black.tmpl: Use 'initrd-modules'
instead of 'initrd'.
 2018-03-03 09:41:21 +01:00
Ludovic Courtès 5a3716aebf
vm: Add missing modules to the 'expression->derivation-in-linux-vm' initrd. 
Fixes a regression introduced in
bc499b113a, 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'.
 2018-03-03 09:41:21 +01:00
Ludovic Courtès 3cb3a4e6e5
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.
 2018-03-03 09:41:21 +01:00
Ricardo Wurmus 3ede1550e8
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.
 2018-03-02 23:44:16 +01:00
Ricardo Wurmus 62a4b952c0
gnu: python-xopen: Update to 0.3.2. 
* gnu/packages/python.scm (python-xopen): Update to 0.3.2.
 2018-03-02 23:43:55 +01:00
Ricardo Wurmus fa5965990d
gnu: Add r-hpar. 
* gnu/packages/bioconductor.scm: New file.
* gnu/local.mk (GNU_SYSTEM_MODULES): Add it.
 2018-03-02 23:24:57 +01:00
Ricardo Wurmus 2a112be09a
gnu: Add r-powerplus. 
* gnu/packages/cran.scm (r-powerplus): New variable.
 2018-03-02 23:07:26 +01:00
Ricardo Wurmus d976454c6b
gnu: Add r-np. 
* gnu/packages/cran.scm (r-np): New variable.
 2018-03-02 23:07:20 +01:00
Ricardo Wurmus 7b81a7eabf
gnu: Add r-phontools. 
* gnu/packages/cran.scm (r-phontools): New variable.
 2018-03-02 23:07:12 +01:00
Ricardo Wurmus 68b6a67e94
gnu: Add r-complexplus. 
* gnu/packages/cran.scm (r-complexplus): New variable.
 2018-03-02 23:07:04 +01:00
Ricardo Wurmus f96eda90d5
gnu: Add r-expm. 
* gnu/packages/cran.scm (r-expm): New variable.
 2018-03-02 23:06:57 +01:00
Ricardo Wurmus 7531ee842c
gnu: Add r-trend. 
* gnu/packages/cran.scm (r-trend): New variable.
 2018-03-02 23:06:50 +01:00
Ricardo Wurmus d32e572489
gnu: Add r-cubature. 
* gnu/packages/cran.scm (r-cubature): New variable.
 2018-03-02 23:06:41 +01:00
Ricardo Wurmus 6615a36421
gnu: Add r-urca. 
* gnu/packages/cran.scm (r-urca): New variable.
 2018-03-02 23:06:33 +01:00
Ricardo Wurmus 5b25bc55dc
gnu: Add r-fractal. 
* gnu/packages/cran.scm (r-fractal): New variable.
 2018-03-02 23:06:26 +01:00
Ricardo Wurmus 19da7fe314
gnu: Add r-extradistr. 
* gnu/packages/cran.scm (r-extradistr): New variable.
 2018-03-02 23:06:17 +01:00
Ricardo Wurmus 4993a02ad7
gnu: Add r-tsa. 
* gnu/packages/cran.scm (r-tsa): New variable.
 2018-03-02 23:06:10 +01:00
Ricardo Wurmus a2c079a780
gnu: Add r-wmtsa. 
* gnu/packages/cran.scm (r-wmtsa): New variable.
 2018-03-02 23:06:00 +01:00
Ricardo Wurmus b6dc325538
gnu: Add r-tseries. 
* gnu/packages/cran.scm (r-tseries): New variable.
 2018-03-02 23:05:52 +01:00
Ricardo Wurmus dceb159206
gnu: Add r-quantmod. 
* gnu/packages/cran.scm (r-quantmod): New variable.
 2018-03-02 23:05:43 +01:00
Ricardo Wurmus 0be7effefa
gnu: Add r-sapa. 
* gnu/packages/cran.scm (r-sapa): New variable.
 2018-03-02 23:05:35 +01:00
Ricardo Wurmus 034ac9d67a
gnu: Add r-ifultools. 
* gnu/packages/cran.scm (r-ifultools): New variable.
 2018-03-02 23:05:14 +01:00
Ricardo Wurmus d3cb62e58d
gnu: Add r-splus2r. 
* gnu/packages/cran.scm (r-splus2r): New variable.
 2018-03-02 23:05:02 +01:00
Ricardo Wurmus 0b64332c74
gnu: Add r-leaps. 
* gnu/packages/cran.scm (r-leaps): New variable.
 2018-03-02 23:03:10 +01:00
Ricardo Wurmus 93c21ddc86
gnu: Add r-ttr. 
* gnu/packages/cran.scm (r-ttr): New variable.
 2018-03-02 22:55:10 +01:00
Ricardo Wurmus 4e35c4290e
gnu: Add r-rbiofabric. 
* gnu/packages/graph.scm (r-rbiofabric): New variable.
 2018-03-02 22:23:18 +01:00