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21439 Commits

Author SHA1 Message Date
Mathieu Othacehe a6b055d453
mailmap: Add an entry for Mathieu Othacehe. 
This avoids duplicated entries with Othacehe in uppercase.
 2017-05-22 21:50:05 +02:00
Ricardo Wurmus 9117448e76
gnu: Remove GCJ. 
* gnu/packages/patches/gcj-arm-mode.patch: Remove file.
* gnu/local.mk (dist_patch_DATA): Delete it.
* gnu/packages/gcc.scm (javac.in, gcj, ecj-bootstrap): Remove variables.
 2017-05-22 18:56:35 +02:00
Ricardo Wurmus e441fc564b
gnu: ant: Implement in terms of ant/java8. 
* gnu/packages/java.scm (ant): Inherit from ant/java8.
 2017-05-22 18:56:35 +02:00
Ricardo Wurmus 8bbd040840
gnu: Add ant/java8. 
* gnu/packages/java.scm (ant/java8): New variable.
 2017-05-22 18:56:35 +02:00
Ricardo Wurmus 5c7952fbf4
gnu: ant: Move after bootstrap packages. 
* gnu/packages/java.scm (ant): Move package.
 2017-05-22 18:56:35 +02:00
Ricardo Wurmus e7a5d73ea9
gnu: ant: Delete bundled jars. 
* gnu/packages/java.scm (ant)[source]: Delete bundled jars in a snippet.
 2017-05-22 18:56:35 +02:00
Ricardo Wurmus fded0c69dd
gnu: ant: Inherit from ant-bootstrap. 
* gnu/packages/java.scm (ant)[build-system]
[home-page][synopsis][description][license]: Remove fields.
[arguments]: Adapt arguments of ant-bootstrap package.
 2017-05-22 18:56:35 +02:00
Ricardo Wurmus fc6e27271d
gnu: clojure: Move below bootstrap packages. 
* gnu/packages/java.scm (clojure): Move package.
 2017-05-22 18:56:34 +02:00
Ricardo Wurmus 5490480c42
gnu: java-swt: Move below the bootstrap packages. 
* gnu/packages/java.scm (java-swt): Move the package.
 2017-05-22 18:56:34 +02:00
Ricardo Wurmus e2098e2d58
gnu: icedtea-7: Use icedtea-6 for bootstrapping. 
* gnu/packages/java.scm (icedtea-7)[source]: Remove Makefile.in patch to link
with GCJ libs.
[arguments]: Remove (ice-9 rdelim) module; adjust configure flags; do not add
GCJ headers to CPATH in build phase "set-additional-paths".
[native-inputs]: Remove gcj and ant; add icedtea-6 and ant-bootstrap.  Remove
autoconf and automake.
(icedtea-8)[native-inputs]: Delete "icedtea" from the inherited inputs, not
"gcj".
 2017-05-22 18:56:34 +02:00
Ricardo Wurmus 9841931668
gnu: Add icedtea-6. 
* gnu/packages/java.scm (icedtea-6): New variable.
 2017-05-22 18:56:34 +02:00
Ricardo Wurmus 1bf56c7233
gnu: Add ecj-javac-on-jamvm-wrapper-final. 
* gnu/packages/java.scm (ecj-javac-on-jamvm-wrapper-final): New variable.
 2017-05-22 18:56:34 +02:00
Ricardo Wurmus 8c6091e3a6
gnu: Add jamvm. 
* gnu/packages/java.scm (jamvm): New variable.
 2017-05-22 18:56:33 +02:00
Ricardo Wurmus 72885a4c8f
gnu: Add classpath-devel. 
* gnu/packages/java.scm (classpath-devel): New variable.
 2017-05-22 18:56:33 +02:00
Ricardo Wurmus 7292d69419
gnu: Add ecj-javac-on-jamvm-wrapper. 
* gnu/packages/java.scm (ecj-javac-on-jamvm-wrapper): New variable.
 2017-05-22 18:56:33 +02:00
Ricardo Wurmus 04d7cae2c4
gnu: Add classpath-jamvm-wrappers. 
* gnu/packages/java.scm (classpath-jamvm-wrappers): New variable.
 2017-05-22 18:56:33 +02:00
Ricardo Wurmus 5f4402c7a3
gnu: Add jamvm-bootstrap. 
* gnu/packages/java.scm (jamvm-bootstrap): New variable.
 2017-05-22 18:56:33 +02:00
Ricardo Wurmus d3551e861e
gnu: Add classpath. 
* gnu/packages/java.scm (classpath): New variable.
 2017-05-22 18:56:33 +02:00
Ricardo Wurmus 6a5829d995
gnu: Add ecj-javac-wrapper. 
* gnu/packages/java.scm (ecj-javac-wrapper): New variable.
 2017-05-22 18:56:32 +02:00
Ricardo Wurmus 5461721fa0
gnu: Add ecj-bootstrap. 
* gnu/packages/java.scm (ecj-bootstrap): New variable.
 2017-05-22 18:56:32 +02:00
Ricardo Wurmus 5783bd7730
gnu: Add ant-bootstrap. 
* gnu/packages/java.scm (ant-bootstrap): New variable.
 2017-05-22 18:56:32 +02:00
Ricardo Wurmus 57f6c50db1
gnu: Add sablevm. 
* gnu/packages/java.scm (sablevm): New variable.
 2017-05-22 18:56:32 +02:00
Ricardo Wurmus 2551fee8a0
gnu: Add sablevm-classpath. 
* gnu/packages/java.scm (sablevm-classpath): New variable.
 2017-05-22 18:56:32 +02:00
Ricardo Wurmus e1ae3587d2
gnu: Add jikes. 
* gnu/packages/java.scm (jikes): New variable.
 2017-05-22 18:55:34 +02:00
Ricardo Wurmus 296b3c631c
gnu: Add r-edaseq. 
* gnu/packages/bioinformatics.scm (r-edaseq): New variable.
 2017-05-22 18:54:59 +02:00
Ricardo Wurmus 7b46532779
gnu: Add r-deseq. 
* gnu/packages/bioinformatics.scm (r-deseq): New variable.
 2017-05-22 18:54:59 +02:00
Ricardo Wurmus d4b83651d1
gnu: Add r-aroma-light. 
* gnu/packages/bioinformatics.scm (r-aroma-light): New variable.
 2017-05-22 18:54:58 +02:00
Marius Bakke fd3782d13b
Merge branch 'version-0.13.0' 2017-05-22 18:25:01 +02:00
Ludovic Courtès 7c63fff6d0
Update NEWS. 2017-05-22 17:25:08 +02:00
Marius Bakke 52d2a2be1f
gnu: vte-ng: Update to 0.48.3.a. 
* gnu/packages/gnome.scm (vte-ng): Update to 0.48.3.a.
 2017-05-22 15:28:59 +02:00
Marius Bakke b7c0c756da
gnu: gexiv2: Update to 0.10.6. 
* gnu/packages/gnome.scm (gexiv2): Update to 0.10.6.
 2017-05-22 15:17:12 +02:00
Marius Bakke 123e816816
gnu: dconf-editor: Update to 3.22.3. 
* gnu/packages/gnome.scm (dconf-editor): Update to 3.22.3.
 2017-05-22 15:17:08 +02:00
Marius Bakke e6a36cf2f3
gnu: aisleriot: Update to 3.22.2. 
* gnu/packages/gnome.scm (aisleriot): Update to 3.22.2.
 2017-05-22 15:17:01 +02:00
Marius Bakke f2da7c861b
gnu: vte: Update to 0.48.3. 
* gnu/packages/gnome.scm (vte): Update to 0.48.3.
 2017-05-22 15:16:40 +02:00
Ben Woodcroft 74297231be
gnu: fraggenescan: Update to 1.30. 
* gnu/packages/bioinformatics.scm (fraggenescan): Update to 1.30.
[arguments]: Update patching of paths, install procedure.  Add new test
case.
 2017-05-22 11:44:20 +01:00
Ben Woodcroft 7569613076
gnu: roary: Update to 3.8.2. 
* gnu/packages/bioinformatics.scm (roary): Update to 3.8.2.
 2017-05-22 11:44:20 +01:00
Ben Woodcroft 3cbfc149c3
gnu: taxtastic: Update to 0.6.4. 
* gnu/packages/bioinformatics.scm (taxtastic): Update to 0.6.4.
[source]: Use PyPI URI.
 2017-05-22 11:44:19 +01:00
Roel Janssen b458413721
gnu: r-mutationalpatterns: Update to 1.2.1. 
* gnu/packages/bioinformatics.scm (r-mutationalpatterns): Update to 1.2.1.
 2017-05-22 09:44:08 +02:00
Mathieu Othacehe 65efb3c031
bootloader: extlinux: Add a warning message on top of generated conf file. 
* gnu/bootloader/extlinux.scm (extlinux-configuration-file): Warn users about
  the fact that the configuration file is automatically generated.
 2017-05-21 18:56:03 +02:00
Marius Bakke f1d1ef71ea
gnu: v4l-utils: Update to 1.12.5. 
* gnu/packages/video.scm (v4l-utils): Update to 1.12.5.
 2017-05-21 17:12:48 +02:00
Marius Bakke cfa7473c2b
gnu: x265: Update to 2.4. 
* gnu/packages/video.scm (x265): Update to 2.4.
 2017-05-21 17:12:48 +02:00
Marius Bakke 3bc45ad460
gnu: vlc: Update to 2.2.5.1. 
* gnu/packages/video.scm (vlc): Update to 2.2.5.1.
[source]: Remove obsolete snippet.
 2017-05-21 17:12:48 +02:00
Marius Bakke ba58886a8c
gnu: libaacs: Update to 0.9.0. 
* gnu/packages/video.scm (libaacs): Update to 0.9.0.
 2017-05-21 17:12:48 +02:00
Ben Woodcroft ef81341f0e
gnu: diamond: Update to 0.9.0. 
* gnu/packages/bioinformatics.scm (diamond): Update to 0.9.0.
[license]: Change to AGPL3+.
 2017-05-21 16:08:03 +01:00
Ludovic Courtès e9c53359e7
gnu: guix: Update to a6d728b. 2017-05-21 16:59:04 +02:00
Ludovic Courtès a6d728b7aa
gnu: guix: Update to 0.13.0. 2017-05-21 16:58:53 +02:00
Ben Woodcroft 88682c9a72
gnu: fasttree: Update to 2.1.10. 
* gnu/packages/bioinformatics.scm (fasttree): Update to 2.1.10.
 2017-05-21 15:42:08 +01:00
Ben Woodcroft abc08cbae6
gnu: python-biom-format: Update to 2.1.6. 
* gnu/packages/bioinformatics.scm (python-biom-format): Update to 2.1.6.
[propagated-inputs]: Add python-pandas.
 2017-05-21 15:42:08 +01:00
Ben Woodcroft c522f57e22
gnu: python-future: Update to 0.16.0. 
* gnu/packages/python.scm (python-future): Update to 0.16.0.
 2017-05-21 15:42:08 +01:00
Marius Bakke 1d0aa4d8c2
gnu: ccid: Update to 1.4.27. 
* gnu/packages/security-token.scm (ccid): Update to 1.4.27.
 2017-05-21 16:37:54 +02:00