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* gnu: diamond: Update to 0.9.1.Ben Woodcroft2017-05-22
| | | | * gnu/packages/bioinformatics.scm (diamond): Update to 0.9.1.
* gnu: Remove GCJ.Ricardo Wurmus2017-05-22
| | | | | | * 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.
* gnu: ant: Implement in terms of ant/java8.Ricardo Wurmus2017-05-22
| | | | * gnu/packages/java.scm (ant): Inherit from ant/java8.
* gnu: Add ant/java8.Ricardo Wurmus2017-05-22
| | | | * gnu/packages/java.scm (ant/java8): New variable.
* gnu: ant: Move after bootstrap packages.Ricardo Wurmus2017-05-22
| | | | * gnu/packages/java.scm (ant): Move package.
* gnu: ant: Delete bundled jars.Ricardo Wurmus2017-05-22
| | | | * gnu/packages/java.scm (ant)[source]: Delete bundled jars in a snippet.
* gnu: ant: Inherit from ant-bootstrap.Ricardo Wurmus2017-05-22
| | | | | | * gnu/packages/java.scm (ant)[build-system] [home-page][synopsis][description][license]: Remove fields. [arguments]: Adapt arguments of ant-bootstrap package.
* gnu: clojure: Move below bootstrap packages.Ricardo Wurmus2017-05-22
| | | | * gnu/packages/java.scm (clojure): Move package.
* gnu: java-swt: Move below the bootstrap packages.Ricardo Wurmus2017-05-22
| | | | * gnu/packages/java.scm (java-swt): Move the package.
* gnu: icedtea-7: Use icedtea-6 for bootstrapping.Ricardo Wurmus2017-05-22
| | | | | | | | | | | * 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".
* gnu: Add icedtea-6.Ricardo Wurmus2017-05-22
| | | | * gnu/packages/java.scm (icedtea-6): New variable.
* gnu: Add ecj-javac-on-jamvm-wrapper-final.Ricardo Wurmus2017-05-22
| | | | * gnu/packages/java.scm (ecj-javac-on-jamvm-wrapper-final): New variable.
* gnu: Add jamvm.Ricardo Wurmus2017-05-22
| | | | * gnu/packages/java.scm (jamvm): New variable.
* gnu: Add classpath-devel.Ricardo Wurmus2017-05-22
| | | | * gnu/packages/java.scm (classpath-devel): New variable.
* gnu: Add ecj-javac-on-jamvm-wrapper.Ricardo Wurmus2017-05-22
| | | | * gnu/packages/java.scm (ecj-javac-on-jamvm-wrapper): New variable.
* gnu: Add classpath-jamvm-wrappers.Ricardo Wurmus2017-05-22
| | | | * gnu/packages/java.scm (classpath-jamvm-wrappers): New variable.
* gnu: Add jamvm-bootstrap.Ricardo Wurmus2017-05-22
| | | | * gnu/packages/java.scm (jamvm-bootstrap): New variable.
* gnu: Add classpath.Ricardo Wurmus2017-05-22
| | | | * gnu/packages/java.scm (classpath): New variable.
* gnu: Add ecj-javac-wrapper.Ricardo Wurmus2017-05-22
| | | | * gnu/packages/java.scm (ecj-javac-wrapper): New variable.
* gnu: Add ecj-bootstrap.Ricardo Wurmus2017-05-22
| | | | * gnu/packages/java.scm (ecj-bootstrap): New variable.
* gnu: Add ant-bootstrap.Ricardo Wurmus2017-05-22
| | | | * gnu/packages/java.scm (ant-bootstrap): New variable.
* gnu: Add sablevm.Ricardo Wurmus2017-05-22
| | | | * gnu/packages/java.scm (sablevm): New variable.
* gnu: Add sablevm-classpath.Ricardo Wurmus2017-05-22
| | | | * gnu/packages/java.scm (sablevm-classpath): New variable.
* gnu: Add jikes.Ricardo Wurmus2017-05-22
| | | | * gnu/packages/java.scm (jikes): New variable.
* gnu: Add r-edaseq.Ricardo Wurmus2017-05-22
| | | | * gnu/packages/bioinformatics.scm (r-edaseq): New variable.
* gnu: Add r-deseq.Ricardo Wurmus2017-05-22
| | | | * gnu/packages/bioinformatics.scm (r-deseq): New variable.
* gnu: Add r-aroma-light.Ricardo Wurmus2017-05-22
| | | | * gnu/packages/bioinformatics.scm (r-aroma-light): New variable.
* Merge branch 'version-0.13.0'Marius Bakke2017-05-22
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| * gnu: guix: Update to a6d728b.Ludovic Courtès2017-05-21
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| * gnu: guix: Update to 0.13.0.Ludovic Courtès2017-05-21
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| * gnu: unionfs-fuse-static: Remove 'unionfsctl' executable.Ludovic Courtès2017-05-21
| | | | | | | | | | | | | | | | | | This avoids pulling in glibc & co. Fixes a regression introduced in 2f861edf5cf5118ad560737343312c9a5efe5b2f (the 'unionfsctl' executable did not exist in unionfs-fuse 0.26). * gnu/packages/linux.scm (unionfs-fuse/static)[arguments] <post-install>: Remove 'unionfsctl' binary.
| * gnu: icedtea@2: Update to 2.6.10 [security fixes].Leo Famulari2017-05-20
| | | | | | | | | | | | Fixes CVE-2017-{3509,3511,3512,3514,3526,3533,3539,3544}. * gnu/packages/java.scm (icedtea-7): Update to 2.6.10.
| * gnu: dropbear: Update to 2017.75 [fixes CVE-2017-{9078,9079}].Leo Famulari2017-05-20
| | | | | | | | * gnu/packages/ssh.scm (dropbear): Update to 2017.75.
| * gnu: guile-ssh: Fix potential double-free/use-after-free issue.Ludovic Courtès2017-05-20
| | | | | | | | | | | | | | | | | | Fixes <http://bugs.gnu.org/26976>. Reported by Mark H Weaver <mhw@netris.org>. * gnu/packages/patches/guile-ssh-double-free.patch: New file. * gnu/local.mk (dist_patch_DATA): Add it. * gnu/packages/ssh.scm (guile-ssh)[source](patches): Add it.
| * gnu: aspell: 'dict-dir' set to ~/.guix-profile/lib/aspell or $ASPELL_DICT_DIR.Ludovic Courtès2017-05-20
| | | | | | | | | | | | | | | | | | See <https://bugs.gnu.org/25836> for background. * gnu/packages/patches/aspell-default-dict-dir.patch: New file. * gnu/packages/aspell.scm (aspell)[source](patches): New field. [native-search-paths]: New field. * gnu/local.mk (dist_patch_DATA): Add it.
| * gnu: qemu: Fix CVE-2017-7493.Leo Famulari2017-05-20
| | | | | | | | | | | | * gnu/packages/patches/qemu-CVE-2017-7493.patch: New file. * gnu/local.mk (dist_patch_DATA): Add it. * gnu/packages/qemu.scm (qemu)[source]: Use it.
| * gnu: glibc/hurd: Do not apply i686 patch.Ricardo Wurmus2017-05-20
| | | | | | | | | | | | | | This is a follow-up to commit c2e4f14ac8cd3e1ce7f46a192ad0c9acc084b210. * gnu/packages/base.scm (glibc/hurd)[arguments]: Override pre-configure phase with a copy that does not include the patch application.
| * gnu: glibc/hurd: Use modify-phases syntax.Ricardo Wurmus2017-05-20
| | | | | | | | * gnu/packages/base.scm (glibc/hurd)[arguments]: Use modify-phases syntax.
| * gnu: tor: Update to 0.3.0.7.Efraim Flashner2017-05-20
| | | | | | | | * gnu/packages/tor.scm (tor): Update to 0.3.0.7.
| * gnu: guix: Update snapshot.Ludovic Courtès2017-05-16
| | | | | | | | * gnu/packages/package-management.scm (guix): Update to ce92d26.
* | gnu: vte-ng: Update to 0.48.3.a.Marius Bakke2017-05-22
| | | | | | | | * gnu/packages/gnome.scm (vte-ng): Update to 0.48.3.a.
* | gnu: gexiv2: Update to 0.10.6.Marius Bakke2017-05-22
| | | | | | | | * gnu/packages/gnome.scm (gexiv2): Update to 0.10.6.
* | gnu: dconf-editor: Update to 3.22.3.Marius Bakke2017-05-22
| | | | | | | | * gnu/packages/gnome.scm (dconf-editor): Update to 3.22.3.
* | gnu: aisleriot: Update to 3.22.2.Marius Bakke2017-05-22
| | | | | | | | * gnu/packages/gnome.scm (aisleriot): Update to 3.22.2.
* | gnu: vte: Update to 0.48.3.Marius Bakke2017-05-22
| | | | | | | | * gnu/packages/gnome.scm (vte): Update to 0.48.3.
* | gnu: fraggenescan: Update to 1.30.Ben Woodcroft2017-05-22
| | | | | | | | | | | | * gnu/packages/bioinformatics.scm (fraggenescan): Update to 1.30. [arguments]: Update patching of paths, install procedure. Add new test case.
* | gnu: roary: Update to 3.8.2.Ben Woodcroft2017-05-22
| | | | | | | | * gnu/packages/bioinformatics.scm (roary): Update to 3.8.2.
* | gnu: taxtastic: Update to 0.6.4.Ben Woodcroft2017-05-22
| | | | | | | | | | * gnu/packages/bioinformatics.scm (taxtastic): Update to 0.6.4. [source]: Use PyPI URI.
* | gnu: r-mutationalpatterns: Update to 1.2.1.Roel Janssen2017-05-22
| | | | | | | | * gnu/packages/bioinformatics.scm (r-mutationalpatterns): Update to 1.2.1.
* | gnu: v4l-utils: Update to 1.12.5.Marius Bakke2017-05-21
| | | | | | | | * gnu/packages/video.scm (v4l-utils): Update to 1.12.5.
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