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2017-05-22gnu: Add jikes.Ricardo Wurmus
* gnu/packages/java.scm (jikes): New variable.
2017-05-22gnu: Add r-edaseq.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-edaseq): New variable.
2017-05-22gnu: Add r-deseq.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-deseq): New variable.
2017-05-22gnu: Add r-aroma-light.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-aroma-light): New variable.
2017-05-22Merge branch 'version-0.13.0'Marius Bakke
2017-05-22gnu: vte-ng: Update to 0.48.3.a.Marius Bakke
* gnu/packages/gnome.scm (vte-ng): Update to 0.48.3.a.
2017-05-22gnu: gexiv2: Update to 0.10.6.Marius Bakke
* gnu/packages/gnome.scm (gexiv2): Update to 0.10.6.
2017-05-22gnu: dconf-editor: Update to 3.22.3.Marius Bakke
* gnu/packages/gnome.scm (dconf-editor): Update to 3.22.3.
2017-05-22gnu: aisleriot: Update to 3.22.2.Marius Bakke
* gnu/packages/gnome.scm (aisleriot): Update to 3.22.2.
2017-05-22gnu: vte: Update to 0.48.3.Marius Bakke
* gnu/packages/gnome.scm (vte): Update to 0.48.3.
2017-05-22gnu: fraggenescan: Update to 1.30.Ben Woodcroft
* gnu/packages/bioinformatics.scm (fraggenescan): Update to 1.30. [arguments]: Update patching of paths, install procedure. Add new test case.
2017-05-22gnu: roary: Update to 3.8.2.Ben Woodcroft
* gnu/packages/bioinformatics.scm (roary): Update to 3.8.2.
2017-05-22gnu: taxtastic: Update to 0.6.4.Ben Woodcroft
* gnu/packages/bioinformatics.scm (taxtastic): Update to 0.6.4. [source]: Use PyPI URI.
2017-05-22gnu: r-mutationalpatterns: Update to 1.2.1.Roel Janssen
* gnu/packages/bioinformatics.scm (r-mutationalpatterns): Update to 1.2.1.
2017-05-21gnu: v4l-utils: Update to 1.12.5.Marius Bakke
* gnu/packages/video.scm (v4l-utils): Update to 1.12.5.
2017-05-21gnu: x265: Update to 2.4.Marius Bakke
* gnu/packages/video.scm (x265): Update to 2.4.
2017-05-21gnu: vlc: Update to 2.2.5.1.Marius Bakke
* gnu/packages/video.scm (vlc): Update to 2.2.5.1. [source]: Remove obsolete snippet.
2017-05-21gnu: libaacs: Update to 0.9.0.Marius Bakke
* gnu/packages/video.scm (libaacs): Update to 0.9.0.
2017-05-21gnu: diamond: Update to 0.9.0.Ben Woodcroft
* gnu/packages/bioinformatics.scm (diamond): Update to 0.9.0. [license]: Change to AGPL3+.
2017-05-21gnu: guix: Update to a6d728b.Ludovic Courtès
2017-05-21gnu: guix: Update to 0.13.0.Ludovic Courtès
2017-05-21gnu: fasttree: Update to 2.1.10.Ben Woodcroft
* gnu/packages/bioinformatics.scm (fasttree): Update to 2.1.10.
2017-05-21gnu: python-biom-format: Update to 2.1.6.Ben Woodcroft
* gnu/packages/bioinformatics.scm (python-biom-format): Update to 2.1.6. [propagated-inputs]: Add python-pandas.
2017-05-21gnu: python-future: Update to 0.16.0.Ben Woodcroft
* gnu/packages/python.scm (python-future): Update to 0.16.0.
2017-05-21gnu: ccid: Update to 1.4.27.Marius Bakke
* gnu/packages/security-token.scm (ccid): Update to 1.4.27.
2017-05-21gnu: fio: Update to 2.20.Marius Bakke
* gnu/packages/benchmark.scm (fio): Update to 2.20. [arguments]<#:phases>: Drop removed script from 'move-outputs' phase.
2017-05-21gnu: nano: Update to 2.8.4.Marius Bakke
* gnu/packages/nano.scm (nano): Update to 2.8.4.
2017-05-21gnu: vim: Update to 8.0.0600.Marius Bakke
* gnu/packages/vim.scm (vim, vim-full): Update to 8.0.0600.
2017-05-21gnu: vim-full: Disable failing test.Marius Bakke
* gnu/packages/vim.scm (vim-full)[arguments]<#:phases>: Add substitution.
2017-05-21gnu: linux-libre: Update to 4.11.2.Mark H Weaver
* gnu/packages/linux.scm (%linux-libre-version): Update to 4.11.2. (%linux-libre-hash): Update hash.
2017-05-21gnu: linux-libre: Remove CONFIG_SMC from x86 kernel configurations.Mark H Weaver
This removes support for the "shared memory communications over RDMA" (SMC-R) networking protocol, which was added in 4.11 without the knowledge of the RDMA maintainers, and which is thought to contain significant security flaws. For details, see <https://lwn.net/Articles/723081> and <https://lwn.net/Articles/723070>. * gnu/packages/aux-files/linux-libre/4.11-x86_64.conf, gnu/packages/aux-files/linux-libre/4.11-i686.conf: Disable CONFIG_SMC. 723# 0001-gnu-libevent-2.0-Add-fix-from-upstream.patch
2017-05-21gnu: linux-libre@4.9: Update to 4.9.29.Mark H Weaver
* gnu/packages/linux.scm (linux-libre-4.9): Update to 4.9.29.
2017-05-21gnu: linux-libre@4.4: Update to 4.4.69.Mark H Weaver
* gnu/packages/linux.scm (linux-libre-4.4): Update to 4.4.69.
2017-05-21gnu: unionfs-fuse-static: Remove 'unionfsctl' executable.Ludovic Courtès
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.
2017-05-21gnu: unionfs-fuse-static: Remove 'unionfsctl' executable.Ludovic Courtès
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.
2017-05-20gnu: ghostscript: Add TODO comment about bundled jbig2dec.Leo Famulari
* gnu/packages/ghostscript.scm (ghostscript): Add comment.
2017-05-20gnu: jbig2dec: Fix CVE-2017-{7885,7975,7976}.Leo Famulari
* gnu/packages/patches/jbig2dec-CVE-2017-7885.patch, gnu/packages/patches/jbig2dec-CVE-2017-7975.patch, gnu/packages/patches/jbig2dec-CVE-2017-7976.patch: New files. * gnu/local.mk (dist_patch_DATA): Add them. * gnu/packages/image.scm (jbig2dec)[source]: Use them.
2017-05-20gnu: pcsc-lite: Update to 1.8.21.Marius Bakke
* gnu/packages/security-token.scm (pcsc-lite): Update to 1.8.21.
2017-05-20gnu: icedtea@3: Add aarch32-drop.Leo Famulari
* gnu/packages/java.scm (icedtea-8)[native-inputs]: Add aarch32-drop.
2017-05-20gnu: icedtea@3: Update to 3.4.0 [security fixes].Leo Famulari
Fixes CVE-2017-{3509,3511,3512,3514,3526,3533,3539,3544}. * gnu/packages/java.scm (icedtea-8): Update to 3.4.0.
2017-05-20gnu: imagemagick: Update to 6.9.8-6.Leo Famulari
* gnu/packages/imagemagick.scm (imagemagick): Update to 6.9.8-6.
2017-05-20gnu: guix: Add 'guile2.0-guix'.Ludovic Courtès
* gnu/packages/package-management.scm (guile2.0-guix): New variable.
2017-05-20gnu: libssh, guile-ssh: Add a "debug" output.Ludovic Courtès
* gnu/packages/ssh.scm (libssh)[outputs]: New field. (guile-ssh)[outputs]: New field.
2017-05-20gnu: icedtea@2: Update to 2.6.10 [security fixes].Leo Famulari
Fixes CVE-2017-{3509,3511,3512,3514,3526,3533,3539,3544}. * gnu/packages/java.scm (icedtea-7): Update to 2.6.10.
2017-05-20gnu: dropbear: Update to 2017.75 [fixes CVE-2017-{9078,9079}].Leo Famulari
* gnu/packages/ssh.scm (dropbear): Update to 2017.75.
2017-05-20gnu: guile-ssh: Fix potential double-free/use-after-free issue.Ludovic Courtès
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.
2017-05-20gnu: aspell: 'dict-dir' set to ~/.guix-profile/lib/aspell or $ASPELL_DICT_DIR.Ludovic Courtès
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.
2017-05-20gnu: qemu: Fix CVE-2017-7493.Leo Famulari
* 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.
2017-05-20gnu: glibc/hurd: Do not apply i686 patch.Ricardo Wurmus
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.
2017-05-20gnu: glibc/hurd: Use modify-phases syntax.Ricardo Wurmus
* gnu/packages/base.scm (glibc/hurd)[arguments]: Use modify-phases syntax.
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