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2017-05-23gnu: gobject-introspection: Update to 1.52.1.Kei Kebreau
* gnu/packages/glib.scm (gobject-introspection): Update to 1.52.1.
2017-05-22Merge branch 'master' into stagingMarius Bakke
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.
2017-05-21bootloader: extlinux: Add a warning message on top of generated conf file.Mathieu Othacehe
* gnu/bootloader/extlinux.scm (extlinux-configuration-file): Warn users about the fact that the configuration file is automatically generated.
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: 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.
2017-05-21vm: Increase default disk size to account for ESP partition.Marius Bakke
Fixes a test regression introduced by ecf5d5376979fadd971559367bf553df89fcc62b. * gnu/system/vm.scm (system-qemu-image/shared-store-script): 30MiB -> 70MiB.
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.
2017-05-20download: Prune the ImageMagick mirror list.Leo Famulari
These sites' TLS certificates are invalid. * guix/download.scm (%mirrors) <imagemagick>: Remove mirrors-{au,ru,uk}.go-parts.com.
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.
2017-05-20pack: Use 'guile2.0-json' when building with Guile 2.0.Ludovic Courtès
Fixes <http://bugs.gnu.org/27005>. Reported by Pjotr Prins <pjotr.public12@thebird.nl>. Fixes a regression introduced in commit 2252f087d4bd450ab41a71379320467887edfc0f. * guix/scripts/pack.scm (docker-image)[json]: New variable. [build]: Use it.
2017-05-19gnu: 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: Add loksh.ng0
* gnu/packages/shells.scm (loksh): New variable. Signed-off-by: Marius Bakke <mbakke@fastmail.com>
2017-05-19gnu: dropbear: Update to 2017.75 [fixes CVE-2017-{9078,9079}].Leo Famulari
* gnu/packages/ssh.scm (dropbear): Update to 2017.75.
2017-05-19gnu: calibre: Don't create uninstaller.Brendan Tildesley
* gnu/packages/ebook.scm (calibre)[arguments]<#:phases>. Add 'patch-source' phase. Co-authored-by: Marius Bakke <mbakke@fastmail.com>
2017-05-19gnu: calibre: Add exhaustive license list.Brendan Tildesley
* gnu/packages/ebook.scm (calibre): Add exhaustive license list. (chmlib)[license]: Use license: prefix. Co-authored-by: Marius Bakke <mbakke@fastmail.com>
2017-05-19gnu: calibre: Add missing dependencies.Brendan Tildesley
* gnu/packages/ebook.scm (calibre)[inputs]: Add poppler, python2-dnspython, and python2-pygments. [arguments]: Remove old TODO comments. libwmf and psutil are no longer used. Signed-off-by: Marius Bakke <mbakke@fastmail.com>
2017-05-19gnu: calibre: Unbundle chardet.Brendan Tildesley
* gnu/packages/ebook.scm (calibre)[source]: Delete bundled chardet. [inputs]: Add python2-chardet. Signed-off-by: Marius Bakke <mbakke@fastmail.com>
2017-05-19gnu: calibre: Unbundle liberation fonts.Brendan Tildesley
*gnu/packages/ebook.scm (calibre)[source]: Delete liberation .ttf files. [native-inputs]: Add font-liberation. [arguments]: Calibre still references the bundled fonts, so we install the packaged fonts to the directory the bundled fonts would have been. Signed-off-by: Marius Bakke <mbakke@fastmail.com>
2017-05-19gnu: calibre: Unbundle python2-markdown.Brendan Tildesley
* gnu/packages/ebook.scm (calibre)[snippet]: Replace python references to bundled markdown with packaged. Remove markdown from source. [inputs]: Add python2-markdown as a dependency. Signed-off-by: Marius Bakke <mbakke@fastmail.com>
2017-05-19gnu: calibre: Import unbundle feedparser patch from debian.Brendan Tildesley
* gnu/packages/ebook.scm (calibre)[source]: Reference new patch file. [inputs]: Add python2-feedparser as an input. * gnu/packages/patches/calibre-use-packaged-feedparser.patch: New file. * gnu/local.mk (dist_patch_DATA): Add it. Signed-off-by: Marius Bakke <mbakke@fastmail.com>
2017-05-19gnu: calibre: Import dont-load-icons patch from debian.Brendan Tildesley
* gnu/packages/patches/calibre-dont-load-remote-icons.patch: New file. * gnu/packages/ebooks.scm (calibre)[source]: Add reference to patch file. * gnu/local.mk (dist_path_DATA): Add it. Signed-off-by: Marius Bakke <mbakke@fastmail.com>
2017-05-19gnu: calibre: Update to 2.85.1.Brendan Tildesley
* gnu/packages/ebooks.scm (calibre): Update to 2.85.1. * gnu/packages/patches/calibre-drop-unrar.patch: Delete incompatible patch file. Recreate debian patch file from the latest calibre git revision. Signed-off-by: Marius Bakke <mbakke@fastmail.com>
2017-05-19system: Use Guile 2.2 rather than 2.0 in %BASE-PACKAGES.Ludovic Courtès
* gnu/system.scm (%base-packages): Change GUILE-2.0 to GUILE-2.2.
2017-05-19gnu: python-pyqt@4: Update to 4.12.Marius Bakke
* gnu/packages/qt.scm (python-pyqt-4): Update to 4.12. [source]: Adjust URI to file rename.
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