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21118 Commits (7569613076eec7c90d32246da6cebb3543f05708)

Author SHA1 Message Date
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
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
Marius Bakke 20d2e1faa9
gnu: fio: Update to 2.20. 
* gnu/packages/benchmark.scm (fio): Update to 2.20.
[arguments]<#:phases>: Drop removed script from 'move-outputs' phase.
 2017-05-21 16:33:42 +02:00
Marius Bakke 31044e6ff2
gnu: nano: Update to 2.8.4. 
* gnu/packages/nano.scm (nano): Update to 2.8.4.
 2017-05-21 16:17:01 +02:00
Marius Bakke 18f61e002b
gnu: vim: Update to 8.0.0600. 
* gnu/packages/vim.scm (vim, vim-full): Update to 8.0.0600.
 2017-05-21 14:34:45 +02:00
Marius Bakke 8b1ff6f0ab
gnu: vim-full: Disable failing test. 
* gnu/packages/vim.scm (vim-full)[arguments]<#:phases>: Add substitution.
 2017-05-21 14:34:45 +02:00
Mark H Weaver 718448e176
gnu: linux-libre: Update to 4.11.2. 
* gnu/packages/linux.scm (%linux-libre-version): Update to 4.11.2.
(%linux-libre-hash): Update hash.
 2017-05-21 02:03:32 -04:00
Mark H Weaver a08691dfbb
gnu: linux-libre: Remove CONFIG_SMC from x86 kernel configurations. 
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
 2017-05-21 01:47:09 -04:00
Mark H Weaver 519fd6c367
gnu: linux-libre@4.9: Update to 4.9.29. 
* gnu/packages/linux.scm (linux-libre-4.9): Update to 4.9.29.
 2017-05-21 01:45:21 -04:00
Mark H Weaver ec8d69ebfe
gnu: linux-libre@4.4: Update to 4.4.69. 
* gnu/packages/linux.scm (linux-libre-4.4): Update to 4.4.69.
 2017-05-21 01:44:25 -04:00
Ludovic Courtès 9f8d6eb24a
gnu: unionfs-fuse-static: Remove 'unionfsctl' executable. 
This avoids pulling in glibc & co.  Fixes a regression introduced in
2f861edf5c (the 'unionfsctl' executable
did not exist in unionfs-fuse 0.26).

* gnu/packages/linux.scm (unionfs-fuse/static)[arguments]
<post-install>: Remove 'unionfsctl' binary.
 2017-05-21 01:14:51 +02:00
Marius Bakke 9a1bfe7648
vm: Increase default disk size to account for ESP partition. 
Fixes a test regression introduced by ecf5d53769.

* gnu/system/vm.scm (system-qemu-image/shared-store-script): 30MiB -> 70MiB.
 2017-05-21 01:07:12 +02:00
Leo Famulari fda33e495b
gnu: ghostscript: Add TODO comment about bundled jbig2dec. 
* gnu/packages/ghostscript.scm (ghostscript): Add comment.
 2017-05-20 16:26:29 -04:00
Leo Famulari 10cb88f85c
gnu: jbig2dec: Fix CVE-2017-{7885,7975,7976}. 
* 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.
 2017-05-20 16:26:29 -04:00
Marius Bakke fefd4c197f
gnu: pcsc-lite: Update to 1.8.21. 
* gnu/packages/security-token.scm (pcsc-lite): Update to 1.8.21.
 2017-05-20 21:42:58 +02:00
Leo Famulari 12eecbf0bb
gnu: icedtea@3: Add aarch32-drop. 
* gnu/packages/java.scm (icedtea-8)[native-inputs]: Add aarch32-drop.
 2017-05-20 14:57:22 -04:00
Leo Famulari db531f734a
gnu: icedtea@3: Update to 3.4.0 [security fixes]. 
Fixes CVE-2017-{3509,3511,3512,3514,3526,3533,3539,3544}.

* gnu/packages/java.scm (icedtea-8): Update to 3.4.0.
 2017-05-20 14:57:22 -04:00
Leo Famulari b17bd261b0
gnu: imagemagick: Update to 6.9.8-6. 
* gnu/packages/imagemagick.scm (imagemagick): Update to 6.9.8-6.
 2017-05-20 14:06:20 -04:00
Leo Famulari 40fd5600a2
download: Prune the ImageMagick mirror list. 
These sites' TLS certificates are invalid.

* guix/download.scm (%mirrors) <imagemagick>: Remove
mirrors-{au,ru,uk}.go-parts.com.
 2017-05-20 14:06:20 -04:00
Ludovic Courtès 82ce81ba06
gnu: guix: Add 'guile2.0-guix'. 
* gnu/packages/package-management.scm (guile2.0-guix): New variable.
 2017-05-20 20:00:53 +02:00
Ludovic Courtès 74460d1121
gnu: libssh, guile-ssh: Add a "debug" output. 
* gnu/packages/ssh.scm (libssh)[outputs]: New field.
(guile-ssh)[outputs]: New field.
 2017-05-20 19:49:36 +02:00
Ludovic Courtès d6bf931cb2
pack: Use 'guile2.0-json' when building with Guile 2.0. 
Fixes <http://bugs.gnu.org/27005>.
Reported by Pjotr Prins <pjotr.public12@thebird.nl>.

Fixes a regression introduced in commit
2252f087d4.

* guix/scripts/pack.scm (docker-image)[json]: New variable.
[build]: Use it.
 2017-05-20 14:30:01 +02:00
Leo Famulari d30ce4a7e2
gnu: icedtea@2: Update to 2.6.10 [security fixes]. 
Fixes CVE-2017-{3509,3511,3512,3514,3526,3533,3539,3544}.

* gnu/packages/java.scm (icedtea-7): Update to 2.6.10.
 2017-05-19 21:40:26 -04:00
ng0 cc5a76a74c
gnu: Add loksh. 
* gnu/packages/shells.scm (loksh): New variable.

Signed-off-by: Marius Bakke <mbakke@fastmail.com>
 2017-05-20 02:42:04 +02:00
Leo Famulari 70f8242b13
gnu: dropbear: Update to 2017.75 [fixes CVE-2017-{9078,9079}]. 
* gnu/packages/ssh.scm (dropbear): Update to 2017.75.
 2017-05-19 20:32:26 -04:00
Brendan Tildesley 1326166ebe
gnu: calibre: Don't create uninstaller. 
* gnu/packages/ebook.scm (calibre)[arguments]<#:phases>. Add 'patch-source' phase.

Co-authored-by: Marius Bakke <mbakke@fastmail.com>
 2017-05-19 23:49:21 +02:00
Brendan Tildesley affaf98f77
gnu: calibre: Add exhaustive license list. 
* gnu/packages/ebook.scm (calibre): Add exhaustive license list.
(chmlib)[license]: Use license: prefix.

Co-authored-by: Marius Bakke <mbakke@fastmail.com>
 2017-05-19 23:49:21 +02:00
Brendan Tildesley 9b7dcc2703
gnu: calibre: Add missing dependencies. 
* 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>
 2017-05-19 23:49:21 +02:00
Brendan Tildesley eeba7d3a07
gnu: calibre: Unbundle chardet. 
* gnu/packages/ebook.scm (calibre)[source]: Delete bundled chardet.
[inputs]: Add python2-chardet.

Signed-off-by: Marius Bakke <mbakke@fastmail.com>
 2017-05-19 23:49:21 +02:00
Brendan Tildesley b3399a0985
gnu: calibre: Unbundle liberation fonts. 
*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>
 2017-05-19 23:49:21 +02:00
Brendan Tildesley 29ec085170
gnu: calibre: Unbundle python2-markdown. 
* 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>
 2017-05-19 23:49:21 +02:00
Brendan Tildesley d94a99ec66
gnu: calibre: Import unbundle feedparser patch from debian. 
* 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>
 2017-05-19 23:49:20 +02:00
Brendan Tildesley 7010d231db
gnu: calibre: Import dont-load-icons patch from debian. 
* 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>
 2017-05-19 23:49:20 +02:00
Brendan Tildesley cd6171c1b4
gnu: calibre: Update to 2.85.1. 
* 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>
 2017-05-19 23:49:20 +02:00
Ludovic Courtès b55dd31660
system: Use Guile 2.2 rather than 2.0 in %BASE-PACKAGES. 
* gnu/system.scm (%base-packages): Change GUILE-2.0 to GUILE-2.2.
 2017-05-19 23:38:52 +02:00
Marius Bakke 41fa164aa0
gnu: python-pyqt@4: Update to 4.12. 
* gnu/packages/qt.scm (python-pyqt-4): Update to 4.12.
[source]: Adjust URI to file rename.
 2017-05-19 21:33:43 +02:00
Marius Bakke 5ac3a671d8
gnu: python-pyqt: Update to 5.8.2. 
* gnu/packages/qt.scm (python-pyqt): Update to 5.8.2.
 2017-05-19 21:24:11 +02:00
Marius Bakke f6da41b54d
gnu: python-sip: Update to 4.19.2. 
* gnu/packages/qt.scm (python-sip): Update to 4.19.2.
 2017-05-19 21:24:11 +02:00
Marius Bakke 8ea98ee10c
doc: Update for UEFI systems. 
* doc/guix.texi (USB Stick Installation): Mention UEFI.
(Preparing for Installation): Add notes about EFI System Partition, and
mounting partitions before init.
(Proceeding with the Installation): Mention the GRUB-EFI package.
(Using the Configuration System): Lightweight desktop is now a UEFI system.
(GRUB Configuration): Expand on package field. Add indexes.
* gnu/system/examples/lightweight-desktop.tmpl: Adjust to native EFI configuration.
 2017-05-19 13:52:49 +02:00