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21355 Commits

Author SHA1 Message Date
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
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
Ludovic Courtès df671177f8
doc: Replace fingerprint of OpenPGP signing key. 
* doc/guix.texi (OPENPGP-SIGNING-KEY-ID): Change to Ludo's key.
 2017-05-21 13:46:35 +02:00
Ludovic Courtès 31025edc94
Update NEWS. 2017-05-21 13:45:54 +02:00
Ludovic Courtès 9d0c24d1be
tests: ssh: Use 'guile2.0-ssh'. 
Fixes a regression introduced in 4d8806c3d6.

* gnu/tests/ssh.scm (run-ssh-test): Use GUILE2.0-SSH instead of GUILE-SSH.
 2017-05-21 11:56:29 +02:00
Ludovic Courtès 8a29dc07a4
guix system: Don't warn about old distros for "guix system init". 
* guix/scripts/system.scm (process-action): Don't call
'warn-about-old-distro' when ACTION is 'init' or 'build'.
 2017-05-21 11:49:07 +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 092c58e745
guix system: Increase image size for 'guix system vm'. 
This is a followup to 9a1bfe7648.

* guix/scripts/system.scm (system-derivation-for-action): Add 40MiB to
the default size for 'vm'.
 2017-05-21 01:25:16 +02:00
Ludovic Courtès 324499184a
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 01:17:11 +02:00
Marius Bakke a588e34e0d
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 01:17:08 +02:00
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
Ricardo Wurmus 402f241da4
Update NEWS. 2017-05-20 23:39:30 +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 96afb480f8
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 14:39:50 +02:00
Leo Famulari 7dccad95b6
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.
 2017-05-20 14:39:50 +02:00
Leo Famulari 6a9defd747
gnu: dropbear: Update to 2017.75 [fixes CVE-2017-{9078,9079}]. 
* gnu/packages/ssh.scm (dropbear): Update to 2017.75.
 2017-05-20 14:39:50 +02:00
Ludovic Courtès 429046e9dd
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.
 2017-05-20 14:39:49 +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
Marius Bakke 6520904b3e
vm: Add UEFI loader to disk images. 
* gnu/build/vm.scm (install-efi): New procedure.
(initialize-hard-disk): Generate EFI blob when ESP is present.
* gnu/system/vm.scm (qemu-image): Append 40MiB EFI System Partition.

(cherry picked from commit ecf5d53769)
 2017-05-20 10:57:00 +02:00
Marius Bakke 03119da211
vm: Support creating FAT partitions. 
* gnu/build/vm.scm (create-ext-file-system, create-fat-file-system): New procedures.
(format-partition): Use them. Error for unknown file systems.
* gnu/system/vm.scm (qemu-image): Include DOSFSTOOLS.
* gnu/system/linux-initrd.scm (base-initrd): Always add nls_is8859-1.ko.
 2017-05-20 10:20:35 +02:00