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* gnu: Add r-deseq.•••* gnu/packages/bioinformatics.scm (r-deseq): New variable. Ricardo Wurmus2017-05-22
* gnu: Add r-aroma-light.•••* gnu/packages/bioinformatics.scm (r-aroma-light): New variable. Ricardo Wurmus2017-05-22
* Merge branch 'version-0.13.0'Marius Bakke2017-05-22
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| * gnu: guix: Update to a6d728b.Ludovic Courtès2017-05-21
| * gnu: guix: Update to 0.13.0.Ludovic Courtès2017-05-21
| * tests: ssh: Use 'guile2.0-ssh'.•••Fixes a regression introduced in 4d8806c3d662c74e6d48d0f0d6ce423fce9a3a08. * gnu/tests/ssh.scm (run-ssh-test): Use GUILE2.0-SSH instead of GUILE-SSH. Ludovic Courtès2017-05-21
| * gnu: unionfs-fuse-static: Remove 'unionfsctl' executable.•••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. Ludovic Courtès2017-05-21
| * vm: Increase default disk size to account for ESP partition.•••Fixes a test regression introduced by ecf5d5376979fadd971559367bf553df89fcc62b. * gnu/system/vm.scm (system-qemu-image/shared-store-script): 30MiB -> 70MiB. Marius Bakke2017-05-21
| * 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. Leo Famulari2017-05-20
| * gnu: dropbear: Update to 2017.75 [fixes CVE-2017-{9078,9079}].•••* gnu/packages/ssh.scm (dropbear): Update to 2017.75. Leo Famulari2017-05-20
| * 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. Ludovic Courtès2017-05-20
| * 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 ecf5d5376979fadd971559367bf553df89fcc62b) Marius Bakke2017-05-20
| * 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. Marius Bakke2017-05-20
| * vm: Support arbitrary partition flags.•••* gnu/build/vm.scm (<partition>): Change BOOTABLE? to FLAGS. (initialize-partition-table): Pass each flag to parted. (initialize-hard-disk): Locate boot partition. * gnu/system/vm.scm (qemu-image): Adjust partition flags. Marius Bakke2017-05-20
| * gnu: guile-ssh: Fix potential double-free/use-after-free issue.•••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. Ludovic Courtès2017-05-20
| * services: user-homes: Do not create home directories marked as no-create.•••Fixes a bug whereby GuixSD would create the /nonexistent directory, from user 'nobody', even though it has 'create-home-directory?' set to #f. * gnu/build/activation.scm (activate-users+groups): Add comment for \#:create-home?. (activate-user-home)[ensure-user-home]: Skip when CREATE-HOME? is #f or SYSTEM? is #t. * gnu/tests/base.scm (run-basic-test)["no extra home directories"]: New tests. Ludovic Courtès2017-05-20
| * install: Enable SSH in installation image.•••* gnu/system/install.scm (%installation-services): Add OPENSSH-SERVICE-TYPE. * doc/guix.texi (Preparing for Installation)[Networking]: Document it. Marius Bakke2017-05-20
| * services: openssh: Don't depend on networking.•••* gnu/services/ssh.scm (openssh-shepherd-service): Drop requirement. Marius Bakke2017-05-20
| * maint: The 'release' target builds a VM image.•••* gnu/system/examples/vm-image.tmpl: New file. * Makefile.am (GUIXSD_VM_SYSTEMS, GUIXSD_VM_IMAGE_BASE, GUIXSD_VM_IMAGE_SIZE): New variables. (release): Add logic to build a VM image. (EXAMPLES): Add 'gnu/system/examples/vm-image.tmpl'. * doc/guix.texi (Running GuixSD in a VM, Installing GuixSD in a VM): Mention the pre-built VM image. Leo Famulari2017-05-20
| * gnu: aspell: 'dict-dir' set to ~/.guix-profile/lib/aspell or $ASPELL_DICT_DIR.•••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. Ludovic Courtès2017-05-20
| * gnu: qemu: Fix CVE-2017-7493.•••* 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. Leo Famulari2017-05-20
| * gnu: glibc/hurd: Do not apply i686 patch.•••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. Ricardo Wurmus2017-05-20
| * gnu: glibc/hurd: Use modify-phases syntax.•••* gnu/packages/base.scm (glibc/hurd)[arguments]: Use modify-phases syntax. Ricardo Wurmus2017-05-20
| * gnu: tor: Update to 0.3.0.7.•••* gnu/packages/tor.scm (tor): Update to 0.3.0.7. Efraim Flashner2017-05-20
| * gnu: guix: Update snapshot.•••* gnu/packages/package-management.scm (guix): Update to ce92d26. Ludovic Courtès2017-05-16
* | gnu: vte-ng: Update to 0.48.3.a.•••* gnu/packages/gnome.scm (vte-ng): Update to 0.48.3.a. Marius Bakke2017-05-22
* | gnu: gexiv2: Update to 0.10.6.•••* gnu/packages/gnome.scm (gexiv2): Update to 0.10.6. Marius Bakke2017-05-22
* | gnu: dconf-editor: Update to 3.22.3.•••* gnu/packages/gnome.scm (dconf-editor): Update to 3.22.3. Marius Bakke2017-05-22
* | gnu: aisleriot: Update to 3.22.2.•••* gnu/packages/gnome.scm (aisleriot): Update to 3.22.2. Marius Bakke2017-05-22
* | gnu: vte: Update to 0.48.3.•••* gnu/packages/gnome.scm (vte): Update to 0.48.3. Marius Bakke2017-05-22
* | 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. Ben Woodcroft2017-05-22
* | gnu: roary: Update to 3.8.2.•••* gnu/packages/bioinformatics.scm (roary): Update to 3.8.2. Ben Woodcroft2017-05-22
* | gnu: taxtastic: Update to 0.6.4.•••* gnu/packages/bioinformatics.scm (taxtastic): Update to 0.6.4. [source]: Use PyPI URI. Ben Woodcroft2017-05-22
* | gnu: r-mutationalpatterns: Update to 1.2.1.•••* gnu/packages/bioinformatics.scm (r-mutationalpatterns): Update to 1.2.1. Roel Janssen2017-05-22
* | 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. Mathieu Othacehe2017-05-21
* | gnu: v4l-utils: Update to 1.12.5.•••* gnu/packages/video.scm (v4l-utils): Update to 1.12.5. Marius Bakke2017-05-21
* | gnu: x265: Update to 2.4.•••* gnu/packages/video.scm (x265): Update to 2.4. Marius Bakke2017-05-21
* | gnu: vlc: Update to 2.2.5.1.•••* gnu/packages/video.scm (vlc): Update to 2.2.5.1. [source]: Remove obsolete snippet. Marius Bakke2017-05-21
* | gnu: libaacs: Update to 0.9.0.•••* gnu/packages/video.scm (libaacs): Update to 0.9.0. Marius Bakke2017-05-21
* | gnu: diamond: Update to 0.9.0.•••* gnu/packages/bioinformatics.scm (diamond): Update to 0.9.0. [license]: Change to AGPL3+. Ben Woodcroft2017-05-21
* | gnu: fasttree: Update to 2.1.10.•••* gnu/packages/bioinformatics.scm (fasttree): Update to 2.1.10. Ben Woodcroft2017-05-21
* | 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. Ben Woodcroft2017-05-21
* | gnu: python-future: Update to 0.16.0.•••* gnu/packages/python.scm (python-future): Update to 0.16.0. Ben Woodcroft2017-05-21
* | gnu: ccid: Update to 1.4.27.•••* gnu/packages/security-token.scm (ccid): Update to 1.4.27. Marius Bakke2017-05-21
* | gnu: fio: Update to 2.20.•••* gnu/packages/benchmark.scm (fio): Update to 2.20. [arguments]<#:phases>: Drop removed script from 'move-outputs' phase. Marius Bakke2017-05-21
* | gnu: nano: Update to 2.8.4.•••* gnu/packages/nano.scm (nano): Update to 2.8.4. Marius Bakke2017-05-21
* | gnu: vim: Update to 8.0.0600.•••* gnu/packages/vim.scm (vim, vim-full): Update to 8.0.0600. Marius Bakke2017-05-21
* | gnu: vim-full: Disable failing test.•••* gnu/packages/vim.scm (vim-full)[arguments]<#:phases>: Add substitution. Marius Bakke2017-05-21
* | 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. Mark H Weaver2017-05-21
* | 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 Mark H Weaver2017-05-21
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