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* gnu: perl-dbd-mysql: Fix CVE-2017-10788.Kei Kebreau2017-07-25
| | | | | | * gnu/packages/patches/perl-dbd-mysql-CVE-2017-10788.patch: New file. * gnu/local.mk (dist_patch_DATA): Add it. * gnu/packages/databases.scm (perl-dbd-mysql)[source]: Use it.
* gnu: openmpi: Description mentions MPI 3.0.Dave Love2017-07-25
| | | | | | * gnu/packages/mpi.scm (openmpi): It's MPI 3, not MPI 2. Signed-off-by: Ludovic Courtès <ludo@gnu.org>
* gnu: openmpi: Update to 1.10.7.Dave Love2017-07-25
| | | | | | * gnu/packages/mpi.scm (openmpi): Update to 1.10.7. Signed-off-by: Ludovic Courtès <ludo@gnu.org>
* hydra: Add 'guix.SYSTEM' jobs.Ludovic Courtès2017-07-25
| | | | | * build-aux/hydra/guix.scm (package->alist): Disable grafting. (hydra-jobs): Return 'guix.SYSTEM' jobs in addition to 'tarball'.
* hydra: Simplify 'tarball' job.Ludovic Courtès2017-07-25
| | | | | * build-aux/hydra/guix.scm (tarball-package): Remove. (hydra-jobs): Use 'dist-package' instead of 'tarball-package'.
* gnu: Add guile2.0-git.Ludovic Courtès2017-07-25
| | | | * gnu/packages/guile.scm (guile2.0-git): New variable.
* gnu: Add guile2.0-bytestructures.Ludovic Courtès2017-07-25
| | | | | | | | | * gnu/packages/patches/guile-bytestructures-name-clash.patch: New file. * gnu/local.mk (dist_patch_DATA): Add it. * gnu/packages/guile.scm (guile-bytestructures)[source]: Use it. [arguments]: Unpack the source. [native-inputs]: New field. (guile2.0-bytestructures): New variable.
* gnu: maxima: Ensure binutils are available at runtime.Kei Kebreau2017-07-25
| | | | | * gnu/packages/maths.scm (maxima)[arguments]: Use modify-phases syntax. Modify 'post-install' phase.
* Revert "gnu: maxima: Ensure gcc is available at runtime."Kei Kebreau2017-07-25
| | | | | | This reverts commit f2fa86cc82b5941bde63b666337eea59aa609e55. Commit 5ea8dbf0c906d51779ba0cf775ec9967f5f42382 fixes the underlying issue in GNU Common Lisp.
* gnu: gcl: Ensure gcc and binutils are available at runtime.Kei Kebreau2017-07-25
| | | | | * gnu/packages/lisp.scm (gcl)[arguments]: Add -fgnu89-inline to CFLAGS. Add GCC path to make-flags. Modify 'pre-conf' phase. Add 'wrap' phase.
* gnu: webkitgtk: Update to 2.16.6 [security fixes].Mark H Weaver2017-07-25
| | | | | | | | Includes fixes for CVE-2017-7039, CVE-2017-7018, CVE-2017-7030, CVE-2017-7037, CVE-2017-7034, CVE-2017-7055, CVE-2017-7056, CVE-2017-7064, CVE-2017-7061, CVE-2017-7048, and CVE-2017-7046. * gnu/packages/webkit.scm (webkitgtk): Update to 2.16.6.
* system: Add a default '.guile' skeleton.Ludovic Courtès2017-07-25
| | | | * gnu/system/shadow.scm (default-skeletons): Add ".guile".
* Add 'guix weather'.Ludovic Courtès2017-07-25
| | | | | | | | | | * guix/scripts/weather.scm: New file. * Makefile.am (MODULES): Add it. * doc/guix.texi (Substitutes, Invoking guix publish): Mention "guix weather". (Invoking guix weather): New node. Co-authored-by: Ricardo Wurmus <rekado@elephly.net>
* gnu: xterm: Update to 330.Leo Famulari2017-07-24
| | | | * gnu/packages/xorg.scm (xterm): Update to 330.
* gnu: dialog: Update to 1.3-20170509.Leo Famulari2017-07-24
| | | | * gnu/packages/ncurses.scm (dialog): Update to 1.3-20170509.
* gnu: opus: Update to 1.2.1.Leo Famulari2017-07-24
| | | | | * gnu/packages/xiph.scm (opus): Update to 1.2.1. [source]: Use new source URL.
* gnu: gnome: Add deja-dup.Christopher Baines2017-07-24
| | | | | | * gnu/packages/gnome.scm (deja-dup): New variable. * gnu/packages/patches/deja-dup-use-ref-keyword-for-iter.patch: New file. * gnu/local.mk (dist_patch_DATA): Add patch file entry.
* import: cpan: Updater returns a list of URLs.Ludovic Courtès2017-07-24
| | | | | * guix/import/cpan.scm (latest-release): Return a list in the 'urls' field of 'upstream-source'.
* gnu: guix: Update snapshot.Ludovic Courtès2017-07-24
| | | | * gnu/packages/package-management.scm (guix): Update to f1ddfe4.
* gnu: python-flaky: Fix Texinfo markup in description.Ludovic Courtès2017-07-24
| | | | * gnu/packages/python.scm (python-flaky)[description]: Escape "@".
* gnu: isc-dhcp: Update bundled bind to 9.9.10-P3.Leo Famulari2017-07-23
| | | | | | | | | This fixes a regression introduced in the fix for CVE-2017-3142, in BIND 9.9.10-P2, commit ecb232bdfcb2718de5944bcf4d9c4e288ec41519. See 'CHANGELOG' in the source distribution for more information. * gnu/packages/admin.scm (isc-dhcp): Update bundled bind to 9.9.10-P3.
* gnu: bind: Update to 9.11.1-P3.Leo Famulari2017-07-23
| | | | | | | | | This fixes a regression introduced in the fix for CVE-2017-3142, in BIND 9.11.1-P2, commit faa1369e3cb72bda4ba8b63029d0ad780df9cf78. See 'CHANGELOG' in the source distribution for more information. * gnu/packages/dns.scm (isc-bind): Update to 9.11.1-P3.
* gnu: ncurses/gpm: Move to (gnu packages ncurses).Mark H Weaver2017-07-23
| | | | | | | | | This is needed to avoid compilation problems caused by the cyclic dependency between (gnu packages ncurses) and (gnu packages linux). * gnu/packages/linux.scm (ncurses/gpm): Move to ... * gnu/packages/ncurses.scm (ncurses/gpm): ... here. Fix misleading indentation. Add (gnu packages linux) to the module imports.
* gnu: Add support for aarch64's compiled kernel.Efraim Flashner2017-07-23
| | | | | | * gnu/packages/linux.scm (linux-libre)[arguments]: Add to the regex to find and install the aarch64-linux kernel. * gnu/system.scm (system-linux-image-file-name): Add entry for aarch64.
* gnu: Add xf86-video-freedreno.Efraim Flashner2017-07-23
| | | | * gnu/packages/xorg.scm (xf86-video-freedreno): New variable.
* gnu: Add u-boot-odroid-c2.Efraim Flashner2017-07-23
| | | | * gnu/packages/bootloaders.scm (u-boot-odroid-c2): New variable.
* gnu: u-boot: Update to 2017.07.Efraim Flashner2017-07-23
| | | | * gnu/packages/bootloaders.scm (u-boot): Update to 2017.07.
* gnu: tevent: Update to 0.9.33.Marius Bakke2017-07-23
| | | | * gnu/packages/samba.scm (tevent): Update to 0.9.33.
* gnu: talloc: Update to 2.1.10.Marius Bakke2017-07-23
| | | | * gnu/packages/samba.scm (talloc): Update to 2.1.10.
* gnu: ldb: Update to 1.1.31.Marius Bakke2017-07-23
| | | | | * gnu/packages/samba.scm (ldb): Update to 1.1.31. [native-inputs]: Add CMOCKA.
* gnu: cmocka: Update to 1.1.1.Marius Bakke2017-07-23
| | | | * gnu/packages/check.scm (cmocka): Update to 1.1.1.
* gnu: tdb: Update to 1.3.14.Marius Bakke2017-07-23
| | | | * gnu/packages/databases.scm (tdb): Update to 1.3.14.
* gnu: python-scipy: Update to 0.19.1.Marius Bakke2017-07-23
| | | | | * gnu/packages/python.scm (python-scipy): Update to 0.19.1. [source]: Use 'pypi-uri'.
* gnu: python-matplotlib: Update to 2.0.2.Marius Bakke2017-07-23
| | | | | * gnu/packages/python.scm (python-matplotlib): Update to 2.0.2. [source]: Use 'pypi-uri'.
* gnu: python-pyparsing: Update to 2.2.0.Marius Bakke2017-07-23
| | | | | * gnu/packages/python.scm (python-pyparsing, python2-pyparsing): Update to 2.2.0.
* gnu: python-pyparsing: Use 'modify-phases' syntax.Marius Bakke2017-07-23
| | | | | * gnu/packages/python.scm (python-pyparsing)[arguments]<#:phases>: Use 'modify-phases'.
* gnu: Add xmobar.Oleg Pykhalov2017-07-23
| | | | | | gnu/packages/wm.scm (xmobar): New variable. Signed-off-by: Leo Famulari <leo@famulari.name>
* gnu: bash-completion: Update to 2.7.Efraim Flashner2017-07-23
| | | | * gnu/packages/bash.scm (bash-completion): Update to 2.7.
* gnu: getmail: Update to 5.1.ng02017-07-22
| | | | | | * gnu/packages/mail.scm (getmail): Update to 5.1. Signed-off-by: Leo Famulari <leo@famulari.name>
* gnu: metabat: Update to 2.11.1.Ben Woodcroft2017-07-23
| | | | | | | | * gnu/packages/bioinformatics.scm (metabat): Update to 2.11.1. [source]: Add patch to fix compilation. [arguments]: Adjust regular expressions modifying 'SConstruct'. * gnu/packages/patches/metabat-fix-compilation.patch: New file. * gnu/local.mk (dist_patch_DATA): Add it.
* gnu: python-plastid: Update to 0.4.8.Ben Woodcroft2017-07-23
| | | | * gnu/packages/bioinformatics.scm (python-plastid): Update to 0.4.8.
* gnu: bcftools: Update to 1.5.Ben Woodcroft2017-07-23
| | | | | | | | | * gnu/packages/bioinformatics.scm (bcftools): Update to 1.5. [origin]: Remove fix-makefile patch. [arguments]: Add configure flags, add LIBS make flag. Do not delete configure phase. * gnu/packages/patches/bcftools-fix-makefile.patch: Remove file. * gnu/local.mk (dist_patch_DATA): Remove it.
* gnu: samtools: Update to 1.5.Ben Woodcroft2017-07-23
| | | | * gnu/packages/bioinformatics.scm (samtools): Update to 1.5.
* gnu: htslib: Update to 1.5.Ben Woodcroft2017-07-23
| | | | * gnu/packages/bioinformatics.scm (htslib): Update to 1.5.
* gnu: python-pysam: Update to 0.11.2.2.Ben Woodcroft2017-07-23
| | | | * gnu/packages/bioinformatics.scm (python-pysam): Update to 0.11.2.2.
* gnu: bamm: Use htslib-1.3.Ben Woodcroft2017-07-23
| | | | | * gnu/packages/bioinformatics (htslib-1.3): New variable. (bamm)[inputs]: Replace htslib with htslib-1.3.
* gnu: bcftools: Update to 1.4.1.Ben Woodcroft2017-07-23
| | | | | | | | * gnu/packages/bioinformatics.scm (bcftools): Update to 1.4.1. [arguments]: Move Makefile modifications from here ... [source]: ... to added patch. Adjust patch for update to 1.4. * gnu/packages/patches/bcftools-fix-makefile.patch: New file. * gnu/local.mk (dist_patch_DATA): Register it.
* gnu: samtools: Update to 1.4.1.Ben Woodcroft2017-07-23
| | | | | | * gnu/packages/bioinformatics.scm (samtools): Update to 1.4.1. [arguments]: Add '--with-htslib=system' configure flag. [inputs]: Add htslib.
* gnu: htslib: Update to 1.4.1.Ben Woodcroft2017-07-23
| | | | | * gnu/packages/bioinformatics.scm (htslib): Update to 1.4.1. [inputs]: Add curl, openssl.
* gnu: samtools: Use "modify-phases" syntax.Ben Woodcroft2017-07-23
| | | | | * gnu/packages/bioinformatics.scm (samtools)[arguments]: Use "modify-phases" syntax.
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