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2015-07-04gnu: icecat: Fix CVE-2015-{2722,2724,2728,2733,2735,2736,2738,2739,2740,2743}.Mark H Weaver
* gnu/packages/patches/icecat-CVE-2015-2722-pt1.patch, gnu/packages/patches/icecat-CVE-2015-2722-pt2.patch, gnu/packages/patches/icecat-CVE-2015-2724-pt1.patch, gnu/packages/patches/icecat-CVE-2015-2724-pt2.patch, gnu/packages/patches/icecat-CVE-2015-2724-pt3.patch, gnu/packages/patches/icecat-CVE-2015-2724-pt4.patch, gnu/packages/patches/icecat-CVE-2015-2728-pt1.patch, gnu/packages/patches/icecat-CVE-2015-2728-pt2.patch, gnu/packages/patches/icecat-CVE-2015-2733-pt1.patch, gnu/packages/patches/icecat-CVE-2015-2733-pt2.patch, gnu/packages/patches/icecat-CVE-2015-2735.patch, gnu/packages/patches/icecat-CVE-2015-2736.patch, gnu/packages/patches/icecat-CVE-2015-2738.patch, gnu/packages/patches/icecat-CVE-2015-2739.patch, gnu/packages/patches/icecat-CVE-2015-2740.patch, gnu/packages/patches/icecat-CVE-2015-2743.patch: New files. * gnu-system.am (dist_patch_DATA): Add them. * gnu/packages/gnuzilla.scm (icecat)[source]: Add patches.
2015-07-03gnu: unrtf: Fix download location.Andreas Enge
* gnu/packages/unrtf.scm (unrtf): Fix download location.
2015-07-03gnu: r: Replace "atlas" with "openblas".Ricardo Wurmus
* gnu/packages/statistics.scm (r)[inputs]: Replace "atlas" with "openblas".
2015-07-03gnu: gnutls: Move man3 pages to "doc" output.Ludovic Courtès
* gnu/packages/gnutls.scm (gnutls)[arguments]: Add #:phases.
2015-07-03gnu: qt-4: Remove reference from "out" to "doc".Ludovic Courtès
* gnu/packages/qt.scm (qt-4)[arguments]: Remove '-docdir' configure flag. Add 'move-doc' phase.
2015-07-03gnu: qt-4: Use a more standard directory layout.Ludovic Courtès
* gnu/packages/qt.scm (qt-4)[arguments]: Pass -datadir, -importdir, -plugindir, and -translationdir.
2015-07-03gnu: qt-4: Use 'modify-phases'.Ludovic Courtès
* gnu/packages/qt.scm (qt-4)[arguments]: Use 'modify-phases' instead of 'alist-replace'.
2015-07-03gnu: cups-filter: Install backends and filters under lib/cups.Ludovic Courtès
This ensures that they are stripped during the 'strip' phase, thereby removing references to GCC and linux-libre-headers that would otherwise be found in debugging symbols. * gnu/packages/cups.scm (cups-filters)[source]: Change pkgbackenddir and pkgfilterdir to $(PREFIX)/lib/cups/{filter,backend}. (cups)[arguments]: Adjust accordingly.
2015-07-03gnu: mysql: Remove unnecessary binaries.Ludovic Courtès
This saves ~42 MiB on x86_64. * gnu/packages/databases.scm (mysql)[arguments]: Add 'remove-extra-binaries' phase.
2015-07-03gnu: mysql: Strip references and GCC and other build-time dependencies.Ludovic Courtès
* gnu/packages/databases.scm (mysql)[arguments]: Add 'strip-extra-references' phase.
2015-07-03gnu: mutt: Don't retain reference to GCC.Ludovic Courtès
* gnu/packages/patches/mutt-store-references.patch: New file. * gnu/packages/mail.scm (mutt)[source]: Use it. * gnu-system.am (dist_patch_DATA): Add it.
2015-07-03gnu: ghostscript: Add "doc" output.Ludovic Courtès
* gnu/packages/ghostscript.scm (ghostscript)[source](snippet): New field. [outputs]: New field. [arguments]: Add 'remove-doc-reference' phase.
2015-07-02gnu: gnupg: Enable TLS support.Mark H Weaver
* gnu/packages/gnupg.scm (gnupg)[native-inputs]: Add pkg-config. [inputs]: Add gnutls. (gnupg-2.0, gnupg-1)[native-inputs]: Override inherited value to be '().
2015-07-02gnu: gnupg: Update to 2.1.6.Mark H Weaver
* gnu/packages/gnupg.scm (gnupg): Update to 2.1.6.
2015-07-02gnu: Add WarpedLMM.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (python2-warpedlmm): New variable.
2015-07-02gnu: r: Set default pager.Ricardo Wurmus
* gnu/packages/statistics.scm (r)[arguments]: Add phase "set-default-pager" to avoid "false" as a default pager.
2015-07-01environment: Define 'GUIX_ENVIRONMENT'.Ludovic Courtès
* guix/scripts/environment.scm (create-environment): Define 'GUIX_ENVIRONMENT'. * doc/guix.texi (Invoking guix environment): Document it. * gnu/system/shadow.scm (default-skeletons): Adjust 'PS1' depending on whether 'GUIX_ENVIRONMENT' is defined.
2015-07-01gnu: powertabeditor: Replace "gcc" with "libiberty".Ricardo Wurmus
* gnu/packages/music.scm (powertabeditor)[inputs]: Replace "gcc" with "libiberty".
2015-07-01gnu: Add Hydrogen.Ricardo Wurmus
* gnu/packages/music.scm (hydrogen): New variable.
2015-07-01gnu: linux-libre: Update to 4.1.1.Mark H Weaver
* gnu/packages/linux.scm (linux-libre): Update to 4.1.1.
2015-06-30gnu: git: Add inputs for send-email.Eric Bavier
* gnu/packages/version-control.scm (package-transitive-propagated-labels*) (package-propagated-input-refs): New procedures. (git)[inputs]: Add perl-authen-sasl, perl-net-smtp-ssl, and perl-io-socket-ssl. [outputs]: Add send-email output. [arguments]: Add #:modules argument with srfi-1. In 'split phase, wrap git-send-email.
2015-06-30gnu: Add perl-authen-sasl.Eric Bavier
* gnu/packages/web.scm (perl-authen-sasl): New variable.
2015-06-30gnu: Add perl-gssapi.Eric Bavier
* gnu/packages/web.scm (perl-gssapi): New variable.
2015-06-30gnu: Add perl-net-smtp-ssl.Eric Bavier
* gnu/packages/web.scm (perl-net-smtp-ssl): New variable.
2015-06-30gnu: curl: Disable test that fails on Hydra.Mark H Weaver
* gnu/packages/curl.scm (arguments): Disable test 1510.
2015-06-30gnu: curl: Update to 7.43.0.Mark H Weaver
* gnu/packages/curl.scm (curl): Update to 7.43.0.
2015-06-29gnu: Add deal.II.Eric Bavier
* gnu/packages/maths.scm (dealii, dealii-openmpi): New variables. * gnu/packages/patches/dealii-p4est-interface.patch: New patch. * gnu-system.am (dist_patch_DATA): Add it.
2015-06-29gnu: Add SLEPc.Eric Bavier
* gnu/packages/maths.scm (slepc, slepc-complex, slepc-openmpi) (slepc-complex-openmpi): New variables.
2015-06-29gnu: Add arpack-ng-openmpi.Eric Bavier
* gnu/packages/maths.scm (arpack-ng-openmpi): New variable.
2015-06-29gnu: petsc: Upgrade to 3.6.0.Eric Bavier
* gnu/packages/maths.scm (petsc): Upgrade to 3.6.0. * gnu/packages/patches/petsc-fix-threadcomm.patch: Delete patch. * gnu-system.am (dist_patch_DATA): Remove it.
2015-06-29gnu: Add MUMPS.Eric Bavier
* gnu/packages/maths.scm (mumps, mumps-metis, mumps-openmpi) (mumps-metis-openmpi): New variables. * gnu/packages/patches/mumps-build-parallelism.patch: New patch. * gnu-system.am (dist_patch_DATA): Add it.
2015-06-29gnu: Add METIS.Eric Bavier
* gnu/packages/maths.scm (metis): New variable.
2015-06-29gnu: Add p4est.Eric Bavier
* gnu/packages/maths.scm (p4est, p4est-openmpi): New variables.
2015-06-29gnu: Add ScaLAPACK.Eric Bavier
* gnu/packages/maths.scm (scalapack): New variable.
2015-06-29gnu: scotch, pt-scotch: Build esmumps libraries.Eric Bavier
* gnu/packages/maths.scm (scotch)[arguments]: Add 'build-esmumps phase. Install esmumps libraries and headers in 'install phase. (pt-scotch)[arguments]: Build ptesmumps in 'build phase. Add make parallelism.
2015-06-29gnu: scotch, pt-scotch: Use modify-phases.Eric Bavier
* gnu/packages/maths.scm (scotch, pt-scotch)[arguments]: Use modify-phases.
2015-06-29gnu: Update scotch to 6.0.4.Eric Bavier
* gnu/packages/maths.scm (scotch): Update to 6.0.4. [arguments]: Add -fPIC to CFLAGS. * gnu/packages/patches/scotch-test-threading.patch: Adjust patch for a new set of test fixes. * gnu/packages/patches/pt-scotch-build-parallelism.patch: New patch. * gnu-system.am (dist_patch_DATA): Add it.
2015-06-29gnu: openmpi: Upgrade to 1.8.5.Eric Bavier
* gnu/packages/mpi.scm (openmpi): Upgrade to 1.8.5. [native-inputs]: Add perl. [arguments]: Add configure flags for thread support.
2015-06-29gnu: hwloc: Move numactl to inputs.Eric Bavier
* gnu/packages/mpi.scm (hwloc)[propagated-inputs]: Move numactl from here... [inputs]: ...to here. [arguments]: New 'refine-libnuma' phase.
2015-06-29gnu: hwloc: Upgrade to 1.10.1.Eric Bavier
* gnu/packages/patches/hwloc-gather-topology-lstopo.patch: New patch. * gnu/packages/mpi.scm (hwloc): Upgrade to 1.10.1. [source]: Use patch. [propagated-inputs]: Remove libpci. [inputs]: Add libpciaccess. * gnu-system.am (dist_patch_DATA): Add patch.
2015-06-29gnu: python-mccabe: Fix license field.Eric Bavier
* gnu/packages/python.scm (python-mccabe)[license]: 'expat' -> 'license:expat'.
2015-06-30gnu: Add python-flake8.Cyril Roelandt
* gnu/packages/python.scm (python-flake8, python2-flake8): New variables.
2015-06-30gnu: Add python-mccabe.Cyril Roelandt
* gnu/packages/python.scm (python-mccabe, python2-mccabe): New variables.
2015-06-30gnu: Add python-pyflakes.Cyril Roelandt
* gnu/packages/python.scm (python-pyflakes, python2-pyflakes): New variables.
2015-06-30gnu: Add python-pep8.Cyril Roelandt
* gnu/packages/python.scm (python-pep8, python2-pep8): New variables.
2015-06-29gnu: withershins: Use new "libiberty" package.Ricardo Wurmus
* gnu/packages/code.scm (withershins)[inputs]: Replace "gcc" with "libiberty". [arguments]: Simplify "find-libiberty" phase.
2015-06-29gnu: Add libiberty.Ricardo Wurmus
* gnu/packages/gcc.scm (make-libiberty, libiberty): New variables.
2015-06-29gnu: r: Update to 3.2.1.Ricardo Wurmus
* gnu/packages/statistics.scm (r): Update to 3.2.1. * gnu/packages/patches/r-fix-15899.patch: Remove file. * gnu-system.am (dist_patch_DATA): Remove it.
2015-06-29gnu: Add Blast+.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (blast+): New variable.
2015-06-29gnu: global: Update to 6.5.Ludovic Courtès
* gnu/packages/code.scm (global): Update to 6.5.
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