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* gnu: petsc: Upgrade to 3.6.0.Eric Bavier2015-06-29
| | | | | | * 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.
* gnu: Add MUMPS.Eric Bavier2015-06-29
| | | | | | | * 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.
* gnu: Add METIS.Eric Bavier2015-06-29
| | | | * gnu/packages/maths.scm (metis): New variable.
* gnu: Add p4est.Eric Bavier2015-06-29
| | | | * gnu/packages/maths.scm (p4est, p4est-openmpi): New variables.
* gnu: Add ScaLAPACK.Eric Bavier2015-06-29
| | | | * gnu/packages/maths.scm (scalapack): New variable.
* gnu: scotch, pt-scotch: Build esmumps libraries.Eric Bavier2015-06-29
| | | | | | | * 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.
* gnu: scotch, pt-scotch: Use modify-phases.Eric Bavier2015-06-29
| | | | * gnu/packages/maths.scm (scotch, pt-scotch)[arguments]: Use modify-phases.
* gnu: Update scotch to 6.0.4.Eric Bavier2015-06-29
| | | | | | | | | * 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.
* gnu: openmpi: Upgrade to 1.8.5.Eric Bavier2015-06-29
| | | | | | * gnu/packages/mpi.scm (openmpi): Upgrade to 1.8.5. [native-inputs]: Add perl. [arguments]: Add configure flags for thread support.
* gnu: hwloc: Move numactl to inputs.Eric Bavier2015-06-29
| | | | | | * gnu/packages/mpi.scm (hwloc)[propagated-inputs]: Move numactl from here... [inputs]: ...to here. [arguments]: New 'refine-libnuma' phase.
* gnu: hwloc: Upgrade to 1.10.1.Eric Bavier2015-06-29
| | | | | | | | | * 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.
* gnu: python-mccabe: Fix license field.Eric Bavier2015-06-29
| | | | | * gnu/packages/python.scm (python-mccabe)[license]: 'expat' -> 'license:expat'.
* gnu: Add python-flake8.Cyril Roelandt2015-06-30
| | | | * gnu/packages/python.scm (python-flake8, python2-flake8): New variables.
* gnu: Add python-mccabe.Cyril Roelandt2015-06-30
| | | | * gnu/packages/python.scm (python-mccabe, python2-mccabe): New variables.
* gnu: Add python-pyflakes.Cyril Roelandt2015-06-30
| | | | * gnu/packages/python.scm (python-pyflakes, python2-pyflakes): New variables.
* gnu: Add python-pep8.Cyril Roelandt2015-06-30
| | | | * gnu/packages/python.scm (python-pep8, python2-pep8): New variables.
* gnu: withershins: Use new "libiberty" package.Ricardo Wurmus2015-06-29
| | | | | * gnu/packages/code.scm (withershins)[inputs]: Replace "gcc" with "libiberty". [arguments]: Simplify "find-libiberty" phase.
* gnu: Add libiberty.Ricardo Wurmus2015-06-29
| | | | * gnu/packages/gcc.scm (make-libiberty, libiberty): New variables.
* gnu: r: Update to 3.2.1.Ricardo Wurmus2015-06-29
| | | | | | * 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.
* gnu: Add Blast+.Ricardo Wurmus2015-06-29
| | | | * gnu/packages/bioinformatics.scm (blast+): New variable.
* gnu: global: Update to 6.5.Ludovic Courtès2015-06-29
| | | | * gnu/packages/code.scm (global): Update to 6.5.
* gnu: help2man: Update to 1.47.1.Ludovic Courtès2015-06-29
| | | | * gnu/packages/man.scm (help2man): Update to 1.47.1.
* gnu: parallel: Update to 20150622.Ludovic Courtès2015-06-29
| | | | * gnu/packages/parallel.scm (parallel): Update to 20150622.
* gnu: screen: Update to 4.3.1.Ludovic Courtès2015-06-29
| | | | * gnu/packages/screen.scm (screen): Update to 4.3.1.
* gnu: texinfo: Add version 6.0.Ludovic Courtès2015-06-29
| | | | * gnu/packages/texinfo.scm (texinfo-6): New variable.
* gnu: gcc-4.8: Update to 4.8.5.Ludovic Courtès2015-06-29
| | | | * gnu/packages/gcc.scm (gcc-4.8): Update to 4.8.5.
* gnu: Add plink.Ricardo Wurmus2015-06-29
| | | | | * gnu/packages/bioinformatics.scm (plink): New variable. * gnu/packages/patches/plink-1.07-unclobber-i.patch: New file.
* gnu: synergy: Upgrade to 1.7.3.Eric Bavier2015-06-28
| | | | | | | | | * gnu/packages/synergy.scm (synergy)[version]: Upgrade to 1.7.3 [source]: Use github for source download. Add snippet to remove bundled source and binaries. [inputs]: Add openssl. [arguments]: Copy example configuration files to out during 'install phase.
* gnu: Add sfarkxtc.Ricardo Wurmus2015-06-28
| | | | * gnu/packages/compression.scm (sfarkxtc): New variable.
* gnu: Add sfarklib.Ricardo Wurmus2015-06-28
| | | | * gnu/packages/compression.scm (sfarklib): New variable.
* gnu: Add Guitarix.Ricardo Wurmus2015-06-28
| | | | * gnu/packages/audio.scm (guitarix): New variable.
* gnu: ardour: Update to 4.1.Ricardo Wurmus2015-06-28
| | | | * gnu/packages/audio.scm (ardour): Update to 4.1.
* gnu: Add libtar.Ricardo Wurmus2015-06-28
| | | | * gnu/packages/compression.scm (libtar): New variable.
* gnu: Add pv.Claes Wallin2015-06-27
| | | | | | | * gnu/package/pv.scm (pv): New file. * gnu-system.am (GNU_SYSTEM_MODULES): Add it. Signed-off-by: Alex Kost <alezost@gmail.com>
* gnu: Refer to 'gcc' instead of 'gcc-4.9'.Ludovic Courtès2015-06-26
| | | | | | | | | | * gnu/packages/commencement.scm (gcc-boot0, cross-gcc-wrapper, libstdc++, gcc-final): Refer to GCC instead of GCC-4.9. * gnu/packages/cross-base.scm (%xgcc): New variable. (cross-gcc-arguments, cross-gcc): Refer to %XGCC instead of GCC-4.9. * gnu/packages/llvm.scm (clang-from-llvm): Refer to GCC instead of GCC-4.9. * gnu/packages/make-bootstrap.scm (package-with-relocatable-glibc, %gcc-static, %gcc-stripped): Likewise.
* gnu: youtube-dl: Update to 2015.06.25.Ludovic Courtès2015-06-26
| | | | * gnu/packages/video.scm (youtube-dl): Update to 2015.06.25.
* gnu: Add python2-fastlmm.Ricardo Wurmus2015-06-26
| | | | * gnu/packages/python.scm (python2-fastlmm): New variable.
* gnu: Add python2-pysnptools.Ricardo Wurmus2015-06-26
| | | | * gnu/packages/python.scm (python2-pysnptools): New variable.
* gnu: nettle: Disable ifunc method of library initialization.Mark H Weaver2015-06-25
| | | | | * gnu/packages/nettle.scm (nettle)[arguments]: Add 'disable-ifunc-init-method' phase.
* gnu: Replace versioned gfortran inputs with just "gfortran".Ricardo Wurmus2015-06-25
| | | | | | | | | | | | | | | * gnu/packages/julia.scm (julia)[inputs]: Replace "gfortran-4.8" with "gfortran". * gnu/packages/machine-learning.scm (randomjungle)[native-inputs]: Likewise. * gnu/packages/maths.scm (arpack-ng, lapack, petsc, superlu) (superlu-dist, openblas, openspecfun, atlas)[inputs]: Likewise. (octave)[native-inputs]: Likewise. (gmsh)[propagated-inputs]: Likewise. * gnu/packages/mpi.scm (openmpi)[inputs]: Likewise. * gnu/packages/python.scm (python-numpy-bootstrap)[native-inputs]: Likewise. * gnu/packages/python.scm (python-scipy)[native-inputs]: Likewise. * gnu/packages/statistics.scm (r)[inputs]: Replace "gfortran-4.9" with "gfortran".
* gnu: Add default GCC and default gfortran.Ricardo Wurmus2015-06-25
| | | | | * gnu/packages/gcc.scm (gcc): New variable. * gnu/packages/gcc.scm (gfortran): New variable.
* gnu: gstreamer: Add search path specification for 'GST_PLUGIN_SYSTEM_PATH'.宋文武2015-06-25
| | | | | | | This reverts commit e53fc0c8a, which add it wrongly to gst-plugins-base. * gnu/packages/gstreamer.scm (gstreamer)[native-search-paths]: New field. (gst-plugins-base)[native-search-paths]: Remove.
* linux-initrd: Produce cpio archives with zeroed timestamps, etc.Ludovic Courtès2015-06-24
| | | | | | * guix/cpio.scm (file->cpio-header*): New procedure. * gnu/build/linux-initrd.scm (write-cpio-archive): Add #:file->header argument to 'cpio:write-cpio-archive'.
* linux-initrd: Populate cpio archives in a deterministic order.Ludovic Courtès2015-06-24
| | | | | * gnu/build/linux-initrd.scm (write-cpio-archive)[files]: Use 'sort' instead of 'reverse'.
* linux-initrd: Use (guix cpio) instead of GNU cpio.Ludovic Courtès2015-06-24
| | | | | | | | | * gnu/build/linux-initrd.scm (write-cpio-archive): Remove 'open-pipe*' and related calls. Compute list of files in 'files' variable. Use 'cpio:write-cpio-archive'. Remove #:cpio parameter. (build-initrd): Remove #:cpio parameter. * gnu/system/linux-initrd.scm (expression->initrd): Likewise, and adjust BUILDER accordingly. Add (guix cpio) to #:modules.
* gnu: pius: Depend on GnuPG 2.0 rather than 2.1.Ludovic Courtès2015-06-24
| | | | * gnu/packages/gnupg.scm (pius)[inputs]: Change GNUPG to GNUPG-2.0.
* gnu: julia: Use modify-phases syntax and add return values.Ricardo Wurmus2015-06-24
| | | | | * gnu/packages/julia.scm (julia)[arguments]: Use modify-phases syntax for build phases and add missing return values.
* gnu: r: Use gfortran-4.9.Ricardo Wurmus2015-06-24
| | | | | * gnu/packages/statistics.scm (r)[inputs]: Replace gfortran-4.8 with gfortran-4.9.
* gnu: Add gfortran 4.9.Ricardo Wurmus2015-06-24
| | | | * gnu/packages/gcc.scm (gfortran-4.9): New variable.
* gnu: Add hmmer.Ben Woodcroft2015-06-24
| | | | * gnu/packages/bioinformatics.scm (hmmer): New variable.
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