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2015-07-21gnu: julia: Update to 0.3.10.Ricardo Wurmus
* gnu/packages/julia.scm (julia): Update to 0.3.10. * gnu/packages/patches/julia-0.3.10-fix-empty-array.patch: New file. * gnu-system.am (dist_patch_DATA): Add it.
2015-07-21gnu: libmad: Apply fixes for ARMv7 Thumb, etc.Mark H Weaver
* gnu/packages/patches/libmad-armv7-thumb-pt1.patch, gnu/packages/patches/libmad-armv7-thumb-pt2.patch, gnu/packages/patches/libmad-frame-length.patch: New files. * gnu-system.am (dist_patch_DATA): Add them. * gnu/packages/mp3.scm (libmad)[source]: Add patches.
2015-07-20gnu: tidy: Add fixes for CVE-2015-5522 and CVE-2015-5523.Mark H Weaver
* gnu/packages/patches/tidy-CVE-2015-5522+5523.patch: New file. * gnu-system.am (dist_patch_DATA): Add it. * gnu/packages/web.scm (tidy)[source]: Add patch.
2015-07-19Merge branch 'master' into core-updatesMark H Weaver
2015-07-18gnu: ninja: Do not report files with mtime = 0 as missing.Ludovic Courtès
This is a followup to 47f315a. * gnu/packages/patches/ninja-zero-mtime.patch: New file. * gnu-system.am (dist_patch_DATA): Add it. * gnu/packages/ninja.scm (ninja)[source]: Reinstate 'patches' field and add this patch. [arguments]: Remove 'apply-ninja-tests.patch' phase.
2015-07-18gnu: crda: Add forgotten patch.Ludovic Courtès
This file should have been added as part of commit cc205da. * gnu/packages/patches/crda-optional-gcrypt.patch: New file. * gnu-system.am (dist_patch_DATA): Add it.
2015-07-17gnu: icecat: Add patch to adapt to freetype 2.6.Mark H Weaver
* gnu/packages/patches/icecat-freetype-2.6.patch: New file. * gnu-system.am (dist_patch_DATA): Add it. * gnu/packages/gnuzilla.scm (icecat)[source]: Add patch.
2015-07-16gnu: subversion: Skip the faulty test.Ludovic Courtès
The added patch from upstream didn't help, nor did downgrading to SQLite 3.8.9. Thus, shamelessly skip the offending test. * gnu/packages/patches/subversion-sqlite-3.8.9-fix.patch: Add one hunk to skip the faulty test, and another one from upstream.
2015-07-15gnu: unzip: Fix CVE-2014-9636 and some other bugs.Mark H Weaver
* gnu/packages/patches/unzip-CVE-2014-9636.patch, gnu/packages/patches/unzip-allow-greater-hostver-values.patch, gnu/packages/patches/unzip-increase-size-of-cfactorstr.patch, gnu/packages/patches/unzip-initialize-symlink-flag.patch, gnu/packages/patches/unzip-remove-build-date.patch: New files. * gnu-system.am (dist_patch_DATA): Add them. * gnu/packages/zip.scm (unzip)[source]: Add patches. [arguments]: Use 'modify-phases'. Remove custom 'configure' phase; pass additional make-flags instead. Add custom 'build' phase that builds "generic_gcc" target; remove "generic_gcc" from make-flags.
2015-07-15Merge branch 'master' into core-updatesMark H Weaver
2015-07-15gnu: icecat: Update to 31.8.0-gnu1.Mark H Weaver
* gnu/packages/patches/icecat-enable-acceleration-and-webgl.patch: New file. * 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: Remove files. * gnu-system.am (dist_patch_DATA): Remove them, and add the new file. * gnu/packages/gnuzilla.scm (icecat): Update to 31.8.0-gnu1. Remove the outdated patches and add the new one.
2015-07-15Merge branch 'master' into core-updatesMark H Weaver
2015-07-13gnu: boost: Patch to avoid -m32 flag on mips.Andreas Enge
* gnu/packages/patches/boost-mips-avoid-m32.patch: New file. * gnu-system.am (dist_patch_DATA): Register patch. * gnu/packages/boost.scm (boost): Use it.
2015-07-10gnu: gettext: Update to 0.19.5.Mark H Weaver
* gnu/packages/patches/gettext-msgunfmt.patch: Remove file. * gnu-system.am (dist_patch_DATA): Remove it. * gnu/packages/gettext.scm (gnu-gettext): Update to 0.19.5. Remove patch.
2015-07-10gnu: coreutils: Update to 8.24.Mark H Weaver
* gnu/packages/patches/coreutils-dummy-man.patch: Remove file. * gnu-system.am (dist_patch_DATA): Remove it. * gnu/packages/base.scm (coreutils): Update to 8.24. Remove patch.
2015-07-08gnu: wpa-supplicant: Fix WPS and P2P NFC NDEF record payload length validation.Mark H Weaver
* gnu/packages/patches/wpa-supplicant-2015-5-fix.patch: New file. * gnu-system.am (dist_patch_DATA): Add it. * gnu/packages/admin.scm (wpa-supplicant-light)[source]: Add patch.
2015-07-08gnu: Add preseq.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (preseq): New variable. * gnu/packages/patches/preseq-1.0.2-install-to-PREFIX.patch: New file. * gnu/packages/patches/preseq-1.0.2-link-with-libbam.patch: New file. * gnu-system.am (dist_patch_DATA): Add them.
2015-07-07gnu: liba52: Build shared library.Mark H Weaver
* gnu/packages/patches/liba52-enable-pic.patch, gnu/packages/patches/liba52-link-with-libm.patch, gnu/packages/patches/liba52-set-soname.patch, gnu/packages/patches/liba52-use-mtune-not-mcpu.patch: New files. * gnu-system.am (dist_patch_DATA): Add them. * gnu/packages/video.scm (liba52)[source]: Add patches. [native-inputs]: Add autoconf, automake, and libtool. [arguments]: Add "--enable-shared" to configure-flags. Add 'bootstrap' phase.
2015-07-07gnu: icecat: Apply more libvpx-1.4 fixes.Mark H Weaver
This is a followup to commit c803ffcb3a9d5669bf5bae62b66fa058d697545c. * gnu/packages/patches/icecat-libvpx-1.4.patch: Augment existing patch to include fixes for content/media/encoder/VP8TrackEncoder.cpp.
2015-07-06gnu: icecat: Fix build against libvpx 1.4.Mark H Weaver
* gnu/packages/patches/icecat-libvpx-1.4.patch: New file. * gnu-system.am (dist_patch_DATA): Add it. * gnu/packages/gnuzilla.scm (icecat)[source]: Add patch.
2015-07-06gnu: libvpx: Update to 1.4.0.Mark H Weaver
* gnu/packages/patches/libvpx-fix-armhf-link.patch, gnu/packages/patches/libvpx-fix-ssse3-quantize.patch, gnu/packages/patches/libvpx-vp9-out-of-bounds-access.patch: Remove files. * gnu-system.am (dist_patch_DATA): Remove them. * gnu/packages/video.scm (libvpx): Update to 1.4.0. Remove patches. Update source URI.
2015-07-06gnu: libwmf: Fix CVE-2006-3376, CVE-2009-1364, CVE-2015-{0848,4588,4695,4696}.Mark H Weaver
* gnu/packages/patches/libwmf-CVE-2006-3376.patch, gnu/packages/patches/libwmf-CVE-2009-1364.patch, gnu/packages/patches/libwmf-CVE-2015-0848+4588+4695+4696.patch: New files. * gnu-system.am (dist_patch_DATA): Add them. * gnu/packages/image.scm (libwmf)[source]: Add patches.
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: 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.
2015-06-29gnu: 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: 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: 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: 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: 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 plink.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (plink): New variable. * gnu/packages/patches/plink-1.07-unclobber-i.patch: New file.
2015-06-21Merge branch 'master' into core-updatesMark H Weaver
2015-06-20gnu: gsl: Fix poly test on i686.Mark H Weaver
* gnu/packages/patches/gsl-poly-test-fix-pt1.patch, gnu/packages/patches/gsl-poly-test-fix-pt2.patch: New files. * gnu-system.am (dist_patch_DATA): Add them. * gnu/packages/maths.scm (gsl)[source]: Add patches.
2015-06-19gnu: mdadm: Add compilation fix for gcc-4.9.Mark H Weaver
* gnu/packages/patches/mdadm-gcc-4.9-fix.patch: New file. * gnu-system.am (dist_patch_DATA): Add it. * gnu/packages/linux.scm (mdadm): Add patch.
2015-06-19gnu: clang: Allow 'clang' to link executables.Ludovic Courtès
* gnu/packages/patches/clang-libc-search-path.patch: New file. * gnu-system.am (dist_patch_DATA): Add it. * gnu/packages/llvm.scm (clang-from-llvm)[source]: Use it. [inputs]: Add "gcc-lib". [arguments]. Add -DGCC_INSTALL_PREFIX and -DC_INCLUDE_DIRS to #:configure-flags. Add #:phases argument.
2015-06-19gnu: Make 'mount' interface in static Guile consistent with Guix API.David Thompson
Rather than expecting a pointer, the version of 'mount' in guile-static-stripped now takes a string for the 'options' argument, just like the 'mount' procedure in (guix build syscalls). * gnu/packages/patches/guile-linux-syscalls.patch (mount): Expect a string or #f for 'options' argument. * gnu/build/file-systems.scm (mount-file-system): Use new 'mount' interface.
2015-06-17gnu: cpio: Fix symlink-bad-length test.Mark H Weaver
* gnu/packages/patches/cpio-fix-symlink-bad-length-test.patch: New file. * gnu-system.am (dist_patch_DATA): Add it. * gnu/packages/cpio.scm (cpio): Add patch.
2015-06-16gnu: libtiff: Add fixes for several CVEs.Mark H Weaver
* gnu/packages/patches/libtiff-CVE-2012-4564.patch, gnu/packages/patches/libtiff-CVE-2013-1960.patch, gnu/packages/patches/libtiff-CVE-2013-1961.patch, gnu/packages/patches/libtiff-CVE-2013-4231.patch, gnu/packages/patches/libtiff-CVE-2013-4232.patch, gnu/packages/patches/libtiff-CVE-2013-4243.patch, gnu/packages/patches/libtiff-CVE-2013-4244.patch, gnu/packages/patches/libtiff-CVE-2014-8127-pt1.patch, gnu/packages/patches/libtiff-CVE-2014-8127-pt2.patch, gnu/packages/patches/libtiff-CVE-2014-8127-pt3.patch, gnu/packages/patches/libtiff-CVE-2014-8127-pt4.patch, gnu/packages/patches/libtiff-CVE-2014-8128-pt1.patch, gnu/packages/patches/libtiff-CVE-2014-8128-pt2.patch, gnu/packages/patches/libtiff-CVE-2014-8128-pt3.patch, gnu/packages/patches/libtiff-CVE-2014-8128-pt4.patch, gnu/packages/patches/libtiff-CVE-2014-8128-pt5.patch, gnu/packages/patches/libtiff-CVE-2014-8129.patch, gnu/packages/patches/libtiff-CVE-2014-9330.patch, gnu/packages/patches/libtiff-CVE-2014-9655.patch: New files. * gnu-system.am (dist_patch_DATA): Add them. * gnu/packages/image.scm (libtiff)[source]: Add patches.
2015-06-16Merge branch 'master' into core-updatesMark H Weaver
2015-06-16gnu: qemu: Add fixes for CVE-2015-{4037,4103,4104,4105,4106}.Mark H Weaver
* gnu/packages/patches/qemu-CVE-2015-4037.patch, gnu/packages/patches/qemu-CVE-2015-4103.patch, gnu/packages/patches/qemu-CVE-2015-4104.patch, gnu/packages/patches/qemu-CVE-2015-4105.patch, gnu/packages/patches/qemu-CVE-2015-4106-pt1.patch, gnu/packages/patches/qemu-CVE-2015-4106-pt2.patch, gnu/packages/patches/qemu-CVE-2015-4106-pt3.patch, gnu/packages/patches/qemu-CVE-2015-4106-pt4.patch, gnu/packages/patches/qemu-CVE-2015-4106-pt5.patch, gnu/packages/patches/qemu-CVE-2015-4106-pt6.patch, gnu/packages/patches/qemu-CVE-2015-4106-pt7.patch, gnu/packages/patches/qemu-CVE-2015-4106-pt8.patch: New files. * gnu-system.am (dist_patch_DATA): Add them. * gnu/packages/qemu.scm (qemu-headless)[source]: Add patches.
2015-06-16gnu: tar: Skip tests that rely on undefined unlinkat(2) behavior.Ludovic Courtès
Fixes <http://bugs.gnu.org/20597>. Reported by Andrew Patterson <ajpatter@uwaterloo.ca>. * gnu/packages/patches/tar-skip-unreliable-tests.patch: New file. * gnu/packages/base.scm (tar)[source](patches): Add it. * gnu-system.am (dist_patch_DATA): Add it.
2015-06-15gnu: gettext: Fix non-deterministic msgunfmt behavior.Ludovic Courtès
Suggested by Alírio Eyng <alirioeyng@gmail.com>. * gnu/packages/patches/gettext-msgunfmt.patch: New file. * gnu/packages/gettext.scm (gnu-gettext)[source]: Use it. * gnu-system.am (dist_patch_DATA): Add it.
2015-06-14Merge branch 'master' into core-updatesMark H Weaver
Conflicts: gnu/packages/commencement.scm gnu/packages/xml.scm
2015-06-13gnu: perl-net-ssleay: Disable test that fails with openssl-1.0.2b.Mark H Weaver
* gnu/packages/patches/perl-net-ssleay-disable-ede-test.patch: New file. * gnu-system.am (dist_patch_DATA): Add it. * gnu/packages/openssl.scm (perl-net-ssleay): Add patch.
2015-06-13gnu: python: Disable ssl test that fails with openssl-1.0.2b.Mark H Weaver
* gnu/packages/patches/python-disable-ssl-test.patch: New file. * gnu-system.am (dist_patch_DATA): Add it. * gnu/packages/python.scm (python): Add patch.
2015-06-13gnu: Add hydra.Eric Bavier
* gnu/packages/ci.scm: New file. * gnu/packages/patches/hydra-automake-1.15.patch, gnu/packages/patches/hydra-disable-darcs-test.patch: New files. * gnu-system.am (GNU_SYSTEM_MODULES): Add file. (dist_patch_DATA): Add patches.
2015-06-12gnu: patch: Set PATH_MAX for Hurd systems.Manolis Ragkousis
* gnu/packages/patches/patch-hurd-path-max.patch: New file. * gnu-system.am (dist_patch_DATA): Add it.
2015-06-10Merge branch 'master' into core-updatesMark H Weaver
2015-06-10gnu: qemu: Add fix for CVE-2015-3209.Mark H Weaver
* gnu/packages/patches/qemu-CVE-2015-3209.patch: New file. * gnu-system.am (dist_patch_DATA): Add it. * gnu/packages/qemu.scm (qemu): Add patch.
2015-06-09gnu: make-bootstrap: Adjust gawk patch to 4.1.3.Ludovic Courtès
* gnu/packages/patches/gawk-shell.patch: Update for gawk 4.1.3.
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