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2015-07-25gnu: bedtools: Add patch to fix compilation on 32 bit systems.Ben Woodcroft
* gnu/packages/patches/bedtools-32bit-compilation.patch: New file. * gnu/packages/bioinformatics.scm (bedtools)[source]: Add patch. * gnu-system.am (dist_patch_DATA): Register patch. Signed-off-by: Andreas Enge <andreas@enge.fr>
2015-07-24gnu: Add extra-cmake-modules.Andreas Enge
* gnu/packages/kde-frameworks.scm: New file. * gnu-system.am (GNU_SYSTEM_MODULES): Register it.
2015-07-24gnu: ripperX: Update to 2.8.0.Andreas Enge
* gnu/packages/mp3.scm (ripperx): Update to 2.8.0. Drop one patch and add another one. * gnu/packages/patches/ripperx-libm.patch: Remove file. * gnu/packages/patches/ripperx-missing-file.patch: New file. * gnu-system.am (dist_patch_DATA): Register one patch and unregister the other.
2015-07-22gnu: teckit: Update to 2.5.4.Andreas Enge
* gnu/packages/fontutils.scm (teckit): Update to 2.5.4. Drop patch. Use svn-fetch for download. [arguments]: Add phase to call autogen. [native-inputs]: New field. * gnu/packages/patches/teckit-cstdio.patch: Delete file. * gnu-system.am (dist_patch_DATA): Unregister patch.
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.
2015-07-20gnu: Add hoedown.David Thompson
* gnu/packages/markdown.scm: New file. * gnu-system.am (GNU_SYSTEM_MODULES): Add it.
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: Add lxappearance.Mathieu Lirzin
* gnu/packages/lxde.scm: New file. * gnu-system.am (GNU_SYSTEM_MODULES): Add it.
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
2015-07-14gnu: Add dunst.Alex Kost
* gnu/packages/dunst.scm: New file. * gnu-system.am (GNU_SYSTEM_MODULES): Add it.
2015-07-13gnu: Add rc.Jeff Mickey
* gnu/packages/rc.scm: New file. * gnu-system.am (GNU_SYSTEM_MODULES): Add it.
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.
2015-07-12gnu: Add skalibs.Claes Wallin
* gnu/package/skarnet.scm (skalibs): New file. * gnu-system.am (GNU_SYSTEM_MODULES): Add it. Signed-off-by: Ludovic Courtès <ludo@gnu.org>
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.
2015-07-09gnu: build: Add Linux container module.David Thompson
* gnu/build/linux-container.scm: New file. * gnu-system.am (GNU_SYSTEM_MODULES): Add it. * .dir-locals.el: Add Scheme indent rules for 'call-with-container', and 'container-excursion'. * tests/containers.scm: New file. * Makefile.am (SCM_TESTS): Add it.
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.
2015-07-06gnu: 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.
2015-07-05gnu: Move content of openssl module into tls module.Andreas Enge
* gnu/packages/openssl.scm (openssl, perl-net-ssleay): Move to... * gnu/packages/tls.scm: ...here. * gnu/packages/openssl.scm: Delete file. * gnu-system.am (GNU_SYSTEM_MODULES): Unregister deleted file. * gnu/packages/{admin.scm, bittorrent.scm, certs.scm, ci.scm, cyrus-sasl.scm, databases.scm, dns.scm, ebook.scm, enlightenment.scm, gnunet.scm, libreoffice.scm, links.scm, mail.scm, messaging.scm, networking.scm, ntp.scm, openldap.scm, package-management.scm, pdf.scm, python.scm, qt.scm, rdesktop.scm, rdf.scm, ruby.scm, ssh.scm, synergy.scm, tor.scm, version-control.scm, video.scm, vpn.scm, w3m.scm, web.scm, weechat.scm, xiph.scm}: Adapt module import.
2015-07-05gnu: Rename module gnutls to tls.Andreas Enge
* gnu/packages/gnutls.scm: Rename to... * gnu/packages/tls.scm: ... this. Change module name accordingly. * gnu/packages/{admin.scm, cups.scm, curl.scm, dc.scm, dns.scm, emacs.scm, ftp.scm, gnome.scm, gnunet.scm, gnupg.scm, gsasl.scm, lynx.scm, mail.scm, messaging.scm, package-management.scm, shishi.scm, task-management.scm, version-control.scm, video.scm, vpn.scm, webkit.scm, weechat.scm, wget.scm, wine.scm, xml.scm}: Adapt module import to new name. * gnu-system.am (GNU_SYSTEM_MODULES): Rename gnutls module to tls.
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.
2015-06-27gnu: Add pv.Claes Wallin
* gnu/package/pv.scm (pv): New file. * gnu-system.am (GNU_SYSTEM_MODULES): Add it. Signed-off-by: Alex Kost <alezost@gmail.com>
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.
2015-06-17gnu: 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.
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