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Author SHA1 Message Date
Ben Woodcroft b81cb1f2f3 gnu: bedtools: Add patch to fix compilation on 32 bit systems. 
* 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>
 2015-07-25 19:16:49 +02:00
Andreas Enge f272987aa2 gnu: Add extra-cmake-modules. 
* gnu/packages/kde-frameworks.scm: New file.
* gnu-system.am (GNU_SYSTEM_MODULES): Register it.
 2015-07-24 22:25:33 +02:00
Andreas Enge d0dfc06683 gnu: ripperX: Update to 2.8.0. 
* 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.
 2015-07-24 21:16:29 +02:00
Andreas Enge 1436c5c7e8 gnu: teckit: Update to 2.5.4. 
* 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.
 2015-07-22 19:29:17 +02:00
Ricardo Wurmus 5ff0edaee6 gnu: julia: Update to 0.3.10. 
* 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.
 2015-07-21 10:33:59 +02:00
Mark H Weaver c0eac5a862 gnu: libmad: Apply fixes for ARMv7 Thumb, etc. 
* 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.
 2015-07-21 02:05:20 -04:00
Mark H Weaver 4d85391059 gnu: tidy: Add fixes for CVE-2015-5522 and CVE-2015-5523. 
* 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.
 2015-07-20 23:33:41 -04:00
David Thompson 7782d3a6ff gnu: Add hoedown. 
* gnu/packages/markdown.scm: New file.
* gnu-system.am (GNU_SYSTEM_MODULES): Add it.
 2015-07-20 09:16:58 -04:00
Mark H Weaver 1b4e48d498 Merge branch 'master' into core-updates 2015-07-19 18:12:34 -04:00
Ludovic Courtès 2e839545c7 gnu: ninja: Do not report files with mtime = 0 as missing. 
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.
 2015-07-18 23:27:18 +02:00
Ludovic Courtès 82700f0fb3 gnu: crda: Add forgotten patch. 
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.
 2015-07-18 17:15:03 +02:00
Mark H Weaver 2fdc682742 gnu: icecat: Add patch to adapt to freetype 2.6. 
* 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.
 2015-07-17 01:42:35 -04:00
Mathieu Lirzin 889e57f4d8 gnu: Add lxappearance. 
* gnu/packages/lxde.scm: New file.
* gnu-system.am (GNU_SYSTEM_MODULES): Add it.
 2015-07-16 11:56:04 +02:00
Mark H Weaver 385ae063c9 gnu: unzip: Fix CVE-2014-9636 and some other bugs. 
* 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.
 2015-07-15 23:02:27 -04:00
Mark H Weaver 368474150b Merge branch 'master' into core-updates 2015-07-15 16:11:13 -04:00
Mark H Weaver b76c415253 gnu: icecat: Update to 31.8.0-gnu1. 
* 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.
 2015-07-15 15:43:23 -04:00
Mark H Weaver 35995769b5 Merge branch 'master' into core-updates 2015-07-15 15:10:32 -04:00
Alex Kost b0ded08ff7 gnu: Add dunst. 
* gnu/packages/dunst.scm: New file.
* gnu-system.am (GNU_SYSTEM_MODULES): Add it.
 2015-07-14 18:46:18 +03:00
Jeff Mickey 0577ddc45d gnu: Add rc. 
* gnu/packages/rc.scm: New file.
* gnu-system.am (GNU_SYSTEM_MODULES): Add it.
 2015-07-13 19:33:17 -04:00
Andreas Enge 8d662672fc gnu: boost: Patch to avoid -m32 flag on mips. 
* 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.
 2015-07-13 14:53:38 -04:00
Claes Wallin 4e2bd414f8 gnu: Add skalibs. 
* gnu/package/skarnet.scm (skalibs): New file.
* gnu-system.am (GNU_SYSTEM_MODULES): Add it.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2015-07-12 22:00:40 +02:00
Mark H Weaver 79e09ef2fd gnu: gettext: Update to 0.19.5. 
* 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.
 2015-07-10 23:47:07 -04:00
Mark H Weaver c2ba49ef8e gnu: coreutils: Update to 8.24. 
* 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.
 2015-07-10 23:47:07 -04:00
David Thompson c1f6a0c2ed gnu: build: Add Linux container module. 
* 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.
 2015-07-09 08:23:03 -04:00
Mark H Weaver 9fb00f383d gnu: wpa-supplicant: Fix WPS and P2P NFC NDEF record payload length validation. 
* 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.
 2015-07-08 18:27:37 -04:00
Ricardo Wurmus 56e373ef75 gnu: Add preseq. 
* 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.
 2015-07-08 17:05:00 +02:00
Mark H Weaver 23da88f61e gnu: liba52: Build shared library. 
* 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.
 2015-07-07 10:52:04 -04:00
Mark H Weaver c803ffcb3a gnu: icecat: Fix build against libvpx 1.4. 
* 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.
 2015-07-06 23:01:56 -04:00
Mark H Weaver 723e886656 gnu: libvpx: Update to 1.4.0. 
* 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.
 2015-07-06 21:17:05 -04:00
Mark H Weaver 9ed5486439 gnu: libwmf: Fix CVE-2006-3376, CVE-2009-1364, CVE-2015-{0848,4588,4695,4696}. 
* 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.
 2015-07-06 20:04:50 -04:00
Andreas Enge cc2b77dfc7 gnu: Move content of openssl module into tls module. 
* 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.
 2015-07-05 18:27:24 +02:00
Andreas Enge a7fd7b68a6 gnu: Rename module gnutls to tls. 
* 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.
 2015-07-05 17:09:42 +02:00
Mark H Weaver 4463c0d216 gnu: icecat: Fix CVE-2015-{2722,2724,2728,2733,2735,2736,2738,2739,2740,2743}. 
* 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.
 2015-07-04 05:44:10 -04:00
Ludovic Courtès b5b08878b6 gnu: mutt: Don't retain reference to GCC. 
* 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.
 2015-07-03 15:28:06 +02:00
Eric Bavier a17d45641b gnu: Add deal.II. 
* 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.
 2015-06-29 15:34:36 -05:00
Eric Bavier 9a899cceab gnu: petsc: Upgrade to 3.6.0. 
* 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.
 2015-06-29 15:34:36 -05:00
Eric Bavier cec86422b7 gnu: Add MUMPS. 
* 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.
 2015-06-29 15:34:36 -05:00
Eric Bavier 6c7985408f gnu: Update scotch to 6.0.4. 
* 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.
 2015-06-29 15:34:36 -05:00
Eric Bavier ce7d9c989d gnu: hwloc: Upgrade to 1.10.1. 
* 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.
 2015-06-29 15:34:36 -05:00
Ricardo Wurmus 74e03fccd3 gnu: r: Update to 3.2.1. 
* 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.
 2015-06-29 16:13:28 +02:00
Claes Wallin 60def646bb gnu: Add pv. 
* gnu/package/pv.scm (pv): New file.
 * gnu-system.am (GNU_SYSTEM_MODULES): Add it.

Signed-off-by: Alex Kost <alezost@gmail.com>
 2015-06-27 17:27:49 +03:00
Mark H Weaver bf76d98789 Merge branch 'master' into core-updates 2015-06-21 14:30:22 -04:00
Mark H Weaver 180a93c72a gnu: gsl: Fix poly test on i686. 
* 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.
 2015-06-20 01:38:56 -04:00
Mark H Weaver 9a6953d28a gnu: mdadm: Add compilation fix for gcc-4.9. 
* 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.
 2015-06-19 22:42:12 -04:00
Ludovic Courtès fd6ae1b983 gnu: clang: Allow 'clang' to link executables. 
* 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.
 2015-06-19 17:23:48 +02:00
Mark H Weaver 9ae1e92071 gnu: cpio: Fix symlink-bad-length test. 
* 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.
 2015-06-17 23:19:02 -04:00
Mark H Weaver 8e28d22c91 gnu: libtiff: Add fixes for several CVEs. 
* 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.
 2015-06-16 01:02:01 -04:00
Mark H Weaver 7d02724b7b Merge branch 'master' into core-updates 2015-06-16 01:01:54 -04:00
Mark H Weaver fef3cfaaab gnu: qemu: Add fixes for CVE-2015-{4037,4103,4104,4105,4106}. 
* 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.
 2015-06-16 00:29:28 -04:00
Ludovic Courtès d3b4c1358c gnu: tar: Skip tests that rely on undefined unlinkat(2) behavior. 
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.
 2015-06-16 00:27:27 +02:00