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2016-01-24Merge branch 'master' into core-updatesMark H Weaver
2016-01-23gnu: Add TopHat.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (tophat): New variable. * gnu/packages/patches/tophat-build-with-later-seqan.patch: New file. * gnu-system.am (dist_patch_DATA): Add it.
2016-01-21gnu: libtiff: Update to 4.0.6. Add fixes for CVE-2015-{8665,8683}.Mark H Weaver
* gnu/packages/patches/libtiff-CVE-2015-8665+CVE-2015-8683.patch, gnu/packages/patches/libtiff-oob-accesses-in-decode.patch, gnu/packages/patches/libtiff-oob-write-in-nextdecode.patch: New files. * gnu-system.am (dist_patch_DATA): Add them. * gnu/packages/image.scm (libtiff): Update to 4.0.6. [source]: Add patches.
2016-01-20gnu: Add perl-module-pluggable.Eric Bavier
This Perl module was moved out of Perl core in v5.19.0. * gnu/packages/perl.scm (perl-module-pluggable): New variable. * gnu/packages/patches/perl-module-pluggable-search.patch: New patch. * gnu-system.am (dist_patch_DATA): Add it.
2016-01-20gnu: linux-libre: Add fix for CVE-2016-0728.Mark H Weaver
* gnu/packages/patches/linux-libre-CVE-2016-0728.patch: New file. * gnu-system.am (dist_patch_DATA): Add it. * gnu/packages/linux.scm (linux-libre)[source]: Add patch.
2016-01-20gnu: arb: Correct patch.Andreas Enge
* gnu/packages/patches/arb-ldconfig.patch: Correct erroneously committed file. This is a follow-up to commit ffc8f345111566e8336cbb5a77a96973826165d8.
2016-01-20gnu: arb: Update to 2.8.1.Andreas Enge
* gnu/packages/algebra.scm (arb)[source]: Update to 2.8.1. Add patch. * gnu/packages/patches/arb-ldconfig.patch: New file. * gnu-system.am (dist_patch_DATA): Register patch.
2016-01-20gnu: doxygen: Update to 1.8.11.Andreas Enge
* gnu/packages/doxygen.scm (doxygen)[source]: Update to 1.8.11. Drop one patch. [build-system]: Switch to cmake-build-system, since gnu-build-system is not supported any more. [arguments]: Adapt. [native-inputs]: Drop unused perl. * gnu/packages/patches/doxygen-tmake.patch: Remove file. * gnu/packages/patches/doxygen-test.patch: Adapt. * gnu-system.am (dist_patch_DATA): Unregister patch.
2016-01-19Merge branch 'master' into core-updatesMark H Weaver
2016-01-15gnu: librsvg: Update to 2.40.13 [fixes CVE-2015-7558].Mark H Weaver
* gnu/packages/patches/librsvg-tests.patch: Delete file. * gnu-system.am (dist_patch_DATA): Remove it. * gnu/packages/gnome.scm (librsvg): Update to 2.40.13. [source]: Remove patch.
2016-01-15gnu: automake: Adjust to deal with Perl 5.22.Ludovic Courtès
Fixes <http://bugs.gnu.org/22375>. * gnu/packages/patches/automake-regexp-syntax.patch: New file. * gnu/packages/autotools.scm (automake)[source]: Use it. * gnu-system.am (dist_patch_DATA): Add it.
2016-01-14gnu: bowtie: Update to 2.2.6.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (bowtie): Update to 2.2.6. [source]: Remove patch; do not set CC and CPP variables. [inputs]: Add "tbb". [arguments]: Pass "prefix" and "WITH_TBB" make flags; remove custom "install" phase. * gnu/packages/patches/bowtie-fix-makefile.patch: Remove file. * gnu-system.am (dist_patch_DATA): Remove patch file.
2016-01-14gnu: gawk: Protect against random failures of the 'fts' test.Ludovic Courtès
* gnu/packages/patches/gawk-fts-test.patch: New file. * gnu/packages/gawk.scm (gawk)[source]: Use it. * gnu-system.am (dist_patch_DATA): Add it.
2016-01-13Merge branch 'master' into core-updatesLudovic Courtès
2016-01-12gnu: boost: Update to 1.60.0.Eric Bavier
* gnu/packages/boost.scm (boost): Update to 1.60.0. [source]: Remove patch. * gnu/packages/patches/boost-mips-avoid-m32.patch: Delete patch * gnu-system.am (dist_patch_DATA): Remove patch. Also fix dependent packages: * gnu/packages/patches/csound-header-ordering.patch: New patch. * gnu/packages/audio.scm (csound)[source]: Use it. [arguments]: Add 'set-flags phase. * gnu/packages/patches/libcmis-fix-test-onedrive.patch: New patch. * gnu/packages/libreoffice.scm (libcmis)[source]: Use it. (libreoffice)[arguments]: Add LDFLAGS to #:configure-flags. (librevenge)[inputs]: Move boost from here... [propogated-inputs]: to here. [arguments]: Add LDFLAGS to #:configure-flags. * gnu/packages/patches/openimageio-boost-1.60.patch: New patch. * gnu/packages/graphics.scm (openimageio): Use it. * gnu-system.am (dist_patch_DATA): Add patches.
2016-01-12gnu: perl: Add fix for CVE-2015-8607.Mark H Weaver
* gnu/packages/patches/perl-CVE-2015-8607.patch: New file. * gnu-system.am (dist_patch_DATA): Add it. * gnu/packages/perl.scm (perl)[source]: Add patch.
2016-01-12gnu: sudo: Add fix for CVE-2015-5602.Mark H Weaver
* gnu/packages/patches/sudo-CVE-2015-5602.patch: New file. * gnu-system.am (dist_patch_DATA): Add it. * gnu/packages/admin.scm (sudo)[source]: Add patch.
2016-01-11gnu: bedtools: Update to 2.25.0.Ben Woodcroft
* gnu/packages/bioinformatics.scm (bedtools): Update to 0.25.0. [source]: Remove patch merged upstream. [arguments]: Use 'modify-phases'. Remove 'patch-makefile-SHELL-definition' phase. * gnu/packages/patches/bedtools-32bit-compilation.patch: Remove file. * gnu-system.am (dist_patch_DATA): Remove it.
2016-01-08gnu: nss: Update to 3.21 [fixes CVE-2015-7575].Mark H Weaver
* gnu/packages/gnuzilla.scm (nss): Update to 3.21. [arguments]: In configure phase, setenv CC=gcc. * gnu/packages/patches/nss-pkgconfig.patch: Adapt to NSS 3.21.
2016-01-07gnu: w3m: Enable SSL, disable broken protocols and ciphers.Leo Famulari
Fixes <http://bugs.gnu.org/16791>. * gnu/packages/patches/w3m-force-ssl_verify_server-on.patch: New file. * gnu/packages/patches/w3m-disable-sslv2-and-sslv3.patch: New file. * gnu/packages/patches/w3m-disable-weak-ciphers.patch: New file. * gnu/packages/w3m.scm (w3m)[source]: Add patches. * gnu-system.am (dist_patch_DATA): Add the new files.
2016-01-07gnu: w3m: Update patch to use '-p1'.Leo Famulari
* gnu/packages/patches/w3m-fix-compile.patch: Rename this file... * gnu/packages/patches/w3m-libgc.patch: ...to this, and adjust patch prefix level to '-p1'. * gnu-system.am (dist_patch_DATA): Update patch name. * gnu/packages/w3m.scm (w3m)[source]: Update patch name. [source]: Drop patch flag -p0.
2016-01-07gnu: flex: Update to 2.6.0.Efraim Flashner
* gnu/packages/flex.scm (flex): Update to 2.6.0. [source]: Remove flex-bison-tests.patch. * gnu-system.am (dist_patch_DATA): Remove flex-bison-tests.patch. * gnu/packages/patches/flex-bison-tests.patch: Remove it.
2016-01-05gnu: gnutls: Update to 3.4.7.Efraim Flashner
* gnu/packages/tls.scm (gnutls): Update to 3.4.7. [source]: Remove gnutls-doc-fix.patch. [arguments]: Remove delete-prebuilt-unfixed-info-file phase. [native-inputs]: Remove texinfo. * gnu-system.am (dist_patch_DATA): Remove gnutls-doc-fix.patch
2016-01-05gnu: Add LDC.Roel Janssen
* gnu/packages/ldc.scm: New file. * gnu/packages/patches/ldc-disable-tests.patch: New file. * gnu-system.am (GNU_SYSTEM_MODULES): Add ldc.scm. (dist_patch_DATA): Add patch file.
2016-01-05gnu: python: Honor 'C_INCLUDE_PATH'.Ludovic Courtès
This is a followup to 009b53fd. * gnu/packages/patches/python-3-search-paths.patch: Check 'C_INCLUDE_PATH' instead of 'CPATH'. * gnu/packages/patches/python-2.7-search-paths.patch: Likewise.
2016-01-04gnu: gtk+: Add patch to support GUIX_GTK3_PATH.Ricardo Wurmus
* gnu/packages/patches/gtk3-respect-GUIX_GTK3_PATH: New file. * gnu-system.am (dist_patch_DATA): Add it. * gnu/packages/gtk.scm (gtk+) [source]: Add patch. [native-search-paths]: Add search path for GUIX_GTK3_PATH.
2016-01-04gnu: gtk+-2: Add patch to support GUIX_GTK2_PATH.Ricardo Wurmus
* gnu/packages/patches/gtk2-respect-GUIX_GTK2_PATH: New file. * gnu-system.am (dist_patch_DATA): Add it. * gnu/packages/gtk.scm (gtk+-2) [source]: Add patch. [native-search-paths]: Add search path for GUIX_GTK2_PATH.
2016-01-04gnu: julia: Update to 0.4.2.Ricardo Wurmus
* gnu/packages/patches/julia-0.3.10-fix-empty-array.patch: Remove file. * gnu-system.am (dist_patch_DATA): Remove it. * gnu/packages/julia.scm (julia): Update to 0.4.2. [arguments]: Remove phase "fix-building-with-mcjit-llvm"; replace phase "patch-include-path" with "fix-include-and-link-paths"; add phase "hardcode-paths"; add missing make-flags. [inputs]: Replace "pcre" with "pcre2"; replace "git" with "libgit2"; add "coreutils"; add "libuv-julia"; add "wget"; add "which". [native-inputs]: Remove "which".
2016-01-03Merge branch 'master' into core-updatesLudovic Courtès
2016-01-03gnu: grep: Skip timing-sensitive test.Ludovic Courtès
This avoids failures on loaded machines as seen at <http://hydra.gnu.org/build/906900/log/raw>. * gnu/packages/patches/grep-timing-sensitive-test.patch: New file. * gnu-system.am (dist_patch_DATA): Add it. * gnu/packages/base.scm (grep): Use it.
2016-01-02gnu: Add Asymptote.Eric Bavier
* gnu/packages/bdw-gc.scm (libgc-for-c++): New variable. * gnu/packages/plotutils.scm (asymptote): New variable. * gnu/packages/patches/asymptote-gsl2.patch: New file. * gnu-system.am (dist_patch_DATA): Add it.
2016-01-01gnu: findutils: Update to 4.6.0.Ludovic Courtès
* gnu/packages/patches/findutils-absolute-paths.patch: Remove. * gnu/packages/patches/findutils-test-xargs.patch: New file. * gnu-system.am (dist_patch_DATA): Adjust accordingly. * gnu/packages/base.scm (findutils): Update to 4.6.0. Remove 'findutils-absolute-paths.patch' and add 'findutils-test-xargs.patch'.
2015-12-29gnu: fuse: Update to 2.9.4.Leo Famulari
* gnu/packages/patches/fuse-CVE-2015-3202.patch: Delete file. * gnu-system.am (dist_patch_DATA): Remove it. * gnu/packages/linux.scm (fuse): Update to 2.9.4. [source]: Remove patch.
2015-12-23gnu: icecat: Update to 38.5.0-gnu1.Mark H Weaver
* gnu/packages/patches/icecat-CVE-2015-7201-pt1.patch, gnu/packages/patches/icecat-CVE-2015-7201-pt2.patch, gnu/packages/patches/icecat-CVE-2015-7201-pt3.patch, gnu/packages/patches/icecat-CVE-2015-7205.patch, gnu/packages/patches/icecat-CVE-2015-7210.patch, gnu/packages/patches/icecat-CVE-2015-7212.patch, gnu/packages/patches/icecat-CVE-2015-7213-pt1.patch, gnu/packages/patches/icecat-CVE-2015-7213-pt2.patch, gnu/packages/patches/icecat-CVE-2015-7214.patch, gnu/packages/patches/icecat-CVE-2015-7222-pt1.patch, gnu/packages/patches/icecat-CVE-2015-7222-pt2.patch, gnu/packages/patches/icecat-CVE-2015-7222-pt3.patch, gnu/packages/patches/icecat-freetype-2.6.patch: Delete files. * gnu-system.am (dist_patch_DATA): Remove them. * gnu/packages/gnuzilla.scm (icecat): Update to 38.5.0-gnu1. [source]: Remove patches.
2015-12-21gnu: grub: Add fix for CVE-2015-8730.Leo Famulari
* gnu/packages/patches/grub-CVE-2015-8370.patch: New file. * gnu-system.am (dist_patch_DATA): Register patch. * gnu/packages/grub.scm: Apply patch.
2015-12-18gnu: commencement: Use GMP 6.0.0a for bootstrapping.Ludovic Courtès
* gnu/packages/multiprecision.scm (gmp-6.0): New variable. * gnu/packages/commencement.scm (gcc-boot0, gcc-final): Use it. * gnu/packages/patches/gmp-arm-asm-nothumb.patch: New file, reinstated from before e414a7d. * gnu-system.am (dist_patch_DATA): Add it.
2015-12-17gnu: icecat: Add fixes for several security flaws.Mark H Weaver
* gnu/packages/patches/icecat-CVE-2015-7201-pt1.patch, gnu/packages/patches/icecat-CVE-2015-7201-pt2.patch, gnu/packages/patches/icecat-CVE-2015-7201-pt3.patch, gnu/packages/patches/icecat-CVE-2015-7205.patch, gnu/packages/patches/icecat-CVE-2015-7210.patch, gnu/packages/patches/icecat-CVE-2015-7212.patch, gnu/packages/patches/icecat-CVE-2015-7213-pt1.patch, gnu/packages/patches/icecat-CVE-2015-7213-pt2.patch, gnu/packages/patches/icecat-CVE-2015-7214.patch, gnu/packages/patches/icecat-CVE-2015-7222-pt1.patch, gnu/packages/patches/icecat-CVE-2015-7222-pt2.patch, gnu/packages/patches/icecat-CVE-2015-7222-pt3.patch: New files. * gnu-system.am (dist_patch_DATA): Add them. * gnu/packages/gnuzilla.scm (icecat)[source]: Add patches.
2015-12-15gnu: python-ipython: Patch 'ctypes' bug.Federico Beffa
* gnu/packages/patches/python-ipython-inputhook-ctype.patch: New patch. * gnu/packages/python.scm (python-ipython): Use it. * gnu-system.am (dist_patch_DATA): Add it.
2015-12-14gnu: bluez: Update to 5.36.Efraim Flashner
* gnu/packages/linux.scm (bluez): Update to 5.36. [source]: Remove patch. * gnu/packages/patches/bluez-tests.patch: Remove file. * gnu-system.am (dist_patch_DATA): Remove it.
2015-12-13gnu: perl: Build deterministically, and make byproducts deterministic.Ludovic Courtès
With this, a --rounds=2 build passes, and timestamps in POD files can be controlled with 'SOURCE_DATE_EPOCH'. * gnu/packages/patches/perl-deterministic-ordering.patch, gnu/packages/patches/perl-no-build-time.patch, gnu/packages/patches/perl-source-date-epoch.patch: New files. * gnu/packages/perl.scm (perl)[source]: Use them. * gnu-system.am (dist_patch_DATA): Add them.
2015-12-13gnu: perl: Update to 5.22.0.Ludovic Courtès
* gnu/packages/perl.scm (perl)[source]: Update to 5.22.0. Remove "perl-module-pluggable-search.patch" since Module::Pluggable appears to be gone. [arguments] <configure-phase>: Adjust Cwd.pm file name. Replace -std=c89 with -std=gnu89. * gnu/packages/commencement.scm (perl-boot0): Add 'disable-pthreads' phase. * gnu/packages/patches/perl-no-sys-dirs.patch: Update. * gnu/packages/patches/perl-module-pluggable-search.patch: Remove. * gnu-system.am (dist_patch_DATA): Adjust accordingly.
2015-12-12Merge branch 'master' into core-updatesLudovic Courtès
2015-12-09gnu: libarchive: Fix test failure on SELinux systems.Ludovic Courtès
Reported by Jan Synáček <jan.synacek@gmail.com> at <https://lists.gnu.org/archive/html/guix-devel/2015-11/msg00522.html>. * gnu/packages/patches/libarchive-bsdtar-test.patch: New file. * gnu/packages/backup.scm (libarchive)[source]: Use it. * gnu-system.am (dist_patch_DATA): Add it.
2015-12-07gnu: libxml2: Update to 2.9.3.Mark H Weaver
* gnu/packages/patches/libxml2-CVE-2015-1819.patch, gnu/packages/patches/libxml2-CVE-2015-7941-pt1.patch, gnu/packages/patches/libxml2-CVE-2015-7941-pt2.patch, gnu/packages/patches/libxml2-CVE-2015-7942-pt1.patch, gnu/packages/patches/libxml2-CVE-2015-7942-pt2.patch, gnu/packages/patches/libxml2-CVE-2015-8035.patch, gnu/packages/patches/libxml2-bug-737840.patch, gnu/packages/patches/libxml2-bug-738805.patch, gnu/packages/patches/libxml2-bug-746048.patch, gnu/packages/patches/libxml2-bug-747437.patch, gnu/packages/patches/libxml2-bug-751603.patch, gnu/packages/patches/libxml2-bug-751631.patch, gnu/packages/patches/libxml2-bug-754946.patch, gnu/packages/patches/libxml2-bug-754947.patch, gnu/packages/patches/libxml2-bug-755857.patch, gnu/packages/patches/libxml2-fix-catalog-corruption.patch, gnu/packages/patches/libxml2-id-attrs-in-xmlSetTreeDoc.patch, gnu/packages/patches/libxml2-node-sort-order-pt1.patch, gnu/packages/patches/libxml2-node-sort-order-pt2.patch: Delete files. * gnu-system.am (dist_patch_DATA): Remove them. * gnu/packages/xml.scm (libxml2): Update to 2.9.3. Remove patches.
2015-12-05gnu: Add python-configobj.Leo Famulari
* gnu/packages/python.scm (python-configobj, python2-configobj): New variables. * gnu/packages/patches/python-configobj-setuptools.patch: New file. * gnu-system.am (dist_patch_DATA): Add it.
2015-12-04gnu: icecat: Update to 38.4.0-gnu1.Mark H Weaver
* gnu/packages/patches/icecat-CVE-2015-4513-pt01.patch, gnu/packages/patches/icecat-CVE-2015-4513-pt02.patch, gnu/packages/patches/icecat-CVE-2015-4513-pt03.patch, gnu/packages/patches/icecat-CVE-2015-4513-pt04.patch, gnu/packages/patches/icecat-CVE-2015-4513-pt05.patch, gnu/packages/patches/icecat-CVE-2015-4513-pt06.patch, gnu/packages/patches/icecat-CVE-2015-4513-pt07.patch, gnu/packages/patches/icecat-CVE-2015-4513-pt08.patch, gnu/packages/patches/icecat-CVE-2015-4513-pt09.patch, gnu/packages/patches/icecat-CVE-2015-4513-pt10.patch, gnu/packages/patches/icecat-CVE-2015-4513-pt11.patch, gnu/packages/patches/icecat-CVE-2015-7188.patch, gnu/packages/patches/icecat-CVE-2015-7189.patch, gnu/packages/patches/icecat-CVE-2015-7193.patch, gnu/packages/patches/icecat-CVE-2015-7194.patch, gnu/packages/patches/icecat-CVE-2015-7196.patch, gnu/packages/patches/icecat-CVE-2015-7197.patch, gnu/packages/patches/icecat-CVE-2015-7198.patch, gnu/packages/patches/icecat-CVE-2015-7199.patch: Delete files. * gnu-system.am (dist_patch_DATA): Remove them. * gnu/packages/gnuzilla.scm (icecat): Update to 38.4.0-gnu1. Remove the obsolete patches.
2015-12-02gnu: gmp: Drop patch included in release 6.1.0.Andreas Enge
* gnu/packages/multiprecision.scm (gmp)[source]: Drop patch. * gnu/packages/patches/gmp-arm-asm-nothumb.patch: Remove patch. * gnu-system.am (dist_patch_DATA): Unregister patch.
2015-12-02gnu: python-matplotlib: Add 'TkAgg' backend and update to version '1.4.3'.Federico Beffa
* gnu/packages/python.scm (python-matplotlib, python2-matplotlib): Do it. * gnu/packages/patches/matplotlib-setupext-tk.patch: New file. * gnu-system.am (dist_patch_DATA): Add the new patch.
2015-11-29gnu: python: Make 'sys.version' deterministic.Ludovic Courtès
* gnu/packages/patches/python-2-deterministic-build-info.patch, gnu/packages/patches/python-3-deterministic-build-info.patch: New files. * gnu/packages/python.scm (python-2, python): Use them. * gnu-system.am (dist_patch_DATA): Add them.
2015-11-29gnu: python-2: Honor 'SOURCE_DATE_EPOCH'.Ludovic Courtès
* gnu/packages/patches/python-2.7-source-date-epoch.patch: New file. * gnu/packages/python.scm (python-2)[source]: Use it. [arguments]: Set SOURCE_DATE_EPOCH in 'patch-lib-shells' phase. * guix/build/python-build-system.scm (set-SOURCE-DATE-EPOCH): New procedure. (%standard-phases): Add it. * gnu-system.am (dist_patch_DATA): Add patch.
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