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2016-02-15gnu: Add slurm....* gnu/packages/parallel.scm (slurm): New variable. * gnu/packages/patches/slurm-configure-remove-nonfree-contribs.patch: New file. * gnu-system.am (dist_patch_DATA): Add it. * gnu/packages/parallel.scm: Introduce license name space. Co-authored-by: Andreas Enge <andreas@enge.fr> Pjotr Prins
2016-02-15gnu: libsndfile: Update to 1.0.26 [with follow-up fix CVE-2015-7805]....Note: The previous fix for CVE-2015-7805 was incomplete. * gnu/packages/patches/libsndfile-CVE-2014-9496.patch, gnu/packages/patches/libsndfile-CVE-2015-7805.patch: Delete files. * gnu-system.am (dist_patch_DATA): Remove them. * gnu/packages/pulseaudio.scm (libsndfile): Update to 1.0.26. [source]: Remove patches. Mark H Weaver
2016-02-13gnu: Add ocaml-findlib....* gnu/packages/ocaml.scm (ocaml-findlib): New variable. * gnu/packages/patches/ocaml-findlib-make-install.patch: New file. * gnu-system.am (dist_patch_DATA): Register it. Jan Nieuwenhuizen
2016-02-12gnu: gnupg: Add upstream fix for test failures on x86_64....Fixes <https://debbugs.gnu.org/22558>. * gnu/packages/patches/gnupg-simple-query-ignore-status-messages.patch: New file. * gnu-system.am (dist_patch_DATA): Add it. * gnu/packages/gnupg.scm (gnupg)[source]: Add patch. Mark H Weaver
2016-02-12gnu: Add tclxml....* gnu/packages/patches/tclxml-3.2-install.patch: New file. * gnu-system.am (dist_patch_DATA): Add it. * gnu/packages/tcl.scm (tclxml): New variable. Signed-off-by: Leo Famulari <leo@famulari.name> Jan Nieuwenhuizen
2016-02-11gnu: icecat: Update bundled graphite2 to 1.3.5 for security fixes....* gnu/packages/patches/icecat-update-graphite2.patch: New file. * gnu-system.am (dist_patch_DATA): Add it. * gnu/packages/gnuzilla.scm (icecat)[source]: Add patch. Add TODO comment about using the system graphite2 in the future. Mark H Weaver
2016-02-10gnu: mit-krb5: Update to 1.13.3; add fixes for CVE-2015-{8629,8630,8631}....* gnu/packages/patches/mit-krb5-CVE-2015-2695-pt1.patch, gnu/packages/patches/mit-krb5-CVE-2015-2695-pt2.patch, gnu/packages/patches/mit-krb5-CVE-2015-2696.patch, gnu/packages/patches/mit-krb5-CVE-2015-2697.patch, gnu/packages/patches/mit-krb5-CVE-2015-2698-pt1.patch, gnu/packages/patches/mit-krb5-CVE-2015-2698-pt2.patch: Delete files. * gnu/packages/patches/mit-krb5-CVE-2015-8629.patch, gnu/packages/patches/mit-krb5-CVE-2015-8630.patch, gnu/packages/patches/mit-krb5-CVE-2015-8631.patch, gnu/packages/patches/mit-krb5-init-context-null-spnego.patch: New files. * gnu-system.am (dist_patch_DATA): Adjust accordingly. * gnu/packages/mit-krb5.scm (mit-krb5): Update to 1.13.3. [source]: Update URI to download conventional .tar.gz file. Add patches. [native-inputs]: Remove old patches-as-inputs. [arguments]: Remove hacks needed to cope with the older unconventional tarball that contained an inner source tarball and signature: Remove #:modules argument, and the custom 'unpack' and 'apply-patches' phases. Mark H Weaver
2016-02-06gnu: xdotools: Update to 3.20150503.1...* gnu/packages/xdisorg.scm (xdotools): Upgrade to 3.20150503.1. * gnu/packages/patches/xdotool-fix-makefile.patch: New file. * gnu-system.am (dist_patch_DATA): Add it. Christopher Allan Webber
2016-02-06gnu: Add python-pygpgme...* gnu/packages/gnupg.scm (python-pygpgme, python2-pygpgme): New variables. * gnu/packages/patches/pygpgme-disable-problematic-tests.patch: New file. * gnu-system.am (dist_patch_DATA): Add it. Christopher Allan Webber
2016-02-06gnu: icecat: Re-enable the Ephemeral Diffie-Hellman cipher suites....* gnu/packages/patches/icecat-re-enable-DHE-cipher-suites.patch: New file. * gnu-system.am (dist_patch_DATA): Add it. * gnu/packages/gnuzilla.scm (icecat)[source]: Add patch. Mark H Weaver
2016-02-05gnu: icecat: Update to 38.6.0-gnu1....* gnu/packages/patches/icecat-bug-1146335-pt1.patch, gnu/packages/patches/icecat-bug-1146335-pt2.patch, gnu/packages/patches/icecat-limit-max-buffers-size-for-ANGLE.patch, gnu/packages/patches/icecat-CVE-2016-1930-pt01.patch, gnu/packages/patches/icecat-CVE-2016-1930-pt02.patch, gnu/packages/patches/icecat-CVE-2016-1930-pt03.patch, gnu/packages/patches/icecat-CVE-2016-1930-pt04.patch, gnu/packages/patches/icecat-CVE-2016-1930-pt05.patch, gnu/packages/patches/icecat-CVE-2016-1930-pt06.patch, gnu/packages/patches/icecat-CVE-2016-1930-pt07.patch, gnu/packages/patches/icecat-CVE-2016-1930-pt08.patch, gnu/packages/patches/icecat-CVE-2016-1930-pt09.patch, gnu/packages/patches/icecat-CVE-2016-1930-pt10.patch, gnu/packages/patches/icecat-CVE-2016-1930-pt11.patch, gnu/packages/patches/icecat-CVE-2016-1930-pt12.patch, gnu/packages/patches/icecat-CVE-2016-1930-pt13.patch, gnu/packages/patches/icecat-CVE-2016-1930-pt14.patch, gnu/packages/patches/icecat-CVE-2016-1930-pt15.patch, gnu/packages/patches/icecat-CVE-2016-1935.patch: Delete files. * gnu-system.am (dist_patch_DATA): Remove them. * gnu/packages/gnuzilla.scm (icecat): Update to 38.6.0-gnu1. [source]: Remove patches. Mark H Weaver
2016-02-04gnu: jasper: Add fixes for several security flaws....* gnu/packages/patches/jasper-CVE-2007-2721.patch, gnu/packages/patches/jasper-CVE-2008-3520.patch, gnu/packages/patches/jasper-CVE-2011-4516-and-CVE-2011-4517.patch, gnu/packages/patches/jasper-CVE-2014-8137.patch, gnu/packages/patches/jasper-CVE-2014-8138.patch, gnu/packages/patches/jasper-CVE-2014-8157.patch, gnu/packages/patches/jasper-CVE-2014-8158.patch, gnu/packages/patches/jasper-CVE-2014-9029.patch, gnu/packages/patches/jasper-CVE-2016-1867.patch: New files. * gnu-system.am (dist_patch_DATA): Add them. * gnu/packages/image.scm (jasper)[source]: Add patches. Leo Famulari
2016-02-04gnu: perl-io-socket-ssl: Add workaround for OpenSSL-1.0.2f....* gnu/packages/patches/perl-io-socket-ssl-openssl-1.0.2f-fix.patch: New file. * gnu-system.am (dist_patch_DATA): Add it. * gnu/packages/web.scm (perl-io-socket-ssl)[source]: Add patch. Mark H Weaver
2016-02-03gnu: Add emacs-constants....* gnu/packages/emacs.scm (emacs-constants): New variable. * gnu/packages/patches/emacs-constants-lisp-like.patch: New patch. * gnu-system.am (dist_patch_DATA): Add it. Federico Beffa
2016-02-03gnu: Add emacs-scheme-complete....* gnu/packages/emacs.scm (emacs-scheme-complete): New variable. * gnu/packages/patches/emacs-scheme-complete-scheme-r5rs-info.patch: New patch. * gnu-system.am (dist_patch_DATA): Add the new patch. Federico Beffa
2016-02-03gnu: qemu: Update to 2.5.0; add fixes for security flaws....* gnu/packages/patches/qemu-CVE-2015-6855.patch: Delete file. * gnu/packages/patches/qemu-virtio-9p-use-accessor-to-get-thread-pool.patch, gnu/packages/patches/qemu-CVE-2015-8558.patch, gnu/packages/patches/qemu-CVE-2015-8567.patch, gnu/packages/patches/qemu-CVE-2015-8613.patch, gnu/packages/patches/qemu-CVE-2015-8701.patch, gnu/packages/patches/qemu-CVE-2015-8743.patch, gnu/packages/patches/qemu-CVE-2016-1568.patch, gnu/packages/patches/qemu-CVE-2016-1922.patch: New files. * gnu-system.am (dist_patch_DATA): Remove 'qemu-CVE-2015-6855.patch'; add the new patches. * gnu/packages/qemu.scm (qemu): Update to 2.5.0. [source]: Remove old patches and add new ones. [arguments]: Add 'disable-test-qga' phase. (%glib-memory-vtable-patch, %glib-duplicate-test-patch): Remove variables. Mark H Weaver
2016-02-01gnu: linux-libre: Update to 4.4.1....* gnu/packages/patches/linux-libre-CVE-2016-0728.patch: Delete file. * gnu-system.am (dist_patch_DATA): Remove it. * gnu/packages/linux.scm (linux-libre): Update to 4.4.1. [source]: Remove patch. Mark H Weaver
2016-01-31gnu: Add pinball....* gnu/packages/games.scm (pinball): New variable. * gnu/packages/patches/pinball-const-fix.patch, gnu/packages/patches/pinball-cstddef.patch, gnu/packages/patches/pinball-missing-separators.patch, gnu/packages/patches/pinball-src-deps.patch, gnu/packages/patches/pinball-system-ltdl.patch: New patches. * gnu-system.am (dist_patch_DATA): Add them. Eric Bavier
2016-01-31gnu: perl-tk: Update to 804.033....* gnu/packages/tcl.scm (perl-tk): Update to 804.033. [source]: Remove patch. * gnu/packages/patches/perl-tk-x11-discover.patch: Remove file. * gnu-system.am (dist_patch_DATA): Remove patch. Efraim Flashner
2016-01-28gnu: icecat: Add fixes for CVE-2016-{1930,1935} and other bugs....* gnu/packages/patches/icecat-CVE-2016-1930-pt01.patch, gnu/packages/patches/icecat-CVE-2016-1930-pt02.patch, gnu/packages/patches/icecat-CVE-2016-1930-pt03.patch, gnu/packages/patches/icecat-CVE-2016-1930-pt04.patch, gnu/packages/patches/icecat-CVE-2016-1930-pt05.patch, gnu/packages/patches/icecat-CVE-2016-1930-pt06.patch, gnu/packages/patches/icecat-CVE-2016-1930-pt07.patch, gnu/packages/patches/icecat-CVE-2016-1930-pt08.patch, gnu/packages/patches/icecat-CVE-2016-1930-pt09.patch, gnu/packages/patches/icecat-CVE-2016-1930-pt10.patch, gnu/packages/patches/icecat-CVE-2016-1930-pt11.patch, gnu/packages/patches/icecat-CVE-2016-1930-pt12.patch, gnu/packages/patches/icecat-CVE-2016-1930-pt13.patch, gnu/packages/patches/icecat-CVE-2016-1930-pt14.patch, gnu/packages/patches/icecat-CVE-2016-1930-pt15.patch, gnu/packages/patches/icecat-CVE-2016-1935.patch, gnu/packages/patches/icecat-bug-1146335-pt1.patch, gnu/packages/patches/icecat-bug-1146335-pt2.patch, gnu/packages/patches/icecat-limit-max-buffers-size-for-ANGLE.patch: New files. * gnu-system.am (dist_patch_DATA): Add them. * gnu/packages/gnuzilla.scm (icecat)[source]: Add patches. Mark H Weaver
2016-01-24Merge branch 'master' into core-updatesMark H Weaver
2016-01-23gnu: Add TopHat....* 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. Ricardo Wurmus
2016-01-21gnu: libtiff: Update to 4.0.6. Add fixes for CVE-2015-{8665,8683}....* 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. Mark H Weaver
2016-01-20gnu: Add perl-module-pluggable....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. Eric Bavier
2016-01-20gnu: linux-libre: Add fix for CVE-2016-0728....* 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. Mark H Weaver
2016-01-20gnu: arb: Correct patch....* gnu/packages/patches/arb-ldconfig.patch: Correct erroneously committed file. This is a follow-up to commit ffc8f345111566e8336cbb5a77a96973826165d8. Andreas Enge
2016-01-20gnu: arb: Update to 2.8.1....* 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. Andreas Enge
2016-01-20gnu: doxygen: Update to 1.8.11....* 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. Andreas Enge
2016-01-19Merge branch 'master' into core-updatesMark H Weaver
2016-01-15gnu: librsvg: Update to 2.40.13 [fixes CVE-2015-7558]....* 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. Mark H Weaver
2016-01-15gnu: automake: Adjust to deal with Perl 5.22....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. Ludovic Courtès
2016-01-14gnu: bowtie: Update to 2.2.6....* 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. Ricardo Wurmus
2016-01-14gnu: gawk: Protect against random failures of the 'fts' test....* 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. Ludovic Courtès
2016-01-13Merge branch 'master' into core-updatesLudovic Courtès
2016-01-12gnu: boost: Update to 1.60.0....* 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. Eric Bavier
2016-01-12gnu: perl: Add fix for CVE-2015-8607....* 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. Mark H Weaver
2016-01-12gnu: sudo: Add fix for CVE-2015-5602....* 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. Mark H Weaver
2016-01-11gnu: bedtools: Update to 2.25.0....* 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. Ben Woodcroft
2016-01-08gnu: nss: Update to 3.21 [fixes CVE-2015-7575]....* 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. Mark H Weaver
2016-01-07gnu: w3m: Enable SSL, disable broken protocols and ciphers....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. Leo Famulari
2016-01-07gnu: w3m: Update patch to use '-p1'....* 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. Leo Famulari
2016-01-07gnu: flex: Update to 2.6.0....* 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. Efraim Flashner
2016-01-05gnu: gnutls: Update to 3.4.7....* 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 Efraim Flashner
2016-01-05gnu: Add LDC....* 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. Roel Janssen
2016-01-05gnu: python: Honor 'C_INCLUDE_PATH'....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. Ludovic Courtès
2016-01-04gnu: gtk+: Add patch to support GUIX_GTK3_PATH....* 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. Ricardo Wurmus
2016-01-04gnu: gtk+-2: Add patch to support GUIX_GTK2_PATH....* 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. Ricardo Wurmus
2016-01-04gnu: julia: Update to 0.4.2....* 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". Ricardo Wurmus
2016-01-03Merge branch 'master' into core-updatesLudovic Courtès
2016-01-03gnu: grep: Skip timing-sensitive test....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. Ludovic Courtès
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