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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.
2016-01-20gnu: Add NQC.Eric Bavier
* gnu/packages/lego.scm: New file. * gnu-system.am (GNU_SYSTEM_MODULES): 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: 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.
2016-01-15gnu: Add radicale.Leo Famulari
* gnu/packages/dav.scm (radicale): New file. * gnu-system.am (GNU_SYSTEM_MODULES): Add it.
2016-01-14gnu: Add python-docker-py.David Thompson
* gnu/packages/docker.scm: New file. * Makefile.am (GNU_SYSTEM_MODULES): 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.
2016-01-12gnu: 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: 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.
2016-01-07gnu: 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.
2016-01-05gnu: 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.
2016-01-04gnu: 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".
2016-01-02gnu: 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.
2015-12-30gnu: Move cursynth to (gnu packages music).Leo Famulari
* gnu/packages/cursynth.scm: Remove. * gnu/packages/music.scm (cursynth): New variable, from cursynth.scm. * gnu-system.am (GNU_SYSTEM_MODULES): Remove cursynth.scm.
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: Add dovecot serviceAndy Wingo
* gnu/services/mail.scm: New file. (&dovecot-configuration-error, dovecot-configuration-error?) (dovecot-service, dovecot-configuration, dict-configuration) (passdb-configuration, userdb-configuration) (unix-listener-configuration, fifo-listener-configuration) (inet-listener-configuration, service-configuration) (protocol-configuration, plugin-configuration, mailbox-configuration) (namespace-configuration, opaque-dovecot-configuration): New public variables. * gnu-system.am (GNU_SYSTEM_MODULES): Add (gnu services mail). * doc/guix.texi (Mail Services): New node.
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.
2015-12-11gnu: Move sparsehash to datastructures module.Ricardo Wurmus
* gnu/packages/crypto.scm (sparsehash): Move variable to... * gnu/packages/datastructures.scm: ...new file. * gnu-system.am (GNU_SYSTEM_MODULES): 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: 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.
2015-11-30gnu: Add cereal.Ricardo Wurmus
* gnu/packages/serialization.scm: New file. * gnu-system.am (GNU_SYSTEM_MODULES): Add it.
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.
2015-11-29gnu: tcl: Produce 'tclIndex' files deterministically.Ludovic Courtès
* gnu/packages/patches/tcl-mkindex-deterministic.patch: New patch. * gnu/packages/tcl.scm (tcl)[source]: Use it. * gnu-system.am (dist_patch_DATA): Add it.
2015-11-29tk: Hardcode path to TK_LIBRARY.宋文武
Fixes <http://bugs.gnu.org/20889>. * gnu/packages/patches/tk-find-library.patch: New patch. * gnu-system.am (dist_patch_DATA): Add it. * gnu/packages/tcl.scm (tk)[source]: Add patch.
2015-11-29gnu: weechat: Dynamically link against libpython2.7.so.Ludovic Courtès
* gnu/packages/patches/weechat-python.patch: New file. * gnu-system.am (dist_patch_DATA): Add it. * gnu/packages/weechat.scm (weechat)[source]: Use it.
2015-11-28gnu: jasper: Patch CVE-2008-3522.Ludovic Courtès
* gnu/packages/patches/jasper-CVE-2008-3522.patch: New file. * gnu/packages/image.scm (jasper)[source]: Use it. * gnu-system.am (dist_patch_DATA): Add it.
2015-11-25gnu: Add kodi.David Thompson
* gnu/packages/kodi.scm: New file. * gnu-system.am (GNU_SYSTEM_MODULES): Add it.
2015-11-25gnu: Add tinyxml.David Thompson
* gnu/packages/xml.scm (tinyxml): New variable. * gnu/packages/patches/tinyxml-use-stl.patch: New file. * gnu-system.am (dist_patch_DATA): Add it.
2015-11-25gnu: Add Ragel.Ricardo Wurmus
* gnu/packages/ragel.scm: New file. * gnu-system.am (GNU_SYSTEM_MODULES): Add it.
2015-11-25gnu: dico: Sort entries in .a files deterministically.Ludovic Courtès
* gnu/packages/patches/dico-libtool-deterministic.patch: New file. * gnu/packages/dico.scm (dico)[source]: Use it. [arguments]: Add #:make-flags. * gnu-system.am (dist_patch_DATA): Add the patch.
2015-11-24gnu: Add GNU Dico.Ludovic Courtès
* gnu/packages/dico.scm: New file. * gnu-system.am (GNU_SYSTEM_MODULES): Add it.
2015-11-24build: Add rsem patch to the distribution.Ludovic Courtès
This file was added in commit 66e3eff1. * gnu-system.am (dist_patch_DATA): Add rsem-makefile.patch.
2015-11-20gnu: Add Synfig.Ricardo Wurmus
* gnu/packages/animation.scm (synfig): New variable. * gnu/packages/patches/synfig-build-fix.patch: New file. * gnu-system.am (dist_patch_DATA): Add it.
2015-11-20gnu: Add ETL.Ricardo Wurmus
* gnu/packages/animation.scm: New file. * gnu-system.am (GNU_SYSTEM_MODULES): Add it.
2015-11-20gnu: hwloc: Update to 1.11.1.Eric Bavier
* gnu/packages/mpi.scm (hwloc): Update to 1.11.1. [source]: Remove patch. * gnu/packages/patches/hwloc-gather-topology-lstopo.patch: Delete it. * gnu-system.am (dist_patch_DATA): Remove it.
2015-11-20gnu: guitarix: Update to 0.34.0.Ricardo Wurmus
* gnu/packages/audio.scm (guitarix): Update to 0.34.0. [source]: Remove patch. [inputs]: Add webkitgtk/gtk+-2. * gnu/packages/patches/guitarix-c++11: Remove file. * gnu-system.am (dist_patch_DATA): Remove it.
2015-11-20gnu: preseq: Update to 2.0.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (preseq): Update to 2.0. [source]: Add file-name field, remove patches. [arguments]: Remove unused build phases, add make flags. [inputs]: Add smithlab-cpp. * gnu/packages/patches/preseq-1.0.2-link-with-libbam.patch: Remove file. * gnu/packages/patches/preseq-1.0.2-install-to-PREFIX.patch: Remove file. * gnu-system.am (dist_patch_DATA): Remove them.
2015-11-18gnu: libsndfile: Add fixes for CVE-2014-9496 and CVE-2015-7805.Mark H Weaver
* gnu/packages/patches/libsndfile-CVE-2014-9496.patch, gnu/packages/patches/libsndfile-CVE-2015-7805.patch: New files. * gnu-system.am (dist_patch_DATA): Add them. * gnu/packages/pulseaudio.scm (libsndfile)[source]: Add patches.
2015-11-18gnu: libxslt: Add fix for CVE-2015-7995.Mark H Weaver
* gnu/packages/patches/libxslt-CVE-2015-7995.patch: New file. * gnu-system.am (dist_patch_DATA): Add it. * gnu/packages/xml.scm (libxslt)[source]: Add patch.
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