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2017-04-30gnu: glibc/linux: Fix build of glibc-intermediate.Ricardo Wurmus
This is a follow-up to commit b2fd8f63679aa4f244c36fdca62f23c00b8eded9. * gnu/packages/base.scm (glibc/linux)[arguments]: Take patch from either native-inputs or just inputs; fix syntax error; report errors on patch failure.
2017-04-30gnu: femtolisp: Remove aarch64-linux from supported-architectures.Efraim Flashner
* gnu/packages/lisp.scm (femtolisp)[supported-systems]: Remove aarch64-linux from supported-systems.
2017-04-30gnu: Add netcdf-fortran.Thomas Danckaert
* gnu/packages/maths.scm (netcdf-fortran): New variable.
2017-04-30gnu: jemalloc: Disable transparent huge pages on non-Intel systems.Efraim Flashner
* gnu/packages/jemalloc.scm (jemalloc)[arguments]: On non-Intel systems add '--disable-thp' to #:configure-flags. Adjust #:phases to remove offending test which incorrectly tests transparent huge pages.
2017-04-29python-sphinxcontrib-programoutput: Update to 0.10.Christopher Allan Webber
* gnu/packages/python.scm (python-sphinxcontrib-programoutput): Update to 0.10.
2017-04-29gnu: xapian: Update to 1.4.4.Marius Bakke
* gnu/packages/search.scm (xapian): Update to 1.4.4.
2017-04-29gnu: glibc/linux: Fix runtime crashes on i686 systems.Ricardo Wurmus
* gnu/packages/patches/glibc-memchr-overflow-i686.patch: New file. * gnu/local.mk (dist_patch_DATA): Add it. * gnu/packages/commencement.scm (glibc-final-with-bootstrap-bash)[native-inputs]: Add the patch conditionally for i686 systems. * gnu/packages/base.scm (glibc/linux)[native-inputs]: Add the patch conditionally for i686 systems. [arguments]: Apply the patch conditionally on i686 systems.
2017-04-29gnu: lsof: Update to 4.89.Efraim Flashner
* gnu/packages/lsof.scm (lsof): Update to 4.89.
2017-04-29gnu: lsof: Shorten 'install phase.Efraim Flashner
* gnu/packages/lsof.scm (lsof)[arguments]: Use 'install-file during the 'install phase.
2017-04-29gnu: lsof: Use 'modify-phases' syntax.Efraim Flashner
* gnu/packages/lsof.scm (lsof)[arguments]: Use 'modify-phases' syntax.
2017-04-29gnu: lsof: Add to mirror list.Efraim Flashner
* gnu/packages/lsof.scm (lsof)[source]: Add to mirror list.
2017-04-29gnu: r-genomeinfodbdata: Fix source url.Efraim Flashner
* gnu/packages/bioinformatics.scm (r-genomeinfodbdata)[source]: Use source uri and not bioconductor-uri shortener.
2017-04-29gnu: freetype: Fix CVE-2017-{8105,8287}.Leo Famulari
* gnu/packages/patches/freetype-CVE-2017-8105.patch, gnu/packages/patches/freetype-CVE-2017-8287.patch: New files. * gnu/local.mk (dist_patch_DATA): Add them. * gnu/packages/fontutils.scm (freetype)[replacement]: New field. (freetype/fixed): New variable.
2017-04-29gnu: ocaml-qtest: Use ocaml-qcheck.Julien Lepiller
* gnu/packages/ocaml.scm (ocaml-qtest)[propagated-inputs]: Add ocaml-qcheck.
2017-04-29gnu: Add ocaml-qcheck.Julien Lepiller
* gnu/packages/ocaml.scm (ocaml-qcheck): New variable.
2017-04-29gnu: python-openid: Fix package.Danny Milosavljevic
Fixes <https://bugs.gnu.org/26692>. * gnu/packages/python.scm (python-openid)[arguments]: Replace 'check phase. [propagated-inputs]: Add python-defusedxml. [native-inputs]: Add python-psycopg2, python-django.
2017-04-29gnu: ghostscript-with-cups: Avoid inheriting replacement field.Leo Famulari
This is a followup to commit a01f15759a00503101baa23af87cbd6095a1fbd6. * gnu/packages/cups.scm (ghostscript/cups)[replacement]: New field.
2017-04-29gnu: radeontop: Update to 1.0.Tobias Geerinckx-Rice
* gnu/packages/linux.scm (radeontop): Update to 1.0. [inputs]: Add libxcb.
2017-04-28gnu: ghostscript: Fix CVE-2017-8291.Leo Famulari
* gnu/packages/patches/ghostscript-CVE-2017-8291.patch: New file. * gnu/local.mk (dist_patch_DATA): Add it. * gnu/packages/ghostscript.scm (ghostscript)[replacement]: New field. (ghostscript/fixed): New variable. (ghostscript-with-x)[replacement]: New field.
2017-04-28gnu: youtube-dl: Update to 2017.04.28.Arun Isaac
* gnu/packages/video.scm (youtube-dl): Update to 2017.04.28.
2017-04-28gnu: Add enigma.Ricardo Wurmus
* gnu/packages/games.scm (enigma): New variable.
2017-04-28gnu: Add xerces-c.Ricardo Wurmus
* gnu/packages/xml.scm (xerces-c): New variable.
2017-04-28gnu: schismtracker: Update to 20170420.Kei Kebreau
* gnu/packages/music.scm (schismtracker): Update to 20170420.
2017-04-28gnu: awscli: Add python-pyyaml input.David Thompson
Without this input, 'aws ec2 import-key-pair' doesn't work. * gnu/packages/python.scm (awscli)[propagated-inputs]: Add python-pyyaml.
2017-04-28gnu: virt-manager: Update to 1.4.1.宋文武
* gnu/packages/qemu.scm (virt-manager): Update to 1.4.1.
2017-04-28gnu: python-libvirt: Update to 3.2.0.宋文武
* gnu/packages/qemu.scm (python-libvirt, python2-libvirt): Update to 3.2.0.
2017-04-28gnu: libvirt-glib: Update to 1.0.0.宋文武
* gnu/packages/qemu.scm (libvirt-glib): Update to 1.0.0.
2017-04-28gnu: libvirt: Update to 3.2.0.宋文武
* gnu/packages/qemu.scm (libvirt): Update to 3.2.0.
2017-04-28gnu: r-preprocesscore: Update to 1.38.0.Roel Janssen
* gnu/packages/statistics.scm (r-preprocesscore): Update to 1.38.0.
2017-04-28gnu: r-msnid: Update to 1.10.0.Roel Janssen
* gnu/packages/bioinformatics.scm (r-msnid): Update to 1.10.0.
2017-04-28gnu: r-msnbase: Update to 2.2.0.Roel Janssen
* gnu/packages/bioinformatics.scm (r-msnbase): Update to 2.2.0.
2017-04-28gnu: r-pcamethods: Update to 1.68.0.Roel Janssen
* gnu/packages/bioinformatics.scm (r-pcamethods): Update to 1.68.0.
2017-04-28gnu: r-mzid: Update to 1.14.0.Roel Janssen
* gnu/packages/bioinformatics.scm (r-mzid): Update to 1.14.0.
2017-04-28gnu: r-vsn: Update to 3.44.0.Roel Janssen
* gnu/packages/bioinformatics.scm (r-vsn): [source]: Update to 3.44.0, [propagated-inputs]: Add r-hexbin.
2017-04-28gnu: r-affy: Update to 1.54.0.Roel Janssen
* gnu/packages/bioinformatics.scm (r-affy): Update to 1.54.0.
2017-04-28gnu: r-affyio: Update to 1.46.0.Roel Janssen
* gnu/packages/bioinformatics.scm (r-affyio): Update to 1.46.0.
2017-04-28gnu: r-mzr: Update to 2.10.0.Roel Janssen
* gnu/packages/bioinformatics.scm (r-mzr): Update to 2.10.0.
2017-04-28gnu: r-protgenerics: Update to 1.8.0.Roel Janssen
* gnu/packages/bioinformatics.scm (r-protgenerics): Update to 1.8.0.
2017-04-28gnu: r-sva: Update to 3.24.0.Roel Janssen
* gnu/packages/bioinformatics.scm (r-sva): Update to 3.24.0.
2017-04-28gnu: r-copywriter: Update to 2.8.0.Roel Janssen
* gnu/packages/bioinformatics.scm (r-copywriter): Update to 2.8.0.
2017-04-28gnu: r-chipseq: Update to 1.26.0.Roel Janssen
* gnu/packages/bioinformatics.scm (r-chipseq): Update to 1.26.0.
2017-04-28gnu: r-rhdf5: Update to 2.20.0.Roel Janssen
* gnu/packages/bioinformatics.scm (r-rhdf5): Update to 2.20.0.
2017-04-28gnu: r-tximport: Update to 1.4.0.Roel Janssen
* gnu/packages/bioinformatics.scm (r-tximport): Update to 1.4.0.
2017-04-28gnu: r-mutationalpatterns: Update to 1.2.0.Roel Janssen
* gnu/packages/bioinformatics.scm (r-mutationalpatterns): [source]: Update to 1.2.0, [propagated-inputs]: Add r-bsgenome-hsapiens-1000genomes-hs37d5, r-bsgenome-hsapiens-ucsc-hg19.
2017-04-28gnu: r-bamsignals: Update to 1.8.0.Roel Janssen
* gnu/packages/bioinformatics.scm (r-bamsignals): Update to 1.8.0.
2017-04-28gnu: r-rhtslib: Update to 1.8.0.Roel Janssen
* gnu/packages/bioinformatics.scm (r-rhtslib): Update to 1.8.0.
2017-04-28gnu: r-zlibbioc: Update to 1.22.0.Roel Janssen
* gnu/packages/bioinformatics.scm (r-zlibbioc): Update to 1.22.0.
2017-04-28gnu: r-motifrg: Update to 1.20.0.Roel Janssen
* gnu/packages/bioinformatics.scm (r-motifrg): Update to 1.20.0.
2017-04-28gnu: r-seqlogo: Update to 1.42.0.Roel Janssen
* gnu/packages/bioinformatics.scm (r-seqlogo): Update to 1.42.0.
2017-04-28gnu: r-genomation: Update to 1.8.0.Roel Janssen
* gnu/packages/bioinformatics.scm (r-genomation): Update to 1.8.0.
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