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* gnu: qemu: Update to 2.8.1 [security fixes].Leo Famulari2017-04-07
| | | | | | | | | | | | Fixes CVE-2016-{9602,9603} and CVE-2017-{2615,2620,2630,5667,5931}. * gnu/packages/qemu.scm (qemu): Update to 2.8.1. * gnu/packages/patches/qemu-CVE-2017-2615.patch, gnu/packages/patches/qemu-CVE-2017-2620.patch, gnu/packages/patches/qemu-CVE-2017-2630.patch, gnu/packages/patches/qemu-CVE-2017-5667.patch, gnu/packages/patches/qemu-CVE-2017-5931.patch: Delete files. * gnu/local.mk (dist_patch_DATA): Remove them.
* gnu: surf: Update to 2.0.Leo Famulari2017-04-06
| | | | | * gnu/packages/suckless.scm (surf): Update to 2.0. [inputs]: Replace webkitgtk/gtk+-2 with webkitgtk.
* gnu: flann: Move .mex file to a separate "octave" output.Ludovic Courtès2017-04-07
| | | | | | | | That way the closure of flann:out is down from 1 GiB to 290 MiB. * gnu/packages/maths.scm (flann)[outputs]: New field. [arguments]: Add 'set-octave-directory' phase.
* gnu: webkitgtk: Update to 2.16.1.Leo Famulari2017-04-06
| | | | * gnu/packages/webkit.scm (webkitgtk): Update to 2.16.1.
* gnu: armadillo: Change license to ASL 2.0.Ricardo Wurmus2017-04-06
| | | | | | | Armadillo versions 7.800 and onwards are licensed under the Apache License 2.0. * gnu/packages/maths.scm (armadillo)[license]: Change to ASL 2.0.
* gnu: re2: Update to 2017-04-01.Marius Bakke2017-04-06
| | | | * gnu/packages/regex.scm (re2): Update to 2017-04-01.
* gnu: feh: Update to 2.18.3.Marius Bakke2017-04-06
| | | | * gnu/packages/image-viewers.scm (feh): Update to 2.18.3.
* gnu: libusb: Update to 1.0.21.Marius Bakke2017-04-06
| | | | | * gnu/packages/libusb.scm (libusb): Update to 1.0.21. [home-page]: Update to new URL.
* gnu: libmtp: Update to 1.1.13 [security fixes].Marius Bakke2017-04-06
| | | | * gnu/packages/libusb.scm (libmtp): Update to 1.1.13.
* gnu: r-sourcetools: Update to 0.1.6.Ricardo Wurmus2017-04-06
| | | | * gnu/packages/statistics.scm (r-sourcetools): Update to 0.1.6.
* gnu: r-seqinr: Update to 3.3-6.Ricardo Wurmus2017-04-06
| | | | * gnu/packages/bioinformatics.scm (r-seqinr): Update to 3.3-6.
* gnu: Remove armadillo-for-rcpparmadillo.Ricardo Wurmus2017-04-06
| | | | | | | | This package is no longer useful, because upstream does not keep the tarballs of older releases. We use the bundled armadillo sources in the r-rccparmadillo package instead. * gnu/packages/maths.scm (armadillo-for-rcpparmadillo): Remove variable.
* gnu: r-rcpparmadillo: Update to 0.7.700.0.0.Ricardo Wurmus2017-04-06
| | | | | | | | | | | * gnu/packages/statistics.scm (r-rcpparmadillo): Update to 0.7.700.0.0. [source]: Do not delete bundled armadillo sources, because upstream no longer hosts previous versions. [propagated-inputs]: Remove "armadillo-for-rcpparmadillo". [arguments]: Remove because we no longer need to link with the armadillo library. * gnu/packages/bioinformatics.scm (r-deseq2)[arguments]: Remove because we no longer need to link with armadillo library.
* gnu: armadillo: Update to 7.800.2.Ricardo Wurmus2017-04-06
| | | | * gnu/packages/maths.scm (armadillo): Update to 7.800.2.
* gnu: r-annotationforge: Update to 1.16.1.Ricardo Wurmus2017-04-06
| | | | * gnu/packages/bioinformatics.scm (r-annotationforge): Update to 1.16.1.
* gnu: r-shortread: Update to 1.32.1.Ricardo Wurmus2017-04-06
| | | | * gnu/packages/bioinformatics.scm (r-shortread): Update to 1.32.1.
* gnu: r-s4vectors: Update to 0.12.2.Ricardo Wurmus2017-04-06
| | | | * gnu/packages/bioinformatics.scm (r-s4vectors): Update to 0.12.2.
* gnu: r-iranges: Update to 2.8.2.Ricardo Wurmus2017-04-06
| | | | * gnu/packages/bioinformatics.scm (r-iranges): Update to 2.8.2.
* gnu: r-variantannotation: Update to 1.20.3.Ricardo Wurmus2017-04-06
| | | | * gnu/packages/bioinformatics.scm (r-variantannotation): Update to 1.20.3.
* gnu: r-limma: Update to 3.30.13.Ricardo Wurmus2017-04-06
| | | | * gnu/packages/bioinformatics.scm (r-limma): Update to 3.30.13.
* gnu: r-genomicranges: Update to 1.26.4.Ricardo Wurmus2017-04-06
| | | | * gnu/packages/bioinformatics.scm (r-genomicranges): Update to 1.26.4.
* gnu: r-annotationdbi: Update to 1.36.2.Ricardo Wurmus2017-04-06
| | | | * gnu/packages/bioinformatics.scm (r-annotationdbi): Update to 1.36.2.
* gnu: r-genomicalignments: Update to 1.10.1.Ricardo Wurmus2017-04-06
| | | | * gnu/packages/bioinformatics.scm (r-genomicalignments): Update to 1.10.1.
* gnu: r-rtracklayer: Update to 1.34.2.Ricardo Wurmus2017-04-06
| | | | * gnu/packages/bioinformatics.scm (r-rtracklayer): Update to 1.34.2.
* gnu: r-genomicfeatures: Update to 1.26.4.Ricardo Wurmus2017-04-06
| | | | * gnu/packages/bioinformatics.scm (r-genomicfeatures): Update to 1.26.4.
* gnu: r-seqminer: Update to 5.7.Ricardo Wurmus2017-04-06
| | | | * gnu/packages/bioinformatics.scm (r-seqminer): Update to 5.7.
* gnu: r-maldiquant: Update to 1.16.2.Ricardo Wurmus2017-04-06
| | | | * gnu/packages/bioinformatics.scm (r-maldiquant): Update to 1.16.2.
* gnu: r-ranger: Update to 0.7.0.Ricardo Wurmus2017-04-06
| | | | * gnu/packages/statistics.scm (r-ranger): Update to 0.7.0.
* gnu: r-pbkrtest: Update to 0.4-7.Ricardo Wurmus2017-04-06
| | | | * gnu/packages/statistics.scm (r-pbkrtest): Update to 0.4-7.
* gnu: r-rcppeigen: Update to 0.3.2.9.1.Ricardo Wurmus2017-04-06
| | | | * gnu/packages/statistics.scm (r-rcppeigen): Update to 0.3.2.9.1.
* gnu: r-mclust: Update to 5.2.3.Ricardo Wurmus2017-04-06
| | | | * gnu/packages/statistics.scm (r-mclust): Update to 5.2.3.
* gnu: r-ggthemes: Update to 3.4.0.Ricardo Wurmus2017-04-06
| | | | * gnu/packages/statistics.scm (r-ggthemes): Update to 3.4.0.
* gnu: r-statmod: Update to 1.4.29.Ricardo Wurmus2017-04-06
| | | | * gnu/packages/statistics.scm (r-statmod): Update to 1.4.29.
* gnu: r-vipor: Update to 0.4.5.Ricardo Wurmus2017-04-06
| | | | * gnu/packages/statistics.scm (r-vipor): Update to 0.4.5.
* gnu: r-pracma: Update to 2.0.4.Ricardo Wurmus2017-04-06
| | | | * gnu/packages/maths.scm (r-pracma): Update to 2.0.4.
* gnu: r-mixtools: Update to 1.1.0.Ricardo Wurmus2017-04-06
| | | | | * gnu/packages/statistics.scm (r-mixtools): Update to 1.1.0. [propagated-inputs]: Remove "r-boot", add "r-survival".
* gnu: r-viridis: Update to 0.4.0.Ricardo Wurmus2017-04-06
| | | | | * gnu/packages/statistics.scm (r-viridis): Update to 0.4.0. [propagated-inputs]: Add "r-viridislite".
* gnu: r-viridislite: Update to 0.2.0.Ricardo Wurmus2017-04-06
| | | | * gnu/packages/statistics.scm (r-viridislite): Update to 0.2.0.
* gnu: r-matrixstats: Update to 0.52.1.Ricardo Wurmus2017-04-06
| | | | * gnu/packages/statistics.scm (r-matrixstats): Update to 0.52.1.
* gnu: r-mvtnorm: Update to 1.0-6.Ricardo Wurmus2017-04-06
| | | | * gnu/packages/statistics.scm (r-mvtnorm): Update to 1.0-6.
* gnu: r-e1071: Update to 1.6-8.Ricardo Wurmus2017-04-06
| | | | * gnu/packages/statistics.scm (r-e1071): Update to 1.6-8.
* gnu: r-sparsem: Update to 1.76.Ricardo Wurmus2017-04-06
| | | | * gnu/packages/statistics.scm (r-sparsem): Update to 1.76.
* gnu: r-xml: Update to 3.98-1.6.Ricardo Wurmus2017-04-06
| | | | * gnu/packages/statistics.scm (r-xml): Update to 3.98-1.6.
* gnu: r-rsqlite: Update to 1.1-2.Ricardo Wurmus2017-04-06
| | | | * gnu/packages/statistics.scm (r-rsqlite): Update to 1.1-2.
* gnu: r-rmarkdown: Update to 1.4.Ricardo Wurmus2017-04-06
| | | | * gnu/packages/statistics.scm (r-rmarkdown): Update to 1.4.
* gnu: r-bbmisc: Update to 1.11.Ricardo Wurmus2017-04-06
| | | | * gnu/packages/statistics.scm (r-bbmisc): Update to 1.11.
* gnu: r-backports: Update to 1.0.5.Ricardo Wurmus2017-04-06
| | | | * gnu/packages/statistics.scm (r-backports): Update to 1.0.5.
* gnu: r-multitaper: Update to 1.0-13.Ricardo Wurmus2017-04-06
| | | | * gnu/packages/statistics.scm (r-multitaper): Update to 1.0-13.
* gnu: r-xml2: Update to 1.1.1.Ricardo Wurmus2017-04-06
| | | | * gnu/packages/statistics.scm (r-xml2): Update to 1.1.1.
* gnu: r-ade4: Update to 1.7-6.Ricardo Wurmus2017-04-06
| | | | * gnu/packages/statistics.scm (r-ade4): Update to 1.7-6.
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