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2017-08-03gnu: r-hmisc: Update to 4.0-3.Ricardo Wurmus
* gnu/packages/statistics.scm (r-hmisc): Update to 4.0-3. [propagated-inputs]: Remove r-base64.
2017-08-03gnu: r-plotly: Update to 4.7.1.Ricardo Wurmus
* gnu/packages/statistics.scm (r-plotly): Update to 4.7.1. [propagated-inputs]: Add r-crosstalk, r-data-table, r-htmltools, and r-rcolorbrewer.
2017-08-03gnu: r-igraph: Update to 1.1.2.Ricardo Wurmus
* gnu/packages/statistics.scm (r-igraph): Update to 1.1.2. [propagated-inputs]: Remove r-nmf; add r-matrix and r-pkgconfig.
2017-08-03gnu: r-purrr: Update to 0.2.2.2.Ricardo Wurmus
* gnu/packages/statistics.scm (r-purrr): Update to 0.2.2.2. [propagated-inputs]: Remove r-bh and r-dplyr; add r-tibble.
2017-08-03gnu: r-devtools: Update to 1.13.3.Ricardo Wurmus
* gnu/packages/statistics.scm (r-devtools): Update to 1.13.3. [propagated-inputs]: Remove r-curl, r-digest, r-evaluate, r-roxygen2, and r-rversions.
2017-08-03gnu: r-tibble: Update to 1.3.3.Ricardo Wurmus
* gnu/packages/statistics.scm (r-tibble): Update to 1.3.3. [propagated-inputs]: Remove r-lazyeval, add r-rlang.
2017-08-03gnu: r-dplyr: Update to 0.7.2.Ricardo Wurmus
* gnu/packages/statistics.scm (r-dplyr): Update to 0.7.2. [propagated-inputs]: Remove r-lazyeval, r-dbi; add r-rlang, r-plogr, r-glue, r-pkgconfig, r-bindrcpp.
2017-08-03gnu: Add r-bindrcpp.Ricardo Wurmus
* gnu/packages/cran.scm (r-bindrcpp): New variable.
2017-08-03gnu: Add r-bindr.Ricardo Wurmus
* gnu/packages/cran.scm (r-bindr): New variable.
2017-08-03gnu: r-rcpp: Move to (gnu packages cran).Ricardo Wurmus
* gnu/packages/statistics.scm (r-rcpp): Move from here... * gnu/packages/cran.scm (r-rcpp): ...to here.
2017-08-03gnu: r-rcpp: Update to 0.12.12.Ricardo Wurmus
* gnu/packages/statistics.scm (r-rcpp): Update to 0.12.12.
2017-08-03gnu: r-plogr: Move to (gnu packages cran).Ricardo Wurmus
* gnu/packages/statistics.scm (r-plogr): Move from here... * gnu/packages/cran.scm (r-plogr): ...to here.
2017-08-03gnu: Add r-glue.Ricardo Wurmus
* gnu/packages/cran.scm (r-glue): New variable.
2017-08-03gnu: Add grub-hybrid.Danny Milosavljevic
* gnu/packages/bootloaders.scm (grub-hybrid): New variable.
2017-08-03gnu: htseq: Use PyPI URI.Ben Woodcroft
This is a follow-up to 92971d68ac942cd4a38092b4ccb20a8192a56aaf. * gnu/packages/bioinformatics.scm (htseq)[source]: Use 'pypi-uri'.
2017-08-03gnu: htseq: Update to 0.9.1.Ben Woodcroft
* gnu/packages/bioinformatics.scm (htseq): Update to 0.9.1. [arguments]: Use python-3 by removing field. [native-inputs]: Add 'python-cython'. [propagated-inputs]: Use python3 numpy package. [inputs]: Use python3 pysam package. Add 'python-matplotlib'. (python2-htseq): New variable. (clipper)[inputs]: Use it.
2017-08-03gnu: vc: Limit to x86_64 and i686.Efraim Flashner
* gnu/packages/maths.scm (vc)[supported-systems]: New field.
2017-08-03gnu: openscenegraph: Add 'Release' configure flag.Manolis Ragkousis
* gnu/packages/graphics.scm (openscenegraph)[arguments]: Add "-DCMAKE_BUILD_TYPE=Release".
2017-08-03gnu: Add LeoCAD.Eric Bavier
* gnu/packages/lego.scm (leocad): New variable.
2017-08-03gnu: youtube-dl: Update to 2017.07.30.1.Tobias Geerinckx-Rice
* gnu/packages/video.scm (youtube-dl): Update to 2017.07.30.1.
2017-08-03gnu: tor: Update to 0.3.0.10.Tobias Geerinckx-Rice
* gnu/packages/tor.scm (tor): Update to 0.3.0.10.
2017-08-03activation: Make sure /etc exists.Ludovic Courtès
Fixes <http://bugs.gnu.org/27146>. Reported by ng0 <ng0@pragmatique.xyz>. * gnu/build/activation.scm (activate-etc): Add call to 'mkdir-p'.
2017-08-02gnu: glibc@2.22: Fix security issues.Efraim Flashner
Fixes CVE-2015-{5180,7547}, CVE-2016-{3075,3706,4429}. * gnu/packages/base.scm (glibc@2.22)[source]: Add patches. * gnu/packages/patches/glibc-CVE-2015-7547.patch: New file. * gnu/local.mk (dist_patch_DATA): Register it.
2017-08-02gnu: glibc@2.23: Fix CVE-2015-5180, CVE-2016-{3075,3706,4429}.Efraim Flashner
* gnu/packages/base.scm (glibc@2.23)[source]: Add patches. * gnu/packages/patches/glibc-CVE-2016-3075.patch, gnu/packages/patches/glibc-CVE-2016-3706.patch, gnu/packages/patches/glibc-CVE-2016-4429.patch: New files. * gnu/local.mk (dist_patch_DATA): Register them.
2017-08-02gnu: glibc@2.24: Fix CVE-2015-5180.Efraim Flashner
* gnu/packages/base.scm (glibc@2.24)[source]: Add patch. * gnu/packages/patches/glibc-CVE-2015-5180.patch: New file. * gnu/local.mk (dist_patch_DATA): Register it.
2017-08-02gnu: python2-conda: Fix build by building with enum34.Leo Famulari
* gnu/packages/package-management.scm (python2-conda): Use 'python2-variant'. [native-inputs]: Add python2-enum34.
2017-08-02gnu: calibre: Add python2-msgpack as an input.Manolis Ragkousis
* gnu/packages/ebook.scm (calibre)[inputs]: Add python2-msgpack.
2017-08-02gnu: gcc@4.7: Don't built on aarch64.Efraim Flashner
* gnu/packages/gcc.scm (gcc@4.7, gcc@4.8, gcc@4.9)[supported-systems]: New field.
2017-08-02gnu: libpng-apng: Be sure to apply the APNG patch.Leo Famulari
* gnu/packages/image.scm (libpng-apng)[arguments]: Check the return status of the patching procedures.
2017-08-02gnu: libpng-apng: Update to 1.6.28.ng0
Fixes <https://bugs.gnu.org/27556>. * gnu/packages/image.scm (libpng-apng): Update to 1.6.28. Remove inherit of 'libpng'. [version]: Use own version, remove 'package-version libpng'. [source]: Don't inherit the source of libpng. [arguments]: Update hash of libpng-apng source. Signed-off-by: Leo Famulari <leo@famulari.name>
2017-08-02gnu: eyed3: Update to 0.8, build with python3.Thomas Danckaert
* gnu/packages/mp3.scm (eyed3): [source] Update to 0.8. [arguments]: Disable tests; don't use python-2. [propagated-inputs]: Add python-six and python-grako. [native-inputs]: Remove.
2017-08-02gnu: Add python-grakoThomas Danckaert
* gnu/packages/python.scm (python-grako): New variable.
2017-08-02gnu: hdf4: Update to 4.12.13.Thomas Danckaert
* gnu/packages/maths.scm (hdf4): Update to 4.12.13.
2017-08-02gnu: libvirt: Update to 3.6.0.Tobias Geerinckx-Rice
* gnu/packages/virtualization.scm (libvirt): Update to 3.6.0.
2017-08-02gnu: libvirt: Use HTTPS.Tobias Geerinckx-Rice
* gnu/packages/virtualization.scm (libvirt)[source, home-page]: Use HTTPS.
2017-08-02gnu: Add r-rlang.Roel Janssen
* gnu/packages/statistics.scm (r-rlang): New variable.
2017-08-02gnu: r-deseq2: Update to 1.16.1.Roel Janssen
* gnu/packages/bioinformatics.scm (r-deseq2): Update to 1.16.1.
2017-08-02gnu: r-annotationforge: Update to 1.18.1.Roel Janssen
* gnu/packages/bioinformatics.scm (r-annotationforge): Update to 1.18.1.
2017-08-02gnu: r-category: Update to 2.42.1.Roel Janssen
* gnu/packages/bioinformatics.scm (r-category): Update to 2.42.1.
2017-08-02gnu: r-biocstyle: Update to 2.4.1.Roel Janssen
* gnu/packages/bioinformatics.scm (r-biocstyle): Update to 2.4.1.
2017-08-02gnu: r-dnacopy: Update to 1.50.1.Roel Janssen
* gnu/packages/bioinformatics.scm (r-dnacopy): Update to 1.50.1.
2017-08-02gnu: r-iranges: Update to 2.10.2.Roel Janssen
* gnu/packages/bioinformatics.scm (r-iranges): Update to 2.10.2.
2017-08-02gnu: r-genomeinfodb: Update to 1.12.2.Roel Janssen
* gnu/packages/bioinformatics.scm (r-genomeinfodb): Update to 1.12.2.
2017-08-02gnu: r-variantannotation: Update to 1.22.3.Roel Janssen
* gnu/packages/bioinformatics.scm (r-variantannotation): Update to 1.22.3.
2017-08-02gnu: r-limma: Update to 3.32.5.Roel Janssen
* gnu/packages/bioinformatics.scm (r-limma): Update to 3.32.5.
2017-08-02gnu: r-biobase: Update to 2.36.2.Roel Janssen
* gnu/packages/bioinformatics.scm (r-biobase): Update to 2.36.2.
2017-08-02gnu: r-annotationdbi: Update to 1.38.2.Roel Janssen
* gnu/packages/bioinformatics.scm (r-annotationdbi): Update to 1.38.2.
2017-08-02gnu: r-biomart: Update to 2.32.1.Roel Janssen
* gnu/packages/bioinformatics.scm (r-biomart): Update to 2.32.1.
2017-08-02gnu: r-biocparallel: Update to 1.10.1.Roel Janssen
* gnu/packages/bioinformatics.scm (r-biocparallel): Update to 1.10.1.
2017-08-02gnu: r-biostrings: Update to 2.44.2.Roel Janssen
* gnu/packages/bioinformatics.scm (r-biostrings): Update to 2.44.2.
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