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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.
2017-08-02gnu: r-delayedarray: Update to 0.2.7.Roel Janssen
* gnu/packages/bioinformatics.scm (r-delayedarray): Update to 0.2.7.
2017-08-02gnu: r-summarizedexperiment: Update to 1.6.3.Roel Janssen
* gnu/packages/bioinformatics.scm (r-summarizedexperiment): Update to 1.6.3.
2017-08-02gnu: r-genomicalignments: Update to 1.12.1.Roel Janssen
* gnu/packages/bioinformatics.scm (r-genomicalignments): Update to 1.12.1.
2017-08-02gnu: r-rtracklayer: Update to 1.36.4.Roel Janssen
* gnu/packages/bioinformatics.scm (r-rtracklayer): Update to 1.36.4.
2017-08-02gnu: r-genomicfeatures: Update to 1.28.4.Roel Janssen
* gnu/packages/bioinformatics.scm (r-genomicfeatures): Update to 1.28.4.
2017-08-02gnu: r-copywriter: Update to 2.8.1.Roel Janssen
* gnu/packages/bioinformatics.scm (r-copywriter): Update to 2.8.1.
2017-08-02gnu: r-sva: Update to 3.24.4.Roel Janssen
* gnu/packages/bioinformatics.scm (r-sva): Update to 3.24.4.
2017-08-02gnu: r-rsqlite: Update to 2.0.Roel Janssen
* gnu/packages/statistics.scm (r-rsqlite): Update to 2.0.
2017-08-02gnu: Add r-blob.Roel Janssen
* gnu/packages/statistics.scm (r-blob): New variable.
2017-08-02gnu: Add r-pkgconfig.Roel Janssen
* gnu/packages/statistics.scm (r-pkgconfig): New variable.
2017-08-02pull: Honor '--no-grafts'.Ludovic Courtès
* guix/scripts/pull.scm (guix-pull): Parameterize %GRAFT? as a function of OPTS.
2017-08-02pull: Use the commit ID as the version string.Ludovic Courtès
* guix/scripts/pull.scm (build-from-source): Add #:commit parameter. Pass it to BUILD. (build-and-install): Add #:commit and pass it to 'build-from-source'. (guix-pull): Pass #:commit to 'build-and-install'.
2017-08-02pull: Fetch source code from Git.Ludovic Courtès
* guix/scripts/pull.scm (%snapshot-url, with-environment-variable) (with-PATH): Remove. (ensure-guile-git!): New procedure. (%repository-url): New variable. (%default-options): Add 'repository-url' and 'ref'. (show-help, %options): Add '--commit' and '--url'. (temporary-directory, first-directory, interned-then-deleted) (unpack): Remove. (build-from-source): Rename 'tarball' to 'source'. Remove call to 'unpack'. (build-and-install): Rename 'tarball' to 'source'. (honor-lets-encrypt-certificates!, report-git-error): New procedures. (with-git-error-handling): New macro. (guix-pull)[fetch-tarball]: Remove. Wrap body in 'with-git-error-handling'. Rewrite to use 'latest-repository-commit'. * build-aux/build-self.scm (build): Print an error message and exit when GUILE-GIT is #f. * doc/guix.texi (Invoking guix pull): Mention Git. Document '--commit' and '--branch'.
2017-08-02build: Make Guile-Git a hard requirement.Ludovic Courtès
* configure.ac: Error out when (git) is missing. * doc/guix.texi (Requirements): Mention Guile-Git. * Makefile.am (MODULES): Add guix/git.scm unconditionally.
2017-08-01gnu: re2: Update to 2017-08-01.Marius Bakke
* gnu/packages/regex.scm (re2): Update to 2017-08-01.
2017-08-01gnu: maim: Update to 5.4.66.Marius Bakke
* gnu/packages/xdisorg.scm (maim): Update to 5.4.66.
2017-08-01gnu: slop: Update to 7.3.48.Marius Bakke
* gnu/packages/xdisorg.scm (slop): Update to 7.3.48.
2017-08-01gnu: git: Update to 2.13.4.Marius Bakke
* gnu/packages/version-control.scm (git): Update to 2.13.4.
2017-08-01gnu: r-foreign: Update hash after upstream tarball change.Roel Janssen
* gnu/packages/statistics.scm (r-foreign): Update hash. The only difference in the tarball is the metadata. The contents are identical.
2017-08-01gnu: r-foreign: Remove duplicate recipe.Roel Janssen
* gnu/packages/statistics.scm (r-foreign): Remove duplicate recipe.
2017-08-01graph: Provide access to the package record in the emit functions.Roel Janssen
* guix/graph.scm (export-graph): Pass the node to the emit functions, instead of the node's label.
2017-08-01guix package: Allow `guix package -u' to fuction as before.Efraim Flashner
This is a follow up to 6ddf97f81bb99a73f00e30ad5fc19577872b5b49 * guix/scripts/package.scm (%options) <"-u">: Only check for a flag when there is an ARG after '-u'.
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