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* gnu: r-rcpp: Update to 0.12.5.•••* gnu/packages/statistics.scm (r-rcpp): Update to 0.12.5. Ricardo Wurmus2016-05-20
* gnu: r-genomicfeatures: Update to 1.24.2.•••* gnu/packages/bioinformatics.scm (r-genomicfeatures): Update to 1.24.2. Ricardo Wurmus2016-05-20
* gnu: r-summarizedexperiment: Update to 1.2.2.•••* gnu/packages/bioinformatics.scm (r-summarizedexperiment): Update to 1.2.2. Ricardo Wurmus2016-05-20
* gnu: r-biocparallel: Update to 1.6.2.•••* gnu/packages/bioinformatics.scm (r-biocparallel): Update to 1.6.2. Ricardo Wurmus2016-05-20
* gnu: r-annotationdbi: Update to 1.34.2.•••* gnu/packages/bioinformatics.scm (r-annotationdbi): Update to 1.34.2. Ricardo Wurmus2016-05-20
* gnu: r-variantannotation: Update to 1.18.1.•••* gnu/packages/bioinformatics.scm (r-variantannotation): Update to 1.18.1. Ricardo Wurmus2016-05-20
* gnu: r-genomeinfodb: Update to 1.8.1.•••* gnu/packages/bioinformatics.scm (r-genomeinfodb): Update to 1.8.1. Ricardo Wurmus2016-05-20
* gnu: btrfs-progs: Update to 4.5.3.•••* gnu/packages/linux.scm (btrfs-progs): Update to 4.5.3. Leo Famulari2016-05-19
* gnu: jemalloc: Update to 4.2.0.•••* gnu/packages/jemalloc.scm (jemalloc): Update to 4.2.0. Signed-off-by: Efraim Flashner <efraim@flashner.co.il> Jelle Licht2016-05-19
* gnu: expat: Fix CVE-2016-0718. Improve fix for CVE-2015-1283.•••* gnu/packages/patches/expat-CVE-2015-1283-refix.patch, gnu/packages/patches/expat-CVE-2016-0718.patch: New files. * gnu/local.mk (dist_patch_DATA): Add them. * gnu/packages/xml.scm (expat)[replacement]: New field. (expat/fixed): New variable. [source]: Use new patches. Leo Famulari2016-05-19
* gnu: flann: Do not install .a files.•••* gnu/packages/maths.scm (flann)[arguments]: Add #:phases. Ludovic Courtès2016-05-19
* gnu: python: Add 'python' variables for different major/minor versions.•••* gnu/packages/python.scm (python-2): Rename variable to... (python-2.7): ...this. (python-2): Refer to "python-2.7". (python): Rename variable to... (python-3.4): ...this. (python-3): Refer to "python-3.4". (python): Refer to "python-3". Signed-off-by: Ludovic Courtès <ludo@gnu.org> Hartmut Goebel2016-05-19
* gnu: flann: Strip .mex file.•••* gnu/packages/maths.scm (flann)[arguments]: Add #:strip-directories. Ludovic Courtès2016-05-19
* gnu: Add r-biased-urn.•••* gnu/packages/statistics.scm (r-biased-urn): New variable. Ben Woodcroft2016-05-19
* gnu: giflib: Use 'modify-phases'.•••* gnu/packages/image.scm (giflib)[arguments]: Use 'modify-phases'. Efraim Flashner2016-05-19
* gnu: giflib: Update to 5.1.4 [fixes CVE-2015-7555, CVE-2016-3977].•••* gnu/packages/image.scm (giflib): Update to 5.1.4. Efraim Flashner2016-05-19
* gnu: Add emacs-smartparens.•••* gnu/packages/emacs.scm (emacs-smartparens): New variable. Signed-off-by: Alex Kost <alezost@gmail.com> humanitiesNerd2016-05-19
* Update name for Kei Kebreau.•••* .mailmap: Add Kei Kebreau. * gnu/local.mk: Replace "Kei Yamashita" with "Kei Kebreau". * gnu/packages/calendar.scm: Likewise. * gnu/packages/dillo.scm: Likewise. * gnu/packages/fltk.scm: Likewise. * gnu/packages/game-development.scm: Likewise. * gnu/packages/games.scm: Likewise. * gnu/packages/gnome.scm: Likewise. * gnu/packages/gtk.scm: Likewise. * gnu/packages/music.scm: Likewise. * gnu/packages/xfce.scm: Likewise. Signed-off-by: Alex Kost <alezost@gmail.com> Kei Kebreau2016-05-19
* gnu: octave: Update to 4.0.2.•••* gnu/packages/maths.scm (octave): Update to 4.0.2. [inputs]: Added cyrus-sasl, openssl. Signed-off-by: Efraim Flashner <efraim@flashner.co.il> Kei Yamashita2016-05-19
* gnu: Add ntfs-3g.•••* gnu/packages/linux.scm (ntfs-3g): New variable. Ludovic Courtès2016-05-18
* gnu: wmbattery: Fix UPower-related memory leak.•••* gnu/packages/gnustep.scm (wmbattery)[source](snippet): New field. Signed-off-by: Ludovic Courtès <ludo@gnu.org> Kei Yamashita2016-05-18
* gnu: qtkeychain: Update to 0.6.2.•••* gnu/packages/qt.scm (qtkeychain): Update to 0.6.2. Efraim Flashner2016-05-18
* gnu: Add krona-tools.•••* gnu/packages/web.scm (krona-tools): New variable. Ben Woodcroft2016-05-18
* gnu: hurd-headers: Update to 0.8.•••* gnu/packages/hurd.scm (hurd-headers): Update to version 0.8. Manolis Ragkousis2016-05-18
* gnu: mig: Update to 1.7.•••* gnu/packages/hurd.scm (mig): Update to version 1.7. Manolis Ragkousis2016-05-18
* gnu: gnumach-headers: Update to 1.7.•••* gnu/packages/hurd.scm (gnumach-headers): Update to version 1.7. Manolis Ragkousis2016-05-18
* gnu: diamond: Do not specify target architecture.•••* gnu/packages/bioinformatics.scm (diamond)[arguments]: Do not specify target architecture. Ben Woodcroft2016-05-18
* gnu: Add Piranha.•••* gnu/packages/bioinformatics.scm (piranha): New variable. Ricardo Wurmus2016-05-18
* gnu: python2-pandas: Fix native-inputs.•••* gnu/packages/python.scm (python2-pandas)[native-inputs]: Use python2- versions of python-panda's native-inputs, not of inputs. Efraim Flashner2016-05-18
* gnu: Add signify.•••* gnu/packages/crypto.scm (signify): New variable. Leo Famulari2016-05-17
* gnu: libndp: Update to 1.6 [fixes CVE-2016-3698].•••* gnu/packages/networking.scm (libndp): Update to 1.6. Leo Famulari2016-05-17
* gnu: Add emacs-zenburn-theme.•••* gnu/packages/emacs.scm (emacs-zenburn-theme): New variable. Signed-off-by: Alex Kost <alezost@gmail.com> humanitiesNerd2016-05-17
* gnu: gd: Fix-CVE-2016-3074.•••* gnu/packages/patches/gd-CVE-2016-3074.patch: New file. * gnu/local.mk (dist_patch_DATA): Add it. * gnu/packages/gd.scm (gd)[source]: Use it. Leo Famulari2016-05-17
* gnu: gd: Specify 'cpe-name'.•••* gnu/packages/gd.scm (gd)[properties]: New field. Ludovic Courtès2016-05-17
* lint: Honor 'cpe-name' and 'cpe-version' package properties.•••* guix/scripts/lint.scm (package-name->cpe-name): Remove. (package-vulnerabilities): Honor 'cpe-name' and 'cpe-version' properties. * gnu/packages/grub.scm (grub)[properties]: New field. * gnu/packages/gnuzilla.scm (icecat)[properties]: Add 'cpe-name' and 'cpe-version'. * doc/guix.texi (Invoking guix lint): Mention 'cpe-name'. Ludovic Courtès2016-05-17
* gnu: emacs-constants: Remove old patch.•••* gnu/packages/patches/emacs-constants-lisp-like.patch: Remove it. * gnu/local.mk (dist_patch_DATA): Remove entry for above patch. Federico Beffa2016-05-17
* store: Clarify 'query-path-hash' docstring.•••* guix/store.scm (query-path-hash): Clarify docstring. Ludovic Courtès2016-05-17
* import: Gracefully report import failures.•••Previously, something like 'guix import gnu which' would spit out a backtrace if, say, the 'which' tarball could not be authenticated. * guix/upstream.scm (download-tarball): Mention failure modes in docstring. * guix/import/gnu.scm (gnu-package->sexp): Return #f when 'download-tarball' returns #f. * guix/scripts/import.scm (guix-import): Call 'leave' when IMPORTER does not return a (package ...) sexp. Ludovic Courtès2016-05-17
* import: Exit with non-zero when an unknown importer is asked.•••* guix/scripts/import.scm (guix-import): Use 'leave' instead of 'format' when IMPORTER is unknown. Ludovic Courtès2016-05-17
* gnu: emacs-constants: Update to 2.6.•••* gnu/packages/emacs.scm (emacs-constants): Change to versioned repository and update to 2.6. Federico Beffa2016-05-17
* gnu: sortmerna: Update to 2.1b.•••* gnu/packages/bioinformatics.scm (sortmerna): Update to 2.1b. [inputs]: New field. Ben Woodcroft2016-05-17
* gnu: vsearch: Update to 1.11.1.•••* gnu/packages/bioinformatics.scm (vsearch): Update to 1.11.1. Ben Woodcroft2016-05-17
* gnu: diamond: Update to 0.8.1.•••* gnu/packages/bioinformatics.scm (diamond): Update to 0.8.1. [source]: Remove 'snippet'. [build-system]: Use cmake-build-system. [arguments]: Remove modifications to phases. [native-inputs]: Remove field. [inputs]: Remove 'boost'. Ben Woodcroft2016-05-17
* gnu: emacs-constants: Factorize home-page in source URL.•••* gnu/packages/emacs.scm (emacs-constants): Move 'home-page' above. Use it in 'uri'. Ludovic Courtès2016-05-17
* gnu: 'uncompressed-file-fetch' no longer depends on gzip.•••* gnu/packages/emacs.scm (uncompressed-file-fetch): Remove dependency on GZIP. Ludovic Courtès2016-05-17
* gnu: cflow: Update to 1.5.•••* gnu/packages/code.scm (cflow): Update to 1.5. Efraim Flashner2016-05-17
* gnu: Add geiser-next.•••Also, I previously committed to this repository in 2015; add self to copyright headers for that year too. * gnu/packages/emacs.scm (geiser-next): New variable. Christopher Allan Webber2016-05-16
* import cran: latest-bioconductor-release: Wrap Bioconductor URL in list.•••* guix/import/cran.scm (latest-bioconductor-release): Wrap Bioconductor URL in list in the "urls" field of the "upstream-source" value. Ricardo Wurmus2016-05-16
* gnu: r-zlibbioc: Update to 1.18.0.•••* gnu/packages/bioinformatics.scm (r-zlibbioc): Update to 1.18.0. Ricardo Wurmus2016-05-16
* gnu: r-motifrg: Update to 1.16.0.•••* gnu/packages/bioinformatics.scm (r-motifrg): Update to 1.16.0. Ricardo Wurmus2016-05-16
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