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2016-07-28gnu: gnome: Propagate file-roller....* gnu/packages/gnome.scm (gnome)[propagated-inputs]: Add file-roller. Signed-off-by: Ludovic Courtès <ludo@gnu.org> Alex Griffin
2016-07-28doc: Discourage software bundling....Fixes <http://bugs.gnu.org/24008>. Suggested by ng0 <ng0@we.make.ritual.n0.is>. * doc/contributing.texi (Submitting Patches): Add item about bundling. Ludovic Courtès
2016-07-28doc: Send changes in your patch which are related....* doc/contributing.texi (Submitting Patches): New @item: This gives information about sending related changes and examples on what we view as related changes. Co-authored-by: Ludovic Courtès <ludo@gnu.org> ng0
2016-07-28doc: Mention separate branch for packages with many dependents....Suggested by ng0 <ng0@we.make.ritual.n0.is>. * doc/contributing.texi (Submitting Patches): Add note on packages with more than 100 dependents. Ludovic Courtès
2016-07-28gnu: r-genomicfeatures: Update to 1.24.5....* gnu/packages/bioinformatics.scm (r-genomicfeatures): Update to 1.24.5. Ben Woodcroft
2016-07-28gnu: r-bsgenome: Update to 1.40.1....* gnu/packages/bioinformatics.scm (r-bsgenome): Update to 1.40.1. Ben Woodcroft
2016-07-28gnu: r-iranges: Update to 2.6.1....* gnu/packages/bioinformatics.scm (r-iranges): Update to 2.6.1. Ben Woodcroft
2016-07-28gnu: r-limma: Update to 3.28.17....* gnu/packages/bioinformatics.scm (r-limma): Update to 3.28.17. Ben Woodcroft
2016-07-28gnu: r-xvector: Update to 0.12.1....* gnu/packages/bioinformatics.scm (r-xvector): Update to 0.12.1. Ben Woodcroft
2016-07-28gnu: r-genomicranges: Update to 1.24.2....* gnu/packages/bioinformatics.scm (r-genomicranges): Update to 1.24.2. Ben Woodcroft
2016-07-28gnu: r-annotationdbi: Update to 1.34.4....* gnu/packages/bioinformatics.scm (r-annotationdbi): Update to 1.34.4. Ben Woodcroft
2016-07-28gnu: r-biocparallel: Update to 1.6.3....* gnu/packages/bioinformatics.scm (r-biocparallel): Update to 1.6.3. Ben Woodcroft
2016-07-28gnu: r-biostrings: Update to 2.40.2....* gnu/packages/bioinformatics.scm (r-biostrings): Update to 2.40.2. Ben Woodcroft
2016-07-28gnu: r-summarizedexperiment: Update to 1.2.3....* gnu/packages/bioinformatics.scm (r-summarizedexperiment): Update to 1.2.3. Ben Woodcroft
2016-07-28gnu: r-genomicalignments: Update to 1.8.4....* gnu/packages/bioinformatics.scm (r-genomicalignments): Update to 1.8.4. Ben Woodcroft
2016-07-28gnu: r-rtracklayer: Update to 1.32.2....* gnu/packages/bioinformatics.scm (r-rtracklayer): Update to 1.32.2. Ben Woodcroft
2016-07-28gnu: r-genomeinfodb: Update to 1.8.3....* gnu/packages/bioinformatics.scm (r-genomeinfodb): Update to 1.8.3. Ben Woodcroft
2016-07-28gnu: r-s4vectors: Update to 0.10.2....* gnu/packages/bioinformatics.scm (r-s4vectors): Update to 0.10.2. Ben Woodcroft
2016-07-28gnu: mysql: Update to 5.7.13 [fixes CVE-2016-{3477,3521,3615,5440}]....* gnu/packages/patches/mysql-fix-failing-test.patch: New file. * gnu/local.mk (dist_patch_DATA): Add it. * gnu/packages/databases.scm (mysql): Update to 5.7.13. Leo Famulari
2016-07-28gnu: the-silver-searcher: Update to 0.32.0....* gnu/packages/code.scm(the-silver-searcher): Update to 0.32.0. Tomáš Čech
2016-07-27gnu: imagemagick: Update to 6.9.5-3....* gnu/packages/imagemagick.scm (imagemagick): Update to 6.9.5-3. Leo Famulari
2016-07-27gnu: mariadb: Update to 10.1.16....* gnu/packages/databases.scm (mariadb): Update to 10.1.16. Leo Famulari
2016-07-27gnu: calibre: Update to 2.63.0....* gnu/packages/ebook.scm (calibre): Update to 2.63.0. [inputs]: Remove unnecessary imagemagick dependency. [phases]: Use modify-phases. * gnu/packages/patches/calibre-drop-unrar.patch: Update for new version. Signed-off-by: Roel Janssen <roel@gnu.org> Alex Griffin
2016-07-27system: Source /etc/environment before $HOME/.guix-profile/etc/profile....* gnu/system.scm (operating-system-etc-service) <profile>: Move sourcing of /etc/environment before that of $HOME/.guix-profile/etc/profile. Signed-off-by: Ludovic Courtès <ludo@gnu.org> Carlos Sánchez de La Lama
2016-07-27gnu: krona-tools: Update to 2.7....* gnu/packages/web.scm (krona-tools): Update to 2.7. [arguments]: Delete 'build' phase. Install new scripts. Ben Woodcroft
2016-07-27gnu: diamond: Update to 0.8.16....* gnu/packages/bioinformatics.scm (diamond): Update to 0.8.16. Ben Woodcroft
2016-07-27gnu: guix: Update revision number in version....This is a follow-up to commit 95af24a2f1fb58eb9e6ee902c9330534f0aca9f3. Reported by Alex Kost <alezost@gmail.com>. Andreas Enge
2016-07-27tests: Use unbuffered input ports when decompressing from 'guix publish'....Fixes <http://bugs.gnu.org/24060>. Reported by Chris Marusich <cmmarusich@gmail.com>. * tests/publish.scm (http-get-port): Explicitly call 'open-socket-for-uri' and add calls to 'setvbuf'. Ludovic Courtès
2016-07-27zlib: Protect against non-empty port internal buffers....* guix/zlib.scm (make-gzip-input-port)[gzfile]: Error out if (drain-input port) returns a non-empty string. * guix/zlib.scm (make-gzip-output-port)[gzfile]: Call 'force-output'. Ludovic Courtès
2016-07-27zlib: Clarify when 'gzread!' can return zero....* guix/zlib.scm (gzread!): Augment docstring to clarify when zero is returned (based on reading zlib code). (make-gzip-input-port)[read!]: Remove scary comment. Ludovic Courtès
2016-07-27gnu: magit: Fix rebase commands that require perl....* gnu/packages/emacs.scm (magit)[inputs]: Add 'perl'. [arguments]: Adjust 'patch-exec-paths' phase to make some rebase commands find 'perl'. Signed-off-by: Alex Kost <alezost@gmail.com> Alex Griffin
2016-07-27gnu: Add httping....* gnu/packages/networking.scm (httping): New variable. Tobias Geerinckx-Rice
2016-07-27gnu: Add missing copyright symbol....* gnu/packages/networking.scm: Add missing "©" to header comments. Tobias Geerinckx-Rice
2016-07-26gnu: gmime: Remove 'gpg' to 'gpg2' substitution....* gnu/packages/mail.scm (gmime)[arguments]: Remove the substitution which previously changed 'gpg' to 'gpg2' in 'patch-paths-in-tests' phase. Signed-off-by: Leo Famulari <leo@famulari.name> ng0
2016-07-26gnu: dmd: Remove package, superseded by shepherd....* gnu/packages/admin.scm (dmd): Remove variable. Andreas Enge
2016-07-26gnu: Add perl-db-file....* gnu/packages/databases.scm (perl-db_file): New variable. Signed-off-by: Andreas Enge <andreas@enge.fr> Danny Milosavljevic
2016-07-26profiles: Output in 'package->manifest-entry' defaults to "out"....Fixes <http://bugs.gnu.org/24029>. Reported by Dylan Jeffers <sapientech@openmailbox.org>. * guix/profiles.scm (package->manifest-entry): Change #:output to default to "out". (packages->manifest): Add 'package?' in second 'match' clause. * tests/profiles.scm ("package->manifest-entry defaults to \"out\""): New test. Ludovic Courtès
2016-07-26environment: Set 'GUIX_ENVIRONMENT' to the profile....* guix/scripts/environment.scm (create-environment): Set 'GUIX_ENVIRONMENT' to PROFILE. * tests/guix-environment.sh: Test it. * doc/guix.texi (Invoking guix environment): Document it. Ludovic Courtès
2016-07-26import: pypi: Correctly handle new-style URLs....Fixes <http://bugs.gnu.org/23997>. * guix/import/pypi.scm (guix-package->pypi-name): Rewrite using 'basename' and 'hyphen-package-name->name+version'. * tests/pypi.scm ("guix-package->pypi-name, old URL style") ("guix-package->pypi-name, new URL style"): New tests. Ludovic Courtès
2016-07-26doc: Explain authentication in "System Installation"....Suggested by Vincent Legoll <vincent.legoll@gmail.com>. * doc/guix.texi (OPENPGP-SIGNING-KEY-ID): New constant. (Binary Installation): Use it. (USB Stick Installation): Copy and adjust the authentication bit from "Binary Installation". Ludovic Courtès
2016-07-26doc: Better illustration use of package revision numbers....* doc/guix.texi (Version Numbers): Add the revision to the example of the git package used in 7.6.3. Signed-off-by: Ludovic Courtès <ludo@gnu.org> ng0
2016-07-26gnu: icecat: Install icons....* gnu/packages/gnuzilla.scm (icecat)[arguments]: Add 'install-icons' phase. Signed-off-by: Ludovic Courtès <ludo@gnu.org> Alex Griffin
2016-07-26gnu: Add haveged....* gnu/packages/linux.scm (haveged): New variable. Tobias Geerinckx-Rice
2016-07-26gnu: Add perceptualdiff....* gnu/packages/image.scm (perceptualdiff): New variable. Tobias Geerinckx-Rice
2016-07-26gnu: linux-libre@4.1: Update to 4.1.28....* gnu/packages/linux.scm (linux-libre-4.1): Update to 4.1.28. Mark H Weaver
2016-07-26gnu: linux-libre: Update to 4.7....* gnu/packages/linux.scm (linux-libre): Update to 4.7. * gnu/packages/linux-libre-4.7-x86_64.conf, gnu/packages/linux-libre-4.7-i686.conf: New files. * gnu/packages/linux-libre-4.6-x86_64.conf, gnu/packages/linux-libre-4.6-i686.conf: Delete files. * Makefile.am (KCONFIGS): Update accordingly. Mark H Weaver
2016-07-26gnu: calibre: Build with non-modular Qt....* gnu/packages/ebook.scm (calibre)[native-inputs]: Replace QTBASE by QT. [inputs]: Replace QTBASE by QT and PYTHON2-PYQT by PYTHON2-PYQT-5.5. This essentially reverts commit 76806c54ed72f8f04079bbb187b186b833c103e1. Reported by Roel Janssen <roel@gnu.org>. Andreas Enge
2016-07-26gnu: pyqt: Add versions based on non-modular Qt 5.5....* gnu/packages/qt.scm (python-pyqt-5.5, python2-pyqt-5.5): New variables. Andreas Enge
2016-07-25gnu: guix: Update development snapshot....* gnu/packages/package-management.scm (guix-devel): Update to 97c8aef. Andreas Enge
2016-07-25system: Add mapped devices for RAID....* gnu/system/mapped-devices.scm (raid-device-mapping, open-raid-device, close-raid-device): New variables. * doc/guix.texi (Mapped Devices): Add documentation for RAID devices, reorganize documentation for LUKS devices. Co-authored-by: Ludovic Courtès <ludo@gnu.org> Andreas Enge
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