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* gnu: r-genomicfeatures: Update to 1.24.5.Ben Woodcroft2016-07-28
| | | | * gnu/packages/bioinformatics.scm (r-genomicfeatures): Update to 1.24.5.
* gnu: r-bsgenome: Update to 1.40.1.Ben Woodcroft2016-07-28
| | | | * gnu/packages/bioinformatics.scm (r-bsgenome): Update to 1.40.1.
* gnu: r-iranges: Update to 2.6.1.Ben Woodcroft2016-07-28
| | | | * gnu/packages/bioinformatics.scm (r-iranges): Update to 2.6.1.
* gnu: r-limma: Update to 3.28.17.Ben Woodcroft2016-07-28
| | | | * gnu/packages/bioinformatics.scm (r-limma): Update to 3.28.17.
* gnu: r-xvector: Update to 0.12.1.Ben Woodcroft2016-07-28
| | | | * gnu/packages/bioinformatics.scm (r-xvector): Update to 0.12.1.
* gnu: r-genomicranges: Update to 1.24.2.Ben Woodcroft2016-07-28
| | | | * gnu/packages/bioinformatics.scm (r-genomicranges): Update to 1.24.2.
* gnu: r-annotationdbi: Update to 1.34.4.Ben Woodcroft2016-07-28
| | | | * gnu/packages/bioinformatics.scm (r-annotationdbi): Update to 1.34.4.
* gnu: r-biocparallel: Update to 1.6.3.Ben Woodcroft2016-07-28
| | | | * gnu/packages/bioinformatics.scm (r-biocparallel): Update to 1.6.3.
* gnu: r-biostrings: Update to 2.40.2.Ben Woodcroft2016-07-28
| | | | * gnu/packages/bioinformatics.scm (r-biostrings): Update to 2.40.2.
* gnu: r-summarizedexperiment: Update to 1.2.3.Ben Woodcroft2016-07-28
| | | | * gnu/packages/bioinformatics.scm (r-summarizedexperiment): Update to 1.2.3.
* gnu: r-genomicalignments: Update to 1.8.4.Ben Woodcroft2016-07-28
| | | | * gnu/packages/bioinformatics.scm (r-genomicalignments): Update to 1.8.4.
* gnu: r-rtracklayer: Update to 1.32.2.Ben Woodcroft2016-07-28
| | | | * gnu/packages/bioinformatics.scm (r-rtracklayer): Update to 1.32.2.
* gnu: r-genomeinfodb: Update to 1.8.3.Ben Woodcroft2016-07-28
| | | | * gnu/packages/bioinformatics.scm (r-genomeinfodb): Update to 1.8.3.
* gnu: r-s4vectors: Update to 0.10.2.Ben Woodcroft2016-07-28
| | | | * gnu/packages/bioinformatics.scm (r-s4vectors): Update to 0.10.2.
* gnu: mysql: Update to 5.7.13 [fixes CVE-2016-{3477,3521,3615,5440}].Leo Famulari2016-07-28
| | | | | | * 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.
* gnu: the-silver-searcher: Update to 0.32.0.Tomáš Čech2016-07-28
| | | | * gnu/packages/code.scm(the-silver-searcher): Update to 0.32.0.
* gnu: imagemagick: Update to 6.9.5-3.Leo Famulari2016-07-27
| | | | * gnu/packages/imagemagick.scm (imagemagick): Update to 6.9.5-3.
* gnu: mariadb: Update to 10.1.16.Leo Famulari2016-07-27
| | | | * gnu/packages/databases.scm (mariadb): Update to 10.1.16.
* gnu: calibre: Update to 2.63.0.Alex Griffin2016-07-27
| | | | | | | | | | | * 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>
* system: Source /etc/environment before $HOME/.guix-profile/etc/profile.Carlos Sánchez de La Lama2016-07-27
| | | | | | | * 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>
* gnu: krona-tools: Update to 2.7.Ben Woodcroft2016-07-27
| | | | | * gnu/packages/web.scm (krona-tools): Update to 2.7. [arguments]: Delete 'build' phase. Install new scripts.
* gnu: diamond: Update to 0.8.16.Ben Woodcroft2016-07-27
| | | | * gnu/packages/bioinformatics.scm (diamond): Update to 0.8.16.
* gnu: guix: Update revision number in version.Andreas Enge2016-07-27
| | | | | This is a follow-up to commit 95af24a2f1fb58eb9e6ee902c9330534f0aca9f3. Reported by Alex Kost <alezost@gmail.com>.
* tests: Use unbuffered input ports when decompressing from 'guix publish'.Ludovic Courtès2016-07-27
| | | | | | | | 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'.
* zlib: Protect against non-empty port internal buffers.Ludovic Courtès2016-07-27
| | | | | | * 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'.
* zlib: Clarify when 'gzread!' can return zero.Ludovic Courtès2016-07-27
| | | | | | * 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.
* gnu: magit: Fix rebase commands that require perl.Alex Griffin2016-07-27
| | | | | | | | * 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>
* gnu: Add httping.Tobias Geerinckx-Rice2016-07-27
| | | | * gnu/packages/networking.scm (httping): New variable.
* gnu: Add missing copyright symbol.Tobias Geerinckx-Rice2016-07-27
| | | | * gnu/packages/networking.scm: Add missing "©" to header comments.
* gnu: gmime: Remove 'gpg' to 'gpg2' substitution.ng02016-07-26
| | | | | | | * 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>
* gnu: dmd: Remove package, superseded by shepherd.Andreas Enge2016-07-26
| | | | * gnu/packages/admin.scm (dmd): Remove variable.
* gnu: Add perl-db-file.Danny Milosavljevic2016-07-26
| | | | | | * gnu/packages/databases.scm (perl-db_file): New variable. Signed-off-by: Andreas Enge <andreas@enge.fr>
* profiles: Output in 'package->manifest-entry' defaults to "out".Ludovic Courtès2016-07-26
| | | | | | | | | | | 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.
* environment: Set 'GUIX_ENVIRONMENT' to the profile.Ludovic Courtès2016-07-26
| | | | | | | * 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.
* import: pypi: Correctly handle new-style URLs.Ludovic Courtès2016-07-26
| | | | | | | | | 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.
* doc: Explain authentication in "System Installation".Ludovic Courtès2016-07-26
| | | | | | | | | 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".
* doc: Better illustration use of package revision numbers.ng02016-07-26
| | | | | | | * 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>
* gnu: icecat: Install icons.Alex Griffin2016-07-26
| | | | | | | * gnu/packages/gnuzilla.scm (icecat)[arguments]: Add 'install-icons' phase. Signed-off-by: Ludovic Courtès <ludo@gnu.org>
* gnu: Add haveged.Tobias Geerinckx-Rice2016-07-26
| | | | * gnu/packages/linux.scm (haveged): New variable.
* gnu: Add perceptualdiff.Tobias Geerinckx-Rice2016-07-26
| | | | * gnu/packages/image.scm (perceptualdiff): New variable.
* gnu: linux-libre@4.1: Update to 4.1.28.Mark H Weaver2016-07-26
| | | | * gnu/packages/linux.scm (linux-libre-4.1): Update to 4.1.28.
* gnu: linux-libre: Update to 4.7.Mark H Weaver2016-07-26
| | | | | | | | | * 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.
* gnu: calibre: Build with non-modular Qt.Andreas Enge2016-07-26
| | | | | | | | | * 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>.
* gnu: pyqt: Add versions based on non-modular Qt 5.5.Andreas Enge2016-07-26
| | | | * gnu/packages/qt.scm (python-pyqt-5.5, python2-pyqt-5.5): New variables.
* gnu: guix: Update development snapshot.Andreas Enge2016-07-25
| | | | * gnu/packages/package-management.scm (guix-devel): Update to 97c8aef.
* system: Add mapped devices for RAID.Andreas Enge2016-07-25
| | | | | | | | | * 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>
* doc: Explain when guix edit is read-only.myglc22016-07-25
| | | | | | | * doc/guix.texi (Invoking guix edit): Explain when you can and can't edit the recipe. Signed-off-by: Alex Kost <alezost@gmail.com>
* gnu: emacs-solarized-theme: Remove unneeded dependencies.Alex Kost2016-07-25
| | | | | * gnu/packages/emacs.scm (emacs-solarized-theme)[propagated-inputs]: Remove 'emacs-f' and 'emacs-s'.
* gnu: emacs: Install site-start.el in non-versioned directory.Alex Kost2016-07-25
| | | | | | | | Reported by Ricardo Wurmus on #guix. * gnu/packages/emacs.scm (emacs)[arguments]: Put "site-start.el" in "/share/emacs/site-lisp" instead of "/share/emacs/<version>/site-lisp" to let inherited package with another version find it.
* gnu: Add guile-daemon.Alex Kost2016-07-25
| | | | * gnu/packages/guile.scm (guile-daemon): New variable.
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