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* Use HTTPS for bioconductor.org.Tobias Geerinckx-Rice2017-10-21
| | | | | | | | | | | | | | | | | | | | | | | | | | | | * doc/guix.texi (Invoking guix import, Invoking guix refresh): Use HTTPS for bioconductor.org URLs. * gnu/packages/bioinformatics.scm (r-annotate, r-geneplotter, r-genefilter) (r-deseq2, r-dexseq, r-annotationforge, r-rbgl, r-gseabase, r-category) (r-gostats, r-shortread, r-biocgenerics, r-biocinstaller, r-biocviews) (r-biocstyle, r-bioccheck, r-s4vectors, r-iranges, r-genomeinfodbdata) (r-genomeinfodb, r-xvector, r-genomicranges, r-biobase, r-annotationdbi) (r-biomart, r-biocparallel, r-biostrings, r-rsamtools, r-delayedarray) (r-summarizedexperiment, r-genomicalignments, r-rtracklayer) (r-genomicfeatures, r-graph, r-topgo, r-bsgenome, r-impute, r-seqpattern) (r-seqlogo, r-motifrg, r-bamsignals, r-mutationalpatterns, r-tximport) (r-rhdf5, r-chipseq, r-sva, r-affy, r-vsn, r-mzid, r-msnid) (r-interactivedisplaybase, r-annotationhub)[home-page]: Likewise. * gnu/packages/bioinformatics.scm (r-txdb-hsapiens-ucsc-hg19-knowngene) (r-go-db, r-bsgenome-hsapiens-1000genomes-hs37d5, r-org-hs-eg-db) (r-org-ce-eg-db, r-org-dm-eg-db, r-org-mm-eg-db) (r-bsgenome-hsapiens-ucsc-hg19, r-bsgenome-mmusculus-ucsc-mm9) (r-bsgenome-mmusculus-ucsc-mm10, r-txdb-mmusculus-ucsc-mm10-knowngene) (r-bsgenome-celegans-ucsc-ce6, r-bsgenome-celegans-ucsc-ce10) (r-bsgenome-dmelanogaster-ucsc-dm3, r-copyhelper)[source, home-page]: Likewise. * gnu/packages/statistics.scm (r-rcurl)[source]: Likewise. * guix/build-system/r.scm (bioconductor-uri): Likewise. * guix/import/cran.scm (%cran-url, bioconductor-package?) (bioconductor-data-package?, bioconductor-experiment-package?): Likewise.
* gnu: schismtracker: Update to 20170910.Kei Kebreau2017-10-21
| | | | * gnu/packages/music.scm (schismtracker): Update to 20170910.
* gnu: Fix the hashes of mutated GitHub archives.Maxim Cournoyer2017-10-20
| | | | | | | | | | | | | | | Fixes <https://bugs.gnu.org/28745>. * gnu/packages/audio.scm (csound): Fix hash. * gnu/packages/engineering.scm (fritzing): Likewise. * gnu/packages/erlang.scm (erlang): Likewise. * gnu/packages/fonts.scm (font-google-material-design-icons): Likewise. * gnu/packages/graphics.scm (ogre): Likewise. * gnu/packages/java.scm (java-plexus-interpolation, antlr3): Likewise. * gnu/packages/serialization.scm (yaml-cpp): Likewise. * gnu/packages/version-control.scm (libgit2): Likewise. Signed-off-by: Ludovic Courtès <ludo@gnu.org>
* gnu: libvirt: Fix CVE-2017-1000256.Leo Famulari2017-10-20
| | | | | | * gnu/packages/patches/libvirt-CVE-2017-1000256.patch: New file. * gnu/local.mk (dist_patch_DATA): Add it. * gnu/packages/virtualization.scm (libvirt)[source]: Use it.
* gnu: mysql: Update to 5.7.20.Leo Famulari2017-10-20
| | | | * gnu/packages/databases.scm (mysql): Update to 5.7.20.
* gnu: webkitgtk: Update to 2.18.1.Leo Famulari2017-10-20
| | | | * gnu/packages/webkit.scm (webkitgtk): Update to 2.18.1.
* gnu: youtube-dl: Update to 2017.10.20.Tobias Geerinckx-Rice2017-10-20
| | | | * gnu/packages/video.scm (youtube-dl): Update to 2017.10.20.
* gnu: dovecot: Update to 2.2.33.2.Tobias Geerinckx-Rice2017-10-20
| | | | * gnu/packages/mail.scm (dovecot): Update to 2.2.33.2.
* gnu: ola: Build with protobuf@2.Tobias Geerinckx-Rice2017-10-20
| | | | | | | This follows up commit dd12d4aad02fc83e00e7b09d676aa78bcb7dd476. * gnu/packages/protobuf.scm (protobuf-2): New variable. * gnu/packages/lighting.scm (ola)[propagated-inputs]: Use it.
* gnu: font-hack: Update to 3.000.Tobias Geerinckx-Rice2017-10-20
| | | | | | * gnu/packages/fonts.scm (font-hack): Update to 3.000. [source]: Download from new account. [license]: Explicitly list all licences.
* gnu: Add aegisub.Julien Lepiller2017-10-20
| | | | * gnu/packages/video.scm (aegisub): New variable.
* gnu: Add ffms2.Julien Lepiller2017-10-20
| | | | * gnu/packages/video.scm (aegisub): New variable.
* gnu: speexdsp: Fix building on aarch64-linux.Efraim Flashner2017-10-20
| | | | | * gnu/packages/xiph.scm (speexdsp)[arguments]: On aarch64-linux, disable neon optimisations.
* gnu: Add emacs-json-snatcher.Oleg Pykhalov2017-10-20
| | | | | | * gnu/packages/emacs.scm (emacs-json-snatcher): New variable. Signed-off-by: Ludovic Courtès <ludo@gnu.org>
* gnu: shellcheck: Update to 0.4.6.ng02017-10-20
| | | | | | * gnu/packages/haskell.scm (shellcheck): Update to 0.4.6. Signed-off-by: Ludovic Courtès <ludo@gnu.org>
* gnu: dos2unix: Update to 7.4.0.Tobias Geerinckx-Rice2017-10-20
| | | | * gnu/packages/textutils.scm (dos2unix): Update to 7.4.0.
* gnu: cowsay: Swap ‘build’ and ‘install’ phases.Tobias Geerinckx-Rice2017-10-20
| | | | | * gnu/packages/games.scm (cowsay)[arguments]: Invoke ‘install.sh’ during the ‘install’ phase. Delete the ‘build’ phase, as there's nothing to be built.
* gnu: cowsay: Update to 3.04.Tobias Geerinckx-Rice2017-10-20
| | | | | | | * gnu/packages/games.scm (cowsay): Update to 3.04. [source]: Download from new location. [home-page]: Point directly to the relevant page. [description]: Correct mark-up and expand slightly.
* gnu: colordiff: Use HTTPS home page.Tobias Geerinckx-Rice2017-10-20
| | | | * gnu/packages/patchutils.scm (colordiff)[home-page]: Use HTTPS.
* gnu: unbound: Update to 1.6.7.Tobias Geerinckx-Rice2017-10-20
| | | | * gnu/packages/dns.scm (unbound): Update to 1.6.7.
* gnu: neofetch: Update to 3.3.0.Tobias Geerinckx-Rice2017-10-20
| | | | | * gnu/packages/admin.scm (neofetch): Update to 3.3.0. [arguments]: Add ‘install’ phase replacement that manually invokes make.
* gnu: qtox: Update to 1.12.1.Tobias Geerinckx-Rice2017-10-20
| | | | * gnu/packages/messaging.scm (qtox): Update to 1.12.1.
* gnu: speedtest-cli: Update to 1.0.7.Tobias Geerinckx-Rice2017-10-20
| | | | * gnu/packages/networking.scm (speedtest-cli): Update to 1.0.7.
* gnu: cppcheck: Update to 1.81.Tobias Geerinckx-Rice2017-10-20
| | | | * gnu/packages/check.scm (cppcheck): Update to 1.81.
* gnu: python-sge-pygame: Update source URL.Kei Kebreau2017-10-19
| | | | * gnu/packages/game-development.scm (python-sge-pygame)[source]: Update URL.
* gnu: musl: Update to 1.1.17.Leo Famulari2017-10-19
| | | | | | | * gnu/packages/musl.scm (musl): Update to 1.1.17. [source]: Remove patch. * gnu/packages/patches/musl-CVE-2016-8859.patch: Delete file. * gnu/local.mk (dist_patch_DATA): Remove it.
* download: Download a nar when a VCS checkout fails.Ludovic Courtès2017-10-19
| | | | | | | | | | | | Fixes <https://bugs.gnu.org/28709>. * guix/build/download-nar.scm: New file. * Makefile.am (MODULES): Add it. * guix/cvs-download.scm (cvs-fetch)[zlib, config.scm, modules]: New variables. [build]: Use MODULES. Add call to 'download-nar'. * guix/git-download.scm (git-fetch): Likewise. * guix/hg-download.scm (hg-fetch): Likewise.
* Add (guix progress).Ludovic Courtès2017-10-19
| | | | | | | | | | | | | | | | | | Among other things, this removes (guix utils), (guix ui), (guix config), etc. from the closure of (guix build download), as was the case since 798648515b77507c242752457b4dc17c155bad6e. * guix/utils.scm (<progress-reporter>, call-with-progress-reporter): Move to... * guix/progress.scm: ... here. New file. * Makefile.am (MODULES): Add it. * guix/build/download.scm (current-terminal-columns) (nearest-exact-integer, duration->seconds, seconds->string) (byte-count->string, progress-bar, string-pad-middle) (rate-limited, progress-reporter/file, dump-port*) (time-monotonic): Move to progress.scm. * guix/scripts/download.scm: Adjust accordingly. * guix/scripts/substitute.scm: Likewise.
* download: Make 'http-fetch' public.Ludovic Courtès2017-10-19
| | | | | | * guix/build/download.scm (http-fetch): Remove 'file' parameter. Change to return an input port and the content-length. Make public. (url-fetch): Adjust accordingly.
* download: Remove old-Guile leftovers.Ludovic Courtès2017-10-19
| | | | | | | This is a followup to 36626c556ed75219bce196ac93d148f6b9af984c. * guix/build/download.scm (http-fetch): Rename 'port-or-bv' to 'port'. Assume (port? port) is always true, and remove other branch.
* vm: Always use GRUB/i386.Ludovic Courtès2017-10-19
| | | | | | | | Fixes <https://bugs.gnu.org/28768>. Reported by Oleg Pykhalov <go.wigust@gmail.com>. * gnu/system/vm.scm (virtualized-operating-system): Override the 'bootloader' field.
* gnu: linux-libre: Update to 4.13.8.Mark H Weaver2017-10-19
| | | | | * gnu/packages/linux.scm (%linux-libre-version): Update to 4.13.8. (%linux-libre-hash): Update hash.
* gnu: linux-libre@4.9: Update to 4.9.57.Mark H Weaver2017-10-19
| | | | * gnu/packages/linux.scm (linux-libre-4.9): Update to 4.9.57.
* gnu: linux-libre@4.4: Update to 4.4.93.Mark H Weaver2017-10-19
| | | | * gnu/packages/linux.scm (linux-libre-4.4): Update to 4.4.93.
* gnu: linux-libre@4.1: Update to 4.1.45.Mark H Weaver2017-10-19
| | | | | * gnu/packages/linux.scm (linux-libre-4.1): Update to 4.1.45. Remove patch that is now included upstream.
* gnu: yadifa: Update to 2.2.6.Marius Bakke2017-10-19
| | | | * gnu/packages/dns.scm (yadifa): Update to 2.2.6.
* gnu: Add zathura-pdf-mupdf.Marius Bakke2017-10-19
| | | | * gnu/packages/pdf.scm (zathura-pdf-mupdf): New variable.
* gnu: qemu: Build with libjpeg-turbo.Marius Bakke2017-10-19
| | | | | | | | This gets rid of a compile warning since SPICE uses libjpeg-turbo, and reduces the closure size by 0.8MiB. * gnu/packages/virtualization.scm (qemu)[inputs]: Replace LIBJPEG-8 with LIBJPEG-TURBO.
* gnu: emacs: Fix Man default C header file search path.Oleg Pykhalov2017-10-19
| | | | | | | * gnu/packages/emacs.scm (emacs): Make sure Man looks for C header files in the right places. Signed-off-by: Ludovic Courtès <ludo@gnu.org>
* gnu: speex: Build and install 'speexdec' and 'speexenc'.宋文武2017-10-19
| | | | | | | * gnu/packages/xiph.scm (speex)[native-inputs]: Add 'pkg-config'. [inputs]: Add 'speexdsp'. Signed-off-by: Ludovic Courtès <ludo@gnu.org>
* gnu: virt-manager: Fix default URI check.Andy Patterson2017-10-19
| | | | | | | | | Allows virt-manager to connect to qemu://system by default. * gnu/packages/virtualization.scm (virt-manager)[arguments]<#:phases>: Add 'fix-default-uri. Signed-off-by: Ludovic Courtès <ludo@gnu.org>
* gnu: virt-manager: Enable statistics graphing support.Andy Patterson2017-10-19
| | | | | | | * gnu/packages/virtualization.scm (virt-manager)[inputs]: Add python2-pycairo. Signed-off-by: Ludovic Courtès <ludo@gnu.org>
* gnu: qemu: Add OpenGL support.Andy Patterson2017-10-19
| | | | | | | | | | | Enables virgl support with spice 0.13+. * gnu/packages/virtualization.scm (qemu)[arguments]<#:configure-flags>: Add --enable-opengl. [inputs]: Add libdrm and libepoxy. (qemu-minimal)[inputs]: Remove libdrm and libepoxy. Signed-off-by: Ludovic Courtès <ludo@gnu.org>
* gnu: virt-manager: Enable spice-gtk support.Andy Patterson2017-10-19
| | | | | | * gnu/packages/virtualization.scm (virt-manager)[inputs]: Add spice-gtk. Signed-off-by: Ludovic Courtès <ludo@gnu.org>
* gnu: spice-gtk: Enable GObject introspection support.Andy Patterson2017-10-19
| | | | | | | | | Allows virt-manager to use the spice-gtk widget. * gnu/packages/spice.scm (spice-gtk)[inputs]: Add gobject-introspection. [arguments]<#:configure-flags>: Add --enable-introspection. Signed-off-by: Ludovic Courtès <ludo@gnu.org>
* gnu: qemu: Enable spice usb redirection support.Andy Patterson2017-10-19
| | | | | | | | | | | * gnu/packages/virtualization.scm (qemu)[arguments]<#:configure-flags>: New argument. [inputs]: Add usbredir. (qemu-minimal)[arguments]<#:configure-flags>: Restrict them even when they are set by qemu. [inputs]: Remove usbredir. Signed-off-by: Ludovic Courtès <ludo@gnu.org>
* gnu: python-hy: Update to 0.13.0.Ricardo Wurmus2017-10-19
| | | | * gnu/packages/python.scm (python-hy): Update to 0.13.0.
* gnu: Order module imports in (gnu packages mate) alphabetically.ng02017-10-19
| | | | | | * gnu/packages/mate.scm: Order module imports alphabetically. Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
* gnu: Add dirvish.Christopher Allan Webber2017-10-19
| | | | | | * gnu/packages/backup.scm (dirvish): New variable. Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
* gnu: Add perl-libtime-period.Christopher Allan Webber2017-10-19
| | | | * gnu/packages/perl.scm (perl-libtime-period): New variable.
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