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2020-01-21gnu: upower: Install 'dbus-1/system.d/org.freedesktop.UPower.conf' to etc/.Ludovic Courtès
Fixes <https://bugs.gnu.org/39203>. Reported by Jesse Gibbons <jgibbons2357@gmail.com>. * gnu/packages/gnome.scm (upower)[source]: Add 'modules' and 'snippet'.
2020-01-21gnu: Use HTTPS for (gnu packages bioinformatics) home pages.Tobias Geerinckx-Rice
* gnu/packages/bioinformatics (bamm, ribodiff, python-biopython) (discrover, hisat, hisat2, htseq, fastqc, htslib, python2-pbcore, roary) (sortmerna, r-qtl, multiqc, r-deseq, r-fastseg, sambamba, trim-galore) (gess, kentutils, bismark, kallisto, sailfish, python-hicexplorer) (pplacer, python2-checkm-genome, r-velocyto)[home-page]: Use HTTPS.
2020-01-21gnu: r-gage: Update home page.Tobias Geerinckx-Rice
* gnu/packages/bioinformatics.scm (r-gage)[home-page]: Update.
2020-01-21gnu: sra-tools: Update home page.Tobias Geerinckx-Rice
* gnu/packages/bioinformatics.scm (sra-tools)[home-page]: Update.
2020-01-21gnu: raxml: Update home page.Tobias Geerinckx-Rice
* gnu/packages/bioinformatics.scm (raxml)[home-page]: Update.
2020-01-21gnu: prodigal: Update home page.Tobias Geerinckx-Rice
* gnu/packages/bioinformatics.scm (prodigal)[home-page]: Use source code repository as home page.
2020-01-21gnu: miso: Update home page.Tobias Geerinckx-Rice
* gnu/packages/bioinformatics.scm (miso)[home-page]: Update.
2020-01-21gnu: grit: Update home page.Tobias Geerinckx-Rice
* gnu/packages/bioinformatics.scm (grit)[home-page]: Use source code repository as home page.
2020-01-21gnu: express-beta-diversity: Update home page.Tobias Geerinckx-Rice
The original is not coming back: <https://github.com/dparks1134/ExpressBetaDiversity/issues/11>. * gnu/packages/bioinformatics.scm (express-beta-diversity)[home-page]: Use source code repository as home page.
2020-01-21gnu: dendropy: Update home page.Tobias Geerinckx-Rice
* gnu/packages/bioinformatics.scm (dendropy)[home-page]: Update.
2020-01-21gnu: ocaml-markup: Update to 0.8.2.Julien Lepiller
gnu/packages/ocaml.scm (ocaml-markup): Update to 0.8.2.
2020-01-21gnu: ocaml-lwt: Update to 5.1.1.Julien Lepiller
* gnu/packages/ocaml.scm (ocaml-lwt): update to 5.1.1.
2020-01-21gnu: Add ocaml-mmap.Julien Lepiller
* gnu/packages/ocaml.scm (ocaml-mmap): New variable.
2020-01-21gnu: ocaml-bisect-ppx: Update to 1.4.2.Julien Lepiller
* gnu/packages/ocaml.scm (ocaml-bisect-ppx): Update to 1.4.2.
2020-01-21gnu: ocaml-qtest. Update to 2.10.1.Julien Lepiller
* gnu/packages/ocaml.scm (ocaml-qtest): Update to 2.10.1.
2020-01-21gnu: ocaml-qcheck: Update to 0.12.Julien Lepiller
* gnu/packages/ocaml.scm (ocaml-qcheck): Update to 0.12.
2020-01-21gnu: camlp5: Update to 7.10.Julien Lepiller
* gnu/packages/ocaml.scm (camlp5): Upadte to 7.10.
2020-01-21gnu: opam: Update to 2.0.6.Julien Lepiller
* gnu/pckages/ocaml.scm (opam): Update to 2.0.6.
2020-01-21gnu: Use HTTPS for bioconductor.org.Tobias Geerinckx-Rice
* gnu/packages/bioinformatics.scm (r-homo-sapiens)[source]: Use HTTPS. * gnu/packages/bioconductor.scm (r-bsgenome-mmusculus-ucsc-mm9-masked, r-cghcall, r-diffbind, r-cghbase, r-ripseeker, r-chippeakanno, r-qdnaseq, r-marray, r-multtest)[home-page]: Likewise. * gnu/packages/graph.scm (r-rgraphviz)[home-page]: Likewise.
2020-01-21gnu: gzdoom: Update to 4.3.2.Tobias Geerinckx-Rice
* gnu/packages/games.scm (gzdoom): Update to 4.3.2. [source]: Use GIT-FETCH and GIT-FILE-NAME. Apply system libgme patch. Update snippet. [arguments]: Allow system libgme. Update substitution file names. [inputs]: Use fluidsynth@2. * gnu/packages/patches/gzdoom-find-system-libgme.patch: New file. * gnu/local.mk (dist_patch_DATA): Add it.
2020-01-21gnu: supercollider: Update to 3.10.4.Tobias Geerinckx-Rice
* gnu/packages/audio.scm (supercollider): Update to 3.10.4. [source]: Remove patch. * gnu/packages/patches/supercollider-boost-1.70-build-fix.patch: Delete file. * gnu/local.mk (dist_patch_DATA): Remove it.
2020-01-21Revert "gnu: Add guile3.0-commonmark."Ricardo Wurmus
This reverts commit 346386f3f7a3a00720e5423fa5900a1b3facb702. A Guile 3.0 variant had already been added with commit 1fa342323619372326106fb923e72ae7beecb5e6.
2020-01-20gnu: Add guile3.0-pfds.Ricardo Wurmus
* gnu/packages/guile-xyz.scm (guile3.0-pfds): New variable.
2020-01-20gnu: Add guile3.0-wisp.Ricardo Wurmus
* gnu/packages/guile-xyz.scm (guile3.0-wisp): New variable.
2020-01-20gnu: Add guile3.0-commonmark.Ricardo Wurmus
* gnu/packages/guile-xyz.scm (guile3.0-commonmark): New variable. (guile-commonmark)[arguments]: Patch configure file.
2020-01-20installer: Disable F12 hot key.Ludovic Courtès
Fixes <https://bugs.gnu.org/38562>. Reported by Brice Waegeneire <brice@waegenei.re>. Previously, pressing F12 or shift-F2 in one of those forms would cause it to exit, usually with the default value #t because the caller had not provided a useful hotkey "callback". * gnu/installer/newt/page.scm (run-input-page, run-confirmation-page) (run-listbox-selection-page, run-checkbox-tree-page) (run-file-textbox-page): Pass #:flags FLAG-NOF12 to 'make-form'.
2020-01-20installer: Makes sure the installer proceeds after hitting "Edit".Ludovic Courtès
Fixes <https://bugs.gnu.org/39199>. Reported by Jonathan Brielmaier <jonathan.brielmaier@web.de>. * gnu/installer/newt/page.scm (run-file-textbox-page): Move 'loop' to the beginning of the body. Do not call 'loop' from the 'dynamic-wind' exit handler as we would not return the value of the second call to 'loop'.
2020-01-20gnu: guile-git: Update to 0.3.0.Marius Bakke
* gnu/packages/guile.scm (guile-git): Update to 0.3.0. [source]: Download tarball with URL-FETCH. [source](file-name, modules, snippet): Remove. [native-inputs]: Remove AUTOCONF, AUTOMAKE and TEXINFO.
2020-01-20gnu: qt@4: Build with libjpeg-turbo.Marius Bakke
* gnu/packages/qt.scm (qt-4)[inputs]: Change from LIBJPEG-8 to LIBJPEG-TURBO.
2020-01-20gnu: stepmania: Build with libjpeg-turbo.Marius Bakke
* gnu/packages/games.scm (stepmania)[inputs]: Change from LIBJPEG-8 to LIBJPEG-TURBO.
2020-01-20gnu: mame: Build with libjpeg-turbo.Marius Bakke
* gnu/packages/emulators.scm (mame)[inputs]: Change from LIBJPEG-8 to LIBJPEG-TURBO.
2020-01-20gnu: mailutils: Update to 3.8.Marius Bakke
* gnu/packages/mail.scm (mailutils): Update to 3.8. [arguments]: Adjust substitutions.
2020-01-20gnu: xorg-server: Update to 1.20.7.Marius Bakke
* gnu/packages/xorg.scm (xorg-server): Update to 1.20.7.
2020-01-20gnu: libsrtp: Build shared library.Marius Bakke
* gnu/packages/telephony.scm (libsrtp)[arguments]: Add #:phases.
2020-01-20gnu: libsrtp: Update to 2.3.0.Marius Bakke
* gnu/packages/telephony.scm (libsrtp): Update to 2.3.0.
2020-01-20gnu: ffmpeg: Update to 4.2.2.Marius Bakke
* gnu/packages/video.scm (ffmpeg): Update to 4.2.2.
2020-01-20gnu: libvpx: Update to 1.8.2.Marius Bakke
* gnu/packages/video.scm (libvpx): Update to 1.8.2.
2020-01-20gnu: re2: Update to 2020-01-01.Marius Bakke
* gnu/packages/regex.scm (re2): Update to 2020-01-01.
2020-01-20gnu: e2fsprogs: Update to 1.45.5.Marius Bakke
* gnu/packages/linux.scm (e2fsprogs): Update to 1.45.5.
2020-01-20gnu: snappy: Update to 1.1.8.Marius Bakke
* gnu/packages/compression.scm (snappy): Update to 1.1.8.
2020-01-20gnu: python-parameterized: Update to 0.7.1.Marius Bakke
* gnu/packages/patches/python2-parameterized-docstring-test.patch: New file. * gnu/local.mk (dist_patch_DATA): Adjust accordingly. * gnu/packages/check.scm (python-parameterized): Update to 0.7.1. [arguments]: Remove #:tests?. Add #:phases to override 'check' phase. [native-inputs]: Add PYTHON-MOCK and PYTHON-NOSE. [properties]: New field. (python2-parameterized)[source](patches): New field.
2020-01-20gnu: Add python-anytree.Marius Bakke
* gnu/packages/python-xyz.scm (python-anytree): New public variable.
2020-01-20gnu: python-packaging: Add comment about upstream patch status.Marius Bakke
* gnu/packages/python-xyz.scm (python-packaging)[source]: Add comment, to prevent needless rebuild by updating the patch directly.
2020-01-20gnu: guix-data-service: Update to 0.0.1-17.bf25a8d.Christopher Baines
* gnu/packages/web.scm (guix-data-service): Update to 0.0.1-17.bf25a8d.
2020-01-20tests: mail: Remove %getmail-os from the bottom of the file.Christopher Baines
This was left over when debugging the system test. * gnu/tests/mail.scm: Remove %getmail-os from the bottom of the file.
2020-01-20services: getmail: Adjust a couple of default configuration values.Christopher Baines
Change the message-log-syslog and message-log-verbose configuration values to match the Getmail defaults. * gnu/services/getmail.scm (getmail-options-configuration): Change defaults for message-log-syslog and message-log-verbose * doc/guix.texi (Mail Services): Update the Getmail documentation accordingly.
2020-01-20services: getmail: Fix some configuration documentation strings.Christopher Baines
* gnu/services/getmail.scm (getmail-retriever-configuration): Specify proper documentation strings for some of the fields. * doc/guix.texi (Mail Services): Update the documentation accordingly.
2020-01-20services: getmail: Fix stopping the shepherd service.Christopher Baines
* gnu/services/getmail.scm (getmail-shepherd-services): Add a stop component to the shepherd services.
2020-01-20services: Add "sane" service.Danny Milosavljevic
* gnu/services/desktop.scm (%desktop-services): Add "sane" service.
2020-01-20gnu: rust-crossbeam-channel-0.3: Update to 0.3.9.Efraim Flashner
* gnu/packages/crates-io.scm (rust-crossbeam-channel-0.3)[arguments]: Remove rust-smallvec-0.6 from cargo-inputs. Add rust-rust-num-cpus-1.10 to cargo-development-inputs. Replace rust-rand-0.4 with 0.6.
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