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Author SHA1 Message Date
Ludovic Courtès
5dc6d5ce99
gnu: upower: Install 'dbus-1/system.d/org.freedesktop.UPower.conf' to etc/. 
Fixes <https://bugs.gnu.org/39203>.
Reported by Jesse Gibbons <jgibbons2357@gmail.com>.

* gnu/packages/gnome.scm (upower)[source]: Add 'modules' and 'snippet'.
 2020-01-21 15:01:46 +01:00
Tobias Geerinckx-Rice
a19fb6a436
gnu: Use HTTPS for (gnu packages bioinformatics) home pages. 
* 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.
 2020-01-21 02:15:32 +01:00
Tobias Geerinckx-Rice
72607005e4
gnu: r-gage: Update home page. 
* gnu/packages/bioinformatics.scm (r-gage)[home-page]: Update.
 2020-01-21 02:15:32 +01:00
Tobias Geerinckx-Rice
0388046068
gnu: sra-tools: Update home page. 
* gnu/packages/bioinformatics.scm (sra-tools)[home-page]: Update.
 2020-01-21 02:15:31 +01:00
Tobias Geerinckx-Rice
0eeaf1ac3c
gnu: raxml: Update home page. 
* gnu/packages/bioinformatics.scm (raxml)[home-page]: Update.
 2020-01-21 02:15:31 +01:00
Tobias Geerinckx-Rice
5832b88c45
gnu: prodigal: Update home page. 
* gnu/packages/bioinformatics.scm (prodigal)[home-page]: Use source code repository as home page.
 2020-01-21 02:15:31 +01:00
Tobias Geerinckx-Rice
030fe2fb7e
gnu: miso: Update home page. 
* gnu/packages/bioinformatics.scm (miso)[home-page]: Update.
 2020-01-21 02:15:31 +01:00
Tobias Geerinckx-Rice
b725655fce
gnu: grit: Update home page. 
* gnu/packages/bioinformatics.scm (grit)[home-page]: Use source code
repository as home page.
 2020-01-21 02:15:31 +01:00
Tobias Geerinckx-Rice
b56f2b6366
gnu: express-beta-diversity: Update home page. 
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.
 2020-01-21 02:15:31 +01:00
Tobias Geerinckx-Rice
568bd2e382
gnu: dendropy: Update home page. 
* gnu/packages/bioinformatics.scm (dendropy)[home-page]: Update.
 2020-01-21 02:15:31 +01:00
Julien Lepiller
5aa573d8c7
gnu: ocaml-markup: Update to 0.8.2. 
gnu/packages/ocaml.scm (ocaml-markup): Update to 0.8.2.
 2020-01-21 01:12:26 +01:00
Julien Lepiller
16829d3b8a
gnu: ocaml-lwt: Update to 5.1.1. 
* gnu/packages/ocaml.scm (ocaml-lwt): update to 5.1.1.
 2020-01-21 01:12:05 +01:00
Julien Lepiller
2624921a64
gnu: Add ocaml-mmap. 
* gnu/packages/ocaml.scm (ocaml-mmap): New variable.
 2020-01-21 01:11:39 +01:00
Julien Lepiller
2e038f36f8
gnu: ocaml-bisect-ppx: Update to 1.4.2. 
* gnu/packages/ocaml.scm (ocaml-bisect-ppx): Update to 1.4.2.
 2020-01-21 01:11:35 +01:00
Julien Lepiller
73e01ae456
gnu: ocaml-qtest. Update to 2.10.1. 
* gnu/packages/ocaml.scm (ocaml-qtest): Update to 2.10.1.
 2020-01-21 01:11:31 +01:00
Julien Lepiller
795cf2a3b5
gnu: ocaml-qcheck: Update to 0.12. 
* gnu/packages/ocaml.scm (ocaml-qcheck): Update to 0.12.
 2020-01-21 01:11:20 +01:00
Julien Lepiller
c2eb8c7ef7
gnu: camlp5: Update to 7.10. 
* gnu/packages/ocaml.scm (camlp5): Upadte to 7.10.
 2020-01-21 01:10:49 +01:00
Julien Lepiller
efeda080ef
gnu: opam: Update to 2.0.6. 
* gnu/pckages/ocaml.scm (opam): Update to 2.0.6.
 2020-01-21 01:10:42 +01:00
Tobias Geerinckx-Rice
99db6db7be
gnu: Use HTTPS for bioconductor.org. 
* 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.
 2020-01-21 00:43:39 +01:00
Tobias Geerinckx-Rice
570b89f401
gnu: gzdoom: Update to 4.3.2. 
* 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.
 2020-01-21 00:43:24 +01:00
Tobias Geerinckx-Rice
21e733ce4e
gnu: supercollider: Update to 3.10.4. 
* 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.
 2020-01-21 00:43:24 +01:00
Ricardo Wurmus
fa730a9780
Revert "gnu: Add guile3.0-commonmark." 
This reverts commit 346386f3f7.

A Guile 3.0 variant had already been added with commit
1fa3423236.
 2020-01-21 00:05:50 +01:00
Ricardo Wurmus
77c95ee60c
gnu: Add guile3.0-pfds. 
* gnu/packages/guile-xyz.scm (guile3.0-pfds): New variable.
 2020-01-20 23:49:53 +01:00
Ricardo Wurmus
b0b725ed40
gnu: Add guile3.0-wisp. 
* gnu/packages/guile-xyz.scm (guile3.0-wisp): New variable.
 2020-01-20 23:49:53 +01:00
Ricardo Wurmus
346386f3f7
gnu: Add guile3.0-commonmark. 
* gnu/packages/guile-xyz.scm (guile3.0-commonmark): New variable.
(guile-commonmark)[arguments]: Patch configure file.
 2020-01-20 23:49:52 +01:00
Ludovic Courtès
37eda8c044
installer: Disable F12 hot key. 
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'.
 2020-01-20 23:21:00 +01:00
Ludovic Courtès
48659aa221
installer: Makes sure the installer proceeds after hitting "Edit". 
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'.
 2020-01-20 23:20:59 +01:00
Marius Bakke
25623647e9
gnu: guile-git: Update to 0.3.0. 
* 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.
 2020-01-20 21:53:53 +01:00
Marius Bakke
89595f98d0
gnu: qt@4: Build with libjpeg-turbo. 
* gnu/packages/qt.scm (qt-4)[inputs]: Change from LIBJPEG-8 to LIBJPEG-TURBO.
 2020-01-20 21:53:52 +01:00
Marius Bakke
96738cb11f
gnu: stepmania: Build with libjpeg-turbo. 
* gnu/packages/games.scm (stepmania)[inputs]: Change from LIBJPEG-8 to
LIBJPEG-TURBO.
 2020-01-20 21:53:52 +01:00
Marius Bakke
7b24b76b98
gnu: mame: Build with libjpeg-turbo. 
* gnu/packages/emulators.scm (mame)[inputs]: Change from LIBJPEG-8 to
LIBJPEG-TURBO.
 2020-01-20 21:53:52 +01:00
Marius Bakke
43987c977c
gnu: mailutils: Update to 3.8. 
* gnu/packages/mail.scm (mailutils): Update to 3.8.
[arguments]: Adjust substitutions.
 2020-01-20 21:53:52 +01:00
Marius Bakke
37f4454734
gnu: xorg-server: Update to 1.20.7. 
* gnu/packages/xorg.scm (xorg-server): Update to 1.20.7.
 2020-01-20 21:53:52 +01:00
Marius Bakke
d18116d9b5
gnu: libsrtp: Build shared library. 
* gnu/packages/telephony.scm (libsrtp)[arguments]: Add #:phases.
 2020-01-20 21:53:52 +01:00
Marius Bakke
80af75abcf
gnu: libsrtp: Update to 2.3.0. 
* gnu/packages/telephony.scm (libsrtp): Update to 2.3.0.
 2020-01-20 21:53:52 +01:00
Marius Bakke
fd4b27e4e4
gnu: ffmpeg: Update to 4.2.2. 
* gnu/packages/video.scm (ffmpeg): Update to 4.2.2.
 2020-01-20 21:53:51 +01:00
Marius Bakke
0fd80a2556
gnu: libvpx: Update to 1.8.2. 
* gnu/packages/video.scm (libvpx): Update to 1.8.2.
 2020-01-20 21:53:51 +01:00
Marius Bakke
bb06336e81
gnu: re2: Update to 2020-01-01. 
* gnu/packages/regex.scm (re2): Update to 2020-01-01.
 2020-01-20 21:53:51 +01:00
Marius Bakke
07b1d40899
gnu: e2fsprogs: Update to 1.45.5. 
* gnu/packages/linux.scm (e2fsprogs): Update to 1.45.5.
 2020-01-20 21:53:51 +01:00
Marius Bakke
a5407c768d
gnu: snappy: Update to 1.1.8. 
* gnu/packages/compression.scm (snappy): Update to 1.1.8.
 2020-01-20 21:53:51 +01:00
Marius Bakke
ae3909eb4c
gnu: python-parameterized: Update to 0.7.1. 
* 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.
 2020-01-20 21:53:51 +01:00
Marius Bakke
544ea9c2df
gnu: Add python-anytree. 
* gnu/packages/python-xyz.scm (python-anytree): New public variable.
 2020-01-20 21:53:51 +01:00
Marius Bakke
20bf58bff4
gnu: python-packaging: Add comment about upstream patch status. 
* gnu/packages/python-xyz.scm (python-packaging)[source]: Add comment, to
prevent needless rebuild by updating the patch directly.
 2020-01-20 21:53:50 +01:00
Christopher Baines
aa10ad7d46
gnu: guix-data-service: Update to 0.0.1-17.bf25a8d. 
* gnu/packages/web.scm (guix-data-service): Update to 0.0.1-17.bf25a8d.
 2020-01-20 20:32:24 +00:00
Christopher Baines
b3e28b5ef5
tests: mail: Remove %getmail-os from the bottom of the file. 
This was left over when debugging the system test.

* gnu/tests/mail.scm: Remove %getmail-os from the bottom of the file.
 2020-01-20 19:13:17 +00:00
Christopher Baines
c8defb2b2a
services: getmail: Adjust a couple of default configuration values. 
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.
 2020-01-20 19:13:16 +00:00
Christopher Baines
2e1a314871
services: getmail: Fix some configuration documentation strings. 
* 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.
 2020-01-20 19:09:00 +00:00
Christopher Baines
147a7f1fd2
services: getmail: Fix stopping the shepherd service. 
* gnu/services/getmail.scm (getmail-shepherd-services): Add a stop component
to the shepherd services.
 2020-01-20 19:01:23 +00:00
Danny Milosavljevic
19b310901c
services: Add "sane" service. 
* gnu/services/desktop.scm (%desktop-services): Add "sane" service.
 2020-01-20 18:46:07 +01:00
Efraim Flashner
9448d0effc
gnu: rust-crossbeam-channel-0.3: Update to 0.3.9. 
* 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.
 2020-01-20 17:28:45 +02:00