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46770 Commits

Author SHA1 Message Date
zimoun 1502751b32
gnu: Add r-flowsom. 
* gnu/packages/bioconductor.scm (r-flowsom): New variable.

Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
 2019-07-24 23:05:39 +02:00
zimoun e0cb053edb
gnu: Add r-flowmeans. 
* gnu/packages/bioconductor.scm (r-flowmeans): New variable.

Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
 2019-07-24 23:05:39 +02:00
zimoun ed6f49fc41
gnu: Add r-consensusclusterplus. 
* gnu/packages/bioconductor.scm (r-consensusclusterplus): New variable.

Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
 2019-07-24 23:05:39 +02:00
zimoun a0422d18f1
gnu: Add r-flowutils. 
* gnu/packages/bioconductor.scm (r-flowutils): New variable.

Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
 2019-07-24 23:05:39 +02:00
zimoun a6fedf1f37
gnu: Add r-flowcore. 
* gnu/packages/bioconductor.scm (r-flowcore): New variable.

Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
 2019-07-24 23:05:39 +02:00
zimoun ad8f46c69e
gnu: Add r-all. 
* gnu/packages/bioconductor.scm (r-all): New variable.

Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
 2019-07-24 23:05:39 +02:00
zimoun 6deb08a359
gnu: Add r-kableextra. 
* gnu/packages/cran.scm (r-kableextra): New variable.

Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
 2019-07-24 23:05:38 +02:00
zimoun 1c0b2e7483
gnu: Add r-umap. 
* gnu/packages/cran.scm (r-umap): New variable.

Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
 2019-07-24 23:05:38 +02:00
Jelle Licht 97bc8c47bb
gnu: emacs-gitpatch: Update to 0.5.1. 
* gnu/packages/emacs-xyz.scm (emacs-gitpatch): Update to 0.5.1.
 2019-07-24 22:23:19 +02:00
Tobias Geerinckx-Rice 8126142baf
gnu: terminator: Propagate gsettings-desktop-schemas. 
* gnu/packages/gnome.scm (terminator)[propagated-inputs]: Add gsettings-desktop-schemas.
 2019-07-24 21:29:10 +02:00
Tobias Geerinckx-Rice 4f20e0a2f6
gnu: spice-gtk: Update to 0.37. 
* gnu/packages/spice.scm (spice-gtk): Update to 0.37.
[propagated-inputs]: Use latest spice-protocol.
(spice-protocol-0.12): Remove unused variable.
 2019-07-24 21:29:10 +02:00
Tobias Geerinckx-Rice 7e2c050a88
gnu: libvirt-glib: Propagate pkg-config requirements. 
* gnu/packages/virtualization.scm (libvirt-glib)[inputs]: Move glib,
libvirt, libxml2, and gobject-introspection…
[native-inputs]: …here.
 2019-07-24 21:29:10 +02:00
Tobias Geerinckx-Rice 7dfda55ba2
gnu: libvirt-glib: Update to 2.0.0. 
* gnu/packages/virtualization.scm (libvirt-glib): Update to 2.0.0.
[arguments]: Remove ‘fix-tests’ phase.
 2019-07-24 21:29:09 +02:00
Leo Famulari b9a178b6dc
doc: Warn about GPG warning. 
* doc/guix.texi (Binary Installation, USB Stick and DVD Installation): Warn
users about the web-of-trust untrusted key warning from GPG.
 2019-07-24 10:59:27 -04:00
宋文武 3c618b9894
deploy: Handle the '--system' command line option. 
* guix/scripts/deploy.scm (show-help): Add help for '--system'.
(%options): Add '-s' and '--system'.
(guix-deploy): Parameterize %current-system.
 2019-07-24 20:34:01 +08:00
宋文武 2fa23d8f5c
deploy: Honor '--no-grafts'. 
* guix/scripts/deploy.scm (guix-deploy): Parameterize '%graft?'.
 2019-07-24 20:34:01 +08:00
Nicolò Balzarotti 7304d5623a
gnu: julia: Update to 1.1.1. 
* gnu/packages/julia.scm (libuv-julia): Update to commit 26dbe56.
(libunwind-for-julia): Remove.
(llvm-patch-url, llvm-patch): New procedures.
(llvm-julia): New variable.
(julia): Update to 1.1.1.
[arguments]: Adjust 'prepare-deps' to new set of dependencies.
Adjust 'hardcode-soname-map': remove openlibm and libfftw handling.
Update file names in 'fix-include-and-link-paths' and 'hardcode-paths'.
Adjust 'disable-broken-tests'.
Pass PREFIX, LIBFLAS, and LIBBLASNAME in #:make-flags; update other
flags.
[inputs]: Replace LLVM-3.9.1 with LLVM-JULIA.  Replace
LIBUNWIND-FOR-JULIA with LIBUNWIND.  Add "rmath" and "libwhich".
[native-inputs]: Remove "unicode-data".

Co-authored-by: Ludovic Courtès <ludo@gnu.org>
 2019-07-24 00:31:23 +02:00
Ludovic Courtès 96a9a8d398
gnu: llvm: Add 'system->llvm-target' procedure. 
* gnu/packages/llvm.scm (system->llvm-target): New procedure.
 2019-07-24 00:31:22 +02:00
Julien Lepiller c42db89ff9
doc: Add example for generating a secret key with knot DNS. 
* doc/guix.texi (DNS Services): Add an example and more context to the
includes field of the knot-configuration record.
 2019-07-23 21:17:04 +02:00
Efraim Flashner 4d3a2b5ac7
gnu: terminology: Update to 1.5.0. 
* gnu/packages/enlightenment.scm (terminology): Update to 1.5.0.
 2019-07-23 16:35:51 +03:00
Mathieu Lirzin 6583ef601a
gnu: emacs-request: Update to 0.3.1. 
* gnu/packages/emacs-xyz.scm (emacs-request): Update to 0.3.1.

Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
 2019-07-23 10:23:28 +03:00
Mathieu Lirzin d7ab6c9067
gnu: emacs-google-translate: Update to 0.11.18. 
* gnu/packages/emacs-xyz.scm (emacs-google-translate): Update to 0.11.18.

Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
 2019-07-23 10:20:47 +03:00
Robert Vollmert 12277003d3
Makefile: Sort scheme tests alphabetically. 
* Makefile.am (SCM_TESTS): Sort.

Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
 2019-07-23 09:55:05 +03:00
Jack Hill 12cc3da5c1
gnu: mallard-ducktype: Update to 1.0.2. 
* gnu/packages/python-xyz.scm (mallard-ducktype) Update to 1.0.2.

Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
 2019-07-23 09:10:16 +03:00
Julien Lepiller 3755d5cb5e
gnu: harmonist: Update to 0.2. 
* gnu/packages/games.scm (harmonist): Update to 0.2.
 2019-07-22 23:10:48 +02:00
Marius Bakke ccad0e4d69
Merge branch 'master' into core-updates 2019-07-22 18:58:48 +02:00
Marius Bakke 2698654446
gnu: vlc: Build against libvpx@1.8. 
* gnu/packages/video.scm (vlc)[inputs]: Change LIBVPX-1.7 to LIBVPX.
 2019-07-22 16:22:22 +02:00
Marius Bakke a242776178
gnu: libvpx: Update to 1.8.1. 
* gnu/packages/video.scm (libvpx): Update to 1.8.1.
 2019-07-22 16:22:22 +02:00
Marius Bakke fb4ea42340
gnu: zstd: Update to 1.4.1. 
* gnu/packages/compression.scm (zstd): Update to 1.4.1.
 2019-07-22 16:22:22 +02:00
Marius Bakke ec0de9d8bc
gnu: zstd: Move libraries to separate outputs. 
* gnu/packages/compression.scm (zstd)[outputs]: New field.
[arguments]: Add phase 'adjust-libary-locations'.  Pass LIBDIR and INCLUDEDIR
in <#:make-flags>.
* gnu/packages/backup.scm (borg)[inputs]: Change ZSTD to ZSTD:LIB.
* gnu/packages/sync.scm (casync)[inputs]: Likewise.
* gnu/packages/tor.scm (tor)[inputs]: Likewise.
* gnu/packages/linux.scm (btrfs-progs)[inputs]: Likewise.  Add ZSTD:STATIC.
 2019-07-22 16:22:22 +02:00
Marius Bakke 8dea61731b
gnu: whois: Update to 5.5.0. 
* gnu/packages/networking.scm (whois): Update to 5.5.0.
 2019-07-22 16:22:22 +02:00
Marius Bakke 293e4f9f2d
gnu: jsoncpp: Update to 1.9.1. 
* gnu/packages/serialization.scm (jsoncpp): Update to 1.9.1.
 2019-07-22 16:22:22 +02:00
Marius Bakke 8d3167fe23
gnu: ffmpeg: Update to 4.1.4. 
* gnu/packages/video.scm (ffmpeg): Update to 4.1.4.
 2019-07-22 16:22:22 +02:00
Marius Bakke 3c08479ef9
gnu: x265: Update to 3.1.1. 
* gnu/packages/video.scm (x265): Update to 3.1.1.
 2019-07-22 16:22:22 +02:00
Marius Bakke 6a489839a8
gnu: ungoogled-chromium: Enable parallel build. 
...but limit the memory usage.  Tested with --cores=8 on a 16 GiB RAM machine.

* gnu/packages/chromium.scm (ungoogled-chromium)[arguments]: Remove <#:parallel-build?>.
Add "jumbo_file_merge_limit=8" in <#:configure-flags>.
 2019-07-22 16:22:21 +02:00
Ricardo Wurmus 6fd4c6b267
gnu: htslib: Propagate zlib. 
Reported by Vedran Franke <Vedran.Franke@mdc-berlin.de>.

* gnu/packages/bioinformatics.scm (htslib)[inputs]: Move zlib from here...
[propagated-inputs]: ...to here.
 2019-07-22 14:24:51 +02:00
Ludovic Courtès cd9f56ff5a
pack: Pass a list as the entry point for 'build-docker-image'. 
* guix/scripts/pack.scm (docker-image)[build]: Pass a list as
 #:entry-point, not a string.
 2019-07-22 11:53:40 +02:00
Ludovic Courtès 96f1cbeff8
swh: Add basic tests. 
* guix/swh.scm (%swh-base-url): Turn into a parameter and export it.
* tests/swh.scm: New file.
* Makefile.am (SCM_TESTS): Add it.
 2019-07-22 11:53:39 +02:00
Ludovic Courtès 5a90d56352
doc: Update 'guix import json' example. 
This is a followup to d78010b81e.

* doc/guix.texi (Invoking guix import): Change 'guix import json'
example to refer to "gettext", not "gcc".
 2019-07-22 11:53:39 +02:00
Efraim Flashner 1bb4122ce6
gnu: perl-net-http: Update to 6.19. 
* gnu/packages/web.scm (perl-net-httpd): Update to 6.19.
 2019-07-22 10:14:41 +03:00
Efraim Flashner bbbed2e60d
gnu: perl-test-simple: Update to 1.302164. 
* gnu/packages/perl-check.scm (perl-test-simple): Update to 1.302164.
 2019-07-22 10:07:57 +03:00
Efraim Flashner 94b9b67618
gnu: perl-cpan-meta: Update to 2.150010. 
* gnu/packages/perl.scm (perl-cpan-meta): Update to 2.150010.
 2019-07-22 10:07:56 +03:00
Efraim Flashner 6f4d20e387
gnu: perl-clone: Update to 0.42. 
* gnu/packages/perl.scm (perl-clone): Update to 0.42.
 2019-07-22 10:07:56 +03:00
Efraim Flashner 2756ab8058
gnu: perl-hash-merge: Update to 0.300. 
* gnu/packages/perl.scm (perl-hash-merge): Update to 0.300.
[inputs]: Add perl-clone-choose.
 2019-07-22 10:07:51 +03:00
Efraim Flashner 5246655fa1
gnu: mallard-ducktype: Run tests. 
* gnu/packages/python-xyz.scm (mallard-ducktype)[arguments]: Replace
'check phase to run test suite.
 2019-07-22 09:49:19 +03:00
Robert Vollmert 7284b11f6c
gnu: oil-shell: Update to 0.6.0 
* gnu/packages/shells.scm (oil-shell): Update to 0.6.0.

Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
 2019-07-22 09:26:55 +03:00
Chris Marusich afb986e77c
gnu: libreoffice: Fix xdg-open absolute paths. 
Fixes: <https://bugs.gnu.org/36728>.

* gnu/packages/libreoffice.scm (libreoffice) [inputs]: Add xdg-utils.
[arguments][#:phases][prepare-src]: Replace hard-coded absolute paths to
xdg-open in the source with the path to xdg-open in the xdg-utils input.
 2019-07-21 16:47:55 -07:00
Tobias Geerinckx-Rice d1e766e5c6
gnu: libosinfo: Update to 1.5.0. 
* gnu/packages/virtualization.scm (libosinfo): Update to 1.5.0.
[arguments]: Remove ‘disable-broken-test’ phase.
[native-inputs]: Remove check.
 2019-07-21 20:27:42 +02:00
Mark H Weaver 59f79254bb
gnu: linux-libre: Update to 5.2.2. 
* gnu/packages/linux.scm (linux-libre-5.2-version): Update to 5.2.2.
(linux-libre-5.2-pristine-source): Update hash.
 2019-07-21 11:17:43 -04:00
Mark H Weaver c39304ce18
gnu: linux-libre@4.19: Update to 4.19.60. 
* gnu/packages/linux.scm (linux-libre-4.19-version): Update to 4.19.60.
(linux-libre-4.19-pristine-source): Update hash.
 2019-07-21 11:17:41 -04:00