jackhill/guix/guix.git
4 years agoMerge branch 'master' into staging
Marius Bakke [Wed, 18 Dec 2019 22:07:40 +0000 (23:07 +0100)]
Merge branch 'master' into staging

4 years agoguix: swh: Fix example URI in comment for <origin>.
Björn Höfling [Wed, 18 Dec 2019 21:31:05 +0000 (22:31 +0100)]
guix: swh: Fix example URI in comment for <origin>.

This is a one-character follow-up to
356a79becc4061d158c68718ad169abac1ab672f

Reported by Jonathan Brielmaier <jonathan.brielmaier@web.de>.

* guix/swh.scm(<origin>): Remove a slash from example URI witin a comment.

4 years agognu: libdbi-drivers: Adapt to multiple-output MariaDB.
Marius Bakke [Wed, 18 Dec 2019 21:20:07 +0000 (22:20 +0100)]
gnu: libdbi-drivers: Adapt to multiple-output MariaDB.

* gnu/packages/databases.scm (mariadb/fixed-install-db): New public variable.
(libdbi-drivers)[inputs]: Add MARIADB:DEV and MARIADB:LIB.  Remove MARIADB.
[native-inputs]: Add MARIADB/FIXED-INSTALL-DB.
[arguments]: Adjust accordingly.

4 years agogexp: Allow character literals in GEXP->SEXP.
Marius Bakke [Sun, 15 Dec 2019 20:27:31 +0000 (21:27 +0100)]
gexp: Allow character literals in GEXP->SEXP.

Fixes <https://bugs.gnu.org/38628>.

* tests/gexp.scm ("lower-gexp, character literal"): New test.
* guix/gexp.scm (gexp->sexp)[self-quoting?]: Add CHAR? to the tested types.
* guix/repl.scm (self-quoting?): Likewise.
* gnu/tests.scm (marionette-shepherd-service)[self-quoting?]: Likewise.

4 years agognu: darktable: Update to 2.6.3.
Marius Bakke [Thu, 12 Dec 2019 00:28:11 +0000 (01:28 +0100)]
gnu: darktable: Update to 2.6.3.

* gnu/packages/photo.scm (darktable): Update to 2.6.3.

4 years agognu: darktable: Remove redundant inputs.
Marius Bakke [Thu, 12 Dec 2019 00:27:37 +0000 (01:27 +0100)]
gnu: darktable: Remove redundant inputs.

* gnu/packages/photo.scm (darktable)[native-inputs]: Remove.

4 years agognu: darktable: Fix build failure.
Marius Bakke [Thu, 12 Dec 2019 00:24:32 +0000 (01:24 +0100)]
gnu: darktable: Fix build failure.

* gnu/packages/photo.scm (darktable)[arguments]: Move CPATH override from
 #:make-flags to a phase, so the GETENV call returns useful data.

4 years agognu: Remove uses of deprecated Qemu network configuration.
Marius Bakke [Fri, 6 Dec 2019 19:53:08 +0000 (20:53 +0100)]
gnu: Remove uses of deprecated Qemu network configuration.

* gnu/build/vm.scm (load-in-linux-vm): Move Qemu network configuration from
ARCH-SPECIFIC-FLAGS to the Qemu command line.  Use the "-nic" option of Qemu
instead of "-device" and "-net".
* gnu/system/vm.scm (common-qemu-options): Do not add a '-net' command.
(virtual-machine-compiler): Use "-nic user,..." instead of "-net".
* doc/guix.texi (Installing Guix in a VM, Invoking guix system, Running Guix
in a VM): Do the same for examples.

4 years agognu: linux-libre: Update to 5.3.18.
Mark H Weaver [Wed, 18 Dec 2019 19:57:30 +0000 (14:57 -0500)]
gnu: linux-libre: Update to 5.3.18.

* gnu/packages/linux.scm (linux-libre-5.3-version): Update to 5.3.18.
(linux-libre-5.3-pristine-source): Update hash.

4 years agognu: linux-libre: Update deblob scripts.
Mark H Weaver [Wed, 18 Dec 2019 20:08:42 +0000 (15:08 -0500)]
gnu: linux-libre: Update deblob scripts.

* gnu/packages/linux.scm (deblob-scripts-4.19): Update to 4.19.90.
(deblob-scripts-4.14): Update to 4.14.159.
(deblob-scripts-5.3, deblob-scripts-4.9, deblob-scripts-4.4): Update version
numbers to 5.3.17, 4.9.206, and 4.4.206, respectively, although the scripts
themselves have not changed.

4 years agognu: Add r-biodist.
Ricardo Wurmus [Wed, 18 Dec 2019 14:25:50 +0000 (15:25 +0100)]
gnu: Add r-biodist.

* gnu/packages/bioconductor.scm (r-biodist): New variable.

4 years agognu: Add r-biocworkflowtools.
Ricardo Wurmus [Wed, 18 Dec 2019 14:25:45 +0000 (15:25 +0100)]
gnu: Add r-biocworkflowtools.

* gnu/packages/bioconductor.scm (r-biocworkflowtools): New variable.

4 years agognu: Add r-biocset.
Ricardo Wurmus [Wed, 18 Dec 2019 14:25:38 +0000 (15:25 +0100)]
gnu: Add r-biocset.

* gnu/packages/bioconductor.scm (r-biocset): New variable.

4 years agognu: Add r-biocpkgtools.
Ricardo Wurmus [Wed, 18 Dec 2019 14:25:31 +0000 (15:25 +0100)]
gnu: Add r-biocpkgtools.

* gnu/packages/bioconductor.scm (r-biocpkgtools): New variable.

4 years agognu: Add r-biocor.
Ricardo Wurmus [Wed, 18 Dec 2019 14:25:23 +0000 (15:25 +0100)]
gnu: Add r-biocor.

* gnu/packages/bioconductor.scm (r-biocor): New variable.

4 years agognu: Add r-bioconcotk.
Ricardo Wurmus [Wed, 18 Dec 2019 14:25:17 +0000 (15:25 +0100)]
gnu: Add r-bioconcotk.

* gnu/packages/bioconductor.scm (r-bioconcotk): New variable.

4 years agognu: Add r-multiassayexperiment.
Ricardo Wurmus [Wed, 18 Dec 2019 14:25:08 +0000 (15:25 +0100)]
gnu: Add r-multiassayexperiment.

* gnu/packages/bioconductor.scm (r-multiassayexperiment): New variable.

4 years agognu: Add r-experimenthub.
Ricardo Wurmus [Wed, 18 Dec 2019 14:25:00 +0000 (15:25 +0100)]
gnu: Add r-experimenthub.

* gnu/packages/bioconductor.scm (r-experimenthub): New variable.

4 years agognu: Add r-biocgraph.
Ricardo Wurmus [Wed, 18 Dec 2019 14:24:53 +0000 (15:24 +0100)]
gnu: Add r-biocgraph.

* gnu/packages/bioconductor.scm (r-biocgraph): New variable.

4 years agognu: Add r-bioccasestudies.
Ricardo Wurmus [Wed, 18 Dec 2019 14:24:46 +0000 (15:24 +0100)]
gnu: Add r-bioccasestudies.

* gnu/packages/bioconductor.scm (r-bioccasestudies): New variable.

4 years agognu: Add r-ebarrays.
Ricardo Wurmus [Wed, 18 Dec 2019 14:24:27 +0000 (15:24 +0100)]
gnu: Add r-ebarrays.

* gnu/packages/bioconductor.scm (r-ebarrays): New variable.

4 years agognu: Add r-reactomepa.
Ricardo Wurmus [Wed, 18 Dec 2019 14:24:21 +0000 (15:24 +0100)]
gnu: Add r-reactomepa.

* gnu/packages/bioconductor.scm (r-reactomepa): New variable.

4 years agognu: Add r-graphite.
Ricardo Wurmus [Wed, 18 Dec 2019 14:24:13 +0000 (15:24 +0100)]
gnu: Add r-graphite.

* gnu/packages/bioconductor.scm (r-graphite): New variable.

4 years agognu: Add r-influencer.
Ricardo Wurmus [Wed, 18 Dec 2019 14:24:05 +0000 (15:24 +0100)]
gnu: Add r-influencer.

* gnu/packages/cran.scm (r-influencer): New variable.

4 years agognu: Add r-curatedtcgadata.
Ricardo Wurmus [Wed, 18 Dec 2019 14:23:27 +0000 (15:23 +0100)]
gnu: Add r-curatedtcgadata.

* gnu/packages/bioconductor.scm (r-curatedtcgadata): New variable.

4 years agognu: Add r-reactome-db.
Ricardo Wurmus [Wed, 18 Dec 2019 14:23:15 +0000 (15:23 +0100)]
gnu: Add r-reactome-db.

* gnu/packages/bioconductor.scm (r-reactome-db): New variable.

4 years agognu: libmicrohttpd: Update to 0.9.69.
Efraim Flashner [Wed, 18 Dec 2019 08:34:27 +0000 (10:34 +0200)]
gnu: libmicrohttpd: Update to 0.9.69.

* gnu/packages/gnunet.scm (libmicrohttpd): Update to 0.9.69.

4 years agognu: cmst: Update to 2019.01.13.
Efraim Flashner [Wed, 18 Dec 2019 08:29:28 +0000 (10:29 +0200)]
gnu: cmst: Update to 2019.01.13.

* gnu/packages/connman.scm (cmst): Update to 2019.01.13.

4 years agognu: python-ecdsa: Actually run the test suite.
Efraim Flashner [Wed, 18 Dec 2019 07:54:47 +0000 (09:54 +0200)]
gnu: python-ecdsa: Actually run the test suite.

* gnu/packages/python-crypto.scm (python-ecdsa)[arguments]: Replace
'check phase.
[native-inputs]: Add python-pytest.

4 years agognu: python-ecdsa: Update to 0.14.1.
Efraim Flashner [Wed, 18 Dec 2019 07:53:48 +0000 (09:53 +0200)]
gnu: python-ecdsa: Update to 0.14.1.

* gnu/packages/python-crypto.scm (python-ecdsa): Update to 0.14.1.
[inputs]: Move openssl ...
[native-inputs]: ... to here.
[propagated-inputs]: Add python-six.

4 years agoswh: Fix API call for getting origin.
Björn Höfling [Sun, 15 Dec 2019 21:00:56 +0000 (22:00 +0100)]
swh: Fix API call for getting origin.

When using the archival linter, git origins already in the archive where
not recognized due to an API change and where repeatedly asked for archival.
This is fixed here.

* guix/swh.scm (lookup-origin): Fix API URI for getting origin.
(<origin>): Fix comment with API URI example.

4 years agognu: linux-libre: Update to 5.3.17.
Mark H Weaver [Tue, 17 Dec 2019 22:24:23 +0000 (17:24 -0500)]
gnu: linux-libre: Update to 5.3.17.

* gnu/packages/linux.scm (linux-libre-5.3-version): Update to 5.3.17.
(linux-libre-5.3-pristine-source): Update hash.

4 years agognu: linux-libre@4.19: Update to 4.19.90.
Mark H Weaver [Tue, 17 Dec 2019 22:23:42 +0000 (17:23 -0500)]
gnu: linux-libre@4.19: Update to 4.19.90.

* gnu/packages/linux.scm (linux-libre-4.19-version): Update to 4.19.90.
(linux-libre-4.19-pristine-source): Update hash.

4 years agognu: linux-libre@4.14: Update to 4.14.159.
Mark H Weaver [Tue, 17 Dec 2019 22:22:36 +0000 (17:22 -0500)]
gnu: linux-libre@4.14: Update to 4.14.159.

* gnu/packages/linux.scm (linux-libre-4.14-version): Update to 4.14.159.
(linux-libre-4.14-pristine-source): Update hash.

4 years agognu: Add r-biobroom.
Ricardo Wurmus [Tue, 17 Dec 2019 18:48:58 +0000 (19:48 +0100)]
gnu: Add r-biobroom.

* gnu/packages/bioconductor.scm (r-biobroom): New variable.

4 years agognu: Add r-bioassayr.
Ricardo Wurmus [Tue, 17 Dec 2019 18:48:50 +0000 (19:48 +0100)]
gnu: Add r-bioassayr.

* gnu/packages/bioconductor.scm (r-bioassayr): New variable.

4 years agognu: Add r-chemminer.
Ricardo Wurmus [Tue, 17 Dec 2019 18:48:38 +0000 (19:48 +0100)]
gnu: Add r-chemminer.

* gnu/packages/bioconductor.scm (r-chemminer): New variable.

4 years agognu: Add r-bigpint.
Ricardo Wurmus [Tue, 17 Dec 2019 18:48:29 +0000 (19:48 +0100)]
gnu: Add r-bigpint.

* gnu/packages/bioconductor.scm (r-bigpint): New variable.

4 years agognu: Add r-bigmemoryextras.
Ricardo Wurmus [Tue, 17 Dec 2019 18:48:21 +0000 (19:48 +0100)]
gnu: Add r-bigmemoryextras.

* gnu/packages/bioconductor.scm (r-bigmemoryextras): New variable.

4 years agognu: Add r-biggr.
Ricardo Wurmus [Tue, 17 Dec 2019 18:48:13 +0000 (19:48 +0100)]
gnu: Add r-biggr.

* gnu/packages/bioconductor.scm (r-biggr): New variable.

4 years agognu: Add r-hyperdraw.
Ricardo Wurmus [Tue, 17 Dec 2019 18:48:04 +0000 (19:48 +0100)]
gnu: Add r-hyperdraw.

* gnu/packages/bioconductor.scm (r-hyperdraw): New variable.

4 years agognu: Add r-hypergraph.
Ricardo Wurmus [Tue, 17 Dec 2019 18:47:42 +0000 (19:47 +0100)]
gnu: Add r-hypergraph.

* gnu/packages/bioconductor.scm (r-hypergraph): New variable.

4 years agognu: Add r-rsbml.
Ricardo Wurmus [Tue, 17 Dec 2019 18:47:27 +0000 (19:47 +0100)]
gnu: Add r-rsbml.

* gnu/packages/bioconductor.scm (r-rsbml): New variable.

4 years agognu: Add r-bifet.
Ricardo Wurmus [Tue, 17 Dec 2019 18:47:19 +0000 (19:47 +0100)]
gnu: Add r-bifet.

* gnu/packages/bioconductor.scm (r-bifet): New variable.

4 years agognu: Add r-bicare.
Ricardo Wurmus [Tue, 17 Dec 2019 18:47:11 +0000 (19:47 +0100)]
gnu: Add r-bicare.

* gnu/packages/bioconductor.scm (r-bicare): New variable.

4 years agognu: Add r-bhc.
Ricardo Wurmus [Tue, 17 Dec 2019 18:47:00 +0000 (19:47 +0100)]
gnu: Add r-bhc.

* gnu/packages/bioconductor.scm (r-bhc): New variable.

4 years agognu: Add r-bgx.
Ricardo Wurmus [Tue, 17 Dec 2019 18:46:30 +0000 (19:46 +0100)]
gnu: Add r-bgx.

* gnu/packages/bioconductor.scm (r-bgx): New variable.

4 years agognu: Add r-bgmix.
Ricardo Wurmus [Tue, 17 Dec 2019 18:46:18 +0000 (19:46 +0100)]
gnu: Add r-bgmix.

* gnu/packages/bioconductor.scm (r-bgmix): New variable.

4 years agognu: Add r-rsvg.
Ricardo Wurmus [Tue, 17 Dec 2019 18:18:54 +0000 (19:18 +0100)]
gnu: Add r-rsvg.

* gnu/packages/cran.scm (r-rsvg): New variable.

4 years agognu: Add r-shinycssloaders.
Ricardo Wurmus [Tue, 17 Dec 2019 18:18:46 +0000 (19:18 +0100)]
gnu: Add r-shinycssloaders.

* gnu/packages/cran.scm (r-shinycssloaders): New variable.

4 years agognu: Add r-lim.
Ricardo Wurmus [Tue, 17 Dec 2019 18:18:36 +0000 (19:18 +0100)]
gnu: Add r-lim.

* gnu/packages/cran.scm (r-lim): New variable.

4 years agognu: Add r-diagram.
Ricardo Wurmus [Tue, 17 Dec 2019 18:18:26 +0000 (19:18 +0100)]
gnu: Add r-diagram.

* gnu/packages/cran.scm (r-diagram): New variable.

4 years agognu: Add r-poibin.
Ricardo Wurmus [Tue, 17 Dec 2019 18:18:11 +0000 (19:18 +0100)]
gnu: Add r-poibin.

* gnu/packages/cran.scm (r-poibin): New variable.

4 years agognu: Add libsbml.
Ricardo Wurmus [Tue, 17 Dec 2019 18:13:42 +0000 (19:13 +0100)]
gnu: Add libsbml.

* gnu/packages/bioinformatics.scm (libsbml): New variable.

4 years agognu: Add love-nuklear.
Jethro Cao [Wed, 11 Dec 2019 14:33:44 +0000 (21:33 +0700)]
gnu: Add love-nuklear.

* gnu/packages/game-development.scm (love-nuklear): New variable.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
4 years agognu: txr: Update to 229.
Guillaume Le Vaillant [Mon, 16 Dec 2019 11:00:04 +0000 (12:00 +0100)]
gnu: txr: Update to 229.

* gnu/packages/lisp.scm (txr): Update to 229.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
4 years agognu: gfortran: change to a hidden package
Konrad Hinsen [Mon, 16 Dec 2019 11:18:52 +0000 (12:18 +0100)]
gnu: gfortran: change to a hidden package

* gnu/packages/gcc.scm (gfortran-4.8, gfortran-4.9)
(gfortran-5, gfortran-6, gfortran-7, gfortran-8)
(gfortran-9): Wrap in 'hidden-package'.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
4 years agognu: python-elasticsearch: Update to 7.1.0.
Ludovic Courtès [Tue, 17 Dec 2019 14:25:15 +0000 (15:25 +0100)]
gnu: python-elasticsearch: Update to 7.1.0.

* gnu/packages/python-web.scm (python-elasticsearch): Update to 7.1.0.

4 years agognu: r-pracma: Update to 2.2.9.
Ricardo Wurmus [Tue, 17 Dec 2019 13:58:12 +0000 (14:58 +0100)]
gnu: r-pracma: Update to 2.2.9.

* gnu/packages/cran.scm (r-pracma): Update to 2.2.9.

4 years agognu: r-repr: Update to 1.0.2.
Ricardo Wurmus [Tue, 17 Dec 2019 13:58:07 +0000 (14:58 +0100)]
gnu: r-repr: Update to 1.0.2.

* gnu/packages/cran.scm (r-repr): Update to 1.0.2.

4 years agognu: r-ggeffects: Update to 0.14.0.
Ricardo Wurmus [Tue, 17 Dec 2019 13:57:51 +0000 (14:57 +0100)]
gnu: r-ggeffects: Update to 0.14.0.

* gnu/packages/cran.scm (r-ggeffects): Update to 0.14.0.
[propagated-inputs]: Remove r-dplyr and r-rlang.

4 years agognu: r-dvmisc: Update to 1.1.4.
Ricardo Wurmus [Tue, 17 Dec 2019 13:56:17 +0000 (14:56 +0100)]
gnu: r-dvmisc: Update to 1.1.4.

* gnu/packages/cran.scm (r-dvmisc): Update to 1.1.4.
[propagated-inputs]: Add r-tab; remove r-purrr.

4 years agognu: r-ttr: Update to 0.23-6.
Ricardo Wurmus [Tue, 17 Dec 2019 13:56:05 +0000 (14:56 +0100)]
gnu: r-ttr: Update to 0.23-6.

* gnu/packages/cran.scm (r-ttr): Update to 0.23-6.

4 years agognu: r-argparser: Update to 0.6.
Ricardo Wurmus [Tue, 17 Dec 2019 13:56:00 +0000 (14:56 +0100)]
gnu: r-argparser: Update to 0.6.

* gnu/packages/cran.scm (r-argparser): Update to 0.6.

4 years agognu: r-ordinal: Update to 2019.12-10.
Ricardo Wurmus [Tue, 17 Dec 2019 13:55:54 +0000 (14:55 +0100)]
gnu: r-ordinal: Update to 2019.12-10.

* gnu/packages/cran.scm (r-ordinal): Update to 2019.12-10.

4 years agognu: r-seurat: Update to 3.1.2.
Ricardo Wurmus [Tue, 17 Dec 2019 13:55:50 +0000 (14:55 +0100)]
gnu: r-seurat: Update to 3.1.2.

* gnu/packages/bioinformatics.scm (r-seurat): Update to 3.1.2.

4 years agognu: r-bh: Update to 1.72.0-1.
Ricardo Wurmus [Tue, 17 Dec 2019 13:55:42 +0000 (14:55 +0100)]
gnu: r-bh: Update to 1.72.0-1.

* gnu/packages/statistics.scm (r-bh): Update to 1.72.0-1.

4 years agognu: Add r-tab.
Ricardo Wurmus [Tue, 17 Dec 2019 13:55:29 +0000 (14:55 +0100)]
gnu: Add r-tab.

* gnu/packages/cran.scm (r-tab): New variable.

4 years agognu: Add r-gee.
Ricardo Wurmus [Tue, 17 Dec 2019 13:55:18 +0000 (14:55 +0100)]
gnu: Add r-gee.

* gnu/packages/cran.scm (r-gee): New variable.

4 years agognu: shotwell: Clean-up inputs.
Efraim Flashner [Tue, 17 Dec 2019 08:23:02 +0000 (10:23 +0200)]
gnu: shotwell: Clean-up inputs.

* gnu/packages/gnome.scm (shotwell)[arguments]: Add phase to skip
gtk-update-icon-cache.
[inputs]: Sort alphabetically. Move glib:bin ...
[native-inputs]: ... to here. Remove desktop-file-utils, gtk+:bin.

4 years agognu: dia: Fix version number.
Efraim Flashner [Tue, 17 Dec 2019 07:57:21 +0000 (09:57 +0200)]
gnu: dia: Fix version number.

This commit is actually after to 0.97.3 release.

* gnu/packages/gnome.scm (dia)[version]: Use git-version.
[source]: Update to new source uri. Use git-file-name.

4 years agognu: dia: Don't override bootstrap phase.
Efraim Flashner [Tue, 17 Dec 2019 07:51:45 +0000 (09:51 +0200)]
gnu: dia: Don't override bootstrap phase.

* gnu/packages/gnome.scm (dia)[arguments]: Remove custom 'run-autogen
phgase. Add phase before 'bootstrap to not run configure.

4 years agognu: dia: Fix-up inputs.
Efraim Flashner [Tue, 17 Dec 2019 07:49:41 +0000 (09:49 +0200)]
gnu: dia: Fix-up inputs.

* gnu/packages/gnome.scm (dia)[inputs]: Sort alphabetically. Move
glib:bin ...
[native-inputs]: ... to here. Sort alphabetically.

4 years agognu: libidl: Hard-code name in source uri.
Efraim Flashner [Tue, 17 Dec 2019 07:37:11 +0000 (09:37 +0200)]
gnu: libidl: Hard-code name in source uri.

* gnu/packages/gnome.scm (libidl)[source]: Hard-code name.

4 years agognu: libidl: Set upstream name.
Efraim Flashner [Tue, 17 Dec 2019 07:36:31 +0000 (09:36 +0200)]
gnu: libidl: Set upstream name.

* gnu/packages/gnome.scm (libidl)[properties]: New field.

4 years agognu: brasero: Update home-page.
Efraim Flashner [Tue, 17 Dec 2019 07:31:47 +0000 (09:31 +0200)]
gnu: brasero: Update home-page.

* gnu/packages/gnome.scm (brasero)[home-page]: Use new home-page.

4 years agognu: brasero: Fix-up inputs.
Efraim Flashner [Tue, 17 Dec 2019 07:31:21 +0000 (09:31 +0200)]
gnu: brasero: Fix-up inputs.

* gnu/packages/gnome.scm (brasero)[inputs]: Move itstool ...
[native-inputs]: ... to here.

4 years agognu: brasero: Hard-code name in source uri.
Efraim Flashner [Tue, 17 Dec 2019 07:30:40 +0000 (09:30 +0200)]
gnu: brasero: Hard-code name in source uri.

* gnu/packages/gnome.scm (brasero)[source]: Hard-code name.

4 years agognu: pinfo: Use a source file name.
Efraim Flashner [Tue, 17 Dec 2019 07:17:27 +0000 (09:17 +0200)]
gnu: pinfo: Use a source file name.

* gnu/packages/texinfo.scm (pinfo)[source]: Add 'file-name'.

4 years agognu: electron-cash: Use substitute-keyword-arguments from electrum.
Vagrant Cascadian [Mon, 16 Dec 2019 23:16:52 +0000 (23:16 +0000)]
gnu: electron-cash: Use substitute-keyword-arguments from electrum.

* gnu/packages/finance (electron-cash)[arguments]: Use
  substitute-keyword-arguments to re-use arguments from electrum.

4 years agognu: electron-cash: Update to 4.0.12.
Vagrant Cascadian [Mon, 16 Dec 2019 21:20:53 +0000 (21:20 +0000)]
gnu: electron-cash: Update to 4.0.12.

* gnu/packages/finanace (electron-cash): Update to 4.0.12.
  [source] switch to git.
  [inputs] Add libsecp256k1.
  [arguments] Add phase patching to use libsecp256k1 from inputs.

4 years agognu: libsecp256k1: Update to 20191213.
Vagrant Cascadian [Mon, 16 Dec 2019 21:50:55 +0000 (21:50 +0000)]
gnu: libsecp256k1: Update to 20191213.

* gnu/packages/crypto (libsecp256k1): Update to 20191213.

4 years agognu: python-gffutils: Update description.
Ricardo Wurmus [Mon, 16 Dec 2019 22:31:53 +0000 (23:31 +0100)]
gnu: python-gffutils: Update description.

* gnu/packages/bioinformatics.scm (python-gffutils)[description]: Reflow
paragraph and fix spelling of SQLite.

4 years agognu: Add python-gffutils.
Mădălin Ionel Patrașcu [Mon, 16 Dec 2019 15:25:19 +0000 (16:25 +0100)]
gnu: Add python-gffutils.

* gnu/packages/bioinformatics.scm (python-gffutils): New variable.

Co-authored-by: Ricardo Wurmus <rekado@elephly.net>
4 years agognu: Remove python2-dask.
Ricardo Wurmus [Mon, 16 Dec 2019 22:12:25 +0000 (23:12 +0100)]
gnu: Remove python2-dask.

This package can no longer be built with Python 2.

* gnu/packages/python-xyz.scm (python2-dask): Remove variable.

4 years agognu: python-dask: Update to 2.9.0.
Ricardo Wurmus [Mon, 16 Dec 2019 22:11:41 +0000 (23:11 +0100)]
gnu: python-dask: Update to 2.9.0.

* gnu/packages/python-xyz.scm (python-dask): Update to 2.9.0.
[arguments]: Adjust phase to disable broken tests.
[propagated-inputs]: Add python-fsspec and python-packaging.

4 years agognu: Add python-fsspec.
Ricardo Wurmus [Mon, 16 Dec 2019 22:00:43 +0000 (23:00 +0100)]
gnu: Add python-fsspec.

* gnu/packages/python-xyz.scm (python-fsspec): New variable.

4 years agognu: python-pyfaidx: Update to 0.5.7.
Mădălin Ionel Patrașcu [Mon, 16 Dec 2019 15:25:18 +0000 (16:25 +0100)]
gnu: python-pyfaidx: Update to 0.5.7.

* gnu/packages/bioinformatics.scm (python-pyfaidx): Update to 0.5.7.

4 years agognu: guix-data-service: Update to 0.0.1-8.a019a5e.
Christopher Baines [Mon, 16 Dec 2019 21:00:46 +0000 (21:00 +0000)]
gnu: guix-data-service: Update to 0.0.1-8.a019a5e.

* gnu/packages/web.scm (guix-data-service): Update to 0.0.1-8.a019a5e.

4 years agoRevert "gnu: ccls: Configure using -isystem for header files."
Brett Gilio [Mon, 16 Dec 2019 20:05:17 +0000 (14:05 -0600)]
Revert "gnu: ccls: Configure using -isystem for header files."

This reverts commit 2c82d4ad10de8e0ba462d81401385c5e7499f6e2.

4 years agoRevert "gnu: ccls: Adjust indentation"
Brett Gilio [Mon, 16 Dec 2019 20:04:59 +0000 (14:04 -0600)]
Revert "gnu: ccls: Adjust indentation"

This reverts commit 3c80b07a0b4a2f1c2702acd6896f94892c516709.

4 years agognu: Add python-argh.
Mădălin Ionel Patrașcu [Mon, 16 Dec 2019 15:25:17 +0000 (16:25 +0100)]
gnu: Add python-argh.

* gnu/packages/python-xyz.scm (python-argh): New variable.

Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
4 years agognu: Add python-iocapture.
Mădălin Ionel Patrașcu [Mon, 16 Dec 2019 15:25:16 +0000 (16:25 +0100)]
gnu: Add python-iocapture.

* gnu/packages/python-xyz.scm (python-iocapture): New variable.

Co-authored-by: Ricardo Wurmus <rekado@elephly.net>
Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
4 years agognu: gash: Update to 0.2.0.
Jan Nieuwenhuizen [Mon, 16 Dec 2019 10:42:37 +0000 (11:42 +0100)]
gnu: gash: Update to 0.2.0.

* gnu/packages/shells.scm (gash): Update to 0.2.0.

4 years agognu: psmisc: Fix cross-compilation.
Mathieu Othacehe [Mon, 16 Dec 2019 15:41:01 +0000 (16:41 +0100)]
gnu: psmisc: Fix cross-compilation.

* gnu/packages/linux.scm (psmisc)[arguments]: Pass
ac_cv_func_malloc_0_nonnull=yes and ac_cv_func_realloc_0_nonnull=yes options
that are required when cross-compiling.

4 years agognu: iw: Fix cross-compilation.
Mathieu Othacehe [Mon, 16 Dec 2019 11:39:18 +0000 (12:39 +0100)]
gnu: iw: Fix cross-compilation.

* gnu/packages/linux.scm (iw)[arguments]: Set PKG_CONFIG and CC variables
correctly for cross-compilation.

4 years agognu: yoshimi: Update to 1.6.1.
Ricardo Wurmus [Mon, 16 Dec 2019 14:01:39 +0000 (15:01 +0100)]
gnu: yoshimi: Update to 1.6.1.

* gnu/packages/music.scm (yoshimi): Update to 1.6.1.

4 years agognu: emacs-helm-fish-completion: Update to 0.2.
Pierre Neidhardt [Mon, 16 Dec 2019 14:34:51 +0000 (15:34 +0100)]
gnu: emacs-helm-fish-completion: Update to 0.2.

* gnu/packages/emacs-xyz.scm (emacs-helm-fish-completion): Update to 0.2.

4 years agoRevert "gnu: info-reader: Fix cross-compilation."
Mathieu Othacehe [Mon, 16 Dec 2019 14:08:01 +0000 (15:08 +0100)]
Revert "gnu: info-reader: Fix cross-compilation."

This reverts commit 614a1e3fa2d731d4719f03912b1b87fb4fd309cb.
This is broken on master with the following error:

output (`/gnu/store/6rnhfi8zrdajbahbq9ii8bpj7mwfcjba-info-reader-6.6') is not
allowed to refer to path
`/gnu/store/ziinjmbnq004866mwjrczsk12wf35qb8-perl-5.30.0' build of
/gnu/store/nnfvr10713khxp1bkbpwi5wxbj8cm4wb-info-reader-6.6.drv failed View
build log at
'/var/log/guix/drvs/nn/fvr10713khxp1bkbpwi5wxbj8cm4wb-info-reader-6.6.drv.bz2'.

4 years agognu: libreoffice: Update to 6.3.4.2.
Efraim Flashner [Mon, 16 Dec 2019 12:13:16 +0000 (14:13 +0200)]
gnu: libreoffice: Update to 6.3.4.2.

* gnu/packages/libreoffice.scm (libreoffice): Update to 6.3.4.2.