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43060 Commits

Author SHA1 Message Date
Ricardo Wurmus 296da6e624
gnu: r-seurat: Update to 3.0.0. 
* gnu/packages/bioinformatics.scm (r-seurat): Update to 3.0.0.
[propagated-inputs]: Remove r-dosnow, r-dplyr, r-dtw, r-foreach, r-fpc,
r-gplots, r-hdf5r, r-hmisc, r-httr, r-lars, r-mixtools, r-reshape2, and
r-tidyr; add r-future, r-future-apply, r-ggrepel, r-kernsmooth, r-rlang,
r-rsvd, r-scales, and r-sctransform.
 2019-04-19 15:38:47 +02:00
Ricardo Wurmus 9b86fea05f
gnu: Add r-sctransform. 
* gnu/packages/cran.scm (r-sctransform): New variable.
 2019-04-19 15:38:46 +02:00
Ricardo Wurmus 7015ae6881
gnu: r-urltools: Update to 1.7.3. 
* gnu/packages/cran.scm (r-urltools): Update to 1.7.3.
 2019-04-19 14:43:34 +02:00
Ricardo Wurmus f0826fec46
gnu: r-rdpack: Update to 0.11-0. 
* gnu/packages/cran.scm (r-rdpack): Update to 0.11-0.
 2019-04-19 14:43:29 +02:00
Ricardo Wurmus 5ac82ee33b
gnu: r-sdmtools: Update to 1.1-221.1. 
* gnu/packages/cran.scm (r-sdmtools): Update to 1.1-221.1.
 2019-04-19 14:43:23 +02:00
Ricardo Wurmus 3d60c80713
gnu: r-hardyweinberg: Update to 1.6.2. 
* gnu/packages/cran.scm (r-hardyweinberg): Update to 1.6.2.
 2019-04-19 14:43:17 +02:00
Ricardo Wurmus 8e79d820d0
gnu: r-clipr: Update to 0.6.0. 
* gnu/packages/cran.scm (r-clipr): Update to 0.6.0.
 2019-04-19 14:43:10 +02:00
Ricardo Wurmus 664a6bc1a6
gnu: r-caret: Update to 6.0-83. 
* gnu/packages/statistics.scm (r-caret): Update to 6.0-83.
 2019-04-19 14:42:51 +02:00
Ricardo Wurmus f00067dbfb
gnu: klick: Fix build with latest scons. 
* gnu/packages/music.scm (klick)[arguments]: Patch "SConstruct" file to make
it compatible with the current version of scons.
 2019-04-19 14:24:04 +02:00
Christopher Baines 35259437a7
gnu: perl-datetime-timezone: Fix missing timezone data. 
I noticed this when using Sqitch, on systems without /usr/share/zoneinfo,
actions like deploy fail.

* gnu/packages/perl.scm (perl-datetime-timezone)[arguments]: Add 'patch-tzdata
phase to replace /usr/share/zoneinfo with a reference to the tzdata package.
[inputs]: Add the tzdata package.
 2019-04-19 11:42:30 +01:00
Marius Bakke f32164abd3
gnu: python2-send2trash: Don't inherit properties from python-send2trash. 
This is a follow-up to commit 20b3fde776.
Commits and beer do not mix well.

* gnu/packages/python-xyz.scm (python2-send2trash): Inherit using STRIP-PYTHON2-VARIANT.
 2019-04-19 02:29:43 +02:00
Marius Bakke 20b3fde776
gnu: python-send2trash: Really delay Python2 variant. 
This is a follow-up to commit 4782a06f45, which
somehow solved my problem, but did so incorrectly.

* gnu/packages/python-xyz.scm (python-send2trash)[properties]: Refer to
PYTHON2-SEND2TRASH.
 2019-04-19 01:57:34 +02:00
Marius Bakke cbeb891344
gnu: gpgme: Update to 1.13.0. 
* gnu/packages/gnupg.scm (gpgme): Update to 1.13.0.
[source](patches): Remove.
 2019-04-19 01:48:07 +02:00
Marius Bakke 4782a06f45
gnu: python-send2trash: Properly delay python2 variant. 
* gnu/packages/python-xyz.scm (python2-send2trash)[properties]: Move from here ...
(python-send2trash)[properties]: ... to here.
 2019-04-19 01:48:07 +02:00
Marius Bakke c105e50903
gnu: python-service-identity: Update to 18.1.0. 
* gnu/packages/python-crypto.scm (python-service-identity): Update to 18.1.0.
 2019-04-19 01:48:07 +02:00
Marius Bakke 1adde06e4e
gnu: python-jsonschema: Update to 3.0.1. 
* gnu/packages/python-xyz.scm (python-jsonschema): Update to 3.0.1.
[arguments]: Adjust check phase for Twisted instead of nosetests.
[native-inputs]: Remove PYTHON-NOSE and PYTHON-VCVERSIONER.  Add
PYTHON-SETUPTOOLS-SCM and PYTHON-TWISTED.
[propagated-inputs]: Add PYTHON-ATTRS, PYTHON-PYRSISTENT and PYTHON-SIX.
(python2-jsonschema)[native-inputs, propagated-inputs]: Inherit.
 2019-04-19 01:48:07 +02:00
Marius Bakke ea43f0d581
gnu: Add python-pyrsistent. 
* gnu/packages/python-xyz.scm (python-pyrsistent, python2-pyrsistent): New
public variables.
 2019-04-19 01:48:07 +02:00
Marius Bakke 52ca1c4abf
gnu: python-twisted: Update to 19.2.0. 
* gnu/packages/python-xyz.scm (python-twisted): Update to 19.2.0.
[propagated-inputs]: Add PYTHON-PYHAMCREST.
 2019-04-19 01:48:06 +02:00
Marius Bakke 919d80a0e0
gnu: python-automat: Update to 0.7.0. 
* gnu/packages/python-xyz.scm (python-automat): Update to 0.7.0.
 2019-04-19 01:48:06 +02:00
Marius Bakke bcfb8fac36
gnu: python-m2r: Update to 0.2.1. 
* gnu/packages/python-xyz.scm (python-m2r): Update to 0.2.1.
 2019-04-19 01:48:06 +02:00
Marius Bakke e95c983706
gnu: python-idna: Update to 2.8. 
* gnu/packages/python-xyz.scm (python-idna): Update to 2.8.
 2019-04-19 01:48:06 +02:00
Marius Bakke 431a0d26c8
gnu: python-hyperlink: Update to 19.0.0. 
* gnu/packages/python-web.scm (python-hyperlink): Update to 19.0.0.
 2019-04-19 01:48:06 +02:00
Marius Bakke 8142eadd40
gnu: python-zope-interface: Update to 4.6.0. 
* gnu/packages/python-web.scm (python-zope-interface): Update to 4.6.0.
 2019-04-19 01:48:06 +02:00
Marius Bakke e6d782621a
gnu: xmlsec: Update to 1.2.28. 
* gnu/packages/xml.scm (xmlsec): Update to 1.2.28.
 2019-04-19 01:48:06 +02:00
Christopher Baines 3fdb9a375f
guile-build-system: Support building in parallel. 
* guix/build/guile-build-system.scm (build): Use invoke-each, instead of
for-each, to use multiple cores if available.
(invoke-each, report-build-process): New procedures.
 2019-04-18 23:13:48 +01:00
Ludovic Courtès 702c3c7dab
lint: 'check-github-url' uses our own 'open-connection-for-uri'. 
Fixes <https://bugs.gnu.org/35053>.
Reported by Efraim Flashner <efraim@flashner.co.il>.

Previously 'check-github-url' would let Guile 2.2's (web client) module
take care of opening the connection.  Consequently, it wouldn't use the
TLS priority strings that we use in (guix build download),
'open-connection-for-uri'.  In particular, it would not disable TLSv1.3,
which would trigger <https://bugs.gnu.org/34102> for github.com.

* guix/scripts/lint.scm (check-github-url): Add #:timeout parameter.
[follow-redirect]: Change parameter name to 'url' and pass it to
'string->uri'.  Call 'guix:open-connection-for-uri' to open the
connection and pass it to 'http-head' via #:port.
 2019-04-18 17:43:56 +02:00
Efraim Flashner bd5b6ce0d7
gnu: gnuastro: Update to 0.9. 
* gnu/packages/astronomy.scm (gnuastro): Update to 0.9.
[native-inputs]: Add libtool.
 2019-04-18 17:00:46 +03:00
Efraim Flashner 5d450aba1f
gnu: nano: Update to 4.1. 
* gnu/packages/nano.scm (nano): Update to 4.1.
 2019-04-18 16:59:28 +03:00
Rutger Helling fd6d2fd871
gnu: xpra: Update to 2.5.1. 
* gnu/packages/xorg.scm (xpra): Update to 2.5.1.
 2019-04-18 09:25:38 +02:00
Tobias Geerinckx-Rice 2ad0310615
gnu: rclone: Update to 1.47.0. 
* gnu/packages/sync.scm (rclone): Update to 1.47.0.
 2019-04-17 16:25:57 +02:00
Tobias Geerinckx-Rice afcd4438f8
gnu: console-setup: Update to 1.191. 
* gnu/packages/xorg.scm (console-setup): Update to 1.191.
 2019-04-17 15:54:54 +02:00
Ludovic Courtès 9015e63996
installer: Sort keyboard layouts according to language and translations. 
Previously, we would always (1) put English first, and (2) sort the
other layouts based on their English description.  This fixes both
issues.

* gnu/installer/newt/keymap.scm (sort-layouts)[layout<?]: New procedure.
[preferred]: New variable.
Partition according to both the 'name' and 'synopsis' fields.  Sort both
the main layouts and the other layouts according to 'layout<?'.
 2019-04-17 15:16:08 +02:00
Ludovic Courtès 818595a974
installer: Parse the 'shortDescription' field from xkeyboard-config. 
* gnu/installer/keymap.scm (<x11-keymap-layout>)[synopsis]: New field.
(xkb-rules->models+layouts): Fill out the 'synopsis' field.
 2019-04-17 15:13:31 +02:00
Ludovic Courtès feaa83a377
installer: Translate keyboard layout names. 
* gnu/installer.scm (installer-program)[installer-builder]: Call
'bindtextdomain' for "xkeyboard-config".
* gnu/installer/newt/keymap.scm (run-keymap-page): Add calls to
'gettext'.
 2019-04-17 15:11:21 +02:00
Ludovic Courtès 085e021e63
nls: Update 'de' translation. 2019-04-17 14:31:46 +02:00
Ludovic Courtès c04052e4df
nls: Update 'de' translation of the manual. 2019-04-17 14:06:30 +02:00
Ludovic Courtès 72f749dcb8
pull: '--url', '--commit', and '--branch' apply to the 'guix' channel. 
Suggested by pkill9 <pkill9@runbox.com>.

* guix/scripts/pull.scm (channel-list): Apply REF and URL to the 'guix'
channel.
* doc/guix.texi (Invoking guix pull): Adjust accordingly.
 2019-04-17 13:56:40 +02:00
Ludovic Courtès 14755829dc
installer: Sort items with 'string-locale<?'. 
That way "Österreich" comes before "Schweiz" in a German locale (or
pretty much any sane locale.)

* gnu/installer/newt/page.scm (run-listbox-selection-page)[sort-listbox-items]:
Use 'string-locale<?' instead of 'string<=?'.
 2019-04-17 11:53:54 +02:00
Ludovic Courtès 7cb7be17af
installer: Look up timezone name translations in "iso_3166-1". 
* gnu/installer/newt/timezone.scm (run-timezone-page): Add call to
'gettext' for timezone names.
 2019-04-17 11:53:54 +02:00
Ludovic Courtès 7837a57241
installer: Display language and territory names natively. 
* gnu/installer.scm (installer-program): Add calls to 'bindtextdomain'.
* gnu/installer/newt/locale.scm (run-locale-page) <language, territory>:
Add calls to 'gettext'.
 2019-04-17 11:53:54 +02:00
Ludovic Courtès 2d5867a213
installer: Change language as soon as it has been chosen. 
Previously we'd call 'setlocale' only after the complete 'locale' step
had finished.

* gnu/installer/newt/locale.scm (run-language-page): Set the 'LANGUAGE'
environment variable before returning.
 2019-04-17 11:53:54 +02:00
Ludovic Courtès 15dca289b8
gnu: guix: Update to b8b1e4d. 
* gnu/packages/package-management.scm (guix): Update to b8b1e4d.
 2019-04-17 11:53:54 +02:00
Ludovic Courtès 3ad3c55842
installer: Desktop environment page now includes window managers. 
* gnu/installer/services.scm (<system-service>)[snippet]: Change to be a
list of sexps and add default value.
[packages]: New field.
(%system-services): Adjust 'snippet' fields to be lists of sexps.
Add Openbox, awesome, i3, and ratpoison.
(system-services->configuration): Adjust 'snippet' handling.  Honor
'packages' field.
 2019-04-17 11:53:53 +02:00
Ludovic Courtès a0e16bec37
gnu: guix: Don't pass '--with-libgcrypt-prefix'. 
* gnu/packages/package-management.scm (guix)[arguments]: Remove
"--with-libgcrypt-prefix" from the configure flags.
 2019-04-17 11:53:53 +02:00
Ludovic Courtès f2d86ed0b3
build: No longer substitute 'LIBGCRYPT'. 
This had become useless since ca71942445.

* configure.ac (LIBGCRYPT): Remove.
* guix/config.scm.in (%libgcrypt): Remove.
 2019-04-17 11:53:53 +02:00
Ludovic Courtès ab77b69eca
self: Remove unused variable. 
This variable is unused since commit
45779fa676.

* guix/self.scm (%dependency-variables): Remove.
* build-aux/build-self.scm (%dependency-variables): Remove.
 2019-04-17 11:53:53 +02:00
Ludovic Courtès a0158c26e2
gnu: awesome: Update home page. 
* gnu/packages/wm.scm (awesome)[home-page]: Update.
 2019-04-17 11:53:53 +02:00
Danny Milosavljevic 0682f08463
services: fprintd: Fix service. 
* gnu/services/authentication.scm (<fprintd-configuration>)[ntp]: Rename to...
[fprintd]: ...this.
(fprintd-dbus-service): New procedure.
(fprintd-service-type): Use it.
[default-value]: Add value.
 2019-04-17 08:51:11 +02:00
Tobias Geerinckx-Rice 38dd8b6058
gnu: gtkwave: Update to 3.3.100. 
* gnu/packages/fpga.scm (gtkwave): Update to 3.3.100.
 2019-04-17 06:15:36 +02:00
Tobias Geerinckx-Rice 9043c1c561
gnu: qsynth: Update to 0.5.6. 
* gnu/packages/audio.scm (qsynth): Update to 0.5.6.
 2019-04-17 06:15:25 +02:00