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2019-04-19gnu: r-seurat: Update to 3.0.0.Ricardo Wurmus
* 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.
2019-04-19gnu: Add r-sctransform.Ricardo Wurmus
* gnu/packages/cran.scm (r-sctransform): New variable.
2019-04-19gnu: r-urltools: Update to 1.7.3.Ricardo Wurmus
* gnu/packages/cran.scm (r-urltools): Update to 1.7.3.
2019-04-19gnu: r-rdpack: Update to 0.11-0.Ricardo Wurmus
* gnu/packages/cran.scm (r-rdpack): Update to 0.11-0.
2019-04-19gnu: r-sdmtools: Update to 1.1-221.1.Ricardo Wurmus
* gnu/packages/cran.scm (r-sdmtools): Update to 1.1-221.1.
2019-04-19gnu: r-hardyweinberg: Update to 1.6.2.Ricardo Wurmus
* gnu/packages/cran.scm (r-hardyweinberg): Update to 1.6.2.
2019-04-19gnu: r-clipr: Update to 0.6.0.Ricardo Wurmus
* gnu/packages/cran.scm (r-clipr): Update to 0.6.0.
2019-04-19gnu: r-caret: Update to 6.0-83.Ricardo Wurmus
* gnu/packages/statistics.scm (r-caret): Update to 6.0-83.
2019-04-19gnu: klick: Fix build with latest scons.Ricardo Wurmus
* gnu/packages/music.scm (klick)[arguments]: Patch "SConstruct" file to make it compatible with the current version of scons.
2019-04-19gnu: perl-datetime-timezone: Fix missing timezone data.Christopher Baines
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.
2019-04-19gnu: python2-send2trash: Don't inherit properties from python-send2trash.Marius Bakke
This is a follow-up to commit 20b3fde7763a14f605ac8a0aba1abfa73a6e7dda. Commits and beer do not mix well. * gnu/packages/python-xyz.scm (python2-send2trash): Inherit using STRIP-PYTHON2-VARIANT.
2019-04-19gnu: python-send2trash: Really delay Python2 variant.Marius Bakke
This is a follow-up to commit 4782a06f45d515eebc4d1ee8e958def409a0ef9f, which somehow solved my problem, but did so incorrectly. * gnu/packages/python-xyz.scm (python-send2trash)[properties]: Refer to PYTHON2-SEND2TRASH.
2019-04-19gnu: gpgme: Update to 1.13.0.Marius Bakke
* gnu/packages/gnupg.scm (gpgme): Update to 1.13.0. [source](patches): Remove.
2019-04-19gnu: python-send2trash: Properly delay python2 variant.Marius Bakke
* gnu/packages/python-xyz.scm (python2-send2trash)[properties]: Move from here ... (python-send2trash)[properties]: ... to here.
2019-04-19gnu: python-service-identity: Update to 18.1.0.Marius Bakke
* gnu/packages/python-crypto.scm (python-service-identity): Update to 18.1.0.
2019-04-19gnu: python-jsonschema: Update to 3.0.1.Marius Bakke
* 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.
2019-04-19gnu: Add python-pyrsistent.Marius Bakke
* gnu/packages/python-xyz.scm (python-pyrsistent, python2-pyrsistent): New public variables.
2019-04-19gnu: python-twisted: Update to 19.2.0.Marius Bakke
* gnu/packages/python-xyz.scm (python-twisted): Update to 19.2.0. [propagated-inputs]: Add PYTHON-PYHAMCREST.
2019-04-19gnu: python-automat: Update to 0.7.0.Marius Bakke
* gnu/packages/python-xyz.scm (python-automat): Update to 0.7.0.
2019-04-19gnu: python-m2r: Update to 0.2.1.Marius Bakke
* gnu/packages/python-xyz.scm (python-m2r): Update to 0.2.1.
2019-04-19gnu: python-idna: Update to 2.8.Marius Bakke
* gnu/packages/python-xyz.scm (python-idna): Update to 2.8.
2019-04-19gnu: python-hyperlink: Update to 19.0.0.Marius Bakke
* gnu/packages/python-web.scm (python-hyperlink): Update to 19.0.0.
2019-04-19gnu: python-zope-interface: Update to 4.6.0.Marius Bakke
* gnu/packages/python-web.scm (python-zope-interface): Update to 4.6.0.
2019-04-19gnu: xmlsec: Update to 1.2.28.Marius Bakke
* gnu/packages/xml.scm (xmlsec): Update to 1.2.28.
2019-04-18guile-build-system: Support building in parallel.Christopher Baines
* 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.
2019-04-18lint: 'check-github-url' uses our own 'open-connection-for-uri'.Ludovic Courtès
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.
2019-04-18gnu: gnuastro: Update to 0.9.Efraim Flashner
* gnu/packages/astronomy.scm (gnuastro): Update to 0.9. [native-inputs]: Add libtool.
2019-04-18gnu: nano: Update to 4.1.Efraim Flashner
* gnu/packages/nano.scm (nano): Update to 4.1.
2019-04-18gnu: xpra: Update to 2.5.1.Rutger Helling
* gnu/packages/xorg.scm (xpra): Update to 2.5.1.
2019-04-17gnu: rclone: Update to 1.47.0.Tobias Geerinckx-Rice
* gnu/packages/sync.scm (rclone): Update to 1.47.0.
2019-04-17gnu: console-setup: Update to 1.191.Tobias Geerinckx-Rice
* gnu/packages/xorg.scm (console-setup): Update to 1.191.
2019-04-17installer: Sort keyboard layouts according to language and translations.Ludovic Courtès
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<?'.
2019-04-17installer: Parse the 'shortDescription' field from xkeyboard-config.Ludovic Courtès
* gnu/installer/keymap.scm (<x11-keymap-layout>)[synopsis]: New field. (xkb-rules->models+layouts): Fill out the 'synopsis' field.
2019-04-17installer: Translate keyboard layout names.Ludovic Courtès
* gnu/installer.scm (installer-program)[installer-builder]: Call 'bindtextdomain' for "xkeyboard-config". * gnu/installer/newt/keymap.scm (run-keymap-page): Add calls to 'gettext'.
2019-04-17nls: Update 'de' translation.Ludovic Courtès
2019-04-17nls: Update 'de' translation of the manual.Ludovic Courtès
2019-04-17pull: '--url', '--commit', and '--branch' apply to the 'guix' channel.Ludovic Courtès
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.
2019-04-17installer: Sort items with 'string-locale<?'.Ludovic Courtès
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<=?'.
2019-04-17installer: Look up timezone name translations in "iso_3166-1".Ludovic Courtès
* gnu/installer/newt/timezone.scm (run-timezone-page): Add call to 'gettext' for timezone names.
2019-04-17installer: Display language and territory names natively.Ludovic Courtès
* gnu/installer.scm (installer-program): Add calls to 'bindtextdomain'. * gnu/installer/newt/locale.scm (run-locale-page) <language, territory>: Add calls to 'gettext'.
2019-04-17installer: Change language as soon as it has been chosen.Ludovic Courtès
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.
2019-04-17gnu: guix: Update to b8b1e4d.Ludovic Courtès
* gnu/packages/package-management.scm (guix): Update to b8b1e4d.
2019-04-17installer: Desktop environment page now includes window managers.Ludovic Courtès
* 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.
2019-04-17gnu: guix: Don't pass '--with-libgcrypt-prefix'.Ludovic Courtès
* gnu/packages/package-management.scm (guix)[arguments]: Remove "--with-libgcrypt-prefix" from the configure flags.
2019-04-17build: No longer substitute 'LIBGCRYPT'.Ludovic Courtès
This had become useless since ca719424455465fca4b872c371daf2a46de88b33. * configure.ac (LIBGCRYPT): Remove. * guix/config.scm.in (%libgcrypt): Remove.
2019-04-17self: Remove unused variable.Ludovic Courtès
This variable is unused since commit 45779fa676419de8838cb26b6c7a24678a2be1cd. * guix/self.scm (%dependency-variables): Remove. * build-aux/build-self.scm (%dependency-variables): Remove.
2019-04-17gnu: awesome: Update home page.Ludovic Courtès
* gnu/packages/wm.scm (awesome)[home-page]: Update.
2019-04-17services: fprintd: Fix service.Danny Milosavljevic
* 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.
2019-04-17gnu: gtkwave: Update to 3.3.100.Tobias Geerinckx-Rice
* gnu/packages/fpga.scm (gtkwave): Update to 3.3.100.
2019-04-17gnu: qsynth: Update to 0.5.6.Tobias Geerinckx-Rice
* gnu/packages/audio.scm (qsynth): Update to 0.5.6.
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