jackhill/guix/guix.git
4 years agonews: Add entry for the further reduced (aka Scheme-only) bootstrap.
Jan (janneke) Nieuwenhuizen [Fri, 17 Apr 2020 17:27:07 +0000 (19:27 +0200)]
news: Add entry for the further reduced (aka Scheme-only) bootstrap.

* etc/news.scm: Add entry for the further reduced (aka Scheme-only) bootstrap.

4 years agognu: linphone: Reformat code to respect coding style conventions.
Raghav Gururajan [Thu, 16 Apr 2020 03:57:02 +0000 (23:57 -0400)]
gnu: linphone: Reformat code to respect coding style conventions.

* gnu/packages/linphone.scm (bcunit, belr, belcard, bcmatroska2, bzrtp)
(belle-sip, mediastreamer2, msopenh264, mssilk, msamr): Adjust code formatting
to meet the 80 characters line width convention, along with other minor
cosmetic edits.

Signed-off-by: Maxim Cournoyer <maxim.cournoyer@gmail.com>
4 years agoMerge branch 'master' into core-updates
Marius Bakke [Wed, 15 Apr 2020 17:26:55 +0000 (19:26 +0200)]
Merge branch 'master' into core-updates

4 years agodoc: Fix typo.
Nicolas Goaziou [Wed, 15 Apr 2020 17:11:32 +0000 (19:11 +0200)]
doc: Fix typo.

* doc/guix.texi (Running Guix in a VM): Add missing reference to
`spice-vdagent-service' and misuse of @pxref.

4 years agoMerge branch 'version-1.1.0'
Ludovic Courtès [Wed, 15 Apr 2020 14:09:18 +0000 (16:09 +0200)]
Merge branch 'version-1.1.0'

4 years agognu: Add gtkd.
guy fleury iteriteka [Wed, 15 Apr 2020 13:07:29 +0000 (15:07 +0200)]
gnu: Add gtkd.

* gnu/packages/dlang.scm (gtkd): New variable.

4 years agognu: Add g-golf
Vitaliy Shatrov [Wed, 15 Apr 2020 07:15:59 +0000 (07:15 +0000)]
gnu: Add g-golf

* gnu/packages/guile-xyz.scm (g-golf): New variable.

Signed-off-by: Christopher Baines <mail@cbaines.net>
4 years agognu: Remove libvpx@1.7.
Marius Bakke [Wed, 15 Apr 2020 11:50:19 +0000 (13:50 +0200)]
gnu: Remove libvpx@1.7.

* gnu/packages/patches/libvpx-use-after-free-in-postproc.patch: Delete file.
* gnu/local.mk (dist_patch_DATA): Adjust accordingly.
* gnu/packages/video.scm (libvpx-1.7): Remove variable.

4 years agognu: IceCat: Build with the latest libvpx.
Marius Bakke [Wed, 15 Apr 2020 11:48:54 +0000 (13:48 +0200)]
gnu: IceCat: Build with the latest libvpx.

* gnu/packages/gnuzilla.scm (icecat)[inputs]: Change from LIBVPX-1.7 to LIBVPX.

4 years agognu: python-jedi: Update to 0.17.0.
Marius Bakke [Wed, 15 Apr 2020 11:23:40 +0000 (13:23 +0200)]
gnu: python-jedi: Update to 0.17.0.

* gnu/packages/python-xyz.scm (python-jedi): Update to 0.17.0.
[source](patches): Remove.
* gnu/packages/patches/python-jedi-deleted-variables.patch: Delete file.
* gnu/local.mk (dist_patch_DATA): Adjust accordingly.

4 years agognu: emacsy-minimal: Update to v0.4.1-28.d459ca1.
Mike Rosset [Wed, 8 Apr 2020 18:17:13 +0000 (11:17 -0700)]
gnu: emacsy-minimal: Update to v0.4.1-28.d459ca1.

* gnu/packages/guile-xyz.scm (emacsy-minimal): Update to v0.4.1-28.d459ca1.

Signed-off-by: Christopher Baines <mail@cbaines.net>
4 years agognu: gqrx: Add volk to inputs.
Guillaume Le Vaillant [Wed, 15 Apr 2020 08:14:45 +0000 (10:14 +0200)]
gnu: gqrx: Add volk to inputs.

* gnu/packages/radio.scm (gqrx)[inputs]: Add volk.

4 years agognu: gnuradio-iqbalance: Add volk to inputs.
Guillaume Le Vaillant [Wed, 15 Apr 2020 08:10:58 +0000 (10:10 +0200)]
gnu: gnuradio-iqbalance: Add volk to inputs.

* gnu/packages/radio.scm (gnuradio-iqbalance)[inputs]: Add volk.

4 years agognu: gnuradio-osmosdr: Add volk to inputs.
Guillaume Le Vaillant [Wed, 15 Apr 2020 08:07:52 +0000 (10:07 +0200)]
gnu: gnuradio-osmosdr: Add volk to inputs.

* gnu/packages/radio.scm (gnuradio-osmosdr)[inputs]: Add volk.

4 years agognu: gnuradio: Use shared volk instead of bundled one.
Guillaume Le Vaillant [Wed, 15 Apr 2020 08:02:13 +0000 (10:02 +0200)]
gnu: gnuradio: Use shared volk instead of bundled one.

* gnu/packages/radio.scm (gnuradio)[source]: Add snippet to delete bundled
  volk.
  [inputs]: Add volk.
  [arguments]: Add "-DENABLE_INTERNAL_VOLK=OFF" to configure-flags.

4 years agognu: hardware: Add copyright line.
Jan (janneke) Nieuwenhuizen [Wed, 15 Apr 2020 08:03:32 +0000 (10:03 +0200)]
gnu: hardware: Add copyright line.

Add missing copyright line for commit
22a98cda38784107a1d1c9cd7afc0c80944a9027

* gnu/packages/hardware.scm: Add copyright.

4 years agognu: guix: Update to 1.1.0.
Ludovic Courtès [Wed, 15 Apr 2020 07:58:26 +0000 (09:58 +0200)]
gnu: guix: Update to 1.1.0.

4 years agognu: u-boot: Update to 2020.04.
Vagrant Cascadian [Wed, 15 Apr 2020 06:14:01 +0000 (23:14 -0700)]
gnu: u-boot: Update to 2020.04.

* gnu/packages/bootloaders (u-boot): Update to 2020.04.

4 years agognu: guile-parted: Update to 0.0.4.
Mathieu Othacehe [Wed, 15 Apr 2020 06:56:20 +0000 (08:56 +0200)]
gnu: guile-parted: Update to 0.0.4.

* gnu/packages/guile-xyz.scm (guile-parted): Update to 0.0.4.

4 years agognu: linphoneqt: Fix reproducibility issue and improve description.
Maxim Cournoyer [Wed, 15 Apr 2020 06:03:26 +0000 (02:03 -0400)]
gnu: linphoneqt: Fix reproducibility issue and improve description.

* gnu/packages/linphone.scm (linphoneqt)[phases]: Rename the 'patch phase to
'set-version-string, and use the version variable of the package in the
replacement.
{set-qt-rcc-source-date-override, fix-cmake-error}: Add phases.
[synopsis]: Explicit what the package is.
[description]: Mention more useful keywords and features.

4 years agognu: cgit: Update Git source code to 2.25.3.
Leo Famulari [Wed, 15 Apr 2020 05:33:58 +0000 (01:33 -0400)]
gnu: cgit: Update Git source code to 2.25.3.

* gnu/packages/version-control.scm (cgit)[inputs]: Update git-source to 2.25.3.

4 years agognu: Git: Update to 2.26.1 [fixes CVE-2020-5260].
Leo Famulari [Wed, 15 Apr 2020 04:48:18 +0000 (00:48 -0400)]
gnu: Git: Update to 2.26.1 [fixes CVE-2020-5260].

* gnu/packages/version-control.scm (git): Update to 2.26.1.
[native-inputs]: Update git-manpages.

4 years agoUpdate NEWS.
Ludovic Courtès [Tue, 14 Apr 2020 20:29:48 +0000 (22:29 +0200)]
Update NEWS.

4 years agoservices: shepherd: Increase the PID file timeout to 30s.
Ludovic Courtès [Tue, 14 Apr 2020 21:58:55 +0000 (23:58 +0200)]
services: shepherd: Increase the PID file timeout to 30s.

When running the installation image off a DVD, early I/O operations are
extremely slow, to the point that something like dbus-daemon would need
~20s to start.  This change works around the issue.

Fixes <https://bugs.gnu.org/40572>.
Reported by Florian Pelz <pelzflorian@pelzflorian.de>.

* gnu/services/shepherd.scm (shepherd-configuration-file): Set
%pid-file-timeout to 30.

4 years agognu: emacs-helm-ag: Update to 0.59.
Michael Rohleder [Sun, 12 Apr 2020 18:27:39 +0000 (20:27 +0200)]
gnu: emacs-helm-ag: Update to 0.59.

* gnu/packages/emacs-xyz.scm (emacs-helm-ag): Update to 0.59.

4 years agognu: cook: Fix test failure.
Marius Bakke [Tue, 14 Apr 2020 16:05:57 +0000 (18:05 +0200)]
gnu: cook: Fix test failure.

* gnu/packages/cook.scm (cook)[arguments]: Override LC_ALL for one test.

4 years agognu: python-pyrsistent: Update to 0.16.0.
Marius Bakke [Tue, 14 Apr 2020 15:41:37 +0000 (17:41 +0200)]
gnu: python-pyrsistent: Update to 0.16.0.

* gnu/packages/python-xyz.scm (python-pyrsistent): Update to 0.16.0.

4 years agognu: python-gssapi: Update to 1.6.5.
Marius Bakke [Tue, 14 Apr 2020 14:14:37 +0000 (16:14 +0200)]
gnu: python-gssapi: Update to 1.6.5.

* gnu/packages/python-xyz.scm (python-gssapi): Update to 1.6.5.

4 years agognu: python-parso: Update to 0.7.0.
Marius Bakke [Tue, 14 Apr 2020 12:08:05 +0000 (14:08 +0200)]
gnu: python-parso: Update to 0.7.0.

* gnu/packages/python-xyz.scm (python-parso): Update to 0.7.0.

4 years agognu: dune-localfunctions: Fix build failure.
Marius Bakke [Tue, 14 Apr 2020 20:30:05 +0000 (22:30 +0200)]
gnu: dune-localfunctions: Fix build failure.

* gnu/packages/maths.scm (dune-localfunctions)[arguments]: Add phase
'hide-gfortran'.

4 years agognu: dune-istl: Fix build failure.
Marius Bakke [Tue, 14 Apr 2020 20:29:35 +0000 (22:29 +0200)]
gnu: dune-istl: Fix build failure.

* gnu/packages/maths.scm (dune-istl)[arguments]: Add phase 'hide-gfortran'.

4 years agognu: mksh: Update to 58.
Tobias Geerinckx-Rice [Tue, 14 Apr 2020 18:22:27 +0000 (20:22 +0200)]
gnu: mksh: Update to 58.

* gnu/packages/shells.scm (mksh): Update to 58.

4 years agognu: txr: Update to 235.
Tobias Geerinckx-Rice [Tue, 14 Apr 2020 16:54:52 +0000 (18:54 +0200)]
gnu: txr: Update to 235.

* gnu/packages/lisp.scm (txr): Update to 235.
[arguments]: Cosmetic shortening.

4 years agognu: txr: Call ./configure manually instead of patching.
Tobias Geerinckx-Rice [Tue, 14 Apr 2020 16:38:23 +0000 (18:38 +0200)]
gnu: txr: Call ./configure manually instead of patching.

* gnu/packages/lisp.scm (txr)[source]: Remove patch.
[arguments]: Add ‘--prefix’ to #:configure-flags.
Use a custom ‘configure’ phase.
* gnu/packages/patches/txr-shell.patch: Delete file.
* gnu/local.mk (dist_patch_DATA): Remove it.

4 years agognu: txr: Declare test target.
Tobias Geerinckx-Rice [Tue, 14 Apr 2020 16:22:16 +0000 (18:22 +0200)]
gnu: txr: Declare test target.

* gnu/packages/lisp.scm (txr)[arguments]: Use #:test-target instead of
a trivial custom ‘check’ phase.

4 years agognu: i2pd: Update to 2.31.0.
Tobias Geerinckx-Rice [Tue, 14 Apr 2020 15:42:45 +0000 (17:42 +0200)]
gnu: i2pd: Update to 2.31.0.

* gnu/packages/i2p.scm (i2pd): Update to 2.31.0.

4 years agognu: strongswan: Update to 5.8.4.
Tobias Geerinckx-Rice [Tue, 14 Apr 2020 18:10:35 +0000 (20:10 +0200)]
gnu: strongswan: Update to 5.8.4.

* gnu/packages/networking.scm (strongswan): Update to 5.8.4.

4 years agodoc: Fix typo.
Brice Waegeneire [Sun, 12 Apr 2020 17:58:28 +0000 (19:58 +0200)]
doc: Fix typo.

* doc/guix.texi (Web Services)[nginx-php-fpm-location]: Replace
'nginx-php-fpm-location' by 'nginx-php-location'.

Signed-off-by: Christopher Baines <mail@cbaines.net>
4 years agognu: python-podcastparser: Update to 0.6.5.
Tobias Geerinckx-Rice [Tue, 14 Apr 2020 15:17:42 +0000 (17:17 +0200)]
gnu: python-podcastparser: Update to 0.6.5.

* gnu/packages/gpodder.scm (python-podcastparser): Update to 0.6.5.

4 years agognu: man-pages: Update to 5.06.
Tobias Geerinckx-Rice [Tue, 14 Apr 2020 15:16:38 +0000 (17:16 +0200)]
gnu: man-pages: Update to 5.06.

* gnu/packages/man.scm (man-pages): Update to 5.06.

4 years agognu: x265: Update to 3.3.
Tobias Geerinckx-Rice [Tue, 14 Apr 2020 15:12:57 +0000 (17:12 +0200)]
gnu: x265: Update to 3.3.

* gnu/packages/video.scm (x265): Update to 3.3.

4 years agognu: r-glue: Update to 1.4.0.
Ricardo Wurmus [Tue, 14 Apr 2020 14:39:53 +0000 (16:39 +0200)]
gnu: r-glue: Update to 1.4.0.

* gnu/packages/cran.scm (r-glue): Update to 1.4.0.
[native-inputs]: Add commment explaining why r-knitr is not an input.

4 years agognu: r-rcpparmadillo: Update to 0.9.860.2.0.
Ricardo Wurmus [Tue, 14 Apr 2020 14:39:23 +0000 (16:39 +0200)]
gnu: r-rcpparmadillo: Update to 0.9.860.2.0.

* gnu/packages/statistics.scm (r-rcpparmadillo): Update to 0.9.860.2.0.
[native-inputs]: Remove r-knitr, r-rmarkdown, ghc-pandoc, and
ghc-pandoc-citeproc.

4 years agognu: r-atacseqqc: Update to 1.10.4.
Ricardo Wurmus [Tue, 14 Apr 2020 14:14:49 +0000 (16:14 +0200)]
gnu: r-atacseqqc: Update to 1.10.4.

* gnu/packages/bioconductor.scm (r-atacseqqc): Update to 1.10.4.

4 years agognu: r-a4base: Update to 1.34.1.
Ricardo Wurmus [Tue, 14 Apr 2020 14:14:40 +0000 (16:14 +0200)]
gnu: r-a4base: Update to 1.34.1.

* gnu/packages/bioconductor.scm (r-a4base): Update to 1.34.1.

4 years agognu: r-varianttools: Update to 1.28.1.
Ricardo Wurmus [Tue, 14 Apr 2020 14:14:33 +0000 (16:14 +0200)]
gnu: r-varianttools: Update to 1.28.1.

* gnu/packages/bioconductor.scm (r-varianttools): Update to 1.28.1.

4 years agognu: r-genomicinteractions: Update to 1.20.3.
Ricardo Wurmus [Tue, 14 Apr 2020 14:14:17 +0000 (16:14 +0200)]
gnu: r-genomicinteractions: Update to 1.20.3.

* gnu/packages/bioconductor.scm (r-genomicinteractions): Update to 1.20.3.

4 years agognu: r-delayedarray: Update to 0.12.3.
Ricardo Wurmus [Tue, 14 Apr 2020 14:14:02 +0000 (16:14 +0200)]
gnu: r-delayedarray: Update to 0.12.3.

* gnu/packages/bioinformatics.scm (r-delayedarray): Update to 0.12.3.
[native-inputs]: Add r-knitr.

4 years agognu: r-s4vectors: Update to 0.24.4.
Ricardo Wurmus [Tue, 14 Apr 2020 14:12:39 +0000 (16:12 +0200)]
gnu: r-s4vectors: Update to 0.24.4.

* gnu/packages/bioinformatics.scm (r-s4vectors): Update to 0.24.4.

4 years agognu: r-httpcode: Update to 0.3.0.
Ricardo Wurmus [Tue, 14 Apr 2020 14:12:25 +0000 (16:12 +0200)]
gnu: r-httpcode: Update to 0.3.0.

* gnu/packages/cran.scm (r-httpcode): Update to 0.3.0.

4 years agognu: r-isoband: Update to 0.2.1.
Ricardo Wurmus [Tue, 14 Apr 2020 14:12:09 +0000 (16:12 +0200)]
gnu: r-isoband: Update to 0.2.1.

* gnu/packages/cran.scm (r-isoband): Update to 0.2.1.
[native-inputs]: Add r-knitr.

4 years agognu: r-anthropometry: Update to 1.14.
Ricardo Wurmus [Tue, 14 Apr 2020 14:09:57 +0000 (16:09 +0200)]
gnu: r-anthropometry: Update to 1.14.

* gnu/packages/cran.scm (r-anthropometry): Update to 1.14.
[native-inputs]: Add r-knitr.

4 years agognu: r-lhs: Update to 1.0.2.
Ricardo Wurmus [Tue, 14 Apr 2020 14:09:30 +0000 (16:09 +0200)]
gnu: r-lhs: Update to 1.0.2.

* gnu/packages/cran.scm (r-lhs): Update to 1.0.2.
[native-inputs]: Add r-knitr.

4 years agognu: r-txtplot: Update to 1.0-4.
Ricardo Wurmus [Tue, 14 Apr 2020 14:08:06 +0000 (16:08 +0200)]
gnu: r-txtplot: Update to 1.0-4.

* gnu/packages/cran.scm (r-txtplot): Update to 1.0-4.

4 years agognu: r-parameters: Update to 0.6.1.
Ricardo Wurmus [Tue, 14 Apr 2020 14:07:35 +0000 (16:07 +0200)]
gnu: r-parameters: Update to 0.6.1.

* gnu/packages/cran.scm (r-parameters): Update to 0.6.1.

4 years agognu: r-sf: Update to 0.9-1.
Ricardo Wurmus [Tue, 14 Apr 2020 14:07:27 +0000 (16:07 +0200)]
gnu: r-sf: Update to 0.9-1.

* gnu/packages/cran.scm (r-sf): Update to 0.9-1.

4 years agognu: r-spdata: Update to 0.3.5.
Ricardo Wurmus [Tue, 14 Apr 2020 14:07:15 +0000 (16:07 +0200)]
gnu: r-spdata: Update to 0.3.5.

* gnu/packages/cran.scm (r-spdata): Update to 0.3.5.

4 years agognu: r-classint: Update to 0.4-3.
Ricardo Wurmus [Tue, 14 Apr 2020 14:06:18 +0000 (16:06 +0200)]
gnu: r-classint: Update to 0.4-3.

* gnu/packages/cran.scm (r-classint): Update to 0.4-3.
[native-inputs]: Add r-knitr.

4 years agognu: r-lemon: Update to 0.4.4.
Ricardo Wurmus [Tue, 14 Apr 2020 14:05:49 +0000 (16:05 +0200)]
gnu: r-lemon: Update to 0.4.4.

* gnu/packages/cran.scm (r-lemon): Update to 0.4.4.
[propagated-inputs]: Add r-rlang.

4 years agognu: r-compositions: Update to 1.40-5.
Ricardo Wurmus [Tue, 14 Apr 2020 14:05:36 +0000 (16:05 +0200)]
gnu: r-compositions: Update to 1.40-5.

* gnu/packages/cran.scm (r-compositions): Update to 1.40-5.

4 years agognu: r-lmertest: Update to 3.1-2.
Ricardo Wurmus [Tue, 14 Apr 2020 14:04:47 +0000 (16:04 +0200)]
gnu: r-lmertest: Update to 3.1-2.

* gnu/packages/cran.scm (r-lmertest): Update to 3.1-2.

4 years agognu: r-usethis: Update to 1.6.0.
Ricardo Wurmus [Tue, 14 Apr 2020 14:04:24 +0000 (16:04 +0200)]
gnu: r-usethis: Update to 1.6.0.

* gnu/packages/cran.scm (r-usethis): Update to 1.6.0.
[propagated-inputs]: Remove r-clisymbols; add r-cli and r-rematch2.

4 years agognu: r-fs: Update to 1.4.1.
Ricardo Wurmus [Tue, 14 Apr 2020 14:04:03 +0000 (16:04 +0200)]
gnu: r-fs: Update to 1.4.1.

* gnu/packages/cran.scm (r-fs): Update to 1.4.1.

4 years agognu: r-effectsize: Update to 0.3.0.
Ricardo Wurmus [Tue, 14 Apr 2020 14:03:47 +0000 (16:03 +0200)]
gnu: r-effectsize: Update to 0.3.0.

* gnu/packages/cran.scm (r-effectsize): Update to 0.3.0.
[native-inputs]: Add r-knitr.

4 years agognu: r-multcomp: Update to 1.4-13.
Ricardo Wurmus [Tue, 14 Apr 2020 14:03:39 +0000 (16:03 +0200)]
gnu: r-multcomp: Update to 1.4-13.

* gnu/packages/cran.scm (r-multcomp): Update to 1.4-13.

4 years agognu: r-survey: Update to 4.0.
Ricardo Wurmus [Tue, 14 Apr 2020 14:03:32 +0000 (16:03 +0200)]
gnu: r-survey: Update to 4.0.

* gnu/packages/cran.scm (r-survey): Update to 4.0.

4 years agognu: r-sjmisc: Update to 2.8.4.
Ricardo Wurmus [Tue, 14 Apr 2020 14:03:02 +0000 (16:03 +0200)]
gnu: r-sjmisc: Update to 2.8.4.

* gnu/packages/cran.scm (r-sjmisc): Update to 2.8.4.
[native-inputs]: Add r-knitr.

4 years agognu: r-arules: Update to 1.6-5.
Ricardo Wurmus [Tue, 14 Apr 2020 14:02:47 +0000 (16:02 +0200)]
gnu: r-arules: Update to 1.6-5.

* gnu/packages/cran.scm (r-arules): Update to 1.6-5.

4 years agognu: r-xfun: Update to 0.13.
Ricardo Wurmus [Tue, 14 Apr 2020 14:02:20 +0000 (16:02 +0200)]
gnu: r-xfun: Update to 0.13.

* gnu/packages/cran.scm (r-xfun): Update to 0.13.
[native-inputs]: Add comment about not adding r-knitr.

4 years agognu: r-rcpp: Update to 1.0.4.6.
Ricardo Wurmus [Tue, 14 Apr 2020 14:02:05 +0000 (16:02 +0200)]
gnu: r-rcpp: Update to 1.0.4.6.

* gnu/packages/cran.scm (r-rcpp): Update to 1.0.4.6.

4 years agognu: r-lubridate: Update to 1.7.8.
Ricardo Wurmus [Tue, 14 Apr 2020 14:01:34 +0000 (16:01 +0200)]
gnu: r-lubridate: Update to 1.7.8.

* gnu/packages/statistics.scm (r-lubridate): Update to 1.7.8.
[propagated-inputs]: Remove r-stringr; add r-generics.
[native-inputs]: Add r-knitr.

4 years agognu: r-cairo: Update to 1.5-12.
Ricardo Wurmus [Tue, 14 Apr 2020 14:01:24 +0000 (16:01 +0200)]
gnu: r-cairo: Update to 1.5-12.

* gnu/packages/statistics.scm (r-cairo): Update to 1.5-12.

4 years agognu: r-lme4: Update to 1.1-23.
Ricardo Wurmus [Tue, 14 Apr 2020 14:01:07 +0000 (16:01 +0200)]
gnu: r-lme4: Update to 1.1-23.

* gnu/packages/statistics.scm (r-lme4): Update to 1.1-23.
[native-inputs]: Add r-knitr.
[propagated-inputs]: Add r-statmod.

4 years agognu: r-mclust: Update to 5.4.6.
Ricardo Wurmus [Tue, 14 Apr 2020 14:00:44 +0000 (16:00 +0200)]
gnu: r-mclust: Update to 5.4.6.

* gnu/packages/statistics.scm (r-mclust): Update to 5.4.6.
[native-inputs]: Add r-knitr.

4 years agognu: r-sfsmisc: Update to 1.1-6.
Ricardo Wurmus [Tue, 14 Apr 2020 14:00:36 +0000 (16:00 +0200)]
gnu: r-sfsmisc: Update to 1.1-6.

* gnu/packages/statistics.scm (r-sfsmisc): Update to 1.1-6.

4 years agognu: r-plotly: Update to 4.9.2.1.
Ricardo Wurmus [Tue, 14 Apr 2020 14:00:29 +0000 (16:00 +0200)]
gnu: r-plotly: Update to 4.9.2.1.

* gnu/packages/statistics.scm (r-plotly): Update to 4.9.2.1.

4 years agognu: r-devtools: Update to 2.3.0.
Ricardo Wurmus [Tue, 14 Apr 2020 14:00:14 +0000 (16:00 +0200)]
gnu: r-devtools: Update to 2.3.0.

* gnu/packages/statistics.scm (r-devtools): Update to 2.3.0.
[native-inputs]: Add r-knitr.

4 years agognu: r-backports: Update to 1.1.6.
Ricardo Wurmus [Tue, 14 Apr 2020 14:00:04 +0000 (16:00 +0200)]
gnu: r-backports: Update to 1.1.6.

* gnu/packages/statistics.scm (r-backports): Update to 1.1.6.

4 years agognu: r-xml2: Update to 1.3.1.
Ricardo Wurmus [Tue, 14 Apr 2020 13:59:57 +0000 (15:59 +0200)]
gnu: r-xml2: Update to 1.3.1.

* gnu/packages/statistics.scm (r-xml2): Update to 1.3.1.

4 years agognu: r-gdtools: Update to 0.2.2.
Ricardo Wurmus [Tue, 14 Apr 2020 13:59:50 +0000 (15:59 +0200)]
gnu: r-gdtools: Update to 0.2.2.

* gnu/packages/statistics.scm (r-gdtools): Update to 0.2.2.

4 years agognu: r-reshape2: Update to 1.4.4.
Ricardo Wurmus [Tue, 14 Apr 2020 13:59:41 +0000 (15:59 +0200)]
gnu: r-reshape2: Update to 1.4.4.

* gnu/packages/statistics.scm (r-reshape2): Update to 1.4.4.

4 years agognu: r-survival: Update to 3.1-12.
Ricardo Wurmus [Tue, 14 Apr 2020 13:24:55 +0000 (15:24 +0200)]
gnu: r-survival: Update to 3.1-12.

* gnu/packages/statistics.scm (r-survival): Update to 3.1-12.

4 years agognu: r-nlme: Update to 3.1-147.
Ricardo Wurmus [Tue, 14 Apr 2020 13:24:31 +0000 (15:24 +0200)]
gnu: r-nlme: Update to 3.1-147.

* gnu/packages/statistics.scm (r-nlme): Update to 3.1-147.

4 years agognu: Add rkdeveloptool.
Jan (janneke) Nieuwenhuizen [Tue, 14 Apr 2020 14:20:52 +0000 (16:20 +0200)]
gnu: Add rkdeveloptool.

* gnu/packages/hardware.scm (rkdeveloptool): New variable.

4 years agodoc: Improve anchor collection.
Ludovic Courtès [Mon, 13 Apr 2020 10:27:17 +0000 (12:27 +0200)]
doc: Improve anchor collection.

This allows us to catch "operating_002dsystem-1", for instance.

* doc/build.scm (syntax-highlighted-html)[build](anchor-id->key): Drop
"-1" & co. from ID.

4 years agodoc: Avoid invalid 'match' pattern in 'syntax-highlighted-html'.
Ludovic Courtès [Mon, 13 Apr 2020 00:09:09 +0000 (02:09 +0200)]
doc: Avoid invalid 'match' pattern in 'syntax-highlighted-html'.

This is a followup to da9deba13d551e316f5a99a614834efa27ddc7d1.

Last-minute modification of the 'match' pattern would lead to an error:

  "multiple ellipsis patterns not allowed at same level"

* doc/build.scm (syntax-highlighted-html)[build](collect-anchors):
Add 'worthy-entry?' procedure and use it instead of the unsupported
pattern for ('dt ...).

4 years agodoc: Emit hyperlinks in HTML output for @lisp snippets.
Ludovic Courtès [Sun, 12 Apr 2020 22:12:20 +0000 (00:12 +0200)]
doc: Emit hyperlinks in HTML output for @lisp snippets.

This makes it easier to jump to the definition of a procedure or
variable when looking at a code snippet.  There can be false-positive
because scoping rules are ignored, for example, but it should be a good
approximation.

* doc/build.scm (syntax-highlighted-html)[build](highlights->sxml*): Add
'anchors' parameter.  Add clause for ('symbol text).
(syntax-highlight): Add 'anchors' parameter.  Wrap body in named let and
use it in recursive calls.  Pass ANCHORS to 'highlights->sxml*'.
(underscore-decode, anchor-id->key, collect-anchors, html?): New procedures.
(process-file): Add 'anchors' parameter. and honor it.
Rewrite mono-node and multi-node HTML files separately.

4 years agoweather: Delete duplicate entries coming from '--manifest'.
Ludovic Courtès [Tue, 14 Apr 2020 13:19:51 +0000 (15:19 +0200)]
weather: Delete duplicate entries coming from '--manifest'.

* guix/scripts/weather.scm (load-manifest): Call 'delete-duplicates'.

4 years agomaint: Ensure substitutes are available for '%default-xorg-modules'.
Ludovic Courtès [Tue, 14 Apr 2020 12:47:19 +0000 (14:47 +0200)]
maint: Ensure substitutes are available for '%default-xorg-modules'.

* etc/release-manifest.scm (%system-packages): Append
%DEFAULT-XORG-MODULES.

4 years agomaint: Actually check for the availablility of system packages.
Ludovic Courtès [Tue, 14 Apr 2020 13:10:24 +0000 (15:10 +0200)]
maint: Actually check for the availablility of system packages.

* etc/release-manifest.scm (%system-manifest): New variable.
<top level>: Add it in 'concatenate-manifests' call.

4 years agognu: Add moptilities.
Pierre Neidhardt [Tue, 14 Apr 2020 13:48:10 +0000 (15:48 +0200)]
gnu: Add moptilities.

* gnu/packages/lisp-xyz.scm (cl-moptilities, sbcl-moptilities): New variables.

4 years agognu: Add perl-authen-passphrase.
Paul Garlick [Tue, 14 Apr 2020 13:31:23 +0000 (14:31 +0100)]
gnu: Add perl-authen-passphrase.

* gnu/packages/perl.scm (perl-authen-passphrase): New variable.

4 years agognu: Add perl-digest-md4.
Paul Garlick [Tue, 14 Apr 2020 11:53:02 +0000 (12:53 +0100)]
gnu: Add perl-digest-md4.

* gnu/packages/perl.scm (perl-digest-md4): New variable.

4 years agognu: Add perl-crypt-des.
Paul Garlick [Fri, 10 Apr 2020 11:06:56 +0000 (12:06 +0100)]
gnu: Add perl-crypt-des.

* gnu/packages/perl.scm (perl-crypt-des): New variable.

4 years agognu: Add perl-crypt-cbc.
Paul Garlick [Thu, 9 Apr 2020 23:39:29 +0000 (00:39 +0100)]
gnu: Add perl-crypt-cbc.

* gnu/packages/perl.scm (perl-crypt-cbc): New variable.

4 years agognu: Add perl-crypt-mysql.
Paul Garlick [Thu, 9 Apr 2020 17:11:46 +0000 (18:11 +0100)]
gnu: Add perl-crypt-mysql.

* gnu/packages/perl.scm (perl-crypt-mysql): New variable.

4 years agognu: Add perl-crypt-passwdmd5.
Paul Garlick [Wed, 8 Apr 2020 15:13:10 +0000 (16:13 +0100)]
gnu: Add perl-crypt-passwdmd5.

* gnu/packages/perl.scm (perl-crypt-passwdmd5): New variable.

4 years agognu: Add perl-crypt-unixcrypt_xs.
Paul Garlick [Wed, 8 Apr 2020 13:58:28 +0000 (14:58 +0100)]
gnu: Add perl-crypt-unixcrypt_xs.

* gnu/packages/perl.scm (perl-crypt-unixcrypt_xs): New variable.

4 years agognu: sbcl-cl-str: Update to 0.17.
Pierre Neidhardt [Tue, 14 Apr 2020 13:06:02 +0000 (15:06 +0200)]
gnu: sbcl-cl-str: Update to 0.17.

* gnu/packages/lisp-xyz.scm (sbcl-cl-str): Update to 0.17.

4 years agognu: Add cl-change-case.
Pierre Neidhardt [Tue, 14 Apr 2020 13:05:18 +0000 (15:05 +0200)]
gnu: Add cl-change-case.

* gnu/packages/lisp-xyz.scm (cl-change-case, sbcl-cl-change-case): New
  variables.