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34942 Commits

Author SHA1 Message Date
Ludovic Courtès 7df945656c
services: hpcguix-web: Set SSL_CERT_DIR. 
Previously Git pulls over HTTPS would fail with:

  guix/git.scm:132:7: In procedure update-cached-checkout:
  Throw to key `git-error' with args `(#<<git-error> code: -17 message: "the SSL certificate is invalid" class: 16>)'.

* gnu/services/web.scm (hpcguix-web-shepherd-service): Pass
"SSL_CERT_DIR=/etc/ssl/certs".
* doc/guix.texi (Web Services): Mention certificates.
 2018-09-06 13:49:06 +02:00
Ludovic Courtès 3ffcad7df3
build-self: Accomodate upgrades from May 2016 and earlier. 
Reported by Paul Garlick <pgarlick@tourbillion-technology.com>.

Fixes a bug whereby "old" Guix instances (before mid-May 2018) would
fail to pull to current master.

Specifically, Paul reported being unable to upgrade from
6f84dc4314 (a commit that predates that
addition of the 'bootstrap' phase on gnu-build-system on 'master' and
that also predates the new 'guix pull'.)

* build-aux/build-self.scm (guile-gcrypt)[arguments]: New field.
 2018-09-06 12:01:39 +02:00
Eric Brown f66be84d08
gnu: gfortran, gcc-objc, gcc-objc++: Add version 8. 
* gnu/packages/gcc.scm (gfortran-8, gcc-objc-8, gcc-objc++-8): New
variables.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2018-09-06 11:12:40 +02:00
Ludovic Courtès 888b64038d
build: Remove -L flag when $LIBGCRYPT_LIBDIR is empty. 
Reported by Alex Vong <alexvong1995@gmail.com>.

* config-daemon.ac: Do not add "-L$LIBGCRYPT_LIBDIR" to LIBGCRYPT_LIBS
when "$LIBGCRYPT_LIBDIR" is empty.
 2018-09-06 10:59:32 +02:00
Ludovic Courtès b290a631a0
gnu: guile-present: Install .go files to libdir. 
* gnu/packages/plotutils.scm (guile-present)[source](modules, snippet):
Remove.
 2018-09-06 10:49:42 +02:00
Ludovic Courtès 89874fd156
gnu: guile-charting: Install .go files to libdir. 
* gnu/packages/plotutils.scm (guile-charting)[source](modules, snippet):
Remove.
 2018-09-06 10:48:44 +02:00
Ludovic Courtès b3ca2d8883
gnu: hpcguix-web: Update to 9ff40fc. 
* gnu/packages/web.scm (hpcguix-web): Update to 9ff40fc.
[arguments]: In 'wrap-program' phase, add guile-gcrypt, guile-git, and
guile-bytestructures to DEPS.
 2018-09-06 10:46:07 +02:00
Ludovic Courtès 96d6c41dfa
gnu: guile-commonmark: Install .go files to libdir. 
* gnu/packages/guile.scm (guile-commonmark)[source](snippet): Change the
"modir = " and "godir = " line separately, allowing .go files to be
installed to $(libdir).
 2018-09-06 10:43:01 +02:00
Ricardo Wurmus d53aeeafcc
Add missing use-modules clause. 
This is a follow-up to commit 5dfe491290.
Sorry!

* gnu/packages/bioinformatics.scm, gnu/packages/graph.scm: Use (gnu packages
bioconductor).
 2018-09-06 04:53:32 +02:00
Tobias Geerinckx-Rice 79b283e433
gnu: ccache: Update to 3.4.3. 
* gnu/packages/ccache.scm (ccache): Update to 3.4.3.
[arguments]: Remove obsolete 'munge-failing-test' phase.
 2018-09-06 02:33:47 +02:00
Tobias Geerinckx-Rice d83477adf9
gnu: font-fira-code: Update to 1.205. 
* gnu/packages/fonts.scm (font-fira-code): Update to 1.205.
 2018-09-06 02:33:47 +02:00
Tobias Geerinckx-Rice a5c70c2e0e
gnu: libmpdclient: Update to 2.15. 
* gnu/packages/mpd.scm (libmpdclient): Update to 2.15.
 2018-09-06 02:33:47 +02:00
Ludovic Courtès 37a6cdbf1b
git: Don't require users to specifiy "origin/" for branches. 
Fixes <https://bugs.gnu.org/32618>.
Reported by Eric Brown <brown@fastmail.com>.

* guix/git.scm (update-cached-checkout): Remove "origin/" from default
REF.  Define CANONICAL-REF and use it instead of REF.
(latest-repository-commit): Remove "origin/" from default REF.
* guix/channels.scm (%default-channels): Remove "origin/" from
'branch'.
 2018-09-05 23:50:38 +02:00
Ludovic Courtès cb341c1219
channels: Fix external channel builds. 
This fixes a regression introduced in
ca71942445 whereby external channels would
fail to build due to the lack of (gcrypt …) modules.

* guix/channels.scm (channel-instance-derivations): Add 'guile-gcrypt'.
Pass it along CORE to 'build-channel-instance'.
 2018-09-05 23:33:49 +02:00
Ricardo Wurmus 00a43cb81c
gnu: pigx-scrnaseq: Use latest version of Pandoc. 
* gnu/packages/bioinformatics.scm (pigx-scrnaseq)[inputs]: Replace
"ghc-pandoc-citeproc-with-pandoc-1" with "ghc-pandoc-citeproc", and
"ghc-pandoc-1" with "ghc-pandoc".
 2018-09-05 20:03:09 +02:00
Ricardo Wurmus c2b4f81e51
gnu: pigx-bsseq: Use latest version of Pandoc. 
* gnu/packages/bioinformatics.scm (pigx-bsseq)[inputs]: Replace
"ghc-pandoc-citeproc-with-pandoc-1" with "ghc-pandoc-citeproc", and
"ghc-pandoc-1" with "ghc-pandoc".
 2018-09-05 20:03:09 +02:00
Ricardo Wurmus 7cd40c8c5d
gnu: pigx-chipseq: Use latest version of Pandoc. 
* gnu/packages/bioinformatics.scm (pigx-chipseq)[inputs]: Replace
"ghc-pandoc-citeproc-with-pandoc-1" with "ghc-pandoc-citeproc", and
"ghc-pandoc-1" with "ghc-pandoc".
 2018-09-05 20:03:09 +02:00
Ricardo Wurmus ca248f1db9
gnu: pigx-rnaseq: Use latest version of Pandoc. 
* gnu/packages/bioinformatics.scm (pigx-rnaseq)[inputs]: Replace
"ghc-pandoc-citeproc-with-pandoc-1" with "ghc-pandoc-citeproc", and
"ghc-pandoc-1" with "ghc-pandoc".
 2018-09-05 20:03:09 +02:00
Ricardo Wurmus dff5640a59
gnu: r-rcas: Use standard version of ghc-pandoc-citeproc. 
* gnu/packages/bioinformatics.scm (r-rcas)[native-inputs]: Replace
"ghc-pandoc-citeproc-with-pandoc-1" with "ghc-pandoc-citeproc".
 2018-09-05 20:03:09 +02:00
Ricardo Wurmus f33a4748b7
gnu: r-modelmetrics: Update to 1.2.0. 
* gnu/packages/statistics.scm (r-modelmetrics): Update to 1.2.0.
[propagated-inputs]: Add r-data-table.
 2018-09-05 20:03:09 +02:00
Ricardo Wurmus 0d279d607a
gnu: r-robustbase: Update to 0.93-2. 
* gnu/packages/statistics.scm (r-robustbase): Update to 0.93-2.
 2018-09-05 20:03:09 +02:00
Ricardo Wurmus 8e499d756a
gnu: r-rann: Update to 2.6. 
* gnu/packages/statistics.scm (r-rann): Update to 2.6.
 2018-09-05 20:03:09 +02:00
Ricardo Wurmus 314e8e763f
gnu: r-ggthemes: Update to 4.0.1. 
* gnu/packages/statistics.scm (r-ggthemes): Update to 4.0.1.
[propagated-inputs]: Remove r-assertthat and r-colorspace; add r-purrr,
r-stringr, and r-tibble.
 2018-09-05 20:03:09 +02:00
Ricardo Wurmus e5db6890ad
gnu: r-ztable: Update to 0.2.0. 
* gnu/packages/statistics.scm (r-ztable): Update to 0.2.0.
[propagated-inputs]: Add r-flextable, r-magrittr, r-moonbook, r-officer,
r-rcolorbrewer, r-scales, and r-stringr.
 2018-09-05 20:03:08 +02:00
Ricardo Wurmus f0519c8fae
gnu: r-zoo: Update to 1.8-3. 
* gnu/packages/statistics.scm (r-zoo): Update to 1.8-3.
 2018-09-05 20:03:08 +02:00
Ricardo Wurmus 8da236a377
gnu: r-gtools: Update to 3.8.1. 
* gnu/packages/statistics.scm (r-gtools): Update to 3.8.1.
 2018-09-05 20:03:08 +02:00
Ricardo Wurmus c28d8d8db0
gnu: r-kernlab: Update to 0.9-27. 
* gnu/packages/machine-learning.scm (r-kernlab): Update to 0.9-27.
 2018-09-05 20:03:08 +02:00
Ricardo Wurmus c0608f815c
gnu: r-adaptivesparsity: Update to 1.6. 
* gnu/packages/machine-learning.scm (r-adaptivesparsity): Update to 1.6.
[propagated-inputs]: Add r-mass and r-matrix.
 2018-09-05 20:03:08 +02:00
Ricardo Wurmus a207bca2ad
gnu: r-codedepends: Move from cran to bioconductor. 
* gnu/packages/cran.scm (r-codedepends): Move from here...
* gnu/packages/bioconductor.scm (r-codedepends): ...to here.
 2018-09-05 20:03:08 +02:00
Ricardo Wurmus 5dfe491290
gnu: r-graph: Move from bioinformatics to bioconductor. 
* gnu/packages/bioinformatics.scm (r-graph): Move from here...
* gnu/packages/bioconductor.scm (r-graph): ...to here.
 2018-09-05 20:03:08 +02:00
Ricardo Wurmus caaec88651
gnu: r-ggpubr: Update to 0.1.8. 
* gnu/packages/cran.scm (r-ggpubr): Update to 0.1.8.
[propagated-inputs]: Add r-glue and r-polynom.
 2018-09-05 20:03:08 +02:00
Ricardo Wurmus a9b02ddd73
gnu: r-codedepends: Update to 0.6.5. 
* gnu/packages/cran.scm (r-codedepends): Update to 0.6.5.
[propagated-inputs]: Add r-graph.
 2018-09-05 20:03:08 +02:00
Ricardo Wurmus 2e6909baf0
gnu: r-later: Update to 0.7.4. 
* gnu/packages/cran.scm (r-later): Update to 0.7.4.
 2018-09-05 20:03:08 +02:00
Ricardo Wurmus 12132229b0
gnu: r-maptools: Update to 0.9-3. 
* gnu/packages/cran.scm (r-maptools): Update to 0.9-3.
 2018-09-05 20:03:08 +02:00
Ricardo Wurmus 7a96c4e0a0
gnu: r-fnn: Update to 1.1.2.1. 
* gnu/packages/cran.scm (r-fnn): Update to 1.1.2.1.
 2018-09-05 20:03:08 +02:00
Ricardo Wurmus 19950821d7
gnu: r-heatmaply: Update to 0.15.2. 
* gnu/packages/cran.scm (r-heatmaply): Update to 0.15.2.
 2018-09-05 20:03:08 +02:00
Ricardo Wurmus 1fe9919a57
gnu: r-tsa: Update to 1.2. 
* gnu/packages/cran.scm (r-tsa): Update to 1.2.
[propagated-inputs]: Remove r-tseries.
 2018-09-05 20:03:08 +02:00
Ricardo Wurmus be5642eb69
gnu: r-statnet-common: Update to 4.1.4. 
* gnu/packages/cran.scm (r-statnet-common): Update to 4.1.4.
 2018-09-05 20:03:08 +02:00
Ricardo Wurmus e32368c130
gnu: r-metap: Update to 1.0. 
* gnu/packages/cran.scm (r-metap): Update to 1.0.
[propagated-inputs]: Add r-rdpack.
 2018-09-05 20:03:07 +02:00
Ricardo Wurmus d97d98e142
gnu: r-tinytex: Update to 0.8. 
* gnu/packages/cran.scm (r-tinytex): Update to 0.8.
 2018-09-05 20:03:07 +02:00
Ricardo Wurmus 6f5b157e3d
gnu: r-pillar: Update to 1.3.0. 
* gnu/packages/cran.scm (r-pillar): Update to 1.3.0.
[propagated-inputs]: Add r-fansi.
 2018-09-05 20:03:07 +02:00
Ricardo Wurmus 69bf449bf1
gnu: r-xts: Update to 0.11-0. 
* gnu/packages/cran.scm (r-xts): Update to 0.11-0.
[native-inputs]: Remove.
 2018-09-05 20:03:07 +02:00
Ricardo Wurmus 1b3b2a72ee
gnu: r-mice: Update to 3.3.0. 
* gnu/packages/cran.scm (r-mice): Update to 3.3.0.
 2018-09-05 20:03:07 +02:00
Ricardo Wurmus a7265593d3
gnu: r-pan: Update to 1.6. 
* gnu/packages/cran.scm (r-pan): Update to 1.6.
 2018-09-05 20:03:07 +02:00
Ricardo Wurmus e7630cc931
gnu: r-jomo: Update to 2.6-4. 
* gnu/packages/cran.scm (r-jomo): Update to 2.6-4.
[propagated-inputs]: Add r-ordinal.
 2018-09-05 20:03:07 +02:00
Ricardo Wurmus b8f6e2f82a
gnu: Add r-ordinal. 
* gnu/packages/cran.scm (r-ordinal): New variable.
 2018-09-05 20:03:07 +02:00
Ricardo Wurmus dc66835226
gnu: Add r-ucminf. 
* gnu/packages/cran.scm (r-ucminf): New variable.
 2018-09-05 20:03:07 +02:00
Ricardo Wurmus 45c156bf81
gnu: r-broom: Update to 0.5.0. 
* gnu/packages/cran.scm (r-broom): Update to 0.5.0.
[propagated-inputs]: Add r-backports, r-dplyr, r-purrr, and r-tibble; remove
r-plyr and r-psych.
 2018-09-05 20:03:07 +02:00
Ricardo Wurmus 2d2b95d151
gnu: r-ipred: Update to 0.9-7. 
* gnu/packages/cran.scm (r-ipred): Update to 0.9-7.
 2018-09-05 20:03:07 +02:00
Ricardo Wurmus c73752cac5
gnu: r-pls: Update to 2.7-0. 
* gnu/packages/cran.scm (r-pls): Update to 2.7-0.
 2018-09-05 20:03:07 +02:00