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30855 Commits

Author SHA1 Message Date
Ricardo Wurmus dfd7299957
gnu: r-rcpp: Update to 0.12.16. 
* gnu/packages/cran.scm (r-rcpp): Update to 0.12.16.
 2018-04-21 23:07:52 +02:00
Ricardo Wurmus 0e94780446
gnu: r-plogr: Update to 0.2.0. 
* gnu/packages/cran.scm (r-plogr): Update to 0.2.0.
 2018-04-21 23:07:52 +02:00
Ricardo Wurmus 1d612cefc8
gnu: r-readxl: Update to 1.1.0. 
* gnu/packages/cran.scm (r-readxl): Update to 1.1.0.
 2018-04-21 23:07:52 +02:00
Ricardo Wurmus 41e8bd77f3
gnu: r-selectr: Update to 0.4-1. 
* gnu/packages/cran.scm (r-selectr): Update to 0.4-1.
[propagated-inputs]: Add r-r6.
 2018-04-21 23:07:52 +02:00
Ricardo Wurmus aeca5f0c5b
gnu: r-scran: Update to 1.6.9. 
* gnu/packages/bioinformatics.scm (r-scran): Update to 1.6.9.
 2018-04-21 23:07:52 +02:00
Ricardo Wurmus 80323c3c13
gnu: r-hitc: Update to 1.22.1. 
* gnu/packages/bioinformatics.scm (r-hitc): Update to 1.22.1.
 2018-04-21 23:07:52 +02:00
Ricardo Wurmus b6d7deca55
gnu: r-ldblock: Update to 1.8.1. 
* gnu/packages/bioinformatics.scm (r-ldblock): Update to 1.8.1.
 2018-04-21 23:07:52 +02:00
Ricardo Wurmus fb1dcfac46
gnu: r-erma: Update to 0.10.1. 
* gnu/packages/bioinformatics.scm (r-erma): Update to 0.10.1.
 2018-04-21 23:07:52 +02:00
Ricardo Wurmus 8defca1d94
gnu: r-gprofiler: Update to 0.6.6. 
* gnu/packages/bioinformatics.scm (r-gprofiler): Update to 0.6.6.
 2018-04-21 23:07:52 +02:00
Ricardo Wurmus fc6d3e2606
gnu: r-ggbio: Update to 1.26.1. 
* gnu/packages/bioinformatics.scm (r-ggbio): Update to 1.26.1.
 2018-04-21 23:07:52 +02:00
Ricardo Wurmus 0bd5c7b859
gnu: r-genomicalignments: Update to 1.14.2. 
* gnu/packages/bioinformatics.scm (r-genomicalignments): Update to 1.14.2.
 2018-04-21 23:07:52 +02:00
Ricardo Wurmus 4207770218
gnu: r-dexseq: Update to 1.24.4. 
* gnu/packages/bioinformatics.scm (r-dexseq): Update to 1.24.4.
 2018-04-21 23:07:52 +02:00
Ricardo Wurmus 3db5d04ccc
gnu: r-vegan: Update to 2.5-1. 
* gnu/packages/bioinformatics.scm (r-vegan): Update to 2.5-1.
[propagated-inputs]: Add r-knitr.
 2018-04-21 23:07:52 +02:00
Ricardo Wurmus 2ef5ab8749
gnu: r-mapproj: Update to 1.2.6. 
* gnu/packages/geo.scm (r-mapproj): Update to 1.2.6.
 2018-04-21 23:07:52 +02:00
Ricardo Wurmus 5895f238d7
gnu: r-maps: Update to 3.3.0. 
* gnu/packages/geo.scm (r-maps): Update to 3.3.0.
 2018-04-21 23:07:52 +02:00
Ricardo Wurmus 8cf7b28ffe
gnu: r-igraph: Update to 1.2.1. 
* gnu/packages/graph.scm (r-igraph): Update to 1.2.1.
[inputs]: Add glpk and zlib.
[propagated-inputs]: Remove r-irlba.
 2018-04-21 23:07:52 +02:00
Ricardo Wurmus 2bcf5fd337
gnu: r-subplex: Update to 1.5-4. 
* gnu/packages/maths.scm (r-subplex): Update to 1.5-4.
 2018-04-21 23:07:52 +02:00
Ricardo Wurmus 61c868e1f5
gnu: r-shinydashboard: Update to 0.7.0. 
* gnu/packages/web.scm (r-shinydashboard): Update to 0.7.0.
 2018-04-21 23:07:52 +02:00
Ricardo Wurmus 4fe0efddfe
gnu: r-htmlwidgets: Update to 1.2. 
* gnu/packages/web.scm (r-htmlwidgets): Update to 1.2.
 2018-04-21 23:07:52 +02:00
Ricardo Wurmus 75a40e89d9
gnu: r-lme4: Update to 1.1-17. 
* gnu/packages/statistics.scm (r-lme4): Update to 1.1-17.
 2018-04-21 23:07:52 +02:00
Ricardo Wurmus 30d76d442a
gnu: r-futile-options: Update to 1.0.1. 
* gnu/packages/statistics.scm (r-futile-options): Update to 1.0.1.
 2018-04-21 23:07:52 +02:00
Ricardo Wurmus 4184649940
gnu: r-xml: Update to . 
* gnu/packages/statistics.scm (r-xml): Update to .
 2018-04-21 23:07:52 +02:00
Ricardo Wurmus ff91ed7d56
gnu: r-rsqlite: Update to 2.1.0. 
* gnu/packages/statistics.scm (r-rsqlite): Update to 2.1.0.
 2018-04-21 23:07:52 +02:00
Ricardo Wurmus 1aa2ad5b32
gnu: r-survival: Update to 2.42-3. 
* gnu/packages/statistics.scm (r-survival): Update to 2.42-3.
 2018-04-21 23:07:52 +02:00
Ricardo Wurmus 6fa9cf1abb
gnu: r-nlme: Update to 3.1-137. 
* gnu/packages/statistics.scm (r-nlme): Update to 3.1-137.
 2018-04-21 23:07:52 +02:00
Ricardo Wurmus ac6672d539
gnu: r-cluster: Update to 2.0.7-1. 
* gnu/packages/statistics.scm (r-cluster): Update to 2.0.7-1.
 2018-04-21 23:07:52 +02:00
Ricardo Wurmus c43ea99b39
gnu: r-minimal: Update to 3.4.4. 
* gnu/packages/statistics.scm (r-minimal): Update to 3.4.4.
 2018-04-21 23:07:52 +02:00
Efraim Flashner 785f40dfbc
gnu: spindle: Limit supported systems. 
* gnu/packages/admin.scm (spindle)[supported-system]: New field.
 2018-04-21 23:25:42 +03:00
Efraim Flashner c80629e7c2
gnu: freefall: Fix compilation error. 
* gnu/packages/linux.scm (freefall)[arguments]: Add make-flag to set
CC=gcc.
 2018-04-21 23:04:25 +03:00
Tomáš Čech 841f833171
gnu: python-onetimepass: Make python-six a propagated input. 
* gnu/packages/python.scm (python-onetimepass)[inputs]: Move python-six from
here...
[propagated-inputs]: ...to here.
 2018-04-21 17:37:12 +02:00
Mark H Weaver 0ccb104354
gnu: go-github-com-vitrun-qart-qr: Remove duplicate 'description' field. 
* gnu/packages/syncthing.scm (go-github-com-vitrun-qart-qr)[description]:
Remove duplicate 'description' field.
 2018-04-21 05:29:53 -04:00
Mark H Weaver 6b2752526b
gnu: uget: Remove duplicate 'native-inputs' field. 
* gnu/packages/bittorrent.scm (uget)[native-inputs]: Remove duplicate
field initializer.
 2018-04-21 05:29:42 -04:00
Mark H Weaver 3fe49e5015
gnu: linux-libre@4.9: Update to 4.9.95. 
* gnu/packages/linux.scm (linux-libre-4.9): Update to 4.9.95.
 2018-04-21 03:02:57 -04:00
Tomáš Čech 9a58840235
gnu: Add osc. 
* gnu/packages/build-tools.scm (osc): New variable.
 2018-04-21 08:40:40 +02:00
Tomáš Čech 2f69121808
gnu: Add python-m2crypto, python2-m2crypto. 
* gnu/packages/python-crypto.scm (python-m2crypto): New variable.
(python2-m2crypto): New variable.
 2018-04-21 08:40:40 +02:00
Tomáš Čech c596461187
gnu: Add python2-urlgrabber. 
* gnu/packages/python-web (python2-urlgrabber): New variable.
 2018-04-21 08:40:40 +02:00
Tomáš Čech 15ed90b960
gnu: Add python-onetimepass. 
* gnu/packages/python.scm (python-onetimepass): New variable.
 2018-04-21 08:33:34 +02:00
Mark H Weaver b5178b3254
gnu: perl: Hack the replacement perl to think it is version 5.26.1. 
Fixes <https://bugs.gnu.org/31216>.

This is a followup to commits 217b8c2e06,
44b98b0002, and
35fbe194c3da264859a5addc661b9fbc2dc8ecc7.

Complications arise when grafting perl unless the version of the replacement
perl matches that of the original.  So, here we add 'perl/fixed', which is
built from the perl-5.26.2 source but hacked to believe it is version 5.26.1.

* gnu/packages/perl.scm (perl)[replacement]: Use perl/fixed, not perl-5.26.2.
(perl-5.26.2): Remove compatibility symlinks.
(perl/fixed): New variable.
 2018-04-21 01:17:44 -04:00
Mark H Weaver 5618193694
gnu: perl: Add more compatibility symlinks to the replacement perl. 
Fixes <https://bugs.gnu.org/31216>.
Reported by Julien Lepiller <julien@lepiller.eu>.

* gnu/packages/perl.scm (perl-5.26.2)[arguments]: Rename the
'workaround-grafting-version-bug' phase to 'install-compatibility-symlinks'.
Install symlinks in $out/lib/perl5/site_perl/5.26.1 and $out/bin/perl5.26.1,
in addition to $out/lib/perl5/5.26.1.  Simplify the code a bit.
 2018-04-20 23:29:14 -04:00
Arun Isaac b02b6f32a5
gnu: texlive-bin: Patch texlua shebangs. 
* gnu/packages/tex.scm (texlive-bin)[arguments]: Patch texlua shebangs in
postint phase.
 2018-04-21 00:19:33 +05:30
Arun Isaac a9fda571c3
gnu: texlive-bin: Use ghostscript executable "gs" in ps2eps. 
* gnu/packages/tex.scm (texlive-bin)[arguments]: Add fix-unix-detection phase.
Replace system* with invoke in postint phase.
 2018-04-21 00:19:15 +05:30
Nicolas Goaziou 1af4212ae4
gnu: emacs-org, emacs-org-contrib: Update version. 
* gnu/packages/emacs.scm (emacs-org): Update to 9.1.10.
(emacs-org-contrib): Update to 20180416.
 2018-04-20 12:31:28 +02:00
Maxim Cournoyer 582c122e7b
gnu: emacs-sx: Fix byte compilation. 
The package would fail building when attempting to create a cache
directory. This has been fixed upstream but not in a tagged release.

* gnu/packages/emacs.scm (emacs-sx): Update to latest git version.

Signed-off-by: Arun Isaac <arunisaac@systemreboot.net>
 2018-04-20 15:38:32 +05:30
Maxim Cournoyer 9835a71d80
gnu: emacs-esxml: Fix byte compilation. 
* gnu/packages/emacs.scm (emacs-esxml)[arguments]: Add fix-sources phase.

Signed-off-by: Arun Isaac <arunisaac@systemreboot.net>
 2018-04-20 14:49:26 +05:30
Maxim Cournoyer 62950ec7e9
gnu: Add emacs-kv. 
* gnu/packages/emacs.scm (emacs-kv): New variable.

Signed-off-by: Arun Isaac <arunisaac@systemreboot.net>
 2018-04-20 14:49:20 +05:30
Tomáš Čech 9324d92e6a
gnu: lvm2: Enable pkg-config files generation. 
* gnu/packages/linux.scm (lvm2)[arguments]: Enable pkg-config files generation
via configure flag.
 2018-04-20 10:38:50 +02:00
Tomáš Čech e60352e453
gnu: Add go-golang-org-x-crypto-ssh-terminal. 
* gnu/packages/golang.scm (go-golang-org-x-crypto-ssh-terminal): New variable.
 2018-04-20 10:38:31 +02:00
Arun Isaac 5368e67c4e
gnu: emacs-realgud: Update to 1.4.5. 
* gnu/packages/emacs.scm (emacs-realgud): Update to 1.4.5.
 2018-04-20 13:42:58 +05:30
Maxim Cournoyer aea388cf36
gnu: emacs-realgud: Fix autogen.sh after EMACSLOADPATH is set. 
* gnu/packages/emacs.scm (emacs-realgud)[arguments]: Move the
fix-autogen-script phase to after the set-emacs-load-path phase.

Signed-off-by: Arun Isaac <arunisaac@systemreboot.net>
 2018-04-20 13:30:39 +05:30
Mark H Weaver 872bda5de5
gnu: linux-libre: Update to 4.16.3. 
* gnu/packages/linux.scm (%linux-libre-version): Update to 4.16.3.
(%linux-libre-hash): Update hash.
 2018-04-19 18:55:23 -04:00