3121814ef1
gnu: Add r-keggrest.
...
* gnu/packages/bioinformatics.scm (r-keggrest): New variable.
2017-11-07 12:39:51 +01:00
a9540107c6
gnu: antlr3-3.3: Prettify build phases.
...
* gnu/packages/java.scm (antlr3-3.3)[arguments]: Prettify build phases
"bin-install" and "generate-grammar".
2017-11-07 12:39:50 +01:00
9ecc4c69eb
gnu: r-servr: Update to 0.8.
...
* gnu/packages/web.scm (r-servr): Update to 0.8.
2017-11-07 08:15:45 +01:00
60ec9da3aa
gnu: r-tidyselect: Update to 0.2.3.
...
* gnu/packages/statistics.scm (r-tidyselect): Update to 0.2.3.
2017-11-07 08:15:44 +01:00
baa00ee90d
gnu: r-msnbase: Update to 2.4.0.
...
* gnu/packages/bioinformatics.scm (r-msnbase): Update to 2.4.0.
[propagated-inputs]: Add r-lattice; remove r-reshape2.
2017-11-07 08:15:44 +01:00
39d9098def
gnu: r-mutationalpatterns: Update to 1.4.0.
...
* gnu/packages/bioinformatics.scm (r-mutationalpatterns): Update to 1.4.0.
[propagated-inputs]: Add r-cowplot, r-ggdendro, and r-s4vectors.
2017-11-07 08:15:44 +01:00
14b3c71911
gnu: r-annotationhub: Update to 2.10.0.
...
* gnu/packages/bioinformatics.scm (r-annotationhub): Update to 2.10.0.
[propagated-inputs]: Add r-curl.
2017-11-07 08:15:44 +01:00
15ca195979
gnu: r-mzr: Remove bundled copy of boost.
...
* gnu/packages/bioinformatics.scm (r-mzr)[source]: Remove boost source.
[arguments]: Add build phase "use-system-boost" to link with our boost
package and avoid building the bundled sources.
2017-11-07 08:15:44 +01:00
34b9675449
gnu: r-mzr: Update to 2.12.0.
...
* gnu/packages/bioinformatics.scm (r-mzr): Update to 2.12.0.
2017-11-07 08:15:43 +01:00
b500dbcdef
gnu: r-mzid: Update to 1.16.0.
...
* gnu/packages/bioinformatics.scm (r-mzid): Update to 1.16.0.
2017-11-07 08:15:43 +01:00
eeaa6967f9
gnu: r-chipseq: Update to 1.28.0.
...
* gnu/packages/bioinformatics.scm (r-chipseq): Update to 1.28.0.
[propagated-inputs]: Add r-lattice.
2017-11-07 08:15:43 +01:00
158b6743dc
gnu: r-genomicfeatures: Update to 1.30.0.
...
* gnu/packages/bioinformatics.scm (r-genomicfeatures): Update to 1.30.0.
[propagated-inputs]: Add r-rmysql.
2017-11-07 08:15:43 +01:00
74248d22a0
gnu: Add r-rmysql.
...
* gnu/packages/databases.scm (r-rmysql): New variable.
2017-11-07 08:15:43 +01:00
4dd469ef6d
gnu: r-rtracklayer: Update to 1.38.0.
...
* gnu/packages/bioinformatics.scm (r-rtracklayer): Update to 1.38.0.
[arguments]: Adjust patch to use system zlib.
2017-11-07 08:15:42 +01:00
a044c7f4c4
gnu: r-biocparallel: Update to 1.12.0.
...
* gnu/packages/bioinformatics.scm (r-biocparallel): Update to 1.12.0.
[propagated-inputs]: Add r-bh.
2017-11-07 08:15:42 +01:00
42e11d3301
gnu: r-biomart: Update to 2.34.0.
...
* gnu/packages/bioinformatics.scm (r-biomart): Update to 2.34.0.
[propagated-inputs]: Add r-progress and r-stringr.
2017-11-07 08:15:42 +01:00
010ab2ffd2
gnu: r-edger: Update to 3.20.1.
...
* gnu/packages/bioinformatics.scm (r-edger): Update to 3.20.1.
[propagated-inputs]: Add r-rcpp.
2017-11-07 08:15:42 +01:00
eb3f5cc76a
gnu: r-gostats: Update to 2.44.0.
...
* gnu/packages/bioinformatics.scm (r-gostats): Update to 2.44.0.
[propagated-inputs]: Add r-rgraphviz.
2017-11-07 08:15:41 +01:00
2404cc4283
gnu: r-category: Update to 2.44.0.
...
* gnu/packages/bioinformatics.scm (r-category): Update to 2.44.0.
[propagated-inputs]: Remove r-rsqlite; add r-dbi.
2017-11-07 08:15:41 +01:00
65a8cd6676
gnu: r-lubridate: Update to 1.7.1.
...
* gnu/packages/statistics.scm (r-lubridate): Update to 1.7.1.
[propagated-inputs]: Add r-rcpp.
2017-11-07 08:15:41 +01:00
689edf1153
gnu: r-preprocesscore: Update to 1.40.0.
...
* gnu/packages/statistics.scm (r-preprocesscore): Update to 1.40.0.
2017-11-07 08:15:41 +01:00
e7f680f071
gnu: r-r-utils: Update to 2.6.0.
...
* gnu/packages/statistics.scm (r-r-utils): Update to 2.6.0.
2017-11-07 08:15:41 +01:00
ecfe98a17a
gnu: r-openssl: Update to 0.9.8.
...
* gnu/packages/statistics.scm (r-openssl): Update to 0.9.8.
2017-11-07 08:15:40 +01:00
aced057fbc
gnu: r-rlang: Update to 0.1.4.
...
* gnu/packages/statistics.scm (r-rlang): Update to 0.1.4.
2017-11-07 08:15:40 +01:00
1be0f53664
gnu: r-vsn: Update to 3.46.0.
...
* gnu/packages/bioinformatics.scm (r-vsn): Update to 3.46.0.
[propagated-inputs]: Remove r-hexbin.
2017-11-07 08:15:40 +01:00
007424b5a5
gnu: r-motifrg: Rename input label.
...
* gnu/packages/bioinformatics.scm (r-motifrg)[propagated-inputs]:
Rename label of r-bsgenome-hsapiens-ucsc-hg19.
2017-11-07 08:15:40 +01:00
ce59d62519
gnu: r-motifrg: Update to 1.22.0.
...
* gnu/packages/bioinformatics.scm (r-motifrg): Update to 1.22.0.
2017-11-07 08:15:40 +01:00
98791c25c8
gnu: r-qvalue: Update to 2.10.0.
...
* gnu/packages/bioinformatics.scm (r-qvalue): Update to 2.10.0.
2017-11-07 08:15:39 +01:00
87fa5aface
gnu: r-fastseq: Update to 1.24.0.
...
* gnu/packages/bioinformatics.scm (r-fastseq): Update to 1.24.0.
2017-11-07 08:15:39 +01:00
1567c8d91b
gnu: r-interactivedisplaybase: Update to 1.16.0.
...
* gnu/packages/bioinformatics.scm (r-interactivedisplaybase): Update to
1.16.0.
2017-11-07 08:15:39 +01:00
0096127974
gnu: r-edaseq: Update to 2.12.0.
...
* gnu/packages/bioinformatics.scm (r-edaseq): Update to 2.12.0.
2017-11-07 08:15:39 +01:00
22752bef3b
gnu: r-msnid: Update to 1.11.0.
...
* gnu/packages/bioinformatics.scm (r-msnid): Update to 1.11.0.
2017-11-07 08:15:38 +01:00
8140f680ad
gnu: r-deseq: Update to 1.30.0.
...
* gnu/packages/bioinformatics.scm (r-deseq): Update to 1.30.0.
2017-11-07 08:15:38 +01:00
531e80903f
gnu: r-aroma-light: Update to 3.8.0.
...
* gnu/packages/bioinformatics.scm (r-aroma-light): Update to 3.8.0.
2017-11-07 08:15:38 +01:00
a998c9a464
gnu: r-pcamethods: Update to 1.70.0.
...
* gnu/packages/bioinformatics.scm (r-pcamethods): Update to 1.70.0.
2017-11-07 08:15:38 +01:00
8a8138d248
gnu: r-affyio: Update to 1.48.0.
...
* gnu/packages/bioinformatics.scm (r-affyio): Update to 1.48.0.
2017-11-07 08:15:38 +01:00
dad5f83817
gnu: r-affy: Update to 1.56.0.
...
* gnu/packages/bioinformatics.scm (r-affy): Update to 1.56.0.
2017-11-07 08:15:37 +01:00
9a665dfb6f
gnu: r-protgenerics: Update to 1.10.0.
...
* gnu/packages/bioinformatics.scm (r-protgenerics): Update to 1.10.0.
2017-11-07 08:15:37 +01:00
617700895b
gnu: r-seqlogo: Update to 1.44.0.
...
* gnu/packages/bioinformatics.scm (r-seqlogo): Update to 1.44.0.
2017-11-07 08:15:37 +01:00
e127c918f8
gnu: r-genomation: Update to 1.10.0.
...
* gnu/packages/bioinformatics.scm (r-genomation): Update to 1.10.0.
[propagated-inputs]: Remove r-rhtslib.
[inputs]: Remove zlib.
2017-11-07 08:15:37 +01:00
e6ce4bf00d
gnu: r-impute: Update to 1.52.0.
...
* gnu/packages/bioinformatics.scm (r-impute): Update to 1.52.0.
2017-11-07 08:15:37 +01:00
0f948b116b
gnu: r-seqpattern: Update to 1.10.0.
...
* gnu/packages/bioinformatics.scm (r-seqpattern): Update to 1.10.0.
2017-11-07 08:15:36 +01:00
e67850b40d
gnu: r-bsgenome: Update to 1.46.0.
...
* gnu/packages/bioinformatics.scm (r-bsgenome): Update to 1.46.0.
2017-11-07 08:15:36 +01:00
d13a3fea7e
gnu: r-topgo: Update to 2.30.0.
...
* gnu/packages/bioinformatics.scm (r-topgo): Update to 2.30.0.
2017-11-07 08:15:36 +01:00
aeb73879f6
gnu: r-graph: Update to 1.56.0.
...
* gnu/packages/bioinformatics.scm (r-graph): Update to 1.56.0.
2017-11-07 08:15:36 +01:00
96fb465174
gnu: r-genomicalignments: Update to 1.14.0.
...
* gnu/packages/bioinformatics.scm (r-genomicalignments): Update to 1.14.0.
2017-11-07 08:15:35 +01:00
6fcbed7329
gnu: r-summarizedexperiment: Update to 1.8.0.
...
* gnu/packages/bioinformatics.scm (r-summarizedexperiment): Update to 1.8.0.
2017-11-07 08:15:35 +01:00
cb0a9a7493
gnu: r-delayedarray: Update to 0.4.1.
...
* gnu/packages/bioinformatics.scm (r-delayedarray): Update to 0.4.1.
2017-11-07 08:15:35 +01:00
f8068419a6
gnu: r-rsamtools: Update to 1.30.0.
...
* gnu/packages/bioinformatics.scm (r-rsamtools): Update to 1.30.0.
2017-11-07 08:15:35 +01:00
b719435ebb
gnu: r-biostrings: Update to 2.46.0.
...
* gnu/packages/bioinformatics.scm (r-biostrings): Update to 2.46.0.
2017-11-07 08:15:35 +01:00
0f8d98f294
gnu: r-annotationdbi: Update to 1.40.0.
...
* gnu/packages/bioinformatics.scm (r-annotationdbi): Update to 1.40.0.
2017-11-07 08:15:34 +01:00
ca52123611
gnu: r-biobase: Update to 2.38.0.
...
* gnu/packages/bioinformatics.scm (r-biobase): Update to 2.38.0.
2017-11-07 08:15:34 +01:00
aa5c1f61f1
gnu: r-genomicranges: Update to 1.30.0.
...
* gnu/packages/bioinformatics.scm (r-genomicranges): Update to 1.30.0.
2017-11-07 08:15:34 +01:00
2b6ae8bfd5
gnu: r-xvector: Update to 0.18.0.
...
* gnu/packages/bioinformatics.scm (r-xvector): Update to 0.18.0.
2017-11-07 08:15:34 +01:00
f642c0e4c7
gnu: r-limma: Update to 3.34.0.
...
* gnu/packages/bioinformatics.scm (r-limma): Update to 3.34.0.
2017-11-07 08:15:33 +01:00
7f1bac3528
gnu: r-variantannotation: Update to 1.24.0.
...
* gnu/packages/bioinformatics.scm (r-variantannotation): Update to 1.24.0.
2017-11-07 08:15:33 +01:00
8aab0235e0
gnu: r-genomeinfodb: Update to 1.14.0.
...
* gnu/packages/bioinformatics.scm (r-genomeinfodb): Update to 1.14.0.
2017-11-07 08:15:33 +01:00
9e482c2069
gnu: r-iranges: Update to 2.12.0.
...
* gnu/packages/bioinformatics.scm (r-iranges): Update to 2.12.0.
2017-11-07 08:15:33 +01:00
41f0f94976
gnu: r-s4vectors: Update to 0.16.0.
...
* gnu/packages/bioinformatics.scm (r-s4vectors): Update to 0.16.0.
2017-11-07 08:15:33 +01:00
2167eafc1d
gnu: r-biocstyle: Update to 2.6.0.
...
* gnu/packages/bioinformatics.scm (r-biocstyle): Update to 2.6.0.
2017-11-07 08:15:32 +01:00
3241461670
gnu: r-biocinstaller: Update to 1.28.0.
...
* gnu/packages/bioinformatics.scm (r-biocinstaller): Update to 1.28.0.
2017-11-07 08:15:32 +01:00
d61fc4e104
gnu: r-biocgenerics: Update to 0.24.0.
...
* gnu/packages/bioinformatics.scm (r-biocgenerics): Update to 0.24.0.
2017-11-07 08:15:32 +01:00
704fe4d115
gnu: r-grohmm: Update to 1.12.0.
...
* gnu/packages/bioinformatics.scm (r-grohmm): Update to 1.12.0.
2017-11-07 08:15:32 +01:00
843826e262
gnu: r-shortread: Update to 1.36.0.
...
* gnu/packages/bioinformatics.scm (r-shortread): Update to 1.36.0.
2017-11-07 08:15:31 +01:00
b53755258a
gnu: r-systempiper: Update to 1.12.0.
...
* gnu/packages/bioinformatics.scm (r-systempiper): Update to 1.12.0.
2017-11-07 08:15:31 +01:00
9f52e53d5d
gnu: r-gseabase: Update to 1.40.0.
...
* gnu/packages/bioinformatics.scm (r-gseabase): Update to 1.40.0.
2017-11-07 08:15:31 +01:00
fad7c0c7bd
gnu: r-sva: Update to 3.26.0.
...
* gnu/packages/bioinformatics.scm (r-sva): Update to 3.26.0.
2017-11-07 08:15:31 +01:00
91e1867972
gnu: r-methylkit: Update to 1.4.0.
...
* gnu/packages/bioinformatics.scm (r-methylkit): Update to 1.4.0.
2017-11-07 08:15:31 +01:00
c126ba69db
gnu: r-copywriter: Update to 2.10.0.
...
* gnu/packages/bioinformatics.scm (r-copywriter): Update to 2.10.0.
2017-11-07 08:15:30 +01:00
598dacf657
gnu: r-annotationfilter: Update to 1.2.0.
...
* gnu/packages/bioinformatics.scm (r-annotationfilter): Update to 1.2.0.
2017-11-07 08:15:30 +01:00
e6b332d43b
gnu: r-rhdf5: Update to 2.22.0.
...
* gnu/packages/bioinformatics.scm (r-rhdf5): Update to 2.22.0.
2017-11-07 08:15:30 +01:00
19e8929cbd
gnu: r-tximport: Update to 1.6.0.
...
* gnu/packages/bioinformatics.scm (r-tximport): Update to 1.6.0.
2017-11-07 08:15:30 +01:00
da153b7f94
gnu: r-bamsignals: Update to 1.10.0.
...
* gnu/packages/bioinformatics.scm (r-bamsignals): Update to 1.10.0.
2017-11-07 08:15:30 +01:00
5c18470008
gnu: r-zlibbioc: Update to 1.24.0.
...
* gnu/packages/bioinformatics.scm (r-zlibbioc): Update to 1.24.0.
2017-11-07 08:15:29 +01:00
1d0263b44e
gnu: r-rhtslib: Update to 1.10.0.
...
* gnu/packages/bioinformatics.scm (r-rhtslib): Update to 1.10.0.
2017-11-07 08:15:29 +01:00
c25154e5cb
gnu: r-rbgl: Update to 1.54.0.
...
* gnu/packages/bioinformatics.scm (r-rbgl): Update to 1.54.0.
2017-11-07 08:15:29 +01:00
727706ad38
gnu: r-annotationforge: Update to 1.20.0.
...
* gnu/packages/bioinformatics.scm (r-annotationforge): Update to 1.20.0.
2017-11-07 08:15:29 +01:00
3fd010ff30
gnu: r-dexseq: Update to 1.24.0.
...
* gnu/packages/bioinformatics.scm (r-dexseq): Update to 1.24.0.
2017-11-07 08:15:28 +01:00
0166dc07ef
gnu: r-deseq2: Update to 1.18.0.
...
* gnu/packages/bioinformatics.scm (r-deseq2): Update to 1.18.0.
2017-11-07 08:15:28 +01:00
554fac74aa
gnu: r-genefilter: Update to 1.60.0.
...
* gnu/packages/bioinformatics.scm (r-genefilter): Update to 1.60.0.
2017-11-07 08:15:28 +01:00
cb4d3ff2c4
gnu: r-geneplotter: Update to 1.56.0.
...
* gnu/packages/bioinformatics.scm (r-geneplotter): Update to 1.56.0.
2017-11-07 08:15:28 +01:00
2d4e887dc0
gnu: r-annotate: Update to 1.56.0.
...
* gnu/packages/bioinformatics.scm (r-annotate): Update to 1.56.0.
2017-11-07 08:15:28 +01:00
94fd86e5e1
gnu: r-dnacopy: Update to 1.52.0.
...
* gnu/packages/bioinformatics.scm (r-dnacopy): Update to 1.52.0.
2017-11-07 08:15:27 +01:00
c7782c3f1f
gnu: r-biocviews: Update to 1.46.0.
...
* gnu/packages/bioinformatics.scm (r-biocviews): Update to 1.46.0.
[propagated-inputs]: Remove r-knitr.
2017-11-07 08:15:27 +01:00
7373b4167a
gnu: r-bioccheck: Update to 1.14.0.
...
* gnu/packages/bioinformatics.scm (r-bioccheck): Update to 1.14.0.
[native-inputs]: Remove which.
[propagated-inputs]: Add r-stringdist.
2017-11-07 08:15:27 +01:00
a40a04fdbb
gnu: Add r-stringdist.
...
* gnu/packages/cran.scm (r-stringdist): New variable.
2017-11-07 08:15:27 +01:00
8ca2b2b06e
gnu: r-rgraphviz: Update to 2.22.0.
...
* gnu/packages/graph.scm (r-rgraphviz): Update to 2.22.0.
2017-11-07 08:15:27 +01:00
a0e4b41b40
gnu: guile-git: Update snapshot.
...
* gnu/packages/guile.scm (guile-git): Update to commit 951a32c.
2017-11-07 00:12:11 +01:00
fedde43b6d
gnu: moka-icon-theme: Fix license.
...
* gnu/packages/gnome.scm (moka-icon-theme): Add cc-by-sa4.0 to license field.
Signed-off-by: Ludovic Courtès <ludo@gnu.org>
2017-11-07 00:12:11 +01:00
550281fb5f
gnu: moka-icon-theme: Add faba-icon-theme as propagated input.
...
* gnu/packages/gnome.scm (moka-icon-theme)[propagated-inputs]: New field.
Signed-off-by: Ludovic Courtès <ludo@gnu.org>
2017-11-07 00:12:11 +01:00
8b0e4177ee
gnu: moka-icon-theme: Simplify package definition.
...
* gnu/packages/gnome.scm (moka-icon-theme): Inherit faba-icon-theme to avoid
duplicating similar package definition.
Signed-off-by: Ludovic Courtès <ludo@gnu.org>
2017-11-07 00:12:11 +01:00
d935e6a12c
gnu: Add faba-icon-theme.
...
* gnu/packages/gnome.scm (faba-icon-theme): New variable.
Signed-off-by: Ludovic Courtès <ludo@gnu.org>
2017-11-07 00:12:11 +01:00
47bd32d98e
gnu: electrum: Update to 3.0.
...
gnu/packages/finance.scm (electrum): Update to 3.0.
[inputs]: Change to python3 inputs.
[arguments]: Remove python-2. Disable tests.
Signed-off-by: Ludovic Courtès <ludo@gnu.org>
2017-11-07 00:12:10 +01:00
ea0421bbf6
gnu: Add python-jsonrpclib-pelix.
...
* gnu/packages/python.scm (python-jsonrpclib-pelix, python2-jsonrpclib-pelix):
New variables.
Co-authored-by: Ludovic Courtès <ludo@gnu.org>
2017-11-07 00:12:10 +01:00
96dc8f3527
packages: 'fold-packages' takes #:select? parameter.
...
* gnu/packages.scm (fold-packages): Add #:select? parameter and honor it.
2017-11-07 00:12:10 +01:00
0ad5f80982
Fix ambiguous imports.
...
* gnu/packages/ocaml.scm: Hide 'zip' from (srfi srfi-1).
* guix/git.scm: Select 'mkdir-p' from (guix build utils).
2017-11-07 00:12:10 +01:00
913027f383
gnu: nnn: Update to 1.5.
...
* gnu/packages/admin.scm (nnn): Update to 1.5.
2017-11-06 23:07:19 +02:00
6a534909fa
gnu: libuninameslist: Update to 20170807.
...
* gnu/packages/fontutils.scm (libuninameslist): Update to 20170807.
2017-11-06 23:07:13 +02:00
10b159a303
gnu: u-boot: Only install 'MLO' output if it exists.
...
* gnu/packages/bootloaders.scm (u-boot)[arguments]: Add 'MLO' to
uboot-files only if it has been built.
2017-11-06 22:54:28 +02:00
b1a3079347
system: vm: Use 2^32 - 1 as hash size.
...
* gnu/system/vm.scm (operating-system-uuid): Use 2^32 - 1 instead of
2^32 as hash size.
On some 32 bit system (ARM for example), 2^32 exceeds hash max
size (ULONG_MAX = 2^32 - 1).
2017-11-06 20:02:25 +01:00
Ricardo Wurmus
Ludovic Courtès
Brendan Tildesley
Carlo Zancanaro
Efraim Flashner
Mathieu Othacehe