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Author SHA1 Message Date
Mark H Weaver
60065f5bd3
gnu: linux-libre@4.9: Update to 4.9.173. 
* gnu/packages/linux.scm (linux-libre-4.9): Update to 4.9.173.
 2019-05-06 02:10:51 -04:00
Maxim Cournoyer
59781b32d8
gnu: docker: Refer to xz by its absolute path. 
* gnu/packages/docker.scm (docker)[inputs]: Add xz.
[phases]{patch-paths}: Patch the reference to xz.
 2019-05-05 21:21:02 -04:00
Maxim Cournoyer
80fec17f39
gnu: docker: Patch the reference to the docker proxy. 
* gnu/packages/docker.scm (docker)[inputs]: Add docker-libnetwork-cmd-proxy.
* gnu/packages/docker.scm (docker)[phases]{patch-paths}: Patch proxy.go to
refer to the docker-proxy binary by its absolute path.
 2019-05-05 21:21:02 -04:00
Maxim Cournoyer
a01d54f3bd
gnu: docker: Optimize substitution macros. 
This change halves the time needed to patch the paths.

* gnu/packages/docker.scm (docker)[phases]{patch-paths}: Allow passing
multiple SOURCE-TEXT, PACKAGE and RELATIVE-PATH tuples so that the rewrite
rules can be generated and processed by a single use of the SUBSTITUTE*
macro.  Rename SUBSTITUTE-LOOKPATH to SUBSTITUTE-LOOKPATH* and
substitute-Command to SUBSTITUTE-COMMAND* to denote the change.  Adapt the
uses of SUBSTITUTE-LOOKPATH* and SUBSTITUTE-COMMAND*.
 2019-05-05 21:21:02 -04:00
Maxim Cournoyer
079f0eb3d2
gnu: docker: Make macros use a relative path as argument. 
* gnu/packages/docker.scm (docker)[phases]: Move implementation detail inside
the SUBSTITUTE-LOOKPATH and SUBSTITUTE-COMMAND macros definition, so that the
relative path argument can be given as a relative path.
 2019-05-05 21:21:01 -04:00
Maxim Cournoyer
3f280d3950
gnu: docker: Harmonize LookPath regexes. 
* gnu/packages/docker.scm (docker)[phases]: In the patch-paths phase, update
the regexes used by SUBSTITUTE-LOOKPATH and SUBSTITUTE-COMMAND to match at the
start of the word, like it's done later.
 2019-05-05 21:21:01 -04:00
Maxim Cournoyer
1b14e1bccd
gnu: docker: Cleanup extraneous comments. 
* gnu/packages/docker.scm (docker): Remove "parenthesis-balancing" comments.
 2019-05-05 21:21:01 -04:00
Maxim Cournoyer
c627932639
gnu: docker: Fix indentation. 
* gnu/packages/docker.scm (docker): Fix indentation using Emacs.
 2019-05-05 21:20:58 -04:00
Maxim Cournoyer
7a31d93a61
services: docker: Add new fields to support proxy. 
The Docker proxy enables inter-container and outside-to-container loopback,
and is required by the Docker registry server.

* gnu/services/docker.scm (docker-configuration)[proxy,
enable-proxy?]: Add fields.
(docker-shepherd-service): Use them.
(serialize-boolean): New function.
 2019-05-05 20:14:15 -04:00
Maxim Cournoyer
0b94911add
gnu: Add docker-libnetwork-cmd-proxy. 
* gnu/packages/docker.scm (docker-libnetwork-cmd-proxy): New variable.
 2019-05-05 20:14:15 -04:00
Maxim Cournoyer
9c0244abbd
gnu: Add docker-libnetwork. 
* gnu/packages/docker.scm (docker-libnetwork): New private variable.
 2019-05-05 20:14:15 -04:00
Maxim Cournoyer
626de0d13a
gnu: Add go-netlink. 
* gnu/packages/linux.scm (go-netlink): New variable.
 2019-05-05 20:14:15 -04:00
Maxim Cournoyer
03981f9064
gnu: Add go-netns. 
* gnu/packages/networking.scm (go-netns): New variable.
 2019-05-05 20:14:14 -04:00
Maxim Cournoyer
523533ed09
gnu: Add go-sctp. 
* gnu/packages/networking.scm (go-sctp): New variable.
 2019-05-05 20:14:14 -04:00
Ricardo Wurmus
85c1d20fa6
gnu: r-chippeakanno: Update to 3.18.0. 
* gnu/packages/bioconductor.scm (r-chippeakanno): Update to 3.18.0.
[propagated-inputs]: Add r-rtracklayer.
 2019-05-06 00:14:59 +02:00
Ricardo Wurmus
c24adbbf07
gnu: r-arrmnormalization: Update to 1.24.0. 
* gnu/packages/bioconductor.scm (r-arrmnormalization): Update to 1.24.0.
 2019-05-06 00:14:59 +02:00
Ricardo Wurmus
c2bfb978bf
gnu: r-progeny: Update to 1.6.0. 
* gnu/packages/bioconductor.scm (r-progeny): Update to 1.6.0.
 2019-05-06 00:14:59 +02:00
Ricardo Wurmus
7d33d36c52
gnu: r-rbowtie2: Update to 1.6.0. 
* gnu/packages/bioconductor.scm (r-rbowtie2): Update to 1.6.0.
 2019-05-06 00:14:58 +02:00
Ricardo Wurmus
02530c2821
gnu: r-zfpkm: Update to 1.6.0. 
* gnu/packages/bioconductor.scm (r-zfpkm): Update to 1.6.0.
 2019-05-06 00:14:58 +02:00
Ricardo Wurmus
67bc9255d5
gnu: r-webbioc: Update to 1.56.0. 
* gnu/packages/bioconductor.scm (r-webbioc): Update to 1.56.0.
 2019-05-06 00:14:58 +02:00
Ricardo Wurmus
c881b9ef3a
gnu: r-widgettools: Update to 1.62.0. 
* gnu/packages/bioconductor.scm (r-widgettools): Update to 1.62.0.
 2019-05-06 00:14:58 +02:00
Ricardo Wurmus
a6edf33533
gnu: r-wiggleplotr: Update to 1.8.0. 
* gnu/packages/bioconductor.scm (r-wiggleplotr): Update to 1.8.0.
 2019-05-06 00:14:58 +02:00
Ricardo Wurmus
07597c85d8
gnu: r-wrench: Update to 1.2.0. 
* gnu/packages/bioconductor.scm (r-wrench): Update to 1.2.0.
 2019-05-06 00:14:58 +02:00
Ricardo Wurmus
298f7f112f
gnu: r-xcms: Update to 3.6.0. 
* gnu/packages/bioconductor.scm (r-xcms): Update to 3.6.0.
 2019-05-06 00:14:58 +02:00
Ricardo Wurmus
7c888138ef
gnu: r-massspecwavelet: Update to 1.50.0. 
* gnu/packages/bioconductor.scm (r-massspecwavelet): Update to 1.50.0.
 2019-05-06 00:14:58 +02:00
Ricardo Wurmus
88469def75
gnu: r-xbseq: Update to 1.16.0. 
* gnu/packages/bioconductor.scm (r-xbseq): Update to 1.16.0.
 2019-05-06 00:14:57 +02:00
Ricardo Wurmus
0334b203d7
gnu: r-roar: Update to 1.20.0. 
* gnu/packages/bioconductor.scm (r-roar): Update to 1.20.0.
 2019-05-06 00:14:57 +02:00
Ricardo Wurmus
7f4957b24e
gnu: r-yarn: Update to 1.10.0. 
* gnu/packages/bioconductor.scm (r-yarn): Update to 1.10.0.
 2019-05-06 00:14:57 +02:00
Ricardo Wurmus
2feea2d22a
gnu: r-quantro: Update to 1.18.0. 
* gnu/packages/bioconductor.scm (r-quantro): Update to 1.18.0.
 2019-05-06 00:14:57 +02:00
Ricardo Wurmus
f48e29daa3
gnu: r-yaqcaffy: Update to 1.44.0. 
* gnu/packages/bioconductor.scm (r-yaqcaffy): Update to 1.44.0.
 2019-05-06 00:14:57 +02:00
Ricardo Wurmus
38c5d13a73
gnu: r-simpleaffy: Update to 2.60.0. 
* gnu/packages/bioconductor.scm (r-simpleaffy): Update to 2.60.0.
 2019-05-06 00:14:57 +02:00
Ricardo Wurmus
56576bea97
gnu: r-gcrma: Update to 2.56.0. 
* gnu/packages/bioconductor.scm (r-gcrma): Update to 2.56.0.
 2019-05-06 00:14:57 +02:00
Ricardo Wurmus
edba69b2ff
gnu: r-yapsa: Update to 1.10.0. 
* gnu/packages/bioconductor.scm (r-yapsa): Update to 1.10.0.
 2019-05-06 00:14:57 +02:00
Ricardo Wurmus
3cdc5d1a7b
gnu: r-somaticsignatures: Update to 2.20.0. 
* gnu/packages/bioconductor.scm (r-somaticsignatures): Update to 2.20.0.
 2019-05-06 00:14:56 +02:00
Ricardo Wurmus
128c6d59f0
gnu: r-gtrellis: Update to 1.16.0. 
* gnu/packages/bioconductor.scm (r-gtrellis): Update to 1.16.0.
 2019-05-06 00:14:56 +02:00
Ricardo Wurmus
1269a926c0
gnu: r-yamss: Update to 1.10.0. 
* gnu/packages/bioconductor.scm (r-yamss): Update to 1.10.0.
 2019-05-06 00:14:56 +02:00
Ricardo Wurmus
2a6d838337
gnu: r-ebimage: Update to 4.26.0. 
* gnu/packages/bioconductor.scm (r-ebimage): Update to 4.26.0.
 2019-05-06 00:14:56 +02:00
Ricardo Wurmus
b68a9e80f4
gnu: r-aucell: Update to 1.6.0. 
* gnu/packages/bioconductor.scm (r-aucell): Update to 1.6.0.
 2019-05-06 00:14:56 +02:00
Ricardo Wurmus
9da2021f49
gnu: r-allelicimbalance: Update to 1.22.0. 
* gnu/packages/bioconductor.scm (r-allelicimbalance): Update to 1.22.0.
 2019-05-06 00:14:56 +02:00
Ricardo Wurmus
ee1a45d719
gnu: r-annotationtools: Update to 1.58.0. 
* gnu/packages/bioconductor.scm (r-annotationtools): Update to 1.58.0.
 2019-05-06 00:14:56 +02:00
Ricardo Wurmus
69a2ec5447
gnu: r-annotationfuncs: Update to 1.34.0. 
* gnu/packages/bioconductor.scm (r-annotationfuncs): Update to 1.34.0.
 2019-05-06 00:14:56 +02:00
Ricardo Wurmus
e2e1dea2bb
gnu: r-abaenrichment: Update to 1.14.0. 
* gnu/packages/bioconductor.scm (r-abaenrichment): Update to 1.14.0.
 2019-05-06 00:14:55 +02:00
Ricardo Wurmus
bab06a6ff3
gnu: r-gofuncr: Update to 1.4.0. 
* gnu/packages/bioconductor.scm (r-gofuncr): Update to 1.4.0.
 2019-05-06 00:14:55 +02:00
Ricardo Wurmus
bcc233c1a6
gnu: r-atacseqqc: Update to 1.8.0. 
* gnu/packages/bioconductor.scm (r-atacseqqc): Update to 1.8.0.
[propagated-inputs]: Add r-edger.
 2019-05-06 00:14:55 +02:00
Ricardo Wurmus
19ee76379c
gnu: r-genomicscores: Update to 1.8.0. 
* gnu/packages/bioconductor.scm (r-genomicscores): Update to 1.8.0.
 2019-05-06 00:14:55 +02:00
Ricardo Wurmus
aa0ebfd2eb
gnu: r-motifstack: Update to 1.28.0. 
* gnu/packages/bioconductor.scm (r-motifstack): Update to 1.28.0.
[propagated-inputs]: Replace r-grimport with r-grimport2.
 2019-05-06 00:14:55 +02:00
Ricardo Wurmus
f7a495b159
gnu: r-motiv: Update to 1.40.0. 
* gnu/packages/bioconductor.scm (r-motiv): Update to 1.40.0.
 2019-05-06 00:14:55 +02:00
Ricardo Wurmus
a5860ebe87
gnu: r-rgadem: Update to 2.31.0. 
* gnu/packages/bioconductor.scm (r-rgadem): Update to 2.31.0.
 2019-05-06 00:14:54 +02:00
Ricardo Wurmus
e33c25ff2c
gnu: r-bacon: Update to 1.12.0. 
* gnu/packages/bioconductor.scm (r-bacon): Update to 1.12.0.
 2019-05-06 00:14:54 +02:00
Ricardo Wurmus
b7ddf0f048
gnu: r-abseqr: Update to 1.2.0. 
* gnu/packages/bioconductor.scm (r-abseqr): Update to 1.2.0.
 2019-05-06 00:14:54 +02:00
Ricardo Wurmus
1aadddeaa9
gnu: r-a4: Update to 1.32.0. 
* gnu/packages/bioconductor.scm (r-a4): Update to 1.32.0.
 2019-05-06 00:14:54 +02:00
Ricardo Wurmus
ae1730ae1a
gnu: r-a4base: Update to 1.32.0. 
* gnu/packages/bioconductor.scm (r-a4base): Update to 1.32.0.
 2019-05-06 00:14:54 +02:00
Ricardo Wurmus
e5a36543ac
gnu: r-a4reporting: Update to 1.32.0. 
* gnu/packages/bioconductor.scm (r-a4reporting): Update to 1.32.0.
 2019-05-06 00:14:54 +02:00
Ricardo Wurmus
0b6091621f
gnu: r-a4preproc: Update to 1.32.0. 
* gnu/packages/bioconductor.scm (r-a4preproc): Update to 1.32.0.
 2019-05-06 00:14:54 +02:00
Ricardo Wurmus
82de77da5a
gnu: r-a4classif: Update to 1.32.0. 
* gnu/packages/bioconductor.scm (r-a4classif): Update to 1.32.0.
 2019-05-06 00:14:53 +02:00
Ricardo Wurmus
b077e3db2a
gnu: r-a4core: Update to 1.32.0. 
* gnu/packages/bioconductor.scm (r-a4core): Update to 1.32.0.
 2019-05-06 00:14:53 +02:00
Ricardo Wurmus
8bef9df4d4
gnu: r-annaffy: Update to 1.56.0. 
* gnu/packages/bioconductor.scm (r-annaffy): Update to 1.56.0.
 2019-05-06 00:14:53 +02:00
Ricardo Wurmus
8265a1115e
gnu: r-mlinterfaces: Update to 1.64.0. 
* gnu/packages/bioconductor.scm (r-mlinterfaces): Update to 1.64.0.
 2019-05-06 00:14:53 +02:00
Ricardo Wurmus
1a3e33be23
gnu: r-clusterprofiler: Update to 3.12.0. 
* gnu/packages/bioconductor.scm (r-clusterprofiler): Update to 3.12.0.
 2019-05-06 00:14:53 +02:00
Ricardo Wurmus
77d28d665c
gnu: r-enrichplot: Update to 1.4.0. 
* gnu/packages/bioconductor.scm (r-enrichplot): Update to 1.4.0.
 2019-05-06 00:14:53 +02:00
Ricardo Wurmus
1990ff9d10
gnu: r-dose: Update to 3.10.0. 
* gnu/packages/bioconductor.scm (r-dose): Update to 3.10.0.
 2019-05-06 00:14:53 +02:00
Ricardo Wurmus
ebffd24c10
gnu: r-fgsea: Update to 1.10.0. 
* gnu/packages/bioconductor.scm (r-fgsea): Update to 1.10.0.
[propagated-inputs]: Add r-bh.
 2019-05-06 00:14:53 +02:00
Ricardo Wurmus
3e5ee6f69f
gnu: r-sigpathway: Update to 1.52.0. 
* gnu/packages/bioconductor.scm (r-sigpathway): Update to 1.52.0.
 2019-05-06 00:14:53 +02:00
Ricardo Wurmus
0a41b5db95
gnu: r-anota: Update to 1.32.0. 
* gnu/packages/bioconductor.scm (r-anota): Update to 1.32.0.
 2019-05-06 00:14:52 +02:00
Ricardo Wurmus
24cf7bad99
gnu: r-gosemsim: Update to 2.10.0. 
* gnu/packages/bioconductor.scm (r-gosemsim): Update to 2.10.0.
 2019-05-06 00:14:52 +02:00
Ricardo Wurmus
376d1fe759
gnu: r-heatplus: Update to 2.30.0. 
* gnu/packages/bioconductor.scm (r-heatplus): Update to 2.30.0.
 2019-05-06 00:14:52 +02:00
Ricardo Wurmus
c2effdedc0
gnu: r-varianttools: Update to 1.26.0. 
* gnu/packages/bioconductor.scm (r-varianttools): Update to 1.26.0.
 2019-05-06 00:14:52 +02:00
Ricardo Wurmus
bc083ecab8
gnu: r-triform: Update to 1.26.0. 
* gnu/packages/bioconductor.scm (r-triform): Update to 1.26.0.
 2019-05-06 00:14:52 +02:00
Ricardo Wurmus
2ee91179d1
gnu: r-ioniser: Update to 2.8.0. 
* gnu/packages/bioconductor.scm (r-ioniser): Update to 2.8.0.
 2019-05-06 00:14:52 +02:00
Ricardo Wurmus
48c2a7eb39
gnu: r-linnorm: Update to 2.8.0. 
* gnu/packages/bioconductor.scm (r-linnorm): Update to 2.8.0.
 2019-05-06 00:14:52 +02:00
Ricardo Wurmus
5551b07cde
gnu: r-lumi: Update to 2.36.0. 
* gnu/packages/bioconductor.scm (r-lumi): Update to 2.36.0.
 2019-05-06 00:14:51 +02:00
Ricardo Wurmus
2986b51ffe
gnu: r-methylumi: Update to 2.30.0. 
* gnu/packages/bioconductor.scm (r-methylumi): Update to 2.30.0.
 2019-05-06 00:14:51 +02:00
Ricardo Wurmus
8c0fae3cd4
gnu: r-minfi: Update to 1.30.0. 
* gnu/packages/bioconductor.scm (r-minfi): Update to 1.30.0.
 2019-05-06 00:14:51 +02:00
Ricardo Wurmus
693a98056c
gnu: r-bumphunter: Update to 1.26.0. 
* gnu/packages/bioconductor.scm (r-bumphunter): Update to 1.26.0.
 2019-05-06 00:14:51 +02:00
Ricardo Wurmus
409f4dd652
gnu: r-siggenes: Update to 1.58.0. 
* gnu/packages/bioconductor.scm (r-siggenes): Update to 1.58.0.
[propagated-inputs]: Add r-scrime.
 2019-05-06 00:14:51 +02:00
Ricardo Wurmus
fadc6db82d
gnu: r-illuminaio: Update to 0.26.0. 
* gnu/packages/bioconductor.scm (r-illuminaio): Update to 0.26.0.
 2019-05-06 00:14:51 +02:00
Ricardo Wurmus
2d4430877a
gnu: r-geoquery: Update to 2.52.0. 
* gnu/packages/bioconductor.scm (r-geoquery): Update to 2.52.0.
 2019-05-06 00:14:51 +02:00
Ricardo Wurmus
26c72fffc1
gnu: r-scone: Update to 1.8.0. 
* gnu/packages/bioconductor.scm (r-scone): Update to 1.8.0.
 2019-05-06 00:14:50 +02:00
Ricardo Wurmus
7baa59ed4d
gnu: r-scdd: Update to 1.8.0. 
* gnu/packages/bioconductor.scm (r-scdd): Update to 1.8.0.
 2019-05-06 00:14:50 +02:00
Ricardo Wurmus
6a2c58b7e0
gnu: r-noiseq: Update to 2.28.0. 
* gnu/packages/bioconductor.scm (r-noiseq): Update to 2.28.0.
 2019-05-06 00:14:50 +02:00
Ricardo Wurmus
78b6326785
gnu: r-monocle: Update to 2.12.0. 
* gnu/packages/bioconductor.scm (r-monocle): Update to 2.12.0.
 2019-05-06 00:14:50 +02:00
Ricardo Wurmus
a0ff725d6a
gnu: r-mast: Update to 1.10.0. 
* gnu/packages/bioconductor.scm (r-mast): Update to 1.10.0.
[propagated-inputs]: Add r-blme.
 2019-05-06 00:14:50 +02:00
Ricardo Wurmus
3fd2ea8883
gnu: r-icobra: Update to 1.12.0. 
* gnu/packages/bioconductor.scm (r-icobra): Update to 1.12.0.
 2019-05-06 00:14:50 +02:00
Ricardo Wurmus
bcd8b7a9bd
gnu: r-ihw: Update to 1.12.0. 
* gnu/packages/bioconductor.scm (r-ihw): Update to 1.12.0.
 2019-05-06 00:14:50 +02:00
Ricardo Wurmus
61c79d55e3
gnu: r-lpsymphony: Update to 1.12.0. 
* gnu/packages/bioconductor.scm (r-lpsymphony): Update to 1.12.0.
 2019-05-06 00:14:49 +02:00
Ricardo Wurmus
4a3c47e940
gnu: r-ebseq: Update to 1.24.0. 
* gnu/packages/bioconductor.scm (r-ebseq): Update to 1.24.0.
 2019-05-06 00:14:49 +02:00
Ricardo Wurmus
301c4ff12a
gnu: r-deds: Update to 1.58.0. 
* gnu/packages/bioconductor.scm (r-deds): Update to 1.58.0.
 2019-05-06 00:14:49 +02:00
Ricardo Wurmus
d5f3c0d09e
gnu: r-dnacopy: Update to 1.58.0. 
* gnu/packages/bioconductor.scm (r-dnacopy): Update to 1.58.0.
 2019-05-06 00:14:49 +02:00
Ricardo Wurmus
d941918599
gnu: r-copynumber: Update to 1.24.0. 
* gnu/packages/bioconductor.scm (r-copynumber): Update to 1.24.0.
 2019-05-06 00:14:49 +02:00
Ricardo Wurmus
58a43fc28e
gnu: r-chipexoqual: Update to 1.8.0. 
* gnu/packages/bioconductor.scm (r-chipexoqual): Update to 1.8.0.
 2019-05-06 00:14:49 +02:00
Ricardo Wurmus
8d3d0c3abe
gnu: r-savr: Update to 1.22.0. 
* gnu/packages/bioconductor.scm (r-savr): Update to 1.22.0.
 2019-05-06 00:14:49 +02:00
Ricardo Wurmus
0aa72f2d1e
gnu: r-destiny: Update to 2.14.0. 
* gnu/packages/bioconductor.scm (r-destiny): Update to 2.14.0.
[propagated-inputs]: Remove r-fnn and r-hmisc; add r-ggplot2.
 2019-05-06 00:14:48 +02:00
Ricardo Wurmus
6fc161fc3e
gnu: r-biocneighbors: Update to 1.2.0. 
* gnu/packages/bioconductor.scm (r-biocneighbors): Update to 1.2.0.
[propagated-inputs]: Add r-biocgenerics and r-rcpphnsw.
 2019-05-06 00:14:48 +02:00
Ricardo Wurmus
d8771f5fd6
gnu: r-ruvseq: Update to 1.18.0. 
* gnu/packages/bioconductor.scm (r-ruvseq): Update to 1.18.0.
 2019-05-06 00:14:48 +02:00
Ricardo Wurmus
774e499cec
gnu: r-dnabarcodes: Update to 1.14.0. 
* gnu/packages/bioconductor.scm (r-dnabarcodes): Update to 1.14.0.
 2019-05-06 00:14:48 +02:00
Ricardo Wurmus
3649d046a6
gnu: r-inspect: Update to 1.14.0. 
* gnu/packages/bioconductor.scm (r-inspect): Update to 1.14.0.
 2019-05-06 00:14:48 +02:00
Ricardo Wurmus
5dce71535f
gnu: r-plgem: Update to 1.56.0. 
* gnu/packages/bioconductor.scm (r-plgem): Update to 1.56.0.
 2019-05-06 00:14:48 +02:00
Ricardo Wurmus
5bf7eb49f6
gnu: r-rots: Update to 1.12.0. 
* gnu/packages/bioconductor.scm (r-rots): Update to 1.12.0.
 2019-05-06 00:14:48 +02:00
Ricardo Wurmus
07252952b7
gnu: r-glimma: Update to 1.12.0. 
* gnu/packages/bioconductor.scm (r-glimma): Update to 1.12.0.
 2019-05-06 00:14:47 +02:00
Ricardo Wurmus
40f0ee43a0
gnu: r-goseq: Update to 1.36.0. 
* gnu/packages/bioconductor.scm (r-goseq): Update to 1.36.0.
 2019-05-06 00:14:47 +02:00
Ricardo Wurmus
7a5d729af1
gnu: r-ctc: Update to 1.58.0. 
* gnu/packages/bioconductor.scm (r-ctc): Update to 1.58.0.
 2019-05-06 00:14:47 +02:00
Ricardo Wurmus
1236ce8e22
gnu: r-genomicinteractions: Update to 1.18.0. 
* gnu/packages/bioconductor.scm (r-genomicinteractions): Update to 1.18.0.
 2019-05-06 00:14:47 +02:00
Ricardo Wurmus
176a264c7c
gnu: r-interactionset: Update to 1.12.0. 
* gnu/packages/bioconductor.scm (r-interactionset): Update to 1.12.0.
 2019-05-06 00:14:47 +02:00
Ricardo Wurmus
eff6b2eb12
gnu: r-riboseqr: Update to 1.18.0. 
* gnu/packages/bioconductor.scm (r-riboseqr): Update to 1.18.0.
 2019-05-06 00:14:47 +02:00
Ricardo Wurmus
7d5acf7a25
gnu: r-riboprofiling: Update to 1.14.0. 
* gnu/packages/bioconductor.scm (r-riboprofiling): Update to 1.14.0.
 2019-05-06 00:14:47 +02:00
Ricardo Wurmus
1ddd4af5a0
gnu: r-chipcomp: Update to 1.14.0. 
* gnu/packages/bioconductor.scm (r-chipcomp): Update to 1.14.0.
 2019-05-06 00:14:47 +02:00
Ricardo Wurmus
c38de81594
gnu: r-bayseq: Update to 2.18.0. 
* gnu/packages/bioconductor.scm (r-bayseq): Update to 2.18.0.
 2019-05-06 00:14:46 +02:00
Ricardo Wurmus
4f4bed7de5
gnu: r-qdnaseq: Update to 1.20.0. 
* gnu/packages/bioconductor.scm (r-qdnaseq): Update to 1.20.0.
 2019-05-06 00:14:46 +02:00
Ricardo Wurmus
2317730994
gnu: r-cghcall: Update to 2.46.0. 
* gnu/packages/bioconductor.scm (r-cghcall): Update to 2.46.0.
 2019-05-06 00:14:46 +02:00
Ricardo Wurmus
8efb842f11
gnu: r-cghbase: Update to 1.44.0. 
* gnu/packages/bioconductor.scm (r-cghbase): Update to 1.44.0.
 2019-05-06 00:14:46 +02:00
Ricardo Wurmus
bcb95b7aac
gnu: r-marray: Update to 1.62.0. 
* gnu/packages/bioconductor.scm (r-marray): Update to 1.62.0.
 2019-05-06 00:14:46 +02:00
Ricardo Wurmus
a61bcb28f7
gnu: r-graph: Update to 1.62.0. 
* gnu/packages/bioconductor.scm (r-graph): Update to 1.62.0.
 2019-05-06 00:14:46 +02:00
Ricardo Wurmus
588b63c2af
gnu: r-multtest: Update to 2.40.0. 
* gnu/packages/bioconductor.scm (r-multtest): Update to 2.40.0.
 2019-05-06 00:14:45 +02:00
Ricardo Wurmus
0968a44874
gnu: r-ripseeker: Update to 1.24.0. 
* gnu/packages/bioconductor.scm (r-ripseeker): Update to 1.24.0.
 2019-05-06 00:14:45 +02:00
Ricardo Wurmus
4c221b3bbf
gnu: r-diffbind: Update to 2.12.0. 
* gnu/packages/bioconductor.scm (r-diffbind): Update to 2.12.0.
[propagated-inputs]: Add r-rhtslib; remove r-zlibbioc.
 2019-05-06 00:14:45 +02:00
Ricardo Wurmus
e02162f7ba
gnu: r-qvalue: Update to 2.16.0. 
* gnu/packages/bioconductor.scm (r-qvalue): Update to 2.16.0.
 2019-05-06 00:14:45 +02:00
Ricardo Wurmus
3e1bc88c1f
gnu: r-geneplotter: Update to 1.62.0. 
* gnu/packages/bioconductor.scm (r-geneplotter): Update to 1.62.0.
 2019-05-06 00:14:45 +02:00
Ricardo Wurmus
4b53d55e98
gnu: r-regioner: Update to 1.16.0. 
* gnu/packages/bioconductor.scm (r-regioner): Update to 1.16.0.
 2019-05-06 00:14:45 +02:00
Ricardo Wurmus
43a23a0733
gnu: r-hpar: Update to 1.26.0. 
* gnu/packages/bioconductor.scm (r-hpar): Update to 1.26.0.
 2019-05-06 00:14:44 +02:00
Ricardo Wurmus
0c53332a27
gnu: r-annotate: Update to 1.62.0. 
* gnu/packages/bioconductor.scm (r-annotate): Update to 1.62.0.
 2019-05-06 00:14:44 +02:00
Ricardo Wurmus
81a1c45df5
gnu: r-biocgenerics: Update to 0.30.0. 
* gnu/packages/bioconductor.scm (r-biocgenerics): Update to 0.30.0.
 2019-05-06 00:14:44 +02:00
Ricardo Wurmus
3addf736d5
gnu: r-systempiper: Update to 1.18.0. 
* gnu/packages/bioinformatics.scm (r-systempiper): Update to 1.18.0.
[propagated-inputs]: Replace r-batchjobs with r-batchtools; add r-yaml.
 2019-05-06 00:14:44 +02:00
Ricardo Wurmus
9bcbca135b
gnu: r-rsamtools: Update to 2.0.0. 
* gnu/packages/bioinformatics.scm (r-rsamtools): Update to 2.0.0.
[propagated-inputs]: Add r-rhtslib.
 2019-05-06 00:14:44 +02:00
Ricardo Wurmus
82d9340b0c
gnu: r-impute: Update to 1.58.0. 
* gnu/packages/bioinformatics.scm (r-impute): Update to 1.58.0.
[inputs]: Move gfortran from here...
[native-inputs]: ...to here.
 2019-05-06 00:14:44 +02:00
Ricardo Wurmus
2b4ac1d77e
gnu: r-rcas: Update to 1.10.0. 
* gnu/packages/bioinformatics.scm (r-rcas): Update to 1.10.0.
[propagated-inputs]: Add ghc-pandoc.
 2019-05-06 00:14:43 +02:00
Ricardo Wurmus
8322c860f9
gnu: r-methylkit: Update to 1.10.0. 
* gnu/packages/bioinformatics.scm (r-methylkit): Update to 1.10.0.
[propagated-inputs]: Add r-mgcv.
 2019-05-06 00:14:43 +02:00
Ricardo Wurmus
b173dbe617
gnu: r-annotationhub: Update to 2.16.0. 
* gnu/packages/bioinformatics.scm (r-annotationhub): Update to 2.16.0.
[propagated-inputs]: Add r-biocfilecache, r-dplyr, and r-rappdirs.
 2019-05-06 00:14:43 +02:00
Ricardo Wurmus
a8abc8dd3a
gnu: r-fastseg: Update to 1.30.0. 
* gnu/packages/bioinformatics.scm (r-fastseg): Update to 1.30.0.
 2019-05-06 00:14:43 +02:00
Ricardo Wurmus
e699e8e599
gnu: r-keggrest: Update to 1.24.0. 
* gnu/packages/bioinformatics.scm (r-keggrest): Update to 1.24.0.
 2019-05-06 00:14:43 +02:00
Ricardo Wurmus
c798455d87
gnu: r-gage: Update to 2.34.0. 
* gnu/packages/bioinformatics.scm (r-gage): Update to 2.34.0.
 2019-05-06 00:14:43 +02:00
Ricardo Wurmus
d4ef1d59cc
gnu: r-genomicfiles: Update to 1.20.0. 
* gnu/packages/bioinformatics.scm (r-genomicfiles): Update to 1.20.0.
 2019-05-06 00:14:43 +02:00
Ricardo Wurmus
70a3e4499d
gnu: r-complexheatmap: Update to 2.0.0. 
* gnu/packages/bioinformatics.scm (r-complexheatmap): Update to 2.0.0.
[propagated-inputs]: Add r-clue and r-png.
 2019-05-06 00:14:43 +02:00
Ricardo Wurmus
e2cb23404c
gnu: r-dirichletmultinomial: Update to 1.26.0. 
* gnu/packages/bioinformatics.scm (r-dirichletmultinomial): Update to 1.26.0.
 2019-05-06 00:14:42 +02:00
Ricardo Wurmus
0af6efa3c5
gnu: r-ensembldb: Update to 2.8.0. 
* gnu/packages/bioinformatics.scm (r-ensembldb): Update to 2.8.0.
 2019-05-06 00:14:42 +02:00
Ricardo Wurmus
96f98c5b72
gnu: r-organismdbi: Update to 1.26.0. 
* gnu/packages/bioinformatics.scm (r-organismdbi): Update to 1.26.0.
 2019-05-06 00:14:42 +02:00
Ricardo Wurmus
a98c3b4ae4
gnu: r-biovizbase: Update to 1.32.0. 
* gnu/packages/bioinformatics.scm (r-biovizbase): Update to 1.32.0.
 2019-05-06 00:14:42 +02:00
Ricardo Wurmus
d38fbacad1
gnu: r-ggbio: Update to 1.32.0. 
* gnu/packages/bioinformatics.scm (r-ggbio): Update to 1.32.0.
 2019-05-06 00:14:42 +02:00
Ricardo Wurmus
623be1a443
gnu: r-gqtlbase: Update to 1.16.0. 
* gnu/packages/bioinformatics.scm (r-gqtlbase): Update to 1.16.0.
 2019-05-06 00:14:42 +02:00
Ricardo Wurmus
ed7de45655
gnu: r-snpstats: Update to 1.34.0. 
* gnu/packages/bioinformatics.scm (r-snpstats): Update to 1.34.0.
 2019-05-06 00:14:42 +02:00
Ricardo Wurmus
3c5f5b4154
gnu: r-erma: Update to 1.0.0. 
* gnu/packages/bioinformatics.scm (r-erma): Update to 1.0.0.
 2019-05-06 00:14:41 +02:00
Ricardo Wurmus
89ba9a7226
gnu: r-ldblock: Update to 1.14.0. 
* gnu/packages/bioinformatics.scm (r-ldblock): Update to 1.14.0.
 2019-05-06 00:14:41 +02:00
Ricardo Wurmus
a349d57a46
gnu: r-gqtlstats: Update to 1.16.0. 
* gnu/packages/bioinformatics.scm (r-gqtlstats): Update to 1.16.0.
 2019-05-06 00:14:41 +02:00
Ricardo Wurmus
105d9e2cb4
gnu: r-gviz: Update to 1.28.0. 
* gnu/packages/bioinformatics.scm (r-gviz): Update to 1.28.0.
 2019-05-06 00:14:41 +02:00
Ricardo Wurmus
1b454f9f69
gnu: r-gwascat: Update to 2.16.0. 
* gnu/packages/bioinformatics.scm (r-gwascat): Update to 2.16.0.
[propagated-inputs]: Remove r-annotationhub, r-ggbio, r-ggplot2, r-gqtlstats,
r-graph, r-gviz, r-snpstats, r-summarizedexperiment, and r-variantannotation.
 2019-05-06 00:14:41 +02:00
Ricardo Wurmus
256609eb46
gnu: r-sushi: Update to 1.22.0. 
* gnu/packages/bioinformatics.scm (r-sushi): Update to 1.22.0.
 2019-05-06 00:14:41 +02:00
Ricardo Wurmus
7705165882
gnu: r-fithic: Update to 1.10.0. 
* gnu/packages/bioinformatics.scm (r-fithic): Update to 1.10.0.
 2019-05-06 00:14:40 +02:00
Ricardo Wurmus
e998a26e1d
gnu: r-hitc: Update to 1.28.0. 
* gnu/packages/bioinformatics.scm (r-hitc): Update to 1.28.0.
 2019-05-06 00:14:40 +02:00
Ricardo Wurmus
65925573be
gnu: r-hdf5array: Update to 1.12.0. 
* gnu/packages/bioinformatics.scm (r-hdf5array): Update to 1.12.0.
[inputs]: Add zlib.
[propagated-inputs]: Add r-rhdf5lib.
 2019-05-06 00:14:40 +02:00
Ricardo Wurmus
d5625b3a9e
gnu: r-rhdf5lib: Update to 1.6.0. 
* gnu/packages/bioinformatics.scm (r-rhdf5lib): Update to 1.6.0.
 2019-05-06 00:14:40 +02:00
Ricardo Wurmus
583b4fd6e3
gnu: r-beachmat: Update to 2.0.0. 
* gnu/packages/bioinformatics.scm (r-beachmat): Update to 2.0.0.
[inputs]: Remove hdf5 and zlib.
[propagated-inputs]: Rmeove r-hdf5array, r-rcpp, r-rhdf5, and r-rhdf5lib.
 2019-05-06 00:14:40 +02:00
Ricardo Wurmus
029cefdd90
gnu: r-singlecellexperiment: Update to 1.6.0. 
* gnu/packages/bioinformatics.scm (r-singlecellexperiment): Update to 1.6.0.
 2019-05-06 00:14:40 +02:00
Ricardo Wurmus
70d04dc183
gnu: r-scater: Update to 1.12.0. 
* gnu/packages/bioinformatics.scm (r-scater): Update to 1.12.0.
[propagated-inputs]: Add r-biocneighbors and r-biocsingular; remove r-plyr,
r-reshape2, and r-rhdf5lib.
 2019-05-06 00:14:40 +02:00
Ricardo Wurmus
4540727a21
gnu: r-scran: Update to 1.12.0. 
* gnu/packages/bioinformatics.scm (r-scran): Update to 1.12.0.
[propagated-inputs]: Add r-bh, r-biocsingular, and r-dqrng; remove r-rhdf5lib.
 2019-05-06 00:14:39 +02:00
Ricardo Wurmus
f2a63d1588
gnu: r-delayedmatrixstats: Update to 1.6.0. 
* gnu/packages/bioinformatics.scm (r-delayedmatrixstats): Update to 1.6.0.
 2019-05-06 00:14:39 +02:00
Ricardo Wurmus
fbf3494972
gnu: Add r-biocfilecache. 
* gnu/packages/bioconductor.scm (r-biocfilecache): New variable.
 2019-05-06 00:14:39 +02:00
Ricardo Wurmus
fab5f7c8d9
gnu: r-interactivedisplaybase: Update to 1.22.0. 
* gnu/packages/bioinformatics.scm (r-interactivedisplaybase): Update to 1.22.0.
 2019-05-06 00:14:39 +02:00
Ricardo Wurmus
975b72fa10
gnu: r-edaseq: Update to 2.18.0. 
* gnu/packages/bioinformatics.scm (r-edaseq): Update to 2.18.0.
 2019-05-06 00:14:39 +02:00
Ricardo Wurmus
b765fc4a4c
gnu: r-deseq: Update to 1.36.0. 
* gnu/packages/bioinformatics.scm (r-deseq): Update to 1.36.0.
 2019-05-06 00:14:39 +02:00
Ricardo Wurmus
95f3a46630
gnu: r-aroma-light: Update to 3.14.0. 
* gnu/packages/bioinformatics.scm (r-aroma-light): Update to 3.14.0.
 2019-05-06 00:14:39 +02:00
Ricardo Wurmus
dd03589939
gnu: r-msnid: Update to 1.18.0. 
* gnu/packages/bioinformatics.scm (r-msnid): Update to 1.18.0.
 2019-05-06 00:14:38 +02:00
Ricardo Wurmus
b65c264907
gnu: r-msnbase: Update to 2.10.0. 
* gnu/packages/bioinformatics.scm (r-msnbase): Update to 2.10.0.
 2019-05-06 00:14:38 +02:00
Ricardo Wurmus
ee386fcb1a
gnu: r-pcamethods: Update to 1.76.0. 
* gnu/packages/bioinformatics.scm (r-pcamethods): Update to 1.76.0.
 2019-05-06 00:14:38 +02:00
Ricardo Wurmus
f955afdabf
gnu: r-mzid: Update to 1.22.0. 
* gnu/packages/bioinformatics.scm (r-mzid): Update to 1.22.0.
 2019-05-06 00:14:38 +02:00
Ricardo Wurmus
9421e6b610
gnu: r-vsn: Update to 3.52.0. 
* gnu/packages/bioinformatics.scm (r-vsn): Update to 3.52.0.
 2019-05-06 00:14:38 +02:00
Ricardo Wurmus
15f240e317
gnu: r-affy: Update to 1.62.0. 
* gnu/packages/bioinformatics.scm (r-affy): Update to 1.62.0.
 2019-05-06 00:14:38 +02:00
Ricardo Wurmus
fdbaa5c1e5
gnu: r-affyio: Update to 1.54.0. 
* gnu/packages/bioinformatics.scm (r-affyio): Update to 1.54.0.
 2019-05-06 00:14:38 +02:00
Ricardo Wurmus
5498cc46b3
gnu: r-mzr: Update to 2.18.0. 
* gnu/packages/bioinformatics.scm (r-mzr): Update to 2.18.0.
 2019-05-06 00:14:37 +02:00
Ricardo Wurmus
24aabd8fd9
gnu: r-protgenerics: Update to 1.16.0. 
* gnu/packages/bioinformatics.scm (r-protgenerics): Update to 1.16.0.
 2019-05-06 00:14:37 +02:00
Ricardo Wurmus
10cb9919fc
gnu: r-sva: Update to 3.32.0. 
* gnu/packages/bioinformatics.scm (r-sva): Update to 3.32.0.
 2019-05-06 00:14:37 +02:00
Ricardo Wurmus
59bef6eaee
gnu: r-copywriter: Update to 2.16.0. 
* gnu/packages/bioinformatics.scm (r-copywriter): Update to 2.16.0.
 2019-05-06 00:14:37 +02:00
Ricardo Wurmus
70c44443c3
gnu: r-chipseq: Update to 1.34.0. 
* gnu/packages/bioinformatics.scm (r-chipseq): Update to 1.34.0.
 2019-05-06 00:14:37 +02:00
Ricardo Wurmus
dbb4aa4a34
gnu: r-annotationfilter: Update to 1.8.0. 
* gnu/packages/bioinformatics.scm (r-annotationfilter): Update to 1.8.0.
 2019-05-06 00:14:37 +02:00
Ricardo Wurmus
f6ecdafa11
gnu: r-rhdf5: Update to 2.28.0. 
* gnu/packages/bioinformatics.scm (r-rhdf5): Update to 2.28.0.
 2019-05-06 00:14:37 +02:00
Ricardo Wurmus
c030eb50c5
gnu: r-tximport: Update to 1.12.0. 
* gnu/packages/bioinformatics.scm (r-tximport): Update to 1.12.0.
 2019-05-06 00:14:36 +02:00
Ricardo Wurmus
5b65a85949
gnu: r-mutationalpatterns: Update to 1.10.0. 
* gnu/packages/bioinformatics.scm (r-mutationalpatterns): Update to 1.10.0.
 2019-05-06 00:14:36 +02:00
Ricardo Wurmus
45aeb4eb1d
gnu: r-bamsignals: Update to 1.16.0. 
* gnu/packages/bioinformatics.scm (r-bamsignals): Update to 1.16.0.
 2019-05-06 00:14:36 +02:00
Ricardo Wurmus
23ce7f3b0b
gnu: r-rhtslib: Update to 1.16.1. 
* gnu/packages/bioinformatics.scm (r-rhtslib): Update to 1.16.1.
 2019-05-06 00:14:36 +02:00
Ricardo Wurmus
c648e672b7
gnu: r-zlibbioc: Update to 1.30.0. 
* gnu/packages/bioinformatics.scm (r-zlibbioc): Update to 1.30.0.
 2019-05-06 00:14:36 +02:00
Ricardo Wurmus
3be113b706
gnu: r-motifrg: Update to 1.28.0. 
* gnu/packages/bioinformatics.scm (r-motifrg): Update to 1.28.0.
 2019-05-06 00:14:35 +02:00
Ricardo Wurmus
a7143246f8
gnu: r-seqlogo: Update to 1.50.0. 
* gnu/packages/bioinformatics.scm (r-seqlogo): Update to 1.50.0.
 2019-05-06 00:14:35 +02:00
Ricardo Wurmus
6ef47ac82e
gnu: r-genomation: Update to 1.16.0. 
* gnu/packages/bioinformatics.scm (r-genomation): Update to 1.16.0.
 2019-05-06 00:14:35 +02:00
Ricardo Wurmus
d726689a70
gnu: r-seqpattern: Update to 1.16.0. 
* gnu/packages/bioinformatics.scm (r-seqpattern): Update to 1.16.0.
 2019-05-06 00:14:35 +02:00
Ricardo Wurmus
651b62c697
gnu: r-bsgenome: Update to 1.52.0. 
* gnu/packages/bioinformatics.scm (r-bsgenome): Update to 1.52.0.
 2019-05-06 00:14:35 +02:00
Ricardo Wurmus
971df3a784
gnu: r-topgo: Update to 2.36.0. 
* gnu/packages/bioinformatics.scm (r-topgo): Update to 2.36.0.
 2019-05-06 00:14:34 +02:00
Ricardo Wurmus
d31f8d1bd8
gnu: r-genomicfeatures: Update to 1.36.0. 
* gnu/packages/bioinformatics.scm (r-genomicfeatures): Update to 1.36.0.
 2019-05-06 00:14:34 +02:00
Ricardo Wurmus
40d97367f0
gnu: r-rtracklayer: Update to 1.44.0. 
* gnu/packages/bioinformatics.scm (r-rtracklayer): Update to 1.44.0.
 2019-05-06 00:14:34 +02:00
Ricardo Wurmus
6ff6973502
gnu: r-genomicalignments: Update to 1.20.0. 
* gnu/packages/bioinformatics.scm (r-genomicalignments): Update to 1.20.0.
 2019-05-06 00:14:34 +02:00
Ricardo Wurmus
8671d1e9d6
gnu: r-summarizedexperiment: Update to 1.14.0. 
* gnu/packages/bioinformatics.scm (r-summarizedexperiment): Update to 1.14.0.
 2019-05-06 00:14:34 +02:00
Ricardo Wurmus
14561bb9e7
gnu: r-delayedarray: Update to 0.10.0. 
* gnu/packages/bioinformatics.scm (r-delayedarray): Update to 0.10.0.
[propagated-inputs]: Add r-matrix.
 2019-05-06 00:14:34 +02:00
Ricardo Wurmus
d2e165496b
gnu: r-biostrings: Update to 2.52.0. 
* gnu/packages/bioinformatics.scm (r-biostrings): Update to 2.52.0.
 2019-05-06 00:14:33 +02:00
Ricardo Wurmus
e10b67c797
gnu: r-biocparallel: Update to 1.18.0. 
* gnu/packages/bioinformatics.scm (r-biocparallel): Update to 1.18.0.
 2019-05-06 00:14:33 +02:00
Ricardo Wurmus
933571ddcd
gnu: r-biomart: Update to 2.40.0. 
* gnu/packages/bioinformatics.scm (r-biomart): Update to 2.40.0.
 2019-05-06 00:14:33 +02:00
Ricardo Wurmus
a1b9378a8e
gnu: r-annotationdbi: Update to 1.46.0. 
* gnu/packages/bioinformatics.scm (r-annotationdbi): Update to 1.46.0.
 2019-05-06 00:14:33 +02:00
Ricardo Wurmus
4aadfcd296
gnu: r-biobase: Update to 2.44.0. 
* gnu/packages/bioinformatics.scm (r-biobase): Update to 2.44.0.
 2019-05-06 00:14:33 +02:00
Ricardo Wurmus
b35bc56a8a
gnu: r-genomicranges: Update to 1.36.0. 
* gnu/packages/bioinformatics.scm (r-genomicranges): Update to 1.36.0.
 2019-05-06 00:14:33 +02:00
Ricardo Wurmus
bc0e5bc12e
gnu: r-xvector: Update to 0.24.0. 
* gnu/packages/bioinformatics.scm (r-xvector): Update to 0.24.0.
 2019-05-06 00:14:32 +02:00
Ricardo Wurmus
5fadf39280
gnu: r-limma: Update to 3.40.0. 
* gnu/packages/bioinformatics.scm (r-limma): Update to 3.40.0.
 2019-05-06 00:14:32 +02:00
Ricardo Wurmus
0d094ad9ab
gnu: r-variantannotation: Update to 1.30.0. 
* gnu/packages/bioinformatics.scm (r-variantannotation): Update to 1.30.0.
[propagated-inputs]: Add r-rhtslib.
 2019-05-06 00:14:32 +02:00
Ricardo Wurmus
1e3f53a489
gnu: r-edger: Update to 3.26.0. 
* gnu/packages/bioinformatics.scm (r-edger): Update to 3.26.0.
 2019-05-06 00:14:32 +02:00
Ricardo Wurmus
6dc05d0a86
gnu: r-genomeinfodb: Update to 1.20.0. 
* gnu/packages/bioinformatics.scm (r-genomeinfodb): Update to 1.20.0.
 2019-05-06 00:14:32 +02:00
Ricardo Wurmus
38142114b7
gnu: r-iranges: Update to 2.18.0. 
* gnu/packages/bioinformatics.scm (r-iranges): Update to 2.18.0.
 2019-05-06 00:14:32 +02:00
Ricardo Wurmus
192ddab3e5
gnu: r-s4vectors: Update to 0.22.0. 
* gnu/packages/bioinformatics.scm (r-s4vectors): Update to 0.22.0.
 2019-05-06 00:14:31 +02:00
Ricardo Wurmus
8bdf7d55be
gnu: r-bioccheck: Update to 1.20.0. 
* gnu/packages/bioinformatics.scm (r-bioccheck): Update to 1.20.0.
 2019-05-06 00:14:31 +02:00
Ricardo Wurmus
e01b72d225
gnu: r-biocstyle: Update to 2.12.0. 
* gnu/packages/bioinformatics.scm (r-biocstyle): Update to 2.12.0.
 2019-05-06 00:14:31 +02:00
Ricardo Wurmus
440af6482a
gnu: r-biocviews: Update to 1.52.0. 
* gnu/packages/bioinformatics.scm (r-biocviews): Update to 1.52.0.
 2019-05-06 00:14:31 +02:00
Ricardo Wurmus
ce52cab000
gnu: r-grohmm: Update to 1.18.0. 
* gnu/packages/bioinformatics.scm (r-grohmm): Update to 1.18.0.
 2019-05-06 00:14:31 +02:00
Ricardo Wurmus
49f30903f0
gnu: r-shortread: Update to 1.42.0. 
* gnu/packages/bioinformatics.scm (r-shortread): Update to 1.42.0.
 2019-05-06 00:14:31 +02:00
Ricardo Wurmus
fe40f55094
gnu: r-gostats: Update to 2.50.0. 
* gnu/packages/bioinformatics.scm (r-gostats): Update to 2.50.0.
 2019-05-06 00:14:30 +02:00
Ricardo Wurmus
4d88dbe6eb
gnu: r-category: Update to 2.50.0. 
* gnu/packages/bioinformatics.scm (r-category): Update to 2.50.0.
 2019-05-06 00:14:30 +02:00
Ricardo Wurmus
08d2a26d47
gnu: r-gseabase: Update to 1.46.0. 
* gnu/packages/bioinformatics.scm (r-gseabase): Update to 1.46.0.
 2019-05-06 00:14:30 +02:00
Ricardo Wurmus
aa51a241c5
gnu: r-rbgl: Update to 1.60.0. 
* gnu/packages/bioinformatics.scm (r-rbgl): Update to 1.60.0.
[propagated-inputs]: Add r-bh.
 2019-05-06 00:14:30 +02:00
Ricardo Wurmus
7f737246d8
gnu: r-annotationforge: Update to 1.26.0. 
* gnu/packages/bioinformatics.scm (r-annotationforge): Update to 1.26.0.
 2019-05-06 00:14:30 +02:00
Ricardo Wurmus
0a58282de7
gnu: r-dexseq: Update to 1.30.0. 
* gnu/packages/bioinformatics.scm (r-dexseq): Update to 1.30.0.
 2019-05-06 00:14:30 +02:00
Ricardo Wurmus
9a39193d45
gnu: r-deseq2: Update to 1.24.0. 
* gnu/packages/bioinformatics.scm (r-deseq2): Update to 1.24.0.
 2019-05-06 00:14:30 +02:00
Ricardo Wurmus
0183163d1e
gnu: r-genefilter: Update to 1.66.0. 
* gnu/packages/bioinformatics.scm (r-genefilter): Update to 1.66.0.
 2019-05-06 00:14:29 +02:00
Ricardo Wurmus
295f35dfb9
gnu: r-preprocesscore: Update to 1.46.0. 
* gnu/packages/statistics.scm (r-preprocesscore): Update to 1.46.0.
 2019-05-06 00:14:29 +02:00
Ricardo Wurmus
52b4703c08
gnu: r-rgraphviz: Update to 2.28.0. 
* gnu/packages/graph.scm (r-rgraphviz): Update to 2.28.0.
 2019-05-06 00:14:29 +02:00
Ricardo Wurmus
3b13b6d777
gnu: r-units: Update to 0.6-3. 
* gnu/packages/cran.scm (r-units): Update to 0.6-3.
 2019-05-06 00:14:29 +02:00
Ricardo Wurmus
3961b3b900
gnu: Add r-dqrng. 
* gnu/packages/cran.scm (r-dqrng): New variable.
 2019-05-06 00:14:29 +02:00
Ricardo Wurmus
b8d6dffbdd
gnu: Add r-sitmo. 
* gnu/packages/cran.scm (r-sitmo): New variable.
 2019-05-06 00:14:29 +02:00
Ricardo Wurmus
0c8960df13
gnu: Add r-clue. 
* gnu/packages/cran.scm (r-clue): New variable.
 2019-05-06 00:14:29 +02:00
Ricardo Wurmus
be23c491cb
gnu: Add r-batchtools. 
* gnu/packages/cran.scm (r-batchtools): New variable.
 2019-05-06 00:14:28 +02:00
Ricardo Wurmus
04bf86ba9f
gnu: Add r-blme. 
* gnu/packages/cran.scm (r-blme): New variable.
 2019-05-06 00:14:28 +02:00
Ricardo Wurmus
2b9d4f5866
gnu: Add r-scrime. 
* gnu/packages/cran.scm (r-scrime): New variable.
 2019-05-06 00:14:28 +02:00
Ricardo Wurmus
78735b9f34
gnu: Add r-grimport2. 
* gnu/packages/cran.scm (r-grimport2): New variable.
 2019-05-06 00:14:28 +02:00
Ricardo Wurmus
8128189976
gnu: Add r-rcpphnsw. 
* gnu/packages/cran.scm (r-rcpphnsw): New variable.
 2019-05-06 00:14:28 +02:00
Ricardo Wurmus
993912905d
gnu: Add r-biocsingular. 
* gnu/packages/bioconductor.scm (r-biocsingular): New variable.
 2019-05-06 00:14:28 +02:00
Ricardo Wurmus
72032c9d5f
gnu: Add r-base64url. 
* gnu/packages/cran.scm (r-base64url): New variable.
 2019-05-06 00:14:27 +02:00
Miguel
28b26eca45
installer: Fix typo. 
* gnu/installer/newt/menu.scm (run-menu-page): Add missing space after
period.

Signed-off-by: Danny Milosavljevic <dannym@scratchpost.org>
 2019-05-05 17:21:18 +02:00
Brendan Tildesley
dcfa0acd7b
Correct email and license info for Brendan Tildesley. 
* gnu/packages/audio.scm: Correct email and license info.
* gnu/packages/ebook.scm: Correct email and license info.
* gnu/packages/fonts.scm: Correct email and license info.
* gnu/packages/freedesktop.scm: Correct email and license info.
* gnu/packages/gnome.scm: Correct email and license info.
* gnu/packages/linux.scm: Correct email and license info.
* gnu/packages/lxde.scm: Correct email and license info.
* gnu/packages/python-web.scm: Correct email and license info.
* gnu/packages/python-xyz.scm: Correct email and license info.
* gnu/packages/python.scm: Correct email and license info.
* gnu/packages/video.scm: Correct email and license info.
* gnu/packages/web.scm: Correct email and license info.

Signed-off-by: Danny Milosavljevic <dannym@scratchpost.org>
 2019-05-05 17:16:51 +02:00
Danny Milosavljevic
ee3ce0d71d
gnu: calibre: Update to 3.42.0. 
* gnu/packages/ebook.scm (calibre): Update to 3.42.0.

Signed-off-by: Danny Milosavljevic <dannym@scratchpost.org>
 2019-05-05 14:44:21 +02:00
Brendan Tildesley
421c5e92f9
gnu: calibre: Shorten long line. 
* gnu/packages/ebook.scm (calibre)[arguments]<#:phases>[build-extra]: Shorten long line.

Signed-off-by: Danny Milosavljevic <dannym@scratchpost.org>
 2019-05-05 14:44:21 +02:00
Brendan Tildesley
d6dfe8b634
gnu: calibre: Install man pages. 
* gnu/packages/ebook.scm (calibre)[arguments]<#:phases>[install-man-pages]:
New phase.

Signed-off-by: Danny Milosavljevic <dannym@scratchpost.org>
 2019-05-05 14:44:21 +02:00
Brendan Tildesley
f3f017dbf0
gnu: calibre: Delete various junk from source. 
* gnu/packages/ebook.scm (calibre)[source](snippet): Delete various junk from
source.

Signed-off-by: Danny Milosavljevic <dannym@scratchpost.org>
 2019-05-05 14:44:21 +02:00
Brendan Tildesley
62a97dc0fb
gnu: calibre: Remove libxrender as an input. 
* gnu/packages/ebook.scm (calibre)[inputs]: Remove libxrender.

Signed-off-by: Danny Milosavljevic <dannym@scratchpost.org>
 2019-05-05 14:44:21 +02:00
Brendan Tildesley
68435a7f55
gnu: calibre: Unbundle python2-odfpy. 
* gnu/packages/ebook.scm (calibre)[snippet]: Remove all of src/odf.
[inputs]: Add python2-odfpy.

Signed-off-by: Danny Milosavljevic <dannym@scratchpost.org>
 2019-05-05 14:44:21 +02:00
Brendan Tildesley
7312a7d073
gnu: calibre: Remove some comments. 
* gnu/packages/ebook.scm (calibre): There is no unrar in Guix currently, and
  pdftohtml is in poppler, so we can remove this comment.

Signed-off-by: Danny Milosavljevic <dannym@scratchpost.org>
 2019-05-05 14:44:21 +02:00
Brendan Tildesley
eb5f620134
gnu: calibre: Enable tests. 
* gnu/packages/ebook.scm (calibre): Enable tests.

Signed-off-by: Danny Milosavljevic <dannym@scratchpost.org>
 2019-05-05 14:44:20 +02:00
Brendan Tildesley
cbe399e736
gnu: calibre: Disable sqlite test. 
* gnu/packages/patches/calibre-remove-test-sqlite.patch: New file.
* gnu/packages/ebook.scm (calibre)[source]: Use it.
* gnu/local.mk (dist_patch_DATA): Add it.

Signed-off-by: Danny Milosavljevic <dannym@scratchpost.org>
 2019-05-05 14:44:20 +02:00
Brendan Tildesley
4bcd0647b7
gnu: calibre: Disable Qt test. 
* gnu/packages/ebook.scm (calibre)[arguments]<#:phases>[configure]: Disable
Qt test.

Signed-off-by: Danny Milosavljevic <dannym@scratchpost.org>
 2019-05-05 14:44:20 +02:00
Brendan Tildesley
f89f5abada
gnu: calibre: Disable bs4 test. 
* gnu/packages/patches/calibre-remove-test-bs4.patch: New file.
* gnu/packages/ebook.scm (calibre)[source]: Use it.
* gnu/local.mk (dist_patch_DATA): Add it.

Signed-off-by: Danny Milosavljevic <dannym@scratchpost.org>
 2019-05-05 14:44:20 +02:00
Brendan Tildesley
6e1ab5fadb
gnu: calibre: Use "linux.py" to install desktop files. 
* gnu/packages/ebook.scm (calibre)[arguments]<#:phases>[configure]: Modify.
[install-mimetypes]: Remove.

Signed-off-by: Danny Milosavljevic <dannym@scratchpost.org>
 2019-05-05 14:44:20 +02:00
Brendan Tildesley
ad74978a95
gnu: Add python-soupsieve, python2-soupsieve. 
* gnu/packages/python-xyz.scm (python-soupsieve): New variable.
(python2-soupsieve): New variable.

Signed-off-by: Danny Milosavljevic <dannym@scratchpost.org>
 2019-05-05 14:44:20 +02:00
Brendan Tildesley
b01cde1ac9
gnu: calibre: Disable tests that require networking. 
* gnu/packages/ebook.scm (calibre)[arguments]<#:phases>[configure]: Modify.

Signed-off-by: Danny Milosavljevic <dannym@scratchpost.org>
 2019-05-05 14:44:20 +02:00
Brendan Tildesley
15871b4087
gnu: calibre: Remove unrar test. 
* gnu/packages/patches/calibre-remove-test-unrar.patch: New file.
* gnu/packages/ebook.scm (calibre)[source]: Use it.
* gnu/local.mk (dist_patch_DATA): Add it.

Signed-off-by: Danny Milosavljevic <dannym@scratchpost.org>
 2019-05-05 14:44:20 +02:00
Brendan Tildesley
c187c9d786
gnu: python-regex, python2-regex: Update to 2019.04.14. 
* gnu/packages/python.scm (python-regex, python2-regex): Update to 2019.04.14.

Signed-off-by: Danny Milosavljevic <dannym@scratchpost.org>
 2019-05-05 14:44:20 +02:00
Brendan Tildesley
adc25b68b1
gnu: calibre: Add python2-html2text as an input. 
* gnu/packages/ebook.scm (calibre)[inputs]: Add python2-html2text.

Signed-off-by: Danny Milosavljevic <dannym@scratchpost.org>
 2019-05-05 14:44:20 +02:00
Brendan Tildesley
7a82ceb7bb
gnu: Add python-html2text, python2-html2text. 
* gnu/packages/python-web.scm (python-html2text): New variable.
(python2-html2text): New variable.

Signed-off-by: Danny Milosavljevic <dannym@scratchpost.org>
 2019-05-05 14:44:20 +02:00
Brendan Tildesley
13068a8ccf
gnu: calibre: Move font unbundling to after check phase. 
* gnu/packages/ebook.scm (calibre)[snippet]: Modify.
[native-inputs]: Remove font-liberation.
[inputs]: Add font-liberation.
[arguments]<#:phases>[install-font-liberation]: Delete phase.
[unbundle-font-liberation]: New phase.

Signed-off-by: Danny Milosavljevic <dannym@scratchpost.org>
 2019-05-05 14:44:20 +02:00
Brendan Tildesley
4f29902080
gnu: calibre: Add missing dependencies as indicated by tests. 
* gnu/packages/ebook.scm (calibre)[inputs]: Add python2-html5lib,
python2-psutil.

Signed-off-by: Danny Milosavljevic <dannym@scratchpost.org>
 2019-05-05 14:44:20 +02:00