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Author SHA1 Message Date
Ricardo Wurmus 0840352835
gnu: r-hdf5array: Update to 1.8.0. 
* gnu/packages/bioinformatics.scm (r-hdf5array): Update to 1.8.0.
 2018-06-02 13:39:12 +02:00
Ricardo Wurmus 5cd725d002
gnu: r-qvalue: Update to 2.12.0. 
* gnu/packages/bioinformatics.scm (r-qvalue): Update to 2.12.0.
 2018-06-02 13:39:12 +02:00
Ricardo Wurmus c6c619c179
gnu: r-hitc: Update to 1.24.0. 
* gnu/packages/bioinformatics.scm (r-hitc): Update to 1.24.0.
 2018-06-02 13:39:12 +02:00
Ricardo Wurmus 4dedecbe70
gnu: r-fithic: Update to 1.6.0. 
* gnu/packages/bioinformatics.scm (r-fithic): Update to 1.6.0.
 2018-06-02 13:39:12 +02:00
Ricardo Wurmus 8db6256f4b
gnu: r-sushi: Update to 1.18.0. 
* gnu/packages/bioinformatics.scm (r-sushi): Update to 1.18.0.
 2018-06-02 13:39:12 +02:00
Ricardo Wurmus 2d3c172b72
gnu: r-gwascat: Update to 2.12.0. 
* gnu/packages/bioinformatics.scm (r-gwascat): Update to 2.12.0.
 2018-06-02 13:39:12 +02:00
Ricardo Wurmus fecbbac286
gnu: r-gviz: Update to 1.24.0. 
* gnu/packages/bioinformatics.scm (r-gviz): Update to 1.24.0.
 2018-06-02 13:39:12 +02:00
Ricardo Wurmus 6929b97583
gnu: r-gqtlstats: Update to 1.12.0. 
* gnu/packages/bioinformatics.scm (r-gqtlstats): Update to 1.12.0.
[propagated-inputs]: Add r-homo-sapiens; remove r-ldblock.
 2018-06-02 13:39:12 +02:00
Ricardo Wurmus 45c29a6e5c
gnu: r-ldblock: Update to 1.10.0. 
* gnu/packages/bioinformatics.scm (r-ldblock): Update to 1.10.0.
[propagated-inputs]: Add r-biocgenerics.
 2018-06-02 13:39:12 +02:00
Ricardo Wurmus 9b0b108ed9
gnu: r-erma: Update to 0.12.0. 
* gnu/packages/bioinformatics.scm (r-erma): Update to 0.12.0.
[propagated-inputs]: Remove r-foreach; add r-biocparallel, r-genomeinfodb, and
r-iranges.
 2018-06-02 13:39:12 +02:00
Ricardo Wurmus d26f95d079
gnu: r-snpstats: Update to 1.30.0. 
* gnu/packages/bioinformatics.scm (r-snpstats): Update to 1.30.0.
 2018-06-02 13:39:12 +02:00
Ricardo Wurmus dcd1f0236c
gnu: r-gqtlbase: Update to 1.12.0. 
* gnu/packages/bioinformatics.scm (r-gqtlbase): Update to 1.12.0.
 2018-06-02 13:39:12 +02:00
Ricardo Wurmus e214a6e6ff
gnu: r-ggbio: Update to 1.28.0. 
* gnu/packages/bioinformatics.scm (r-ggbio): Update to 1.28.0.
 2018-06-02 13:39:11 +02:00
Ricardo Wurmus 34cc18d4de
gnu: r-biovizbase: Update to 1.28.0. 
* gnu/packages/bioinformatics.scm (r-biovizbase): Update to 1.28.0.
 2018-06-02 13:39:11 +02:00
Ricardo Wurmus 94ae875c0a
gnu: r-organismdbi: Update to 1.22.0. 
* gnu/packages/bioinformatics.scm (r-organismdbi): Update to 1.22.0.
 2018-06-02 13:39:11 +02:00
Ricardo Wurmus bbcd19fb4d
gnu: r-ensembldb: Update to 2.4.1. 
* gnu/packages/bioinformatics.scm (r-ensembldb): Update to 2.4.1.
[propagated-inputs]: Remove r-annotationhub.
 2018-06-02 13:39:11 +02:00
Ricardo Wurmus 19adb89854
gnu: r-dirichletmultinomial: Update to 1.22.0. 
* gnu/packages/bioinformatics.scm (r-dirichletmultinomial): Update to 1.22.0.
 2018-06-02 13:39:11 +02:00
Ricardo Wurmus d3fb2ad834
gnu: r-complexheatmap: Update to 1.18.0. 
* gnu/packages/bioinformatics.scm (r-complexheatmap): Update to 1.18.0.
 2018-06-02 13:39:11 +02:00
Ricardo Wurmus d1463f1b0c
gnu: r-genomicfiles: Update to 1.16.0. 
* gnu/packages/bioinformatics.scm (r-genomicfiles): Update to 1.16.0.
 2018-06-02 13:39:11 +02:00
Ricardo Wurmus 1ba126e0e4
gnu: r-gage: Update to 2.30.0. 
* gnu/packages/bioinformatics.scm (r-gage): Update to 2.30.0.
 2018-06-02 13:39:11 +02:00
Ricardo Wurmus 419e438d52
gnu: r-keggrest: Update to 1.20.0. 
* gnu/packages/bioinformatics.scm (r-keggrest): Update to 1.20.0.
 2018-06-02 13:39:11 +02:00
Ricardo Wurmus 15cc1a6867
gnu: r-fastseg: Update to 1.26.0. 
* gnu/packages/bioinformatics.scm (r-fastseg): Update to 1.26.0.
 2018-06-02 13:39:11 +02:00
Ricardo Wurmus 646439c7e3
gnu: r-annotationhub: Update to 2.12.0. 
* gnu/packages/bioinformatics.scm (r-annotationhub): Update to 2.12.0.
 2018-06-02 13:39:11 +02:00
Ricardo Wurmus 420415b057
gnu: r-interactivedisplaybase: Update to 1.18.0. 
* gnu/packages/bioinformatics.scm (r-interactivedisplaybase): Update to 1.18.0.
 2018-06-02 13:39:11 +02:00
Ricardo Wurmus a67dd4c5e9
gnu: r-edaseq: Update to 2.14.0. 
* gnu/packages/bioinformatics.scm (r-edaseq): Update to 2.14.0.
 2018-06-02 13:39:11 +02:00
Ricardo Wurmus 749b712677
gnu: r-deseq: Update to 1.32.0. 
* gnu/packages/bioinformatics.scm (r-deseq): Update to 1.32.0.
 2018-06-02 13:39:11 +02:00
Ricardo Wurmus 0ebd7a4c9f
gnu: r-aroma-light: Update to 3.10.0. 
* gnu/packages/bioinformatics.scm (r-aroma-light): Update to 3.10.0.
 2018-06-02 13:39:11 +02:00
Ricardo Wurmus bdc8b40af2
gnu: r-msnid: Update to 1.14.0. 
* gnu/packages/bioinformatics.scm (r-msnid): Update to 1.14.0.
 2018-06-02 13:39:10 +02:00
Ricardo Wurmus 250d78eac9
gnu: r-msnbase: Update to 2.6.1. 
* gnu/packages/bioinformatics.scm (r-msnbase): Update to 2.6.1.
[propagated-inputs]: Add r-mass and r-scales.
 2018-06-02 13:39:10 +02:00
Ricardo Wurmus 0f773b90db
gnu: r-pcamethods: Update to 1.72.0. 
* gnu/packages/bioinformatics.scm (r-pcamethods): Update to 1.72.0.
 2018-06-02 13:39:10 +02:00
Ricardo Wurmus 7bd2582971
gnu: r-mzid: Update to 1.18.0. 
* gnu/packages/bioinformatics.scm (r-mzid): Update to 1.18.0.
 2018-06-02 13:39:10 +02:00
Ricardo Wurmus af8710624d
gnu: r-vsn: Update to 3.48.1. 
* gnu/packages/bioinformatics.scm (r-vsn): Update to 3.48.1.
 2018-06-02 13:39:10 +02:00
Ricardo Wurmus 5837f1835b
gnu: r-affy: Update to 1.58.0. 
* gnu/packages/bioinformatics.scm (r-affy): Update to 1.58.0.
[inputs]: Add zlib.
 2018-06-02 13:39:10 +02:00
Ricardo Wurmus 82589f7430
gnu: r-affyio: Update to 1.50.0. 
* gnu/packages/bioinformatics.scm (r-affyio): Update to 1.50.0.
 2018-06-02 13:39:10 +02:00
Ricardo Wurmus 39cc491790
gnu: r-mzr: Update to 2.14.0. 
* gnu/packages/bioinformatics.scm (r-mzr): Update to 2.14.0.
[inputs]: Add zlib.
[propagated-inputs]: Add r-rhdf5lib.
 2018-06-02 13:39:10 +02:00
Ricardo Wurmus a02b82088f
gnu: r-protgenerics: Update to 1.12.0. 
* gnu/packages/bioinformatics.scm (r-protgenerics): Update to 1.12.0.
 2018-06-02 13:39:10 +02:00
Ricardo Wurmus 9547dd8613
gnu: r-sva: Update to 3.28.0. 
* gnu/packages/bioinformatics.scm (r-sva): Update to 3.28.0.
 2018-06-02 13:39:10 +02:00
Ricardo Wurmus 19ad568e79
gnu: r-methylkit: Update to 1.6.0. 
* gnu/packages/bioinformatics.scm (r-methylkit): Update to 1.6.0.
 2018-06-02 13:39:10 +02:00
Ricardo Wurmus aae4f716da
gnu: r-copywriter: Update to 2.12.0. 
* gnu/packages/bioinformatics.scm (r-copywriter): Update to 2.12.0.
 2018-06-02 13:39:10 +02:00
Ricardo Wurmus 8f94487da7
gnu: r-chipseq: Update to 1.30.0. 
* gnu/packages/bioinformatics.scm (r-chipseq): Update to 1.30.0.
 2018-06-02 13:39:10 +02:00
Ricardo Wurmus 62509bbc81
gnu: r-annotationfilter: Update to 1.4.0. 
* gnu/packages/bioinformatics.scm (r-annotationfilter): Update to 1.4.0.
 2018-06-02 13:39:10 +02:00
Ricardo Wurmus d73c5728f3
gnu: r-rhdf5: Update to 2.24.0. 
* gnu/packages/bioinformatics.scm (r-rhdf5): Update to 2.24.0.
[arguments]: Remove.
[propagated-inputs]: Remove r-zlibbioc; add r-rhdf5lib.
[inputs]: Remove perl.
 2018-06-02 13:39:10 +02:00
Ricardo Wurmus c76e8baf9e
gnu: r-tximport: Update to 1.8.0. 
* gnu/packages/bioinformatics.scm (r-tximport): Update to 1.8.0.
 2018-06-02 13:39:10 +02:00
Ricardo Wurmus b6c2c8f781
gnu: r-mutationalpatterns: Update to 1.6.1. 
* gnu/packages/bioinformatics.scm (r-mutationalpatterns): Update to 1.6.1.
 2018-06-02 13:39:09 +02:00
Ricardo Wurmus 72f11ff9c5
gnu: r-bamsignals: Update to 1.12.0. 
* gnu/packages/bioinformatics.scm (r-bamsignals): Update to 1.12.0.
 2018-06-02 13:39:09 +02:00
Ricardo Wurmus 1a08bb8a17
gnu: r-rhtslib: Update to 1.12.1. 
* gnu/packages/bioinformatics.scm (r-rhtslib): Update to 1.12.1.
[native-inputs]: Remove autoconf.
 2018-06-02 13:39:09 +02:00
Ricardo Wurmus 2c480bb012
gnu: r-zlibbioc: Update to 1.26.0. 
* gnu/packages/bioinformatics.scm (r-zlibbioc): Update to 1.26.0.
 2018-06-02 13:39:09 +02:00
Ricardo Wurmus 7e6537e257
gnu: r-motifrg: Update to 1.24.0. 
* gnu/packages/bioinformatics.scm (r-motifrg): Update to 1.24.0.
 2018-06-02 13:39:09 +02:00
Ricardo Wurmus 8217c2d0bc
gnu: r-seqlogo: Update to 1.46.0. 
* gnu/packages/bioinformatics.scm (r-seqlogo): Update to 1.46.0.
 2018-06-02 13:39:09 +02:00
Ricardo Wurmus 17d35de73f
gnu: r-genomation: Update to 1.12.0. 
* gnu/packages/bioinformatics.scm (r-genomation): Update to 1.12.0.
 2018-06-02 13:39:09 +02:00
Ricardo Wurmus 5229cedf57
gnu: r-seqpattern: Update to 1.12.0. 
* gnu/packages/bioinformatics.scm (r-seqpattern): Update to 1.12.0.
 2018-06-02 13:39:09 +02:00
Ricardo Wurmus 25d1df5764
gnu: r-impute: Update to 1.54.0. 
* gnu/packages/bioinformatics.scm (r-impute): Update to 1.54.0.
 2018-06-02 13:39:09 +02:00
Ricardo Wurmus 89ef133ebd
gnu: r-bsgenome: Update to 1.48.0. 
* gnu/packages/bioinformatics.scm (r-bsgenome): Update to 1.48.0.
 2018-06-02 13:39:09 +02:00
Ricardo Wurmus f2eb2e453e
gnu: r-topgo: Update to 2.32.0. 
* gnu/packages/bioinformatics.scm (r-topgo): Update to 2.32.0.
 2018-06-02 13:39:09 +02:00
Ricardo Wurmus 2f66fecd89
gnu: r-graph: Update to 1.58.0. 
* gnu/packages/bioinformatics.scm (r-graph): Update to 1.58.0.
 2018-06-02 13:39:09 +02:00
Ricardo Wurmus b4ad4ec6b4
gnu: r-genomicfeatures: Update to 1.32.0. 
* gnu/packages/bioinformatics.scm (r-genomicfeatures): Update to 1.32.0.
[propagated-inputs]: Remove r-rmysql.
 2018-06-02 13:39:09 +02:00
Ricardo Wurmus a30df29768
gnu: r-rtracklayer: Update to 1.40.2. 
* gnu/packages/bioinformatics.scm (r-rtracklayer): Update to 1.40.2.
[native-inputs]: Add pkg-config.
 2018-06-02 13:39:09 +02:00
Ricardo Wurmus 90102bd06b
gnu: r-genomicalignments: Update to 1.16.0. 
* gnu/packages/bioinformatics.scm (r-genomicalignments): Update to 1.16.0.
 2018-06-02 13:39:09 +02:00
Ricardo Wurmus 9bf4110ea1
gnu: r-summarizedexperiment: Update to 1.10.1. 
* gnu/packages/bioinformatics.scm (r-summarizedexperiment): Update to 1.10.1.
 2018-06-02 13:39:08 +02:00
Ricardo Wurmus 82f593f378
gnu: r-delayedarray: Update to 0.6.0. 
* gnu/packages/bioinformatics.scm (r-delayedarray): Update to 0.6.0.
[propagated-inputs]: Add r-biocparallel.
 2018-06-02 13:39:08 +02:00
Ricardo Wurmus d2367a89dd
gnu: r-rsamtools: Update to 1.32.0. 
* gnu/packages/bioinformatics.scm (r-rsamtools): Update to 1.32.0.
 2018-06-02 13:39:08 +02:00
Ricardo Wurmus 942655add1
gnu: r-biostrings: Update to 2.48.0. 
* gnu/packages/bioinformatics.scm (r-biostrings): Update to 2.48.0.
 2018-06-02 13:39:08 +02:00
Ricardo Wurmus e6eac58d4c
gnu: r-biocparallel: Update to 1.14.1. 
* gnu/packages/bioinformatics.scm (r-biocparallel): Update to 1.14.1.
 2018-06-02 13:39:08 +02:00
Ricardo Wurmus 1763cba80e
gnu: r-biomart: Update to 2.36.1. 
* gnu/packages/bioinformatics.scm (r-biomart): Update to 2.36.1.
 2018-06-02 13:39:08 +02:00
Ricardo Wurmus 77f66feee7
gnu: r-annotationdbi: Update to 1.42.1. 
* gnu/packages/bioinformatics.scm (r-annotationdbi): Update to 1.42.1.
 2018-06-02 13:39:08 +02:00
Ricardo Wurmus 6fd71f1b6a
gnu: r-biobase: Update to 2.40.0. 
* gnu/packages/bioinformatics.scm (r-biobase): Update to 2.40.0.
 2018-06-02 13:39:08 +02:00
Ricardo Wurmus e51afc63b7
gnu: r-genomicranges: Update to 1.32.3. 
* gnu/packages/bioinformatics.scm (r-genomicranges): Update to 1.32.3.
 2018-06-02 13:39:08 +02:00
Ricardo Wurmus c2401d06c5
gnu: r-xvector: Update to 0.20.0. 
* gnu/packages/bioinformatics.scm (r-xvector): Update to 0.20.0.
 2018-06-02 13:39:08 +02:00
Ricardo Wurmus 0a465e5694
gnu: r-limma: Update to 3.36.1. 
* gnu/packages/bioinformatics.scm (r-limma): Update to 3.36.1.
 2018-06-02 13:39:08 +02:00
Ricardo Wurmus d358a5a0c1
gnu: r-variantannotation: Update to 1.26.0. 
* gnu/packages/bioinformatics.scm (r-variantannotation): Update to 1.26.0.
 2018-06-02 13:39:08 +02:00
Ricardo Wurmus 4639025284
gnu: r-edger: Update to 3.22.2. 
* gnu/packages/bioinformatics.scm (r-edger): Update to 3.22.2.
 2018-06-02 13:39:08 +02:00
Ricardo Wurmus 953c8b18f8
gnu: r-genomeinfodb: Update to 1.16.0. 
* gnu/packages/bioinformatics.scm (r-genomeinfodb): Update to 1.16.0.
 2018-06-02 13:39:08 +02:00
Ricardo Wurmus 8b44c28f5d
gnu: r-iranges: Update to 2.14.10. 
* gnu/packages/bioinformatics.scm (r-iranges): Update to 2.14.10.
 2018-06-02 13:39:08 +02:00
Ricardo Wurmus 33cd15fa84
gnu: r-s4vectors: Update to 0.18.2. 
* gnu/packages/bioinformatics.scm (r-s4vectors): Update to 0.18.2.
 2018-06-02 13:39:08 +02:00
Ricardo Wurmus 607acf3194
gnu: r-dnacopy: Update to 1.54.0. 
* gnu/packages/bioinformatics.scm (r-dnacopy): Update to 1.54.0.
 2018-06-02 13:39:07 +02:00
Ricardo Wurmus 3679a2fec4
gnu: r-bioccheck: Update to 1.16.0. 
* gnu/packages/bioinformatics.scm (r-bioccheck): Update to 1.16.0.
 2018-06-02 13:39:07 +02:00
Ricardo Wurmus dc6c168ac1
gnu: r-biocstyle: Update to 2.8.2. 
* gnu/packages/bioinformatics.scm (r-biocstyle): Update to 2.8.2.
 2018-06-02 13:39:07 +02:00
Ricardo Wurmus e5f52b692a
gnu: r-biocviews: Update to 1.48.0. 
* gnu/packages/bioinformatics.scm (r-biocviews): Update to 1.48.0.
 2018-06-02 13:39:07 +02:00
Ricardo Wurmus 97af51ef40
gnu: r-biocinstaller: Update to 1.30.0. 
* gnu/packages/bioinformatics.scm (r-biocinstaller): Update to 1.30.0.
 2018-06-02 13:39:07 +02:00
Ricardo Wurmus e5907a44e1
gnu: r-biocgenerics: Update to 0.26.0. 
* gnu/packages/bioinformatics.scm (r-biocgenerics): Update to 0.26.0.
 2018-06-02 13:39:07 +02:00
Ricardo Wurmus 9370b8ee9f
gnu: r-grohmm: Update to 1.14.0. 
* gnu/packages/bioinformatics.scm (r-grohmm): Update to 1.14.0.
 2018-06-02 13:39:07 +02:00
Ricardo Wurmus 712fe39680
gnu: r-systempiper: Update to 1.14.0. 
* gnu/packages/bioinformatics.scm (r-systempiper): Update to 1.14.0.
 2018-06-02 13:39:07 +02:00
Ricardo Wurmus eabe78faca
gnu: r-shortread: Update to 1.38.0. 
* gnu/packages/bioinformatics.scm (r-shortread): Update to 1.38.0.
 2018-06-02 13:39:07 +02:00
Ricardo Wurmus 9da8e275ca
gnu: r-gostats: Update to 2.46.0. 
* gnu/packages/bioinformatics.scm (r-gostats): Update to 2.46.0.
 2018-06-02 13:39:07 +02:00
Ricardo Wurmus d8410d6610
gnu: r-category: Update to 2.46.0. 
* gnu/packages/bioinformatics.scm (r-category): Update to 2.46.0.
 2018-06-02 13:39:07 +02:00
Ricardo Wurmus f1094f50a7
gnu: r-gseabase: Update to 1.42.0. 
* gnu/packages/bioinformatics.scm (r-gseabase): Update to 1.42.0.
 2018-06-02 13:39:07 +02:00
Ricardo Wurmus 9177ac2295
gnu: r-rbgl: Update to 1.56.0. 
* gnu/packages/bioinformatics.scm (r-rbgl): Update to 1.56.0.
 2018-06-02 13:39:07 +02:00
Ricardo Wurmus 5516db9e70
gnu: r-annotationforge: Update to 1.22.0. 
* gnu/packages/bioinformatics.scm (r-annotationforge): Update to 1.22.0.
 2018-06-02 13:39:07 +02:00
Ricardo Wurmus 16da69b5e6
gnu: r-dexseq: Update to 1.26.0. 
* gnu/packages/bioinformatics.scm (r-dexseq): Update to 1.26.0.
 2018-06-02 13:39:07 +02:00
Ricardo Wurmus 51c1f96ebc
gnu: r-deseq2: Update to 1.20.0. 
* gnu/packages/bioinformatics.scm (r-deseq2): Update to 1.20.0.
 2018-06-02 13:39:07 +02:00
Ricardo Wurmus 41657b15f4
gnu: r-genefilter: Update to 1.62.0. 
* gnu/packages/bioinformatics.scm (r-genefilter): Update to 1.62.0.
 2018-06-02 13:39:06 +02:00
Ricardo Wurmus 4d70c8c486
gnu: r-geneplotter: Update to 1.58.0. 
* gnu/packages/bioinformatics.scm (r-geneplotter): Update to 1.58.0.
 2018-06-02 13:39:06 +02:00
Ricardo Wurmus 14e9235f0c
gnu: r-copynumber: Update to 1.20.0. 
* gnu/packages/bioinformatics.scm (r-copynumber): Update to 1.20.0.
 2018-06-02 13:39:06 +02:00
Ricardo Wurmus 02be818044
gnu: r-annotate: Update to 1.58.0. 
* gnu/packages/bioinformatics.scm (r-annotate): Update to 1.58.0.
 2018-06-02 13:39:06 +02:00
Ricardo Wurmus 81b0181b6f
gnu: r-qdnaseq: Update to 1.16.0. 
* gnu/packages/bioconductor.scm (r-qdnaseq): Update to 1.16.0.
[propagated-inputs]: Add r-biocparallel.
 2018-06-02 13:39:06 +02:00
Ricardo Wurmus 5c0df206cf
gnu: r-cghcall: Update to 2.42.0. 
* gnu/packages/bioconductor.scm (r-cghcall): Update to 2.42.0.
 2018-06-02 13:39:06 +02:00
Ricardo Wurmus 205df4a4cb
gnu: r-cghbase: Update to 1.40.0. 
* gnu/packages/bioconductor.scm (r-cghbase): Update to 1.40.0.
 2018-06-02 13:39:06 +02:00
Ricardo Wurmus 6748708883
gnu: r-marray: Update to 1.58.0. 
* gnu/packages/bioconductor.scm (r-marray): Update to 1.58.0.
[propagated-inputs]: Remove r-biobase.
 2018-06-02 13:39:06 +02:00
Ricardo Wurmus f794e85daa
gnu: r-chippeakanno: Update to 3.14.0. 
* gnu/packages/bioconductor.scm (r-chippeakanno): Update to 3.14.0.
[propagated-inputs]: Add r-biostrings, r-delayedarray, r-genomicranges,
r-iranges, and r-s4vectors.
 2018-06-02 13:39:06 +02:00
Ricardo Wurmus 43734b4727
gnu: r-ripseeker: Update to 1.20.0. 
* gnu/packages/bioconductor.scm (r-ripseeker): Update to 1.20.0.
 2018-06-02 13:39:06 +02:00
Ricardo Wurmus 45bbccf4e7
gnu: r-diffbind: Update to 2.8.0. 
* gnu/packages/bioconductor.scm (r-diffbind): Update to 2.8.0.
[propagated-inputs]: Add r-genomicranges, r-ggplot2, and
r-summarizedexperiment.
 2018-06-02 13:39:06 +02:00
Ricardo Wurmus 72427c721d
gnu: r-regioner: Update to 1.12.0. 
* gnu/packages/bioconductor.scm (r-regioner): Update to 1.12.0.
[propagated-inputs]: Add r-s4vectors.
 2018-06-02 13:39:06 +02:00
Ricardo Wurmus 2f5b3d8e90
gnu: r-hpar: Update to 1.22.2. 
* gnu/packages/bioconductor.scm (r-hpar): Update to 1.22.2.
 2018-06-02 13:39:06 +02:00
Ricardo Wurmus d22546cf80
gnu: r-minimal: Update to 3.5.0. 
* gnu/packages/statistics.scm (r-with-tests): New variable derived from
r-minimal; update to 3.5.0.
[arguments]: Build recommended packages.
(r-minimal): Inherit from r-with-tests.
[arguments]: Disable recommended packages and tests.
 2018-06-02 13:39:06 +02:00
Clément Lassieur d5452aa201
gnu: emacs-elfeed: Update to 3.0.0. 
* gnu/packages/emacs.scm (emacs-elfeed): Update to 3.0.0.
 2018-06-02 13:05:08 +02:00
Mark H Weaver 1a3e3162ac
gnu: icecat: Add more fixes from upstream esr52. 
* gnu/packages/gnuzilla.scm (icecat)[source]: Add selected fixes from
the upstream mozilla-esr52 repository.
 2018-06-01 12:51:43 -04:00
Ricardo Wurmus 65a9f6b6cf
gnu: qtbase: Fix build on older kernels. 
* gnu/packages/qt.scm (qtbase)[arguments]: Add configure flags
"-no-feature-getentropy" and "-no-feature-renameat2".
 2018-06-01 17:33:25 +02:00
Ludovic Courtès 9f160a0d3c
vm: Use 'with-extensions'. 
* gnu/system/vm.scm (system-docker-image)[build]: Use
'with-extensions'.  Remove 'add-to-load-path' calls.
 2018-06-01 15:21:28 +02:00
Ludovic Courtès 33d8a87104
bootloader: grub: Use 'with-extensions'. 
* gnu/bootloader/grub.scm (svg->png): Use 'with-extensions'.  Remove
'add-to-load-path' calls.
* gnu/build/svg.scm: Use (rsvg) and (cairo) the normal way.  Remove
'module-autoload!' calls.
 2018-06-01 15:21:28 +02:00
Ludovic Courtès 31a5d694a3
bootloader: grub: Simplify 'svg->png'. 
* gnu/bootloader/grub.scm (svg->png): Remove now unneeded
  #:guile-for-build argument.
 2018-06-01 15:21:28 +02:00
Ludovic Courtès ff913cf514
tests: ssh: Use 'with-extensions'. 
* gnu/tests/ssh.scm (run-ssh-test)[test]: Wrap body in
'with-extensions'.  Remove %load-path manipulation code.
 2018-06-01 15:21:28 +02:00
Robin Templeton 514026d7de
gnu: rust: Add support for building 32-bit packages on 64-bit hosts. 
* gnu/packages/rust.scm (rust-bootstrap, rust-1.23): Use
nix-system->gnu-triplet to determine the system type.
(rust-1.19): Use readelf instead of nm in the atomic-lock-free test.
(rust-1.23): Disable the cargo_test_env test. Disable parallel execution of
tests.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2018-06-01 13:50:27 +02:00
Timothy Sample a078a6ec3b
gnu: Add git-annex. 
* gnu/packages/version-control.scm (git-annex): New variable.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2018-06-01 13:50:27 +02:00
Timothy Sample 4e5d9bf20e
gnu: Add ghc-disk-free-space. 
* gnu/packages/haskell.scm (ghc-disk-free-space): New variable.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2018-06-01 13:50:27 +02:00
Timothy Sample 1ea3971992
gnu: ghc-psqueues: Allow building with newer versions of QuickCheck. 
* gnu/packages/haskell.scm (ghc-psqueues)[arguments]: Add configure
flag to allow newer versions of QuickCheck.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2018-06-01 13:50:27 +02:00
Timothy Sample 6950a45073
gnu: Add ghc-safesemaphore. 
* gnu/packages/haskell.scm (ghc-safesemaphore): New variable.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2018-06-01 13:50:27 +02:00
Timothy Sample 92c2097bc2
gnu: Add ghc-esqueleto. 
* gnu/packages/haskell.scm (ghc-esqueleto): New variable.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2018-06-01 13:50:26 +02:00
Timothy Sample a39e6faee9
gnu: Add ghc-ifelse. 
* gnu/packages/haskell.scm (ghc-ifelse): New variable.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2018-06-01 13:50:26 +02:00
Timothy Sample e3aae496f9
gnu: Add ghc-feed. 
* gnu/packages/haskell.scm (ghc-feed): New variable.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2018-06-01 13:50:26 +02:00
Timothy Sample 4c798726b4
gnu: Add ghc-bloomfilter. 
* gnu/package/haskell.scm (ghc-bloomfilter): New variable.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2018-06-01 13:50:26 +02:00
Rouby Pierre-Antoine 93b83eb31e
services: Add hpcguix-web. 
* gnu/service/web.scm (<hpcguix-web-configuration>): New record-type.
  (%hpcguix-web-accounts): New variable.
  (%hpcguix-web-activation,hpcguix-web-shepherd-service,
  hpcguix-web-service-type): New procedures.
* gnu/tests/web.scm (run-hpcguix-web-server-test): New procedure.
  (%hpcguix-web-specs, %hpcguix-web-os, %test-hpcguix-web): New variable.
* doc/guix.texi (Web Services): Add 'hpcguix-web'.

Co-authored-by: Ludovic Courtès <ludo@gnu.org>
 2018-06-01 13:50:26 +02:00
Rouby Pierre-Antoine d6a4dfec90
gnu: Add hpcguix-web. 
* gnu/package/web.scm (hpcguix-web): New variable.

Signed-off-by: Ludovic Courtès <ludovic.courtes@inria.fr>
 2018-06-01 13:50:26 +02:00
Ludovic Courtès 7a4e2eaab3
marionette: Add 'wait-for-tcp-port'. 
* gnu/build/marionette.scm (wait-for-tcp-port): New procedure.
* gnu/tests/dict.scm (run-dicod-test)["connect inside"]: Use it instead
of the inline loop.
 2018-06-01 13:50:26 +02:00
Ludovic Courtès 5ede50b850
gnu: emacs-w3m: Update and allow builds with Emacs 26. 
* gnu/packages/emacs.scm (emacs-w3m)[source]: Grab the source from
github.com.
[native-inputs]: Add TEXINFO.
[arguments]: Add 'support-emacs!' phase.  In 'patch-exec-paths' phase,
make w3m.el and w3m-image.el writable.  Remove substitution for
'w3m-image-viewer', which no longer exists.
 2018-06-01 13:50:26 +02:00
Stefan Stefanović 8674abb1dd
gnu: sddm: Fix CMake build. 
* gnu/packages/display-managers.scm (sddm): Fix CMake build.
* gnu/local.mk (dist_patch_DATA): Register it.
* gnu/packages/patches/sddm-fix-build-with-qt-5.11-1024.patch: New file.

Signed-off-by: Rutger Helling <rhelling@mykolab.com>
 2018-06-01 12:17:00 +02:00
Leo Famulari e90322d201
gnu: prosody: Update to 0.10.2 [fixes CVE-2018-10847]. 
* gnu/packages/messaging.scm (prosody): Update to 0.10.2.
 2018-05-31 20:31:46 -04:00
Konrad Hinsen 555ab0853b
gnu: Add emacs-zotxt. 
* gnu/packages/emacs.scm (emacs-zotxt): New variable.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2018-05-31 18:13:09 +02:00
Konrad Hinsen 45dca193a4
gnu: Add emacs-org-caldav. 
* gnu/packages/emacs.scm (emacs-org-caldav): New variable.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2018-05-31 18:13:08 +02:00
Konrad Hinsen ec8a9892d1
gnu: Add python-bigfloat. 
* gnu/packages/python.scm (python-bigfloat, python2-bigfloat): New
variables.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2018-05-31 18:13:08 +02:00
Fis Trivial 73d854232f
gnu: bear: Fix python path. 
* gnu/packages/build-tools.scm (bear)
[inputs]: Add python-wrapper.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2018-05-31 18:13:08 +02:00
Ludovic Courtès b1059b38b2
system: 'read-boot-parameters' provides a more meaningful warning. 
'system' here was bound to Guile's 'system' procedure.

* gnu/system.scm (read-boot-parameters): Fix argument for fallback
warning.
 2018-05-31 18:13:08 +02:00
Ludovic Courtès 69a05eab35
file-systems: Always wait for devices to show up. 
Previously, 'canonicalize-device-spec' would wait for devices when they
were specified as a label or UUID, but would not wait when the user
passed a "/dev" file name directly.  This could cause problems when
the /dev node takes a while to show up.

* gnu/build/file-systems.scm (canonicalize-device-spec): Add 'resolve'
call in the 'string?' case.
 2018-05-31 18:13:08 +02:00
Ricardo Wurmus 404e5c7d7d
gnu: r-servr: Update to 0.10. 
* gnu/packages/web.scm (r-servr): Update to 0.10.
[native-inputs]: Remove r-rcpp.
 2018-05-31 13:21:31 +02:00
Ricardo Wurmus ce8b9e3b1c
gnu: r-seurat: Update to 2.3.1. 
* gnu/packages/bioinformatics.scm (r-seurat): Update to 2.3.1.
[propagated-inputs]: Remove r-gridextra; add r-reticulate.
 2018-05-31 13:21:31 +02:00
Ricardo Wurmus 508dd24abe
gnu: r-shiny: Update to 1.1.0. 
* gnu/packages/web.scm (r-shiny): Update to 1.1.0.
[source]: Fetch from git.
[propagated-inputs]: Add r-crayon.
 2018-05-31 13:21:31 +02:00
Ricardo Wurmus eb0d599a67
gnu: r-rjson: Update to 0.2.19. 
* gnu/packages/web.scm (r-rjson): Update to 0.2.19.
 2018-05-31 13:21:31 +02:00
Ricardo Wurmus 71644c0ee8
gnu: r-htmltable: Update to 1.12. 
* gnu/packages/web.scm (r-htmltable): Update to 1.12.
 2018-05-31 13:21:31 +02:00
Ricardo Wurmus beb0878fe5
gnu: r-directlabels: Update to 2018.05.22. 
* gnu/packages/statistics.scm (r-directlabels): Update to 2018.05.22.
 2018-05-31 13:21:31 +02:00
Ricardo Wurmus 089e037638
gnu: r-ranger: Update to 0.10.0. 
* gnu/packages/statistics.scm (r-ranger): Update to 0.10.0.
 2018-05-31 13:21:31 +02:00
Ricardo Wurmus 14bb6f5f83
gnu: r-tclust: Update to 1.4-1. 
* gnu/packages/statistics.scm (r-tclust): Update to 1.4-1.
 2018-05-31 13:21:31 +02:00
Ricardo Wurmus 9fad62743c
gnu: r-caret: Update to 6.0-80. 
* gnu/packages/statistics.scm (r-caret): Update to 6.0-80.
 2018-05-31 13:21:31 +02:00
Ricardo Wurmus 9bcc68fbf6
gnu: r-quantreg: Update to 5.36. 
* gnu/packages/statistics.scm (r-quantreg): Update to 5.36.
 2018-05-31 13:21:31 +02:00
Ricardo Wurmus 13dc492435
gnu: r-rrcov: Update to 1.4-4. 
* gnu/packages/statistics.scm (r-rrcov): Update to 1.4-4.
 2018-05-31 13:21:31 +02:00
Ricardo Wurmus 6f96c2d89e
gnu: r-ggthemes: Update to 3.5.0. 
* gnu/packages/statistics.scm (r-ggthemes): Update to 3.5.0.
 2018-05-31 13:21:31 +02:00
Ricardo Wurmus 366dd8d7cb
gnu: r-runit: Update to 0.4.32. 
* gnu/packages/statistics.scm (r-runit): Update to 0.4.32.
 2018-05-31 13:21:31 +02:00
Ricardo Wurmus edb29f2986
gnu: r-purrr: Update to 0.2.5. 
* gnu/packages/statistics.scm (r-purrr): Update to 0.2.5.
 2018-05-31 13:21:31 +02:00
Ricardo Wurmus e94d827440
gnu: r-tidyr: Update to 0.8.1. 
* gnu/packages/statistics.scm (r-tidyr): Update to 0.8.1.
 2018-05-31 13:21:31 +02:00
Ricardo Wurmus 1957c20e0c
gnu: r-synchronicity: Update to 1.3.4. 
* gnu/packages/statistics.scm (r-synchronicity): Update to 1.3.4.
 2018-05-31 13:21:31 +02:00
Ricardo Wurmus 7da0790e2a
gnu: r-rngtools: Update to 1.3.1. 
* gnu/packages/statistics.scm (r-rngtools): Update to 1.3.1.
 2018-05-31 13:21:31 +02:00
Ricardo Wurmus 3a6051659d
gnu: r-pkgmaker: Update to 0.27. 
* gnu/packages/statistics.scm (r-pkgmaker): Update to 0.27.
[propagated-inputs]: Add r-bibtex, r-magrittr, r-stringi, and r-withr.
 2018-05-31 13:21:31 +02:00