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2020-12-20gnu: kentutils: Build with OpenSSL 1.1.Marius Bakke
* gnu/packages/bioinformatics.scm (kentutils)[inputs]: Change from OPENSSL-1.0 to OPENSSL.
2020-12-20gnu: kentutils: Add a file name for the "samtabix" input.Marius Bakke
* gnu/packages/bioinformatics.scm (kentutils)[native-inputs]: For "samtabix", add a file name on the origin.
2020-12-09gnu: r-keggrest: Update to 1.30.1.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-keggrest): Update to 1.30.1.
2020-12-09gnu: r-genomeinfodb: Update to 1.26.2.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-genomeinfodb): Update to 1.26.2.
2020-12-09gnu: r-biocstyle: Update to 2.18.1.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-biocstyle): Update to 2.18.1.
2020-12-09gnu: r-rhtslib: Propagate zlib.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-rhtslib)[inputs]: Move zlib from here... [propagated-inputs]: ...to here. (r-variantannotation, r-rsamtools, r-bamsignals, r-rhdf5, r-methylkit)[inputs]: Remove zlib. * gnu/packages/bioconductor.scm (r-diffbind, r-quasr, r-cytolib, r-ncdfflow, r-flowworkspace, r-seqbias)[inputs]: Remove zlib.
2020-12-09gnu: r-gqtlstats: Update to 1.21.3.zimoun
* gnu/packages/bioinformatics.scm (r-gqtlstats): Update to 1.21.3.
2020-12-09gnu: r-gqtlbase: Update to 1.21.1.zimoun
Co-authored-by: Ricardo Wurmus <rekado@elephly.net> * gnu/packages/bioinformatics.scm (r-gqtlbase): Update to 1.21.1. [arguments]: Add phase to patch broken NAMESPACE file.
2020-12-09gnu: r-biocviews: Update to 1.58.1.zimoun
* gnu/packages/bioinformatics.scm (r-biocviews): Update to 1.58.1. Co-authored-by: Ricardo Wurmus <reka@elephly.net>.
2020-12-09gnu: r-rhdf5: Update to 2.34.0.zimoun
* gnu/packages/bioinformatics.scm (r-rhdf5): Update to 2.34.0. [propagated-inputs]: Add r-rhdf5filters. [arguments]: Avoid to have a plain directory on the list of libraries to link. Co-authored-by: Ricardo Wurmus <reka@elephly.net>.
2020-12-09gnu: Add r-rhdf5filters.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-rhdf5filters): New variable.
2020-12-09gnu: r-genomationdata: Update to 1.22.0.zimoun
* gnu/packages/bioinformatics.scm (r-genomationdata): Update to 1.22.0.
2020-12-09gnu: r-sushi: Update to 1.28.0.zimoun
* gnu/packages/bioinformatics.scm (r-sushi): Update to 1.28.0.
2020-12-09gnu: r-gwascat: Update to 2.22.0.zimoun
* gnu/packages/bioinformatics.scm (r-gwascat): Update to 2.22.0. [propagated-inputs]: Add r-biocfilecache, r-readr, r-snpstats, and r-variantannotation; remove r-biocgenerics, r-ggplot2, r-rsamtools, and r-rtracklayer.
2020-12-09gnu: r-gviz: Update to 1.34.0.zimoun
* gnu/packages/bioinformatics.scm (r-gviz): Update to 1.34.0.
2020-12-09gnu: r-ldblock: Update to 1.20.0.zimoun
* gnu/packages/bioinformatics.scm (r-ldblock): Update to 1.20.0.
2020-12-09gnu: r-erma: Update to 1.6.0.zimoun
* gnu/packages/bioinformatics.scm (r-erma): Update to 1.6.0.
2020-12-09gnu: r-snpstats: Update to 1.40.0.zimoun
* gnu/packages/bioinformatics.scm (r-snpstats): Update to 1.40.0.
2020-12-09gnu: r-ggbio: Update to 1.38.0.zimoun
* gnu/packages/bioinformatics.scm (r-ggbio): Update to 1.38.0.
2020-12-09gnu: r-biovizbase: Update to 1.38.0.zimoun
* gnu/packages/bioinformatics.scm (r-biovizbase): Update to 1.38.0.
2020-12-09gnu: r-organismdbi: Update to 1.32.0.zimoun
* gnu/packages/bioinformatics.scm (r-organismdbi): Update to 1.32.0.
2020-12-09gnu: r-ensembldb: Update to 2.14.0.zimoun
* gnu/packages/bioinformatics.scm (r-ensembldb): Update to 2.14.0.
2020-12-09gnu: r-dirichletmultinomial: Update to 1.32.0.zimoun
* gnu/packages/bioinformatics.scm (r-dirichletmultinomial): Update to 1.32.0.
2020-12-09gnu: r-complexheatmap: Update to 2.6.2.Roel Janssen
* gnu/packages/bioinformatics.scm (r-complexheatmap): Update to 2.6.2; [propagated-inputs]: Add r-cairo, r-digest, r-iranges, r-matrixstats, and r-s4vectors.
2020-12-09gnu: r-genomicfiles: Update to 1.26.0.zimoun
* gnu/packages/bioinformatics.scm (r-genomicfiles): Update to 1.26.0. [propagated-inputs]: Add r-matrixgenerics.
2020-12-09gnu: r-gage: Update to 2.40.0.zimoun
* gnu/packages/bioinformatics.scm (r-gage): Update to 2.40.0.
2020-12-09gnu: r-keggrest: Update to 1.30.0.zimoun
* gnu/packages/bioinformatics.scm (r-keggrest): Update to 1.30.0.
2020-12-09gnu: r-fastseg: Update to 1.36.0.zimoun
* gnu/packages/bioinformatics.scm (r-fastseg): Update to 1.36.0.
2020-12-09gnu: r-annotationhub: Update to 2.22.0.zimoun
* gnu/packages/bioinformatics.scm (r-annotationhub): Update to 2.22.0.
2020-12-09gnu: r-interactivedisplaybase: Update to 1.28.0.zimoun
* gnu/packages/bioinformatics.scm (r-interactivedisplaybase): Update to 1.28.0.
2020-12-09gnu: r-edaseq: Update to 2.24.0.zimoun
* gnu/packages/bioinformatics.scm (r-edaseq): Update to 2.24.0.
2020-12-09gnu: r-aroma-light: Update to 3.20.0.zimoun
* gnu/packages/bioinformatics.scm (r-aroma-light): Update to 3.20.0.
2020-12-09gnu: r-msnid: Update to 1.24.0.zimoun
* gnu/packages/bioinformatics.scm (r-msnid): Update to 1.24.0. [propagated-inputs]: Add r-annotationdbi, r-annotationhub, r-biocgenerics, r-biocstyle, r-biostrings, r-ggplot2, r-msmstests, r-purrr, r-rlang, r-runit, r-stringr, r-tibble, and r-xtable.
2020-12-09gnu: r-pcamethods: Update to 1.82.0.zimoun
* gnu/packages/bioinformatics.scm (r-pcamethods): Update to 1.82.0.
2020-12-09gnu: r-mzid: Update to 1.28.0.zimoun
* gnu/packages/bioinformatics.scm (r-mzid): Update to 1.28.0. [propagated-inputs]: Remove r-rcpp.
2020-12-09gnu: r-vsn: Update to 3.58.0.zimoun
* gnu/packages/bioinformatics.scm (r-vsn): Update to 3.58.0.
2020-12-09gnu: r-affy: Update to 1.68.0.zimoun
* gnu/packages/bioinformatics.scm (r-affy): Update to 1.68.0.
2020-12-09gnu: r-affyio: Update to 1.60.0.zimoun
* gnu/packages/bioinformatics.scm (r-affyio): Update to 1.60.0.
2020-12-09gnu: r-mzr: Fix linking.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-mzr)[arguments]: Fix linking with rhdf5 libraries.
2020-12-09gnu: r-mzr: Update to 2.24.1.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-mzr): Update to 2.24.1.
2020-12-09gnu: r-protgenerics: Update to 1.22.0.zimoun
* gnu/packages/bioinformatics.scm (r-protgenerics): Update to 1.22.0.
2020-12-09gnu: r-sva: Update to 3.38.0.zimoun
* gnu/packages/bioinformatics.scm (r-sva): Update to 3.38.0.
2020-12-09gnu: r-methylkit: Update to 1.16.0.zimoun
* gnu/packages/bioinformatics.scm (r-methylkit): Update to 1.16.0.
2020-12-09gnu: r-copywriter: Update to 2.22.0.zimoun
* gnu/packages/bioinformatics.scm (r-copywriter): Update to 2.22.0.
2020-12-09gnu: r-chipseq: Update to 1.40.0.zimoun
* gnu/packages/bioinformatics.scm (r-chipseq): Update to 1.40.0.
2020-12-09gnu: r-annotationfilter: Update to 1.14.0.zimoun
* gnu/packages/bioinformatics.scm (r-annotationfilter): Update to 1.14.0.
2020-12-09gnu: r-tximport: Update to 1.18.0.zimoun
* gnu/packages/bioinformatics.scm (r-tximport): Update to 1.18.0.
2020-12-09gnu: r-mutationalpatterns: Update to 3.0.1.Roel Janssen
* gnu/packages/bioinformatics.scm (r-mutationalpatterns): Update to 3.0.1. [native-inputs]: Add r-knitr. [propagated-inputs]: Add r-bsgenome, r-dplyr, r-ggalluvial, r-magrittr, r-purrr, r-stringr, r-tibble, and r-tidyr; remove r-reshape2 and r-summarizedexperiment.
2020-12-09gnu: r-rcas: Update to 1.16.0.zimoun
* gnu/packages/bioinformatics.scm (r-rcas): Update to 1.16.0.
2020-12-09gnu: r-bamsignals: Update to 1.22.0.zimoun
* gnu/packages/bioinformatics.scm (r-bamsignals): Update to 1.22.0.
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