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Author SHA1 Message Date
Pierre Neidhardt a294eecd98
gnu: Add emacs-helm-switch-to-repl. 
* gnu/packages/emacs-xyz.scm (emacs-helm-switch-to-repl): New variable.
 2020-12-09 17:27:51 +01:00
Nicolas Goaziou 5103459664
gnu: emacs-debbugs: Update to 0.27. 
* gnu/packages/emacs-xyz.scm (emacs-debbugs): Update to 0.27.
 2020-12-09 14:54:27 +01:00
Ludovic Courtès 3d85c3ec65
gnu: pciutils: Fix compilation error on GNU/Hurd. 
* gnu/packages/patches/pciutils-hurd-fix.patch: New file.
* gnu/local.mk (dist_patch_DATA): Add it.
* gnu/packages/pciutils.scm (pciutils)[arguments]: Add
'apply-hurd-patch' phase when (hurd-target?) is true.
[inputs]: Add "hurd-patch" entry when (hurd-target?) is true.
 2020-12-09 14:13:33 +01:00
Ludovic Courtès f066e65713
services: guix-publish: Depend on 'avahi-daemon' when needed. 
* gnu/services/base.scm (guix-publish-shepherd-service): Add
'user-processes' to 'requirement'.  When ADVERTISE? is true, also add
'avahi-daemon'.
 2020-12-09 14:13:32 +01:00
Ludovic Courtès 59a6780f70
services: avahi: Depend on 'user-processes'. 
* gnu/services/avahi.scm (avahi-shepherd-service): Add 'user-processes'
to 'requirement'.
 2020-12-09 14:13:32 +01:00
Ricardo Wurmus ebf11de4e3
gnu: r-diffbind: Update to 3.0.8. 
* gnu/packages/bioconductor.scm (r-diffbind): Update to 3.0.8.
 2020-12-09 12:12:48 +01:00
Ricardo Wurmus 4617cc7fd5
gnu: r-rhtslib: Propagate zlib. 
* 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.
 2020-12-09 12:12:48 +01:00
Ricardo Wurmus 7601015fc9
gnu: r-delayedmatrixstats: Update to 1.12.1. 
* gnu/packages/bioconductor.scm (r-delayedmatrixstats): Update to 1.12.1.
[propagated-inputs]: Add r-matrixgenerics.
 2020-12-09 12:12:48 +01:00
zimoun cde035e67f
gnu: r-gqtlstats: Update to 1.21.3. 
* gnu/packages/bioinformatics.scm (r-gqtlstats): Update to 1.21.3.
 2020-12-09 12:12:48 +01:00
zimoun 6a4818716d
gnu: r-gqtlbase: Update to 1.21.1. 
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.
 2020-12-09 12:12:48 +01:00
zimoun 64f9fb308f
gnu: r-bigmelon: Update to 1.16.0. 
* gnu/packages/bioconductor.scm (r-bigmelon): Update to 1.16.0.
 2020-12-09 12:12:48 +01:00
zimoun 9f6e2bfe1f
gnu: r-watermelon: Update to 1.34.0. 
* gnu/packages/bioconductor.scm (r-watermelon): Update to 1.34.0.
 2020-12-09 12:12:47 +01:00
zimoun 8db36c1f68
gnu: r-yarn: Update to 1.16.0. 
* gnu/packages/bioconductor.scm (r-yarn): Update to 1.16.0.
 2020-12-09 12:12:47 +01:00
zimoun adf6edc750
gnu: r-quantro: Update to 1.24.0. 
* gnu/packages/bioconductor.scm (r-quantro): Update to 1.24.0.
 2020-12-09 12:12:47 +01:00
zimoun 4eeaa159d2
gnu: r-lumi: Update to 2.42.0. 
* gnu/packages/bioconductor.scm (r-lumi): Update to 2.42.0.
 2020-12-09 12:12:47 +01:00
zimoun 0b7dd44706
gnu: r-methylumi: Update to 2.36.0. 
* gnu/packages/bioconductor.scm (r-methylumi): Update to 2.36.0.
 2020-12-09 12:12:47 +01:00
zimoun e5a4198bc3
gnu: r-minfi: Update to 1.36.0. 
* gnu/packages/bioconductor.scm (r-minfi): Update to 1.36.0.
 2020-12-09 12:12:47 +01:00
zimoun 45dfb75166
gnu: Add r-catalyst. 
* gnu/packages/bioconductor.scm (r-catalyst): New variable.
 2020-12-09 12:12:47 +01:00
zimoun 43bf50ecae
gnu: r-ggcyto: Update to 1.18.0. 
* gnu/packages/bioconductor.scm (r-ggcyto): Update to 1.18.0.
 2020-12-09 12:12:47 +01:00
zimoun b856a48768
gnu: r-scdd: Update to 1.14.0. 
* gnu/packages/bioconductor.scm (r-scdd): Update to 1.14.0.
 2020-12-09 12:12:47 +01:00
zimoun 3f04b8167b
gnu: r-chipcomp: Update to 1.20.0. 
* gnu/packages/bioconductor.scm (r-chipcomp): Update to 1.20.0.
 2020-12-09 12:12:47 +01:00
zimoun 1174317e03
gnu: r-pcatools: Update to 2.2.0. 
* gnu/packages/bioconductor.scm (r-pcatools): Update to 2.2.0.
 2020-12-09 12:12:47 +01:00
zimoun 970984237a
gnu: r-biocviews: Update to 1.58.1. 
* gnu/packages/bioinformatics.scm (r-biocviews): Update to 1.58.1.

Co-authored-by: Ricardo Wurmus <reka@elephly.net>.
 2020-12-09 12:12:47 +01:00
zimoun b03c955c6f
gnu: r-scran: Update to 1.18.0. 
* gnu/packages/bioconductor.scm (r-scran): Update to 1.18.0.
[propagated-inputs]: Add r-bluster, r-scuttle.  Remove r-iranges.

Co-authored-by: Ricardo Wurmus <reka@elephly.net>.
 2020-12-09 12:12:47 +01:00
zimoun d4b5d18684
gnu: r-scater: Update to 1.18.3. 
* gnu/packages/bioconductor.scm (r-scater): Update to 1.18.3.
[propagated-inputs]: Add r-gridextra, r-scutlle.  Remove r-beachmat, r-rcpp.

Co-authored-by: Ricardo Wurmus <reka@elephly.net>.
 2020-12-09 12:12:46 +01:00
Ricardo Wurmus 0e60dda0ae
gnu: Add r-scuttle. 
* gnu/packages/bioconductor.scm (r-scuttle): New variable.
 2020-12-09 12:12:46 +01:00
zimoun 10c87ecf77
gnu: r-delayedmatrixstats: Update to 1.12.0. 
* gnu/packages/bioconductor.scm (r-delayedmatrixstats): Update to 1.12.0.

Co-authored-by: Ricardo Wurmus <rekado@elephly.net>.
 2020-12-09 12:12:46 +01:00
zimoun 53affb349a
gnu: r-rhdf5: Update to 2.34.0. 
* 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>.
 2020-12-09 12:12:46 +01:00
Ricardo Wurmus 86fcceeae1
gnu: Add r-rhdf5filters. 
* gnu/packages/bioinformatics.scm (r-rhdf5filters): New variable.
 2020-12-09 12:12:46 +01:00
zimoun 4ef898d449
gnu: r-singlecellexperiment: Update to 1.12.0. 
* gnu/packages/bioconductor.scm (r-singlecellexperiment): Update to 1.12.0.
 2020-12-09 12:12:46 +01:00
zimoun d0db04fcaf
gnu: r-yapsa: Update to 1.16.0. 
* gnu/packages/bioconductor.scm (r-yapsa): Update to 1.16.0.
 2020-12-09 12:12:46 +01:00
zimoun 798ec28916
gnu: r-biocsingular: Update to 1.6.0. 
* gnu/packages/bioconductor.scm (r-biocsingular): Update to 1.6.0.
 2020-12-09 12:12:46 +01:00
zimoun dd9341ffa3
gnu: r-genomicinteractions: Update to 1.24.0. 
* gnu/packages/bioconductor.scm (r-genomicinteractions): Update to 1.24.0.
 2020-12-09 12:12:46 +01:00
zimoun 35dae95110
gnu: r-interactionset: Update to 1.18.0. 
* gnu/packages/bioconductor.scm (r-interactionset): Update to 1.18.0.
 2020-12-09 12:12:46 +01:00
zimoun 60ad3c7b3b
gnu: r-genomationdata: Update to 1.22.0. 
* gnu/packages/bioinformatics.scm (r-genomationdata): Update to 1.22.0.
 2020-12-09 12:12:46 +01:00
Ricardo Wurmus 5e719988f2
gnu: Add r-sparsematrixstats. 
* gnu/packages/bioconductor.scm (r-sparsematrixstats): New variable.
 2020-12-09 12:12:46 +01:00
Roel Janssen a23310ffc2
gnu: Add r-bluster. 
* gnu/packages/bioconductor.scm (r-bluster): New variable.
 2020-12-09 12:12:45 +01:00
Roel Janssen aca4ebe40a
gnu: r-annaffy: Update to 1.62.0. 
* gnu/packages/bioconductor.scm (r-annaffy): Update to 1.62.0.
 2020-12-09 12:12:45 +01:00
zimoun e707820442
gnu: r-sushi: Update to 1.28.0. 
* gnu/packages/bioinformatics.scm (r-sushi): Update to 1.28.0.
 2020-12-09 12:12:45 +01:00
zimoun 83129edfb7
gnu: r-gwascat: Update to 2.22.0. 
* 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.
 2020-12-09 12:12:45 +01:00
zimoun 717e53fdc0
gnu: r-gviz: Update to 1.34.0. 
* gnu/packages/bioinformatics.scm (r-gviz): Update to 1.34.0.
 2020-12-09 12:12:45 +01:00
zimoun 0a8d08e887
gnu: r-ldblock: Update to 1.20.0. 
* gnu/packages/bioinformatics.scm (r-ldblock): Update to 1.20.0.
 2020-12-09 12:12:45 +01:00
zimoun 494010ad3e
gnu: r-erma: Update to 1.6.0. 
* gnu/packages/bioinformatics.scm (r-erma): Update to 1.6.0.
 2020-12-09 12:12:45 +01:00
zimoun 6e338901bf
gnu: r-snpstats: Update to 1.40.0. 
* gnu/packages/bioinformatics.scm (r-snpstats): Update to 1.40.0.
 2020-12-09 12:12:45 +01:00
zimoun 74a11b21be
gnu: r-ggbio: Update to 1.38.0. 
* gnu/packages/bioinformatics.scm (r-ggbio): Update to 1.38.0.
 2020-12-09 12:12:45 +01:00
zimoun 3c6eecdeed
gnu: r-biovizbase: Update to 1.38.0. 
* gnu/packages/bioinformatics.scm (r-biovizbase): Update to 1.38.0.
 2020-12-09 12:12:45 +01:00
zimoun 6e182c237a
gnu: r-organismdbi: Update to 1.32.0. 
* gnu/packages/bioinformatics.scm (r-organismdbi): Update to 1.32.0.
 2020-12-09 12:12:44 +01:00
zimoun 06fe3b7a53
gnu: r-ensembldb: Update to 2.14.0. 
* gnu/packages/bioinformatics.scm (r-ensembldb): Update to 2.14.0.
 2020-12-09 12:12:44 +01:00
zimoun 8962a13afe
gnu: r-dirichletmultinomial: Update to 1.32.0. 
* gnu/packages/bioinformatics.scm (r-dirichletmultinomial): Update to 1.32.0.
 2020-12-09 12:12:44 +01:00
Roel Janssen 4ef1e375b4
gnu: r-complexheatmap: Update to 2.6.2. 
* 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.
 2020-12-09 12:12:44 +01:00
zimoun 0fde2f9ad2
gnu: r-genomicfiles: Update to 1.26.0. 
* gnu/packages/bioinformatics.scm (r-genomicfiles): Update to 1.26.0.
[propagated-inputs]: Add r-matrixgenerics.
 2020-12-09 12:12:44 +01:00
zimoun 78cadd0fef
gnu: r-gage: Update to 2.40.0. 
* gnu/packages/bioinformatics.scm (r-gage): Update to 2.40.0.
 2020-12-09 12:12:44 +01:00
zimoun 143437c623
gnu: r-keggrest: Update to 1.30.0. 
* gnu/packages/bioinformatics.scm (r-keggrest): Update to 1.30.0.
 2020-12-09 12:12:44 +01:00
zimoun b6dd0722c8
gnu: r-fastseg: Update to 1.36.0. 
* gnu/packages/bioinformatics.scm (r-fastseg): Update to 1.36.0.
 2020-12-09 12:12:44 +01:00
zimoun a9dc755e67
gnu: r-annotationhub: Update to 2.22.0. 
* gnu/packages/bioinformatics.scm (r-annotationhub): Update to 2.22.0.
 2020-12-09 12:12:43 +01:00
zimoun 3becce3ff3
gnu: r-interactivedisplaybase: Update to 1.28.0. 
* gnu/packages/bioinformatics.scm (r-interactivedisplaybase): Update to 1.28.0.
 2020-12-09 12:12:43 +01:00
zimoun 8e55b9f502
gnu: r-edaseq: Update to 2.24.0. 
* gnu/packages/bioinformatics.scm (r-edaseq): Update to 2.24.0.
 2020-12-09 12:12:43 +01:00
zimoun 8db8a683b9
gnu: r-aroma-light: Update to 3.20.0. 
* gnu/packages/bioinformatics.scm (r-aroma-light): Update to 3.20.0.
 2020-12-09 12:12:43 +01:00
zimoun 971f3a377c
gnu: r-msnid: Update to 1.24.0. 
* 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.
 2020-12-09 12:12:43 +01:00
zimoun 16f16b5e21
gnu: Add r-msmstests. 
* gnu/packages/bioconductor.scm (r-msmstests): New variable.
 2020-12-09 12:12:43 +01:00
zimoun e520c68fa9
gnu: Add r-msmseda. 
* gnu/packages/bioconductor.scm (r-msmseq): New variable.
 2020-12-09 12:12:43 +01:00
zimoun 2ed937e0aa
gnu: r-pcamethods: Update to 1.82.0. 
* gnu/packages/bioinformatics.scm (r-pcamethods): Update to 1.82.0.
 2020-12-09 12:12:43 +01:00
zimoun b47560c1cf
gnu: r-mzid: Update to 1.28.0. 
* gnu/packages/bioinformatics.scm (r-mzid): Update to 1.28.0.
[propagated-inputs]: Remove r-rcpp.
 2020-12-09 12:12:43 +01:00
zimoun 75bdab83cc
gnu: r-vsn: Update to 3.58.0. 
* gnu/packages/bioinformatics.scm (r-vsn): Update to 3.58.0.
 2020-12-09 12:12:42 +01:00
zimoun 6a6f38b89e
gnu: r-affy: Update to 1.68.0. 
* gnu/packages/bioinformatics.scm (r-affy): Update to 1.68.0.
 2020-12-09 12:12:42 +01:00
zimoun d6750c6587
gnu: r-affyio: Update to 1.60.0. 
* gnu/packages/bioinformatics.scm (r-affyio): Update to 1.60.0.
 2020-12-09 12:12:42 +01:00
Ricardo Wurmus 471ceb5e5e
gnu: r-mzr: Fix linking. 
* gnu/packages/bioinformatics.scm (r-mzr)[arguments]: Fix linking with rhdf5
libraries.
 2020-12-09 12:12:42 +01:00
Ricardo Wurmus badb4678bd
gnu: r-mzr: Update to 2.24.1. 
* gnu/packages/bioinformatics.scm (r-mzr): Update to 2.24.1.
 2020-12-09 12:12:42 +01:00
zimoun 4d9e168db8
gnu: r-protgenerics: Update to 1.22.0. 
* gnu/packages/bioinformatics.scm (r-protgenerics): Update to 1.22.0.
 2020-12-09 12:12:42 +01:00
zimoun 858eb988a0
gnu: r-sva: Update to 3.38.0. 
* gnu/packages/bioinformatics.scm (r-sva): Update to 3.38.0.
 2020-12-09 12:12:42 +01:00
zimoun 99bd4f2d7c
gnu: r-methylkit: Update to 1.16.0. 
* gnu/packages/bioinformatics.scm (r-methylkit): Update to 1.16.0.
 2020-12-09 12:12:42 +01:00
zimoun 2ed79a0a42
gnu: r-copywriter: Update to 2.22.0. 
* gnu/packages/bioinformatics.scm (r-copywriter): Update to 2.22.0.
 2020-12-09 12:12:41 +01:00
zimoun 36fd725b6f
gnu: r-chipseq: Update to 1.40.0. 
* gnu/packages/bioinformatics.scm (r-chipseq): Update to 1.40.0.
 2020-12-09 12:12:41 +01:00
zimoun cad3eb4eb4
gnu: r-annotationfilter: Update to 1.14.0. 
* gnu/packages/bioinformatics.scm (r-annotationfilter): Update to 1.14.0.
 2020-12-09 12:12:41 +01:00
zimoun ec0050c0a9
gnu: r-tximport: Update to 1.18.0. 
* gnu/packages/bioinformatics.scm (r-tximport): Update to 1.18.0.
 2020-12-09 12:12:41 +01:00
Roel Janssen 6d5a4dd0a7
gnu: r-mutationalpatterns: Update to 3.0.1. 
* 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.
 2020-12-09 12:12:41 +01:00
zimoun a823a74525
gnu: r-rcas: Update to 1.16.0. 
* gnu/packages/bioinformatics.scm (r-rcas): Update to 1.16.0.
 2020-12-09 12:12:41 +01:00
zimoun 2c15a1c502
gnu: r-bamsignals: Update to 1.22.0. 
* gnu/packages/bioinformatics.scm (r-bamsignals): Update to 1.22.0.
 2020-12-09 12:12:41 +01:00
zimoun 728369634f
gnu: r-rhtslib: Update to 1.22.0. 
* gnu/packages/bioinformatics.scm (r-rhtslib): Update to 1.22.0.
 2020-12-09 12:12:41 +01:00
zimoun b0d85e36f1
gnu: r-zlibbioc: Update to 1.36.0. 
* gnu/packages/bioinformatics.scm (r-zlibbioc): Update to 1.36.0.
 2020-12-09 12:12:40 +01:00
zimoun 329879b70c
gnu: r-seqlogo: Update to 1.56.0. 
* gnu/packages/bioinformatics.scm (r-seqlogo): Update to 1.56.0.
 2020-12-09 12:12:40 +01:00
zimoun 2a70c96e3d
gnu: r-genomation: Update to 1.22.0. 
* gnu/packages/bioinformatics.scm (r-genomation): Update to 1.22.0.
 2020-12-09 12:12:40 +01:00
zimoun 44bf116f03
gnu: r-seqpattern: Update to 1.22.0. 
* gnu/packages/bioinformatics.scm (r-seqpattern): Update to 1.22.0.
 2020-12-09 12:12:40 +01:00
zimoun a180744b37
gnu: r-impute: Update to 1.64.0. 
* gnu/packages/bioinformatics.scm (r-impute): Update to 1.64.0.
 2020-12-09 12:12:40 +01:00
zimoun e2e11f095f
gnu: r-bsgenome: Update to 1.58.0. 
* gnu/packages/bioinformatics.scm (r-bsgenome): Update to 1.58.0.
 2020-12-09 12:12:40 +01:00
Roel Janssen 6a7de43a58
gnu: r-topgo: Update to 2.42.0. 
* gnu/packages/bioinformatics.scm (r-topgo): Update to 2.42.0.
 2020-12-09 12:12:40 +01:00
Roel Janssen 26e2184fc1
gnu: r-genomicfeatures: Update to 1.42.1. 
* gnu/packages/bioinformatics.scm (r-genomicfeatures): Update to 1.42.1.
 2020-12-09 12:12:40 +01:00
zimoun 92377e7fea
gnu: r-rtracklayer: Update to 1.50.0. 
* gnu/packages/bioinformatics.scm (r-rtracklayer): Update to 1.50.0.
 2020-12-09 12:12:39 +01:00
zimoun 077e813657
gnu: r-genomicalignments: Update to 1.26.0. 
* gnu/packages/bioinformatics.scm (r-genomicalignments): Update to 1.26.0.
 2020-12-09 12:12:39 +01:00
zimoun 3ca5b05474
gnu: r-variantannotation: Update to 1.36.0. 
* gnu/packages/bioinformatics.scm (r-variantannotation): Update to 1.36.0.
[propagated-inputs]: Add r-matrixgenerics.
 2020-12-09 12:12:39 +01:00
zimoun 8607a5394b
gnu: r-summarizedexperiment: Update to 1.20.0. 
* gnu/packages/bioinformatics.scm (r-summarizedexperiment): Update to 1.20.0.
[propagated-inputs]: Add r-matrixgenerics.
 2020-12-09 12:12:39 +01:00
zimoun 9168ab0911
gnu: r-rsamtools: Update to 2.6.0. 
* gnu/packages/bioinformatics.scm (r-rsamtools): Update to 2.6.0.
 2020-12-09 12:12:39 +01:00
zimoun 5d60273b77
gnu: r-biostrings: Update to 2.58.0. 
* gnu/packages/bioinformatics.scm (r-biostrings): Update to 2.58.0.
 2020-12-09 12:12:39 +01:00
Roel Janssen 444b101dc2
gnu: r-biocparallel: Update to 1.24.1. 
* gnu/packages/bioconductor.scm (r-biocparallel): Update to 1.24.1.
 2020-12-09 12:12:39 +01:00
zimoun 4fac3fe67d
gnu: r-biomart: Update to 2.46.0. 
* gnu/packages/bioinformatics.scm (r-biomart): Update to 2.46.0.
 2020-12-09 12:12:39 +01:00
zimoun f517365cef
gnu: r-annotationdbi: Update to 1.52.0. 
* gnu/packages/bioinformatics.scm (r-annotationdbi): Update to 1.52.0.
 2020-12-09 12:12:39 +01:00
zimoun 9103041d13
gnu: r-biobase: Update to 2.50.0. 
* gnu/packages/bioinformatics.scm (r-biobase): Update to 2.50.0.
 2020-12-09 12:12:38 +01:00
zimoun 7641dba3e6
gnu: r-genomicranges: Update to 1.42.0. 
* gnu/packages/bioinformatics.scm (r-genomicranges): Update to 1.42.0.
 2020-12-09 12:12:38 +01:00
zimoun d972ab690e
gnu: r-limma: Update to 3.46.0. 
* gnu/packages/bioinformatics.scm (r-limma): Update to 3.46.0.
 2020-12-09 12:12:38 +01:00
zimoun 5996929b36
gnu: r-edger: Update to 3.32.0. 
* gnu/packages/bioinformatics.scm (r-edger): Update to 3.32.0.
 2020-12-09 12:12:38 +01:00
zimoun cde7fcedf9
gnu: r-genomeinfodb: Update to 1.26.0. 
* gnu/packages/bioinformatics.scm (r-genomeinfodb): Update to 1.26.0.
 2020-12-09 12:12:38 +01:00
zimoun 2ae3b7db24
gnu: r-bioccheck: Update to 1.26.0. 
* gnu/packages/bioinformatics.scm (r-bioccheck): Update to 1.26.0.
 2020-12-09 12:12:38 +01:00
zimoun 1160c83caf
gnu: r-biocstyle: Update to 2.18.0. 
* gnu/packages/bioinformatics.scm (r-biocstyle): Update to 2.18.0.
 2020-12-09 12:12:38 +01:00
zimoun 182a080127
gnu: r-biocviews: Update to 1.58.0. 
* gnu/packages/bioinformatics.scm (r-biocviews): Update to 1.58.0.
 2020-12-09 12:12:38 +01:00
zimoun 16a4822a07
gnu: r-grohmm: Update to 1.24.0. 
* gnu/packages/bioinformatics.scm (r-grohmm): Update to 1.24.0.
 2020-12-09 12:12:37 +01:00
Roel Janssen 5598f53497
gnu: r-systempiper: Update to 1.24.2. 
* gnu/packages/bioinformatics.scm (r-systempiper): Update to 1.24.2.
[propagated-inputs]: Add r-iranges.
 2020-12-09 12:12:37 +01:00
zimoun a05bb428e4
gnu: r-shortread: Update to 1.48.0. 
* gnu/packages/bioinformatics.scm (r-shortread): Update to 1.48.0.
 2020-12-09 12:12:37 +01:00
zimoun 74204b48eb
gnu: r-gostats: Update to 2.56.0. 
* gnu/packages/bioinformatics.scm (r-gostats): Update to 2.56.0.
 2020-12-09 12:12:37 +01:00
zimoun afbc8e1433
gnu: r-category: Update to 2.56.0. 
* gnu/packages/bioinformatics.scm (r-category): Update to 2.56.0.
 2020-12-09 12:12:37 +01:00
zimoun 03312f052a
gnu: r-gseabase: Update to 1.52.0. 
* gnu/packages/bioinformatics.scm (r-gseabase): Update to 1.52.0.
 2020-12-09 12:12:37 +01:00
zimoun 7a57b229b6
gnu: r-rbgl: Update to 1.66.0. 
* gnu/packages/bioinformatics.scm (r-rbgl): Update to 1.66.0.
 2020-12-09 12:12:37 +01:00
zimoun 4451918e3a
gnu: r-annotationforge: Update to 1.32.0. 
* gnu/packages/bioinformatics.scm (r-annotationforge): Update to 1.32.0.
 2020-12-09 12:12:37 +01:00
zimoun a323c1e9b4
gnu: r-dexseq: Update to 1.36.0. 
* gnu/packages/bioinformatics.scm (r-dexseq): Update to 1.36.0.
 2020-12-09 12:12:37 +01:00
zimoun 936227f144
gnu: r-deseq2: Update to 1.30.0. 
* gnu/packages/bioinformatics.scm (r-deseq2): Update to 1.30.0.
 2020-12-09 12:12:37 +01:00
zimoun 64cf667e98
gnu: r-genefilter: Update to 1.72.0. 
* gnu/packages/bioinformatics.scm (r-genefilter): Update to 1.72.0.
 2020-12-09 12:12:36 +01:00
Roel Janssen fe4ce29a5c
gnu: r-beachmat: Update to 2.6.1. 
* gnu/packages/bioconductor.scm (r-beachmat): Update to 2.6.1.
 2020-12-09 12:12:36 +01:00
zimoun 0022e9f4c0
gnu: r-ncdfflow: Fix r-rhdf5libs link. 
* gnu/packages/bioconductor.scm (r-ncdfflow): [arguments]: Avoid to have a
plain directory on the list of libraries to link.

Co-authored-by: Ricardo Wurmus <reka@elephly.net>.
 2020-12-09 12:12:36 +01:00
zimoun 2b224f904a
gnu: r-cytoml: Fix r-rhdf5libs linking. 
* gnu/packages/bioconductor.scm (r-cytoml): [arguments]: Avoid to have
a plain directory on the list of libraries to link.
 2020-12-09 12:12:36 +01:00
zimoun ece564f07d
gnu: r-flowworkspace: Fix r-rhdf5libs linking. 
* gnu/packages/bioconductor.scm (r-flowworkspace): [arguments]: Avoid to have
a plain directory on the list of libraries to link.
 2020-12-09 12:12:36 +01:00
zimoun 26cf5eb568
gnu: r-hdf5array: Fix r-rhdf5libs linking. 
* gnu/packages/bioconductor.scm (r-hdf5array): [arguments]: Avoid to have a
plain directory on the list of libraries to link.

Co-authored-by: Ricardo Wurmus <reka@elephly.net>.
 2020-12-09 12:12:36 +01:00
zimoun b58c4e7613
gnu: r-cytolib: Fix r-rhdf5libs linking. 
* gnu/packages/bioconductor.scm (r-cytolib): [arguments]: Avoid to have a
plain directory on the list of libraries to link.

Co-authored-by: Ricardo Wurmus <reka@elephly.net>.
 2020-12-09 12:12:36 +01:00
Roel Janssen c5ae5c1c40
gnu: r-rhdf5lib: Fix build. 
* gnu/packages/bioconductor.scm (r-rhdf5lib)[arguments]: Fix build.
 2020-12-09 12:12:36 +01:00
zimoun 79cb6af375
gnu: r-rhdf5lib: Update to 1.12.0. 
* gnu/packages/bioconductor.scm (r-rhdf5lib): Update to 1.12.0.
 2020-12-09 12:12:36 +01:00
zimoun 5992c25e7f
gnu: r-hdf5array: Update to 1.18.0. 
* gnu/packages/bioconductor.scm (r-hdf5array): Update to 1.18.0.
 2020-12-09 12:12:36 +01:00
zimoun fafa94b065
gnu: r-delayedarray: Update to 0.16.0. 
* gnu/packages/bioinformatics.scm (r-delayedarray): Update to 0.16.0.
[propagated-inputs]: Add r-matrixgenerics; remove r-matrixstats.
 2020-12-09 12:12:36 +01:00
Roel Janssen c8da013780
gnu: Add r-matrixgenerics. 
* gnu/packages/bioconductor.scm (r-matrixgenerics): New variable.
 2020-12-09 12:12:36 +01:00
Roel Janssen 47f6fd802e
gnu: Add r-ggalluvial. 
* gnu/packages/cran.scm (r-ggalluvial): New variable.
 2020-12-09 12:12:35 +01:00
zimoun cf6033ee6e
gnu: r-iranges: Update to 2.24.0. 
* gnu/packages/bioinformatics.scm (r-iranges): Update to 2.24.0.
 2020-12-09 12:12:35 +01:00
zimoun 57820475db
gnu: r-s4vectors: Update to 0.28.0. 
* gnu/packages/bioinformatics.scm (r-s4vectors): Update to 0.28.0.
 2020-12-09 12:12:35 +01:00
zimoun ed44a72acf
gnu: r-hitc: Update to 1.34.0. 
* gnu/packages/bioconductor.scm (r-hitc): Update to 1.34.0.
 2020-12-09 12:12:35 +01:00
zimoun 7105658e9c
gnu: r-fithic: Update to 1.16.0. 
* gnu/packages/bioconductor.scm (r-fithic): Update to 1.16.0.
 2020-12-09 12:12:35 +01:00
zimoun 724b770678
gnu: r-xvector: Update to 0.30.0. 
* gnu/packages/bioinformatics.scm (r-xvector): Update to 0.30.0.
 2020-12-09 12:12:35 +01:00
zimoun b6348b0edf
gnu: r-rgraphviz: Update to 2.34.0. 
* gnu/packages/bioconductor.scm (r-rgraphviz): Update to 2.34.0.
 2020-12-09 12:12:35 +01:00
zimoun 8fa30df02a
gnu: r-preprocesscore: Update to 1.52.0. 
* gnu/packages/bioconductor.scm (r-preprocesscore): Update to 1.52.0.
 2020-12-09 12:12:35 +01:00
zimoun e5b2c80dc2
gnu: r-fourcseq: Update to 1.24.0. 
* gnu/packages/bioconductor.scm (r-fourcseq): Update to 1.24.0.
 2020-12-09 12:12:35 +01:00
zimoun 3cacc3bdce
gnu: r-icens: Update to 1.62.0. 
* gnu/packages/bioconductor.scm (r-icens): Update to 1.62.0.
 2020-12-09 12:12:35 +01:00
zimoun 126846a0da
gnu: r-m3c: Update to 1.12.0. 
* gnu/packages/bioconductor.scm (r-m3c): Update to 1.12.0.
 2020-12-09 12:12:35 +01:00
zimoun 7a242042ae
gnu: r-rgreat: Update to 1.22.0. 
* gnu/packages/bioconductor.scm (r-rgreat): Update to 1.22.0.
 2020-12-09 12:12:35 +01:00
zimoun 15be98c136
gnu: r-biodist: Update to 1.62.0. 
* gnu/packages/bioconductor.scm (r-biodist): Update to 1.62.0.
 2020-12-09 12:12:34 +01:00
zimoun 7891c83c3e
gnu: r-biocworkflowtools: Update to 1.16.0. 
* gnu/packages/bioconductor.scm (r-biocworkflowtools): Update to 1.16.0.
 2020-12-09 12:12:34 +01:00
zimoun feb0cbf402
gnu: r-biocset: Update to 1.4.0. 
* gnu/packages/bioconductor.scm (r-biocset): Update to 1.4.0.
[propagated-inputs]: Add r-s4vectors; remove r-rtracklayer.
 2020-12-09 12:12:34 +01:00
zimoun ff4834c065
gnu: Add r-biocio. 
* gnu/packages/bioconductor.scm (r-biocio): New variable.
 2020-12-09 12:12:34 +01:00
zimoun 6a5d8cadee
gnu: r-biocpkgtools: Update to 1.8.0. 
* gnu/packages/bioconductor.scm (r-biocpkgtools): Update to 1.8.0.
 2020-12-09 12:12:34 +01:00
zimoun 072f722f8e
gnu: r-biocor: Update to 1.14.0. 
* gnu/packages/bioconductor.scm (r-biocor): Update to 1.14.0.
 2020-12-09 12:12:34 +01:00
zimoun e29b15ee97
gnu: r-bioconcotk: Update to 1.10.0. 
* gnu/packages/bioconductor.scm (r-bioconcotk): Update to 1.10.0.
 2020-12-09 12:12:34 +01:00
zimoun 13d0b780c1
gnu: r-multiassayexperiment: Update to 1.16.0. 
* gnu/packages/bioconductor.scm (r-multiassayexperiment): Update to 1.16.0.
 2020-12-09 12:12:34 +01:00
zimoun 49a728581f
gnu: r-experimenthub: Update to 1.16.0. 
* gnu/packages/bioconductor.scm (r-experimenthub): Update to 1.16.0.
 2020-12-09 12:12:34 +01:00
zimoun abc18fc596
gnu: r-biocgraph: Update to 1.52.0. 
* gnu/packages/bioconductor.scm (r-biocgraph): Update to 1.52.0.
 2020-12-09 12:12:34 +01:00
zimoun 7dced9ad01
gnu: r-bioccasestudies: Update to 1.52.0. 
* gnu/packages/bioconductor.scm (r-bioccasestudies): Update to 1.52.0.
 2020-12-09 12:12:34 +01:00
zimoun b0f3bfe4ae
gnu: r-ebarrays: Update to 2.54.0. 
* gnu/packages/bioconductor.scm (r-ebarrays): Update to 2.54.0.
 2020-12-09 12:12:34 +01:00
zimoun a4f4a55283
gnu: r-reactomepa: Update to 1.34.0. 
* gnu/packages/bioconductor.scm (r-reactomepa): Update to 1.34.0.
 2020-12-09 12:12:34 +01:00
zimoun 26224e09ae
gnu: r-graphite: Update to 1.36.0. 
* gnu/packages/bioconductor.scm (r-graphite): Update to 1.36.0.
 2020-12-09 12:12:34 +01:00
zimoun 95e30d8f6e
gnu: r-biobroom: Update to 1.22.0. 
* gnu/packages/bioconductor.scm (r-biobroom): Update to 1.22.0.
 2020-12-09 12:12:33 +01:00
zimoun 2f36b0406e
gnu: r-bioassayr: Update to 1.28.0. 
* gnu/packages/bioconductor.scm (r-bioassayr): Update to 1.28.0.
 2020-12-09 12:12:33 +01:00
zimoun 95ef268142
gnu: r-chemminer: Update to 3.42.0. 
* gnu/packages/bioconductor.scm (r-chemminer): Update to 3.42.0.
 2020-12-09 12:12:33 +01:00
zimoun 1e28867803
gnu: r-bigpint: Update to 1.6.0. 
* gnu/packages/bioconductor.scm (r-bigpint): Update to 1.6.0.
 2020-12-09 12:12:33 +01:00
zimoun e80f8262f6
gnu: r-bigmemoryextras: Update to 1.38.0. 
* gnu/packages/bioconductor.scm (r-bigmemoryextras): Update to 1.38.0.
 2020-12-09 12:12:33 +01:00
zimoun 0f94a9edb0
gnu: r-biggr: Update to 1.26.0. 
* gnu/packages/bioconductor.scm (r-biggr): Update to 1.26.0.
 2020-12-09 12:12:33 +01:00
zimoun 249b703056
gnu: r-hyperdraw: Update to 1.42.0. 
* gnu/packages/bioconductor.scm (r-hyperdraw): Update to 1.42.0.
 2020-12-09 12:12:33 +01:00
zimoun 294fd58a42
gnu: r-hypergraph: Update to 1.62.0. 
* gnu/packages/bioconductor.scm (r-hypergraph): Update to 1.62.0.
 2020-12-09 12:12:33 +01:00
zimoun 3320f044a3
gnu: r-rsbml: Update to 2.48.0. 
* gnu/packages/bioconductor.scm (r-rsbml): Update to 2.48.0.
 2020-12-09 12:12:33 +01:00
zimoun d57be63323
gnu: r-bifet: Update to 1.10.0. 
* gnu/packages/bioconductor.scm (r-bifet): Update to 1.10.0.
 2020-12-09 12:12:33 +01:00
zimoun 4ec665693d
gnu: r-bicare: Update to 1.48.0. 
* gnu/packages/bioconductor.scm (r-bicare): Update to 1.48.0.
 2020-12-09 12:12:33 +01:00
zimoun 2219bef12f
gnu: r-bhc: Update to 1.42.0. 
* gnu/packages/bioconductor.scm (r-bhc): Update to 1.42.0.
 2020-12-09 12:12:33 +01:00
zimoun 3cebe2745a
gnu: r-bgx: Update to 1.56.0. 
* gnu/packages/bioconductor.scm (r-bgx): Update to 1.56.0.
 2020-12-09 12:12:33 +01:00
zimoun fad5da32dc
gnu: r-bgmix: Update to 1.50.0. 
* gnu/packages/bioconductor.scm (r-bgmix): Update to 1.50.0.
 2020-12-09 12:12:32 +01:00
zimoun fa7e242910
gnu: r-unifiedwmwqpcr: Update to 1.26.0. 
* gnu/packages/bioconductor.scm (r-unifiedwmwqpcr): Update to 1.26.0.
 2020-12-09 12:12:32 +01:00
zimoun 949626f209
gnu: r-htqpcr: Update to 1.44.0. 
* gnu/packages/bioconductor.scm (r-htqpcr): Update to 1.44.0.
 2020-12-09 12:12:32 +01:00
zimoun 44ecd5f77f
gnu: r-variancepartition: Update to 1.20.0. 
* gnu/packages/bioconductor.scm (r-variancepartition): Update to 1.20.0.
 2020-12-09 12:12:32 +01:00
zimoun 45ea773f94
gnu: r-variantfiltering: Update to 1.26.0. 
* gnu/packages/bioconductor.scm (r-variantfiltering): Update to 1.26.0.
 2020-12-09 12:12:32 +01:00
zimoun 87f704b43c
gnu: r-timeseriesexperiment: Update to 1.8.0. 
* gnu/packages/bioconductor.scm (r-timeseriesexperiment): Update to 1.8.0.
 2020-12-09 12:12:32 +01:00
zimoun fd7e23b551
gnu: r-wavcluster: Update to 2.24.0. 
* gnu/packages/bioconductor.scm (r-wavcluster): Update to 2.24.0.
 2020-12-09 12:12:32 +01:00
zimoun 0c53f27dd6
gnu: r-reqon: Update to 1.36.0. 
* gnu/packages/bioconductor.scm (r-reqon): Update to 1.36.0.
 2020-12-09 12:12:32 +01:00
zimoun 42e00c0923
gnu: r-seqbias: Update to 1.38.0. 
* gnu/packages/bioconductor.scm (r-seqbias): Update to 1.38.0.
 2020-12-09 12:12:32 +01:00
zimoun a50779b8a3
gnu: r-gdsfmt: Update to 1.26.0. 
* gnu/packages/bioconductor.scm (r-gdsfmt): Update to 1.26.0.
 2020-12-09 12:12:32 +01:00
zimoun e7b61ba7f6
gnu: r-roc: Update to 1.66.0. 
* gnu/packages/bioconductor.scm (r-roc): Update to 1.66.0.
 2020-12-09 12:12:31 +01:00
zimoun 5d1bd61137
gnu: r-genie3: Update to 1.12.0. 
* gnu/packages/bioconductor.scm (r-genie3): Update to 1.12.0.
 2020-12-09 12:12:31 +01:00
zimoun 7954fe16a0
gnu: r-cicero: Update to 1.8.0. 
* gnu/packages/bioconductor.scm (r-cicero): Update to 1.8.0.
 2020-12-09 12:12:31 +01:00
zimoun 6481357330
gnu: r-rcistarget: Update to 1.10.0. 
* gnu/packages/bioconductor.scm (r-rcistarget): Update to 1.10.0.
 2020-12-09 12:12:31 +01:00
zimoun fafaeab48b
gnu: r-depecher: Update to 1.6.0. 
* gnu/packages/bioconductor.scm (r-depecher): Update to 1.6.0.
 2020-12-09 12:12:31 +01:00
zimoun 0e78ce36f0
gnu: r-mixomics: Update to 6.14.0. 
* gnu/packages/bioconductor.scm (r-mixomics): Update to 6.14.0.
 2020-12-09 12:12:31 +01:00
zimoun 1f7ddaf0fb
gnu: r-flowsom: Update to 1.22.0. 
* gnu/packages/bioconductor.scm (r-flowsom): Update to 1.22.0.
 2020-12-09 12:12:31 +01:00
zimoun 63033b159a
gnu: r-cytoml: Update to 2.2.1. 
* gnu/packages/bioconductor.scm (r-cytoml): Update to 2.2.1.
 2020-12-09 12:12:31 +01:00
zimoun 5abf0a0dd2
gnu: r-opencyto: Update to 2.2.0. 
* gnu/packages/bioconductor.scm (r-opencyto): Update to 2.2.0.
 2020-12-09 12:12:30 +01:00
zimoun fd11c7b80f
gnu: r-flowstats: Update to 4.2.0. 
* gnu/packages/bioconductor.scm (r-flowstats): Update to 4.2.0.
 2020-12-09 12:12:30 +01:00
zimoun 1b347814f8
gnu: r-flowworkspace: Update to 4.2.0. 
* gnu/packages/bioconductor.scm (r-flowworkspace): Update to 4.2.0.
[inputs]: Add zlib.
[propagated-inputs]: Add r-aws-s3 and r-aws-signature.  Remove r-stringr.
 2020-12-09 12:12:30 +01:00
zimoun ffa42c7741
gnu: Add r-aws-s3. 
* gnu/packages/cran.scm (r-aws-s3): New variable.
 2020-12-09 12:12:30 +01:00
zimoun 7f940bd093
gnu: Add r-aws-signature. 
* gnu/packages/cran.scm (r-aws-signature): New variable.
 2020-12-09 12:12:30 +01:00
zimoun 5bab0b7eee
gnu: r-rprotobuflib: Update to 2.2.0. 
* gnu/packages/bioconductor.scm (r-rprotobuflib): Update to 2.2.0.
 2020-12-09 12:12:30 +01:00
zimoun 33c5b6d7ca
gnu: r-flowclust: Update to 3.28.0. 
* gnu/packages/bioconductor.scm (r-flowclust): Update to 3.28.0.
 2020-12-09 12:12:30 +01:00
zimoun d5a53ab76b
gnu: r-flowviz: Update to 1.54.0. 
* gnu/packages/bioconductor.scm (r-flowviz): Update to 1.54.0.
 2020-12-09 12:12:30 +01:00
zimoun eac1eaaa0f
gnu: r-ncdfflow: Update to 2.36.0. 
* gnu/packages/bioconductor.scm (r-ncdfflow): Update to 2.36.0.
 2020-12-09 12:12:30 +01:00
zimoun 2cd78131cc
gnu: r-flowmeans: Update to 1.50.0. 
* gnu/packages/bioconductor.scm (r-flowmeans): Update to 1.50.0.
 2020-12-09 12:12:30 +01:00
zimoun 3f0e93b47b
gnu: r-flowcore: Update to 2.2.0. 
* gnu/packages/bioconductor.scm (r-flowcore): Update to 2.2.0.
[propagated-inputs]: Add r-s4vectors.
 2020-12-09 12:12:29 +01:00
zimoun c6ccd4fcb1
gnu: r-cytolib: Update to 2.2.0. 
* gnu/packages/bioconductor.scm (r-cytolib): Update to 2.2.0.
[native-inputs]: Add pkg-config.
 2020-12-09 12:12:29 +01:00
zimoun a49024e6af
gnu: r-consensusclusterplus: Update to 1.54.0. 
* gnu/packages/bioconductor.scm (r-consensusclusterplus): Update to 1.54.0.
 2020-12-09 12:12:29 +01:00
zimoun d361222d8f
gnu: r-flowutils: Update to 1.54.0. 
* gnu/packages/bioconductor.scm (r-flowutils): Update to 1.54.0.
 2020-12-09 12:12:29 +01:00
zimoun d764f1e7fe
gnu: r-rsubread: Update to 2.4.2. 
* gnu/packages/bioconductor.scm (r-rsubread): Update to 2.4.2.
 2020-12-09 12:12:29 +01:00
zimoun 458aa44622
gnu: r-annotatr: Update to 1.16.0. 
* gnu/packages/bioconductor.scm (r-annotatr): Update to 1.16.0.
 2020-12-09 12:12:29 +01:00
zimoun 26e417063f
gnu: r-biosigner: Update to 1.18.0. 
* gnu/packages/bioconductor.scm (r-biosigner): Update to 1.18.0.
 2020-12-09 12:12:29 +01:00