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2020-12-09gnu: emacs-debbugs: Update to 0.27.Nicolas Goaziou
* gnu/packages/emacs-xyz.scm (emacs-debbugs): Update to 0.27.
2020-12-09gnu: pciutils: Fix compilation error on GNU/Hurd.Ludovic Courtès
* 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.
2020-12-09doc: Document 'advertise?' for 'guix-publish-configuration'.Ludovic Courtès
* doc/guix.texi (Base Services): Document the 'advertise?' field of 'guix-publish-configuration'.
2020-12-09services: guix-publish: Depend on 'avahi-daemon' when needed.Ludovic Courtès
* gnu/services/base.scm (guix-publish-shepherd-service): Add 'user-processes' to 'requirement'. When ADVERTISE? is true, also add 'avahi-daemon'.
2020-12-09services: avahi: Depend on 'user-processes'.Ludovic Courtès
* gnu/services/avahi.scm (avahi-shepherd-service): Add 'user-processes' to 'requirement'.
2020-12-09gnu: r-diffbind: Update to 3.0.8.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-diffbind): Update to 3.0.8.
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-delayedmatrixstats: Update to 1.12.1.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-delayedmatrixstats): Update to 1.12.1. [propagated-inputs]: Add r-matrixgenerics.
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-bigmelon: Update to 1.16.0.zimoun
* gnu/packages/bioconductor.scm (r-bigmelon): Update to 1.16.0.
2020-12-09gnu: r-watermelon: Update to 1.34.0.zimoun
* gnu/packages/bioconductor.scm (r-watermelon): Update to 1.34.0.
2020-12-09gnu: r-yarn: Update to 1.16.0.zimoun
* gnu/packages/bioconductor.scm (r-yarn): Update to 1.16.0.
2020-12-09gnu: r-quantro: Update to 1.24.0.zimoun
* gnu/packages/bioconductor.scm (r-quantro): Update to 1.24.0.
2020-12-09gnu: r-lumi: Update to 2.42.0.zimoun
* gnu/packages/bioconductor.scm (r-lumi): Update to 2.42.0.
2020-12-09gnu: r-methylumi: Update to 2.36.0.zimoun
* gnu/packages/bioconductor.scm (r-methylumi): Update to 2.36.0.
2020-12-09gnu: r-minfi: Update to 1.36.0.zimoun
* gnu/packages/bioconductor.scm (r-minfi): Update to 1.36.0.
2020-12-09gnu: Add r-catalyst.zimoun
* gnu/packages/bioconductor.scm (r-catalyst): New variable.
2020-12-09gnu: r-ggcyto: Update to 1.18.0.zimoun
* gnu/packages/bioconductor.scm (r-ggcyto): Update to 1.18.0.
2020-12-09gnu: r-scdd: Update to 1.14.0.zimoun
* gnu/packages/bioconductor.scm (r-scdd): Update to 1.14.0.
2020-12-09gnu: r-chipcomp: Update to 1.20.0.zimoun
* gnu/packages/bioconductor.scm (r-chipcomp): Update to 1.20.0.
2020-12-09gnu: r-pcatools: Update to 2.2.0.zimoun
* gnu/packages/bioconductor.scm (r-pcatools): Update to 2.2.0.
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-scran: Update to 1.18.0.zimoun
* 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>.
2020-12-09gnu: r-scater: Update to 1.18.3.zimoun
* 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>.
2020-12-09gnu: Add r-scuttle.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-scuttle): New variable.
2020-12-09gnu: r-delayedmatrixstats: Update to 1.12.0.zimoun
* gnu/packages/bioconductor.scm (r-delayedmatrixstats): Update to 1.12.0. Co-authored-by: Ricardo Wurmus <rekado@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-singlecellexperiment: Update to 1.12.0.zimoun
* gnu/packages/bioconductor.scm (r-singlecellexperiment): Update to 1.12.0.
2020-12-09gnu: r-yapsa: Update to 1.16.0.zimoun
* gnu/packages/bioconductor.scm (r-yapsa): Update to 1.16.0.
2020-12-09gnu: r-biocsingular: Update to 1.6.0.zimoun
* gnu/packages/bioconductor.scm (r-biocsingular): Update to 1.6.0.
2020-12-09gnu: r-genomicinteractions: Update to 1.24.0.zimoun
* gnu/packages/bioconductor.scm (r-genomicinteractions): Update to 1.24.0.
2020-12-09gnu: r-interactionset: Update to 1.18.0.zimoun
* gnu/packages/bioconductor.scm (r-interactionset): Update to 1.18.0.
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: Add r-sparsematrixstats.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-sparsematrixstats): New variable.
2020-12-09gnu: Add r-bluster.Roel Janssen
* gnu/packages/bioconductor.scm (r-bluster): New variable.
2020-12-09gnu: r-annaffy: Update to 1.62.0.Roel Janssen
* gnu/packages/bioconductor.scm (r-annaffy): Update to 1.62.0.
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.
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