Merge remote-tracking branch 'origin/master' into staging

1 files changed, 0 insertions, 405 deletions

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 96fa22f1a3..512abcd8fd 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -10484,411 +10484,6 @@ high-level packages for biological data visualization.  This saves development
 effort and encourages consistency.")
     (license license:artistic2.0)))
 
-(define-public r-ggbio
-  (package
-    (name "r-ggbio")
-    (version "1.38.0")
-    (source
-     (origin
-       (method url-fetch)
-       (uri (bioconductor-uri "ggbio" version))
-       (sha256
-        (base32
-         "0vabil4jzrlv01aibqjhdkvrv2bf2kkpsidrkjj06isqr5fz54lw"))))
-    (build-system r-build-system)
-    (arguments
-     `(#:phases
-       (modify-phases %standard-phases
-         ;; See https://github.com/tengfei/ggbio/issues/117
-         ;; This fix will be included in the next release.
-         (add-after 'unpack 'fix-typo
-           (lambda _
-             (substitute* "R/GGbio-class.R"
-               (("fechable") "fetchable"))
-             #t)))))
-    (propagated-inputs
-     `(("r-annotationdbi" ,r-annotationdbi)
-       ("r-annotationfilter" ,r-annotationfilter)
-       ("r-biobase" ,r-biobase)
-       ("r-biocgenerics" ,r-biocgenerics)
-       ("r-biostrings" ,r-biostrings)
-       ("r-biovizbase" ,r-biovizbase)
-       ("r-bsgenome" ,r-bsgenome)
-       ("r-ensembldb" ,r-ensembldb)
-       ("r-genomeinfodb" ,r-genomeinfodb)
-       ("r-genomicalignments" ,r-genomicalignments)
-       ("r-genomicfeatures" ,r-genomicfeatures)
-       ("r-genomicranges" ,r-genomicranges)
-       ("r-ggally" ,r-ggally)
-       ("r-ggplot2" ,r-ggplot2)
-       ("r-gridextra" ,r-gridextra)
-       ("r-gtable" ,r-gtable)
-       ("r-hmisc" ,r-hmisc)
-       ("r-iranges" ,r-iranges)
-       ("r-organismdbi" ,r-organismdbi)
-       ("r-reshape2" ,r-reshape2)
-       ("r-rlang" ,r-rlang)
-       ("r-rsamtools" ,r-rsamtools)
-       ("r-rtracklayer" ,r-rtracklayer)
-       ("r-s4vectors" ,r-s4vectors)
-       ("r-scales" ,r-scales)
-       ("r-summarizedexperiment" ,r-summarizedexperiment)
-       ("r-variantannotation" ,r-variantannotation)))
-    (native-inputs
-     `(("r-knitr" ,r-knitr)))
-    (home-page "http://www.tengfei.name/ggbio/")
-    (synopsis "Visualization tools for genomic data")
-    (description
-     "The ggbio package extends and specializes the grammar of graphics for
-biological data.  The graphics are designed to answer common scientific
-questions, in particular those often asked of high throughput genomics data.
-All core Bioconductor data structures are supported, where appropriate.  The
-package supports detailed views of particular genomic regions, as well as
-genome-wide overviews.  Supported overviews include ideograms and grand linear
-views.  High-level plots include sequence fragment length, edge-linked
-interval to data view, mismatch pileup, and several splicing summaries.")
-    (license license:artistic2.0)))
-
-(define-public r-gqtlbase
-  (package
-    (name "r-gqtlbase")
-    (version "1.21.1")
-    (source
-     (origin
-       (method url-fetch)
-       (uri (bioconductor-uri "gQTLBase" version))
-       (sha256
-        (base32
-         "0nipibm1bk9k70ajbw1f6vjmz0dh7gk21l17q3m54bnawxsggrfh"))))
-    (properties `((upstream-name . "gQTLBase")))
-    (build-system r-build-system)
-    (arguments
-     `(#:phases
-       (modify-phases %standard-phases
-         ;; This is an upstream bug.
-         (add-after 'unpack 'fix-imports
-           (lambda _
-             (substitute* "NAMESPACE"
-               ((".*maxffmode.*") "")
-               (("importFrom\\(ff,.*") "import(ff)\n"))
-             #t)))))
-    (propagated-inputs
-     `(("r-batchjobs" ,r-batchjobs)
-       ("r-bbmisc" ,r-bbmisc)
-       ("r-biocgenerics" ,r-biocgenerics)
-       ("r-bit" ,r-bit)
-       ("r-doparallel" ,r-doparallel)
-       ("r-ff" ,r-ff)
-       ("r-ffbase" ,r-ffbase)
-       ("r-foreach" ,r-foreach)
-       ("r-genomicfiles" ,r-genomicfiles)
-       ("r-genomicranges" ,r-genomicranges)
-       ("r-rtracklayer" ,r-rtracklayer)
-       ("r-s4vectors" ,r-s4vectors)
-       ("r-summarizedexperiment" ,r-summarizedexperiment)))
-    (native-inputs
-     `(("r-knitr" ,r-knitr)))
-    (home-page "https://bioconductor.org/packages/gQTLBase")
-    (synopsis "Infrastructure for eQTL, mQTL and similar studies")
-    (description
-     "The purpose of this package is to simplify the storage and interrogation
-of @dfn{quantitative trait loci} (QTL) archives, such as eQTL, mQTL, dsQTL,
-and more.")
-    (license license:artistic2.0)))
-
-(define-public r-snpstats
-  (package
-    (name "r-snpstats")
-    (version "1.40.0")
-    (source
-     (origin
-       (method url-fetch)
-       (uri (bioconductor-uri "snpStats" version))
-       (sha256
-        (base32
-         "1298a71swwav53yf9kfqkdpach3818plqcbw0lgb6sibs8y8ff24"))))
-    (properties `((upstream-name . "snpStats")))
-    (build-system r-build-system)
-    (inputs `(("zlib" ,zlib)))
-    (propagated-inputs
-     `(("r-biocgenerics" ,r-biocgenerics)
-       ("r-matrix" ,r-matrix)
-       ("r-survival" ,r-survival)
-       ("r-zlibbioc" ,r-zlibbioc)))
-    (home-page "https://bioconductor.org/packages/snpStats")
-    (synopsis "Methods for SNP association studies")
-    (description
-     "This package provides classes and statistical methods for large
-@dfn{single-nucleotide polymorphism} (SNP) association studies.  This extends
-the earlier snpMatrix package, allowing for uncertainty in genotypes.")
-    (license license:gpl3)))
-
-(define-public r-homo-sapiens
-  (package
-    (name "r-homo-sapiens")
-    (version "1.3.1")
-    (source (origin
-              (method url-fetch)
-              ;; We cannot use bioconductor-uri here because this tarball is
-              ;; located under "data/annotation/" instead of "bioc/".
-              (uri (string-append "https://www.bioconductor.org/packages/"
-                                  "release/data/annotation/src/contrib/"
-                                  "Homo.sapiens_"
-                                  version ".tar.gz"))
-              (sha256
-               (base32
-                "151vj7h5p1c8yd5swrchk46z469p135wk50hvkl0nhgndvy0jj01"))))
-    (properties
-     `((upstream-name . "Homo.sapiens")))
-    (build-system r-build-system)
-    (propagated-inputs
-     `(("r-genomicfeatures" ,r-genomicfeatures)
-       ("r-go-db" ,r-go-db)
-       ("r-org-hs-eg-db" ,r-org-hs-eg-db)
-       ("r-txdb-hsapiens-ucsc-hg19-knowngene" ,r-txdb-hsapiens-ucsc-hg19-knowngene)
-       ("r-organismdbi" ,r-organismdbi)
-       ("r-annotationdbi" ,r-annotationdbi)))
-    (home-page "https://bioconductor.org/packages/Homo.sapiens/")
-    (synopsis "Annotation package for the Homo.sapiens object")
-    (description
-     "This package contains the Homo.sapiens object to access data from
-several related annotation packages.")
-    (license license:artistic2.0)))
-
-(define-public r-erma
-  (package
-    (name "r-erma")
-    (version "1.6.0")
-    (source
-     (origin
-       (method url-fetch)
-       (uri (bioconductor-uri "erma" version))
-       (sha256
-        (base32
-         "1k2j1xhv0vwn45xmh8ds0gz812px5hnpgzvp37ngsdn4j5ai1l0k"))))
-    (build-system r-build-system)
-    (propagated-inputs
-     `(("r-annotationdbi" ,r-annotationdbi)
-       ("r-biobase" ,r-biobase)
-       ("r-biocgenerics" ,r-biocgenerics)
-       ("r-biocparallel" ,r-biocparallel)
-       ("r-genomeinfodb" ,r-genomeinfodb)
-       ("r-genomicfiles" ,r-genomicfiles)
-       ("r-genomicranges" ,r-genomicranges)
-       ("r-ggplot2" ,r-ggplot2)
-       ("r-homo-sapiens" ,r-homo-sapiens)
-       ("r-iranges" ,r-iranges)
-       ("r-rtracklayer" ,r-rtracklayer)
-       ("r-s4vectors" ,r-s4vectors)
-       ("r-shiny" ,r-shiny)
-       ("r-summarizedexperiment" ,r-summarizedexperiment)))
-    (native-inputs
-     `(("r-knitr" ,r-knitr)))
-    (home-page "https://bioconductor.org/packages/erma")
-    (synopsis "Epigenomic road map adventures")
-    (description
-     "The epigenomics road map describes locations of epigenetic marks in DNA
-from a variety of cell types.  Of interest are locations of histone
-modifications, sites of DNA methylation, and regions of accessible chromatin.
-This package presents a selection of elements of the road map including
-metadata and outputs of the ChromImpute procedure applied to ENCODE cell lines
-by Ernst and Kellis.")
-    (license license:artistic2.0)))
-
-(define-public r-ldblock
-  (package
-    (name "r-ldblock")
-    (version "1.20.0")
-    (source
-     (origin
-       (method url-fetch)
-       (uri (bioconductor-uri "ldblock" version))
-       (sha256
-        (base32
-         "09i3ikv0axks9g842z1pjsc8x0fba51zyyc218h0bylbi1n9cdkm"))))
-    (build-system r-build-system)
-    (propagated-inputs
-     `(("r-biocgenerics" ,r-biocgenerics)
-       ("r-ensdb-hsapiens-v75" ,r-ensdb-hsapiens-v75)
-       ("r-ensembldb" ,r-ensembldb)
-       ("r-genomeinfodb" ,r-genomeinfodb)
-       ("r-genomicfiles" ,r-genomicfiles)
-       ("r-httr" ,r-httr)
-       ("r-matrix" ,r-matrix)
-       ("r-rsamtools" ,r-rsamtools)
-       ("r-snpstats" ,r-snpstats)
-       ("r-variantannotation" ,r-variantannotation)))
-    (native-inputs
-     `(("r-knitr" ,r-knitr)))
-    (home-page "https://bioconductor.org/packages/ldblock")
-    (synopsis "Data structures for linkage disequilibrium measures in populations")
-    (description
-     "This package defines data structures for @dfn{linkage
-disequilibrium} (LD) measures in populations.  Its purpose is to simplify
-handling of existing population-level data for the purpose of flexibly
-defining LD blocks.")
-    (license license:artistic2.0)))
-
-(define-public r-gqtlstats
-  (package
-    (name "r-gqtlstats")
-    (version "1.21.3")
-    (source
-     (origin
-       (method url-fetch)
-       (uri (bioconductor-uri "gQTLstats" version))
-       (sha256
-        (base32
-         "1h78l23idf867djmdk97b02jxgmz4vfr2dai01fp648d0lsx5mkl"))))
-    (properties `((upstream-name . "gQTLstats")))
-    (build-system r-build-system)
-    (propagated-inputs
-     `(("r-annotationdbi" ,r-annotationdbi)
-       ("r-batchjobs" ,r-batchjobs)
-       ("r-bbmisc" ,r-bbmisc)
-       ("r-beeswarm" ,r-beeswarm)
-       ("r-biobase" ,r-biobase)
-       ("r-biocgenerics" ,r-biocgenerics)
-       ("r-doparallel" ,r-doparallel)
-       ("r-dplyr" ,r-dplyr)
-       ("r-erma" ,r-erma)
-       ("r-ffbase" ,r-ffbase)
-       ("r-foreach" ,r-foreach)
-       ("r-genomeinfodb" ,r-genomeinfodb)
-       ("r-genomicfeatures" ,r-genomicfeatures)
-       ("r-genomicfiles" ,r-genomicfiles)
-       ("r-genomicranges" ,r-genomicranges)
-       ("r-ggbeeswarm" ,r-ggbeeswarm)
-       ("r-ggplot2" ,r-ggplot2)
-       ("r-gqtlbase" ,r-gqtlbase)
-       ("r-hardyweinberg" ,r-hardyweinberg)
-       ("r-homo-sapiens" ,r-homo-sapiens)
-       ("r-iranges" ,r-iranges)
-       ("r-limma" ,r-limma)
-       ("r-mgcv" ,r-mgcv)
-       ("r-plotly" ,r-plotly)
-       ("r-reshape2" ,r-reshape2)
-       ("r-s4vectors" ,r-s4vectors)
-       ("r-shiny" ,r-shiny)
-       ("r-snpstats" ,r-snpstats)
-       ("r-summarizedexperiment" ,r-summarizedexperiment)
-       ("r-variantannotation" ,r-variantannotation)))
-    (native-inputs
-     `(("r-knitr" ,r-knitr)))
-    (home-page "https://bioconductor.org/packages/gQTLstats")
-    (synopsis "Computationally efficient analysis for eQTL and allied studies")
-    (description
-     "This package provides tools for the computationally efficient analysis
-of @dfn{quantitative trait loci} (QTL) data, including eQTL, mQTL, dsQTL, etc.
-The software in this package aims to support refinements and functional
-interpretation of members of a collection of association statistics on a
-family of feature/genome hypotheses.")
-    (license license:artistic2.0)))
-
-(define-public r-gviz
-  (package
-    (name "r-gviz")
-    (version "1.34.0")
-    (source
-     (origin
-       (method url-fetch)
-       (uri (bioconductor-uri "Gviz" version))
-       (sha256
-        (base32
-         "0v7bz46b91dnrr55ah42ljj1i2xs3090s4w0lw8098pag00p4vh2"))))
-    (properties `((upstream-name . "Gviz")))
-    (build-system r-build-system)
-    (propagated-inputs
-     `(("r-annotationdbi" ,r-annotationdbi)
-       ("r-biobase" ,r-biobase)
-       ("r-biocgenerics" ,r-biocgenerics)
-       ("r-biomart" ,r-biomart)
-       ("r-biostrings" ,r-biostrings)
-       ("r-biovizbase" ,r-biovizbase)
-       ("r-bsgenome" ,r-bsgenome)
-       ("r-digest" ,r-digest)
-       ("r-ensembldb" ,r-ensembldb)
-       ("r-genomeinfodb" ,r-genomeinfodb)
-       ("r-genomicalignments" ,r-genomicalignments)
-       ("r-genomicfeatures" ,r-genomicfeatures)
-       ("r-genomicranges" ,r-genomicranges)
-       ("r-iranges" ,r-iranges)
-       ("r-lattice" ,r-lattice)
-       ("r-latticeextra" ,r-latticeextra)
-       ("r-matrixstats" ,r-matrixstats)
-       ("r-rcolorbrewer" ,r-rcolorbrewer)
-       ("r-rsamtools" ,r-rsamtools)
-       ("r-rtracklayer" ,r-rtracklayer)
-       ("r-s4vectors" ,r-s4vectors)
-       ("r-xvector" ,r-xvector)))
-    (native-inputs
-     `(("r-knitr" ,r-knitr)))
-    (home-page "https://bioconductor.org/packages/Gviz")
-    (synopsis "Plotting data and annotation information along genomic coordinates")
-    (description
-     "Genomic data analyses requires integrated visualization of known genomic
-information and new experimental data.  Gviz uses the biomaRt and the
-rtracklayer packages to perform live annotation queries to Ensembl and UCSC
-and translates this to e.g. gene/transcript structures in viewports of the
-grid graphics package.  This results in genomic information plotted together
-with your data.")
-    (license license:artistic2.0)))
-
-(define-public r-gwascat
-  (package
-    (name "r-gwascat")
-    (version "2.22.0")
-    (source
-     (origin
-       (method url-fetch)
-       (uri (bioconductor-uri "gwascat" version))
-       (sha256
-        (base32
-         "1aqi1ny93virnzsxkh9ccx3mws70bgv0r8nwgla09vffb7f16nna"))))
-    (build-system r-build-system)
-    (propagated-inputs
-     `(("r-annotationdbi" ,r-annotationdbi)
-       ("r-biocfilecache" ,r-biocfilecache)
-       ("r-biostrings" ,r-biostrings)
-       ("r-genomeinfodb" ,r-genomeinfodb)
-       ("r-genomicfeatures" ,r-genomicfeatures)
-       ("r-genomicranges" ,r-genomicranges)
-       ("r-iranges" ,r-iranges)
-       ("r-readr" ,r-readr)
-       ("r-s4vectors" ,r-s4vectors)
-       ("r-snpstats" ,r-snpstats)
-       ("r-variantannotation" ,r-variantannotation)))
-    (native-inputs
-     `(("r-knitr" ,r-knitr)))
-    (home-page "https://bioconductor.org/packages/gwascat")
-    (synopsis "Tools for data in the EMBL-EBI GWAS catalog")
-    (description
-     "This package provides tools for representing and modeling data in the
-EMBL-EBI GWAS catalog.")
-    (license license:artistic2.0)))
-
-(define-public r-sushi
-  (package
-    (name "r-sushi")
-    (version "1.28.0")
-    (source (origin
-              (method url-fetch)
-              (uri (bioconductor-uri "Sushi" version))
-              (sha256
-               (base32
-                "0ksj4f9z14mjsv6ssg5dwhpldw4r7wpdsln2if5g486mm1c56r8p"))))
-    (properties `((upstream-name . "Sushi")))
-    (build-system r-build-system)
-    (propagated-inputs
-     `(("r-biomart" ,r-biomart)
-       ("r-zoo" ,r-zoo)))
-    (home-page "https://bioconductor.org/packages/Sushi")
-    (synopsis "Tools for visualizing genomics data")
-    (description
-     "This package provides flexible, quantitative, and integrative genomic
-visualizations for publication-quality multi-panel figures.")
-    (license license:gpl2+)))
-
 (define-public r-dropbead
   (let ((commit "d746c6f3b32110428ea56d6a0001ce52a251c247")
         (revision "2"))