add r-tcgabiolinks

2 files changed, 154 insertions, 0 deletions

diff --git a/.SRCINFO b/.SRCINFO
new file mode 100644
index 000000000000..2cbb48b6721b
--- /dev/null
+++ b/.SRCINFO
@@ -0,0 +1,69 @@
+pkgbase = r-tcgabiolinks
+	pkgdesc = TCGAbiolinks: An R/Bioconductor package for integrative analysis with GDC data
+	pkgver = 2.24.1
+	pkgrel = 3
+	url = https://bioconductor.org/packages/TCGAbiolinks
+	arch = any
+	license = GPL
+	depends = r
+	depends = r-biomart
+	depends = r-data.table
+	depends = r-downloader
+	depends = r-dplyr
+	depends = r-genomicranges
+	depends = r-ggplot2
+	depends = r-httr
+	depends = r-iranges
+	depends = r-jsonlite
+	depends = r-knitr
+	depends = r-plyr
+	depends = r-purrr
+	depends = r-r.utils
+	depends = r-readr
+	depends = r-rvest
+	depends = r-s4vectors
+	depends = r-stringr
+	depends = r-summarizedexperiment
+	depends = r-tcgabiolinksgui.data
+	depends = r-tibble
+	depends = r-tidyr
+	depends = r-xml
+	depends = r-xml2
+	optdepends = r-affy
+	optdepends = r-biobase
+	optdepends = r-biocstyle
+	optdepends = r-c3net
+	optdepends = r-circlize
+	optdepends = r-clusterprofiler
+	optdepends = r-complexheatmap
+	optdepends = r-consensusclusterplus
+	optdepends = r-devtools
+	optdepends = r-dnet
+	optdepends = r-doparallel
+	optdepends = r-edaseq
+	optdepends = r-edger
+	optdepends = r-genefilter
+	optdepends = r-ggrepel
+	optdepends = r-grid
+	optdepends = r-gridextra
+	optdepends = r-igraph
+	optdepends = r-jpeg
+	optdepends = r-limma
+	optdepends = r-maftools
+	optdepends = r-minet
+	optdepends = r-parallel
+	optdepends = r-parmigene
+	optdepends = r-pathview
+	optdepends = r-png
+	optdepends = r-rmarkdown
+	optdepends = r-scales
+	optdepends = r-sesame
+	optdepends = r-suprahex
+	optdepends = r-survival
+	optdepends = r-survminer
+	optdepends = r-sva
+	optdepends = r-testthat
+	source = https://bioconductor.org/packages/release/bioc/src/contrib/TCGAbiolinks_2.24.1.tar.gz
+	sha256sums = 24dc728f1ba157047a01f6061af3b4b32275a4e339c0e38ebc11d48e5ea6844f
+
+pkgname = r-tcgabiolinks
diff --git a/PKGBUILD b/PKGBUILD
new file mode 100644
index 000000000000..c459512c41ba
--- /dev/null
+++ b/PKGBUILD
@@ -0,0 +1,85 @@
+# Maintainer: Guoyi Zhang <guoyizhang at malacology dot net>
+
+_pkgname=TCGAbiolinks
+_pkgver=2.24.1
+pkgname=r-${_pkgname,,}
+pkgver=2.24.1
+pkgrel=3
+pkgdesc='TCGAbiolinks: An R/Bioconductor package for integrative analysis with GDC data'
+arch=('any')
+url="https://bioconductor.org/packages/${_pkgname}"
+license=('GPL')
+depends=(
+  r
+  r-biomart
+  r-data.table
+  r-downloader
+  r-dplyr
+  r-genomicranges
+  r-ggplot2
+  r-httr
+  r-iranges
+  r-jsonlite
+  r-knitr
+  r-plyr
+  r-purrr
+  r-r.utils
+  r-readr
+  r-rvest
+  r-s4vectors
+  r-stringr
+  r-summarizedexperiment
+  r-tcgabiolinksgui.data
+  r-tibble
+  r-tidyr
+  r-xml
+  r-xml2
+)
+optdepends=(
+  r-affy
+  r-biobase
+  r-biocstyle
+  r-c3net
+  r-circlize
+  r-clusterprofiler
+  r-complexheatmap
+  r-consensusclusterplus
+  r-devtools
+  r-dnet
+  r-doparallel
+  r-edaseq
+  r-edger
+  r-genefilter
+  r-ggrepel
+  r-grid
+  r-gridextra
+  r-igraph
+  r-jpeg
+  r-limma
+  r-maftools
+  r-minet
+  r-parallel
+  r-parmigene
+  r-pathview
+  r-png
+  r-rmarkdown
+  r-scales
+  r-sesame
+  r-suprahex
+  r-survival
+  r-survminer
+  r-sva
+  r-testthat
+)
+source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz")
+sha256sums=('24dc728f1ba157047a01f6061af3b4b32275a4e339c0e38ebc11d48e5ea6844f')
+
+build() {
+  R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}"
+}
+
+package() {
+  install -dm0755 "${pkgdir}/usr/lib/R/library"
+  cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library"
+}
+# vim:set ts=2 sw=2 et: