add r-tcgautils

2 files changed, 110 insertions, 0 deletions

diff --git a/.SRCINFO b/.SRCINFO
new file mode 100644
index 000000000000..0f987ba2d657
--- /dev/null
+++ b/.SRCINFO
@@ -0,0 +1,47 @@
+pkgbase = r-tcgautils
+	pkgdesc = TCGA utility functions for data management
+	pkgver = 1.16.0
+	pkgrel = 1
+	url = https://bioconductor.org/packages/TCGAutils
+	arch = any
+	license = Artistic2.0
+	depends = r
+	depends = r-annotationdbi
+	depends = r-biocgenerics
+	depends = r-genomeinfodb
+	depends = r-genomicdatacommons
+	depends = r-genomicfeatures
+	depends = r-genomicranges
+	depends = r-iranges
+	depends = r-multiassayexperiment
+	depends = r-raggedexperiment
+	depends = r-rvest
+	depends = r-s4vectors
+	depends = r-stringr
+	depends = r-summarizedexperiment
+	depends = r-xml2
+	optdepends = r-biocfilecache
+	optdepends = r-biocstyle
+	optdepends = r-complexheatmap
+	optdepends = r-curatedtcgadata
+	optdepends = r-devtools
+	optdepends = r-dplyr
+	optdepends = r-illuminahumanmethylation450kanno.ilmn12.hg19
+	optdepends = r-impute
+	optdepends = r-knitr
+	optdepends = r-magrittr
+	optdepends = r-mirbase.db
+	optdepends = r-org.hs.eg.db
+	optdepends = r-r.utils
+	optdepends = r-rcolorbrewer
+	optdepends = r-readr
+	optdepends = r-rmarkdown
+	optdepends = r-rtcgatoolbox
+	optdepends = r-rtracklayer
+	optdepends = r-testthat
+	optdepends = r-txdb.hsapiens.ucsc.hg18.knowngene
+	optdepends = r-txdb.hsapiens.ucsc.hg19.knowngene
+	source = https://bioconductor.org/packages/release/bioc/src/contrib/TCGAutils_1.16.0.tar.gz
+	sha256sums = 0ce2b04849c7c9fafb3193fb26d0df249e9e3e953a0f25b285e6ab5200fa0276
+
+pkgname = r-tcgautils
diff --git a/PKGBUILD b/PKGBUILD
new file mode 100644
index 000000000000..3a631b2059ed
--- /dev/null
+++ b/PKGBUILD
@@ -0,0 +1,63 @@
+# Maintainer: Guoyi Zhang <guoyizhang at malacology dot net>
+
+_pkgname=TCGAutils
+_pkgver=1.16.0
+pkgname=r-${_pkgname,,}
+pkgver=1.16.0
+pkgrel=1
+pkgdesc='TCGA utility functions for data management'
+arch=('any')
+url="https://bioconductor.org/packages/${_pkgname}"
+license=('Artistic2.0')
+depends=(
+  r
+  r-annotationdbi
+  r-biocgenerics
+  r-genomeinfodb
+  r-genomicdatacommons
+  r-genomicfeatures
+  r-genomicranges
+  r-iranges
+  r-multiassayexperiment
+  r-raggedexperiment
+  r-rvest
+  r-s4vectors
+  r-stringr
+  r-summarizedexperiment
+  r-xml2
+)
+optdepends=(
+  r-biocfilecache
+  r-biocstyle
+  r-complexheatmap
+  r-curatedtcgadata
+  r-devtools
+  r-dplyr
+  r-illuminahumanmethylation450kanno.ilmn12.hg19
+  r-impute
+  r-knitr
+  r-magrittr
+  r-mirbase.db
+  r-org.hs.eg.db
+  r-r.utils
+  r-rcolorbrewer
+  r-readr
+  r-rmarkdown
+  r-rtcgatoolbox
+  r-rtracklayer
+  r-testthat
+  r-txdb.hsapiens.ucsc.hg18.knowngene
+  r-txdb.hsapiens.ucsc.hg19.knowngene
+)
+source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz")
+sha256sums=('0ce2b04849c7c9fafb3193fb26d0df249e9e3e953a0f25b285e6ab5200fa0276')
+
+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: