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# Maintainer: Pekka Ristola <pekkarr [at] protonmail [dot] com>
_pkgname=factR
_pkgver=1.6.0
pkgname=r-${_pkgname,,}
pkgver=${_pkgver//-/.}
pkgrel=1
pkgdesc="Functional Annotation of Custom Transcriptomes"
arch=(any)
url="https://bioconductor.org/packages/$_pkgname"
license=('Apache-2.0')
depends=(
r-biocgenerics
r-biocparallel
r-biostrings
r-crayon
r-data.table
r-dplyr
r-drawproteins
r-genomeinfodb
r-genomicfeatures
r-genomicranges
r-ggplot2
r-iranges
r-pbapply
r-purrr
r-rcurl
r-rlang
r-rtracklayer
r-s4vectors
r-stringr
r-tibble
r-tidyr
r-wiggleplotr
r-xml
)
checkdepends=(
r-annotationhub
r-bsgenome.mmusculus.ucsc.mm10
r-testthat
)
optdepends=(
r-annotationhub
r-bio3d
r-bsgenome
r-bsgenome.mmusculus.ucsc.mm10
r-covr
r-knitr
r-markdown
r-patchwork
r-rmarkdown
r-rmdformats
r-signalhsmm
r-testthat
r-tidyverse
r-zeallot
)
source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz")
md5sums=('71444320c46af980fffd92815ed30e84')
b2sums=('a3ac343c955a2b8b5a5fbc367c655baeb10af39083fce20ebba202136f7ed5467609aaf7d22f183004924346e98db517a5a6559f4e9af039897d3fb2b9646aa0')
build() {
mkdir build
R CMD INSTALL -l build "$_pkgname"
}
check() {
cd "$_pkgname/tests"
R_LIBS="$srcdir/build" NOT_CRAN=true Rscript --vanilla testthat.R
}
package() {
install -d "$pkgdir/usr/lib/R/library"
cp -a --no-preserve=ownership "build/$_pkgname" "$pkgdir/usr/lib/R/library"
}
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