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# Maintainer: Pekka Ristola <pekkarr [at] protonmail [dot] com>
_pkgname=syntenet
_pkgver=1.14.0
pkgname=r-${_pkgname,,}
pkgver=${_pkgver//-/.}
pkgrel=1
pkgdesc="Inference And Analysis Of Synteny Networks"
arch=(x86_64)
url="https://bioconductor.org/packages/$_pkgname"
license=('GPL-3.0-only')
depends=(
r-biocparallel
r-biostrings
r-genomicranges
r-ggnetwork
r-ggplot2
r-igraph
r-intergraph
r-pheatmap
r-rcolorbrewer
r-rcpp
r-rlang
)
makedepends=(
r-testthat
)
checkdepends=(
r-xml2
)
optdepends=(
r-biocstyle
r-covr
r-ggtree
r-knitr
r-labdsv
r-networkd3
r-rmarkdown
r-rtracklayer
r-testthat
r-xml2
)
source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz")
md5sums=('37b2833ca59ffa90209216f5fd842d49')
b2sums=('18a74408f5df4936ddfd10ea9e9a870fc1c334bf7ca98e3ea13d27a575c5d32a1d87c118fa7029394ac678fdaf4c49a150596a7ec2f4f08dde4581cf213b3fca')
#prepare() {
# skip tests that cause a coredump
# sed -i '1i skip("dumps core")' "$_pkgname/tests/testthat/test-03_synteny_detection.R"
#}
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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