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# Maintainer: Pekka Ristola <pekkarr [at] protonmail [dot] com>
_pkgname=MSA2dist
_pkgver=1.8.0
pkgname=r-${_pkgname,,}
pkgver=${_pkgver//-/.}
pkgrel=1
pkgdesc="MSA2dist calculates pairwise distances between all sequences of a DNAStringSet or a AAStringSet using a custom score matrix and conducts codon based analysis"
arch=(x86_64)
url="https://bioconductor.org/packages/$_pkgname"
license=('GPL-3.0-only')
depends=(
r-ape
r-biostrings
r-doparallel
r-dplyr
r-foreach
r-genomicranges
r-iranges
r-pwalign
r-rcpp
r-rlang
r-seqinr
r-stringi
r-stringr
r-tibble
r-tidyr
)
makedepends=(
r-rcppthread
)
checkdepends=(
r-testthat
)
optdepends=(
r-biocstyle
r-devtools
r-ggplot2
r-knitr
r-rmarkdown
r-testthat
)
source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz")
md5sums=('f2246da253b2a0d5b3464c228774ad38')
b2sums=('20df7449d220733b87dbe20c42984398fadda3a04b06fd5443aaaf3a1687383609ac03584195af8884070498560412470a1c8f667eeae2e866f20e80246526af')
build() {
mkdir build
R CMD INSTALL -l build "$_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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