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# Maintainer: Pekka Ristola <pekkarr [at] protonmail [dot] com>
_pkgname=SVMDO
_pkgver=1.4.7
pkgname=r-${_pkgname,,}
pkgver=${_pkgver//-/.}
pkgrel=1
pkgdesc="Identification of Tumor-Discriminating mRNA Signatures via Support Vector Machines Supported by Disease Ontology"
arch=(any)
url="https://bioconductor.org/packages/$_pkgname"
license=('GPL-3.0-only')
depends=(
r-annotationdbi
r-bsda
r-caret
r-catools
r-data.table
r-dose
r-dplyr
r-dt
r-e1071
r-golem
r-klar
r-nortest
r-org.hs.eg.db
r-shiny
r-shinyfiles
r-shinytitle
r-sjmisc
r-summarizedexperiment
)
checkdepends=(
r-testthat
)
optdepends=(
r-biocstyle
r-knitr
r-rmarkdown
r-testthat
)
source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz"
"fix-tests.patch")
md5sums=('2b0d486ce1b3279cfbac4b9626a41666'
'ace8dbf4ccc927c5fee18f3403240bd2')
b2sums=('26d38cbf1b6fa773acdfb75bd55efc6a6b83bd4b15d513e6162bc9498610687be1181031e9f1e193f07810ca408e86552a367227e3b9aea87d3d46a9e6e3c410'
'f2a0015c8d43679b7e388b8183c4f1b67422f62fe2b1b58371bf65f341c8fcea91fddaf6f91bb8811997bedb0045590c5f97e6e1f9d2c373a5fffab3b31a430c')
prepare() {
# skip failing tests
patch -Np1 -i fix-tests.patch
}
build() {
mkdir build
R CMD INSTALL -l build "$_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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