summarylogtreecommitdiffstats
path: root/PKGBUILD
blob: 8ac74e7f5c525081b31a34382107612fa2ed9cd9 (plain)
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
# Maintainer: Pekka Ristola <pekkarr [at] protonmail [dot] com>

_pkgname=lineagespot
_pkgver=1.8.0
pkgname=r-${_pkgname,,}
pkgver=${_pkgver//-/.}
pkgrel=1
pkgdesc="Detection of SARS-CoV-2 lineages in wastewater samples using next-generation sequencing"
arch=(any)
url="https://bioconductor.org/packages/$_pkgname"
license=('MIT')
depends=(
  r-data.table
  r-httr
  r-matrixgenerics
  r-stringr
  r-summarizedexperiment
  r-variantannotation
)
checkdepends=(
  r-testthat
)
optdepends=(
  r-biocstyle
  r-knitr
  r-refmanager
  r-rmarkdown
  r-testthat
)
source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz")
md5sums=('774c39427111843ee37e6cb07d38aa65')
b2sums=('39d1997b025158202722f62fc44a5909ce69b532a873415d0e5fcb3668a4fb42a6be52ef85ab6f6b15be8d56fd393bdfa454c87aa925ad2c56e3fdd41f669a44')

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"

  install -d "$pkgdir/usr/share/licenses/$pkgname"
  ln -s "/usr/lib/R/library/$_pkgname/LICENSE" "$pkgdir/usr/share/licenses/$pkgname"
}