PKGBUILD


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
51
52
53
54
55

# Maintainer: Pekka Ristola <pekkarr [at] protonmail [dot] com>

_pkgname=cytofQC
_pkgver=1.6.0
pkgname=r-${_pkgname,,}
pkgver=${_pkgver//-/.}
pkgrel=1
pkgdesc="Labels normalized cells for CyTOF data and assigns probabilities for each label"
arch=(any)
url="https://bioconductor.org/packages/$_pkgname"
license=('Artistic-2.0')
depends=(
  r-catalyst
  r-e1071
  r-eztune
  r-flowcore
  r-gbm
  r-ggplot2
  r-hrbrthemes
  r-matrixstats
  r-randomforest
  r-rmarkdown
  r-s4vectors
  r-singlecellexperiment
  r-ssc
  r-summarizedexperiment
)
checkdepends=(
  r-testthat
)
optdepends=(
  r-gridextra
  r-knitr
  r-rcolorbrewer
  r-testthat
  r-uwot
)
source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz")
md5sums=('3884c0b74e8168170174b23717c1f6fe')
b2sums=('e7165719cb253f34a2270bad88e381786271637ac0bbc6ee9a0059a8f0b04d3922b1fa70b1d887bd72df4d02a5f24c06f989a633cac84dbbf428086c20c75228')

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"
}