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

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

_pkgname=VDJdive
_pkgver=1.6.0
pkgname=r-${_pkgname,,}
pkgver=${_pkgver//-/.}
pkgrel=1
pkgdesc="Analysis Tools for 10X V(D)J Data"
arch=(x86_64)
url="https://bioconductor.org/packages/$_pkgname"
license=('Artistic-2.0')
depends=(
  r-biocparallel
  r-cowplot
  r-ggplot2
  r-gridextra
  r-iranges
  r-rcolorbrewer
  r-rcpp
  r-s4vectors
  r-singlecellexperiment
  r-summarizedexperiment
)
checkdepends=(
  r-breakaway
  r-testthat
)
optdepends=(
  r-biocstyle
  r-breakaway
  r-covr
  r-knitr
  r-rmarkdown
  r-testthat
)
source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz")
md5sums=('1207027ee0cda0d82755db2892a9a327')
b2sums=('d97b8b2660bbff766d256e449057c1460daf1047f19b0e83c52077db6495b2983906bb6ff16c7780a4006c1708615a1e0795053294bb046f86b0d92cbb718903')

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"
}