blob: 62175bfd8fe499111234a6a9011e279e950ee74e (
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
51
52
53
54
55
56
57
58
59
60
|
# Maintainer: Pekka Ristola <pekkarr [at] protonmail [dot] com>
_pkgname=HiCExperiment
_pkgver=1.6.0
pkgname=r-${_pkgname,,}
pkgver=${_pkgver//-/.}
pkgrel=1
pkgdesc="Bioconductor class for interacting with Hi-C files in R"
arch=(any)
url="https://bioconductor.org/packages/$_pkgname"
license=('MIT')
depends=(
r-biocgenerics
r-biocio
r-biocparallel
r-dplyr
r-genomeinfodb
r-genomicranges
r-interactionset
r-iranges
r-rhdf5
r-s4vectors
r-strawr
r-vroom
)
checkdepends=(
r-hicontactsdata
r-testthat
)
optdepends=(
r-biocfilecache
r-biocstyle
r-hicontacts
r-hicontactsdata
r-knitr
r-rmarkdown
r-rtracklayer
r-testthat
)
source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz")
md5sums=('78ff18f540ccf6d3459097f2575c3ef0')
b2sums=('5b806e653a63257c8f0ee442dbb701926a913c150a27592182975fab472a2e7c61cc68a92299d85dc5232d22ae922390b4995d22797f79ac6d9283014e7c817d')
build() {
mkdir build
R CMD INSTALL -l build "$_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"
}
|