blob: c1162eb75bff350512a0f8d868c99f75edc2b7e8 (
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
61
|
# Maintainer: Pekka Ristola <pekkarr [at] protonmail [dot] com>
_pkgname=gDNAx
_pkgver=1.0.1
pkgname=r-${_pkgname,,}
pkgver=${_pkgver//-/.}
pkgrel=1
pkgdesc="Diagnostics for assessing genomic DNA contamination in RNA-seq data"
arch=(any)
url="https://bioconductor.org/packages/$_pkgname"
license=('Artistic-2.0')
depends=(
r-annotationdbi
r-annotationhub
r-biocgenerics
r-biocparallel
r-biostrings
r-bitops
r-genomeinfodb
r-genomicalignments
r-genomicfeatures
r-genomicfiles
r-genomicranges
r-iranges
r-plotrix
r-rcolorbrewer
r-rsamtools
r-s4vectors
r-summarizedexperiment
)
checkdepends=(
r-gdnainrnaseqdata
r-runit
r-txdb.hsapiens.ucsc.hg38.knowngene
)
optdepends=(
r-biocstyle
r-gdnainrnaseqdata
r-knitr
r-rmarkdown
r-runit
r-txdb.hsapiens.ucsc.hg38.knowngene
)
source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz")
md5sums=('4f51a23263fff85c936d0319a2c0e1de')
b2sums=('9563776d06f41efe8bd315cd2b3a16d451010e6a33f2f4dee3670c91d1f0ffdb8ecae228a4b6851d03431d1ed1930808f0899ce8dd4889ac32ef027cc5ec9bc1')
build() {
mkdir build
R CMD INSTALL -l build "$_pkgname"
}
check() {
cd "$_pkgname/tests"
R_LIBS="$srcdir/build" Rscript --vanilla runTests.R
}
package() {
install -d "$pkgdir/usr/lib/R/library"
cp -a --no-preserve=ownership "build/$_pkgname" "$pkgdir/usr/lib/R/library"
}
|