blob: 575339a2c8be71f44f8a70505cb6573a3cc90e3d (
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
62
63
64
65
66
67
68
69
70
71
72
73
74
75
|
# Maintainer: Pekka Ristola <pekkarr [at] protonmail [dot] com>
_pkgname=HiContacts
_pkgver=1.8.0
pkgname=r-${_pkgname,,}
pkgver=${_pkgver//-/.}
pkgrel=1
pkgdesc="Analysing cool files in R with HiContacts"
arch=(any)
url="https://bioconductor.org/packages/$_pkgname"
license=('MIT')
depends=(
r-biocgenerics
r-biocio
r-biocparallel
r-dplyr
r-genomeinfodb
r-genomicranges
r-ggplot2
r-ggrastr
r-hicexperiment
r-interactionset
r-iranges
r-readr
r-rspectra
r-s4vectors
r-scales
r-stringr
r-summarizedexperiment
r-tibble
r-tidyr
)
checkdepends=(
r-bsgenome.scerevisiae.ucsc.saccer3
r-hicontactsdata
r-rfast
r-testthat
r-wgcna
)
optdepends=(
r-biocstyle
r-biostrings
r-bsgenome.scerevisiae.ucsc.saccer3
r-genomicfeatures
r-hicontactsdata
r-knitr
r-patchwork
r-rfast
r-rmarkdown
r-rtracklayer
r-terra
r-testthat
r-wgcna
)
source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz")
md5sums=('04024808b535cef83529e36f47032b54')
b2sums=('0780302845de4f255a1d53433ec2f259d38d8de02c29069ecf9bac07d4a9160b83fa994f22030bcae18a6b0b114da0b0f528544e52bccf6d11d03c701de710e1')
build() {
mkdir build
R CMD INSTALL -l build "$_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"
}
|