blob: b35fdccf24f096805aa42bd3048dbf0a59a2d1f3 (
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: peippo <christoph+aur@christophfink.com>
# Contributor: Viktor Drobot (aka dviktor) linux776 [at] gmail [dot] com
# Contributor: Grey Christoforo <first name at last name dot net>
_bcname=GenomeInfoDb
_bcver=1.34.9
pkgname="r-${_bcname,,}"
pkgver="${_bcver//[:-]/.}"
pkgrel=2
pkgdesc="Utilities for manipulating chromosome names, including modifying them to follow a particular naming style"
arch=("any")
url="https://bioconductor.org/packages/release/bioc/html/${_bcname}.html"
license=("Artistic2.0")
depends=(
"r>=4.0.0"
"r-biocgenerics>=0.37.0"
"r-s4vectors>=0.25.12"
"r-iranges>=2.13.12"
"r-rcurl"
"r-genomeinfodbdata"
)
optdepends=(
"r-genomicranges"
"r-rsamtools"
"r-genomicalignments"
"r-genomicfeatures"
"r-txdb.dmelanogaster.ucsc.dm3.ensgene"
"r-bsgenome"
"r-bsgenome.scerevisiae.ucsc.saccer2"
"r-bsgenome.celegans.ucsc.ce2"
"r-bsgenome.hsapiens.ncbi.grch38"
"r-runit"
"r-biocstyle"
"r-knitr"
)
checkdepends=(
"${optdepends[@]}"
"r-rcmdcheck"
)
source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_bcname}_${_bcver}.tar.gz")
b2sums=('d6e3e86125cc3f5e1ac703a75cee215da5da74321729a4b0b9956883049ca61a5bd1f104809c895ebb13aae75618b2d644607a63a779388d54443a738c9a9afd')
build() {
mkdir -p "${srcdir}/build/"
R CMD INSTALL ${_bcname}_${_bcver}.tar.gz -l "${srcdir}/build/"
}
check() {
cd "${srcdir}/${_bcname}/"
R_LIBS="${srcdir}/build/" R CMD check --no-manual --no-multiarch --no-vignettes .
}
package() {
install -dm0755 "${pkgdir}/usr/lib/R/library"
cp -a --no-preserve=ownership "${srcdir}/build/${_bcname}" "${pkgdir}/usr/lib/R/library"
if [[ -f "${_cranname}/LICENSE" ]]; then
install -Dm0644 "${_cranname}/LICENSE" "${pkgdir}/usr/share/licenses/${pkgname}/LICENSE"
fi
}
|