blob: b2fd64882285ba67d741182e83a0124f4786fda1 (
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
|
# Maintainer: Pekka Ristola <pekkarr [at] protonmail [dot] com>
# Contributor: Guoyi Zhang <guoyizhang at malacology dot net>
_pkgname=GenomicDataCommons
_pkgver=1.28.2
pkgname=r-${_pkgname,,}
pkgver=${_pkgver//-/.}
pkgrel=1
pkgdesc="NIH / NCI Genomic Data Commons Access"
arch=(any)
url="https://bioconductor.org/packages/$_pkgname"
license=('Artistic-2.0')
depends=(
r-dplyr
r-genomicranges
r-httr
r-iranges
r-jsonlite
r-magrittr
r-rappdirs
r-readr
r-rlang
r-tibble
r-tidyr
r-xml2
)
checkdepends=(
r-testthat
)
optdepends=(
r-biocparallel
r-biocstyle
r-data.table
r-dt
r-genomicalignments
r-ggplot2
r-knitr
r-listviewer
r-maftools
r-r.utils
r-rmarkdown
r-rsamtools
r-testthat
r-txdb.hsapiens.ucsc.hg38.knowngene
r-variantannotation
)
source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz")
md5sums=('6d6759e675b94f49938c1a7ae741ce47')
b2sums=('71a59742e510a17d9b2dd0de9c84e21e12f72b732738d76dbc69bd45910ba7566030bdf630f3ffb6611beb328faf05e5240cede25f5d62c6ab150210e03045b3')
build() {
mkdir build
R CMD INSTALL -l build "$_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"
}
|