blob: 5b62a0663cb8209d793ba58503b5805b5ead3990 (
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
76
77
78
79
80
|
# Maintainer: Pekka Ristola <pekkarr [at] protonmail [dot] com>
_pkgname=epimutacions
_pkgver=1.8.0
pkgname=r-${_pkgname,,}
pkgver=${_pkgver//-/.}
pkgrel=1
pkgdesc="Robust outlier identification for DNA methylation data"
arch=(x86_64)
url="https://bioconductor.org/packages/$_pkgname"
license=('MIT')
depends=(
r-annotationdbi
r-annotationhub
r-biocgenerics
r-biocparallel
r-biomart
r-bumphunter
r-ensembldb
r-epimutacionsdata
r-experimenthub
r-genomeinfodb
r-genomicfeatures
r-genomicranges
r-ggplot2
r-ggrepel
r-gridextra
r-gviz
r-homo.sapiens
r-illuminahumanmethylation450kanno.ilmn12.hg19
r-illuminahumanmethylation450kmanifest
r-illuminahumanmethylationepicanno.ilm10b2.hg19
r-illuminahumanmethylationepicmanifest
r-iranges
r-isotree
r-matrixstats
r-minfi
r-purrr
r-reshape2
r-robustbase
r-rtracklayer
r-s4vectors
r-summarizedexperiment
r-tibble
r-txdb.hsapiens.ucsc.hg18.knowngene
r-txdb.hsapiens.ucsc.hg19.knowngene
r-txdb.hsapiens.ucsc.hg38.knowngene
)
checkdepends=(
r-testthat
)
optdepends=(
r-a4base
r-biocstyle
r-kableextra
r-knitr
r-rmarkdown
r-testthat
)
source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz")
md5sums=('694c3b410dc04c920577d6b16d905fe1')
b2sums=('aa049bfa3553767e84651b2e307ebd73711db57e961d214c5728ce1d53ca0ed21c9838242add7c952b2b62ae4190ce0bacda059a652f3e93dcf0832a8183bf3b')
build() {
mkdir build
R CMD INSTALL -l build "$_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"
}
|