blob: eeb376ec152c7f861548886fe2f5fd0db89c2751 (
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
|
# Maintainer: Pekka Ristola <pekkarr [at] protonmail [dot] com>
_pkgname=decontX
_pkgver=1.2.0
pkgname=r-${_pkgname,,}
pkgver=${_pkgver//-/.}
pkgrel=1
pkgdesc="Decontamination of single cell genomics data"
arch=(x86_64)
url="https://bioconductor.org/packages/$_pkgname"
license=('MIT')
depends=(
onetbb
r-celda
r-dbscan
r-delayedarray
r-ggplot2
r-mcmcprecision
r-patchwork
r-plyr
r-rcpp
r-rcppparallel
r-reshape2
r-rstan
r-rstantools
r-s4vectors
r-scater
r-seurat
r-singlecellexperiment
r-summarizedexperiment
r-withr
)
makedepends=(
r-bh
r-rcppeigen
r-stanheaders
)
checkdepends=(
r-testthat
)
optdepends=(
r-biocstyle
r-dplyr
r-knitr
r-rmarkdown
r-scran
r-singlecellmultimodal
r-tenxpbmcdata
r-testthat
)
source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz")
md5sums=('3d4a6f83a54c9f4cad51d594335a63ae')
b2sums=('b990dd26e924d7979e2215bb1982165534e1e060b2aa550043cf481de40452bb064953cfab5ee2d2ae1db4e3d16687def13b34ef60e94faf83243734b41bb1a2')
build() {
mkdir build
R CMD INSTALL -l build "$_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"
}
|