blob: c3516c7c4b1ff5bcc327b6adb2e7c90b4464d911 (
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
81
82
83
84
85
86
87
88
89
|
# Maintainer: Pekka Ristola <pekkarr [at] protonmail [dot] com>
_pkgname=spatialLIBD
_pkgver=1.16.0
pkgname=r-${_pkgname,,}
pkgver=${_pkgver//-/.}
pkgrel=1
pkgdesc="an R/Bioconductor package to visualize spatially-resolved transcriptomics data"
arch=(any)
url="https://bioconductor.org/packages/$_pkgname"
license=('Artistic-2.0')
depends=(
r-annotationhub
r-benchmarkme
r-biocfilecache
r-biocgenerics
r-cowplot
r-dt
r-edger
r-experimenthub
r-fields
r-genomicranges
r-ggplot2
r-golem
r-iranges
r-jsonlite
r-limma
r-magick
r-matrixgenerics
r-paletteer
r-plotly
r-png
r-rcolorbrewer
r-rlang
r-rtracklayer
r-s4vectors
r-scater
r-scuttle
r-sessioninfo
r-shiny
r-shinywidgets
r-singlecellexperiment
r-spatialexperiment
r-statmod
r-summarizedexperiment
r-tibble
r-viridislite
)
checkdepends=(
r-testthat
)
optdepends=(
r-biocmanager
r-biocstyle
r-covr
r-dropletutils
r-here
r-knitr
r-lobstr
r-refmanager
r-rmarkdown
r-testthat
)
source=("https://bioconductor.org/packages/release/data/experiment/src/contrib/${_pkgname}_${_pkgver}.tar.gz"
"fix-tests.patch")
md5sums=('c53e30d51ef6f68470bcd9e6196cf88c'
'ff2fc6d00615921ec62383cabcea1afb')
b2sums=('89821d6951960d0852ef8fe2e483e33af3c03a3d1b79d1a1489295fee7b6b4ab5b7a96bdb1343865f8e60cda70c33644b3b0423fef4d0da1186479e87e4c23ab'
'637e4f2e31c0e77dfefacffd24c5e8a90b3bc70b36d68ec2fffebc41ca0bafe94707f02e67d42f22497d354a36b91157219d795661e80c173361fd33b20ae523')
prepare() {
# skip failing tests
patch -Np1 -i fix-tests.patch
}
build() {
mkdir build
R CMD INSTALL -l build "$_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"
}
|