blob: bce2ba8a9306dd0ca9e61357fa9b2c9c9cb88123 (
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
|
# Maintainer: Pekka Ristola <pekkarr [at] protonmail [dot] com>
# Contributor: Guoyi Zhang <guoyizhang at malacology dot net>
_pkgname=CytoML
_pkgver=2.16.0
pkgname=r-${_pkgname,,}
pkgver=${_pkgver//-/.}
pkgrel=1
pkgdesc="A GatingML Interface for Cross Platform Cytometry Data Sharing"
arch=(x86_64)
url="https://bioconductor.org/packages/$_pkgname"
license=('AGPL-3.0-only')
depends=(
boost-libs
libxml2
r-biobase
r-cytolib
r-data.table
r-dplyr
r-flowcore
r-flowworkspace
r-ggcyto
r-graph
r-jsonlite
r-opencyto
r-rbgl
r-rgraphviz
r-tibble
r-xml
r-yaml
)
makedepends=(
boost
r-bh
r-cpp11
r-rhdf5lib
r-rprotobuflib
)
checkdepends=(
r-flowworkspacedata
r-testthat
)
optdepends=(
r-flowworkspacedata
r-knitr
r-rmarkdown
r-testthat
)
source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz"
"system-hdf5.patch")
md5sums=('54cae297dff28f9f6a8b7b23cdc1c427'
'c830342f553f0cfc7ac954ec93b429c2')
b2sums=('f3773f14b2933afe3118704dd7a6d7b3ee984055b51c955d3ee87aefb67e66163896f3272d6256355884a20cc56cf9449a0953eae9f0c81e1bf31158fa6389f9'
'841b451423480c8a53debd7b63f5d83e27ffb064e2eff8051f284560f658cac1826fbf0172fad09aa3810f78e7a4cfd3ad41bdaf3fc28ec4c8d76ed2f418e666')
prepare() {
# use system hdf5
patch -Np1 -i system-hdf5.patch
}
build() {
mkdir build
R CMD INSTALL -l build "$_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"
}
|