blob: b756c3e35cfe115ce094c0b3079c2e16655a65e2 (
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
|
# Maintainer: Pekka Ristola <pekkarr [at] protonmail [dot] com>
# Contributor: Guoyi Zhang <guoyizhang at malacology dot net>
_pkgname=flowWorkspace
_pkgver=4.14.3
pkgname=r-${_pkgname,,}
pkgver=${_pkgver//-/.}
pkgrel=1
pkgdesc="Infrastructure for representing and interacting with gated and ungated cytometry data sets"
arch=(x86_64)
url="https://bioconductor.org/packages/$_pkgname"
license=('AGPL-3.0-only')
depends=(
boost-libs
hdf5
r-biobase
r-biocgenerics
r-cytolib
r-data.table
r-delayedarray
r-dplyr
r-flowcore
r-ggplot2
r-graph
r-matrixstats
r-ncdfflow
r-rbgl
r-rgraphviz
r-rprotobuflib
r-s4vectors
r-scales
r-xml
)
makedepends=(
boost
r-bh
r-cpp11
r-rhdf5lib
)
checkdepends=(
r-flowworkspacedata
r-testthat
)
optdepends=(
r-cytoml
r-flowworkspacedata
r-ggcyto
r-knitr
r-opencyto
r-rmarkdown
r-testthat
)
source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz"
"system-hdf5.patch")
md5sums=('84495f076b13f32e0f98817c8ff03ede'
'd83db00432ba74621da54d24fce960fc')
b2sums=('7d241283522c1eaab9e5124b73504d83f76de210d42dccebcdc292f9a5cce78c1701ef89d33021f9aaf416d4a192b296b920cf75fcd8b768b1a345655737142c'
'5f693100c9198981f8ff28aca945499054570fb5957ae22c908f2e4c19cf79704e5961589632e6568a5e62229b678ab748c02333919a18193b773c1ed602bbaf')
prepare() {
# use system hdf5 and skip failing tests
patch -Np1 -i system-hdf5.patch
}
build() {
mkdir build
R CMD INSTALL -l build "$_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"
}
|