[lilac] updated to 2.12.2-2

1 files changed, 38 insertions, 20 deletions

diff --git a/PKGBUILD b/PKGBUILD
index 6688608088d9..d7721748376f 100644
--- a/PKGBUILD
+++ b/PKGBUILD
@@ -1,29 +1,33 @@
-# system requirements: GNU make, C++11
-# Maintainer: Guoyi Zhang <guoyizhang at malacology dot net>
+# Maintainer: Pekka Ristola <pekkarr [at] protonmail [dot] com>
+# Contributor: Guoyi Zhang <guoyizhang at malacology dot net>
+# Contributor: Nick B <Shirakawasuna at gmail _dot_com>
 
 _pkgname=flowCore
 _pkgver=2.12.2
 pkgname=r-${_pkgname,,}
-pkgver=2.12.2
-pkgrel=1
-pkgdesc='flowCore: Basic structures for flow cytometry data'
-arch=('x86_64')
+pkgver=${_pkgver//-/.}
+pkgrel=2
+pkgdesc="flowCore: Basic structures for flow cytometry data"
+arch=(x86_64)
 url="https://bioconductor.org/packages/${_pkgname}"
-license=('Artistic2.0')
+license=(Artistic2.0)
 depends=(
-  gcc
-  make
-  r
-  r-bh
   r-biobase
   r-biocgenerics
-  r-cpp11
   r-cytolib
   r-matrixstats
   r-rcpp
-  r-rprotobuflib
   r-s4vectors
 )
+makedepends=(
+  r-bh
+  r-cpp11
+  r-rprotobuflib
+)
+checkdepends=(
+  r-flowworkspacedata
+  r-testthat
+)
 optdepends=(
   r-flowstats
   r-flowviz
@@ -36,15 +40,29 @@ optdepends=(
   r-rgraphviz
   r-testthat
 )
-source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz")
-sha256sums=('1064a2941dbca4a25ff129ca8d62c9341b545aa070d6221987b2edeac3d57dfc')
-options=(!lto !buildflags staticlibs)
+source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz"
+        "fix-build.patch")
+md5sums=('92bb3f604d43aef47d1b8d4ecbb5f28d'
+         '219c62c718ad269fd5e832397a354e83')
+sha256sums=('1064a2941dbca4a25ff129ca8d62c9341b545aa070d6221987b2edeac3d57dfc'
+            '73e075b8ce2f0e9f3dea2e8778c6174586b71fb3c2b64c6ded4e5fb50ccd350c')
+
+prepare() {
+  # fix build and remove unnecessary import from tests
+  patch -Np1 -i fix-build.patch
+}
+
 build() {
-  R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}"
+  mkdir -p build
+  R CMD INSTALL "$_pkgname" -l build
+}
+
+check() {
+  cd "$_pkgname/tests"
+  R_LIBS="$srcdir/build" NOT_CRAN=true Rscript --vanilla testthat.R
 }
 
 package() {
-  install -dm0755 "${pkgdir}/usr/lib/R/library"
-  cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library"
+  install -d "$pkgdir/usr/lib/R/library"
+  cp -a --no-preserve=ownership "build/$_pkgname" "$pkgdir/usr/lib/R/library"
 }
-# vim:set ts=2 sw=2 et: