[lilac] updated to 2.12.0-2

3 files changed, 74 insertions, 32 deletions

diff --git a/.SRCINFO b/.SRCINFO
index 69d7324be058..ac4018549b79 100644
--- a/.SRCINFO
+++ b/.SRCINFO
@@ -1,17 +1,20 @@
 pkgbase = r-cytoml
 	pkgdesc = A GatingML Interface for Cross Platform Cytometry Data Sharing
 	pkgver = 2.12.0
-	pkgrel = 1
+	pkgrel = 2
 	url = https://bioconductor.org/packages/CytoML
 	arch = x86_64
-	license = custom
-	depends = gcc
+	license = AGPL3
+	checkdepends = r-flowworkspacedata
+	checkdepends = r-testthat
+	makedepends = boost
+	makedepends = r-bh
+	makedepends = r-cpp11
+	makedepends = r-rhdf5lib
+	makedepends = r-rprotobuflib
+	depends = boost-libs
 	depends = libxml2
-	depends = make
-	depends = r
-	depends = r-bh
 	depends = r-biobase
-	depends = r-cpp11
 	depends = r-cytolib
 	depends = r-data.table
 	depends = r-dplyr
@@ -23,17 +26,18 @@ pkgbase = r-cytoml
 	depends = r-opencyto
 	depends = r-rbgl
 	depends = r-rgraphviz
-	depends = r-rhdf5lib
-	depends = r-rprotobuflib
 	depends = r-tibble
 	depends = r-xml
 	depends = r-yaml
 	optdepends = r-flowworkspacedata
 	optdepends = r-knitr
-	optdepends = r-parallel
 	optdepends = r-rmarkdown
 	optdepends = r-testthat
 	source = https://bioconductor.org/packages/release/bioc/src/contrib/CytoML_2.12.0.tar.gz
+	source = system-hdf5.patch
+	md5sums = 5118f217fc4d383753ddb7c749b5c949
+	md5sums = c830342f553f0cfc7ac954ec93b429c2
 	sha256sums = 6e03532826526949599a15f615472c9c7f4577c51772a2ea2e4088694b7834a7
+	sha256sums = f97522aab6e311702e9606c370d4e2eed01169a83d7fc01bf6bb5ad90b115a05
 
 pkgname = r-cytoml
diff --git a/PKGBUILD b/PKGBUILD
index 0a76a7a644c5..c0489e5fb21e 100644
--- a/PKGBUILD
+++ b/PKGBUILD
@@ -1,23 +1,19 @@
-# system requirements: xml2, 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>
 
 _pkgname=CytoML
 _pkgver=2.12.0
 pkgname=r-${_pkgname,,}
-pkgver=2.12.0
-pkgrel=1
-pkgdesc='A GatingML Interface for Cross Platform Cytometry Data Sharing'
-arch=('x86_64')
+pkgver=${_pkgver//-/.}
+pkgrel=2
+pkgdesc="A GatingML Interface for Cross Platform Cytometry Data Sharing"
+arch=(x86_64)
 url="https://bioconductor.org/packages/${_pkgname}"
-license=('custom')
+license=(AGPL3)
 depends=(
-  gcc
+  boost-libs
   libxml2
-  make
-  r
-  r-bh
   r-biobase
-  r-cpp11
   r-cytolib
   r-data.table
   r-dplyr
@@ -29,29 +25,50 @@ depends=(
   r-opencyto
   r-rbgl
   r-rgraphviz
-  r-rhdf5lib
-  r-rprotobuflib
   r-tibble
   r-xml
   r-yaml
 )
+makedepends=(
+  boost
+  r-bh
+  r-cpp11
+  r-rhdf5lib
+  r-rprotobuflib
+)
+checkdepends=(
+  r-flowworkspacedata
+  r-testthat
+)
 optdepends=(
   r-flowworkspacedata
   r-knitr
-  r-parallel
   r-rmarkdown
   r-testthat
 )
-source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz")
-sha256sums=('6e03532826526949599a15f615472c9c7f4577c51772a2ea2e4088694b7834a7')
+source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz"
+        "system-hdf5.patch")
+md5sums=('5118f217fc4d383753ddb7c749b5c949'
+         'c830342f553f0cfc7ac954ec93b429c2')
+sha256sums=('6e03532826526949599a15f615472c9c7f4577c51772a2ea2e4088694b7834a7'
+            'f97522aab6e311702e9606c370d4e2eed01169a83d7fc01bf6bb5ad90b115a05')
+
+prepare() {
+  # use system hdf5
+  patch -Np1 -i system-hdf5.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}" "${pkgdir}/usr/lib/R/library"
-  install -Dm644 "${_pkgname}/LICENSE" -t "${pkgdir}/usr/share/licenses/${pkgname}"
+  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:
diff --git a/system-hdf5.patch b/system-hdf5.patch
new file mode 100644
index 000000000000..a05e902d587e
--- /dev/null
+++ b/system-hdf5.patch
@@ -0,0 +1,21 @@
+diff --git a/CytoML/src/Makevars.in b/CytoML/src/Makevars.in
+index 9b169a2..d12c8be 100644
+--- a/CytoML/src/Makevars.in
++++ b/CytoML/src/Makevars.in
+@@ -6,13 +6,10 @@ ifneq (,)
+ This makefile requires GNU Make.
+ endif
+ 	
+-CXX_STD = CXX11
++CXX_STD = CXX17
+ 
+ PKG_CPPFLAGS =-DROUT -I../inst/include/ @PKG_CPPFLAGS@ -DBOOST_NO_AUTO_PTR 
+ 
+-RHDF5_LIBS= $(shell echo 'Rhdf5lib::pkgconfig("PKG_CXX_LIBS")'|\
+-    "${R_HOME}/bin/R" --vanilla --slave)
++CLINK_CPPFLAGS := -I/usr/lib/R/library/cpp11/include -I/usr/lib/R/library/RProtoBufLib/include -I/usr/lib/R/library/cytolib/include -I/usr/lib/R/library/flowWorkspace/include
+ 
+-PKG_LIBS = `${R_HOME}/bin/Rscript -e "cytolib:::cytolib_LdFlags()"` $(RHDF5_LIBS) $(LAPACK_LIBS) $(BLAS_LIBS) @PKG_LIBS@   
+-
+-  
++PKG_LIBS = `${R_HOME}/bin/Rscript -e "cytolib:::cytolib_LdFlags()"` $(LAPACK_LIBS) $(BLAS_LIBS) @PKG_LIBS@