[lilac] updated to 1.16.0-2

3 files changed, 50 insertions, 25 deletions

diff --git a/.SRCINFO b/.SRCINFO
index 54b428202052..2f80b4fb8d82 100644
--- a/.SRCINFO
+++ b/.SRCINFO
@@ -1,11 +1,13 @@
 pkgbase = r-scgps
 	pkgdesc = A complete analysis of single cell subpopulations, from identifying subpopulations to analysing their relationship (scGPS = single cell Global Predictions of Subpopulation)
 	pkgver = 1.16.0
-	pkgrel = 1
+	pkgrel = 2
 	url = https://bioconductor.org/packages/scGPS
 	arch = x86_64
-	license = GPL
-	depends = r
+	license = GPL-3.0-only
+	checkdepends = r-testthat
+	depends = blas
+	depends = lapack
 	depends = r-caret
 	depends = r-deseq2
 	depends = r-dplyr
@@ -19,7 +21,6 @@ pkgbase = r-scgps
 	depends = r-rcppparallel
 	depends = r-singlecellexperiment
 	depends = r-summarizedexperiment
-	depends = make
 	optdepends = r-biocparallel
 	optdepends = r-clusterprofiler
 	optdepends = r-cowplot
@@ -28,10 +29,8 @@ pkgbase = r-scgps
 	optdepends = r-dose
 	optdepends = r-e1071
 	optdepends = r-knitr
-	optdepends = r-matrix
 	optdepends = r-networkd3
 	optdepends = r-org.hs.eg.db
-	optdepends = r-parallel
 	optdepends = r-rcolorbrewer
 	optdepends = r-reactomepa
 	optdepends = r-reshape2
@@ -41,6 +40,10 @@ pkgbase = r-scgps
 	optdepends = r-wgcna
 	optdepends = r-xlsx
 	source = https://bioconductor.org/packages/release/bioc/src/contrib/scGPS_1.16.0.tar.gz
-	sha256sums = 3a30413a462684cd657530d996dc35dfdb79361d1fc7eb41900e868bfc1ae4f6
+	source = fix-build.patch
+	md5sums = 5d11fe3a4af0d56d3028d97c6090ccfb
+	md5sums = 10f827551e2b78263235e157e5b6a4b2
+	b2sums = 3c265f5702b0701dfc63efef0a5b10f35b326bdc736c03cef0bef699c561fc1956e86cd466dcbb90eaa754d8f8b461f08dc97f429e329d526d568ef8342e4e57
+	b2sums = e2f840b1d0e9a8897ac8233ce695ea40e658797e01ad46f50bb5e7528efcf3797ec402b22c92d0b8a16c96bd7f4146664b81f9e7998525057426b61d05693e89
 
 pkgname = r-scgps
diff --git a/PKGBUILD b/PKGBUILD
index 4e2610b4e242..fe79bce7cb69 100644
--- a/PKGBUILD
+++ b/PKGBUILD
@@ -1,17 +1,18 @@
-# system requirements: GNU make
-# 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=scGPS
 _pkgver=1.16.0
 pkgname=r-${_pkgname,,}
-pkgver=1.16.0
-pkgrel=1
-pkgdesc='A complete analysis of single cell subpopulations, from identifying subpopulations to analysing their relationship (scGPS = single cell Global Predictions of Subpopulation)'
-arch=('x86_64')
-url="https://bioconductor.org/packages/${_pkgname}"
-license=('GPL')
+pkgver=${_pkgver//-/.}
+pkgrel=2
+pkgdesc="A complete analysis of single cell subpopulations, from identifying subpopulations to analysing their relationship (scGPS = single cell Global Predictions of Subpopulation)"
+arch=(x86_64)
+url="https://bioconductor.org/packages/$_pkgname"
+license=('GPL-3.0-only')
 depends=(
-  r
+  blas
+  lapack
   r-caret
   r-deseq2
   r-dplyr
@@ -25,7 +26,9 @@ depends=(
   r-rcppparallel
   r-singlecellexperiment
   r-summarizedexperiment
-  make
+)
+checkdepends=(
+  r-testthat
 )
 optdepends=(
   r-biocparallel
@@ -36,10 +39,8 @@ optdepends=(
   r-dose
   r-e1071
   r-knitr
-  r-matrix
   r-networkd3
   r-org.hs.eg.db
-  r-parallel
   r-rcolorbrewer
   r-reactomepa
   r-reshape2
@@ -49,15 +50,29 @@ optdepends=(
   r-wgcna
   r-xlsx
 )
-source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz")
-sha256sums=('3a30413a462684cd657530d996dc35dfdb79361d1fc7eb41900e868bfc1ae4f6')
+source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz"
+        "fix-build.patch")
+md5sums=('5d11fe3a4af0d56d3028d97c6090ccfb'
+         '10f827551e2b78263235e157e5b6a4b2')
+b2sums=('3c265f5702b0701dfc63efef0a5b10f35b326bdc736c03cef0bef699c561fc1956e86cd466dcbb90eaa754d8f8b461f08dc97f429e329d526d568ef8342e4e57'
+        'e2f840b1d0e9a8897ac8233ce695ea40e658797e01ad46f50bb5e7528efcf3797ec402b22c92d0b8a16c96bd7f4146664b81f9e7998525057426b61d05693e89')
+
+prepare() {
+  # fix linking with onetbb
+  patch -Np1 -i fix-build.patch
+}
 
 build() {
-  R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}"
+  mkdir build
+  R CMD INSTALL -l build "$_pkgname"
+}
+
+check() {
+  cd "$_pkgname/tests"
+  R_LIBS="$srcdir/build" NOT_CRAN=true Rscript --vanilla testthat.R
 }
 
 package() {
-  install -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:
diff --git a/fix-build.patch b/fix-build.patch
new file mode 100644
index 000000000000..38527a72b4d3
--- /dev/null
+++ b/fix-build.patch
@@ -0,0 +1,7 @@
+diff --git a/scGPS/src/Makevars b/scGPS/src/Makevars
+index 22ebc63..532cff9 100644
+--- a/scGPS/src/Makevars
++++ b/scGPS/src/Makevars
+@@ -1 +1,2 @@
+ PKG_LIBS = $(LAPACK_LIBS) $(BLAS_LIBS) $(FLIBS)
++PKG_LIBS += $(shell "${R_HOME}/bin/Rscript" -e "RcppParallel::LdFlags()")