Version 1.0.10

2 files changed, 114 insertions, 0 deletions

diff --git a/.SRCINFO b/.SRCINFO
new file mode 100644
index 000000000000..cbdad04185a2
--- /dev/null
+++ b/.SRCINFO
@@ -0,0 +1,44 @@
+pkgbase = r-simona
+	pkgdesc = Semantic Similarity in Bio-Ontologies
+	pkgver = 1.0.10
+	pkgrel = 1
+	url = https://bioconductor.org/packages/simona
+	arch = x86_64
+	license = MIT
+	checkdepends = r-go.db
+	checkdepends = r-org.hs.eg.db
+	checkdepends = r-proxyc
+	checkdepends = r-testthat
+	depends = java-runtime
+	depends = perl
+	depends = r-circlize
+	depends = r-complexheatmap
+	depends = r-getoptlong
+	depends = r-globaloptions
+	depends = r-igraph
+	depends = r-matrixstats
+	depends = r-polychrome
+	depends = r-rcpp
+	depends = r-s4vectors
+	depends = r-shiny
+	depends = r-xml2
+	optdepends = r-annotationdbi
+	optdepends = r-annotationhub
+	optdepends = r-biocmanager
+	optdepends = r-diagrammer
+	optdepends = r-go.db
+	optdepends = r-interactivecomplexheatmap
+	optdepends = r-jsonlite
+	optdepends = r-knitr
+	optdepends = r-org.hs.eg.db
+	optdepends = r-png
+	optdepends = r-proxyc
+	optdepends = r-ragg
+	optdepends = r-simplifyenrichment
+	optdepends = r-testthat
+	optdepends = r-uniprotkeywords
+	source = https://bioconductor.org/packages/release/bioc/src/contrib/simona_1.0.10.tar.gz
+	md5sums = 3c9d33cfa91dc8e3e071da9fb3bff761
+	b2sums = 00f3ed8cce6c401558d4e08365ac82111a00fd7e8f973b438868d58e602efe90b13d528170da13c323d16a4d6eab32ad4445938027834a068ba29c9228656b14
+
+pkgname = r-simona
diff --git a/PKGBUILD b/PKGBUILD
new file mode 100644
index 000000000000..aa7951badad8
--- /dev/null
+++ b/PKGBUILD
@@ -0,0 +1,70 @@
+# Maintainer: Pekka Ristola <pekkarr [at] protonmail [dot] com>
+
+_pkgname=simona
+_pkgver=1.0.10
+pkgname=r-${_pkgname,,}
+pkgver=${_pkgver//-/.}
+pkgrel=1
+pkgdesc="Semantic Similarity in Bio-Ontologies"
+arch=(x86_64)
+url="https://bioconductor.org/packages/$_pkgname"
+license=('MIT')
+depends=(
+  java-runtime
+  perl
+  r-circlize
+  r-complexheatmap
+  r-getoptlong
+  r-globaloptions
+  r-igraph
+  r-matrixstats
+  r-polychrome
+  r-rcpp
+  r-s4vectors
+  r-shiny
+  r-xml2
+)
+checkdepends=(
+  r-go.db
+  r-org.hs.eg.db
+  r-proxyc
+  r-testthat
+)
+optdepends=(
+  r-annotationdbi
+  r-annotationhub
+  r-biocmanager
+  r-diagrammer
+  r-go.db
+  r-interactivecomplexheatmap
+  r-jsonlite
+  r-knitr
+  r-org.hs.eg.db
+  r-png
+  r-proxyc
+  r-ragg
+  r-simplifyenrichment
+  r-testthat
+  r-uniprotkeywords
+)
+source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz")
+md5sums=('3c9d33cfa91dc8e3e071da9fb3bff761')
+b2sums=('00f3ed8cce6c401558d4e08365ac82111a00fd7e8f973b438868d58e602efe90b13d528170da13c323d16a4d6eab32ad4445938027834a068ba29c9228656b14')
+
+build() {
+  mkdir build
+  R CMD INSTALL -l build "$_pkgname"
+}
+
+check() {
+  cd "$_pkgname/tests"
+  R_LIBS="$srcdir/build" NOT_CRAN=true Rscript --vanilla test-all.R
+}
+
+package() {
+  install -d "$pkgdir/usr/lib/R/library"
+  cp -a --no-preserve=ownership "build/$_pkgname" "$pkgdir/usr/lib/R/library"
+
+  install -d "$pkgdir/usr/share/licenses/$pkgname"
+  ln -s "/usr/lib/R/library/$_pkgname/LICENSE" "$pkgdir/usr/share/licenses/$pkgname"
+}