Version 1.2.4

2 files changed, 100 insertions, 0 deletions

diff --git a/.SRCINFO b/.SRCINFO
new file mode 100644
index 000000000000..71951ec42aad
--- /dev/null
+++ b/.SRCINFO
@@ -0,0 +1,35 @@
+pkgbase = r-syntenet
+	pkgdesc = Inference And Analysis Of Synteny Networks
+	pkgver = 1.2.4
+	pkgrel = 1
+	url = https://bioconductor.org/packages/syntenet
+	arch = x86_64
+	license = GPL3
+	checkdepends = r-xml2
+	makedepends = r-testthat
+	depends = r-biocparallel
+	depends = r-biostrings
+	depends = r-genomicranges
+	depends = r-ggnetwork
+	depends = r-ggplot2
+	depends = r-igraph
+	depends = r-intergraph
+	depends = r-networkd3
+	depends = r-pheatmap
+	depends = r-rcolorbrewer
+	depends = r-rcpp
+	depends = r-rlang
+	depends = r-rtracklayer
+	optdepends = r-biocstyle
+	optdepends = r-covr
+	optdepends = r-ggtree
+	optdepends = r-knitr
+	optdepends = r-labdsv
+	optdepends = r-rmarkdown
+	optdepends = r-testthat
+	optdepends = r-xml2
+	source = https://bioconductor.org/packages/release/bioc/src/contrib/syntenet_1.2.4.tar.gz
+	md5sums = 81bd02bbba83fcb7f62098b5fd2a1fc6
+	sha256sums = d5cb3ad5a92be38fa9a538dc856002464d4d353400d126f6840ed4e3bd74a02e
+
+pkgname = r-syntenet
diff --git a/PKGBUILD b/PKGBUILD
new file mode 100644
index 000000000000..5de24f2765be
--- /dev/null
+++ b/PKGBUILD
@@ -0,0 +1,65 @@
+# Maintainer: Pekka Ristola <pekkarr [at] protonmail [dot] com>
+
+_pkgname=syntenet
+_pkgver=1.2.4
+pkgname=r-${_pkgname,,}
+pkgver=${_pkgver//-/.}
+pkgrel=1
+pkgdesc="Inference And Analysis Of Synteny Networks"
+arch=(x86_64)
+url="https://bioconductor.org/packages/${_pkgname}"
+license=(GPL3)
+depends=(
+  r-biocparallel
+  r-biostrings
+  r-genomicranges
+  r-ggnetwork
+  r-ggplot2
+  r-igraph
+  r-intergraph
+  r-networkd3
+  r-pheatmap
+  r-rcolorbrewer
+  r-rcpp
+  r-rlang
+  r-rtracklayer
+)
+makedepends=(
+  r-testthat
+)
+checkdepends=(
+  r-xml2
+)
+optdepends=(
+  r-biocstyle
+  r-covr
+  r-ggtree
+  r-knitr
+  r-labdsv
+  r-rmarkdown
+  r-testthat
+  r-xml2
+)
+source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz")
+md5sums=('81bd02bbba83fcb7f62098b5fd2a1fc6')
+sha256sums=('d5cb3ad5a92be38fa9a538dc856002464d4d353400d126f6840ed4e3bd74a02e')
+
+prepare() {
+  # skip tests that cause a coredump
+  sed -i '1i skip("dumps core")' "$_pkgname/tests/testthat/test-03_synteny_detection.R"
+}
+
+build() {
+  mkdir -p build
+  R CMD INSTALL "$_pkgname" -l build
+}
+
+check() {
+  cd "$_pkgname/tests"
+  R_LIBS="$srcdir/build" NOT_CRAN=true Rscript --vanilla testthat.R
+}
+
+package() {
+  install -d "$pkgdir/usr/lib/R/library"
+  cp -a --no-preserve=ownership "build/$_pkgname" "$pkgdir/usr/lib/R/library"
+}