upgpkg: r-genomicranges 1.48.0-1

upstream release

upstream release

2 files changed, 80 insertions, 32 deletions

diff --git a/.SRCINFO b/.SRCINFO
index 257e7a64d908..48b751df5208 100644
--- a/.SRCINFO
+++ b/.SRCINFO
@@ -1,6 +1,6 @@
 pkgbase = r-genomicranges
 	pkgdesc = Representation and manipulation of genomic intervals
-	pkgver = 1.46.1
+	pkgver = 1.48.0
 	pkgrel = 1
 	url = https://bioconductor.org/packages/release/bioc/html/GenomicRanges.html
 	arch = i686
@@ -12,41 +12,42 @@ pkgbase = r-genomicranges
 	depends = r-iranges>=2.23.9
 	depends = r-genomeinfodb>=1.15.2
 	depends = r-xvector>=0.29.2
-	optdepends = r-biobase
-	optdepends = r-annotationdbi
 	optdepends = r-annotate
-	optdepends = r-biostrings
-	optdepends = r-summarizedexperiment
-	optdepends = r-rsamtools
-	optdepends = r-genomicalignments
-	optdepends = r-rtracklayer
-	optdepends = r-bsgenome
-	optdepends = r-genomicfeatures
-	optdepends = r-gviz
-	optdepends = r-variantannotation
+	optdepends = r-annotationdbi
 	optdepends = r-annotationhub
+	optdepends = r-biobase
+	optdepends = r-biocstyle
+	optdepends = r-biostrings>=2.25.3
+	optdepends = r-bsgenome
+	optdepends = r-bsgenome.hsapiens.ucsc.hg19
+	optdepends = r-bsgenome.mmusculus.ucsc.mm10
+	optdepends = r-bsgenome.scerevisiae.ucsc.saccer2
 	optdepends = r-deseq2
 	optdepends = r-dexseq
+	optdepends = r-digest
 	optdepends = r-edger
-	optdepends = r-kegggraph
-	optdepends = r-rnaseqdata.hnrnpc.bam.chr14
-	optdepends = r-pasillabamsubset
-	optdepends = r-keggrest
+	optdepends = r-genomicalignments
+	optdepends = r-genomicfeatures
+	optdepends = r-gviz
 	optdepends = r-hgu95av2.db
 	optdepends = r-hgu95av2probe
-	optdepends = r-bsgenome.scerevisiae.ucsc.saccer2
-	optdepends = r-bsgenome.hsapiens.ucsc.hg19
-	optdepends = bsgenome.mmusculus.ucsc.mm10
+	optdepends = r-kegggraph
+	optdepends = r-keggrest
+	optdepends = r-knitr
+	optdepends = r-matrix
+	optdepends = r-pasillabamsubset
+	optdepends = r-rmarkdown
+	optdepends = r-rnaseqdata.hnrnpc.bam.chr14
+	optdepends = r-rsamtools>=1.13.53
+	optdepends = r-rtracklayer
+	optdepends = r-runit
+	optdepends = r-summarizedexperiment>=0.1.5
 	optdepends = r-txdb.athaliana.biomart.plantsmart22
-	optdepends = txdb.dmelanogaster.ucsc.dm3.ensgene
+	optdepends = r-txdb.dmelanogaster.ucsc.dm3.ensgene
 	optdepends = r-txdb.hsapiens.ucsc.hg19.knowngene
 	optdepends = r-txdb.mmusculus.ucsc.mm10.knowngene
-	optdepends = r-runit
-	optdepends = r-digest
-	optdepends = r-knitr
-	optdepends = r-rmarkdown
-	optdepends = r-biocstyle
-	source = https://bioconductor.org/packages/release/bioc/src/contrib/GenomicRanges_1.46.1.tar.gz
-	sha256sums = 9df774cd514343a29f57d45a13889bf400d0abeaa2013cd396f7faa6f911798c
+	optdepends = r-variantannotation
+	source = https://bioconductor.org/packages/release/bioc/src/contrib/GenomicRanges_1.48.0.tar.gz
+	sha256sums = d623d25b9eb20d4b48f42f6e30771101503b8e9e1592d76e310273ca54d81921
 
 pkgname = r-genomicranges
diff --git a/PKGBUILD b/PKGBUILD
index 68f3263f16cc..38f3953a5a56 100644
--- a/PKGBUILD
+++ b/PKGBUILD
@@ -1,8 +1,9 @@
+# Maintainer: peippo <christoph+aur@christophfink.com>
 # Contributor: Viktor Drobot (aka dviktor) linux776 [at] gmail [dot] com
 # Contributor: Grey Christoforo <first name at last name dot net>
 
 _bcname=GenomicRanges
-_bcver=1.46.1
+_bcver=1.48.0
 pkgname=r-${_bcname,,}
 pkgver=${_bcver//[:-]/.}
 pkgrel=1
@@ -10,10 +11,53 @@ pkgdesc="Representation and manipulation of genomic intervals"
 arch=(i686 x86_64)
 url="https://bioconductor.org/packages/release/bioc/html/${_bcname}.html"
 license=(Artistic-2.0)
-depends=('r>=4.0.0' 'r-biocgenerics>=0.37.0' 'r-s4vectors>=0.27.12' 'r-iranges>=2.23.9' 'r-genomeinfodb>=1.15.2' 'r-xvector>=0.29.2')
-optdepends=(r-biobase r-annotationdbi r-annotate r-biostrings r-summarizedexperiment r-rsamtools r-genomicalignments r-rtracklayer r-bsgenome r-genomicfeatures r-gviz r-variantannotation r-annotationhub r-deseq2 r-dexseq r-edger r-kegggraph r-rnaseqdata.hnrnpc.bam.chr14 r-pasillabamsubset r-keggrest r-hgu95av2.db r-hgu95av2probe r-bsgenome.scerevisiae.ucsc.saccer2 r-bsgenome.hsapiens.ucsc.hg19 bsgenome.mmusculus.ucsc.mm10 r-txdb.athaliana.biomart.plantsmart22 txdb.dmelanogaster.ucsc.dm3.ensgene r-txdb.hsapiens.ucsc.hg19.knowngene r-txdb.mmusculus.ucsc.mm10.knowngene r-runit r-digest r-knitr r-rmarkdown r-biocstyle)
+depends=(
+    "r>=4.0.0"
+	"r-biocgenerics>=0.37.0"
+	"r-s4vectors>=0.27.12"
+	"r-iranges>=2.23.9"
+	"r-genomeinfodb>=1.15.2"
+	"r-xvector>=0.29.2"
+)
+optdepends=(
+	r-annotate
+	r-annotationdbi
+	r-annotationhub
+    r-biobase
+	r-biocstyle
+	"r-biostrings>=2.25.3"
+	r-bsgenome
+	r-bsgenome.hsapiens.ucsc.hg19
+	r-bsgenome.mmusculus.ucsc.mm10
+	r-bsgenome.scerevisiae.ucsc.saccer2
+	r-deseq2
+	r-dexseq
+	r-digest
+	r-edger
+	r-genomicalignments
+	r-genomicfeatures
+	r-gviz
+	r-hgu95av2.db
+	r-hgu95av2probe
+	r-kegggraph
+	r-keggrest
+	r-knitr
+    r-matrix
+	r-pasillabamsubset
+	r-rmarkdown
+	r-rnaseqdata.hnrnpc.bam.chr14
+	"r-rsamtools>=1.13.53"
+	r-rtracklayer
+	r-runit
+	"r-summarizedexperiment>=0.1.5"
+	r-txdb.athaliana.biomart.plantsmart22
+	r-txdb.dmelanogaster.ucsc.dm3.ensgene
+	r-txdb.hsapiens.ucsc.hg19.knowngene
+	r-txdb.mmusculus.ucsc.mm10.knowngene
+	r-variantannotation
+)
 source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_bcname}_${_bcver}.tar.gz")
-sha256sums=('9df774cd514343a29f57d45a13889bf400d0abeaa2013cd396f7faa6f911798c')
+sha256sums=("d623d25b9eb20d4b48f42f6e30771101503b8e9e1592d76e310273ca54d81921")
 
 build() {
   R CMD INSTALL ${_bcname}_${_bcver}.tar.gz -l "${srcdir}"
@@ -21,6 +65,9 @@ build() {
 
 package() {
   install -dm0755 "${pkgdir}/usr/lib/R/library"
-
   cp -a --no-preserve=ownership "${_bcname}" "${pkgdir}/usr/lib/R/library"
+
+  if [[ -f "${_cranname}/LICENSE" ]]; then
+    install -Dm0644 "${_cranname}/LICENSE" "${pkgdir}/usr/share/licenses/${pkgname}/LICENSE"
+  fi
 }