Fixed PKGBUILD

3 files changed, 41 insertions, 27 deletions

diff --git a/.SRCINFO b/.SRCINFO
index 66a39b963166..bc57aac30ecd 100644
--- a/.SRCINFO
+++ b/.SRCINFO
@@ -1,26 +1,33 @@
 pkgbase = r-shortread
 	pkgdesc = FASTQ input and manipulation
-	pkgver = 1.44.0
+	pkgver = 1.44.1
 	pkgrel = 1
 	url = https://bioconductor.org/packages/release/bioc/html/ShortRead.html
+	arch = i686
 	arch = x86_64
 	license = Artistic-2.0
+	makedepends = gcc
 	depends = r
-	depends = r-biocgenerics
+	depends = r-biocgenerics>=0.23.3
 	depends = r-biocparallel
-	depends = r-biostrings
-	depends = r-rsamtools
-	depends = r-genomicalignments
+	depends = r-biostrings>=2.47.6
+	depends = r-rsamtools>=1.31.2
+	depends = r-genomicalignments>=1.15.6
 	depends = r-biobase
-	depends = r-s4vectors
-	depends = r-iranges
-	depends = r-genomeinfodb
-	depends = r-genomicranges
+	depends = r-s4vectors>=0.17.25
+	depends = r-iranges>=2.13.12
+	depends = r-genomeinfodb>=1.15.2
+	depends = r-genomicranges>=1.31.8
 	depends = r-hwriter
 	depends = r-zlibbioc
 	depends = r-latticeextra
-	source = https://bioconductor.org/packages/release/bioc/src/contrib/ShortRead_1.44.0.tar.gz
-	sha1sums = 5a60229c2eb98dcbdc13cc4c99cd693887d171fd
+	optdepends = r-biocstyle
+	optdepends = r-runit
+	optdepends = r-biomart
+	optdepends = r-genomicfeatures
+	optdepends = r-yeastnagalakshmi
+	source = https://bioconductor.org/packages/release/bioc/src/contrib/ShortRead_1.44.1.tar.gz
+	md5sums = 6db17bc451e51ef0e0bc6e6d5089e401
 
 pkgname = r-shortread
 
diff --git a/.gitignore b/.gitignore
deleted file mode 100644
index 6ae0b18a1f6c..000000000000
--- a/.gitignore
+++ /dev/null
@@ -1,4 +0,0 @@
-/pkg
-/src
-*.tar.gz
-*.tar.xz
diff --git a/PKGBUILD b/PKGBUILD
index c9c22d4b11fc..f46c47ad9a2c 100644
--- a/PKGBUILD
+++ b/PKGBUILD
@@ -1,19 +1,30 @@
+# Contributor: Viktor Drobot (aka dviktor) linux776 [at] gmail [dot] com
 # Contributor: Grey Christoforo <first name at last name dot net>
-pkgname=r-shortread
-_bc_name=ShortRead
-pkgver=1.44.0
+
+_bcname=ShortRead
+_bcver=1.44.1
+pkgname=r-${_bcname,,}
+pkgver=${_bcver//[:-]/.}
 pkgrel=1
 pkgdesc="FASTQ input and manipulation"
-url="https://bioconductor.org/packages/release/bioc/html/${_bc_name}.html"
-arch=("x86_64")
-license=('Artistic-2.0')
-depends=('r' 'r-biocgenerics' 'r-biocparallel' 'r-biostrings' 'r-rsamtools' 'r-genomicalignments' 'r-biobase' 'r-s4vectors' 'r-iranges' 'r-genomeinfodb' 'r-genomicranges' 'r-hwriter' 'r-zlibbioc' 'r-latticeextra')
-source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_bc_name}_${pkgver}.tar.gz")
-sha1sums=('5a60229c2eb98dcbdc13cc4c99cd693887d171fd')
+arch=(i686 x86_64)
+url="https://bioconductor.org/packages/release/bioc/html/${_bcname}.html"
+license=(Artistic-2.0)
+depends=(r 'r-biocgenerics>=0.23.3' r-biocparallel 'r-biostrings>=2.47.6' 'r-rsamtools>=1.31.2' 'r-genomicalignments>=1.15.6' r-biobase 'r-s4vectors>=0.17.25' 'r-iranges>=2.13.12' 'r-genomeinfodb>=1.15.2' 'r-genomicranges>=1.31.8' r-hwriter r-zlibbioc r-latticeextra)
+makedepends=(gcc)
+optdepends=(r-biocstyle r-runit r-biomart r-genomicfeatures r-yeastnagalakshmi)
+source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_bcname}_${_bcver}.tar.gz")
+md5sums=('6db17bc451e51ef0e0bc6e6d5089e401')
+
+build() {
+  cd "${srcdir}"
+
+  R CMD INSTALL ${_bcname}_${_bcver}.tar.gz -l ${srcdir}
+}
 
 package() {
- mkdir -p $pkgdir/usr/lib/R/library
- cd $srcdir
+  cd "${srcdir}"
 
- R CMD INSTALL -l $pkgdir/usr/lib/R/library ./${_bc_name}
+  install -dm0755 "${pkgdir}/usr/lib/R/library"
+  cp -a --no-preserve=ownership "${_bcname}" "${pkgdir}/usr/lib/R/library"
 }