upgpkg: r-genomeinfodb 1.36.0-2

2 files changed, 26 insertions, 23 deletions

diff --git a/.SRCINFO b/.SRCINFO
index 23ce51128c04..03d4a992753f 100644
--- a/.SRCINFO
+++ b/.SRCINFO
@@ -1,23 +1,10 @@
 pkgbase = r-genomeinfodb
 	pkgdesc = Utilities for manipulating chromosome names, including modifying them to follow a particular naming style
 	pkgver = 1.36.0
-	pkgrel = 1
+	pkgrel = 2
 	url = https://bioconductor.org/packages/release/bioc/html/GenomeInfoDb.html
 	arch = any
 	license = Artistic2.0
-	checkdepends = r-genomicranges
-	checkdepends = r-rsamtools
-	checkdepends = r-genomicalignments
-	checkdepends = r-genomicfeatures
-	checkdepends = r-txdb.dmelanogaster.ucsc.dm3.ensgene
-	checkdepends = r-bsgenome
-	checkdepends = r-bsgenome.scerevisiae.ucsc.saccer2
-	checkdepends = r-bsgenome.celegans.ucsc.ce2
-	checkdepends = r-bsgenome.hsapiens.ncbi.grch38
-	checkdepends = r-runit
-	checkdepends = r-biocstyle
-	checkdepends = r-knitr
-	checkdepends = r-rcmdcheck
 	depends = r>=4.0.0
 	depends = r-biocgenerics>=0.37.0
 	depends = r-s4vectors>=0.25.12
diff --git a/PKGBUILD b/PKGBUILD
index 88c2ee4b3dcb..4ac73f0ce819 100644
--- a/PKGBUILD
+++ b/PKGBUILD
@@ -6,11 +6,12 @@ _bcname=GenomeInfoDb
 _bcver=1.36.0
 pkgname="r-${_bcname,,}"
 pkgver="${_bcver//[:-]/.}"
-pkgrel=1
+pkgrel=2
 pkgdesc="Utilities for manipulating chromosome names, including modifying them to follow a particular naming style"
 arch=("any")
 url="https://bioconductor.org/packages/release/bioc/html/${_bcname}.html"
 license=("Artistic2.0")
+
 depends=(
     "r>=4.0.0"
 	"r-biocgenerics>=0.37.0"
@@ -33,10 +34,25 @@ optdepends=(
     "r-biocstyle"
     "r-knitr"
 )
-checkdepends=(
-    "${optdepends[@]}"
-    "r-rcmdcheck"
-)
+
+# The unittests for `r-pkgcache` have circular
+# dependency chains.
+
+# As such, the tests can not be run on first build.
+# While R packages from CRAN, generally, are well-tested
+# before they are released, in some situations, you want to
+# have thorough testing on your own end.
+
+# To run the tests, first build this package without `check()`
+# (i.e., as-is) to bootstrap `r-pkgcache`. Then, on subsequent builds,
+# (assumining you have a local repository that is accessible from
+# the build chroot), uncomment the lines defining `checkdepends`, below,
+# as well as the `check()` function further down
+
+# checkdepends=(
+#     "${optdepends[@]}"
+#     "r-rcmdcheck"
+# )
 
 source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_bcname}_${_bcver}.tar.gz")
 b2sums=("2bd7ed553f7a2bbe37f71d4eee98152907f47f206f657fbdbfc192d385671715be397407e3a3feb827ec73f2f1e52ce1beac68a0460de0224ed3b3c1368eddd5")
@@ -46,10 +62,10 @@ build() {
     R CMD INSTALL ${_bcname}_${_bcver}.tar.gz -l "${srcdir}/build/"
 }
 
-check() {
-    cd "${srcdir}/${_bcname}/"
-    R_LIBS="${srcdir}/build/" R CMD check --no-manual --no-multiarch --no-vignettes .
-}
+# check() {
+#     cd "${srcdir}/${_bcname}/"
+#     R_LIBS="${srcdir}/build/" R CMD check --no-manual --no-multiarch --no-vignettes .
+# }
 
 package() {
     install -dm0755 "${pkgdir}/usr/lib/R/library"