r-genomicdatacommons: fix depends, use metadata checks

BioArchLinux/r-genomicdatacommons/PKGBUILD

@@ -1,16 +1,16 @@
-# Maintainer: Guoyi Zhang <guoyizhang at malacology dot net>
+# Maintainer: Pekka Ristola <pekkarr [at] protonmail [dot] com>
+# Contributor: Guoyi Zhang <guoyizhang at malacology dot net>
 
 _pkgname=GenomicDataCommons
-_pkgver=1.24.2
+_pkgver=1.24.3
 pkgname=r-${_pkgname,,}
-pkgver=1.24.2
-pkgrel=1
-pkgdesc='NIH / NCI Genomic Data Commons Access'
-arch=('any')
+pkgver=${_pkgver//-/.}
+pkgrel=0
+pkgdesc="NIH / NCI Genomic Data Commons Access"
+arch=(any)
 url="https://bioconductor.org/packages/${_pkgname}"
-license=('Artistic2.0')
+license=(Artistic2.0)
 depends=(
-  r
   r-dplyr
   r-genomicranges
   r-httr
@@ -21,8 +21,12 @@ depends=(
   r-readr
   r-rlang
   r-tibble
+  r-tidyr
   r-xml2
 )
+checkdepends=(
+  r-testthat
+)
 optdepends=(
   r-biocparallel
   r-biocstyle
@@ -41,14 +45,20 @@ optdepends=(
   r-variantannotation
 )
 source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz")
-sha256sums=('747cda20f437796b0bec7400bf9b5ab58bd65f1a5970ce5bde38b0654d84fb35')
+md5sums=('ad52387795de8e7bdbfb93c3835e548f')
+sha256sums=('6840570e4512e0d8e459ade8464349dddd158804d1233efc05f7747a54cc3bbf')
 
 build() {
-  R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}"
+  mkdir -p build
+  R CMD INSTALL "$_pkgname" -l build
+}
+
+check() {
+  cd "$_pkgname/tests"
+  R_LIBS="$srcdir/build" NOT_CRAN=true Rscript --vanilla testthat.R
 }
 
 package() {
-  install -dm0755 "${pkgdir}/usr/lib/R/library"
-  cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library"
+  install -d "$pkgdir/usr/lib/R/library"
+  cp -a --no-preserve=ownership "build/$_pkgname" "$pkgdir/usr/lib/R/library"
 }
-# vim:set ts=2 sw=2 et:

BioArchLinux/r-genomicdatacommons/lilac.py

@@ -1,12 +1,13 @@
 #!/usr/bin/env python3
 from lilaclib import *
 
+import os
+import sys
+sys.path.append(os.path.normpath(f'{__file__}/../../../lilac-extensions'))
+from lilac_r_utils import r_pre_build
+
 def pre_build():
-    for line in edit_file('PKGBUILD'):
-        if line.startswith('_pkgver='):
-            line = f'_pkgver={_G.newver}'
-        print(line)
-    update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.'))
+    r_pre_build(_G)
 
 def post_build():
     git_pkgbuild_commit()

BioArchLinux/r-genomicdatacommons/lilac.yaml

@@ -1,7 +1,7 @@
 build_prefix: extra-x86_64
 maintainers:
-- github: starsareintherose
-  email: kuoi@bioarchlinux.org
+- github: pekkarr
+  email: pekkarr@protonmail.com
 repo_depends:
 - r-dplyr
 - r-genomicranges
@@ -13,9 +13,13 @@ repo_depends:
 - r-readr
 - r-rlang
 - r-tibble
+- r-tidyr
 - r-xml2
+repo_makedepends:
+- r-testthat
 update_on:
-- regex: GenomicDataCommons_([\d._-]+).tar.gz
-  source: regex
-  url: https://bioconductor.org/packages/GenomicDataCommons
+- source: rpkgs
+  pkgname: GenomicDataCommons
+  repo: bioc
+  md5: true
 - alias: r