r-gcatest: use metadata checks

BioArchLinux/r-gcatest/PKGBUILD

@@ -1,36 +1,43 @@
-# 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=gcatest
 _pkgver=2.0.7
 pkgname=r-${_pkgname,,}
-pkgver=2.0.7
+pkgver=${_pkgver//-/.}
 pkgrel=1
-pkgdesc='Genotype Conditional Association TEST'
-arch=('x86_64')
+pkgdesc="Genotype Conditional Association TEST"
+arch=(any)
 url="https://bioconductor.org/packages/${_pkgname}"
-license=('GPL')
+license=(GPL3)
 depends=(
-  r
   r-lfa
 )
+checkdepends=(
+  r-testthat
+)
 optdepends=(
+  r-bedmatrix
+  r-genio
   r-ggplot2
   r-knitr
+  r-testthat
 )
-makedepends=('git')
-source=("git+https://git.bioconductor.org/packages/${_pkgname}")
-sha256sums=('SKIP')
-
-prepare(){
-  tar -czf ${_pkgname}_$_pkgver.tar.gz ${_pkgname}
-}
+source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz")
+md5sums=('e0cfb7c0ad56c72aaf703b153456d091')
+sha256sums=('f162ba2d4acfaececbe491d030e8538e74b7ac3caab88d4eb52f044c436a1dd8')
 
 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-gcatest/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-gcatest/lilac.yaml

@@ -1,11 +1,14 @@
 build_prefix: extra-x86_64
 maintainers:
-- github: starsareintherose
-  email: kuoi@bioarchlinux.org
+- github: pekkarr
+  email: pekkarr@protonmail.com
 repo_depends:
 - r-lfa
+repo_makedepends:
+- r-testthat
 update_on:
-- regex: <td>(\d+.\d+.\d+)</td>
-  source: regex
-  url: https://bioconductor.org/packages/gcatest
+- source: rpkgs
+  pkgname: gcatest
+  repo: bioc
+  md5: true
 - alias: r