r-mfa: use metadata checks

BioArchLinux/r-mfa/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=mfa
 _pkgver=1.22.0
 pkgname=r-${_pkgname,,}
-pkgver=1.22.0
+pkgver=${_pkgver//-/.}
 pkgrel=1
-pkgdesc='Bayesian hierarchical mixture of factor analyzers for modelling genomic bifurcations'
-arch=('x86_64')
+pkgdesc="Bayesian hierarchical mixture of factor analyzers for modelling genomic bifurcations"
+arch=(x86_64)
 url="https://bioconductor.org/packages/${_pkgname}"
-license=('GPL')
+license=(GPL)
 depends=(
-  r
   r-biobase
   r-coda
   r-dplyr
@@ -22,6 +22,9 @@ depends=(
   r-rcpp
   r-tibble
 )
+checkdepends=(
+  r-testthat
+)
 optdepends=(
   r-biocstyle
   r-knitr
@@ -29,20 +32,20 @@ optdepends=(
   r-testthat
 )
 source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz")
+md5sums=('a47205412204ffd49737d41b7b78574d')
 sha256sums=('043a7b884c4d454c12b0c9066f114faf1824eb531630a92053cb42ac684488e5')
 
-prepare() {
-  sed -i "s#PI#M_PI#" "${_pkgname}/src/gibbs.cpp"
-  tar cfz "${_pkgname}.tar.gz" "${_pkgname}"
+build() {
+  mkdir -p build
+  R CMD INSTALL "$_pkgname" -l build
 }
 
-build() {
-  #R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}"
-  R CMD INSTALL ${_pkgname}.tar.gz -l "${srcdir}"
+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-mfa/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-mfa/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-biobase
 - r-coda
@@ -13,8 +13,11 @@ repo_depends:
 - r-mcmcpack
 - r-rcpp
 - r-tibble
+repo_makedepends:
+- r-testthat
 update_on:
-- regex: mfa_([\d._-]+).tar.gz
-  source: regex
-  url: https://bioconductor.org/packages/mfa
+- source: rpkgs
+  pkgname: mfa
+  repo: bioc
+  md5: true
 - alias: r