r-rstanarm: use metadata checks

BioArchLinux/r-rstanarm/PKGBUILD

@@ -1,30 +1,39 @@
-# system requirements: GNU make, pandoc (>= 1.12.3), pandoc-citeproc
-# Maintainer: sukanka <su975853527@gmail.com>
+# Maintainer: Pekka Ristola <pekkarr [at] protonmail [dot] com>
+# Contributor: sukanka <su975853527@gmail.com>
 
 _pkgname=rstanarm
 _pkgver=2.26.1
 pkgname=r-${_pkgname,,}
-pkgver=2.26.1
+pkgver=${_pkgver//-/.}
 pkgrel=1
-pkgdesc='Bayesian Applied Regression Modeling via Stan'
-arch=('x86_64')
+pkgdesc="Bayesian Applied Regression Modeling via Stan"
+arch=(x86_64)
 url="https://cran.r-project.org/package=${_pkgname}"
-license=('GPL')
+license=(GPL3)
 depends=(
-  r
+  pandoc
   r-bayesplot
-  r-bh
   r-ggplot2
   r-lme4
   r-loo
+  r-posterior
   r-rcpp
-  r-rcppeigen
   r-rcppparallel
   r-rstan
   r-rstantools
   r-shinystan
+)
+makedepends=(
+  r-bh
+  r-rcppeigen
   r-stanheaders
-  pandoc
+)
+checkdepends=(
+  r-betareg
+  r-biglm
+  r-data.table
+  r-hsaur3
+  r-testthat
 )
 optdepends=(
   r-betareg
@@ -35,24 +44,39 @@ optdepends=(
   r-gridextra
   r-hsaur3
   r-knitr
-  r-mass
-  r-mgcv
   r-rmarkdown
   r-roxygen2
   r-shiny
   r-stanheaders
   r-testthat
 )
-makedepends=('make')
 source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz")
+md5sums=('8505a33ae9ff139e9f0b3d5b8cc6ee7e')
 sha256sums=('4a54792d6e035931b613647aebfc98b81d1aac646a5a3f6f116b6f560d544444')
 
+prepare() {
+  cd "$_pkgname/tests/testthat"
+  # skip tests that make a coredump
+  sed -e '/"stan_betareg ok when modeling x and z (link.phi = '\'sqrt\'')"/a\ \ skip("dumps core")' \
+      -e '/"heavy tailed priors work with stan_betareg"/a\ \ skip("dumps core")' \
+      -i test_stan_betareg.R
+  sed -i '1i skip("dumps core")' test_stan_jm.R
+  sed -i '/"multiple grouping factors are ok"/a\ \ skip("dumps core")' test_stan_mvmer.R
+}
+
 build() {
-  R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}"
+  mkdir -p build
+  # compilation needs a lot of memory
+  MAKEFLAGS+=" -j1"
+  R CMD INSTALL "$_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-rstanarm/lilac.py

@@ -1,17 +1,17 @@
 #!/usr/bin/env python3
 from lilaclib import *
 
-# we use 2 threads in BioArchLinux, but it should not be pushed to aur.
+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}'
-        elif line.startswith('build()'):
-            line += '\n' + 'export MAKE="make -j2"'
-        print(line)
-    update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.'))
+    r_pre_build(
+        _G,
+        expect_systemrequirements = "GNU make, pandoc (>= 1.12.3), pandoc-citeproc",
+    )
 
 def post_build():
-    run_cmd(['sh', '-c', "sed -i '/export MAKE/d' PKGBUILD"])
     git_pkgbuild_commit()
     update_aur_repo()

BioArchLinux/r-rstanarm/lilac.yaml

@@ -1,22 +1,30 @@
 build_prefix: extra-x86_64
 maintainers:
-  - github: sukanka
+- github: pekkarr
+  email: pekkarr@protonmail.com
 repo_depends:
-  - r-bayesplot
-  - r-bh
-  - r-ggplot2
-  - r-lme4
-  - r-loo
-  - r-rcpp
-  - r-rcppeigen
-  - r-rcppparallel
-  - r-rstan
-  - r-rstantools
-  - r-shinystan
-  - r-stanheaders
+- r-bayesplot
+- r-ggplot2
+- r-lme4
+- r-loo
+- r-posterior
+- r-rcpp
+- r-rcppparallel
+- r-rstan
+- r-rstantools
+- r-shinystan
+repo_makedepends:
+- r-bh
+- r-rcppeigen
+- r-stanheaders
+- r-betareg
+- r-biglm
+- r-data.table
+- r-hsaur3
+- r-testthat
 update_on:
-  - regex: rstanarm_([\d._-]+).tar.gz
-    source: regex
-    url: https://cran.r-project.org/package=rstanarm
-  - alias: r
-time_limit_hours: 10
+- source: rpkgs
+  pkgname: rstanarm
+  repo: cran
+  md5: true
+- alias: r