r-tenxplore: use metadata checks

BioArchLinux/r-tenxplore/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=tenXplore
 _pkgver=1.22.0
 pkgname=r-${_pkgname,,}
-pkgver=1.22.0
+pkgver=${_pkgver//-/.}
 pkgrel=1
-pkgdesc='ontological exploration of scRNA-seq of 1.3 million mouse neurons from 10x genomics'
-arch=('any')
+pkgdesc="ontological exploration of scRNA-seq of 1.3 million mouse neurons from 10x genomics"
+arch=(any)
 url="https://bioconductor.org/packages/${_pkgname}"
-license=('Artistic2.0')
+license=(Artistic2.0)
 depends=(
-  r
   r-annotationdbi
   r-matrixstats
   r-ontoproc
@@ -19,6 +19,9 @@ depends=(
   r-shiny
   r-summarizedexperiment
 )
+checkdepends=(
+  r-testthat
+)
 optdepends=(
   r-biocstyle
   r-knitr
@@ -27,21 +30,20 @@ optdepends=(
   r-testthat
 )
 source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz")
+md5sums=('96c18d808ccb0106111ce4bf1d00ec5c')
 sha256sums=('a3abc9e04879cc200d71d8ac5aa0d1b0e5d4c5037cd110824ce4b4b77de96e1f')
 
-prepare(){
-  # Do not import RESTfulSummarizedExperiment from RESTfulSE
-  sed -i '/RESTfulSummarizedExperiment/d' ${_pkgname}/R/${_pkgname}.R ${_pkgname}/NAMESPACE
-  tar -zcvf ${_pkgname}_${_pkgver}_1.tar.gz  ${_pkgname}
-
+build() {
+  mkdir -p build
+  R CMD INSTALL "$_pkgname" -l build
 }
 
-build() {
-  R CMD INSTALL ${_pkgname}_${_pkgver}_1.tar.gz -l "${srcdir}"
+check() {
+  cd "$_pkgname/tests"
+  R_LIBS="$srcdir/build" NOT_CRAN=true Rscript --vanilla test.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-tenxplore/lilac.py

@@ -1,12 +1,14 @@
 #!/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()
+    update_aur_repo()

BioArchLinux/r-tenxplore/lilac.yaml

@@ -1,7 +1,7 @@
 build_prefix: extra-x86_64
 maintainers:
-- github: starsareintherose
-  email: starsareintherose@outlook.com
+- github: pekkarr
+  email: pekkarr@protonmail.com
 repo_depends:
 - r-annotationdbi
 - r-matrixstats
@@ -10,8 +10,11 @@ repo_depends:
 - r-restfulse
 - r-shiny
 - r-summarizedexperiment
+repo_makedepends:
+- r-testthat
 update_on:
-- regex: tenXplore_([\d._-]+).tar.gz
-  source: regex
-  url: https://bioconductor.org/packages/tenXplore
+- source: rpkgs
+  pkgname: tenXplore
+  repo: bioc
+  md5: true
 - alias: r