r-humantranscriptomecompendium: fix depends, use metadata checks

BioArchLinux/r-humantranscriptomecompendium/PKGBUILD

@@ -1,21 +1,27 @@
-# 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=HumanTranscriptomeCompendium
-_pkgver=1.16.0
+_pkgver=1.16.3
 pkgname=r-${_pkgname,,}
-pkgver=1.16.0
-pkgrel=1
-pkgdesc='Tools to work with a Compendium of 181000 human transcriptome sequencing studies'
-arch=('any')
+pkgver=${_pkgver//-/.}
+pkgrel=0
+pkgdesc="Tools to work with a Compendium of 181000 human transcriptome sequencing studies"
+arch=(any)
 url="https://bioconductor.org/packages/${_pkgname}"
-license=('Artistic2.0')
+license=(Artistic2.0)
 depends=(
-  r
+  r-biocmanager
   r-s4vectors
   r-shiny
   r-ssrch
   r-summarizedexperiment
 )
+checkdepends=(
+  r-biocfilecache
+  r-rhdf5client
+  r-testthat
+)
 optdepends=(
   r-beeswarm
   r-biocfilecache
@@ -31,14 +37,20 @@ optdepends=(
   r-tximportdata
 )
 source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz")
-sha256sums=('ef7f7e47313cbacd888f1030e8c17c5b7c14b538530a26ebd13d07f5e4b5ee86')
+md5sums=('91a351c2b23e0407ba8d67abfda46c2d')
+sha256sums=('289705a6fcc798fa93e9ae43a2418ac5dcd758ac228960f84086f4d848263c3a')
 
 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-humantranscriptomecompendium/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-humantranscriptomecompendium/lilac.yaml

@@ -1,14 +1,20 @@
 build_prefix: extra-x86_64
 maintainers:
-- github: starsareintherose
-  email: kuoi@bioarchlinux.org
+- github: pekkarr
+  email: pekkarr@protonmail.com
 repo_depends:
+- r-biocmanager
 - r-s4vectors
 - r-shiny
 - r-ssrch
 - r-summarizedexperiment
+repo_makedepends:
+- r-biocfilecache
+- r-rhdf5client
+- r-testthat
 update_on:
-- regex: HumanTranscriptomeCompendium_([\d._-]+).tar.gz
-  source: regex
-  url: https://bioconductor.org/packages/HumanTranscriptomeCompendium
+- source: rpkgs
+  pkgname: HumanTranscriptomeCompendium
+  repo: bioc
+  md5: true
 - alias: r