r-biodb: fix depends, use metadata checks

BioArchLinux/r-biodb/PKGBUILD

@@ -1,18 +1,19 @@
-# 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=biodb
-_pkgver=1.8.0
+_pkgver=1.8.1
 pkgname=r-${_pkgname,,}
-pkgver=1.8.0
-pkgrel=1
-pkgdesc='biodb, a library and a development framework for connecting to chemical and biological databases'
-arch=('x86_64')
+pkgver=${_pkgver//-/.}
+pkgrel=0
+pkgdesc="biodb, a library and a development framework for connecting to chemical and biological databases"
+arch=(x86_64)
 url="https://bioconductor.org/packages/${_pkgname}"
-license=('AGPL')
+license=(AGPL3)
 depends=(
-  r
   r-biocfilecache
   r-chk
+  r-git2r
   r-jsonlite
   r-lgr
   r-lifecycle
@@ -25,16 +26,20 @@ depends=(
   r-rcurl
   r-rsqlite
   r-stringr
-  r-testthat
   r-withr
   r-xml
   r-yaml
 )
+makedepends=(
+  r-testthat
+)
+checkdepends=(
+  r-xml2
+)
 optdepends=(
   r-biocstyle
   r-covr
   r-devtools
-  r-git2r
   r-knitr
   r-rmarkdown
   r-roxygen2
@@ -42,14 +47,20 @@ optdepends=(
   r-xml2
 )
 source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz")
-sha256sums=('b394a2bea684f3c406cbdb5564893dc289ad995716cf8cf13d0c66e57ec092d1')
+md5sums=('f69fe1c97541bcf6b7a21503029dca6e')
+sha256sums=('93fd88720be908517d594ab00b24d98a994edee00efd7f311664e182540547a2')
 
 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-biodb/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-biodb/lilac.yaml

@@ -1,10 +1,11 @@
 build_prefix: extra-x86_64
 maintainers:
-- github: starsareintherose
-  email: kuoi@bioarchlinux.org
+- github: pekkarr
+  email: pekkarr@protonmail.com
 repo_depends:
 - r-biocfilecache
 - r-chk
+- r-git2r
 - r-jsonlite
 - r-lgr
 - r-lifecycle
@@ -17,12 +18,15 @@ repo_depends:
 - r-rcurl
 - r-rsqlite
 - r-stringr
-- r-testthat
 - r-withr
 - r-xml
 - r-yaml
+repo_makedepends:
+- r-testthat
+- r-xml2
 update_on:
-- regex: biodb_([\d._-]+).tar.gz
-  source: regex
-  url: https://bioconductor.org/packages/biodb
+- source: rpkgs
+  pkgname: biodb
+  repo: bioc
+  md5: true
 - alias: r