diff --git a/BioArchLinux/r-biodb/PKGBUILD b/BioArchLinux/r-biodb/PKGBUILD index 3f4b6a347d..c15c898f3e 100644 --- a/BioArchLinux/r-biodb/PKGBUILD +++ b/BioArchLinux/r-biodb/PKGBUILD @@ -1,18 +1,19 @@ -# Maintainer: Guoyi Zhang +# Maintainer: Pekka Ristola +# Contributor: Guoyi Zhang _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: diff --git a/BioArchLinux/r-biodb/lilac.py b/BioArchLinux/r-biodb/lilac.py index bd219c037c..b5cdb057c5 100644 --- a/BioArchLinux/r-biodb/lilac.py +++ b/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() diff --git a/BioArchLinux/r-biodb/lilac.yaml b/BioArchLinux/r-biodb/lilac.yaml index 254b302f0e..84e5ee79fc 100644 --- a/BioArchLinux/r-biodb/lilac.yaml +++ b/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