diff --git a/BioArchLinux/r-glmmtmb/PKGBUILD b/BioArchLinux/r-glmmtmb/PKGBUILD index 80af1bdd68..52932dbc4c 100644 --- a/BioArchLinux/r-glmmtmb/PKGBUILD +++ b/BioArchLinux/r-glmmtmb/PKGBUILD @@ -1,26 +1,33 @@ -# system requirements: GNU make -# Maintainer: Guoyi Zhang +# Maintainer: Pekka Ristola +# Contributor: Guoyi Zhang _pkgname=glmmTMB _pkgver=1.1.7 pkgname=r-${_pkgname,,} -pkgver=1.1.7 +pkgver=${_pkgver//-/.} pkgrel=2 -pkgdesc='Generalized Linear Mixed Models using Template Model Builder' -arch=('x86_64') +pkgdesc="Generalized Linear Mixed Models using Template Model Builder" +arch=(x86_64) url="https://cran.r-project.org/package=${_pkgname}" -license=('AGPL') +license=(AGPL3) depends=( - r r-lme4 r-numderiv - r-rcppeigen r-tmb - make +) +makedepends=( + r-rcppeigen +) +checkdepends=( + r-car + r-effects + r-emmeans + r-mvabund + r-pscl + r-testthat ) optdepends=( r-bbmle - r-boot r-broom r-broom.mixed r-car @@ -33,13 +40,10 @@ optdepends=( r-ggplot2 r-huxtable r-knitr - r-lattice - r-mass r-mlmrev r-multcomp r-mumin r-mvabund - r-parallel r-plyr r-png r-pscl @@ -50,14 +54,20 @@ optdepends=( r-xtable ) source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +md5sums=('97dac1dddc453e0e9b5d7c072e4d4766') sha256sums=('a38be6e3b8a65a928d19970aee2b13d28535e42b97a046b2f00014f78475c1f1') 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 AAAtest-all.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-glmmtmb/lilac.py b/BioArchLinux/r-glmmtmb/lilac.py index bd219c037c..6cfc1b802b 100644 --- a/BioArchLinux/r-glmmtmb/lilac.py +++ b/BioArchLinux/r-glmmtmb/lilac.py @@ -1,12 +1,16 @@ #!/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, + expect_systemrequirements = "GNU make", + ) def post_build(): git_pkgbuild_commit() diff --git a/BioArchLinux/r-glmmtmb/lilac.yaml b/BioArchLinux/r-glmmtmb/lilac.yaml index 5726b6201b..037ff819cc 100644 --- a/BioArchLinux/r-glmmtmb/lilac.yaml +++ b/BioArchLinux/r-glmmtmb/lilac.yaml @@ -1,14 +1,24 @@ build_prefix: extra-x86_64 maintainers: -- github: starsareintherose - email: kuoi@bioarchlinux.org +- github: pekkarr + email: pekkarr@protonmail.com repo_depends: - r-lme4 - r-numderiv -- r-rcppeigen - r-tmb +repo_makedepends: +- r-rcppeigen +- r-car +- r-effects +- r-emmeans +- r-mvabund +- r-pscl +- r-testthat update_on: -- regex: glmmTMB_([\d._-]+).tar.gz - source: regex - url: https://cran.r-project.org/package=glmmTMB +- source: rpkgs + pkgname: glmmTMB + repo: cran + md5: true - alias: r +update_on_build: +- pkgbase: r-tmb diff --git a/lilac-extensions/lilac_r_utils.py b/lilac-extensions/lilac_r_utils.py index e1c02c9f98..3bad04bf90 100644 --- a/lilac-extensions/lilac_r_utils.py +++ b/lilac-extensions/lilac_r_utils.py @@ -185,6 +185,7 @@ class Pkgbuild: # maps the license field in the DESCRIPTION file to a PKGBUILD license value license_map = { + "AGPL-3": "AGPL3", "Apache License": "Apache", "Apache License (== 2.0)": "Apache", "Apache License 2.0": "Apache",