diff --git a/BioArchLinux/r-dharma/PKGBUILD b/BioArchLinux/r-dharma/PKGBUILD new file mode 100644 index 0000000000..b6ddc3f773 --- /dev/null +++ b/BioArchLinux/r-dharma/PKGBUILD @@ -0,0 +1,53 @@ +# Maintainer: Pekka Ristola + +_pkgname=DHARMa +_pkgver=0.4.6 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//-/.} +pkgrel=1 +pkgdesc="Residual Diagnostics for Hierarchical (Multi-Level / Mixed) Regression Models" +arch=(any) +url="https://cran.r-project.org/package=$_pkgname" +license=('GPL-3.0-or-later') +depends=( + r-ape + r-gap + r-lme4 + r-lmtest + r-qgam +) +checkdepends=( + r-glmmadaptive + r-glmmtmb + r-mgcviz + r-spamm + r-testthat +) +optdepends=( + r-glmmadaptive + r-glmmtmb + r-knitr + r-mgcviz + r-rmarkdown + r-sfsmisc + r-spamm + r-testthat +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +md5sums=('1bc0e3ce3b7761689efc8ad828b55e5d') +b2sums=('c344045c2adeedad2f17f318ddbbe9f8d6214368a50c97d0874f292197941f0c329ba68a18d099a7ec8160ffb294fccb7783762906692203b073bb9e76e0dbca') + +build() { + mkdir build + R CMD INSTALL -l build "$_pkgname" +} + +check() { + cd "$_pkgname/tests" + R_LIBS="$srcdir/build" NOT_CRAN=true Rscript --vanilla testthat.R +} + +package() { + install -d "$pkgdir/usr/lib/R/library" + cp -a --no-preserve=ownership "build/$_pkgname" "$pkgdir/usr/lib/R/library" +} diff --git a/BioArchLinux/r-dharma/lilac.py b/BioArchLinux/r-dharma/lilac.py new file mode 100644 index 0000000000..b5cdb057c5 --- /dev/null +++ b/BioArchLinux/r-dharma/lilac.py @@ -0,0 +1,14 @@ +#!/usr/bin/env python3 +from lilaclib import * + +import os +import sys +sys.path.append(os.path.normpath(f'{__file__}/../../../lilac-extensions')) +from lilac_r_utils import r_pre_build + +def pre_build(): + r_pre_build(_G) + +def post_build(): + git_pkgbuild_commit() + update_aur_repo() diff --git a/BioArchLinux/r-dharma/lilac.yaml b/BioArchLinux/r-dharma/lilac.yaml new file mode 100644 index 0000000000..bb22ae76d0 --- /dev/null +++ b/BioArchLinux/r-dharma/lilac.yaml @@ -0,0 +1,22 @@ +build_prefix: extra-x86_64 +maintainers: +- github: pekkarr + email: pekkarr@protonmail.com +repo_depends: +- r-ape +- r-gap +- r-lme4 +- r-lmtest +- r-qgam +repo_makedepends: +- r-glmmadaptive +- r-glmmtmb +- r-mgcviz +- r-spamm +- r-testthat +update_on: +- source: rpkgs + pkgname: DHARMa + repo: cran + md5: true +- alias: r diff --git a/BioArchLinux/r-gamm4/PKGBUILD b/BioArchLinux/r-gamm4/PKGBUILD new file mode 100644 index 0000000000..7a340c6061 --- /dev/null +++ b/BioArchLinux/r-gamm4/PKGBUILD @@ -0,0 +1,27 @@ +# Maintainer: Pekka Ristola + +_pkgname=gamm4 +_pkgver=0.2-6 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//-/.} +pkgrel=1 +pkgdesc="Generalized Additive Mixed Models using 'mgcv' and 'lme4'" +arch=(any) +url="https://cran.r-project.org/package=$_pkgname" +license=('GPL-2.0-or-later') +depends=( + r-lme4 +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +md5sums=('dff478c7c80f51c0356df39347fdf9f5') +b2sums=('1d6ea478da815f23c9c986c8d4c3acf9c5b57eaa923e627a3bf8d1b8c07920f48fffd98aaeff5ef8b8afafa5176337f2fb42002633eb0e04b8c6eecec0dce02d') + +build() { + mkdir build + R CMD INSTALL -l build "$_pkgname" +} + +package() { + install -d "$pkgdir/usr/lib/R/library" + cp -a --no-preserve=ownership "build/$_pkgname" "$pkgdir/usr/lib/R/library" +} diff --git a/BioArchLinux/r-gamm4/lilac.py b/BioArchLinux/r-gamm4/lilac.py new file mode 100644 index 0000000000..b5cdb057c5 --- /dev/null +++ b/BioArchLinux/r-gamm4/lilac.py @@ -0,0 +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(): + r_pre_build(_G) + +def post_build(): + git_pkgbuild_commit() + update_aur_repo() diff --git a/BioArchLinux/r-gamm4/lilac.yaml b/BioArchLinux/r-gamm4/lilac.yaml new file mode 100644 index 0000000000..683ac9dd48 --- /dev/null +++ b/BioArchLinux/r-gamm4/lilac.yaml @@ -0,0 +1,12 @@ +build_prefix: extra-x86_64 +maintainers: +- github: pekkarr + email: pekkarr@protonmail.com +repo_depends: +- r-lme4 +update_on: +- source: rpkgs + pkgname: gamm4 + repo: cran + md5: true +- alias: r diff --git a/BioArchLinux/r-genepop/lilac.py b/BioArchLinux/r-genepop/lilac.py index 9de86aa0f5..b5cdb057c5 100644 --- a/BioArchLinux/r-genepop/lilac.py +++ b/BioArchLinux/r-genepop/lilac.py @@ -7,10 +7,7 @@ sys.path.append(os.path.normpath(f'{__file__}/../../../lilac-extensions')) from lilac_r_utils import r_pre_build def pre_build(): - r_pre_build( - _G, - expect_license = "CeCILL-2", - ) + r_pre_build(_G) def post_build(): git_pkgbuild_commit() diff --git a/BioArchLinux/r-glmmadaptive/PKGBUILD b/BioArchLinux/r-glmmadaptive/PKGBUILD new file mode 100644 index 0000000000..97861ca32a --- /dev/null +++ b/BioArchLinux/r-glmmadaptive/PKGBUILD @@ -0,0 +1,38 @@ +# Maintainer: Pekka Ristola + +_pkgname=GLMMadaptive +_pkgver=0.9-1 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//-/.} +pkgrel=1 +pkgdesc="Generalized Linear Mixed Models using Adaptive Gaussian Quadrature" +arch=(any) +url="https://cran.r-project.org/package=$_pkgname" +license=('GPL-3.0-or-later') +depends=( + r-matrixstats +) +optdepends=( + r-dharma + r-effects + r-emmeans + r-estimability + r-knitr + r-multcomp + r-optimparallel + r-pkgdown + r-rmarkdown +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +md5sums=('5425f98c02d9ed56c6190b5c2b11dc8e') +b2sums=('d2e8007729a569ebeb2b7d498bf4ed38076526c3a6610537ef79f28ecb32c757d31b2350b99c17bdea39a3e70276f6fa563001909464c6baa9d47fefe727d75a') + +build() { + mkdir build + R CMD INSTALL -l build "$_pkgname" +} + +package() { + install -d "$pkgdir/usr/lib/R/library" + cp -a --no-preserve=ownership "build/$_pkgname" "$pkgdir/usr/lib/R/library" +} diff --git a/BioArchLinux/r-glmmadaptive/lilac.py b/BioArchLinux/r-glmmadaptive/lilac.py new file mode 100644 index 0000000000..b5cdb057c5 --- /dev/null +++ b/BioArchLinux/r-glmmadaptive/lilac.py @@ -0,0 +1,14 @@ +#!/usr/bin/env python3 +from lilaclib import * + +import os +import sys +sys.path.append(os.path.normpath(f'{__file__}/../../../lilac-extensions')) +from lilac_r_utils import r_pre_build + +def pre_build(): + r_pre_build(_G) + +def post_build(): + git_pkgbuild_commit() + update_aur_repo() diff --git a/BioArchLinux/r-glmmadaptive/lilac.yaml b/BioArchLinux/r-glmmadaptive/lilac.yaml new file mode 100644 index 0000000000..8826ed8f3c --- /dev/null +++ b/BioArchLinux/r-glmmadaptive/lilac.yaml @@ -0,0 +1,12 @@ +build_prefix: extra-x86_64 +maintainers: +- github: pekkarr + email: pekkarr@protonmail.com +repo_depends: +- r-matrixstats +update_on: +- source: rpkgs + pkgname: GLMMadaptive + repo: cran + md5: true +- alias: r diff --git a/BioArchLinux/r-mgcviz/PKGBUILD b/BioArchLinux/r-mgcviz/PKGBUILD new file mode 100644 index 0000000000..35d5ac918b --- /dev/null +++ b/BioArchLinux/r-mgcviz/PKGBUILD @@ -0,0 +1,52 @@ +# Maintainer: Pekka Ristola + +_pkgname=mgcViz +_pkgver=0.1.11 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//-/.} +pkgrel=1 +pkgdesc="Visualisations for Generalized Additive Models" +arch=(any) +url="https://cran.r-project.org/package=$_pkgname" +license=('GPL-3.0-only') +depends=( + r-gamm4 + r-ggally + r-ggplot2 + r-gridextra + r-matrixstats + r-miniui + r-plyr + r-qgam + r-shiny + r-viridis +) +checkdepends=( + r-hexbin + r-testthat +) +optdepends=( + r-knitr + r-rgl + r-rmarkdown + r-testthat + r-webshot2 +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +md5sums=('8b1f6454bc0d2d2a91f638ed6a25cfa6') +b2sums=('02c27902655eadd9be2b2b7a11b767cbf7d02baf784e4fb03d4428ee52743dd999643a1c70d491eb23dc6617a0133638244b833c3eb893aff29fd61d0e9561e1') + +build() { + mkdir build + R CMD INSTALL -l build "$_pkgname" +} + +check() { + cd "$_pkgname/tests" + R_LIBS="$srcdir/build" NOT_CRAN=true Rscript --vanilla testthat.R +} + +package() { + install -d "$pkgdir/usr/lib/R/library" + cp -a --no-preserve=ownership "build/$_pkgname" "$pkgdir/usr/lib/R/library" +} diff --git a/BioArchLinux/r-mgcviz/lilac.py b/BioArchLinux/r-mgcviz/lilac.py new file mode 100644 index 0000000000..b5cdb057c5 --- /dev/null +++ b/BioArchLinux/r-mgcviz/lilac.py @@ -0,0 +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(): + r_pre_build(_G) + +def post_build(): + git_pkgbuild_commit() + update_aur_repo() diff --git a/BioArchLinux/r-mgcviz/lilac.yaml b/BioArchLinux/r-mgcviz/lilac.yaml new file mode 100644 index 0000000000..07f8ccca02 --- /dev/null +++ b/BioArchLinux/r-mgcviz/lilac.yaml @@ -0,0 +1,24 @@ +build_prefix: extra-x86_64 +maintainers: +- github: pekkarr + email: pekkarr@protonmail.com +repo_depends: +- r-gamm4 +- r-ggally +- r-ggplot2 +- r-gridextra +- r-matrixstats +- r-miniui +- r-plyr +- r-qgam +- r-shiny +- r-viridis +repo_makedepends: +- r-hexbin +- r-testthat +update_on: +- source: rpkgs + pkgname: mgcViz + repo: cran + md5: true +- alias: r diff --git a/BioArchLinux/r-performance/PKGBUILD b/BioArchLinux/r-performance/PKGBUILD index ef024649b0..b33dd43a7a 100644 --- a/BioArchLinux/r-performance/PKGBUILD +++ b/BioArchLinux/r-performance/PKGBUILD @@ -2,10 +2,10 @@ # Contributor: Hu Butui _pkgname=performance -_pkgver=0.10.9 +_pkgver=0.11.0 pkgname=r-${_pkgname,,} pkgver=${_pkgver//-/.} -pkgrel=1 +pkgrel=0 pkgdesc="Assessment of Regression Models Performance" arch=(any) url="https://cran.r-project.org/package=$_pkgname" @@ -23,6 +23,7 @@ checkdepends=( r-bigutilsr r-curl r-dbscan + r-dharma r-estimatr r-fixest r-glmmtmb @@ -59,6 +60,7 @@ optdepends=( r-correlation r-cplm r-dbscan + r-dharma r-estimatr r-fixest r-flextable @@ -106,8 +108,8 @@ optdepends=( r-withr ) source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") -md5sums=('07a07184ab81c70c92646ab990e0fd5f') -b2sums=('029a8b72203e719ac7520d903f3eb510de573fd16a3efc2249a16b22dd11223f25a5e0680a4a114cd87fff4dd0e08504a4f7449e031cea683873059ac7823933') +md5sums=('003d46ccb28030be151595396c4315fd') +b2sums=('1e442ea24bcba7dd8a0a8504adc76a8686aa07e3bb25a73f161d4c2aa92aa2d965c69bde462fe2b7fb0c1ed55e5b10c10f7654dc396de75e277bbfedfe590231') prepare() { # skip failing tests diff --git a/BioArchLinux/r-performance/lilac.yaml b/BioArchLinux/r-performance/lilac.yaml index 05d62cf139..8cf74b4670 100644 --- a/BioArchLinux/r-performance/lilac.yaml +++ b/BioArchLinux/r-performance/lilac.yaml @@ -14,6 +14,7 @@ repo_makedepends: - r-bigutilsr - r-curl - r-dbscan +- r-dharma - r-estimatr - r-fixest - r-glmmtmb diff --git a/BioArchLinux/r-spamm/PKGBUILD b/BioArchLinux/r-spamm/PKGBUILD new file mode 100644 index 0000000000..c98b7c40a6 --- /dev/null +++ b/BioArchLinux/r-spamm/PKGBUILD @@ -0,0 +1,71 @@ +# Maintainer: Pekka Ristola + +_pkgname=spaMM +_pkgver=4.4.16 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//-/.} +pkgrel=1 +pkgdesc="Mixed-Effect Models, with or without Spatial Random Effects" +arch=(x86_64) +url="https://cran.r-project.org/package=$_pkgname" +license=('CECILL-2.0') +depends=( + gsl + r-backports + r-crayon + r-geometry + r-gmp + r-minqa + r-nloptr + r-numderiv + r-pbapply + r-proxy + r-rcpp + r-roi +) +makedepends=( + r-rcppeigen +) +checkdepends=( + r-testthat +) +optdepends=( + r-agridat + r-blackbox + r-foreach + r-future + r-future.apply + r-infusion + r-isorix + r-lme4 + r-maps + r-multilevel + r-rcdd + r-roi.plugin.glpk + r-rsae + r-rspectra + r-testthat +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz" + "$_pkgname-LICENSE::http://www.cecill.info/licences/Licence_CeCILL_V2-en.txt") +md5sums=('0e525101ec9034092e125b132e38ee5c' + '599cf91b33571e942d3ba5f9623b8011') +b2sums=('b0a969682e9f004e2a879a4156fe8eede308f5e16c2a7a05fd0e9cd8b46469791df8f094125fe457c75264c6a4d2f50554bddf85c5c1d4679fc7135758cb4d64' + 'ff97dacc39b8597e670dbaf5bc0f0e4db73eada273708433fc227fa72c054a30a67dbc7b2416089d68f09ab65da721e5b30711022c41047d9cf706731d568038') + +build() { + mkdir build + R CMD INSTALL -l build "$_pkgname" +} + +check() { + cd "$_pkgname/tests" + R_LIBS="$srcdir/build" NOT_CRAN=true Rscript --vanilla test-all.R +} + +package() { + install -d "$pkgdir/usr/lib/R/library" + cp -a --no-preserve=ownership "build/$_pkgname" "$pkgdir/usr/lib/R/library" + + install -Dm644 "$_pkgname-LICENSE" "$pkgdir/usr/share/licenses/$pkgname/LICENSE" +} diff --git a/BioArchLinux/r-spamm/lilac.py b/BioArchLinux/r-spamm/lilac.py new file mode 100644 index 0000000000..44d2780fa1 --- /dev/null +++ b/BioArchLinux/r-spamm/lilac.py @@ -0,0 +1,17 @@ +#!/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(): + r_pre_build( + _G, + expect_systemrequirements = "GNU Scientific Library (GSL)", + ) + +def post_build(): + git_pkgbuild_commit() + update_aur_repo() diff --git a/BioArchLinux/r-spamm/lilac.yaml b/BioArchLinux/r-spamm/lilac.yaml new file mode 100644 index 0000000000..fe9d9e75e6 --- /dev/null +++ b/BioArchLinux/r-spamm/lilac.yaml @@ -0,0 +1,29 @@ +build_prefix: extra-x86_64 +maintainers: +- github: pekkarr + email: pekkarr@protonmail.com +repo_depends: +- r-backports +- r-crayon +- r-geometry +- r-gmp +- r-minqa +- r-nloptr +- r-numderiv +- r-pbapply +- r-proxy +- r-rcpp +- r-roi +repo_makedepends: +- r-rcppeigen +- r-testthat +update_on: +- source: rpkgs + pkgname: spaMM + repo: cran + md5: true +- alias: r +- source: alpmfiles + pkgname: gsl + filename: usr/lib/libgsl\.so\.([^.]+) + repo: extra diff --git a/lilac-extensions/lilac_r_utils.py b/lilac-extensions/lilac_r_utils.py index 89e85ab119..77f4d95f04 100644 --- a/lilac-extensions/lilac_r_utils.py +++ b/lilac-extensions/lilac_r_utils.py @@ -200,6 +200,7 @@ license_map = { "CC BY-NC-SA 4.0": "CC-BY-NC-SA-4.0", "CC0": "CC0-1.0", "CeCILL": "CECILL-2.0", + "CeCILL-2": "CECILL-2.0", "EPL": "EPL", "GNU General Public License version 2": "GPL-2.0-only", "GPL": "GPL-2.0-or-later",