diff --git a/BioArchLinux/r-analogue/PKGBUILD b/BioArchLinux/r-analogue/PKGBUILD new file mode 100644 index 0000000000..ec9d91c7b5 --- /dev/null +++ b/BioArchLinux/r-analogue/PKGBUILD @@ -0,0 +1,40 @@ +# Maintainer: Pekka Ristola + +_pkgname=analogue +_pkgver=0.17-6 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//-/.} +pkgrel=1 +pkgdesc="Analogue and Weighted Averaging Methods for Palaeoecology" +arch=(x86_64) +url="https://cran.r-project.org/package=${_pkgname}" +license=(GPL2) +depends=( + r-brglm + r-princurve + r-vegan +) +checkdepends=( + r-testthat +) +optdepends=( + r-testthat +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +md5sums=('f4fcf06d896fa95e76d79da19c19e6ff') +sha256sums=('71070f4e669b161a8bec355bf678cc94bb78ba87ee0625cbd8cd53b7ac45b030') + +build() { + mkdir -p build + R CMD INSTALL "$_pkgname" -l build +} + +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" "$pkgdir/usr/lib/R/library" +} diff --git a/BioArchLinux/r-analogue/lilac.py b/BioArchLinux/r-analogue/lilac.py new file mode 100644 index 0000000000..b5cdb057c5 --- /dev/null +++ b/BioArchLinux/r-analogue/lilac.py @@ -0,0 +1,14 @@ +#!/usr/bin/env python3 +from lilaclib import * + +import os +import sys +sys.path.append(os.path.normpath(f'{__file__}/../../../lilac-extensions')) +from lilac_r_utils import r_pre_build + +def pre_build(): + r_pre_build(_G) + +def post_build(): + git_pkgbuild_commit() + update_aur_repo() diff --git a/BioArchLinux/r-analogue/lilac.yaml b/BioArchLinux/r-analogue/lilac.yaml new file mode 100644 index 0000000000..71948bb4b0 --- /dev/null +++ b/BioArchLinux/r-analogue/lilac.yaml @@ -0,0 +1,16 @@ +build_prefix: extra-x86_64 +maintainers: +- github: pekkarr + email: pekkarr@protonmail.com +repo_depends: +- r-brglm +- r-princurve +- r-vegan +repo_makedepends: +- r-testthat +update_on: +- source: rpkgs + pkgname: analogue + repo: cran + md5: true +- alias: r diff --git a/BioArchLinux/r-fcps/PKGBUILD b/BioArchLinux/r-fcps/PKGBUILD new file mode 100644 index 0000000000..8588917292 --- /dev/null +++ b/BioArchLinux/r-fcps/PKGBUILD @@ -0,0 +1,88 @@ +# Maintainer: Pekka Ristola + +_pkgname=FCPS +_pkgver=1.3.4 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//-/.} +pkgrel=1 +pkgdesc="Fundamental Clustering Problems Suite" +arch=(any) +url="https://cran.r-project.org/package=${_pkgname}" +license=(GPL3) +depends=( + pandoc + r-datavisualizations + r-ggplot2 + r-mclust +) +optdepends=( + r-abcanalysis + r-adpclust + r-apcluster + r-cclust + r-cec + r-clusterability + r-clusterr + r-clustersim + r-clustmixtype + r-clustrd + r-clustvarsel + r-databionicswarm + r-dbscan + r-dendextend + r-densityclust + r-emcluster + r-energy + r-fastcluster + r-flexclust + r-generalizedumatrix + r-genie + r-hdclassif + r-igraph + r-kernlab + r-knitr + r-kohonen + r-leiden + r-mcl + r-mixtools + r-mlpack + r-moments + r-mstknnclust + r-networktoolbox + r-orclus + r-paralleldist + r-partitioncomparison + r-pdfcluster + r-plotly + r-ppci + r-prabclus + r-pracma + r-prclust + r-projectionbasedclustering + r-protoclust + r-r.utils + r-reshape2 + r-rgl + r-rmarkdown + r-signal + r-smacof + r-sparcl + r-spectrum + r-subspace + r-tclust + r-varsellcm + r-yardstick +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +md5sums=('749ba6fd6322916b39cfcbc8843280a8') +sha256sums=('d1e5e06700a81fe529f52ef1f65977d3c786f33df262f4f89238d2622dc7ba97') + +build() { + mkdir -p build + R CMD INSTALL "$_pkgname" -l build +} + +package() { + install -d "$pkgdir/usr/lib/R/library" + cp -a --no-preserve=ownership "build/$_pkgname" "$pkgdir/usr/lib/R/library" +} diff --git a/BioArchLinux/r-fcps/lilac.py b/BioArchLinux/r-fcps/lilac.py new file mode 100644 index 0000000000..a7bdacf2c5 --- /dev/null +++ b/BioArchLinux/r-fcps/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 = "Pandoc (>= 1.12.3)", + ) + +def post_build(): + git_pkgbuild_commit() + update_aur_repo() diff --git a/BioArchLinux/r-fcps/lilac.yaml b/BioArchLinux/r-fcps/lilac.yaml new file mode 100644 index 0000000000..801738408a --- /dev/null +++ b/BioArchLinux/r-fcps/lilac.yaml @@ -0,0 +1,14 @@ +build_prefix: extra-x86_64 +maintainers: +- github: pekkarr + email: pekkarr@protonmail.com +repo_depends: +- r-datavisualizations +- r-ggplot2 +- r-mclust +update_on: +- source: rpkgs + pkgname: FCPS + repo: cran + md5: true +- alias: r diff --git a/BioArchLinux/r-fusesom/PKGBUILD b/BioArchLinux/r-fusesom/PKGBUILD new file mode 100644 index 0000000000..619d03c877 --- /dev/null +++ b/BioArchLinux/r-fusesom/PKGBUILD @@ -0,0 +1,50 @@ +# Maintainer: Pekka Ristola + +_pkgname=FuseSOM +_pkgver=1.4.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//-/.} +pkgrel=1 +pkgdesc="A Correlation Based Multiview Self Organizing Maps Clustering For IMC Datasets" +arch=(x86_64) +url="https://bioconductor.org/packages/${_pkgname}" +license=(GPL2) +depends=( + r-analogue + r-coop + r-diptest + r-fastcluster + r-fcps + r-fpc + r-ggplot2 + r-ggplotify + r-ggpubr + r-pheatmap + r-proxy + r-psych + r-s4vectors + r-stringr + r-summarizedexperiment +) +makedepends=( + r-rcpp +) +optdepends=( + r-biocstyle + r-knitr + r-rmarkdown + r-singlecellexperiment +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +md5sums=('8f53b251d77ea648cb8e56bb5eb72b18') +sha256sums=('34faa781054e961cb06eab6f477680dcc07933003370ffd98e1558975f462bd7') + +build() { + mkdir -p build + R CMD INSTALL "$_pkgname" -l build +} + +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-fusesom/lilac.py b/BioArchLinux/r-fusesom/lilac.py new file mode 100644 index 0000000000..b5cdb057c5 --- /dev/null +++ b/BioArchLinux/r-fusesom/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-fusesom/lilac.yaml b/BioArchLinux/r-fusesom/lilac.yaml new file mode 100644 index 0000000000..84e9e94958 --- /dev/null +++ b/BioArchLinux/r-fusesom/lilac.yaml @@ -0,0 +1,28 @@ +build_prefix: extra-x86_64 +maintainers: +- github: pekkarr + email: pekkarr@protonmail.com +repo_depends: +- r-analogue +- r-coop +- r-diptest +- r-fastcluster +- r-fcps +- r-fpc +- r-ggplot2 +- r-ggplotify +- r-ggpubr +- r-pheatmap +- r-proxy +- r-psych +- r-s4vectors +- r-stringr +- r-summarizedexperiment +repo_makedepends: +- r-rcpp +update_on: +- source: rpkgs + pkgname: FuseSOM + repo: bioc + md5: true +- alias: r