r-fusesom: init

BioArchLinux/r-analogue/PKGBUILD

@@ -0,0 +1,40 @@
+# Maintainer: Pekka Ristola <pekkarr [at] protonmail [dot] com>
+
+_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"
+}

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()

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

BioArchLinux/r-fcps/PKGBUILD

@@ -0,0 +1,88 @@
+# Maintainer: Pekka Ristola <pekkarr [at] protonmail [dot] com>
+
+_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"
+}

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()

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

BioArchLinux/r-fusesom/PKGBUILD

@@ -0,0 +1,50 @@
+# Maintainer: Pekka Ristola <pekkarr [at] protonmail [dot] com>
+
+_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"
+}

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()

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