r-tdbasedufe: init

BioArchLinux/r-mofadata/PKGBUILD

@@ -0,0 +1,33 @@
+# Maintainer: Pekka Ristola <pekkarr [at] protonmail [dot] com>
+
+_pkgname=MOFAdata
+_pkgver=1.18.0
+pkgname=r-${_pkgname,,}
+pkgver=${_pkgver//-/.}
+pkgrel=1
+pkgdesc="Data package for Multi-Omics Factor Analysis (MOFA)"
+arch=(any)
+url="https://bioconductor.org/packages/${_pkgname}"
+license=(LGPL3)
+depends=(
+  r
+)
+optdepends=(
+  r-biocstyle
+  r-knitr
+  r-multiassayexperiment
+  r-rmarkdown
+)
+source=("https://bioconductor.org/packages/release/data/experiment/src/contrib/${_pkgname}_${_pkgver}.tar.gz")
+md5sums=('23e46e209a43d7e62cfd6accc6a6fb44')
+sha256sums=('c1e32c68192a91e9174f345cfbc97b73879594b0182fd51642ef2047db4885de')
+
+build() {
+  mkdir -p build
+  R CMD INSTALL "$_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-mofadata/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_needscompilation = True,
+    )
+
+def post_build():
+    git_pkgbuild_commit()
+    update_aur_repo()

BioArchLinux/r-mofadata/lilac.yaml

@@ -0,0 +1,10 @@
+build_prefix: extra-x86_64
+maintainers:
+- github: pekkarr
+  email: pekkarr@protonmail.com
+update_on:
+- source: rpkgs
+  pkgname: MOFAdata
+  repo: bioc-data-experiment
+  md5: true
+- alias: r

BioArchLinux/r-tdbasedufe/PKGBUILD

@@ -0,0 +1,47 @@
+# Maintainer: Pekka Ristola <pekkarr [at] protonmail [dot] com>
+
+_pkgname=TDbasedUFE
+_pkgver=1.2.0
+pkgname=r-${_pkgname,,}
+pkgver=${_pkgver//-/.}
+pkgrel=1
+pkgdesc="Tensor Decomposition Based Unsupervised Feature Extraction"
+arch=(any)
+url="https://bioconductor.org/packages/${_pkgname}"
+license=(GPL3)
+depends=(
+  r-genomicranges
+  r-mofadata
+  r-readr
+  r-rtensor
+  r-shiny
+  r-tximport
+  r-tximportdata
+)
+checkdepends=(
+  r-testthat
+)
+optdepends=(
+  r-biocstyle
+  r-knitr
+  r-rmarkdown
+  r-testthat
+)
+source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz")
+md5sums=('5557e1128d1d6ffab09670bf90b8947c')
+sha256sums=('66ed99fd2677d840b52079fd72eaaea8c67e0be06a87e8eba26848e6629514d8')
+
+build() {
+  mkdir -p build
+  R CMD INSTALL "$_pkgname" -l build
+}
+
+check() {
+  cd "$_pkgname/tests"
+  R_LIBS="$srcdir/build" NOT_CRAN=true Rscript --vanilla testthat.R
+}
+
+package() {
+  install -d "$pkgdir/usr/lib/R/library"
+  cp -a --no-preserve=ownership "build/$_pkgname" "$pkgdir/usr/lib/R/library"
+}

BioArchLinux/r-tdbasedufe/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-tdbasedufe/lilac.yaml

@@ -0,0 +1,20 @@
+build_prefix: extra-x86_64
+maintainers:
+- github: pekkarr
+  email: pekkarr@protonmail.com
+repo_depends:
+- r-genomicranges
+- r-mofadata
+- r-readr
+- r-rtensor
+- r-shiny
+- r-tximport
+- r-tximportdata
+repo_makedepends:
+- r-testthat
+update_on:
+- source: rpkgs
+  pkgname: TDbasedUFE
+  repo: bioc
+  md5: true
+- alias: r

BioArchLinux/r-tximportdata/PKGBUILD

@@ -0,0 +1,31 @@
+# Maintainer: Pekka Ristola <pekkarr [at] protonmail [dot] com>
+
+_pkgname=tximportData
+_pkgver=1.30.0
+pkgname=r-${_pkgname,,}
+pkgver=${_pkgver//-/.}
+pkgrel=1
+pkgdesc="tximportData"
+arch=(any)
+url="https://bioconductor.org/packages/${_pkgname}"
+license=(GPL)
+depends=(
+  r
+)
+optdepends=(
+  r-knitr
+  r-markdown
+)
+source=("https://bioconductor.org/packages/release/data/experiment/src/contrib/${_pkgname}_${_pkgver}.tar.gz")
+md5sums=('4494d764fc087333e5c04ee7977c85c8')
+sha256sums=('0f8218398e976c5930ecebf45663feba4af8b8f165d47f01f91f4fbade78554f')
+
+build() {
+  mkdir -p build
+  R CMD INSTALL "$_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-tximportdata/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-tximportdata/lilac.yaml

@@ -0,0 +1,10 @@
+build_prefix: extra-x86_64
+maintainers:
+- github: pekkarr
+  email: pekkarr@protonmail.com
+update_on:
+- source: rpkgs
+  pkgname: tximportData
+  repo: bioc-data-experiment
+  md5: true
+- alias: r