r-*: add some missing Bioconductor packages

BioArchLinux/r-metabinr/PKGBUILD

@@ -0,0 +1,49 @@
+# Maintainer: Pekka Ristola <pekkarr [at] protonmail [dot] com>
+
+_pkgname=metabinR
+_pkgver=1.4.0
+pkgname=r-${_pkgname,,}
+pkgver=${_pkgver//-/.}
+pkgrel=1
+pkgdesc="Abundance and Compositional Based Binning of Metagenomes"
+arch=(any)
+url="https://bioconductor.org/packages/$_pkgname"
+license=('GPL-3.0-only')
+depends=(
+  r-rjava
+)
+checkdepends=(
+  r-testthat
+)
+optdepends=(
+  r-biocstyle
+  r-cvms
+  r-data.table
+  r-dplyr
+  r-ggplot2
+  r-gridextra
+  r-knitr
+  r-r.utils
+  r-rmarkdown
+  r-sabre
+  r-spelling
+  r-testthat
+)
+source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz")
+md5sums=('7080ae8eac49640aeae95bda1185ac7d')
+b2sums=('aca5dc5305cd8218c5fe4086629d46ad848d9e9a9836dac76e844ba20a2b77e891fb42f1604ec446dbe9cd27615869d7db75e93a9e12536647b0dc5b6dbd92eb')
+
+build() {
+  mkdir build
+  R CMD INSTALL -l build "$_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"
+}

BioArchLinux/r-metabinr/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 = "Java (>= 8)",
+    )
+
+def post_build():
+    git_pkgbuild_commit()
+    update_aur_repo()

BioArchLinux/r-metabinr/lilac.yaml

@@ -0,0 +1,14 @@
+build_prefix: extra-x86_64
+maintainers:
+- github: pekkarr
+  email: pekkarr@protonmail.com
+repo_depends:
+- r-rjava
+repo_makedepends:
+- r-testthat
+update_on:
+- source: rpkgs
+  pkgname: metabinR
+  repo: bioc
+  md5: true
+- alias: r

BioArchLinux/r-regionalst/PKGBUILD

@@ -0,0 +1,58 @@
+# Maintainer: Pekka Ristola <pekkarr [at] protonmail [dot] com>
+
+_pkgname=RegionalST
+_pkgver=1.0.1
+pkgname=r-${_pkgname,,}
+pkgver=${_pkgver//-/.}
+pkgrel=1
+pkgdesc="Investigating regions of interest and performing cross-regional analysis with spatial transcriptomics data"
+arch=(any)
+url="https://bioconductor.org/packages/$_pkgname"
+license=('GPL-3.0-only')
+depends=(
+  r-assertthat
+  r-bayesspace
+  r-colorspace
+  r-dplyr
+  r-fgsea
+  r-ggplot2
+  r-gridextra
+  r-magrittr
+  r-rcolorbrewer
+  r-s4vectors
+  r-scater
+  r-seurat
+  r-shiny
+  r-singlecellexperiment
+  r-summarizedexperiment
+  r-tibble
+  r-toast
+)
+checkdepends=(
+  r-testthat
+)
+optdepends=(
+  r-biocstyle
+  r-gplots
+  r-knitr
+  r-rmarkdown
+  r-testthat
+)
+source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz")
+md5sums=('d9589bef7f1408c77dee510baa14b4ad')
+b2sums=('82d2fe4733e6bbfc397e0f52e30b13dafd96c5305ac67b8461ceb9edb86c3671d7924b05b441665a1b86c864ae8def6d0687773984f60731a0049132e3257749')
+
+build() {
+  mkdir build
+  R CMD INSTALL -l build "$_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"
+}

BioArchLinux/r-regionalst/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-regionalst/lilac.yaml

@@ -0,0 +1,30 @@
+build_prefix: extra-x86_64
+maintainers:
+- github: pekkarr
+  email: pekkarr@protonmail.com
+repo_depends:
+- r-assertthat
+- r-bayesspace
+- r-colorspace
+- r-dplyr
+- r-fgsea
+- r-ggplot2
+- r-gridextra
+- r-magrittr
+- r-rcolorbrewer
+- r-s4vectors
+- r-scater
+- r-seurat
+- r-shiny
+- r-singlecellexperiment
+- r-summarizedexperiment
+- r-tibble
+- r-toast
+repo_makedepends:
+- r-testthat
+update_on:
+- source: rpkgs
+  pkgname: RegionalST
+  repo: bioc
+  md5: true
+- alias: r

BioArchLinux/r-reusedata/PKGBUILD

@@ -0,0 +1,39 @@
+# Maintainer: Pekka Ristola <pekkarr [at] protonmail [dot] com>
+
+_pkgname=ReUseData
+_pkgver=1.2.2
+pkgname=r-${_pkgname,,}
+pkgver=${_pkgver//-/.}
+pkgrel=1
+pkgdesc="Reusable and reproducible Data Management"
+arch=(any)
+url="https://bioconductor.org/packages/$_pkgname"
+license=('GPL-3.0-only')
+depends=(
+  r-basilisk
+  r-biocfilecache
+  r-jsonlite
+  r-rcwl
+  r-rcwlpipelines
+  r-s4vectors
+  r-yaml
+)
+optdepends=(
+  r-biocstyle
+  r-knitr
+  r-rmarkdown
+  r-testthat
+)
+source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz")
+md5sums=('c0041ec5d810d0d043c7375e04e78c06')
+b2sums=('994e05474d8b9b21045c24b1900055009135f5b5cf8e0d362b15175f719c3cdba80633092cdc9ef8fc26f101cd9f2ef1577560263f7a31727494e43cb330f6d3')
+
+build() {
+  mkdir build
+  R CMD INSTALL -l build "$_pkgname"
+}
+
+package() {
+  install -d "$pkgdir/usr/lib/R/library"
+  cp -a --no-preserve=ownership "build/$_pkgname" "$pkgdir/usr/lib/R/library"
+}

BioArchLinux/r-reusedata/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-reusedata/lilac.yaml

@@ -0,0 +1,18 @@
+build_prefix: extra-x86_64
+maintainers:
+- github: pekkarr
+  email: pekkarr@protonmail.com
+repo_depends:
+- r-basilisk
+- r-biocfilecache
+- r-jsonlite
+- r-rcwl
+- r-rcwlpipelines
+- r-s4vectors
+- r-yaml
+update_on:
+- source: rpkgs
+  pkgname: ReUseData
+  repo: bioc
+  md5: true
+- alias: r

BioArchLinux/r-scarray.sat/PKGBUILD

@@ -0,0 +1,52 @@
+# Maintainer: Pekka Ristola <pekkarr [at] protonmail [dot] com>
+
+_pkgname=SCArray.sat
+_pkgver=1.2.1
+pkgname=r-${_pkgname,,}
+pkgver=${_pkgver//-/.}
+pkgrel=1
+pkgdesc="Large-scale single-cell RNA-seq data analysis using GDS files and Seurat"
+arch=(any)
+url="https://bioconductor.org/packages/$_pkgname"
+license=('GPL-3.0-only')
+depends=(
+  r-biocgenerics
+  r-biocparallel
+  r-biocsingular
+  r-delayedarray
+  r-gdsfmt
+  r-s4vectors
+  r-scarray
+  r-seurat
+  r-seuratobject
+  r-summarizedexperiment
+)
+checkdepends=(
+  r-runit
+)
+optdepends=(
+  r-biocstyle
+  r-future
+  r-knitr
+  r-markdown
+  r-rmarkdown
+  r-runit
+)
+source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz")
+md5sums=('dfa447cd634a432486a982a719e27451')
+b2sums=('c5578e0249789ce5b09ccaf8209b12109f18c68dd37230e2c25259bcbf59eba958d99d56076b0b3d8ac12dcd48e871c0ad16cf7d9ba9933259ee89214823df54')
+
+build() {
+  mkdir build
+  R CMD INSTALL -l build "$_pkgname"
+}
+
+check() {
+  cd "$_pkgname/tests"
+  R_LIBS="$srcdir/build" Rscript --vanilla runTests.R
+}
+
+package() {
+  install -d "$pkgdir/usr/lib/R/library"
+  cp -a --no-preserve=ownership "build/$_pkgname" "$pkgdir/usr/lib/R/library"
+}

BioArchLinux/r-scarray.sat/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-scarray.sat/lilac.yaml

@@ -0,0 +1,23 @@
+build_prefix: extra-x86_64
+maintainers:
+- github: pekkarr
+  email: pekkarr@protonmail.com
+repo_depends:
+- r-biocgenerics
+- r-biocparallel
+- r-biocsingular
+- r-delayedarray
+- r-gdsfmt
+- r-s4vectors
+- r-scarray
+- r-seurat
+- r-seuratobject
+- r-summarizedexperiment
+repo_makedepends:
+- r-runit
+update_on:
+- source: rpkgs
+  pkgname: SCArray.sat
+  repo: bioc
+  md5: true
+- alias: r

BioArchLinux/r-simona/PKGBUILD

@@ -0,0 +1,70 @@
+# Maintainer: Pekka Ristola <pekkarr [at] protonmail [dot] com>
+
+_pkgname=simona
+_pkgver=1.0.10
+pkgname=r-${_pkgname,,}
+pkgver=${_pkgver//-/.}
+pkgrel=1
+pkgdesc="Semantic Similarity in Bio-Ontologies"
+arch=(x86_64)
+url="https://bioconductor.org/packages/$_pkgname"
+license=('MIT')
+depends=(
+  java-runtime
+  perl
+  r-circlize
+  r-complexheatmap
+  r-getoptlong
+  r-globaloptions
+  r-igraph
+  r-matrixstats
+  r-polychrome
+  r-rcpp
+  r-s4vectors
+  r-shiny
+  r-xml2
+)
+checkdepends=(
+  r-go.db
+  r-org.hs.eg.db
+  r-proxyc
+  r-testthat
+)
+optdepends=(
+  r-annotationdbi
+  r-annotationhub
+  r-biocmanager
+  r-diagrammer
+  r-go.db
+  r-interactivecomplexheatmap
+  r-jsonlite
+  r-knitr
+  r-org.hs.eg.db
+  r-png
+  r-proxyc
+  r-ragg
+  r-simplifyenrichment
+  r-testthat
+  r-uniprotkeywords
+)
+source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz")
+md5sums=('3c9d33cfa91dc8e3e071da9fb3bff761')
+b2sums=('00f3ed8cce6c401558d4e08365ac82111a00fd7e8f973b438868d58e602efe90b13d528170da13c323d16a4d6eab32ad4445938027834a068ba29c9228656b14')
+
+build() {
+  mkdir build
+  R CMD INSTALL -l build "$_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" "$pkgdir/usr/lib/R/library"
+
+  install -d "$pkgdir/usr/share/licenses/$pkgname"
+  ln -s "/usr/lib/R/library/$_pkgname/LICENSE" "$pkgdir/usr/share/licenses/$pkgname"
+}

BioArchLinux/r-simona/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 = "Perl, Java",
+    )
+
+def post_build():
+    git_pkgbuild_commit()
+    update_aur_repo()

BioArchLinux/r-simona/lilac.yaml

@@ -0,0 +1,27 @@
+build_prefix: extra-x86_64
+maintainers:
+- github: pekkarr
+  email: pekkarr@protonmail.com
+repo_depends:
+- r-circlize
+- r-complexheatmap
+- r-getoptlong
+- r-globaloptions
+- r-igraph
+- r-matrixstats
+- r-polychrome
+- r-rcpp
+- r-s4vectors
+- r-shiny
+- r-xml2
+repo_makedepends:
+- r-go.db
+- r-org.hs.eg.db
+- r-proxyc
+- r-testthat
+update_on:
+- source: rpkgs
+  pkgname: simona
+  repo: bioc
+  md5: true
+- alias: r