r-moonlight2r: init

BioArchLinux/r-fuzzyjoin/PKGBUILD

@@ -0,0 +1,58 @@
+# Maintainer: Pekka Ristola <pekkarr [at] protonmail [dot] com>
+
+_pkgname=fuzzyjoin
+_pkgver=0.1.6
+pkgname=r-${_pkgname,,}
+pkgver=${_pkgver//-/.}
+pkgrel=1
+pkgdesc="Join Tables Together on Inexact Matching"
+arch=(any)
+url="https://cran.r-project.org/package=${_pkgname}"
+license=(MIT)
+depends=(
+  r-dplyr
+  r-geosphere
+  r-purrr
+  r-stringdist
+  r-stringr
+  r-tibble
+  r-tidyr
+)
+checkdepends=(
+  r-ggplot2
+  r-iranges
+  r-testthat
+)
+optdepends=(
+  r-covr
+  r-ggplot2
+  r-iranges
+  r-knitr
+  r-maps
+  r-qdapdictionaries
+  r-readr
+  r-rmarkdown
+  r-rvest
+  r-testthat
+)
+source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz")
+md5sums=('d472d77dec7889760a9323a90aacc89e')
+sha256sums=('47eaefb73ce8553301e15359bc0e071222fc463c334ca486fa04c68d3e86b968')
+
+build() {
+  mkdir -p build
+  R CMD INSTALL "$_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" "$pkgdir/usr/lib/R/library"
+
+  install -d "$pkgdir/usr/share/licenses/$pkgname"
+  ln -s "/usr/lib/R/library/$_pkgname/LICENSE" "$pkgdir/usr/share/licenses/$pkgname"
+}

BioArchLinux/r-fuzzyjoin/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-fuzzyjoin/lilac.yaml

@@ -0,0 +1,22 @@
+build_prefix: extra-x86_64
+maintainers:
+- github: pekkarr
+  email: pekkarr@protonmail.com
+repo_depends:
+- r-dplyr
+- r-geosphere
+- r-purrr
+- r-stringdist
+- r-stringr
+- r-tibble
+- r-tidyr
+repo_makedepends:
+- r-ggplot2
+- r-iranges
+- r-testthat
+update_on:
+- source: rpkgs
+  pkgname: fuzzyjoin
+  repo: cran
+  md5: true
+- alias: r

BioArchLinux/r-moonlight2r/PKGBUILD

@@ -0,0 +1,73 @@
+# Maintainer: Pekka Ristola <pekkarr [at] protonmail [dot] com>
+
+_pkgname=Moonlight2R
+_pkgver=1.0.0
+pkgname=r-${_pkgname,,}
+pkgver=${_pkgver//-/.}
+pkgrel=1
+pkgdesc="Identify oncogenes and tumor suppressor genes from omics data"
+arch=(any)
+url="https://bioconductor.org/packages/${_pkgname}"
+license=(GPL3)
+depends=(
+  r-annotationhub
+  r-biobase
+  r-circlize
+  r-clusterprofiler
+  r-complexheatmap
+  r-doparallel
+  r-dose
+  r-dplyr
+  r-easypubmed
+  r-foreach
+  r-fuzzyjoin
+  r-genomicranges
+  r-geoquery
+  r-gplots
+  r-hiver
+  r-magrittr
+  r-org.hs.eg.db
+  r-parmigene
+  r-purrr
+  r-qpdf
+  r-randomforest
+  r-rcolorbrewer
+  r-readr
+  r-rismed
+  r-rtracklayer
+  r-seqminer
+  r-stringr
+  r-tibble
+  r-tidyheatmap
+  r-tidyr
+)
+checkdepends=(
+  r-testthat
+)
+optdepends=(
+  r-biocstyle
+  r-devtools
+  r-knitr
+  r-png
+  r-rmarkdown
+  r-roxygen2
+  r-testthat
+)
+source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz")
+md5sums=('45af1bc580f9231cb2a83eae7517d3b8')
+sha256sums=('e306a3aa11700652a2f1ada4cec3eed4112ec43d3392da550538b8c4bf6ee909')
+
+build() {
+  mkdir -p build
+  R CMD INSTALL "$_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-moonlight2r/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 = "CScapeSomatic",
+    )
+
+def post_build():
+    git_pkgbuild_commit()
+    update_aur_repo()

BioArchLinux/r-moonlight2r/lilac.yaml

@@ -0,0 +1,43 @@
+build_prefix: extra-x86_64
+maintainers:
+- github: pekkarr
+  email: pekkarr@protonmail.com
+repo_depends:
+- r-annotationhub
+- r-biobase
+- r-circlize
+- r-clusterprofiler
+- r-complexheatmap
+- r-doparallel
+- r-dose
+- r-dplyr
+- r-easypubmed
+- r-foreach
+- r-fuzzyjoin
+- r-genomicranges
+- r-geoquery
+- r-gplots
+- r-hiver
+- r-magrittr
+- r-org.hs.eg.db
+- r-parmigene
+- r-purrr
+- r-qpdf
+- r-randomforest
+- r-rcolorbrewer
+- r-readr
+- r-rismed
+- r-rtracklayer
+- r-seqminer
+- r-stringr
+- r-tibble
+- r-tidyheatmap
+- r-tidyr
+repo_makedepends:
+- r-testthat
+update_on:
+- source: rpkgs
+  pkgname: Moonlight2R
+  repo: bioc
+  md5: true
+- alias: r

BioArchLinux/r-spelling/PKGBUILD

@@ -0,0 +1,43 @@
+# Maintainer: Pekka Ristola <pekkarr [at] protonmail [dot] com>
+# Contributor: Viktor Drobot (aka dviktor) linux776 [at] gmail [dot] com
+# Contributor: Kibouo <csonka.mihaly@hotmail.com>
+
+_pkgname=spelling
+_pkgver=2.2.1
+pkgname=r-${_pkgname,,}
+pkgver=${_pkgver//-/.}
+pkgrel=0
+pkgdesc="Tools for Spell Checking in R"
+arch=(any)
+url="https://cran.r-project.org/package=${_pkgname}"
+license=(MIT)
+depends=(
+  r-commonmark
+  r-hunspell
+  r-knitr
+  r-xml2
+)
+optdepends=(
+  r-pdftools
+)
+source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz")
+md5sums=('47128c93e6cace1644edddfbb127de7b')
+sha256sums=('4fd4afcb5caa010630372c2dd32c34e8fc02ae385425c1f4b7dae697f8ab256f')
+
+build() {
+  mkdir -p build
+  R CMD INSTALL "$_pkgname" -l build
+}
+
+check() {
+  cd "$_pkgname/tests"
+  R_LIBS="$srcdir/build" NOT_CRAN=true Rscript --vanilla spelling.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-spelling/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-spelling/lilac.yaml

@@ -0,0 +1,15 @@
+build_prefix: extra-x86_64
+maintainers:
+- github: pekkarr
+  email: pekkarr@protonmail.com
+repo_depends:
+- r-commonmark
+- r-hunspell
+- r-knitr
+- r-xml2
+update_on:
+- source: rpkgs
+  pkgname: spelling
+  repo: cran
+  md5: true
+- alias: r

BioArchLinux/r-tidyheatmap/PKGBUILD

@@ -0,0 +1,74 @@
+# Maintainer: Pekka Ristola <pekkarr [at] protonmail [dot] com>
+
+_pkgname=tidyHeatmap
+_pkgver=1.8.1
+pkgname=r-${_pkgname,,}
+pkgver=${_pkgver//-/.}
+pkgrel=1
+pkgdesc="A Tidy Implementation of Heatmap"
+arch=(any)
+url="https://cran.r-project.org/package=${_pkgname}"
+license=(GPL3)
+depends=(
+  r-circlize
+  r-complexheatmap
+  r-dendextend
+  r-dplyr
+  r-lifecycle
+  r-magrittr
+  r-patchwork
+  r-purrr
+  r-rcolorbrewer
+  r-rlang
+  r-tibble
+  r-tidyr
+  r-viridis
+)
+checkdepends=(
+  r-spelling
+  r-testthat
+  r-vdiffr
+)
+optdepends=(
+  r-biocmanager
+  r-covr
+  r-forcats
+  r-ggplot2
+  r-knitr
+  r-qpdf
+  r-rmarkdown
+  r-roxygen2
+  r-spelling
+  r-testthat
+  r-vdiffr
+)
+source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz")
+md5sums=('043abb0854964eceb2fccc711ae64a35')
+sha256sums=('9544d397b4a2c2666d703bbb6c7d49847ed20f447d1be1edc7c0e83a2ebaf7a5')
+
+prepare() {
+  # skip failing snapshot tests
+  sed -e '/"grouped double and annotated plot"/a\\tskip("fails")' \
+      -e '/"grouped and annotated plot both vertical and horizontal"/a\\tskip("fails")' \
+      -e '/"pass arguments with ..."/a\\tskip("fails")' \
+      -e '/"multi-type"/a\\tskip("fails")' \
+      -e '/"legend"/a\\tskip("fails")' \
+      -e '/"size annotation"/a\\tskip("fails")' \
+      -e '/"wrap heatmap for patchwork"/a\\tskip("fails")' \
+      -i "$_pkgname/tests/testthat/tests.R"
+}
+
+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-tidyheatmap/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-tidyheatmap/lilac.yaml

@@ -0,0 +1,28 @@
+build_prefix: extra-x86_64
+maintainers:
+- github: pekkarr
+  email: pekkarr@protonmail.com
+repo_depends:
+- r-circlize
+- r-complexheatmap
+- r-dendextend
+- r-dplyr
+- r-lifecycle
+- r-magrittr
+- r-patchwork
+- r-purrr
+- r-rcolorbrewer
+- r-rlang
+- r-tibble
+- r-tidyr
+- r-viridis
+repo_makedepends:
+- r-spelling
+- r-testthat
+- r-vdiffr
+update_on:
+- source: rpkgs
+  pkgname: tidyHeatmap
+  repo: cran
+  md5: true
+- alias: r