r-signifinder: init

BioArchLinux/r-canvasxpress.data/PKGBUILD

@@ -0,0 +1,33 @@
+# Maintainer: Pekka Ristola <pekkarr [at] protonmail [dot] com>
+
+_pkgname=canvasXpress.data
+_pkgver=1.34.2
+pkgname=r-${_pkgname,,}
+pkgver=${_pkgver//-/.}
+pkgrel=1
+pkgdesc="Datasets for the 'canvasXpress' Package"
+arch=(any)
+url="https://cran.r-project.org/package=${_pkgname}"
+license=(GPL3)
+depends=(
+  r
+)
+optdepends=(
+  r-dplyr
+  r-tibble
+  r-tidyr
+  r-usethis
+)
+source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz")
+md5sums=('0df166053851e54ba49dca573d21080a')
+sha256sums=('7af8d537f7f2f39b80001169953ebbbfd39c1db3b5aa26c728a997ebc3a2cd81')
+
+build() {
+  mkdir -p build
+  R CMD INSTALL "$_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-canvasxpress.data/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-canvasxpress.data/lilac.yaml

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

BioArchLinux/r-canvasxpress/PKGBUILD

@@ -0,0 +1,61 @@
+# Maintainer: Pekka Ristola <pekkarr [at] protonmail [dot] com>
+
+_pkgname=canvasXpress
+_pkgver=1.46.9-1
+pkgname=r-${_pkgname,,}
+pkgver=${_pkgver//-/.}
+pkgrel=1
+pkgdesc="Visualization Package for CanvasXpress in R"
+arch=(any)
+url="https://cran.r-project.org/package=${_pkgname}"
+license=(GPL3)
+depends=(
+  r-htmltools
+  r-htmlwidgets
+  r-httr
+  r-jsonlite
+)
+checkdepends=(
+  r-canvasxpress.data
+  r-dplyr
+  r-ggplot2
+  r-readr
+  r-shiny
+  r-testthat
+)
+optdepends=(
+  r-canvasxpress.data
+  r-dplyr
+  r-dt
+  r-ggplot2
+  r-glue
+  r-knitr
+  r-limma
+  r-png
+  r-readr
+  r-rlang
+  r-rmarkdown
+  r-shiny
+  r-stringr
+  r-testthat
+  r-tibble
+  r-tidyr
+)
+source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz")
+md5sums=('f25e77795fcb5dc87488793b343c60e0')
+sha256sums=('a6e382b05f6d4f7c29c3a1bfc1a49b30c69f404f7c2ff5652122b5dfef63667d')
+
+build() {
+  mkdir -p build
+  R CMD INSTALL "$_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-canvasxpress/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-canvasxpress/lilac.yaml

@@ -0,0 +1,22 @@
+build_prefix: extra-x86_64
+maintainers:
+- github: pekkarr
+  email: pekkarr@protonmail.com
+repo_depends:
+- r-htmltools
+- r-htmlwidgets
+- r-httr
+- r-jsonlite
+repo_makedepends:
+- r-canvasxpress.data
+- r-dplyr
+- r-ggplot2
+- r-readr
+- r-shiny
+- r-testthat
+update_on:
+- source: rpkgs
+  pkgname: canvasXpress
+  repo: cran
+  md5: true
+- alias: r

BioArchLinux/r-dgeobj.utils/PKGBUILD

@@ -0,0 +1,67 @@
+# Maintainer: Pekka Ristola <pekkarr [at] protonmail [dot] com>
+
+_pkgname=DGEobj.utils
+_pkgver=1.0.6
+pkgname=r-${_pkgname,,}
+pkgver=${_pkgver//-/.}
+pkgrel=1
+pkgdesc="Differential Gene Expression (DGE) Analysis Utility Toolkit"
+arch=(any)
+url="https://cran.r-project.org/package=${_pkgname}"
+license=(GPL3)
+depends=(
+  r-assertthat
+  r-dgeobj
+  r-dplyr
+  r-stringr
+)
+checkdepends=(
+  r-biomart
+  r-canvasxpress
+  r-edger
+  r-ggplot2
+  r-ihw
+  r-limma
+  r-qvalue
+  r-rnaseqpower
+  r-statmod
+  r-sva
+  r-testthat
+  r-zfpkm
+)
+optdepends=(
+  r-biomart
+  r-canvasxpress
+  r-conflicted
+  r-edger
+  r-ggplot2
+  r-glue
+  r-ihw
+  r-knitr
+  r-limma
+  r-qvalue
+  r-rmarkdown
+  r-rnaseqpower
+  r-statmod
+  r-sva
+  r-testthat
+  r-zfpkm
+)
+source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz")
+md5sums=('8acaeb2945ce80bd2f83f88ef365c88f')
+sha256sums=('734c961fcb346643707e693825b4d6d5f1ee4fea4c9bb952d5d1ab2dccf7eb06')
+
+build() {
+  mkdir -p build
+  R CMD INSTALL "$_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-dgeobj.utils/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-dgeobj.utils/lilac.yaml

@@ -0,0 +1,28 @@
+build_prefix: extra-x86_64
+maintainers:
+- github: pekkarr
+  email: pekkarr@protonmail.com
+repo_depends:
+- r-assertthat
+- r-dgeobj
+- r-dplyr
+- r-stringr
+repo_makedepends:
+- r-biomart
+- r-canvasxpress
+- r-edger
+- r-ggplot2
+- r-ihw
+- r-limma
+- r-qvalue
+- r-rnaseqpower
+- r-statmod
+- r-sva
+- r-testthat
+- r-zfpkm
+update_on:
+- source: rpkgs
+  pkgname: DGEobj.utils
+  repo: cran
+  md5: true
+- alias: r

BioArchLinux/r-dgeobj/PKGBUILD

@@ -0,0 +1,51 @@
+# Maintainer: Pekka Ristola <pekkarr [at] protonmail [dot] com>
+
+_pkgname=DGEobj
+_pkgver=1.1.2
+pkgname=r-${_pkgname,,}
+pkgver=${_pkgver//-/.}
+pkgrel=1
+pkgdesc="Differential Gene Expression (DGE) Analysis Results Data Object"
+arch=(any)
+url="https://cran.r-project.org/package=${_pkgname}"
+license=(GPL3)
+depends=(
+  r-assertthat
+  r-magrittr
+  r-stringr
+)
+checkdepends=(
+  r-biomart
+  r-edger
+  r-genomicranges
+  r-testthat
+)
+optdepends=(
+  r-biomart
+  r-conflicted
+  r-dplyr
+  r-edger
+  r-genomicranges
+  r-glue
+  r-knitr
+  r-rmarkdown
+  r-testthat
+)
+source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz")
+md5sums=('8d84369964ade6ee4707681568feb390')
+sha256sums=('c3deabb98e90085373a4a438f40e7b481e7cc37e9ebd9ade356ee43599a1cd02')
+
+build() {
+  mkdir -p build
+  R CMD INSTALL "$_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-dgeobj/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-dgeobj/lilac.yaml

@@ -0,0 +1,19 @@
+build_prefix: extra-x86_64
+maintainers:
+- github: pekkarr
+  email: pekkarr@protonmail.com
+repo_depends:
+- r-assertthat
+- r-magrittr
+- r-stringr
+repo_makedepends:
+- r-biomart
+- r-edger
+- r-genomicranges
+- r-testthat
+update_on:
+- source: rpkgs
+  pkgname: DGEobj
+  repo: cran
+  md5: true
+- alias: r

BioArchLinux/r-openair/PKGBUILD

@@ -0,0 +1,44 @@
+# Maintainer: Pekka Ristola <pekkarr [at] protonmail [dot] com>
+
+_pkgname=openair
+_pkgver=2.18-0
+pkgname=r-${_pkgname,,}
+pkgver=${_pkgver//-/.}
+pkgrel=1
+pkgdesc="Tools for the Analysis of Air Pollution Data"
+arch=(x86_64)
+url="https://cran.r-project.org/package=${_pkgname}"
+license=(GPL)
+depends=(
+  r-cli
+  r-dplyr
+  r-hexbin
+  r-latticeextra
+  r-lubridate
+  r-mapproj
+  r-purrr
+  r-rcpp
+  r-readr
+  r-rlang
+  r-tibble
+  r-tidyr
+)
+optdepends=(
+  r-mapdata
+  r-maps
+  r-quantreg
+  r-spelling
+)
+source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz")
+md5sums=('301c3df8314138c6193499cff523c396')
+sha256sums=('e06febbe421a6493dff0a3c05b894bb1fffdfb1c4fed576288974f5dae597cc3')
+
+build() {
+  mkdir -p build
+  R CMD INSTALL "$_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-openair/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-openair/lilac.yaml

@@ -0,0 +1,23 @@
+build_prefix: extra-x86_64
+maintainers:
+- github: pekkarr
+  email: pekkarr@protonmail.com
+repo_depends:
+- r-cli
+- r-dplyr
+- r-hexbin
+- r-latticeextra
+- r-lubridate
+- r-mapproj
+- r-purrr
+- r-rcpp
+- r-readr
+- r-rlang
+- r-tibble
+- r-tidyr
+update_on:
+- source: rpkgs
+  pkgname: openair
+  repo: cran
+  md5: true
+- alias: r

BioArchLinux/r-signifinder/PKGBUILD

@@ -0,0 +1,68 @@
+# Maintainer: Pekka Ristola <pekkarr [at] protonmail [dot] com>
+
+_pkgname=signifinder
+_pkgver=1.4.0
+pkgname=r-${_pkgname,,}
+pkgver=${_pkgver//-/.}
+pkgrel=1
+pkgdesc="Implementations of transcriptional cancer signatures"
+arch=(any)
+url="https://bioconductor.org/packages/${_pkgname}"
+license=(AGPL3)
+depends=(
+  r-annotationdbi
+  r-biocgenerics
+  r-complexheatmap
+  r-consensusov
+  r-cowplot
+  r-dgeobj.utils
+  r-dplyr
+  r-ensembldb
+  r-ggplot2
+  r-ggridges
+  r-gsva
+  r-iranges
+  r-magrittr
+  r-matrixstats
+  r-maxstat
+  r-openair
+  r-org.hs.eg.db
+  r-patchwork
+  r-rcolorbrewer
+  r-spatialexperiment
+  r-summarizedexperiment
+  r-survminer
+  r-txdb.hsapiens.ucsc.hg19.knowngene
+  r-txdb.hsapiens.ucsc.hg38.knowngene
+  r-viridis
+)
+checkdepends=(
+  r-edger
+  r-testthat
+)
+optdepends=(
+  r-biocstyle
+  r-edger
+  r-kableextra
+  r-knitr
+  r-limma
+  r-testthat
+)
+source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz")
+md5sums=('f24a46dbbbc9b688450e9f2a0e2e221e')
+sha256sums=('330b2ae04fd1b4d02053dfecc4698efe3543c7ea42e430e0df2598915c2464fa')
+
+build() {
+  mkdir -p build
+  R CMD INSTALL "$_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-signifinder/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-signifinder/lilac.yaml

@@ -0,0 +1,39 @@
+build_prefix: extra-x86_64
+maintainers:
+- github: pekkarr
+  email: pekkarr@protonmail.com
+repo_depends:
+- r-annotationdbi
+- r-biocgenerics
+- r-complexheatmap
+- r-consensusov
+- r-cowplot
+- r-dgeobj.utils
+- r-dplyr
+- r-ensembldb
+- r-ggplot2
+- r-ggridges
+- r-gsva
+- r-iranges
+- r-magrittr
+- r-matrixstats
+- r-maxstat
+- r-openair
+- r-org.hs.eg.db
+- r-patchwork
+- r-rcolorbrewer
+- r-spatialexperiment
+- r-summarizedexperiment
+- r-survminer
+- r-txdb.hsapiens.ucsc.hg19.knowngene
+- r-txdb.hsapiens.ucsc.hg38.knowngene
+- r-viridis
+repo_makedepends:
+- r-edger
+- r-testthat
+update_on:
+- source: rpkgs
+  pkgname: signifinder
+  repo: bioc
+  md5: true
+- alias: r