r-gnosis: init

BioArchLinux/r-comparegroups/PKGBUILD

@@ -0,0 +1,47 @@
+# Maintainer: Pekka Ristola <pekkarr [at] protonmail [dot] com>
+
+_pkgname=compareGroups
+_pkgver=4.7.2
+pkgname=r-${_pkgname,,}
+pkgver=${_pkgver//-/.}
+pkgrel=1
+pkgdesc="Descriptive Analysis by Groups"
+arch=(any)
+url="https://cran.r-project.org/package=${_pkgname}"
+license=(GPL)
+depends=(
+  r-chron
+  r-flextable
+  r-hardyweinberg
+  r-kableextra
+  r-knitr
+  r-officer
+  r-rmarkdown
+  r-writexl
+)
+optdepends=(
+  r-dt
+  r-haven
+  r-readxl
+  r-shiny
+  r-shinybs
+  r-shinydashboardplus
+  r-shinyjqui
+  r-shinyjs
+  r-shinythemes
+  r-shinywidgets
+  r-tcltk2
+)
+source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz")
+md5sums=('e9dbc5905e2f1d7bfb7bb5fe372d4e7a')
+sha256sums=('a83f3e4cd8e83c24f8e867cbbca9f1fbeea611cbb77af31bab6506008772779b')
+
+build() {
+  mkdir -p build
+  R CMD INSTALL "$_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-comparegroups/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-comparegroups/lilac.yaml

@@ -0,0 +1,19 @@
+build_prefix: extra-x86_64
+maintainers:
+- github: pekkarr
+  email: pekkarr@protonmail.com
+repo_depends:
+- r-chron
+- r-flextable
+- r-hardyweinberg
+- r-kableextra
+- r-knitr
+- r-officer
+- r-rmarkdown
+- r-writexl
+update_on:
+- source: rpkgs
+  pkgname: compareGroups
+  repo: cran
+  md5: true
+- alias: r

BioArchLinux/r-dashboardthemes/PKGBUILD

@@ -0,0 +1,46 @@
+# Maintainer: Pekka Ristola <pekkarr [at] protonmail [dot] com>
+
+_pkgname=dashboardthemes
+_pkgver=1.1.6
+pkgname=r-${_pkgname,,}
+pkgver=${_pkgver//-/.}
+pkgrel=1
+pkgdesc="Customise the Appearance of 'shinydashboard' Applications using Themes"
+arch=(any)
+url="https://cran.r-project.org/package=${_pkgname}"
+license=(MIT)
+depends=(
+  r-htmltools
+)
+checkdepends=(
+  r-testthat
+)
+optdepends=(
+  r-covr
+  r-glue
+  r-knitr
+  r-lintr
+  r-rmarkdown
+  r-testthat
+)
+source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz")
+md5sums=('0412aef1b3d96fb04a725bfeb02938d2')
+sha256sums=('cc80bcd4b66d2418fe08636a25425083574d406e4bd9dfa8d170663aeb23717a')
+
+build() {
+  mkdir -p build
+  R CMD INSTALL "$_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-dashboardthemes/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-dashboardthemes/lilac.yaml

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

BioArchLinux/r-gnosis/PKGBUILD

@@ -0,0 +1,59 @@
+# Maintainer: Pekka Ristola <pekkarr [at] protonmail [dot] com>
+
+_pkgname=GNOSIS
+_pkgver=1.0.0
+pkgname=r-${_pkgname,,}
+pkgver=${_pkgver//-/.}
+pkgrel=1
+pkgdesc="Genomics explorer using statistical and survival analysis in R"
+arch=(any)
+url="https://bioconductor.org/packages/${_pkgname}"
+license=(MIT)
+depends=(
+  r-car
+  r-cbioportaldata
+  r-comparegroups
+  r-dashboardthemes
+  r-desctools
+  r-dt
+  r-fabricatr
+  r-fontawesome
+  r-maftools
+  r-magrittr
+  r-operator.tools
+  r-partykit
+  r-rcolorbrewer
+  r-reshape2
+  r-rstatix
+  r-shiny
+  r-shinycssloaders
+  r-shinydashboard
+  r-shinydashboardplus
+  r-shinyjs
+  r-shinylogs
+  r-shinymeta
+  r-shinywidgets
+  r-survminer
+  r-tidyverse
+)
+optdepends=(
+  r-biocstyle
+  r-knitr
+  r-rmarkdown
+)
+source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz")
+md5sums=('e3cbf07a76da1ae0aa6e669bad2cb778')
+sha256sums=('ae75596cfc64be63f8c782b447c35bd8d1977c646374c861a4e32d65ff8c6037')
+
+build() {
+  mkdir -p build
+  R CMD INSTALL "$_pkgname" -l build
+}
+
+package() {
+  install -d "$pkgdir/usr/lib/R/library"
+  cp -a --no-preserve=ownership "build/$_pkgname" "$pkgdir/usr/lib/R/library"
+
+  install -d "$pkgdir/usr/share/licenses/$pkgname"
+  ln -s "/usr/lib/R/library/$_pkgname/LICENSE" "$pkgdir/usr/share/licenses/$pkgname"
+}

BioArchLinux/r-gnosis/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-gnosis/lilac.yaml

@@ -0,0 +1,36 @@
+build_prefix: extra-x86_64
+maintainers:
+- github: pekkarr
+  email: pekkarr@protonmail.com
+repo_depends:
+- r-car
+- r-cbioportaldata
+- r-comparegroups
+- r-dashboardthemes
+- r-desctools
+- r-dt
+- r-fabricatr
+- r-fontawesome
+- r-maftools
+- r-magrittr
+- r-operator.tools
+- r-partykit
+- r-rcolorbrewer
+- r-reshape2
+- r-rstatix
+- r-shiny
+- r-shinycssloaders
+- r-shinydashboard
+- r-shinydashboardplus
+- r-shinyjs
+- r-shinylogs
+- r-shinymeta
+- r-shinywidgets
+- r-survminer
+- r-tidyverse
+update_on:
+- source: rpkgs
+  pkgname: GNOSIS
+  repo: bioc
+  md5: true
+- alias: r

BioArchLinux/r-shinylogs/PKGBUILD

@@ -0,0 +1,53 @@
+# Maintainer: Pekka Ristola <pekkarr [at] protonmail [dot] com>
+
+_pkgname=shinylogs
+_pkgver=0.2.1
+pkgname=r-${_pkgname,,}
+pkgver=${_pkgver//-/.}
+pkgrel=1
+pkgdesc="Record Everything that Happens in a 'Shiny' Application"
+arch=(any)
+url="https://cran.r-project.org/package=${_pkgname}"
+license=(GPL3)
+depends=(
+  r-anytime
+  r-bit64
+  r-data.table
+  r-digest
+  r-htmltools
+  r-jsonlite
+  r-nanotime
+  r-shiny
+)
+checkdepends=(
+  r-dbi
+  r-rsqlite
+  r-testthat
+)
+optdepends=(
+  r-covr
+  r-dbi
+  r-googledrive
+  r-knitr
+  r-rmarkdown
+  r-rsqlite
+  r-testthat
+)
+source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz")
+md5sums=('25ffc5c472d557ee69e2d18aa4ae352d')
+sha256sums=('527e362c0f00571d2463187c90486563922e813c988037d989764cc13ff829f0')
+
+build() {
+  mkdir -p build
+  R CMD INSTALL "$_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-shinylogs/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-shinylogs/lilac.yaml

@@ -0,0 +1,23 @@
+build_prefix: extra-x86_64
+maintainers:
+- github: pekkarr
+  email: pekkarr@protonmail.com
+repo_depends:
+- r-anytime
+- r-bit64
+- r-data.table
+- r-digest
+- r-htmltools
+- r-jsonlite
+- r-nanotime
+- r-shiny
+repo_makedepends:
+- r-dbi
+- r-rsqlite
+- r-testthat
+update_on:
+- source: rpkgs
+  pkgname: shinylogs
+  repo: cran
+  md5: true
+- alias: r

BioArchLinux/r-shinymeta/PKGBUILD

@@ -0,0 +1,58 @@
+# Maintainer: Pekka Ristola <pekkarr [at] protonmail [dot] com>
+
+_pkgname=shinymeta
+_pkgver=0.2.0.3
+pkgname=r-${_pkgname,,}
+pkgver=${_pkgver//-/.}
+pkgrel=1
+pkgdesc="Export Domain Logic from Shiny using Meta-Programming"
+arch=(any)
+url="https://cran.r-project.org/package=${_pkgname}"
+license=(GPL3)
+depends=(
+  r-callr
+  r-fastmap
+  r-fs
+  r-htmltools
+  r-rlang
+  r-shiny
+  r-sourcetools
+  r-styler
+)
+checkdepends=(
+  r-knitr
+  r-rmarkdown
+  r-testthat
+)
+optdepends=(
+  r-clipr
+  r-cranlogs
+  r-dplyr
+  r-ggplot2
+  r-knitr
+  r-magrittr
+  r-rmarkdown
+  r-shinyace
+  r-stringr
+  r-testthat
+  r-xfun
+  r-zoo
+)
+source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz")
+md5sums=('5452325a791296ba7fb6725d937f9fb0')
+sha256sums=('095dffe6d8763edf42eabf91f606aad12f3a08271fcd9d7257c2812775793fd2')
+
+build() {
+  mkdir -p build
+  R CMD INSTALL "$_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-shinymeta/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-shinymeta/lilac.yaml

@@ -0,0 +1,23 @@
+build_prefix: extra-x86_64
+maintainers:
+- github: pekkarr
+  email: pekkarr@protonmail.com
+repo_depends:
+- r-callr
+- r-fastmap
+- r-fs
+- r-htmltools
+- r-rlang
+- r-shiny
+- r-sourcetools
+- r-styler
+repo_makedepends:
+- r-knitr
+- r-rmarkdown
+- r-testthat
+update_on:
+- source: rpkgs
+  pkgname: shinymeta
+  repo: cran
+  md5: true
+- alias: r