r-screpertoire: fix depends, use metadata checks

BioArchLinux/r-inext/PKGBUILD

@@ -0,0 +1,44 @@
+# Maintainer: Pekka Ristola <pekkarr [at] protonmail [dot] com>
+
+_pkgname=iNEXT
+_pkgver=3.0.1
+pkgname=r-${_pkgname,,}
+pkgver=${_pkgver//-/.}
+pkgrel=1
+pkgdesc="Interpolation and Extrapolation for Species Diversity"
+arch=(x86_64)
+url="https://cran.r-project.org/package=$_pkgname"
+license=('GPL-3.0-or-later')
+depends=(
+  r-ggplot2
+  r-rcpp
+  r-reshape2
+)
+checkdepends=(
+  r-testthat
+)
+optdepends=(
+  r-ggthemes
+  r-gridextra
+  r-knitr
+  r-rmarkdown
+  r-testthat
+)
+source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz")
+md5sums=('1cc313937b3f3f3eb86c094dea0c54b9')
+b2sums=('5b56b746da5935edae098a5972f0161e231411d5939d21d324d9870435eb40ffe4a8ef32e862ed639bea7c76432f647a175180e3c46536ed67a967222ae1c6ad')
+
+build() {
+  mkdir build
+  R CMD INSTALL -l build "$_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-inext/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-inext/lilac.yaml

@@ -0,0 +1,16 @@
+build_prefix: extra-x86_64
+maintainers:
+- github: pekkarr
+  email: pekkarr@protonmail.com
+repo_depends:
+- r-ggplot2
+- r-rcpp
+- r-reshape2
+repo_makedepends:
+- r-testthat
+update_on:
+- source: rpkgs
+  pkgname: iNEXT
+  repo: cran
+  md5: true
+- alias: r

BioArchLinux/r-screpertoire/PKGBUILD

@@ -1,35 +1,43 @@
 # Maintainer: Guoyi Zhang <guoyizhang at malacology dot net>
 
 _pkgname=scRepertoire
-_pkgver=1.12.0
+_pkgver=2.0.0
 pkgname=r-${_pkgname,,}
-pkgver=1.12.0
-pkgrel=2
-pkgdesc='A toolkit for single-cell immune receptor profiling'
-arch=('any')
-url="https://bioconductor.org/packages/${_pkgname}"
-license=('Apache')
+pkgver=${_pkgver//-/.}
+pkgrel=0
+pkgdesc="A toolkit for single-cell immune receptor profiling"
+arch=(x86_64)
+url="https://bioconductor.org/packages/$_pkgname"
+license=('MIT')
 depends=(
-  r
-  r-doparallel
+  r-cubature
   r-dplyr
+  r-evmix
   r-ggalluvial
+  r-ggdendro
   r-ggplot2
   r-ggraph
+  r-hash
   r-igraph
+  r-inext
   r-plyr
-  r-powertcr
+  r-quantreg
+  r-rcpp
   r-reshape2
+  r-rjson
   r-rlang
+  r-s4vectors
   r-seuratobject
   r-singlecellexperiment
   r-stringdist
   r-stringr
   r-summarizedexperiment
   r-tidygraph
-  r-vegan
+  r-truncdist
+  r-vgam
 )
 optdepends=(
+  r-biocmanager
   r-biocstyle
   r-circlize
   r-knitr
@@ -37,16 +45,23 @@ optdepends=(
   r-scales
   r-scater
   r-seurat
+  r-spelling
+  r-testthat
+  r-vdiffr
 )
 source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz")
-sha256sums=('818aec659cc0f055dfe1cb454667bc6223fc82e6851be4238b02d15f7643faf1')
+md5sums=('cada6940cf1146f26526d4dcdd6f68f4')
+b2sums=('42c8ea83ae496d8d53b639c4c890b590953125c166c043effbf3ac214635ae33328805a44339ec11d2bb1c6199eb3375170b218d895fc608e9f28f66328fbb41')
 
 build() {
-  R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}"
+  mkdir build
+  R CMD INSTALL -l build "$_pkgname"
 }
 
 package() {
-  install -dm0755 "${pkgdir}/usr/lib/R/library"
-  cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library"
+  install -d "$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"
 }
-# vim:set ts=2 sw=2 et:

BioArchLinux/r-screpertoire/lilac.py

@@ -1,12 +1,13 @@
 #!/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():
-    for line in edit_file('PKGBUILD'):
-        if line.startswith('_pkgver='):
-            line = f'_pkgver={_G.newver}'
-        print(line)
-    update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.'))
+    r_pre_build(_G)
 
 def post_build():
     git_pkgbuild_commit()

BioArchLinux/r-screpertoire/lilac.yaml

@@ -3,25 +3,34 @@ maintainers:
 - github: starsareintherose
   email: kuoi@bioarchlinux.org
 repo_depends:
-- r-doparallel
+- r-cubature
 - r-dplyr
+- r-evmix
 - r-ggalluvial
+- r-ggdendro
 - r-ggplot2
 - r-ggraph
+- r-hash
 - r-igraph
+- r-inext
 - r-plyr
-- r-powertcr
+- r-quantreg
+- r-rcpp
 - r-reshape2
+- r-rjson
 - r-rlang
+- r-s4vectors
 - r-seuratobject
 - r-singlecellexperiment
 - r-stringdist
 - r-stringr
 - r-summarizedexperiment
 - r-tidygraph
-- r-vegan
+- r-truncdist
+- r-vgam
 update_on:
-- regex: scRepertoire_([\d._-]+).tar.gz
-  source: regex
-  url: https://bioconductor.org/packages/scRepertoire
+- source: rpkgs
+  pkgname: scRepertoire
+  repo: bioc
+  md5: true
 - alias: r