r-scp: fix depends, use metadata checks

BioArchLinux/r-nipals/PKGBUILD

@@ -0,0 +1,40 @@
+# Maintainer: Pekka Ristola <pekkarr [at] protonmail [dot] com>
+
+_pkgname=nipals
+_pkgver=0.8
+pkgname=r-${_pkgname,,}
+pkgver=${_pkgver//-/.}
+pkgrel=1
+pkgdesc="Principal Components Analysis using NIPALS or Weighted EMPCA, with Gram-Schmidt Orthogonalization"
+arch=(any)
+url="https://cran.r-project.org/package=$_pkgname"
+license=('GPL-3.0-only')
+depends=(
+  r
+)
+checkdepends=(
+  r-testthat
+)
+optdepends=(
+  r-knitr
+  r-rmarkdown
+  r-testthat
+)
+source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz")
+md5sums=('5fd148499e1c906423ee3eec530ff079')
+b2sums=('bf9f3b7acbeecfe797264133fefdf271ebae6de8be65fe490efd0bd3ebe75e093a540dbf1587a5b2d2687b31e4148ca5c71c1bb3e94cd2c5463b23d8a841cc3c')
+
+build() {
+  mkdir build
+  R CMD INSTALL -l build "$_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-nipals/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-nipals/lilac.yaml

@@ -0,0 +1,12 @@
+build_prefix: extra-x86_64
+maintainers:
+- github: pekkarr
+  email: pekkarr@protonmail.com
+repo_makedepends:
+- r-testthat
+update_on:
+- source: rpkgs
+  pkgname: nipals
+  repo: cran
+  md5: true
+- alias: r

BioArchLinux/r-scp/PKGBUILD

@@ -1,31 +1,35 @@
 # Maintainer: Guoyi Zhang <guoyizhang at malacology dot net>
 
 _pkgname=scp
-_pkgver=1.12.0
+_pkgver=1.14.0
 pkgname=r-${_pkgname,,}
-pkgver=1.12.0
-pkgrel=2
-pkgdesc='Mass Spectrometry-Based Single-Cell Proteomics Data Analysis'
-arch=('any')
-url="https://bioconductor.org/packages/${_pkgname}"
-license=('Artistic2.0')
+pkgver=${_pkgver//-/.}
+pkgrel=0
+pkgdesc="Mass Spectrometry-Based Single-Cell Proteomics Data Analysis"
+arch=(any)
+url="https://bioconductor.org/packages/$_pkgname"
+license=('Artistic-2.0')
 depends=(
-  r
   r-dplyr
-  r-magrittr
+  r-ggplot2
+  r-ggrepel
+  r-ihw
   r-matrixstats
+  r-metapod
   r-mscoreutils
   r-multiassayexperiment
+  r-nipals
   r-qfeatures
+  r-rcolorbrewer
   r-s4vectors
   r-singlecellexperiment
   r-summarizedexperiment
 )
 optdepends=(
   r-biocstyle
-  r-ggplot2
   r-impute
   r-knitr
+  r-msdatahub
   r-patchwork
   r-preprocesscore
   r-rmarkdown
@@ -37,14 +41,15 @@ optdepends=(
   r-vsn
 )
 source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz")
-sha256sums=('f0b301a02fc703dec1b439e7eb3f44235e60ab8195f19d4775c27c67381c9575')
+md5sums=('6d0918024a41e466059a694476266f3a')
+b2sums=('de9333382576510dad4ffb409842d0d46e43a55b24a86aea6409f9d79a4744d95b21e24d34bed06005c4a5af898a17e44fbd79d4747aac18703dd1ace394877b')
 
 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"
 }
-# vim:set ts=2 sw=2 et:

BioArchLinux/r-scp/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-scp/lilac.yaml

@@ -4,16 +4,22 @@ maintainers:
   email: kuoi@bioarchlinux.org
 repo_depends:
 - r-dplyr
-- r-magrittr
+- r-ggplot2
+- r-ggrepel
+- r-ihw
 - r-matrixstats
+- r-metapod
 - r-mscoreutils
 - r-multiassayexperiment
+- r-nipals
 - r-qfeatures
+- r-rcolorbrewer
 - r-s4vectors
 - r-singlecellexperiment
 - r-summarizedexperiment
 update_on:
-- regex: scp_([\d._-]+).tar.gz
-  source: regex
-  url: https://bioconductor.org/packages/scp
+- source: rpkgs
+  pkgname: scp
+  repo: bioc
+  md5: true
 - alias: r