From 1fa950a74cbd3a0853205671b4c7138ba4343791 Mon Sep 17 00:00:00 2001
From: Pekka Ristola <pekkarr@protonmail.com>
Date: Sun, 15 Oct 2023 19:31:23 +0300
Subject: [PATCH] r-residualmatrix: use metadata checks

---
 BioArchLinux/r-residualmatrix/PKGBUILD   | 29 ++++++++++++++++--------
 BioArchLinux/r-residualmatrix/lilac.py   | 11 +++++----
 BioArchLinux/r-residualmatrix/lilac.yaml | 13 +++++++----
 3 files changed, 33 insertions(+), 20 deletions(-)

diff --git a/BioArchLinux/r-residualmatrix/PKGBUILD b/BioArchLinux/r-residualmatrix/PKGBUILD
index aa2fd6ca38..5158388ce1 100644
--- a/BioArchLinux/r-residualmatrix/PKGBUILD
+++ b/BioArchLinux/r-residualmatrix/PKGBUILD
@@ -1,19 +1,22 @@
-# Maintainer: Guoyi Zhang <guoyizhang at malacology dot net>
+# Maintainer: Pekka Ristola <pekkarr [at] protonmail [dot] com>
+# Contributor: Guoyi Zhang <guoyizhang at malacology dot net>
 
 _pkgname=ResidualMatrix
 _pkgver=1.10.0
 pkgname=r-${_pkgname,,}
-pkgver=1.10.0
+pkgver=${_pkgver//-/.}
 pkgrel=1
-pkgdesc='Creating a DelayedMatrix of Regression Residuals'
-arch=('any')
+pkgdesc="Creating a DelayedMatrix of Regression Residuals"
+arch=(any)
 url="https://bioconductor.org/packages/${_pkgname}"
-license=('GPL')
+license=(GPL3)
 depends=(
-  r
   r-delayedarray
   r-s4vectors
 )
+checkdepends=(
+  r-testthat
+)
 optdepends=(
   r-biocsingular
   r-biocstyle
@@ -22,14 +25,20 @@ optdepends=(
   r-testthat
 )
 source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz")
+md5sums=('7d4291731f44ec7111ac14306ce53f18')
 sha256sums=('1be3c4247e23d2b157f64cc19052a15ea78100aef652ec55195d096841045ef9')
 
 build() {
-  R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}"
+  mkdir -p build
+  R CMD INSTALL "$_pkgname" -l build
+}
+
+check() {
+  cd "$_pkgname/tests"
+  R_LIBS="$srcdir/build" NOT_CRAN=true Rscript --vanilla testthat.R
 }
 
 package() {
-  install -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:
diff --git a/BioArchLinux/r-residualmatrix/lilac.py b/BioArchLinux/r-residualmatrix/lilac.py
index bd219c037c..b5cdb057c5 100644
--- a/BioArchLinux/r-residualmatrix/lilac.py
+++ b/BioArchLinux/r-residualmatrix/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()
diff --git a/BioArchLinux/r-residualmatrix/lilac.yaml b/BioArchLinux/r-residualmatrix/lilac.yaml
index c556f35500..d1759c068d 100644
--- a/BioArchLinux/r-residualmatrix/lilac.yaml
+++ b/BioArchLinux/r-residualmatrix/lilac.yaml
@@ -1,12 +1,15 @@
 build_prefix: extra-x86_64
 maintainers:
-- github: starsareintherose
-  email: kuoi@bioarchlinux.org
+- github: pekkarr
+  email: pekkarr@protonmail.com
 repo_depends:
 - r-delayedarray
 - r-s4vectors
+repo_makedepends:
+- r-testthat
 update_on:
-- regex: ResidualMatrix_([\d._-]+).tar.gz
-  source: regex
-  url: https://bioconductor.org/packages/ResidualMatrix
+- source: rpkgs
+  pkgname: ResidualMatrix
+  repo: bioc
+  md5: true
 - alias: r