From c38651057a29b740c3ba84ea33edd44266a9474a Mon Sep 17 00:00:00 2001
From: Pekka Ristola <pekkarr@protonmail.com>
Date: Sun, 3 Mar 2024 09:47:01 +0200
Subject: [PATCH] r-bcseq: use metadata checks

---
 BioArchLinux/r-bcseq/PKGBUILD   | 22 +++++++++++-----------
 BioArchLinux/r-bcseq/lilac.py   | 11 ++++++-----
 BioArchLinux/r-bcseq/lilac.yaml |  7 ++++---
 3 files changed, 21 insertions(+), 19 deletions(-)

diff --git a/BioArchLinux/r-bcseq/PKGBUILD b/BioArchLinux/r-bcseq/PKGBUILD
index 950b1fdb85..d0a56c8d42 100644
--- a/BioArchLinux/r-bcseq/PKGBUILD
+++ b/BioArchLinux/r-bcseq/PKGBUILD
@@ -3,14 +3,13 @@
 _pkgname=bcSeq
 _pkgver=1.24.0
 pkgname=r-${_pkgname,,}
-pkgver=1.24.0
+pkgver=${_pkgver//-/.}
 pkgrel=1
-pkgdesc='Fast Sequence Mapping in High-Throughput shRNA and CRISPR Screens'
-arch=('x86_64')
-url="https://bioconductor.org/packages/${_pkgname}"
-license=('GPL')
+pkgdesc="Fast Sequence Mapping in High-Throughput shRNA and CRISPR Screens"
+arch=(x86_64)
+url="https://bioconductor.org/packages/$_pkgname"
+license=('GPL-2.0-or-later')
 depends=(
-  r
   r-biostrings
   r-rcpp
 )
@@ -18,14 +17,15 @@ optdepends=(
   r-knitr
 )
 source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz")
-sha256sums=('338514ad92f5db3bcfecd825ef75a3fed1b503f2821ad3cc9c94236563821914')
+md5sums=('e582b114bc4743a328b6ada2953a74da')
+b2sums=('fbc7c77d884307b41b040199be7ab592b1fef0ce82acac0069367db039e62757abad8c96f591fbd40f0e2f2c0140e188f340de002d5ed3358b8c84f0a2757002')
 
 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:
diff --git a/BioArchLinux/r-bcseq/lilac.py b/BioArchLinux/r-bcseq/lilac.py
index bd219c037c..b5cdb057c5 100644
--- a/BioArchLinux/r-bcseq/lilac.py
+++ b/BioArchLinux/r-bcseq/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-bcseq/lilac.yaml b/BioArchLinux/r-bcseq/lilac.yaml
index 5e14047577..048699ff0d 100644
--- a/BioArchLinux/r-bcseq/lilac.yaml
+++ b/BioArchLinux/r-bcseq/lilac.yaml
@@ -6,7 +6,8 @@ repo_depends:
 - r-biostrings
 - r-rcpp
 update_on:
-- regex: bcSeq_([\d._-]+).tar.gz
-  source: regex
-  url: https://bioconductor.org/packages/bcSeq
+- source: rpkgs
+  pkgname: bcSeq
+  repo: bioc
+  md5: true
 - alias: r