From d6993e824cf9f0440496abd29ace8e2d409143f1 Mon Sep 17 00:00:00 2001
From: Pekka Ristola <pekkarr@protonmail.com>
Date: Tue, 9 Apr 2024 14:53:46 +0300
Subject: [PATCH] r-monocle: use metadata checks

---
 BioArchLinux/r-monocle/PKGBUILD   | 23 +++++++++++------------
 BioArchLinux/r-monocle/lilac.py   | 11 ++++++-----
 BioArchLinux/r-monocle/lilac.yaml |  8 ++++----
 3 files changed, 21 insertions(+), 21 deletions(-)

diff --git a/BioArchLinux/r-monocle/PKGBUILD b/BioArchLinux/r-monocle/PKGBUILD
index b08e4e3699..39c17298c9 100644
--- a/BioArchLinux/r-monocle/PKGBUILD
+++ b/BioArchLinux/r-monocle/PKGBUILD
@@ -3,14 +3,13 @@
 _pkgname=monocle
 _pkgver=2.30.1
 pkgname=r-${_pkgname,,}
-pkgver=2.30.1
+pkgver=${_pkgver//-/.}
 pkgrel=1
-pkgdesc='Clustering, differential expression, and trajectory analysis for single- cell RNA-Seq'
-arch=('x86_64')
-url="https://bioconductor.org/packages/${_pkgname}"
-license=('Artistic2.0')
+pkgdesc="Clustering, differential expression, and trajectory analysis for single- cell RNA-Seq"
+arch=(x86_64)
+url="https://bioconductor.org/packages/$_pkgname"
+license=('Artistic-2.0')
 depends=(
-  r
   r-biobase
   r-biocgenerics
   r-biocviews
@@ -28,7 +27,6 @@ depends=(
   r-pheatmap
   r-plyr
   r-proxy
-  r-qlcmatrix
   r-rann
   r-rcpp
   r-reshape2
@@ -48,14 +46,15 @@ optdepends=(
   r-testthat
 )
 source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz")
-sha256sums=('3503b014eb460f7dd9dd56b7e24b4696d672c4f1ea5eca87cd9595de51d16241')
+md5sums=('d958f3bb9af54d59a472f6ee6ddae596')
+b2sums=('06b8938300de4c4d1e482ad2e9fa26a6773ae22c7cdb256799f29a7038dca5a4f50a2365765c1e69a4127d625a66cd3b60b6359a7ccc9631a69e936ea1ee4094')
 
 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-monocle/lilac.py b/BioArchLinux/r-monocle/lilac.py
index bd219c037c..b5cdb057c5 100644
--- a/BioArchLinux/r-monocle/lilac.py
+++ b/BioArchLinux/r-monocle/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-monocle/lilac.yaml b/BioArchLinux/r-monocle/lilac.yaml
index ba7528508f..09cec54673 100644
--- a/BioArchLinux/r-monocle/lilac.yaml
+++ b/BioArchLinux/r-monocle/lilac.yaml
@@ -20,7 +20,6 @@ repo_depends:
 - r-pheatmap
 - r-plyr
 - r-proxy
-- r-qlcmatrix
 - r-rann
 - r-rcpp
 - r-reshape2
@@ -31,7 +30,8 @@ repo_depends:
 - r-vgam
 - r-viridis
 update_on:
-- regex: monocle_([\d._-]+).tar.gz
-  source: regex
-  url: https://bioconductor.org/packages/monocle
+- source: rpkgs
+  pkgname: monocle
+  repo: bioc
+  md5: true
 - alias: r