From 83b06123517b7d4514ee155652fd826812394bf5 Mon Sep 17 00:00:00 2001
From: Pekka Ristola <pekkarr@protonmail.com>
Date: Tue, 20 Feb 2024 07:54:38 +0200
Subject: [PATCH] r-edger: use metadata checks

---
 BioArchLinux/r-edger/PKGBUILD   | 28 +++++++++++++---------------
 BioArchLinux/r-edger/lilac.py   | 11 ++++++-----
 BioArchLinux/r-edger/lilac.yaml | 15 ++++++++++++---
 3 files changed, 31 insertions(+), 23 deletions(-)

diff --git a/BioArchLinux/r-edger/PKGBUILD b/BioArchLinux/r-edger/PKGBUILD
index 5b6b077eab..ac02909051 100644
--- a/BioArchLinux/r-edger/PKGBUILD
+++ b/BioArchLinux/r-edger/PKGBUILD
@@ -1,21 +1,20 @@
-# system requirements: C++11
 # Maintainer: Guoyi Zhang <guoyizhang at malacology dot net>
 
 _pkgname=edgeR
 _pkgver=4.0.16
 pkgname=r-${_pkgname,,}
-pkgver=4.0.16
+pkgver=${_pkgver//-/.}
 pkgrel=1
-pkgdesc='Empirical Analysis of Digital Gene Expression Data in R'
-arch=('x86_64')
-url="https://bioconductor.org/packages/${_pkgname}"
-license=('GPL')
+pkgdesc="Empirical Analysis of Digital Gene Expression Data in R"
+arch=(x86_64)
+url="https://bioconductor.org/packages/$_pkgname"
+license=('GPL-2.0-or-later')
 depends=(
-  r
+  blas
+  lapack
   r-limma
   r-locfit
   r-rcpp
-  gcc
 )
 optdepends=(
   r-annotationdbi
@@ -23,23 +22,22 @@ optdepends=(
   r-biocstyle
   r-jsonlite
   r-knitr
-  r-matrix
   r-org.hs.eg.db
   r-readr
   r-rhdf5
   r-seuratobject
-  r-splines
   r-summarizedexperiment
 )
 source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz")
-sha256sums=('d145e4f8423632dbea1cf1c2e53ae72ea05a937924090f3c4aff6bcd035cd449')
+md5sums=('8fb1c6c67e29d299c991d16d0f6c5f5b')
+b2sums=('535ad59062196733724e9bbeca903a99f4de3201b807baa851b4a68c58240ec340439ea305e43e22951cd40d907453e7c7c4e08a27d69bd02d3444e9a0aae637')
 
 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-edger/lilac.py b/BioArchLinux/r-edger/lilac.py
index bd219c037c..b5cdb057c5 100644
--- a/BioArchLinux/r-edger/lilac.py
+++ b/BioArchLinux/r-edger/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-edger/lilac.yaml b/BioArchLinux/r-edger/lilac.yaml
index a97646ec7f..27a2d9e683 100644
--- a/BioArchLinux/r-edger/lilac.yaml
+++ b/BioArchLinux/r-edger/lilac.yaml
@@ -7,7 +7,16 @@ repo_depends:
 - r-locfit
 - r-rcpp
 update_on:
-- regex: edgeR_([\d._-]+).tar.gz
-  source: regex
-  url: https://bioconductor.org/packages/edgeR
+- source: rpkgs
+  pkgname: edgeR
+  repo: bioc
+  md5: true
 - alias: r
+- source: alpmfiles
+  pkgname: blas
+  filename: usr/lib/libblas\.so\.([^.]+)
+  repo: extra
+- source: alpmfiles
+  pkgname: lapack
+  filename: usr/lib/liblapack\.so\.([^.]+)
+  repo: extra