From 3dbe4bf43c6af9a4c81eedf37e96d3e8612931f5 Mon Sep 17 00:00:00 2001
From: Pekka Ristola <pekkarr@protonmail.com>
Date: Thu, 19 Dec 2024 00:45:07 +0200
Subject: [PATCH] r-rjava: improve PKGBUILD, push to AUR

---
 BioArchLinux/r-rjava/PKGBUILD   | 16 +++++++---------
 BioArchLinux/r-rjava/lilac.py   |  1 +
 BioArchLinux/r-rjava/lilac.yaml |  2 ++
 3 files changed, 10 insertions(+), 9 deletions(-)

diff --git a/BioArchLinux/r-rjava/PKGBUILD b/BioArchLinux/r-rjava/PKGBUILD
index 901256404c..c02070c758 100644
--- a/BioArchLinux/r-rjava/PKGBUILD
+++ b/BioArchLinux/r-rjava/PKGBUILD
@@ -1,5 +1,7 @@
 # Maintainer: Guoyi Zhang <guoyizhang at malacology dot net>
 # Contributor: Viktor Drobot (aka dviktor) linux776 [at] gmail [dot] com
+# Contributor: peippo <christoph+aur@christophfink.com>
+# Contributor: Dimitris Kiziridis <ragouel at outlook dot com>
 
 _pkgname=rJava
 _pkgver=1.0-11
@@ -12,11 +14,9 @@ url="https://cran.r-project.org/package=$_pkgname"
 license=('LGPL-2.1-only')
 depends=(
   java-runtime
-  openmp
   r
 )
 makedepends=(
-  clang
   java-environment
   patchelf
 )
@@ -25,10 +25,7 @@ md5sums=('4d8eff03a23cb797f01e710ea7528dd2')
 b2sums=('13ecb4a3c545505f047474027d586e0bf7ca02676bbe0bcd142bba786b3380714937f71efa2ca324fcf6efa0c20112f9ef8bc01d8093d3eea17e63176048d6b4')
 
 
-package() {
-  export CC=clang
-  export CXX=clang++
-  export LD=clang
+build() {
   export JAVA_HOME=/usr/lib/jvm/default
   export JAR=$JAVA_HOME/bin/jar
   export JAVA=$JAVA_HOME/bin/java
@@ -38,12 +35,13 @@ package() {
   export JAVA_LIBS="-L$JAVA_HOME/lib/server -ljvm"
   export LD_LIBRARY_PATH="$LD_LIBRARY_PATH:$JAVA_HOME/lib/server"
 
-  archlinux-java fix
   mkdir build
   R CMD INSTALL -l build "$_pkgname"
 
+  patchelf --set-rpath "$JAVA_LD_LIBRARY_PATH" "build/$_pkgname/libs/rJava.so"
+}
+
+package() {
   install -d "$pkgdir/usr/lib/R/library"
   cp -a --no-preserve=ownership "build/$_pkgname" "$pkgdir/usr/lib/R/library"
-
-  patchelf --set-rpath "${JAVA_LD_LIBRARY_PATH}" ${pkgdir}/usr/lib/R/library/rJava/libs/rJava.so
 }
diff --git a/BioArchLinux/r-rjava/lilac.py b/BioArchLinux/r-rjava/lilac.py
index 559a362456..30ee62ff10 100644
--- a/BioArchLinux/r-rjava/lilac.py
+++ b/BioArchLinux/r-rjava/lilac.py
@@ -14,3 +14,4 @@ def pre_build():
 
 def post_build():
     git_pkgbuild_commit()
+    update_aur_repo()
diff --git a/BioArchLinux/r-rjava/lilac.yaml b/BioArchLinux/r-rjava/lilac.yaml
index 41610a2535..0ab211fb3f 100644
--- a/BioArchLinux/r-rjava/lilac.yaml
+++ b/BioArchLinux/r-rjava/lilac.yaml
@@ -8,3 +8,5 @@ update_on:
   repo: cran
   md5: true
 - alias: r
+- source: manual
+  manual: 1