From c3dc063d66bc656007078aef4b89d0a82873cbd9 Mon Sep 17 00:00:00 2001
From: Pekka Ristola <pekkarr@protonmail.com>
Date: Tue, 10 Oct 2023 14:47:04 +0300
Subject: [PATCH] r-rnetcdf: fix systemrequirements, use openmpi

---
 BioArchLinux/r-rnetcdf/PKGBUILD   | 26 +++++++++++++++++++-------
 BioArchLinux/r-rnetcdf/lilac.py   |  2 +-
 BioArchLinux/r-rnetcdf/lilac.yaml |  9 ++++++++-
 3 files changed, 28 insertions(+), 9 deletions(-)

diff --git a/BioArchLinux/r-rnetcdf/PKGBUILD b/BioArchLinux/r-rnetcdf/PKGBUILD
index d1871bd719..fc35c1a14e 100644
--- a/BioArchLinux/r-rnetcdf/PKGBUILD
+++ b/BioArchLinux/r-rnetcdf/PKGBUILD
@@ -1,32 +1,44 @@
 # Maintainer: Pekka Ristola <pekkarr [at] protonmail [dot] com>
 
 _pkgname=RNetCDF
-_pkgver=2.6-2
+_pkgver=2.7-1
 pkgname=r-${_pkgname,,}
 pkgver=${_pkgver//-/.}
-pkgrel=2
+pkgrel=0
 pkgdesc="Interface to 'NetCDF' Datasets"
 arch=(x86_64)
 url="https://cran.r-project.org/package=${_pkgname}"
 license=(GPL)
 depends=(
-  netcdf
+  netcdf-openmpi
+  openmpi
   r
   udunits
 )
 checkdepends=(
   r-bit64
+  r-pbdmpi
+  r-rmpi
 )
 optdepends=(
   r-bit64
 )
-source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz")
-md5sums=('faa65d9a33a7dd02fcf2a204d5c89819')
-sha256sums=('b4de45798fc5f3021f23187bc52d5931a86a4f5c91fcdba7ca4f92c966ec022e')
+source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz"
+        "$_pkgname-fix-build.patch::https://github.com/mjwoods/RNetCDF/pull/128.patch")
+md5sums=('4ea0d88f5bb0b80ac2befd5903367977'
+         '218440db93cdbfd1c963e73461176ecd')
+sha256sums=('80626172829077807c6f14506782ffd85a316f0c09539c3d64d4594edc756d0b'
+            '186ebb62ea7b289108475ead24044f9d71f3bfdae06998f92e70faf1ceb74952')
+
+prepare() {
+  # fix build
+  patch -Np1 -d "$_pkgname" < "$_pkgname-fix-build.patch"
+}
 
 build() {
   mkdir -p build
-  R CMD INSTALL "$_pkgname" -l build
+  R CMD INSTALL "$_pkgname" -l build \
+      --configure-args="--with-mpicc=/usr/bin/mpicc --with-mpiexec=mpiexec"
 }
 
 check() {
diff --git a/BioArchLinux/r-rnetcdf/lilac.py b/BioArchLinux/r-rnetcdf/lilac.py
index 0de0579edd..d6769ca166 100644
--- a/BioArchLinux/r-rnetcdf/lilac.py
+++ b/BioArchLinux/r-rnetcdf/lilac.py
@@ -10,7 +10,7 @@ def pre_build():
     r_pre_build(
         _G,
         expect_license = "GPL (>= 2) | file LICENSE",
-        expect_systemrequirements = "netcdf udunits-2",
+        expect_systemrequirements = "netcdf (>=4.1.3), udunits-2 (>=2.0.4)",
     )
 
 def post_build():
diff --git a/BioArchLinux/r-rnetcdf/lilac.yaml b/BioArchLinux/r-rnetcdf/lilac.yaml
index c302370407..db8eb788ea 100644
--- a/BioArchLinux/r-rnetcdf/lilac.yaml
+++ b/BioArchLinux/r-rnetcdf/lilac.yaml
@@ -6,6 +6,8 @@ repo_depends:
 - udunits
 repo_makedepends:
 - r-bit64
+- r-pbdmpi
+- r-rmpi
 update_on:
 - source: rpkgs
   pkgname: RNetCDF
@@ -13,6 +15,11 @@ update_on:
   md5: true
 - alias: r
 - source: alpmfiles
-  pkgname: netcdf
+  pkgname: netcdf-openmpi
   filename: usr/lib/libnetcdf\.so\.([^.]+)
   repo: extra
+- source: alpm
+  alpm: openmpi
+  repo: extra
+  provided: libmpi.so
+  strip_release: true