From e9895844c56d0013c4bb2ebc8c087d913442dfd2 Mon Sep 17 00:00:00 2001
From: Pekka Ristola <pekkarr@protonmail.com>
Date: Tue, 10 Oct 2023 14:43:14 +0300
Subject: [PATCH] r-pbdmpi: init, checkdependency of r-rnetcdf

---
 BioArchLinux/r-pbdmpi/PKGBUILD    | 28 ++++++++++++++++++++++++++++
 BioArchLinux/r-pbdmpi/lilac.py    | 17 +++++++++++++++++
 BioArchLinux/r-pbdmpi/lilac.yaml  | 17 +++++++++++++++++
 lilac-extensions/lilac_r_utils.py |  1 +
 4 files changed, 63 insertions(+)
 create mode 100644 BioArchLinux/r-pbdmpi/PKGBUILD
 create mode 100644 BioArchLinux/r-pbdmpi/lilac.py
 create mode 100644 BioArchLinux/r-pbdmpi/lilac.yaml

diff --git a/BioArchLinux/r-pbdmpi/PKGBUILD b/BioArchLinux/r-pbdmpi/PKGBUILD
new file mode 100644
index 0000000000..bcf2f7734d
--- /dev/null
+++ b/BioArchLinux/r-pbdmpi/PKGBUILD
@@ -0,0 +1,28 @@
+# Maintainer: Pekka Ristola <pekkarr [at] protonmail [dot] com>
+
+_pkgname=pbdMPI
+_pkgver=0.5-0
+pkgname=r-${_pkgname,,}
+pkgver=${_pkgver//-/.}
+pkgrel=1
+pkgdesc="R Interface to MPI for HPC Clusters (Programming with Big Data Project)"
+arch=(x86_64)
+url="https://cran.r-project.org/package=${_pkgname}"
+license=(MPL2)
+depends=(
+  openmpi
+  r-float
+)
+source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz")
+md5sums=('a643799993c8ecf9c2d1cff9e3e615b9')
+sha256sums=('fd70950c4d0df37713e50df9b999873a11e7c5473b5d0dd94997e706e518dd71')
+
+build() {
+  mkdir -p build
+  R CMD INSTALL "$_pkgname" -l build
+}
+
+package() {
+  install -d "$pkgdir/usr/lib/R/library"
+  cp -a --no-preserve=ownership "build/$_pkgname" "$pkgdir/usr/lib/R/library"
+}
diff --git a/BioArchLinux/r-pbdmpi/lilac.py b/BioArchLinux/r-pbdmpi/lilac.py
new file mode 100644
index 0000000000..b968413ff6
--- /dev/null
+++ b/BioArchLinux/r-pbdmpi/lilac.py
@@ -0,0 +1,17 @@
+#!/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():
+    r_pre_build(
+        _G,
+        expect_systemrequirements = "OpenMPI (>= 1.5.4) on Linux, Mac, and FreeBSD. MS-MPI (Microsoft MPI v7.1 (SDK) and Microsoft HPC Pack 2012 R2 MS-MPI Redistributable Package) on Windows.",
+    )
+
+def post_build():
+    git_pkgbuild_commit()
+    update_aur_repo()
diff --git a/BioArchLinux/r-pbdmpi/lilac.yaml b/BioArchLinux/r-pbdmpi/lilac.yaml
new file mode 100644
index 0000000000..c3547a0124
--- /dev/null
+++ b/BioArchLinux/r-pbdmpi/lilac.yaml
@@ -0,0 +1,17 @@
+build_prefix: extra-x86_64
+maintainers:
+- github: pekkarr
+  email: pekkarr@protonmail.com
+repo_depends:
+- r-float
+update_on:
+- source: rpkgs
+  pkgname: pbdMPI
+  repo: cran
+  md5: true
+- alias: r
+- source: alpm
+  alpm: openmpi
+  repo: extra
+  provided: libmpi.so
+  strip_release: true
diff --git a/lilac-extensions/lilac_r_utils.py b/lilac-extensions/lilac_r_utils.py
index 8b5f5c1e2c..abfc73241b 100644
--- a/lilac-extensions/lilac_r_utils.py
+++ b/lilac-extensions/lilac_r_utils.py
@@ -208,6 +208,7 @@ license_map = {
     "LGPL-3": "LGPL3",
     "Lucent Public License": "custom:LPL",
     "MIT + file LICENSE": "MIT",
+    "Mozilla Public License 2.0": "MPL2",
 }
 
 def get_default_r_pkgs() -> set: