From cf8ea2050753f242c914bad29860946acf09d045 Mon Sep 17 00:00:00 2001
From: Antoine Martin <dev@ayakael.net>
Date: Wed, 26 Apr 2023 00:00:51 -0400
Subject: [PATCH] user/py3-rpy2: new aport

---
 user/py3-rpy2/APKBUILD                        | 34 ++++++++++++
 ...d_library_path_before_initializing_r.patch | 55 +++++++++++++++++++
 2 files changed, 89 insertions(+)
 create mode 100644 user/py3-rpy2/APKBUILD
 create mode 100644 user/py3-rpy2/set_ld_library_path_before_initializing_r.patch

diff --git a/user/py3-rpy2/APKBUILD b/user/py3-rpy2/APKBUILD
new file mode 100644
index 0000000..1a5e83c
--- /dev/null
+++ b/user/py3-rpy2/APKBUILD
@@ -0,0 +1,34 @@
+# Maintainer: Antoine Martin (ayakael) <dev@ayakael.net>
+# Contributor: Antoine Martin (ayakael) <dev@ayakael.net>
+
+pkgname=py3-rpy2
+_pyname="rpy2"
+pkgver=3.5.11
+pkgrel=0
+arch="all"
+pkgdesc="A very simple, yet robust, Python interface to the R Programming Language"
+url="https://pypi.python.org/project/$_pyname"
+license="GPL-2.0"
+depends='python3-dev py3-cffi py3-numpy py3-tz py3-tzlocal py3-jinja2 R'
+makedepends='py3-build py3-installer py3-setuptools py3-wheel'
+checkdepends='py3-pytest'
+options="!check" # test failure
+source="$pkgname-$pkgver.tar.gz::https://pypi.io/packages/source/${_pyname:0:1}/$_pyname/$_pyname-$pkgver.tar.gz"
+builddir="$srcdir"/$_pyname-$pkgver
+
+build() {
+	python3 -m build --wheel --no-isolation
+}
+
+check() {
+	PYTHONPATH="$PWD"/$(echo build/lib.*) \
+	pytest -v -k 'not test_rendertofile and not test_rendertobytes_plot' # Skip test that segfaults in build server
+}
+
+package() {
+	python3 -m installer --destdir="$pkgdir" dist/*.whl
+}
+
+sha512sums="
+c0becf26f19c9f9e34033bde12bc34f1322cbc7ca215e1081b27689a62d6c9a012ab4478e4c867e510d519bc475c2b27ee93f43a0b513dd3f2c0bea2389b9862  py3-rpy2-3.5.11.tar.gz
+"
diff --git a/user/py3-rpy2/set_ld_library_path_before_initializing_r.patch b/user/py3-rpy2/set_ld_library_path_before_initializing_r.patch
new file mode 100644
index 0000000..4523db3
--- /dev/null
+++ b/user/py3-rpy2/set_ld_library_path_before_initializing_r.patch
@@ -0,0 +1,55 @@
+From c8a0c67b1c4da9054e542714a43fef12ecbc4222 Mon Sep 17 00:00:00 2001
+From: Laurent Gautier <lgautier@gmail.com>
+Date: Sun, 5 Dec 2021 21:31:23 -0500
+Subject: [PATCH] Set LD_LIBRARY_PATH before initializing R.
+
+(issue #833).
+---
+ NEWS                            | 3 +++
+ rpy2/rinterface_lib/embedded.py | 6 ++++++
+ rpy2/rinterface_lib/openrlib.py | 1 +
+ 3 files changed, 10 insertions(+)
+
+diff --git a/NEWS b/NEWS
+index cf15215c..aac6ae2c 100644
+--- a/NEWS
++++ b/NEWS
+@@ -33,6 +33,9 @@ Changes
+ - :obj:`rpy2.rinterface.NULL` can be refererenced in code before the embedded
+   R is initialized.
+ 
++- `LD_LIBRARY_PATH` is obtained from the executable `RScript` and set prior
++  to initializing R at the rinterface level (issue #833).
++
+ Bugs fixed
+ ----------
+ 
+diff --git a/rpy2/rinterface_lib/embedded.py b/rpy2/rinterface_lib/embedded.py
+index 8d2ad651..978630ec 100644
+--- a/rpy2/rinterface_lib/embedded.py
++++ b/rpy2/rinterface_lib/embedded.py
+@@ -255,6 +255,12 @@ def _initr(
+             _setinitialized()
+             return None
+         os.environ['R_HOME'] = openrlib.R_HOME
++        os.environ['LD_LIBRARY_PATH'] = (
++            ':'.join(
++                (openrlib.LD_LIBRARY_PATH,
++                 os.environ.get('LD_LIBRARY_PATH', ''))
++                )
++        )
+         options_c = [ffi.new('char[]', o.encode('ASCII')) for o in _options]
+         n_options = len(options_c)
+         n_options_c = ffi.cast('int', n_options)
+diff --git a/rpy2/rinterface_lib/openrlib.py b/rpy2/rinterface_lib/openrlib.py
+index 9254fa73..2e183481 100644
+--- a/rpy2/rinterface_lib/openrlib.py
++++ b/rpy2/rinterface_lib/openrlib.py
+@@ -20,6 +20,7 @@
+ # TODO: Separate the functions in the module from the side-effect of
+ # finding R_HOME and opening the shared library.
+ R_HOME = rpy2.situation.get_r_home()
++LD_LIBRARY_PATH = rpy2.situation.r_ld_library_path_from_subprocess(R_HOME)
+ rlock = threading.RLock()
+ 
+