From 9d68e4e3da4ce68e28506d926c7de9fd6ffbf6a3 Mon Sep 17 00:00:00 2001
From: Daniel Baumann <daniel.baumann@progress-linux.org>
Date: Mon, 4 Apr 2022 20:42:14 +0200
Subject: Merging upstream version 2.18.1.

Signed-off-by: Daniel Baumann <daniel.baumann@progress-linux.org>
---
 pre_commit/languages/r.py | 38 +++++++++++++++++++++++++++++---------
 1 file changed, 29 insertions(+), 9 deletions(-)

(limited to 'pre_commit/languages/r.py')

diff --git a/pre_commit/languages/r.py b/pre_commit/languages/r.py
index e034e39..c736b38 100644
--- a/pre_commit/languages/r.py
+++ b/pre_commit/languages/r.py
@@ -1,10 +1,11 @@
+from __future__ import annotations
+
 import contextlib
 import os
 import shlex
 import shutil
 from typing import Generator
 from typing import Sequence
-from typing import Tuple
 
 from pre_commit.envcontext import envcontext
 from pre_commit.envcontext import PatchesT
@@ -58,7 +59,11 @@ def _prefix_if_non_local_file_entry(
 
 
 def _rscript_exec() -> str:
-    return os.path.join(os.getenv('R_HOME', ''), 'Rscript')
+    r_home = os.environ.get('R_HOME')
+    if r_home is None:
+        return 'Rscript'
+    else:
+        return os.path.join(r_home, 'bin', 'Rscript')
 
 
 def _entry_validate(entry: Sequence[str]) -> None:
@@ -80,7 +85,7 @@ def _entry_validate(entry: Sequence[str]) -> None:
         )
 
 
-def _cmd_from_hook(hook: Hook) -> Tuple[str, ...]:
+def _cmd_from_hook(hook: Hook) -> tuple[str, ...]:
     entry = shlex.split(hook.entry)
     _entry_validate(entry)
 
@@ -102,9 +107,7 @@ def install_environment(
         shutil.copy(prefix.path('renv.lock'), env_dir)
         shutil.copytree(prefix.path('renv'), os.path.join(env_dir, 'renv'))
 
-        cmd_output_b(
-            _rscript_exec(), '--vanilla', '-e',
-            f"""\
+        r_code_inst_environment = f"""\
             prefix_dir <- {prefix.prefix_dir!r}
             options(
                 repos = c(CRAN = "https://cran.rstudio.com"),
@@ -131,24 +134,41 @@ def install_environment(
             if (is_package) {{
                 renv::install(prefix_dir)
             }}
-            """,
+            """
+
+        cmd_output_b(
+            _rscript_exec(), '--vanilla', '-e',
+            _inline_r_setup(r_code_inst_environment),
             cwd=env_dir,
         )
         if additional_dependencies:
+            r_code_inst_add = 'renv::install(commandArgs(trailingOnly = TRUE))'
             with in_env(prefix, version):
                 cmd_output_b(
                     _rscript_exec(), *RSCRIPT_OPTS, '-e',
-                    'renv::install(commandArgs(trailingOnly = TRUE))',
+                    _inline_r_setup(r_code_inst_add),
                     *additional_dependencies,
                     cwd=env_dir,
                 )
 
 
+def _inline_r_setup(code: str) -> str:
+    """
+    Some behaviour of R cannot be configured via env variables, but can
+    only be configured via R options once R has started. These are set here.
+    """
+    with_option = f"""\
+    options(install.packages.compile.from.source = "never")
+    {code}
+    """
+    return with_option
+
+
 def run_hook(
         hook: Hook,
         file_args: Sequence[str],
         color: bool,
-) -> Tuple[int, bytes]:
+) -> tuple[int, bytes]:
     with in_env(hook.prefix, hook.language_version):
         return helpers.run_xargs(
             hook, _cmd_from_hook(hook), file_args, color=color,
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