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better r path detection

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This commit is contained in:
Lorenz Walthert 2021-12-11 18:35:57 +01:00
parent 44687a3cda
commit ba496b8369
1 changed files with 9 additions and 2 deletions
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11
pre_commit/languages/r.py
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@ -54,6 +54,12 @@ def _prefix_if_non_local_file_entry(
path = prefix.path(entry[1]) path = prefix.path(entry[1])
return (path,) return (path,)
def _rscript_exec():
"""
When invoked in a sub-process of R, use full path
"""
return os.path.join(os.getenv('R_HOME', ""), 'Rscript')
def _entry_validate(entry: Sequence[str]) -> None: def _entry_validate(entry: Sequence[str]) -> None:
""" """
@ -95,8 +101,9 @@ def install_environment(
os.makedirs(env_dir, exist_ok=True) os.makedirs(env_dir, exist_ok=True)
shutil.copy(prefix.path('renv.lock'), env_dir) shutil.copy(prefix.path('renv.lock'), env_dir)
shutil.copytree(prefix.path('renv'), os.path.join(env_dir, 'renv')) shutil.copytree(prefix.path('renv'), os.path.join(env_dir, 'renv'))
cmd_output_b( cmd_output_b(
'Rscript', '--vanilla', '-e', _rscript_exec(), '--vanilla', '-e',
f"""\ f"""\
prefix_dir <- {prefix.prefix_dir!r} prefix_dir <- {prefix.prefix_dir!r}
options( options(
@ -130,7 +137,7 @@ def install_environment(
if additional_dependencies: if additional_dependencies:
with in_env(prefix, version): with in_env(prefix, version):
cmd_output_b( cmd_output_b(
'Rscript', *RSCRIPT_OPTS, '-e', _rscript_exec(), *RSCRIPT_OPTS, '-e',
'renv::install(commandArgs(trailingOnly = TRUE))', 'renv::install(commandArgs(trailingOnly = TRUE))',
*additional_dependencies, *additional_dependencies,
cwd=env_dir, cwd=env_dir,