diff options
Diffstat (limited to 'pre_commit')
| -rw-r--r-- | pre_commit/languages/r.py | 53 |
1 files changed, 37 insertions, 16 deletions
diff --git a/pre_commit/languages/r.py b/pre_commit/languages/r.py index 138a26e..6feb065 100644 --- a/pre_commit/languages/r.py +++ b/pre_commit/languages/r.py @@ -4,6 +4,8 @@ import contextlib import os import shlex import shutil +import tempfile +import textwrap from typing import Generator from typing import Sequence @@ -21,6 +23,19 @@ get_default_version = lang_base.basic_get_default_version health_check = lang_base.basic_health_check +@contextlib.contextmanager +def _r_code_in_tempfile(code: str) -> Generator[str, None, None]: + """ + To avoid quoting and escaping issues, avoid `Rscript [options] -e {expr}` + but use `Rscript [options] path/to/file_with_expr.R` + """ + with tempfile.TemporaryDirectory() as tmpdir: + fname = os.path.join(tmpdir, 'script.R') + with open(fname, 'w') as f: + f.write(_inline_r_setup(textwrap.dedent(code))) + yield fname + + def get_env_patch(venv: str) -> PatchesT: return ( ('R_PROFILE_USER', os.path.join(venv, 'activate.R')), @@ -93,6 +108,8 @@ def install_environment( version: str, additional_dependencies: Sequence[str], ) -> None: + lang_base.assert_version_default('r', version) + env_dir = lang_base.environment_dir(prefix, ENVIRONMENT_DIR, version) os.makedirs(env_dir, exist_ok=True) shutil.copy(prefix.path('renv.lock'), env_dir) @@ -127,20 +144,19 @@ def install_environment( }} """ - cmd_output_b( - _rscript_exec(), '--vanilla', '-e', - _inline_r_setup(r_code_inst_environment), - cwd=env_dir, - ) + with _r_code_in_tempfile(r_code_inst_environment) as f: + cmd_output_b(_rscript_exec(), '--vanilla', f, 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', - _inline_r_setup(r_code_inst_add), - *additional_dependencies, - cwd=env_dir, - ) + with _r_code_in_tempfile(r_code_inst_add) as f: + cmd_output_b( + _rscript_exec(), *RSCRIPT_OPTS, + f, + *additional_dependencies, + cwd=env_dir, + ) def _inline_r_setup(code: str) -> str: @@ -148,11 +164,16 @@ 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", pkgType = "binary") - {code} - """ - return with_option + with_option = [ + textwrap.dedent("""\ + options( + install.packages.compile.from.source = "never", + pkgType = "binary" + ) + """), + code, + ] + return '\n'.join(with_option) def run_hook( |