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More robust R hooks for Windows #2885

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Merged
asottile merged 1 commit into from
May 17, 2023
Merged

More robust R hooks for Windows #2885

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51 changes: 35 additions & 16 deletions pre_commit/languages/r.py
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Original file line number Diff line number Diff line change
Expand Up @@ -4,6 +4,8 @@
import os
import shlex
import shutil
import tempfile
import textwrap
from typing import Generator
from typing import Sequence

Expand All @@ -21,6 +23,19 @@
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')),
Expand Down Expand Up @@ -129,32 +144,36 @@ 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:
"""
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(
Expand Down