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lorenzwalthertasottile
lorenzwalthert
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asottile
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add support for R via renv
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15 files changed

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‎azure-pipelines.yml‎

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@@ -26,6 +26,10 @@ jobs:
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Write-Host "##vso[task.prependpath]C:\Strawberry\perl\site\bin"
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Write-Host "##vso[task.prependpath]C:\Strawberry\c\bin"
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displayName: Add strawberry perl to PATH
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- task: PowerShell@2
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inputs:
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filePath: "testing/get-r.ps1"
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displayName: install R
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- template: job--python-tox.yml@asottile
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parameters:
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toxenvs: [py37]
@@ -42,6 +46,8 @@ jobs:
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testing/get-swift.sh
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echo '##vso[task.prependpath]/tmp/swift/usr/bin'
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displayName: install swift
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- bash: testing/get-r.sh
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displayName: install R
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- template: job--python-tox.yml@asottile
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parameters:
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toxenvs: [pypy3, py36, py37, py38, py39]
@@ -56,3 +62,5 @@ jobs:
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testing/get-swift.sh
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echo '##vso[task.prependpath]/tmp/swift/usr/bin'
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displayName: install swift
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- bash: testing/get-r.sh
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displayName: install R

‎pre_commit/languages/all.py‎

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@@ -16,6 +16,7 @@
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from pre_commit.languages import perl
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from pre_commit.languages import pygrep
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from pre_commit.languages import python
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from pre_commit.languages import r
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from pre_commit.languages import ruby
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from pre_commit.languages import rust
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from pre_commit.languages import script
@@ -52,6 +53,7 @@ class Language(NamedTuple):
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'perl': Language(name='perl', ENVIRONMENT_DIR=perl.ENVIRONMENT_DIR, get_default_version=perl.get_default_version, healthy=perl.healthy, install_environment=perl.install_environment, run_hook=perl.run_hook), # noqa: E501
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'pygrep': Language(name='pygrep', ENVIRONMENT_DIR=pygrep.ENVIRONMENT_DIR, get_default_version=pygrep.get_default_version, healthy=pygrep.healthy, install_environment=pygrep.install_environment, run_hook=pygrep.run_hook), # noqa: E501
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'python': Language(name='python', ENVIRONMENT_DIR=python.ENVIRONMENT_DIR, get_default_version=python.get_default_version, healthy=python.healthy, install_environment=python.install_environment, run_hook=python.run_hook), # noqa: E501
56+
'r': Language(name='r', ENVIRONMENT_DIR=r.ENVIRONMENT_DIR, get_default_version=r.get_default_version, healthy=r.healthy, install_environment=r.install_environment, run_hook=r.run_hook), # noqa: E501
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'ruby': Language(name='ruby', ENVIRONMENT_DIR=ruby.ENVIRONMENT_DIR, get_default_version=ruby.get_default_version, healthy=ruby.healthy, install_environment=ruby.install_environment, run_hook=ruby.run_hook), # noqa: E501
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'rust': Language(name='rust', ENVIRONMENT_DIR=rust.ENVIRONMENT_DIR, get_default_version=rust.get_default_version, healthy=rust.healthy, install_environment=rust.install_environment, run_hook=rust.run_hook), # noqa: E501
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'script': Language(name='script', ENVIRONMENT_DIR=script.ENVIRONMENT_DIR, get_default_version=script.get_default_version, healthy=script.healthy, install_environment=script.install_environment, run_hook=script.run_hook), # noqa: E501

‎pre_commit/languages/r.py‎

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@@ -0,0 +1,141 @@
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import contextlib
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import os
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import shlex
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import shutil
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from typing import Generator
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from typing import Sequence
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from typing import Tuple
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9+
from pre_commit.envcontext import envcontext
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from pre_commit.envcontext import PatchesT
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from pre_commit.hook import Hook
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from pre_commit.languages import helpers
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from pre_commit.prefix import Prefix
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from pre_commit.util import clean_path_on_failure
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from pre_commit.util import cmd_output_b
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17+
ENVIRONMENT_DIR = 'renv'
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get_default_version = helpers.basic_get_default_version
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healthy = helpers.basic_healthy
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21+
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def get_env_patch(venv: str) -> PatchesT:
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return (
24+
('R_PROFILE_USER', os.path.join(venv, 'activate.R')),
25+
)
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@contextlib.contextmanager
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def in_env(
30+
prefix: Prefix,
31+
language_version: str,
32+
) -> Generator[None, None, None]:
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envdir = _get_env_dir(prefix, language_version)
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with envcontext(get_env_patch(envdir)):
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yield
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def _get_env_dir(prefix: Prefix, version: str) -> str:
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return prefix.path(helpers.environment_dir(ENVIRONMENT_DIR, version))
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41+
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def _prefix_if_file_entry(
43+
entry: Sequence[str],
44+
prefix: Prefix,
45+
) -> Sequence[str]:
46+
if entry[1] == '-e':
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return entry[1:]
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else:
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return (prefix.path(entry[1]),)
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51+
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def _entry_validate(entry: Sequence[str]) -> None:
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"""
54+
Allowed entries:
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# Rscript -e expr
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# Rscript path/to/file
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"""
58+
if entry[0] != 'Rscript':
59+
raise ValueError('entry must start with `Rscript`.')
60+
61+
if entry[1] == '-e':
62+
if len(entry) > 3:
63+
raise ValueError('You can supply at most one expression.')
64+
elif len(entry) > 2:
65+
raise ValueError(
66+
'The only valid syntax is `Rscript -e {expr}`',
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'or `Rscript path/to/hook/script`',
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)
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def _cmd_from_hook(hook: Hook) -> Tuple[str, ...]:
72+
opts = ('--no-save', '--no-restore', '--no-site-file', '--no-environ')
73+
entry = shlex.split(hook.entry)
74+
_entry_validate(entry)
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76+
return (
77+
*entry[:1], *opts,
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*_prefix_if_file_entry(entry, hook.prefix),
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*hook.args,
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)
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def install_environment(
84+
prefix: Prefix,
85+
version: str,
86+
additional_dependencies: Sequence[str],
87+
) -> None:
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env_dir = _get_env_dir(prefix, version)
89+
with clean_path_on_failure(env_dir):
90+
os.makedirs(env_dir, exist_ok=True)
91+
path_desc_source = prefix.path('DESCRIPTION')
92+
if os.path.exists(path_desc_source):
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shutil.copy(path_desc_source, env_dir)
94+
shutil.copy(prefix.path('renv.lock'), env_dir)
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cmd_output_b(
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'Rscript', '--vanilla', '-e',
97+
"""\
98+
missing_pkgs <- setdiff(
99+
"renv", unname(installed.packages()[, "Package"])
100+
)
101+
options(
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repos = c(CRAN = "https://cran.rstudio.com"),
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renv.consent = TRUE
104+
)
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install.packages(missing_pkgs)
106+
renv::activate()
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renv::restore()
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activate_statement <- paste0(
109+
'renv::activate("', file.path(getwd()), '"); '
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)
111+
writeLines(activate_statement, 'activate.R')
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is_package <- tryCatch(
113+
suppressWarnings(
114+
unname(read.dcf('DESCRIPTION')[,'Type'] == "Package")
115+
),
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error = function(...) FALSE
117+
)
118+
if (is_package) {
119+
renv::install(normalizePath('.'))
120+
}
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""",
122+
cwd=env_dir,
123+
)
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if additional_dependencies:
125+
cmd_output_b(
126+
'Rscript', '-e',
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'renv::install(commandArgs(trailingOnly = TRUE))',
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*additional_dependencies,
129+
cwd=env_dir,
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)
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132+
133+
def run_hook(
134+
hook: Hook,
135+
file_args: Sequence[str],
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color: bool,
137+
) -> Tuple[int, bytes]:
138+
with in_env(hook.prefix, hook.language_version):
139+
return helpers.run_xargs(
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hook, _cmd_from_hook(hook), file_args, color=color,
141+
)

‎pre_commit/resources/empty_template_renv.lock‎

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{
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"R": {
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"Version": "4.0.3",
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"Repositories": [
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{
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"Name": "CRAN",
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"URL": "https://cran.rstudio.com"
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}
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]
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},
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"Packages": {
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"renv": {
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"Package": "renv",
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"Version": "0.12.5",
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"Source": "Repository",
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"Repository": "CRAN",
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"Hash": "5c0cdb37f063c58cdab3c7e9fbb8bd2c"
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}
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}
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}

‎pre_commit/store.py‎

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@@ -189,7 +189,7 @@ def _git_cmd(*args: str) -> None:
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LOCAL_RESOURCES = (
190190
'Cargo.toml', 'main.go', 'go.mod', 'main.rs', '.npmignore',
191191
'package.json', 'pre_commit_dummy_package.gemspec', 'setup.py',
192-
'environment.yml', 'Makefile.PL',
192+
'environment.yml', 'Makefile.PL', 'renv.lock',
193193
)
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195195
def make_local(self, deps: Sequence[str]) -> str:

‎testing/gen-languages-all‎

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@@ -2,9 +2,9 @@
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import sys
33

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LANGUAGES = [
5-
'conda', 'coursier', 'docker', 'dotnet', 'docker_image', 'fail', 'golang',
6-
'node', 'perl', 'pygrep', 'python', 'ruby', 'rust', 'script', 'swift',
7-
'system',
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'conda', 'coursier', 'docker', 'docker_image', 'dotnet', 'fail', 'golang',
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'node', 'perl', 'pygrep', 'python', 'r', 'ruby', 'rust', 'script',
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'swift', 'system',
88
]
99
FIELDS = [
1010
'ENVIRONMENT_DIR', 'get_default_version', 'healthy', 'install_environment',

‎testing/get-r.ps1‎

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$dir = $Env:Temp
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$urlR = "https://cran.r-project.org/bin/windows/base/old/4.0.4/R-4.0.4-win.exe"
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$outputR = "$dir\R-win.exe"
4+
$wcR = New-Object System.Net.WebClient
5+
$wcR.DownloadFile($urlR, $outputR)
6+
Start-Process -FilePath $outputR -ArgumentList "/S /v/qn"

‎testing/get-r.sh‎

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#!/usr/bin/env bash
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sudo apt install r-base
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# create empty folder for user library.
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# necessary for non-root users who have
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# never installed an R package before.
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# Alternatively, we require the renv
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# package to be installed already, then we can
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# omit that.
9+
Rscript -e 'dir.create(Sys.getenv("R_LIBS_USER"), recursive = TRUE)'

‎testing/resources/r_hooks_repo/.pre-commit-hooks.yaml‎

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# parsing file
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- id: parse-file-no-opts-no-args
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name: Say hi
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entry: Rscript parse-file-no-opts-no-args.R
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language: r
6+
types: [r]
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- id: parse-file-no-opts-args
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name: Say hi
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entry: Rscript parse-file-no-opts-args.R
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args: [--no-cache]
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language: r
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types: [r]
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## parsing expr
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- id: parse-expr-no-opts-no-args-1
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name: Say hi
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entry: Rscript -e '1+1'
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language: r
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types: [r]
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- id: parse-expr-args-in-entry-2
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name: Say hi
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entry: Rscript -e '1+1' -e '3' --no-cache3
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language: r
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types: [r]
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# real world
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- id: hello-world
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name: Say hi
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entry: Rscript hello-world.R
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args: [blibla]
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language: r
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types: [r]
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- id: hello-world-inline
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name: Say hi
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entry: |
34+
Rscript -e
35+
'stopifnot(
36+
packageVersion("rprojroot") == "1.0",
37+
packageVersion("gli.clu") == "0.0.0.9000"
38+
)
39+
cat(commandArgs(trailingOnly = TRUE), "from R!\n", sep = ", ")
40+
'
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args: ['Hi-there']
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language: r
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types: [r]
44+
- id: additional-deps
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name: Check additional deps
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entry: Rscript additional-deps.R
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language: r
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types: [r]

‎testing/resources/r_hooks_repo/DESCRIPTION‎

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Package: gli.clu
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Title: What the Package Does (One Line, Title Case)
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Type: Package
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Version: 0.0.0.9000
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Authors@R:
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person(given = "First",
7+
family = "Last",
8+
role = c("aut", "cre"),
9+
email = "first.last@example.com",
10+
comment = c(ORCID = "YOUR-ORCID-ID"))
11+
Description: What the package does (one paragraph).
12+
License: `use_mit_license()`, `use_gpl3_license()` or friends to
13+
pick a license
14+
Encoding: UTF-8
15+
LazyData: true
16+
Roxygen: list(markdown = TRUE)
17+
RoxygenNote: 7.1.1
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Imports:
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rprojroot

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