Rscript not found

[jaskozi]

I have a problem when I want to commit after activating precommit with use_precommit()

I have the latest version, did the autoupdate, everything described here: https://lorenzwalthert.github.io/precommit/articles/precommit.html

My .pre-commit-config.yaml is the default one created after executing use_precommit()

The log file is as follows:

pre-commit version: 2.20.0
git --version: git version 2.33.0.windows.2
sys.version:
    3.9.7 | packaged by conda-forge | (default, Sep 23 2021, 07:24:41) [MSC v.1916 64 bit (AMD64)]
sys.executable: C:\Users\username\AppData\Local\MAMBAF~1\python.exe
os.name: nt
sys.platform: win32

### error information

An unexpected error has occurred: CalledProcessError: command: ('C:/PROGRA~1/R/R-41~1.0\\bin\\Rscript', '--vanilla', '-e', '    options(install.packages.compile.from.source = "never")\n                prefix_dir <- \'C:\\\\Users\\\\username\\\\.cache\\\\pre-commit\\\\repoz11tusy_\'\n            options(\n                repos = c(CRAN = "https://cran.rstudio.com"),\n                renv.consent = TRUE\n            )\n            source("renv/activate.R")\n            renv::restore()\n            activate_statement <- paste0(\n              \'suppressWarnings({\',\n              \'old <- setwd("\', getwd(), \'"); \',\n              \'source("renv/activate.R"); \',\n              \'setwd(old); \',\n              \'renv::load("\', getwd(), \'");})\'\n            )\n            writeLines(activate_statement, \'activate.R\')\n            is_package <- tryCatch(\n              {\n                  path_desc <- file.path(prefix_dir, \'DESCRIPTION\')\n                  suppressWarnings(desc <- read.dcf(path_desc))\n                  "Package" %in% colnames(desc)\n              },\n              error = function(...) FALSE\n            )\n            if (is_package) {\n                renv::install(prefix_dir)\n            }\n            \n    ')
return code: 1
expected return code: 0
stdout:
    Executable `C:/PROGRA~1/R/R-41~1.0\bin\Rscript` not found
stderr: (none)


Traceback (most recent call last):
  File "C:\Users\username\AppData\Roaming\Python\Python39\site-packages\pre_commit\error_handler.py", line 73, in error_handler
    yield
  File "C:\Users\username\AppData\Roaming\Python\Python39\site-packages\pre_commit\main.py", line 358, in main
    return hook_impl(
  File "C:\Users\username\AppData\Roaming\Python\Python39\site-packages\pre_commit\commands\hook_impl.py", line 254, in hook_impl
    return retv | run(config, store, ns)
  File "C:\Users\username\AppData\Roaming\Python\Python39\site-packages\pre_commit\commands\run.py", line 424, in run
    install_hook_envs(to_install, store)
  File "C:\Users\username\AppData\Roaming\Python\Python39\site-packages\pre_commit\repository.py", line 223, in install_hook_envs
    _hook_install(hook)
  File "C:\Users\username\AppData\Roaming\Python\Python39\site-packages\pre_commit\repository.py", line 79, in _hook_install
    lang.install_environment(
  File "C:\Users\username\AppData\Roaming\Python\Python39\site-packages\pre_commit\languages\r.py", line 139, in install_environment
    cmd_output_b(
  File "C:\Users\username\AppData\Roaming\Python\Python39\site-packages\pre_commit\util.py", line 146, in cmd_output_b
    raise CalledProcessError(returncode, cmd, retcode, stdout_b, stderr_b)
pre_commit.util.CalledProcessError: command: ('C:/PROGRA~1/R/R-41~1.0\\bin\\Rscript', '--vanilla', '-e', '    options(install.packages.compile.from.source = "never")\n                prefix_dir <- \'C:\\\\Users\\\\username\\\\.cache\\\\pre-commit\\\\repoz11tusy_\'\n            options(\n                repos = c(CRAN = "https://cran.rstudio.com"),\n                renv.consent = TRUE\n            )\n            source("renv/activate.R")\n            renv::restore()\n            activate_statement <- paste0(\n              \'suppressWarnings({\',\n              \'old <- setwd("\', getwd(), \'"); \',\n              \'source("renv/activate.R"); \',\n              \'setwd(old); \',\n              \'renv::load("\', getwd(), \'");})\'\n            )\n            writeLines(activate_statement, \'activate.R\')\n            is_package <- tryCatch(\n              {\n                  path_desc <- file.path(prefix_dir, \'DESCRIPTION\')\n                  suppressWarnings(desc <- read.dcf(path_desc))\n                  "Package" %in% colnames(desc)\n              },\n              error = function(...) FALSE\n            )\n            if (is_package) {\n                renv::install(prefix_dir)\n            }\n            \n    ')
return code: 1
expected return code: 0
stdout:
    Executable `C:/PROGRA~1/R/R-41~1.0\bin\Rscript` not found
stderr: (none)

The executable Rscript in the named folder is present, I checked manually
Thank you for your time!

[lorenzwalthert]

Did you run pre-commit clean?

[jaskozi]

Before filing a bug

• I have installed the latest dev version of {precommit} with remotes::install_github('lorenzwalthert/precommit')
• I have installed the latest hook revisions (update with precommit::autoupdate())
• I have installed the latest release of the upstream Python framework pre-comit as described under the update instructions.

Describe the bug
I did run pre-commit clean, cleared the file in .git/hooks/, also tried reinstalling, and I also did try via pip and conda, still got the same message. I also created a new blank project, wanted to commit a readme.md, got the same error message

Additional context

• My operating system is: Windows 10
• My project uses {renv}.

[lorenzwalthert]

To me, this looks suspicious:

pre_commit.util.CalledProcessError: command: ('C:/PROGRA~1/R/R-41~1.0\\bin\\Rscript', '--vanilla', '-e', '    ...

I.e. is pre-commit shortening the path to the executable somewhere and then you have a string with a bunch of ~ in it?

[lorenzwalthert]

Plus the direction of the slashes changes: First forward, than backward slashes...

[jaskozi]

Yes it is, because the actual path is C:\Program Files\R\R-4.1.0\bin, and I don't understand why is it shortening

[jaskozi]

A small update:

The problem is only present if I use this repo. If I remove it from the hooks, I can use precommit without problems.

Hopefully this helps.

[lorenzwalthert]

What is this repo? Do you mean if you put github.com/lorenzwalthert/precommit into your .pre-commit-config.yaml?

[lorenzwalthert]

Just to confirm? Are you using {renv}, as indicated in the issue description? Are you using pre-commit from inside RStudio or from where?

[jaskozi]

What is this repo? Do you mean if you put github.com/lorenzwalthert/precommit into your .pre-commit-config.yaml?

Yes exactly. And I am using renv.

[lorenzwalthert]

From inside RStudio?

[jaskozi]

From inside RStudio?

Yes, from inside RStudio.

[lorenzwalthert]

Can you try outside of RStudio $ git commit ...?

[jaskozi]

Can you try outside of RStudio $ git commit ...?

Same error.

[lorenzwalthert]

Can you set the environment variable R_HOME to the full path (C:\Program Files\R\R-4.1.0) and try again? In unix, I would

export R_HOME=/path/to/r/home

Because pre-commit then appends "/bin/Rscript" to R_HOME when running the hooks.

[lorenzwalthert]

If that works, we know that your env variable R_HOME is wrongly set.