Executable Rscript not found in VS Code

[joshpersi]

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 am able to use the precommit package successfully in RStudio but if I try to use precommit (on the same computer) in VS code, I receive errors like:

$ git commit
style-files..............................................................Failed
- hook id: style-files
- exit code: 1

Executable `Rscript` not found

lintr....................................................................Failed
- hook id: lintr
- exit code: 1

Executable `Rscript` not found

parsable-R...............................................................Failed
- hook id: parsable-R
- exit code: 1

Executable `Rscript` not found

no-browser-statement.....................................................Failed
- hook id: no-browser-statement
- exit code: 1

Executable `Rscript` not found

To Reproduce
Steps to reproduce the behavior:

1. Create a new folder and open it in VS Code
2. Create an empty R script
3. Init git
4. Run precommit::use_precommit()
5. Stage changes and attempt to commit

Expected behavior
I expect precommit's checks to run on VS

Additional context

• My operating system is:
• My project uses {renv}.
• the output of packageVersion('renv')

[lorenzwalthert]

Thanks for the report. Is Rscript on your PATH?

[lorenzwalthert]

Also see #441 (comment).

[joshpersi]

I honestly don't know how to tell if Rscript is on my PATH.

If I run Sys.getenv("PATH") in RStudio, where precommit works, this is the output (I've broken lines at ; for readability):

C:\\rtools43\\x86_64-w64-mingw32.static.posix\\bin
C:\\rtools43\\usr\\bin
C:\\Users\\joshpersi\\AppData\\Local\\Programs\\R\\R-4.3.1\\bin\\x64
C:\\Program Files (x86)\\Common Files\\Oracle\\Java\\javapath
C:\\Oracle\\product\\12.1\\bin
C:\\WINDOWS\\System32
C:\\WINDOWS
C:\\WINDOWS\\System32\\Wbem
C:\\WINDOWS\\System32\\Windowspowershell\\V1.0\\
C:\\WINDOWS\\System32\\Openssh\\
C:\\WINDOWS\\system32
C:\\WINDOWS
C:\\WINDOWS\\System32\\Wbem
C:\\WINDOWS\\System32\\WindowsPowerShell\\v1.0\\
C:\\WINDOWS\\System32\\OpenSSH\\
C:\\Program Files\\1E\\Client\\Extensibility\\NomadBranch
C:\\Program Files\\dotnet\\
C:\\Program Files\\Docker\\Docker\\resources\\bin
C:\\Users\\joshpersi\\AppData\\Local\\Programs\\Quarto\\bin
C:\\Users\\joshpersi\\AppData\\Local\\Microsoft\\WindowsApps
C:\\Users\\joshpersi\\AppData\\Local\\Programs\\Git\\cmd
C:\\Users\\joshpersi\\AppData\\Roaming\\TinyTeX\\bin\\win32
C:\\Users\\joshpersi\\AppData\\Local\\Pandoc\\
C:\\Users\\joshpersi\\AppData\\Local\\Programs\\Microsoft VS Code\\bin
C:\\Users\\joshpersi\\AppData\\Local\\Programs\\Quarto\\bin
C:\\Program Files\\RStudio\\resources\\app\\bin\\postback

And here's what I get if I run Sys.getenv("PATH") in VS Code:

C:\\rtools43/x86_64-w64-mingw32.static.posix/bin
C:\\rtools43/usr/bin
C:\\Users\\joshpersi\\AppData\\Local\\r-miniconda
C:\\Users\\joshpersi\\AppData\\Local\\r-miniconda\\Library\\mingw-w64\\bin
C:\\Users\\joshpersi\\AppData\\Local\\r-miniconda\\Library\\usr\\bin
C:\\Users\\joshpersi\\AppData\\Local\\r-miniconda\\Library\\bin
C:\\Users\\joshpersi\\AppData\\Local\\r-miniconda\\Scripts
C:\\Users\\joshpersi\\AppData\\Local\\r-miniconda\\bin
C:\\Users\\joshpersi\\AppData\\Local\\r-miniconda\\condabin
C:\\Users\\joshpersi\\AppData\\Local\\Programs\\Git\\mingw64\\bin
C:\\Users\\joshpersi\\AppData\\Local\\Programs\\Git\\usr\\bin
C:\\Users\\joshpersi\\bin
C:\\Program Files (x86)\\Common Files\\Oracle\\Java\\javapath
C:\\Oracle\\product\\12.1\\bin
C:\\WINDOWS\\System32
C:\\WINDOWS
C:\\WINDOWS\\System32\\Wbem
C:\\WINDOWS\\System32\\Windowspowershell\\V1.0
C:\\WINDOWS\\System32\\Openssh
C:\\WINDOWS\\system32
C:\\WINDOWS
C:\\WINDOWS\\System32\\Wbem
C:\\WINDOWS\\System32\\WindowsPowerShell\\v1.0
C:\\WINDOWS\\System32\\OpenSSH
C:\\Program Files\\1E\\Client\\Extensibility\\NomadBranch
C:\\Program Files\\dotnet
C:\\Program Files\\Docker\\Docker\\resources\\bin
C:\\Users\\joshpersi\\AppData\\Local\\Programs\\Quarto\\bin
C:\\Users\\joshpersi\\AppData\\Local\\Microsoft\\WindowsApps
C:\\Users\\joshpersi\\AppData\\Local\\Programs\\Git\\cmd
C:\\Users\\joshpersi\\AppData\\Roaming\\TinyTeX\\bin\\win32
C:\\Users\\joshpersi\\AppData\\Local\\Pandoc
C:\\Users\\joshpersi\\AppData\\Local\\Programs\\Microsoft VS Code\\bin
C:\\Program Files (x86)\\Common Files\\Oracle\\Java\\javapath
C:\\Oracle\\product\\12.1\\bin
C:\\WINDOWS\\System32
C:\\WINDOWS
C:\\WINDOWS\\System32\\Wbem
C:\\WINDOWS\\System32\\Windowspowershell\\V1.0\\
C:\\WINDOWS\\System32\\Openssh\\
C:\\WINDOWS\\system32
C:\\WINDOWS
C:\\WINDOWS\\System32\\Wbem
C:\\WINDOWS\\System32\\WindowsPowerShell\\v1.0\\
C:\\WINDOWS\\System32\\OpenSSH\\
C:\\Program Files\\1E\\Client\\Extensibility\\NomadBranch
C:\\Program Files\\dotnet\\
C:\\Program Files\\Docker\\Docker\\resources\\bin
C:\\Users\\joshpersi\\AppData\\Local\\Programs\\Quarto\\bin
C:\\Users\\joshpersi\\AppData\\Local\\Microsoft\\WindowsApps
C:\\Users\\joshpersi\\AppData\\Local\\Programs\\Git\\cmd
C:\\Users\\joshpersi\\AppData\\Roaming\\TinyTeX\\bin\\win32
C:\\Users\\joshpersi\\AppData\\Local\\Pandoc\\
C:\\Users\\joshpersi\\AppData\\Local\\Programs\\Microsoft VS Code\\bin

If it's helpful, here are two VS code settings I've manually configured:

"r.rterm.windows": "C:\\Users\\persij\\AppData\\Local\\Programs\\R\\R-4.3.1\\bin\\x64\\R.exe",
"r.rpath.windows": "C:\\Users\\persij\\AppData\\Local\\Programs\\R\\R-4.3.1",

I tried to set the path environment in VS code to be the same as the one in RStudio but to no avail.

Please let me know if there's anything else I can do to help!

[lorenzwalthert]

Ok finding out how Rscript gets ob your PATH is not a pre-commit issue. Does the same problem happen when you open a terminal with Apple‘s terminal app and try to git commit in that repo? I don’t know how you installed R but seems not a common installation avenue…

[joshpersi]

Thanks for your patience - I now appreciate this isn't a precommit issue. I'll look into it a bit more on my own. Thanks for your help!

[lorenzwalthert]

I think if you use VS Code and a reasonable recent version of macOS, then your default shell is zsh (and there should be no difference to opening a new zsh shell with the Apple terminal app) and you can add the location of your R executable to the PATH by adding it to the respective profile file (there are a few different files that have different behaviour mainly based on how you start the shell).

Or you just install R again with an installation method that places the executable on the PATH, or you symlink the current executable in a place that is already on the PATH.

[skwde]

@lorenzwalthert I have the same issue, Rscript is not found.

I basically use two different conda environments, one for pre-commit and another one for R.
Of course Rscript is not available in the pre-commit environment.

To my understanding pre-commit will fetch what is needed on pre-commit run --all.
Why doesn't it fetch Rscript as well?
Isn't that the power of pre-commit to just specify a hook in pre-commit-config.yaml and forget about the setup?

[lorenzwalthert]

Ok. I don't think I accounted for the situation where you don’t have a global R executable but instead only one in a conda environment. In fact, I think this would require a change to the python pre-commit package because when you call git to commit, git calls pre-commit which calls Rscript on the PATH to activate renv to call the hooks. Temporary workaround is to have a global R installation you can fall back on that is on the PATH.

[lorenzwalthert]

How can you reliably detect if a directory uses a conda environment? And how to find the R executable?

[skwde]

Ok, the availability of Rscript (and R in general) is a dependency of pre-commit itself and not your hook (https://pre-commit.com/#r). So it makes actually sense to put this along side the pre-commit install (i.e. into the pre-commit environment).

So in that case it would be enough to look for Rscript in the environment where pre-commit is installed.

Regarding your question, does this https://pre-commit.com/#conda help?
I.e. pre-commit supports conda as long as a environment.yml is present.
Hmm I think it would be better though if one can specify a environment.yml to use. Mine are often called something like environment.<name>.yml.

[lorenzwalthert]

Ok, the availability of Rscript (and R in general) is a dependency of pre-commit itself and not your hook (https://pre-commit.com/#r)

In pre-commit, there are different levels of languages, r is implemented as a second level language. This means that a global R executable is required, but R package dependencies will be managed in an isolated fashion (with {renv}).

So it makes actually sense to put this along side the pre-commit install (i.e. into the pre-commit environment).

Usually though, pre-commit is installed globally (at least I haven't come across a project where pre-commit was listed as a dev requirement), and there is not necessarily a pre-commit conda or venv virtual environment associated with it.

Also note that for example in R, the {renv} environment that pre-commit uses is not same as the user created for his project (if any), but these are separate virtual environments. While most R projects don't use {renv}, some do, and pre-commit's {renv} environment is separate from it. So if you are using conda to manage your project's dependencies, it does not mean that pre-commit has to use conda as well. In fact if you install {precommit} into your conda environment, it is only useful as far as the R API goes, e.g. to precommit::install() or perform other operations from the R console interactively.

Regarding your question, does this https://pre-commit.com/#conda help?

If this repository's hooks were implemented with language: conda instead of language: r (see .pre-commit-hooks.yaml), then probably a global R installation would not be required, yes, because the Rscript executable would be bootstrapped as part of the conda environment. Unfortunately, I think a hook repo (like lorenzwalthert/precommit) can only contain an implementation of one language, so we had to create a second repo to do this.

Summa summarum, I think the easiest is just to install R globally so you can use it for pre-commit. Using the hooks from this repo won't install any packages in your global R package library, except maybe {renv}.