renv::load() duplicating paths in the PATH environment variable

[lucygarner]

Hi,

renv::load() appears to be duplicating some of the paths in the PATH environment variable.

In my R project, I run the following prior to loading renv.
renv:::renv_envvar_get("PATH")

[1] "/Users/lucy/Library/r-miniconda/condabin:/Users/lucy/Documents/2022/devel/10x/R/.conda_env/bin:/usr/local/bin:/usr/bin:/bin:/usr/sbin:/sbin:/Library/TeX/texbin:/opt/X11/bin:/Library/Apple/usr/bin:/Users/lucy/Applications/quarto/bin:/usr/texbin:/Applications/RStudio.app/Contents/MacOS"

Then I run renv::load() and renv:::renv_envvar_get("PATH").

[1] "/Users/lucy/Library/r-miniconda/condabin:/Users/lucy/Documents/2022/devel/10x/R/.conda_env/bin:/usr/local/bin:/usr/bin:/bin:/usr/sbin:/sbin:/Library/Apple/usr/bin:/opt/X11/bin:/Library/TeX/texbin:/Users/lucy/Library/r-miniconda/condabin:/Users/lucy/Documents/2022/devel/10x/R/.conda_env/bin:/Users/lucy/Applications/quarto/bin:/usr/texbin:/Applications/RStudio.app/Contents/MacOS"

I have RENV_AUTOLOADER_ENABLED = FALSE in my .Renviron.

Best wishes,
Lucy

[kevinushey]

IIUC these are the two path entries getting duplicated:

/Users/lucy/Library/r-miniconda/condabin
/Users/lucy/Documents/2022/devel/10x/R/.conda_env/bin

Do you know where these path entries are originally being set?

The output of the following might be helpful:

trace(Sys.setenv, quote({
  dots <- list(...)
  if ("PATH" %in% names(dots)) {
    print(rlang::trace_back())
  }
}), print = FALSE)
renv::load()

[lucygarner]

Yes correct.

trace(Sys.setenv, quote({
  dots <- list(...)
  if ("PATH" %in% names(dots)) {
    print(rlang::trace_back())
  }
}), print = FALSE)

Tracing function "Sys.setenv" in package "base"
[1] "Sys.setenv"

Is that what you wanted me to run?

[kevinushey]

Please also run renv::load() after running that code.

[lucygarner]

I had to run renv::load() prior to trace since otherwise I get an error that there is no package called rlang.

So I ran:

renv::load()
trace(Sys.setenv, quote({
    dots <- list(...)
    if ("PATH" %in% names(dots)) {
        print(rlang::trace_back())
    }
}), print = FALSE)
renv::load()

And got the following:

    ▆
 1. └─renv::load()
 2.   └─renv:::renv_load_path(project)
 3.     └─base::Sys.setenv(PATH = paste(mix, collapse = .Platform$path.sep))
    ▆
 1. └─renv::load()
 2.   └─renv:::renv_load_python(project, lockfile$Python)
 3.     └─renv:::renv_envvar_prepend("PATH", bindir)
 4.       └─renv:::renv_envvar_modify(envvar, value, TRUE)
 5.         ├─base::do.call(Sys.setenv, as.list(new))
 6.         └─base (local) `<fnctnWtT>`(PATH = "/Users/lucy/Documents/2022/devel/10x/R/.conda_env/bin:/usr/local/bin:/usr/bin:/bin:/usr/sbin:/sbin:/Library/Apple/usr/bin:/opt/X11/bin:/Library/TeX/texbin:/Users/lucy/Library/r-miniconda/condabin:/Users/lucy/Documents/2022/devel/10x/R/.conda_env/bin:/Users/lucy/Applications/quarto/bin:/usr/texbin:/Applications/RStudio.app/Contents/MacOS")
    ▆
 1. └─renv::load()
 2.   └─renv:::renv_load_python(project, lockfile$Python)
 3.     └─renv:::renv_envvar_prepend("PATH", dirname(conda))
 4.       └─renv:::renv_envvar_modify(envvar, value, TRUE)
 5.         ├─base::do.call(Sys.setenv, as.list(new))
 6.         └─base (local) `<fnctnWtT>`(PATH = "/Users/lucy/Library/r-miniconda/condabin:/Users/lucy/Documents/2022/devel/10x/R/.conda_env/bin:/usr/local/bin:/usr/bin:/bin:/usr/sbin:/sbin:/Library/Apple/usr/bin:/opt/X11/bin:/Library/TeX/texbin:/Users/lucy/Library/r-miniconda/condabin:/Users/lucy/Documents/2022/devel/10x/R/.conda_env/bin:/Users/lucy/Applications/quarto/bin:/usr/texbin:/Applications/RStudio.app/Contents/MacOS")

[kevinushey]

Thanks! I believe this will be fixed via 97f6620.

[lucygarner]

I gave it a go. This doesn't seem to have fixed it unfortunately.

packageVersion("renv")

[1] ‘0.16.0.15’

Sys.getenv("PATH")

[1] "/Users/lucy/Library/r-miniconda/condabin:/Users/lucy/Documents/2022/devel/10x/R/.conda_env/bin:/usr/local/bin:/usr/bin:/bin:/usr/sbin:/sbin:/Library/TeX/texbin:/opt/X11/bin:/Library/Apple/usr/bin:/Users/lucy/Applications/quarto/bin:/usr/texbin:/Applications/RStudio.app/Contents/MacOS"

renv::load()

* Project '~/Documents/2022/devel/10x/R' loaded. [renv 0.16.0-15]

Sys.getenv("PATH")

[1] "/Users/lucy/Library/r-miniconda/condabin:/Users/lucy/Documents/2022/devel/10x/R/.conda_env/bin:/usr/local/bin:/usr/bin:/bin:/usr/sbin:/sbin:/Library/Apple/usr/bin:/opt/X11/bin:/Library/TeX/texbin:/Users/lucy/Library/r-miniconda/condabin:/Users/lucy/Documents/2022/devel/10x/R/.conda_env/bin:/Users/lucy/Applications/quarto/bin:/usr/texbin:/Applications/RStudio.app/Contents/MacOS"

The following paths are still duplicated:
/Users/lucy/Documents/2022/devel/10x/R/.conda_env/bin
/Users/lucy/Library/r-miniconda/condabin

Best wishes,
Lucy

[kevinushey]

Thanks -- I'll have to take another look and see if I can figure out why...

[hadley]

I'm still seeing this too:

Sys.setenv("PATH" = "/opt/homebrew/bin/:/bin")
renv::scaffold()
#> * renv infrastructure has been generated for project "/private/tmp/RtmpQVJX13/reprex-13dda40d69662-odd-tuna".
strsplit(Sys.getenv("PATH")[[1]], ":")
#> [[1]]
#> [1] "/opt/homebrew/bin/" "/bin"
renv::load()
strsplit(Sys.getenv("PATH")[[1]], ":")
#> [[1]]
#> [1] "/opt/homebrew/bin/" "/opt/homebrew/bin/" "/bin"

^{Created on 2023-05-11 with reprex v2.0.2}