bash code in Rmd chunks behaving differently than bash in terminal

Question

Take two simple commands executed in an Rmd file.

pwd works fine
but when I try to run conda list I get an error that conda: command not found, even though conda list executes fine in my terminal.

```{bash}
pwd
```

```{bash}
conda list
```

What would be the process to make conda findable in an Rmd chunk?

The symptoms suggest that you have a different `PATH` in the environment where it doesn't work, but your question doesn't contain any details about why or how it's different. We have a ton of `PATH` troubleshooting questions so I'm simply voting to close this as lacking debugging details and/or search effort. Starting your R environment from a place where the `PATH` is correct is probably the simplest immediate workaround. — tripleee, May 31 '22 at 17:15
@GoinOff adding the full path was successful. Thank you. /Users/jpowers4/miniconda3/bin/conda list — Joe, May 31 '22 at 17:30
Possible duplicate of https://stackoverflow.com/questions/135688/setting-environment-variables-on-os-x — tripleee, Jun 01 '22 at 03:16

score 0 · Answer 1 · edited May 31 '22 at 18:07

0

This issue can be solved in two ways both alluded to in comments:

Adding the full path to conda

/Users/jpowers4/miniconda3/bin/conda list

Adding the "full path to conda" to my PATH variable in R

old_path <- Sys.getenv("PATH")

Sys.setenv(PATH = paste(old_path, "/Users/jpowers4/miniconda3/bin/", sep = ":"))

Then conda list will execute

conda list

edited May 31 '22 at 18:07

John Kugelman

answered May 31 '22 at 17:38

Joe

1 Answers1