Terminal and R won't work together

RStudio Cloud
#1

I have installed a python program using the Terminal Tab. I then added the path to the installed library to the environment PATH; and checked that I can find the installed program

python3 -m pip install --user --upgrade cutadapt
PATH=$HOME/bin:"$PATH"
which cutadapt

And that works. The problem is when I try to use that program through an R script

system2("which", args = "cutadapt")

then it can't find it.

Any best practices out there to use unix installed programs with Rstudio cloud?

#2

Can you check which shell the Rstudio cloud is using? Make sure you use the same one as Rstudio.

Run

system2("echo", "$SHELL")

#3

Thanks for the reply - The result is interesting: running echo $SHELL from the Terminal Tab (within Rstudio cloud) returns /bin/bash;
system2("echo", "$SHELL") returns nothing

#4

Do you have a .zshrc or any type of rc file that contains a path export?

Can you run any commands through system2?

Say system2("whoami")

#5

Hi there,

  • In some of my Rstudiocloud projects I have a .bash_profile with a PATH variable, but not in other projects. It does not seem to make a difference on whether system2 returns the same paths that directly looking at the terminal.
  • I just run system2("whoami") and it returned
rstudio-user

I looked at the environment vars in both cases - I used
system2("printenv")
and
printenv from the terminal tab in Rstudiocloud.
I made them into a df and these are the entries that are different between the two

image
image939×146 13.2 KB

#6

We have clearly found the problem, the two environments are completely different, now we just need to resolve it.

Can you run

system2("export", ".bash_profile")

Where in the profile you have the path for the binary cutadapt?

#7

Cool! The path sits in a .bash_profile file I created in the project root (/cloud/project/.bash_profile), but system2("export", ".bash_profile") does not work.

#8

Sorry, I mean place the following statement

export PATH="path to cutadapt your-dir:$PATH"
at the last line of your .bash_profile and run system2("source", "path_to_bash_profile/.bash_profile")