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I am trying to run a compiled program (idemp - https://github.com/yhwu/idemp ) from a script in R Studio. I just installed the latest version of R studio and R on November 15, 2021 four days ago.

I followed the directions on the idemp page to download and compile idemp within Ubuntu (Windows Subsystem for Linux) in Windows 10. I can see the files in the correct path for idemp.

R Studio doesn't seem to run anything. Here is the code I am trying:

idemp <- "C:/Users/User/Downloads/idemp-master/idemp"
system2(idemp)

There is no output to the RStudio console.

Then I set up the arguments and tried to run with arguments and again, there is no output to the RStudio console and the 'running' stop sign doesn't appear at the top right corner of the RStudio console.

flags = paste("-b", barcode, "-I1", I1, "-R1", R1, "-R2", R2, "-o", demultiplexed_path)
system2(idemp, args = flags)

Can anyone suggest how I can get RStudio to run idemp?

I know that system2() will work because it works in this script using a different program as intended.

neuron
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aminards
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1 Answers1

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I ended up figuring out my issue. I think system2() is trying to run a Windows program. Idemp is a command-line program.
I got this to work using the following:

system('bash -c idemp')
aminards
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