.Rprofile and .libPaths with Dada2 exit code -11

Hi @ebolyen,
In the exit code -11 and .Rprofile thread, I accidentally forgot to include all the .Rprofile info. I also included the .libPaths output you requested.

LSB4139A-4DM:~ msullivan$ cat ~/.Rprofile
.libPaths(.libPaths()[2])LSB4139A-4DM:~ msullivan$ 
(qiime2-2017.9) LSB4139A-4DM:~ msullivan$ R -e ".libPaths()"
> .libPaths()
[1] "/Users/msullivan/Library/R/3.3/library"                      
[2] "/Users/msullivan/miniconda3/envs/qiime2-2017.9/lib/R/library"
> 
> 

Also, which command did you want me to include the --verbose output from?

Thanks,
Madsen

Thanks @MSullivan!

Based on the .libPaths() output, it looks like the instructions should still generally work. I think what might be wrong is your file doesn’t seem to end with a newline. I’m not sure how much that matters to R, but just in case, run the following:

echo ".libPaths(.libPaths()[2])" > ~/.Rprofile

That should dump exactly one line (with a newline character) overwriting whatever’s in .Rprofile at the moment.

Let me know if that helps, otherwise, if you could post the result of running --verbose on the dada2 denoise command that is currently failing, that would be great!

This topic was automatically closed 31 days after the last reply. New replies are no longer allowed.