.Rprofile and .libPaths with Dada2 exit code -11

User Support
1

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

3

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!