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
(qiime2-2017.9) LSB4139A-4DM:~ msullivan$ R -e ".libPaths()"
Also, which command did you want me to include the
--verbose output from?
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())" > ~/.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!
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