I am attempting to run the differential_abundance.py script and I continue to receive this error:

burrito.util.ApplicationError: R library not installed:


Library optparse not found.

To install, open R and run the command:

If you already have the optparse package installed in a local directory,
please store the path to that directory in an environment variable
called "R_LIBRARY_PATH". This may be necessary if you are running
QIIME on a cluster, and the cluster instances of R don't know about
your local R libraries. If you don't know your R library paths, you
can list them by opening R and running with the command, ".libPaths()".
The current R instance knows about these paths:

I have the latest version of R installed and I have already installed optparse and getopt in R and know they are fully functional. When .libPaths() is run in R I receive:

[1] "/Library/Frameworks/R.framework/Versions/3.4/Resources/library"

I have already attempted to move optparse into the known path and I have attempted to move the directory into that pathway but I receive the same error every time. What do I need to do?

Hi @Kitkat14! differential_abundance.py is a QIIME 1 script. Can you please post your question on the QIIME 1 Forum? This forum is reserved for QIIME 2 support. Thanks!

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