I am attempting to run the differential_abundance.py script and I continue to receive this error:
burrito.util.ApplicationError: R library not installed:
stdout:
stderr:
Library optparse not found.
To install, open R and run the command:
install.packages("optparse")
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:
[/Users/bioresearch/miniconda3/envs/qiime2/lib/R/library]
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?