Hi,

I installed qiime 1 via bioconda and am trying to run the script differential_abundance.py. This has dependencies with some R packages like biom format, which is giving me the following error: I ran: differential_abundance.py -i otu_table_L2.biom -a DESeq2_nbinom -m mappingfile.txt -c Disease -x A -y B -o differential_abundance_L2

ERROR: Library biom not found.

To install, open R and run the command: install.packages("biom")

If you already have the biom 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/pbanerjee/anaconda3/envs/qiime1/lib/R/library]

Warning message: In librarylib.name, character.only = TRUE, logical.return = TRUE, : there is no package called ‘biom’

I checked my library, it has a package named biomformat, but nothing named biom, as that seem to be deprecated package in R.

Anyone else faced similar problem and knows how to solve this?

Thanks. Payal