Hi thank you for this great tool
I also had the same error and the package was initially installed from github, but I had to reinstall it from github again, still get the error even if installed form github
'Error in parse_taxonomy(taxonomy) :
Table does not match expected format. ie does not have columns Feature.ID and Taxon"
Skipping install of 'qiime2R' from a github remote, the SHA1 (2a3cee18) has not changed since last install.
force = TRUE to force installation
remotes::install_github("jbisanz/qiime2R", force =TRUE)