When I am using the divergence_stratigraphy function with ds.value = FALSE, as follows:
result <- divergence_stratigraphy( query_file = query_file, subject_file = subject_file, eval = "1E-5", ortho_detection = "RBH", comp_cores = 1, ds.values = FALSE, quiet = TRUE, clean_folders = TRUE )

I am getting the following error:
Error in dNdS_tbl[, list(dNdS, query_id)]: ! Can't subset columns with list(dNdS, query_id). ✖ list(dNdS, query_id)must be logical, numeric, or character, not a list. Runrlang::last_trace() to see where the error occurred.

rlang::last_trace() <error/vctrs_error_subscript_type> Error indNdS_tbl[, list(dNdS, query_id)]: ! Can't subset columns with list(dNdS, query_id). ✖ list(dNdS, query_id)` must be logical, numeric, or character, not a list.

Backtrace:
▆

1. ├─orthologr::divergence_stratigraphy(...)
2. │ ├─stats::na.omit(dNdS_tbl[, list(dNdS, query_id)])
3. │ ├─dNdS_tbl[, list(dNdS, query_id)]
4. │ └─tibble:::[.tbl_df(dNdS_tbl, , list(dNdS, query_id))
5. │ └─tibble:::vectbl_as_col_location(...)
6. │ ├─tibble:::subclass_col_index_errors(...)
7. │ │ └─base::withCallingHandlers(...)
8. │ └─vctrs::vec_as_location(j, n, names, missing = "error", call = call)
9. └─rlang::cnd_signal(x)
   `

I think this is an issue with data.table way of subsetting and might be fixed with dNdS_tbl[, .(dNdS, query_id)] instead of the list() method.