phenoscape / rphenoscape

R package to make phenotypic traits from the Phenoscape Knowledgebase available from within R.
https://rphenoscape.phenoscape.org/
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OntoTrace tests issue a warning when taxon not found #258

Closed hlapp closed 2 years ago

hlapp commented 2 years ago

It's likely that the (default?) behavior in response to unmatched taxa has changed. It seems the warning is suppressed under CRAN settings, but should be eliminated, either by removing the test, or expecting the warning.

Warning (test-ontotrace.R:11:3): Ontotrace basics
Could not find "Ictalurus TT" in the database. Please check your input.
Backtrace:
 1. testthat::expect_error(...)
      at test-ontotrace.R:11:2
 6. rphenoscape::get_ontotrace_data(...)
 7. rphenoscape:::apply_term_iris(...)
      at rphenoscape/R/ontotrace.R:92:4
 8. base::lapply(names, FUN = get_term_iri, as = as, exactOnly = exactOnly)
      at rphenoscape/R/ontotrace.R:142:2
 9. rphenoscape (local) FUN(X[[i]], ...)