Error: report with compoundsConsensus fails

[LeonSaal]

Hi Rick,

I was trying the workflow with:

...
compounds = consensus(compoundsLibrary, compoundsMetFrag)
...
fGroupsSusp = screenSuspects(fGroups, suspects)

# annotate suspects 
fGroupsSusp <-
  annotateSuspects(
    fGroupsSusp,
    formulas = formulas,
    compounds = compounds,
    MSPeakLists = mslists,
    IDFile = "idlevelrules.yml"
  )

# reporting
report(
  fGroupsSusp,
  MSPeakLists =  mslists,
  formulas = formulas,
  compounds = compounds
)

...but generating the report failed with the following error:

Generating report parts: Feature groups... Features... MS peak lists... Formulas... Compounds... 
Quitting from lines 38-370 [unnamed-chunk-12] (./details.Rmd)

Quitting from lines 38-370 [unnamed-chunk-3] (./details.Rmd)
Error in `if (tolower(db) == "chemspider") ...`:
! missing value where TRUE/FALSE needed
Backtrace:
  1. bslib::layout_column_wrap(...)
 20. utils$genCompoundsTable()
 21. patRoon:::makeAnnReactable(...)
 22. patRoon:::makeReactable(...)
 23. reactable::reactable(...)
     ...
 27. reactable (local) FUN(X[[i]], ...)
 28. reactable:::callFunc(details, index, key)
 30. patRoon (local) `<fn>`(7L)
 33. patRoon (local) detailsTabFunc(index)
 35. patRoon:::makeDBIdentLink(db, ct[[col]])
Warning message:
call dbDisconnect() when finished working with a connection

with compoundsMetFrag everything worked as expected.

Kind regards,

Leon

[rickhelmus]

Hi @LeonSaal ,

Sorry for my slow response, your issue got buried under while being on holidays... Anyway, I just pushed a small fix for this. Feel free to re-open if there are still issues.

Thanks,
Rick