Closed LeonSaal closed 1 week ago
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.
compoundsMetFrag
Kind regards,
Leon
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
Hi Rick,
I was trying the workflow with:
...but generating the report failed with the following error:
with
compoundsMetFrag
everything worked as expected.Kind regards,
Leon