Generating taxonomic dictionary error

[jamie-thompson]

What does this mean? Every other time I have used this it has worked fine.

Generating taxonomic dictionary ...
Invalid taxonomy
Unexpected Error : Invalid taxonomy

[ShixiangWang]

@jamie-thompson Could you provide a minimal reproducible example for debugging purposes?

[mrubenss]

Hi,

Thank you for your efforts in developing and maintaining phylotaR.

I'm also encountering an error at the taxonomic dictionary generation stage:

Generating taxonomic dictionary ...
Unexpected Error in recs[[x]]@prnt : 
  no applicable method for `@` applied to an object of class "NULL"

Error in stages_run(wd = wd, frm = 1, to = nstages, stgs_msg = stgs_msg) : 
  Unexpected Error in recs[[x]]@prnt : 
  no applicable method for `@` applied to an object of class "NULL"

This issue arises with txid8509 (and some other related clades). I've tested other txids, and they work fine. Could this be related to a problem with the NCBI taxonomy database, or is there something else I should check?

Any guidance would be greatly appreciated. Thanks again!

Best regards,
Matheus R Barbosa

[ShixiangWang]

Hi @mrubenss , thanks for your report and details, especially the clue of txid8509 for reproducing the error. Recently I am quite busy, I will reproduce this with provided info and try resolving the issue in about a week. :)