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ropensci / rentrez

talk with NCBI entrez using R
https://docs.ropensci.org/rentrez
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Error in ans[[1]] : subscript out of bounds #84

Closed Andreas-Bio closed 7 years ago

Andreas-Bio commented 8 years ago

What is happening?

snail_coi <- entrez_search(db="nuccore", term="COI[Gene] AND Gastropoda[ORGN]", use_history=TRUE) Error in ans[[1]] : subscript out of bounds

query <- "Gastropoda[Organism] AND COI[Gene]" entrez_search(db="nuccore", term=query, use_history=TRUE,retmode="json") Error in if (nchar(x$QueryTranslation) > 50) { : argument has length 0

It's completely broken :(

Andreas-Bio commented 8 years ago

It turns out that nuccore is down! The world is ending!

http://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=nucleotide&term=biomol+trna[prop]

Search Backend failed: Database is not supported: nuccore
htc502 commented 8 years ago

Hi @dwinter ,I think it's better to add an extra feature that is able to notify the user when the database is down. error information like this is quite misleading...

dwinter commented 8 years ago

Hi @htc502 -- I agree, unfortunately this is one of those "Happy families are all alike; every unhappy family is unhappy in its own way" situations. There are many different ways in which the NCBI might return "intermittent" errors and Eutils doesn't flag them in a consistent way.

If there are specific examples we can catch we should. In the mean time we should include a not about intermittent outages in vignette, encouring bug reports by making the point that sometimes it will fix itself before we look at it