Anyone having problems with rentrez's latest release?

Package Use Questions
1

Hi all,

I am trying to get to the bottom of a bug reported for rentrez (the ropensci package for the EUtils api): https://github.com/ropensci/rentrez/issues/29

I can’t reproduce the bug on any of the NCBI databases (or, it seems, get any more information from the bug’s reporter). I’m hesitant to close the issue while it might be effecting the package, so thought I’d check in here and see if anyone using rentrez or fulltext (which uses the function in question) has run into problems in the last couple of weeks?

Cheers,
David

1 Like
2

hi @dwinter - I"ll have a look and see if I can replicate the error

S

3

@dwinter i thought older versions of jsonlite or httr might cause that problem, but to no avail thus far

perhaps require that the user have a certain version or greater of jsonlite or httr that you know work, then when user installs they need to have those versions.

4

Thanks @sckott, requiring a package version seems like a good idea, I’ve only developed it alongside pretty recent versions of those packages.

For anyone else that has rentrez at their fingertips and wants to help out, here’s a shorti-ish way to hit the summary endpoint for every database (almost all of them have human records):

f <- function(db){
   db_id <- entrez_search(db=db, term="Homo", retmax=1)
   print(db)
   entrez_summary(db=db, id=db_id$id)
} 
dbs <- entrez_dbs()
sapply(dbs, f)

If that chokes on any database in your system I’d like to know about it :smile: