Updated rentrez package today and having issues with run

gadepallivs commented 9 years ago

UPDATE I think you can delete this issue. I re-installed the latest developer version and it solved the issue.

library(devtools)
install_github("ropensci/rentrez")

Hi David, I updated rentrez package today. When I run my code, I am running into some issues. Pubmed search used to show Qeury Translation. I don't see that now, when I do a summary of the pubmed_search

summary(pubmed_search)
       Length Class               Mode       
ids    18     -none-              character  
count   1     -none-              character  
retmax  1     -none-              character  
file    1     XMLInternalDocument externalptr

new error I noticed with entrex_query to explicit the db name. It was not an issue earlier. earlier code gives an error

links <- entrez_link( dbfrom = "pubmed", id = pubmed_search$ids, cmd = "prlinks" )
Error in make_entrez_query("elink", db = db, dbfrom = dbfrom, config = config,  : 
  argument "db" is missing, with no default

added db = "pmc"

links <- entrez_link(db = "pmc", dbfrom = "pubmed", id = pubmed_search$ids, cmd = "prlinks" )
links
elink result with ids from 0 databases:
character(0)

gadepallivs commented 9 years ago

Hi david, Error in as.vector(x, "character") : cannot coerce type 'externalptr' to vector of type 'character' Have you came across this error ? Is it related to parse_pubmed_xml ? I get this error when I try to output the table generated from parse_pubmed_xml to RenderDataTable in Rshiny

dwinter commented 9 years ago

Hi @Monty9 -- as you worked out the first error came from accidently downgrading rentrez to the current CRAN version. I hope to get the goodies in the development version onto CRAN this week so that will be fine.

Can you start a new issue for you new error? And provide a reproducably example and the output of traceback() run after the error?

ropensci / rentrez

Updated rentrez package today and having issues with run #62