What does this warning mean from RISmed?

Question

I just opened a package for R to get an abstract from pubmed, which is great. But while receiving the data, I get a warning message:

R2009 <- pubmed.search("R+package[tiab]+AND+2009/01/01[dp]:2009/12/31[dp]",dest="temp",format="ris") Warning message: In download.file(e.query, dest = temp, quiet = TRUE) : downloaded length 2565 != reported length 200 > nrow(as.data.frame(R2009)) [1] 82 

I manually searched in pubmed and found the same number of articles (82).

I wonder what the warning message means, is there something you need to fix? Thanks.

Answer 1

This means that any pubmed.search() file was loaded, it was 2565 long (bytes, what do I assume?), But the length reported during the connection negotiations was only 200 bytes.

I don’t know that this is good, but you can imagine a situation where the data file containing the loaded search results is generated "on the fly" and the final file size is unknown, so the size of the dummy file is first, but the actual download stream goes beyond this size . You can visually see this when using the browser from time to time - sometimes the browser does not know how large the load is, so the time until completion is not reported, just the amount of data downloaded.

Answer 2

200 is the HTTP status value for OK, not the length of the downloaded file. The Alert Warning identifies a problem with the download.file function and depends on the method that it uses internally to execute the download request.