[BioC] function pubmed and large requests

[Kimpel, Mark W]

I am having problems with R blowing up (Windows error window) when
trying to retrieve large amounts of data from PubMed using the function
"pubmed". I had originally thought this might be due to inadequate
memory, but increasing the memory allocated to R to 4 GB did not solve
the problem (thank you, however, to those whose suggestions allowed me
to try this).

The process works well up to about 380 pubmed id's. I reviewed the NCBI
policy on such requests and have been running them at night as
suggested. I am nowhere near the set limit of 5,000 requests per day per
user.

One possibility would be to simply break up the request into smaller
chunks, but for my purposes I would like just one resultant data object.
I did try breaking up my request into smaller chunks, which works, but
cannot figure out if it is possible to somehow merge the resultant
list-objects into one.

Any help you can give this struggling biologist would be most
appreciated!

Thanks,

Mark

Mark W. Kimpel MD
Indiana U. School of Medicine

 

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