[BioC] biomaRt and hapmap "virtualSchema" parameter mis-specification

Andrew McDavid amcdavid at fhcrc.org
Fri Aug 20 21:46:23 CEST 2010

It looks like biomaRt is passing mal-formed queries to biomart.org for hapmap.  Following instructions I found at https://stat.ethz.ch/pipermail/bioconductor/2010-March/032297.html I traced the urls that biomaRt is using.

> trace(biomaRt:::bmRequest, quote(print(request)), quote(print("done")))
Tracing function "bmRequest" in package "biomaRt (not-exported)"
[1] "bmRequest"

> mart = useMart("HapMap_rel27")
Tracing bmRequest(paste("http://", host, ":", port, path, "?type=registry&requestid=biomaRt",  .... on entry 
[1] "http://www.biomart.org:80/biomart/martservice?type=registry&requestid=biomaRt"
Tracing bmRequest(paste("http://", host, ":", port, path, "?type=registry&requestid=biomaRt",  .... on exit 
[1] "done"
> mart = useDataset("hm27_variation", mart)
Checking attributes ...Tracing bmRequest(request) on entry 
[1] "http://www.biomart.org:80/biomart/martservice?type=attributes&dataset=hm27_variation&requestid=biomaRt&mart=HapMap_rel27&virtualSchema=rel27_NCBI_Build36"
Tracing bmRequest(request) on exit 
[1] "done"
Error in bmAttrFilt("attributes", mart) : 
  biomaRt error: looks like we're connecting to incompatible version of BioMart suite.

When I change the above url to http://www.biomart.org:80/biomart/martservice?type=attributes&dataset=hm27_variation&requestid=biomaRt&mart=HapMap_rel27&virtualSchema=default
and paste into a browser, the server returns some convincing-looking csv output about the available attributes.  I'm not overly-motivated to teach myself the internals of biomaRt right now, so if someone with more experience with the package wants to take a stab at fixing this...

Andrew McDavid
Systems Analyst
amcdavid at fhcrc.org

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