Hi Andrew,

Which version of biomaRt are you using?
This should be fixed in the devel version of biomaRt which you can download
from here:

http://www.bioconductor.org/packages/devel/bioc/html/biomaRt.html

Let me know if this doesn't work.

Cheers,
Steffen


On Fri, Aug 20, 2010 at 12:46 PM, Andrew McDavid <amcdavid@fhcrc.org> wrote:

> Hello,
> 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@fhcrc.org
> 206.667.6407
>
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