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&reque stid=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&dat aset=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/marts ervice?type=attributes&dataset=hm27_variation&requestid=biomaRt&mart=H apMap_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 206.667.6407

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&requesti d=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&datase t=hm27_variation&requestid=biomaRt&mart=HapMap_rel27&virtualSchema=rel 27_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&datase t=hm27_variation&requestid=biomaRt&mart=HapMap_rel27&virtualSchema=def ault > 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 > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > [[alternative HTML version deleted]]