[BioC] problems when trying to use biomaRt

[Martin Morgan]

Hi Jenny --

On 03/17/2010 08:13 AM, Jenny Drnevich wrote:
> Hi Martin,
> 
>> now try debug(useDataset), and so on. Some functions might not be
>> exported from biomaRt's name space, and then you will need to
>> debug(biomaRt:::bmAttrFilter), for instance. When you do get to the
>> 'bottom' of the problem, it would be good to know what the variable
>> values are, e.g., some biomaRt functions seem to compose a variable
>> named 'request' that contains the string to be sent to biomaRt.
>>
>> >From Jenny's post, I'm not sure how successful this will be in the long
>> run, but it would be helpful to have a precise location of the problem.
> 
> Here are my variable values:
> 
> debug: tryCatchList(expr, classes, parentenv, handlers)
> Browse[2]> expr
> [1] "\n<MartRegistry>\n  <MartURLLocation database=\"ensembl_mart_57\"
> default=\"1\" displayName=\"ENSEMBL GENES 57 (SANGER UK)\"

hmm, a little too deep. Let's try

  trace(biomaRt:::bmRequest,
        quote(print(request)), quote(print("done")))
  useMart("ensembl", dataset="hsapiens_gene_ensembl")

My output is below, what does yours look like? Each of those http://...
should be executable in a web browser (watch for line endings -- these
should just be one line long). If the url doesn't load in the browser,
then it seems very likely that it is a BioMart issue (e.g., blocked
ports) and not an R issue, which is where your previous thread ended up.
If it does load in the browser, it might be interesting to try the
troublesome (i.e., last reported) url in a new R session with RCurl directly

  library(RCurl)
  getURL("http://...", ssl.verifypeer=TRUE)

perhaps one or several times

Martin

> trace(biomaRt:::bmRequest, quote(print(request)), quote(print("done")))
Tracing function "bmRequest" in package "biomaRt (not-exported)"
[1] "bmRequest"
> useMart("ensembl", dataset="hsapiens_gene_ensembl")
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"
Checking attributes ...Tracing bmRequest(request) on entry
[1]
"http://www.biomart.org:80/biomart/martservice?type=attributes&dataset=hsapiens_gene_ensembl&requestid=biomaRt&mart=ensembl&virtualSchema=default"
Tracing bmRequest(request) on exit
[1] "done"
 ok
Checking filters ...Tracing bmRequest(request) on entry
[1]
"http://www.biomart.org:80/biomart/martservice?type=filters&dataset=hsapiens_gene_ensembl&requestid=biomaRt&mart=ensembl&virtualSchema=default"
Tracing bmRequest(request) on exit
[1] "done"
 ok

-- 
Martin Morgan
Computational Biology / Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N.
PO Box 19024 Seattle, WA 98109

Location: Arnold Building M1 B861
Phone: (206) 667-2793