[BioC] biomaRt proxy issues

[Bill Raynor]

"James W. MacDonald" <jmacdon at uw.edu> wrote:
> Hi Bill,
> 
> I am not sure you need to pass anything to listMarts() unless you aren't 
> sure what mart to use. It seems to me that the critical function would 
> be getBM() to which you can pass an already formed curl object.
> 
> Can you do something like this?
> 
> mart <- useMart("ensembl","hsapiens_gene_ensembl")
> curl <- getCurlHandle()
> curlSetOpt(.opts = 
> list(proxy="xxx.yyy.com:8080",proxyuserpwd="myid:mypassword"),curl = curl)
> 
> getBM(c("entrezgene","uniprot_genename"), "entrezgene", 
> c(1,10,100,1000), mart, curl)
> 
> 
> Best,
> 
> Jim
> 
> 
> 
> On 5/23/2014 12:00 PM, Bill Raynor [guest] wrote:
>> biomart does not seem to honor the http_proxy and http_proxy_user
>> settings. How can I pass Rcurl options into it.
>> 
>> if I debug(listMart) and step through the function, it is attempting to
>> request "http://www.biomart.org:80/biomart/martservice?type=registry&requestid=biomaRt",
>> however bmRequest returns the error page from our proxy.
>> 
>> if I do a
>> curl = getCurlHandle()
>> curlSetOpt( .opts =
>> list(proxy="xxx.yyy.com:8080",proxyuserpwd="myid:mypassword"),curl = curl)
>>  
>> getURL("http://www.biomart.org/biomart/martservice?type=registry&requestid=bioma
>> t", curl=curl)
>> 
>> I get the same output that I would get via internet explorer.
>> 
>> So how do I get biomaRt to work through a proxy that requires authentication?
>> 
>> 
>> 
>>   -- output of sessionInfo():
>> 
>>> sessionInfo()
>> R version 3.1.0 (2014-04-10)
>> Platform: x86_64-w64-mingw32/x64 (64-bit)
>> 
>> locale:
>> [1] LC_COLLATE=English_United States.1252  LC_CTYPE=English_United States.1252
>> [3] LC_MONETARY=English_United States.1252 LC_NUMERIC=C
>> [5] LC_TIME=English_United States.1252
>> 
>> attached base packages:
>> [1] grDevices datasets  splines   graphics  utils     grid      stats     methods   base
>> 
>> other attached packages:
>>   [1] biomaRt_2.20.0  RCurl_1.95-4.1  bitops_1.0-6    graph_1.42.0   
>> R2HTML_2.2.1    Hmisc_3.14-4
>>   [7] Formula_1.1-1   survival_2.37-7 lattice_0.20-29 foreign_0.8-61  ggplot2_1.0.0
>> 
>> loaded via a namespace (and not attached):
>>   [1] AnnotationDbi_1.26.0 Biobase_2.24.0       BiocGenerics_0.10.0 
>> cluster_1.15.2       colorspace_1.2-4
>>   [6] DBI_0.2-7            digest_0.6.4         GenomeInfoDb_1.0.2  
>> gtable_0.1.2         IRanges_1.22.7
>> [11] latticeExtra_0.6-26  MASS_7.3-33          munsell_0.4.2       
>> parallel_3.1.0       plyr_1.8.1
>> [16] proto_0.3-10         RColorBrewer_1.0-5   Rcpp_0.11.1         
>> reshape2_1.4         RSQLite_0.11.4
>> [21] scales_0.2.4         stats4_3.1.0         stringr_0.6.2       
>> tools_3.1.0          XML_3.98-1.1
>> 
>> --
>> Sent via the guest posting facility at bioconductor.org.
>> 
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Thanks Jim, 
I'm away from the office & proxy server till teusday. I will try that then.