[BioC] biomaRt proxy issues

[Bill Raynor [guest]]

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=biomaRt", 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 

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