[BioC] biomaRt proxy issues

Sun Jun 29 15:24:53 CEST 2014

Enrico,
Glad it helped. Another trick that may be useful is the "no-proxy" option. (E.g. RCytoscape)Curl respects that, too.  I gather that most of the developers don't have to fight corporate firewalls in all their manifold forms, or have cooperative MIS staffs.

Sent from my iPhone

On Jun 27, 2014, at 4:11 AM, "Enrico Ferrero" <enricoferrero86 at gmail.com<mailto:enricoferrero86 at gmail.com>> wrote:

Bill,

Thanks very much for this. I had proxy issues with biomaRt for the longest time and they're finally over.
Can the biomaRt maintainers please update the package vignette? Proxy issues are mentioned, but a non-working solution is currently provided instead of this one.

Cheers,

On 28 May 2014 21:45, Raynor, Bill <Bill.Raynor at kcc.com<mailto:Bill.Raynor at kcc.com>> wrote:
Jim,

Yes and No, the code failed on the useMart statement, which attempts to establish a connection through the firewall.

However, a google search on "RCurl Proxy authentication" turned up a passing mention to "RCurlOptions", which led me into the RCurl docs, where it is revealed that RCurl will look at that option automatically.

So this works:

options(RCurlOptions = list(proxy="uscache.kcc.com:80<http://uscache.kcc.com:80>",proxyuserpwd="------:-------"))
# getOption("RCurlOptions")  # just checking
getURLContent("http://www.omegahat.org")
mart <- useMart("ensembl","hsapiens_gene_ensembl")

Regards,
Bill

-----Original Message-----
From: James W. MacDonald [mailto:jmacdon at uw.edu<mailto:jmacdon at uw.edu>]
Sent: Friday, May 23, 2014 1:28 PM
To: Bill Raynor [guest]
Cc: bioconductor at r-project.org<mailto:bioconductor at r-project.org>; Raynor, Bill
Subject: Re: [BioC] biomaRt proxy issues

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<http://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<http://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
>
> --
> Sent via the guest posting facility at bioconductor.org<http://bioconductor.org>.
>
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--
James W. MacDonald, M.S.
Biostatistician
University of Washington
Environmental and Occupational Health Sciences
4225 Roosevelt Way NE, # 100
Seattle WA 98105-6099

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Enrico Ferrero
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