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@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 > ",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@uw.edu] > Sent: Friday, May 23, 2014 1:28 PM > To: Bill Raynor [guest] > Cc: bioconductor@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",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&requesti d=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=b iomaRt", > 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. > > > > _______________________________________________ > > Bioconductor mailing list > > Bioconductor@r-project.org > > https://stat.ethz.ch/mailman/listinfo/bioconductor > > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > > -- > James W. MacDonald, M.S. > Biostatistician > University of Washington > Environmental and Occupational Health Sciences > 4225 Roosevelt Way NE, # 100 > Seattle WA 98105-6099 > > > ________________________________ > > > This e-mail is intended for the use of the addressee(s) only and may > contain privileged, confidential, or proprietary information that is exempt > from disclosure under law. If you have received this message in error, > please inform us promptly by reply e-mail, then delete the e-mail and > destroy any printed copy. Thank you. > > _______________________________________________ > Bioconductor mailing list > Bioconductor@r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > -- Enrico Ferrero [[alternative HTML version deleted]]

Thanks Enrico, I'll update the biomaRt vignette with this working code. Best, Steffen On Fri, Jun 27, 2014 at 2:10 AM, Enrico Ferrero <enricoferrero86@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@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 > > ",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@uw.edu] > > Sent: Friday, May 23, 2014 1:28 PM > > To: Bill Raynor [guest] > > Cc: bioconductor@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",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&requesti d=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=b iomaRt > ", > > 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. > > > > > > _______________________________________________ > > > Bioconductor mailing list > > > Bioconductor@r-project.org > > > https://stat.ethz.ch/mailman/listinfo/bioconductor > > > Search the archives: > > http://news.gmane.org/gmane.science.biology.informatics.conductor > > > > -- > > James W. MacDonald, M.S. > > Biostatistician > > University of Washington > > Environmental and Occupational Health Sciences > > 4225 Roosevelt Way NE, # 100 > > Seattle WA 98105-6099 > > > > > > ________________________________ > > > > > > This e-mail is intended for the use of the addressee(s) only and may > > contain privileged, confidential, or proprietary information that is > exempt > > from disclosure under law. If you have received this message in error, > > please inform us promptly by reply e-mail, then delete the e-mail and > > destroy any printed copy. Thank you. > > > > _______________________________________________ > > Bioconductor mailing list > > Bioconductor@r-project.org > > https://stat.ethz.ch/mailman/listinfo/bioconductor > > Search the archives: > > http://news.gmane.org/gmane.science.biology.informatics.conductor > > > > > > -- > Enrico Ferrero > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor@r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > [[alternative HTML version deleted]]

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.k="" cc.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@uw.edu<mailto:jmacdon@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="m yid: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=registr y&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&r equestid=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="">. > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org<mailto:bioconductor at="" r-project.org=""> > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor -- James W. MacDonald, M.S. Biostatistician University of Washington Environmental and Occupational Health Sciences 4225 Roosevelt Way NE, # 100 Seattle WA 98105-6099 ________________________________ This e-mail is intended for the use of the addressee(s) only and may contain privileged, confidential, or proprietary information that is exempt from disclosure under law. If you have received this message in error, please inform us promptly by reply e-mail, then delete the e-mail and destroy any printed copy. Thank you. _______________________________________________ Bioconductor mailing list Bioconductor at r-project.org<mailto:bioconductor at="" r-project.org=""> https://stat.ethz.ch/mailman/listinfo/bioconductor Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor -- Enrico Ferrero ________________________________ This e-mail is intended for the use of the addressee(s) only and may contain privileged, confidential, or proprietary information that is exempt from disclosure under law. If you have received this message in error, please inform us promptly by reply e-mail, then delete the e-mail and destroy any printed copy. Thank you. ________________________________