Question: Problems with url/download and http_proxy
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gravatar for Warnes, Gregory R
17.3 years ago by
Warnes, Gregory R460 wrote:
I would like to use the getBioC.R script from http://www.bioconductor.org/getBioC.R to install the biobase packages. Unfortunately, url() and download.file() die when trying to talk to my proxy: > getBioC("exprs") connect: Cannot assign requested address unable to connect to 'gproxy1.pfizer.com'. connect: Cannot assign requested address unable to connect to 'gproxy1.pfizer.com'. connect: Cannot assign requested address unable to connect to 'gproxy1.pfizer.com'. connect: Cannot assign requested address unable to connect to 'gproxy1.pfizer.com'. connect: Cannot assign requested address unable to connect to 'gproxy1.pfizer.com'. connect: Cannot assign requested address unable to connect to 'gproxy1.pfizer.com'. connect: Cannot assign requested address unable to connect to 'gproxy1.pfizer.com'. [1] "Get Biobase failed" "Get annotate failed" "Get genefilter failed" [4] "Get geneplotter failed" "Get edd failed" "Get ROC failed" [7] "Get tkWidgets failed" Which is caused by: > url(getUrl("unix","Biobase", F),'r') connect: Cannot assign requested address unable to connect to 'gproxy1.pfizer.com'. Error in url(getUrl("unix", "Biobase", F), "r") : cannot open URL `http://www.bioconductor.org/packages/release/distrib/Source/Biobase_1 .0.tar .gz' and similarly: > download.file(getUrl("unix","Biobase", F),dest="test.tgz") trying URL `http://www.bioconductor.org/packages/release/distrib/Source/Biobase_1 .0.tar .gz' connect: Cannot assign requested address unable to connect to 'gproxy1.pfizer.com'. Error in download.file(getUrl("unix", "Biobase", F), dest = "test.tgz") : cannot open URL `http://www.bioconductor.org/packages/release/distrib/Source/Biobase_1 .0.tar .gz' So, it looks like R's internal http code can't handle my proxy settings: > Sys.getenv("http_proxy") http_proxy "http://gproxy1.pfizer.com" However, this proxy value works just fine for wget/lynx etc: > download.file(getUrl("unix","Biobase", F),dest="test.gz", method="wget") --11:12:07-- http://www.bioconductor.org:80/packages/release/distrib/Source/Biobase _1.0.t ar.gz => `affy.tar.gz' Connecting to gproxy1.pfizer.com:80... connected! Proxy request sent, awaiting response... 200 OK Length: 292,800 [application/x-tar] 0K -> .......... .......... .......... .......... .......... [ 17%] 50K -> .......... .......... .......... .......... .......... [ 34%] ... So, does R need the proxy settings to be in a different format? Other ideas on what might be wrong? Obligatory version info: > version _ platform sparc-sun-solaris2.8 arch sparc os solaris2.8 system sparc, solaris2.8 status Patched major 1 minor 5.1 year 2002 month 06 day 18 language R -Greg LEGAL NOTICE Unless expressly stated otherwise, this message is confidential and may be privileged. It is intended for the addressee(s) only. Access to this E-mail by anyone else is unauthorized. If you are not an addressee, any disclosure or copying of the contents of this E-mail or any action taken (or not taken) in reliance on it is unauthorized and may be unlawful. If you are not an addressee, please inform the sender immediately.
ADD COMMENTlink modified 17.3 years ago by ripley@stats.ox.ac.uk50 • written 17.3 years ago by Warnes, Gregory R460
Answer: Problems with url/download and http_proxy
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gravatar for ripley@stats.ox.ac.uk
17.3 years ago by
ripley@stats.ox.ac.uk50 wrote:
The code (which you do have available to you) says http_proxy * Should be like http://myproxy/ or http://myproxy:3128/ which yours is not, so please try that format. The code suggests that the traling / can be omitted, but the words do not. -- Brian D. Ripley, ripley@stats.ox.ac.uk Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/ University of Oxford, Tel: +44 1865 272861 (self) 1 South Parks Road, +44 1865 272860 (secr) Oxford OX1 3TG, UK Fax: +44 1865 272595
ADD COMMENTlink written 17.3 years ago by ripley@stats.ox.ac.uk50
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