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Request to BioMart web service failed. Verify if you are still connected to the internet

Dear All, I am using Rstudio on windows machine --

R version 3.3.1 (2016-06-21) Platform: x86_64-w64-mingw32/x64 (64-bit) Running under: Windows 7 x64 (build 7601) Service Pack 1

I installed biomaRt package. But, when I try to use this gives error. Please see the following command and errors-

command

ensembl <- useMart("ENSEMBL_MART_ENSEMBL", dataset="hsapiens_gene_ensembl", host='may2009.archive.ensembl.org')

Errors

Request to BioMart web service failed. Verify if you are still connected to the internet. Alternatively the BioMart web service is temporarily down. Check http://www.biomart.org and verify if this website is available. Error: XML content does not seem to be XML:

Please suggest the work around if possible. Thanks in advance

r
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updated by jim.paredes • jim.paredes • written by Mamoon • Mamoon

I don't see any mistake. Are you connected to internet

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written by sysbiocoder sysbiocoder

I tried with double quotes too but failed. Yes, the site is working.

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written by Mamoon • Mamoon

This error comes and goes due to over-usage of the resource, I believe. Keep trying and eventually you'll get a slot. Limits are placed on these resources so that they don't crash.

Ensure, in addition, that you close your session correctly so that your slot is made available to others who are trying to use it.

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written by Kevin Blighe Kevin Blighe

Hi! i had the same error and tried to solve it as you did, but now it gives me this error: Error: XML content does not seem to be XML: I don´t know to fix it. Could you help me please?

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written by jim.paredes • jim.paredes

1 answer

Now I knew what was wrong with me. I am working under a proxy server and I doubted this was creating problem. The solution is setting the proxy configuration--

options(RCurlOptions = list(proxy="http://proxyIP:8080", proxyuserpwd="user:pwd"))
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updated by GenoMax GenoMax • written by Mamoon • Mamoon

Thank you for posting this!!!

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written by wichaidi • wichaidi

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