Request to BioMart web service failed. Verify if you are still connected to the internet
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5.9 years ago
Mamoon ▴ 20

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 • 4.7k views
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I don't see any mistake. Are you connected to internet

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You are using single quotes for may2009.archive.ensembl.org. Can you make sure you are able to open http://may2009.archive.ensembl.org in a browser?

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

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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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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 donĀ“t know to fix it. Could you help me please?

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5.9 years ago
Mamoon ▴ 20

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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Thank you for posting this!!!

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