Question: Request to BioMart web service failed. Verify if you are still connected to the internet
0
gravatar for Mamoon
2.7 years ago by
Mamoon20
Saudi Arab
Mamoon20 wrote:

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 • 3.2k views
ADD COMMENTlink modified 2.3 years ago by jim.paredes0 • written 2.7 years ago by Mamoon20

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

ADD REPLYlink written 2.7 years ago by sysbiocoder170

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?

ADD REPLYlink written 2.7 years ago by genomax71k

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

ADD REPLYlink written 2.7 years ago by Mamoon20

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.

ADD REPLYlink written 19 months ago by Kevin Blighe48k

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?

ADD REPLYlink written 2.3 years ago by jim.paredes0
2
gravatar for Mamoon
2.7 years ago by
Mamoon20
Saudi Arab
Mamoon20 wrote:

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"))

ADD COMMENTlink modified 2.7 years ago by genomax71k • written 2.7 years ago by Mamoon20

Thank you for posting this!!!

ADD REPLYlink written 10 months ago by wichaidi0
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