Hi Steffen,
thanks for getting back to me. I tried the same commands now again and did not 
experience any problems any more. I didn't change anything with my R version. It 
seems to be repaired again. Odd, but good that it works again. 
 My session info is:
> sessionInfo()
R version 2.12.1 (2010-12-16)
Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit)

locale:
[1] en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/en_US.UTF-8

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] biomaRt_2.6.0

loaded via a namespace (and not attached):
[1] RCurl_1.4-3 XML_3.2-0  
 
Thanks for the feedback,
Stefanie




Hi Stefanie,

As Jim suggested you might be running a version of R and biomaRt that is too old 
to be compatible with the current BioMart servers.
What do you get when you run sessionInfo() after loading the biomaRt library?

It should look like:


> library(biomaRt)
> sessionInfo()
R version 2.12.1 (2010-12-16)
Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit)

locale:
[1] en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/en_US.UTF-8

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] biomaRt_2.6.0

loaded via a namespace (and not attached):
[1] RCurl_1.4-3 XML_3.2-0  


Cheers,
Steffen


On Mon, Feb 21, 2011 at 9:13 AM, Stefanie Carola Gerstberger <scg74@cornell.edu> 
wrote:

Hi,
>I'm having recently a problem with biomaRt in R.  I tried to access the human 
>ensembl genes. I didn't have a problem until last week, but over the weekend I 
>received this:
>
>> > library(biomaRt)
>> > ensembl=useMart("ensembl")
>> > listDatasets(ensembl)
>> > ens_sap=useMart("ensembl", dataset="hsapiens_gene_ensembl")
>> > attr_sap=listAttributes(ens_sap)
>> > filter_sap=listFilters(ens_sap)
>> >
>>
>> > getBM(attributes="ensembl_gene_id", filters="hgnc_symbol",
>> values="FUS",
>> >mart=ens_sap)
>>
>> Error in getBM(attributes = "ensembl_gene_id", filters =
>> "hgnc_symbol",  :
>>  Query ERROR: caught BioMart::Exception::Database: Could not connect
>> to mysql
>> database ensembl_mart_61: DBI
>> connect('database=ensembl_mart_61;host=dcc-qa-
>> db.oicr.on.ca;port=3306','bm_web',...)
>>  failed: Can't connect to MySQL server on 'dcc-qa-db.oicr.on.ca' (113)
>> at
>> /srv/biomart_server/biomart.org/biomart-
>> perl/lib/BioMart/Configuration/DBLocation.pm
>>  line 98
>
>Exactly this line happend for any kind of query, e.g. instead of hgnc_symbol I 
>tried refseq_dna, ensembl_gene_id etc...
>
>I contacted Ensembl and they suggested to go through the ensembl server by 
using
>
>library(biomaRt)
>ensembl=useMart("ENSEMBL_MART_ENSEMBL", host="www.ensembl.org")
>dataset="hsapiens_gene_ensembl"
>ensembl=useDataset(dataset, mart=ensembl)
>
>however at command line :
>
>>ensembl=useMart("ENSEMBL_MART_ENSEMBL", host="www.ensembl.org")
>
>I get :
>
>
>>Space required after the Public Identifier
>>SystemLiteral " or ' expected
>>SYSTEM or PUBLIC, the URI is missing
>>Error: 1: Space required after the Public Identifier
>>2: SystemLiteral " or ' expected
>>3: SYSTEM or PUBLIC, the URI is missing
>
>
>Does anyone know how to fix this problem?
>Thanks,
>Stefanie
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