[BioC] getBM weird error

[Dick Beyer]

Hi Jim,

I tried that, but got this:

  mart <- useMart("ENSEMBL_MART_ENSEMBL","mmusculus_gene_ensembl", host="www.ensembl.org")
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

I might have to read the manual (queue Edvard Munch's The Scream).

Thanks
Dick
*******************************************************************************
Richard P. Beyer, Ph.D.	University of Washington
Tel.:(206) 616 7378	Env. & Occ. Health Sci. , Box 354695
Fax: (206) 685 4696	4225 Roosevelt Way NE, # 100
 			Seattle, WA 98105-6099
http://depts.washington.edu/ceeh/members_fc_IEHSFC.html
http://staff.washington.edu/dbeyer
*******************************************************************************

On Thu, 4 Oct 2012, James W. MacDonald wrote:

> Hi Dick,
>
> On 10/4/2012 2:25 PM, Dick Beyer wrote:
>> I'm hoping someone might have a work-around for this getBM problem:
>> 
>> library(biomaRt)
>> mart <- useMart( "ensembl", dataset="mmusculus_gene_ensembl")
>> tmp <- getBM(attributes=c("uniprot_swissprot_accession","ipi"), 
>> filters="ipi", values="IPI00134704", mart=mart)
>> 
>> Error in getBM(attributes = c("uniprot_swissprot_accession", "ipi"), 
>> filters = "ipi",  :
>>   Query ERROR: caught BioMart::Exception::Database: Could not connect to 
>> mysql database ensembl_mart_68: DBI 
>> connect('database=ensembl_mart_68;host=bmdccdb.oicr.on.ca;port=3306','bm_web',...) 
>> failed: Host 'bmdcc1.oicr.on.ca' is blocked because of many connection 
>> errors; unblock with 'mysqladmin flush-hosts' at 
>> /srv/biomart_server/biomart.org/biomart-perl/lib/BioMart/Configuration/DBLocation.pm 
>> line 98
>
> That server looks borked. You could switch to the ensembl one:
>
>> mart <- useMart("ENSEMBL_MART_ENSEMBL","mmusculus_gene_ensembl", 
> host="www.ensembl.org")
>> getBM(c("uniprot_swissprot_accession","ipi"), "ipi","IPI00124704", mart)
> [1] uniprot_swissprot_accession ipi
> <0 rows> (or 0-length row.names)
>
> Best,
>
> Jim
>
>
>> 
>> Thanks much,
>> Dick
>> ******************************************************************************* 
>> Richard P. Beyer, Ph.D.    University of Washington
>> Tel.:(206) 616 7378    Env. & Occ. Health Sci. , Box 354695
>> Fax: (206) 685 4696    4225 Roosevelt Way NE, # 100
>>             Seattle, WA 98105-6099
>> http://depts.washington.edu/ceeh/members_fc_IEHSFC.html
>> http://staff.washington.edu/dbeyer
>> 
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>
> -- 
> James W. MacDonald, M.S.
> Biostatistician
> University of Washington
> Environmental and Occupational Health Sciences
> 4225 Roosevelt Way NE, # 100
> Seattle WA 98105-6099
>
>