[BioC] getBM weird error

[James W. MacDonald]

Hi Dick,

What is your version? It works for me...


 > mart <- useMart("ENSEMBL_MART_ENSEMBL","mmusculus_gene_ensembl", 
host="www.ensembl.org")
 > sessionInfo()
R version 2.15.1 (2012-06-22)
Platform: x86_64-unknown-linux-gnu (64-bit)

locale:
  [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C
  [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8
  [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8
  [7] LC_PAPER=C                 LC_NAME=C
  [9] LC_ADDRESS=C               LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C

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

other attached packages:
  [1] biomaRt_2.14.0            affycoretools_1.31.0
  [3] KEGG.db_2.8.0             GO.db_2.8.0
  [5] AnnotationDbi_1.20.0      affy_1.36.0
  [7] pd.mogene.1.0.st.v1_3.8.0 RSQLite_0.11.2
  [9] DBI_0.2-5                 limma_3.13.20
[11] oligo_1.22.0              Biobase_2.17.8
[13] oligoClasses_1.20.0       BiocGenerics_0.4.0


On 10/4/2012 3:56 PM, Dick Beyer wrote:
> 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
>>
>>
>

-- 
James W. MacDonald, M.S.
Biostatistician
University of Washington
Environmental and Occupational Health Sciences
4225 Roosevelt Way NE, # 100
Seattle WA 98105-6099