[BioC] problem with biomaRt

[Teresa Colombo]

Hi,

I am also having troubles with biomaRt since last Monday. I've been
following threads on the topic in the Bioconductor mailing list these
days trying to find a solution, but could not solve it yet.
Following Jim suggestion's, today I tried updating R from version 2.11
to 2.12 and so the biomaRt package from 2.4 to 2.6, but this
unfortunately did not solve the problem.

Any further suggestion?

thank you in advance,

Teresa

____________________________
Teresa Colombo, PhD
Dept of Cellular Biotechnology and Hematology
'Sapienza' University of Rome
Phone/Fax: +39 06 4457731



> library(biomaRt)
> mart <- useMart("ensembl","hsapiens_gene_ensembl")
> getBM("ensembl_gene_id","hgnc_symbol", "FUS", mart)
Errore in getBM("ensembl_gene_id", "hgnc_symbol", "FUS", mart) :
  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
> sessionInfo()
R version 2.12.0 (2010-10-15)
Platform: x86_64-redhat-linux-gnu (64-bit)

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

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_1.5-0 XML_3.2-0







2011/2/22 James W. MacDonald <jmacdon at med.umich.edu>:
> Hi Stephanie,
>
>
> On 2/21/2011 6:29 PM, Stefanie Carola Gerstberger wrote:
>>
>> Hi all,
>> I frequently use R biomaRt for querying ensembl. Over the weekend I
>> experienced a problem with biomaRt. whatever I query I get
>>
>>> 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)
>
> I get
>
>> library(biomaRt)
>> mart <- useMart("ensembl","hsapiens_gene_ensembl")
>> getBM("ensembl_gene_id","hgnc_symbol", "FUS", mart)
>  ensembl_gene_id
> 1 ENSG00000089280
>> sessionInfo()
> R version 2.12.0 Patched (2010-11-23 r53652)
> Platform: x86_64-unknown-linux-gnu (64-bit)
>
> locale:
>  [1] LC_CTYPE=en_US.iso885915       LC_NUMERIC=C
>  [3] LC_TIME=en_US.iso885915        LC_COLLATE=en_US.iso885915
>  [5] LC_MONETARY=C                  LC_MESSAGES=en_US.iso885915
>  [7] LC_PAPER=en_US.iso885915       LC_NAME=C
>  [9] LC_ADDRESS=C                   LC_TELEPHONE=C
> [11] LC_MEASUREMENT=en_US.iso885915 LC_IDENTIFICATION=C
>
> 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_1.5-0 XML_3.2-0
>
>
> What is the output of sessionInfo() for you?
>
> Best,
>
> Jim
>
>
>>>
>>
>>> 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
>>
>>> getBM(attributes="ensembl_gene_id", filters="refseq_dna",
>>> values="NM_001134363", mart=ens_sap)
>>
>>
>> I asked ensembl help desk and they advised me to use directly ensembl mart
>> through this:
>>
>>> library(biomaRt)
>>> ensembl=useMart("ENSEMBL_MART_ENSEMBL", host="www.ensembl.org")
>>> dataset="hsapiens_gene_ensembl"
>>> ensembl=useDataset(dataset, mart=ensembl)
>>
>> ..however when I try this command I get the following:
>>
>>> ensembl=useMart("ENSEMBL_MART_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
>>
>>
>> Does anyone know how to fix this problem?
>>
>> Thanks a lot,
>> Stefanie
>>
>> _______________________________________________
>> Bioconductor mailing list
>> Bioconductor at r-project.org
>> https://stat.ethz.ch/mailman/listinfo/bioconductor
>> Search the archives:
>> http://news.gmane.org/gmane.science.biology.informatics.conductor
>
> --
> James W. MacDonald, M.S.
> Biostatistician
> Douglas Lab
> University of Michigan
> Department of Human Genetics
> 5912 Buhl
> 1241 E. Catherine St.
> Ann Arbor MI 48109-5618
> 734-615-7826
> **********************************************************
> Electronic Mail is not secure, may not be read every day, and should not be
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