[BioC] getBM weird error
Dick Beyer
dbeyer at u.washington.edu
Thu Oct 4 23:09:20 CEST 2012
Hi Jim,
Sorry, I forgot my sessionInfo():
> sessionInfo()
R version 2.15.1 (2012-06-22)
Platform: x86_64-redhat-linux-gnu (64-bit)
locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 LC_MONETARY=en_US.UTF-8
[6] LC_MESSAGES=en_US.UTF-8 LC_PAPER=C LC_NAME=C 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_2.12.0
loaded via a namespace (and not attached):
[1] RCurl_1.91-1 XML_3.9-4
I know biomaRt should be at 2.14.0. This sessionInfo is after I just did:
source("http://bioconductor.org/biocLite.R")
biocLite("biomaRt")
and restarted R with library(biomaRt).
I also had the same problem on my windows machine. I was able to update to biomaRt_2.14.0 by downloading the http://www.bioconductor.org/packages/2.11/bioc/bin/windows/contrib/2.15/biomaRt_2.14.0.zip file and use the Packages/Install package(s) from local zip files... process.
Not sure why I'd see this odd biocLite behavior.
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,
>
> 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
>>>>
>>>> _______________________________________________
>>>> Bioconductor mailing list
>>>> Bioconductor at r-project.org
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>>>> Search the archives:
>>>> http://news.gmane.org/gmane.science.biology.informatics.conductor
>>>
>>> --
>>> 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
>
>
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