[BioC] getBM weird error

Dan Tenenbaum dtenenba at fhcrc.org
Thu Oct 4 23:14:13 CEST 2012 

Hi Dick,

On Thu, Oct 4, 2012 at 2:09 PM, Dick Beyer <dbeyer at u.washington.edu> wrote:
> 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.

What you want is to be able to download Bioconductor 2.11 packages. To
upgrade from BioC 2.10 do this:

source("http://bioconductor.org/biocLite.R")
biocLite("BiocUpgrade")

Dan


>
> 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
>>>>> 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
>>>> 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
>>
>>
>
> _______________________________________________
> 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

More information about the Bioconductor mailing list