[BioC] getBM weird error
Dick Beyer
dbeyer at u.washington.edu
Fri Oct 5 00:23:53 CEST 2012
Thanks Dan and Steffen and Jim,
All is well now. Sorry to bother everyone due to not completely updating my installation.
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
*******************************************************************************
On Thu, 4 Oct 2012, Steffen Durinck wrote:
> As Jim suggested, it looks like something is up with the central BioMart server in Canada.
> Default queries, when one does not specify a host, go there and these seem to fail. Jim's suggestion to specify the Ensembl host works.
> I'll contact the Biomart team to see what is up, they should be able to fix this soon.
>
> Cheers,
> Steffen
>
>
>
>
> On Thu, Oct 4, 2012 at 2:14 PM, Dan Tenenbaum <dtenenba at fhcrc.org> wrote:
> 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
>
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