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@fhcrc.org> wrote:

> Hi Dick,
>
> On Thu, Oct 4, 2012 at 2:09 PM, Dick Beyer <dbeyer@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@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@r-project.org
> > https://stat.ethz.ch/mailman/listinfo/bioconductor
> > Search the archives:
> > http://news.gmane.org/gmane.science.biology.informatics.conductor
>
> _______________________________________________
> Bioconductor mailing list
> Bioconductor@r-project.org
> https://stat.ethz.ch/mailman/listinfo/bioconductor
> Search the archives:
> http://news.gmane.org/gmane.science.biology.informatics.conductor
>

	[[alternative HTML version deleted]]

