getBM weird error
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Dick Beyer ★ 1.4k
@dick-beyer-26
Last seen 9.6 years ago
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 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
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Dan Tenenbaum ★ 8.2k
@dan-tenenbaum-4256
Last seen 3.1 years ago
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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=3 306','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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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]]
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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 > > _______________________________________________ > 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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@james-w-macdonald-5106
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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
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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 > >
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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=330 6','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
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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.or g/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=33 06','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 > >
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