biomaRt error
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@iain-gallagher-2532
Last seen 9.3 years ago
United Kingdom
Hello List Can anyone shed any light on the following biomaRt error? Has something changed at Ensembl? > library(biomaRt) > > mart <- useMart("ensembl", dataset="hsapiens_gene_ensembl") Error: non-BioMart die(): not well-formed (invalid token) at line 1, column 11797, byte 11797 at /usr/lib/perl5/XML/Parser.pm line 187 does not seem to be XML, nor to identify a file name > sessionInfo() R version 2.10.1 (2009-12-14) x86_64-pc-linux-gnu locale: [1] LC_CTYPE=en_GB.UTF-8 LC_NUMERIC=C [3] LC_TIME=en_GB.UTF-8 LC_COLLATE=en_GB.UTF-8 [5] LC_MONETARY=C LC_MESSAGES=en_GB.UTF-8 [7] LC_PAPER=en_GB.UTF-8 LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=en_GB.UTF-8 LC_IDENTIFICATION=C attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] biomaRt_2.2.0 loaded via a namespace (and not attached): [1] RCurl_1.3-1 XML_2.6-0 > Thanks Iain
biomaRt biomaRt • 1.4k views
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@iain-gallagher-2532
Last seen 9.3 years ago
United Kingdom
Seems to be ok this morning. Ran the same query with no problems. Perhaps some transient changes at the server end. Cheers Iain --- On Wed, 13/1/10, Paul Leo <p.leo at="" uq.edu.au=""> wrote: > From: Paul Leo <p.leo at="" uq.edu.au=""> > Subject: Re: [BioC] biomaRt error > To: "Iain Gallagher" <iaingallagher at="" btopenworld.com=""> > Cc: bioconductor at stat.math.ethz.ch > Date: Wednesday, 13 January, 2010, 23:45 > Dito. > Actually 3 days ago some of my old queries started > returning different > numbers of rows > > > length(unique(ann.all[ann.all[,"gene_biotype"]=="protein_coding" > , > "ensembl_gene_id"])) > [1] 19940 > > > > length(unique(ann.all.entrez[ann.all.entrez[,"gene_biotype"]=="prote in_coding" > , "ensembl_gene_id"])) # 22836 > [1] 22836 > > vs for months before hand and 4 days previous > > length(unique(ann.all[ann.all[,"gene_biotype"]=="protein_coding" > , > "ensembl_gene_id"])) > [1] 22836 > > > > length(unique(ann.all.entrez[ann.all.entrez[,"gene_biotype"]=="prote in_coding" > , "ensembl_gene_id"])) # 22836 > [1] 22836 > > FOR > a.filter<-c( "chromosome_name", "start" , "end") > fil.vals<-list(chrom,? low.cut, high.cut) > > ann.all<-getBM(attributes = > c("ensembl_gene_id","external_gene_id","chromosome_name","start_posi tion","end_position","strand","gene_biotype","mgi_symbol","description "), > filters = a.filter, values=fil.vals, mart = mart) > > ann.all.entrez<-getBM(attributes = > c( > "ensembl_gene_id","external_gene_id","ensembl_transcript_id","chromo some_name","start_position","end_position","strand","gene_biotype","en trezgene","mgi_symbol","description"), > filters = a.filter, values=fil.vals, mart = mart) > > No idea why the first query was affected and not the > second.... This did > coincide with a bioC update I did two days ago... but that > may be a > coincidence.... > > > > > Today I get the same error > > listMarts() > Error: non-BioMart die(): > not well-formed (invalid token) at line 1, column 11797, > byte 11797 > at /usr/lib/perl5/XML/Parser.pm line 187 > > ? does not seem to be XML, nor to identify a file > name > > > > > > sessionInfo() > R version 2.10.1 (2009-12-14) > x86_64-pc-linux-gnu > > locale: > [1] LC_CTYPE=en_AU.UTF-8? ? > ???LC_NUMERIC=C? ? ? ? > ? ? ? > [3] LC_TIME=en_AU.UTF-8? ? ? ? > LC_COLLATE=en_AU.UTF-8? ? > [5] LC_MONETARY=C? ? ? ? ? ? > ? LC_MESSAGES=en_AU.UTF-8??? > [7] LC_PAPER=en_AU.UTF-8? ? > ???LC_NAME=C? ? ? ? > ? ? ? ??? > [9] LC_ADDRESS=C? ? ? ? ? ? > ???LC_TELEPHONE=C? ? ? ? > ? ? > [11] LC_MEASUREMENT=en_AU.UTF-8 LC_IDENTIFICATION=C? > ? ??? > > attached base packages: > [1] stats? ???graphics? grDevices > utils? ???datasets? methods > base? ??? > > other attached packages: > [1] org.Mm.eg.db_2.3.6? RSQLite_0.8-1? ? > ???DBI_0.2-5? ? ? ? > ? > [4] AnnotationDbi_1.8.1 Biobase_2.6.1? ? > ???biomaRt_2.2.0? ? ? > > loaded via a namespace (and not attached): > [1] RCurl_1.3-1? tcltk_2.10.1 tools_2.10.1 > XML_2.6-0? > > > > -----Original Message----- > From: Iain Gallagher <iaingallagher at="" btopenworld.com=""> > To: bioconductor at stat.math.ethz.ch > Subject: [BioC] biomaRt error > Date: Wed, 13 Jan 2010 19:00:14 +0000 (GMT) > > Hello List > > Can anyone shed any light on the following biomaRt error? > Has something changed at Ensembl? > > > library(biomaRt) > > > > mart <- useMart("ensembl", > dataset="hsapiens_gene_ensembl") > Error: non-BioMart die(): > not well-formed (invalid token) at line 1, column 11797, > byte 11797 at /usr/lib/perl5/XML/Parser.pm line 187 > > ? does not seem to be XML, nor to identify a file > name > > sessionInfo() > R version 2.10.1 (2009-12-14) > x86_64-pc-linux-gnu > > locale: > [1] LC_CTYPE=en_GB.UTF-8? ? > ???LC_NUMERIC=C? ? ? ? > ? ? ? > [3] LC_TIME=en_GB.UTF-8? ? ? ? > LC_COLLATE=en_GB.UTF-8? ? > [5] LC_MONETARY=C? ? ? ? ? ? > ? LC_MESSAGES=en_GB.UTF-8??? > [7] LC_PAPER=en_GB.UTF-8? ? > ???LC_NAME=C? ? ? ? > ? ? ? ??? > [9] LC_ADDRESS=C? ? ? ? ? ? > ???LC_TELEPHONE=C? ? ? ? > ? ? > [11] LC_MEASUREMENT=en_GB.UTF-8 LC_IDENTIFICATION=C? > ? ??? > > attached base packages: > [1] stats? ???graphics? grDevices > utils? ???datasets? > methods???base? ??? > > other attached packages: > [1] biomaRt_2.2.0 > > loaded via a namespace (and not attached): > [1] RCurl_1.3-1 XML_2.6-0? > > > > Thanks > > Iain > > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor > >
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Hi Iain Yes there seems to have been problems connecting to the www.biomart.org registry which have now been resolved by the Biomart team at the OICR. As an alternative, you can also access the Ensembl databases from the Ensembl biomart installation at www.ensembl.org using the following biomaRt commands: > library(biomaRt) > listMarts(host = "www.ensembl.org"); biomart version 1 ENSEMBL_MART_ENSEMBL Ensembl 56 2 ENSEMBL_MART_SNP Ensembl variation 56 3 ENSEMBL_MART_FUNCGEN Ensembl functional genomics 56 4 ENSEMBL_MART_VEGA Vega 36 5 REACTOME Reactome 6 wormbase_current WormBase (CSHL US) 7 pride PRIDE (EBI UK) > mart = useMart("ENSEMBL_MART_ENSEMBL", host = "www.ensembl.org") etc... Regards Rhoda On 14 Jan 2010, at 09:37, Iain Gallagher wrote: > Seems to be ok this morning. Ran the same query with no problems. > Perhaps some transient changes at the server end. > > Cheers > > Iain > > --- On Wed, 13/1/10, Paul Leo <p.leo at="" uq.edu.au=""> wrote: > >> From: Paul Leo <p.leo at="" uq.edu.au=""> >> Subject: Re: [BioC] biomaRt error >> To: "Iain Gallagher" <iaingallagher at="" btopenworld.com=""> >> Cc: bioconductor at stat.math.ethz.ch >> Date: Wednesday, 13 January, 2010, 23:45 >> Dito. >> Actually 3 days ago some of my old queries started >> returning different >> numbers of rows >> >> >> length(unique(ann.all[ann.all[,"gene_biotype"]=="protein_coding" >> , >> "ensembl_gene_id"])) >> [1] 19940 >> >>> >> length >> (unique >> (ann.all.entrez[ann.all.entrez[,"gene_biotype"]=="protein_coding" >> , "ensembl_gene_id"])) # 22836 >> [1] 22836 >> >> vs for months before hand and 4 days previous >> >> length(unique(ann.all[ann.all[,"gene_biotype"]=="protein_coding" >> , >> "ensembl_gene_id"])) >> [1] 22836 >> >>> >> length >> (unique >> (ann.all.entrez[ann.all.entrez[,"gene_biotype"]=="protein_coding" >> , "ensembl_gene_id"])) # 22836 >> [1] 22836 >> >> FOR >> a.filter<-c( "chromosome_name", "start" , "end") >> fil.vals<-list(chrom, low.cut, high.cut) >> >> ann.all<-getBM(attributes = >> c >> ("ensembl_gene_id >> ","external_gene_id >> ","chromosome_name >> ","start_position >> ","end_position","strand","gene_biotype","mgi_symbol","description"), >> filters = a.filter, values=fil.vals, mart = mart) >> >> ann.all.entrez<-getBM(attributes = >> c( >> "ensembl_gene_id >> ","external_gene_id >> ","ensembl_transcript_id >> ","chromosome_name >> ","start_position >> ","end_position >> ","strand","gene_biotype","entrezgene","mgi_symbol","description"), >> filters = a.filter, values=fil.vals, mart = mart) >> >> No idea why the first query was affected and not the >> second.... This did >> coincide with a bioC update I did two days ago... but that >> may be a >> coincidence.... >> >> >> >> >> Today I get the same error >>> listMarts() >> Error: non-BioMart die(): >> not well-formed (invalid token) at line 1, column 11797, >> byte 11797 >> at /usr/lib/perl5/XML/Parser.pm line 187 >> >> does not seem to be XML, nor to identify a file >> name >> >> >> >> >>> sessionInfo() >> R version 2.10.1 (2009-12-14) >> x86_64-pc-linux-gnu >> >> locale: >> [1] LC_CTYPE=en_AU.UTF-8 >> LC_NUMERIC=C >> >> [3] LC_TIME=en_AU.UTF-8 >> LC_COLLATE=en_AU.UTF-8 >> [5] LC_MONETARY=C >> LC_MESSAGES=en_AU.UTF-8 >> [7] LC_PAPER=en_AU.UTF-8 >> LC_NAME=C >> >> [9] LC_ADDRESS=C >> LC_TELEPHONE=C >> >> [11] LC_MEASUREMENT=en_AU.UTF-8 LC_IDENTIFICATION=C >> >> >> attached base packages: >> [1] stats graphics grDevices >> utils datasets methods >> base >> >> other attached packages: >> [1] org.Mm.eg.db_2.3.6 RSQLite_0.8-1 >> DBI_0.2-5 >> >> [4] AnnotationDbi_1.8.1 Biobase_2.6.1 >> biomaRt_2.2.0 >> >> loaded via a namespace (and not attached): >> [1] RCurl_1.3-1 tcltk_2.10.1 tools_2.10.1 >> XML_2.6-0 >> >> >> >> -----Original Message----- >> From: Iain Gallagher <iaingallagher at="" btopenworld.com=""> >> To: bioconductor at stat.math.ethz.ch >> Subject: [BioC] biomaRt error >> Date: Wed, 13 Jan 2010 19:00:14 +0000 (GMT) >> >> Hello List >> >> Can anyone shed any light on the following biomaRt error? >> Has something changed at Ensembl? >> >>> library(biomaRt) >>> >>> mart <- useMart("ensembl", >> dataset="hsapiens_gene_ensembl") >> Error: non-BioMart die(): >> not well-formed (invalid token) at line 1, column 11797, >> byte 11797 at /usr/lib/perl5/XML/Parser.pm line 187 >> >> does not seem to be XML, nor to identify a file >> name >>> sessionInfo() >> R version 2.10.1 (2009-12-14) >> x86_64-pc-linux-gnu >> >> locale: >> [1] LC_CTYPE=en_GB.UTF-8 >> LC_NUMERIC=C >> >> [3] LC_TIME=en_GB.UTF-8 >> LC_COLLATE=en_GB.UTF-8 >> [5] LC_MONETARY=C >> LC_MESSAGES=en_GB.UTF-8 >> [7] LC_PAPER=en_GB.UTF-8 >> LC_NAME=C >> >> [9] LC_ADDRESS=C >> LC_TELEPHONE=C >> >> [11] LC_MEASUREMENT=en_GB.UTF-8 LC_IDENTIFICATION=C >> >> >> attached base packages: >> [1] stats graphics grDevices >> utils datasets >> methods base >> >> other attached packages: >> [1] biomaRt_2.2.0 >> >> loaded via a namespace (and not attached): >> [1] RCurl_1.3-1 XML_2.6-0 >>> >> >> Thanks >> >> Iain >> >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor at stat.math.ethz.ch >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor >> >> > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor Rhoda Kinsella Ph.D. Ensembl Bioinformatician, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton Cambridge CB10 1SD, UK.
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Thank you Rhoda. Very useful. Cheers Iain --- On Thu, 14/1/10, Rhoda Kinsella <rhoda at="" ebi.ac.uk=""> wrote: > From: Rhoda Kinsella <rhoda at="" ebi.ac.uk=""> > Subject: Re: [BioC] biomaRt error > To: "Iain Gallagher" <iaingallagher at="" btopenworld.com=""> > Cc: bioconductor at stat.math.ethz.ch > Date: Thursday, 14 January, 2010, 9:46 > Hi Iain > Yes there seems to have been problems connecting to the > www.biomart.org registry which have now been resolved by the > Biomart team at the OICR. As an alternative,? you can > also access the Ensembl databases from the Ensembl biomart > installation at www.ensembl.org using the following biomaRt > commands: > > > library(biomaRt) > > listMarts(host = "www.ensembl.org"); > biomart version > 1 ENSEMBL_MART_ENSEMBL Ensembl 56 > 2 ENSEMBL_MART_SNP Ensembl variation 56 > 3 ENSEMBL_MART_FUNCGEN Ensembl functional genomics 56 > 4 ENSEMBL_MART_VEGA Vega 36 > 5 REACTOME Reactome > 6 wormbase_current WormBase (CSHL US) > 7 pride PRIDE (EBI UK) > > mart = useMart("ENSEMBL_MART_ENSEMBL", host = > "www.ensembl.org") > etc... > > Regards > Rhoda > > > On 14 Jan 2010, at 09:37, Iain Gallagher wrote: > > > Seems to be ok this morning. Ran the same query with > no problems. Perhaps some transient changes at the server > end. > > > > Cheers > > > > Iain > > > > --- On Wed, 13/1/10, Paul Leo <p.leo at="" uq.edu.au=""> > wrote: > > > >> From: Paul Leo <p.leo at="" uq.edu.au=""> > >> Subject: Re: [BioC] biomaRt error > >> To: "Iain Gallagher" <iaingallagher at="" btopenworld.com=""> > >> Cc: bioconductor at stat.math.ethz.ch > >> Date: Wednesday, 13 January, 2010, 23:45 > >> Dito. > >> Actually 3 days ago some of my old queries > started > >> returning different > >> numbers of rows > >> > >> > >> > length(unique(ann.all[ann.all[,"gene_biotype"]=="protein_coding" > >> , > >> "ensembl_gene_id"])) > >> [1] 19940 > >> > >>> > >> > length(unique(ann.all.entrez[ann.all.entrez[,"gene_biotype"]=="prote in_coding" > >> , "ensembl_gene_id"])) # 22836 > >> [1] 22836 > >> > >> vs for months before hand and 4 days previous > >> > >> > length(unique(ann.all[ann.all[,"gene_biotype"]=="protein_coding" > >> , > >> "ensembl_gene_id"])) > >> [1] 22836 > >> > >>> > >> > length(unique(ann.all.entrez[ann.all.entrez[,"gene_biotype"]=="prote in_coding" > >> , "ensembl_gene_id"])) # 22836 > >> [1] 22836 > >> > >> FOR > >> a.filter<-c( "chromosome_name", "start" , > "end") > >> fil.vals<-list(chrom,? low.cut, high.cut) > >> > >> ann.all<-getBM(attributes = > >> > c("ensembl_gene_id","external_gene_id","chromosome_name","start_posi tion","end_position","strand","gene_biotype","mgi_symbol","description "), > >> filters = a.filter, values=fil.vals, mart = mart) > >> > >> ann.all.entrez<-getBM(attributes = > >> c( > >> > "ensembl_gene_id","external_gene_id","ensembl_transcript_id","chromo some_name","start_position","end_position","strand","gene_biotype","en trezgene","mgi_symbol","description"), > >> filters = a.filter, values=fil.vals, mart = mart) > >> > >> No idea why the first query was affected and not > the > >> second.... This did > >> coincide with a bioC update I did two days ago... > but that > >> may be a > >> coincidence.... > >> > >> > >> > >> > >> Today I get the same error > >>> listMarts() > >> Error: non-BioMart die(): > >> not well-formed (invalid token) at line 1, column > 11797, > >> byte 11797 > >> at /usr/lib/perl5/XML/Parser.pm line 187 > >> > >>???does not seem to be XML, nor to > identify a file > >> name > >> > >> > >> > >> > >>> sessionInfo() > >> R version 2.10.1 (2009-12-14) > >> x86_64-pc-linux-gnu > >> > >> locale: > >> [1] LC_CTYPE=en_AU.UTF-8 > >>? ? LC_NUMERIC=C > >> > >> [3] LC_TIME=en_AU.UTF-8 > >> LC_COLLATE=en_AU.UTF-8 > >> [5] LC_MONETARY=C > >>???LC_MESSAGES=en_AU.UTF-8 > >> [7] LC_PAPER=en_AU.UTF-8 > >>? ? LC_NAME=C > >> > >> [9] LC_ADDRESS=C > >>? ? LC_TELEPHONE=C > >> > >> [11] LC_MEASUREMENT=en_AU.UTF-8 > LC_IDENTIFICATION=C > >> > >> > >> attached base packages: > >> [1] stats? ???graphics? > grDevices > >> utils? ???datasets? > methods > >> base > >> > >> other attached packages: > >> [1] org.Mm.eg.db_2.3.6? RSQLite_0.8-1 > >>? ? DBI_0.2-5 > >> > >> [4] AnnotationDbi_1.8.1 Biobase_2.6.1 > >>? ? biomaRt_2.2.0 > >> > >> loaded via a namespace (and not attached): > >> [1] RCurl_1.3-1? tcltk_2.10.1 tools_2.10.1 > >> XML_2.6-0 > >> > >> > >> > >> -----Original Message----- > >> From: Iain Gallagher <iaingallagher at="" btopenworld.com=""> > >> To: bioconductor at stat.math.ethz.ch > >> Subject: [BioC] biomaRt error > >> Date: Wed, 13 Jan 2010 19:00:14 +0000 (GMT) > >> > >> Hello List > >> > >> Can anyone shed any light on the following biomaRt > error? > >> Has something changed at Ensembl? > >> > >>> library(biomaRt) > >>> > >>> mart <- useMart("ensembl", > >> dataset="hsapiens_gene_ensembl") > >> Error: non-BioMart die(): > >> not well-formed (invalid token) at line 1, column > 11797, > >> byte 11797 at /usr/lib/perl5/XML/Parser.pm line > 187 > >> > >>???does not seem to be XML, nor to > identify a file > >> name > >>> sessionInfo() > >> R version 2.10.1 (2009-12-14) > >> x86_64-pc-linux-gnu > >> > >> locale: > >> [1] LC_CTYPE=en_GB.UTF-8 > >>? ? LC_NUMERIC=C > >> > >> [3] LC_TIME=en_GB.UTF-8 > >> LC_COLLATE=en_GB.UTF-8 > >> [5] LC_MONETARY=C > >>???LC_MESSAGES=en_GB.UTF-8 > >> [7] LC_PAPER=en_GB.UTF-8 > >>? ? LC_NAME=C > >> > >> [9] LC_ADDRESS=C > >>? ? LC_TELEPHONE=C > >> > >> [11] LC_MEASUREMENT=en_GB.UTF-8 > LC_IDENTIFICATION=C > >> > >> > >> attached base packages: > >> [1] stats? ???graphics? > grDevices > >> utils? ???datasets > >> methods???base > >> > >> other attached packages: > >> [1] biomaRt_2.2.0 > >> > >> loaded via a namespace (and not attached): > >> [1] RCurl_1.3-1 XML_2.6-0 > >>> > >> > >> Thanks > >> > >> Iain > >> > >> > >> _______________________________________________ > >> Bioconductor mailing list > >> Bioconductor at stat.math.ethz.ch > >> https://stat.ethz.ch/mailman/listinfo/bioconductor > >> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor > >> > >> > > > > _______________________________________________ > > Bioconductor mailing list > > Bioconductor at stat.math.ethz.ch > > https://stat.ethz.ch/mailman/listinfo/bioconductor > > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor > > Rhoda Kinsella Ph.D. > Ensembl Bioinformatician, > European Bioinformatics Institute (EMBL-EBI), > Wellcome Trust Genome Campus, > Hinxton > Cambridge CB10 1SD, > UK. > >
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Paul Leo ▴ 970
@paul-leo-2092
Last seen 10.2 years ago
Dito. Actually 3 days ago some of my old queries started returning different numbers of rows length(unique(ann.all[ann.all[,"gene_biotype"]=="protein_coding" , "ensembl_gene_id"])) [1] 19940 > length(unique(ann.all.entrez[ann.all.entrez[,"gene_biotype"]=="protein _coding" , "ensembl_gene_id"])) # 22836 [1] 22836 vs for months before hand and 4 days previous length(unique(ann.all[ann.all[,"gene_biotype"]=="protein_coding" , "ensembl_gene_id"])) [1] 22836 > length(unique(ann.all.entrez[ann.all.entrez[,"gene_biotype"]=="protein _coding" , "ensembl_gene_id"])) # 22836 [1] 22836 FOR a.filter<-c( "chromosome_name", "start" , "end") fil.vals<-list(chrom, low.cut, high.cut) ann.all<-getBM(attributes = c("ensembl_gene_id","external_gene_id","chromosome_name","start_positi on","end_position","strand","gene_biotype","mgi_symbol","description") , filters = a.filter, values=fil.vals, mart = mart) ann.all.entrez<-getBM(attributes = c( "ensembl_gene_id","external_gene_id","ensembl_transcript_id","chrom osome_name","start_position","end_position","strand","gene_biotype","e ntrezgene","mgi_symbol","description"), filters = a.filter, values=fil.vals, mart = mart) No idea why the first query was affected and not the second.... This did coincide with a bioC update I did two days ago... but that may be a coincidence.... Today I get the same error > listMarts() Error: non-BioMart die(): not well-formed (invalid token) at line 1, column 11797, byte 11797 at /usr/lib/perl5/XML/Parser.pm line 187 does not seem to be XML, nor to identify a file name > sessionInfo() R version 2.10.1 (2009-12-14) x86_64-pc-linux-gnu locale: [1] LC_CTYPE=en_AU.UTF-8 LC_NUMERIC=C [3] LC_TIME=en_AU.UTF-8 LC_COLLATE=en_AU.UTF-8 [5] LC_MONETARY=C LC_MESSAGES=en_AU.UTF-8 [7] LC_PAPER=en_AU.UTF-8 LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=en_AU.UTF-8 LC_IDENTIFICATION=C attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] org.Mm.eg.db_2.3.6 RSQLite_0.8-1 DBI_0.2-5 [4] AnnotationDbi_1.8.1 Biobase_2.6.1 biomaRt_2.2.0 loaded via a namespace (and not attached): [1] RCurl_1.3-1 tcltk_2.10.1 tools_2.10.1 XML_2.6-0 -----Original Message----- From: Iain Gallagher <iaingallagher@btopenworld.com> To: bioconductor at stat.math.ethz.ch Subject: [BioC] biomaRt error Date: Wed, 13 Jan 2010 19:00:14 +0000 (GMT) Hello List Can anyone shed any light on the following biomaRt error? Has something changed at Ensembl? > library(biomaRt) > > mart <- useMart("ensembl", dataset="hsapiens_gene_ensembl") Error: non-BioMart die(): not well-formed (invalid token) at line 1, column 11797, byte 11797 at /usr/lib/perl5/XML/Parser.pm line 187 does not seem to be XML, nor to identify a file name > sessionInfo() R version 2.10.1 (2009-12-14) x86_64-pc-linux-gnu locale: [1] LC_CTYPE=en_GB.UTF-8 LC_NUMERIC=C [3] LC_TIME=en_GB.UTF-8 LC_COLLATE=en_GB.UTF-8 [5] LC_MONETARY=C LC_MESSAGES=en_GB.UTF-8 [7] LC_PAPER=en_GB.UTF-8 LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=en_GB.UTF-8 LC_IDENTIFICATION=C attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] biomaRt_2.2.0 loaded via a namespace (and not attached): [1] RCurl_1.3-1 XML_2.6-0 > Thanks Iain _______________________________________________ Bioconductor mailing list Bioconductor at stat.math.ethz.ch https://stat.ethz.ch/mailman/listinfo/bioconductor Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor
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