biomaRt 'Please report this to the mailing list'
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@john-coulthard-3077
Last seen 10.5 years ago
Hi When following the instructions in the biomaRt.pdf I get the error below which ends 'Please report this to the mailing list'. Did I do something wrong or do I wait for something to be fixed? I am behind a proxy server but I can download packages so I don't think that is the issue. Many thanks John $ R R version 2.15.1 (2012-06-22) -- "Roasted Marshmallows" Copyright (C) 2012 The R Foundation for Statistical Computing ISBN 3-900051-07-0 Platform: x86_64-unknown-linux-gnu (64-bit) R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under certain conditions. Type 'license()' or 'licence()' for distribution details. Natural language support but running in an English locale R is a collaborative project with many contributors. Type 'contributors()' for more information and 'citation()' on how to cite R or R packages in publications. Type 'demo()' for some demos, 'help()' for on-line help, or 'help.start()' for an HTML browser interface to help. Type 'q()' to quit R. > library(biomaRt) > ensembl = useMart("ensembl", dataset = "hsapiens_gene_ensembl") > affyids = c("202763_at", "209310_s_at", "207500_at") > getBM(attributes = c("affy_hg_u133_plus_2", "entrezgene"), filters = "affy_hg_u133_plus_2",values = affyids, mart = ensembl) & nbsp; V1 1 2 <html><head><meta http-equiv="Content-Type" content="text/html;" charset="iso-8859-1"> 3 & nbsp; <title>ERROR: The requested URL could not be retrieved</title> 4 <style type="text/css"></style> 5 & nbsp; </head><body> 6

ERROR

Error in getBM(attributes = c("affy_hg_u133_plus_2", "entrezgene"), filters = "affy_hg_u133_plus_2", : The query to the BioMart webservice returned an invalid result: the number of columns in the result table does not equal the number of attributes in the query. Please report this to the mailing list. That html reads.... ERROR The requested URL could not be retrieved While trying to process the request: POST /biomart/martservice? HTTP/1.1 Host: www.biomart.org Accept: */* Proxy-Connection: Keep-Alive Content-Length: 483 Expect: 100-continue Content-Type: multipart/form- data; boundary=----------------------------2224e5531f52 The following error was encountered: Invalid Request Some aspect of the HTTP Request is invalid. Possible problems: Missing or unknown request method Missing URL Missing HTTP Identifier (HTTP/1.0) Request is too large Content-Length missing for POST or PUT requests Illegal character in hostname; underscores are not allowed Your cache administrator is cacheadmin@udcf.gla.ac.uk. Generated Thu, 02 Aug 2012 11:12:23 GMT by south (squid/2.7.STABLE9) > sessionInfo() R version 2.15.1 (2012-06-22) Platform: x86_64-unknown-linux-gnu (64-bit) 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=en_GB.UTF-8 LC_MESSAGES=en_GB.UTF-8 [7] LC_PAPER=C 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_2.10.0 loaded via a namespace (and not attached): [1] AnnotationDbi_1.16.19 Biobase_2.14.0 Biostrings_2.22.0 [4] BSgenome_1.22.0 DBI_0.2-5 GenomicFeatures_1.6.9 [7] GenomicRanges_1.6.7 IRanges_1.12.6 RCurl_1.91-1 [10] RSQLite_0.11.1 rtracklayer_1.14.4 tools_2.15.1 [13] XML_3.9-4 zlibbioc_1.0.1 > [[alternative HTML version deleted]]
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@sean-davis-490
Last seen 4 days ago
United States
On Thu, Aug 2, 2012 at 9:58 AM, John Coulthard <bahhab@hotmail.com> wrote: > > Hi > > When following the instructions in the biomaRt.pdf I get the > error below which ends 'Please report this to the mailing list'. > > Did I do something wrong or do I wait for something to be fixed? > I am behind a proxy server but I can download packages so I don't think > that is the issue. > > Many thanks > John > > > $ R > > R version 2.15.1 (2012-06-22) -- "Roasted Marshmallows" > Copyright (C) 2012 The R Foundation for Statistical Computing > ISBN 3-900051-07-0 > Platform: x86_64-unknown-linux-gnu (64-bit) > > R is free software and comes with ABSOLUTELY NO WARRANTY. > You are welcome to redistribute it under certain conditions. > Type 'license()' or 'licence()' for distribution details. > > Natural language support but running in an English locale > > R is a collaborative project with many contributors. > Type 'contributors()' for more information and > 'citation()' on how to cite R or R packages in publications. > > Type 'demo()' for some demos, 'help()' for on-line help, or > 'help.start()' for an HTML browser interface to help. > Type 'q()' to quit R. > > > library(biomaRt) > > ensembl = useMart("ensembl", dataset = "hsapiens_gene_ensembl") > > affyids = c("202763_at", "209310_s_at", "207500_at") > > > getBM(attributes = c("affy_hg_u133_plus_2", "entrezgene"), filters = > "affy_hg_u133_plus_2",values = affyids, mart = ensembl) > > > & > nbsp; V1 > 1 > http://www.w3.org/TR/html4/loose.dtd> > 2 > <html><head><meta http-equiv="Content-Type"> CONTENT=text/html; charset=iso-8859-1> > 3 > > & > nbsp; ERROR: The > requested URL could not be retrieved > Hi, John. I note below in sessionInfo() that you are using an outdated version of biomaRt. You might want to update by doing: biocLite('biomaRt') Using the current release version (2.12.0), I was not able to reproduce your problem. That said, it looks like biomaRt cannot connect to biomart. Does listMarts(ensembl) work for you? This could be a temporary problem or it could be that you are behind a firewall and need to set up a proxy for R to connect to the internet. Sean > 4 > <style> > type=text/css></style> > 5 > > & > nbsp; </head><body> > 6 >

ERROR

> Error in getBM(attributes = c("affy_hg_u133_plus_2", "entrezgene"), > filters = "affy_hg_u133_plus_2", : > > The query to the BioMart webservice returned an invalid result: the > number of columns in the result table does not equal the number of > attributes in the query. Please report this to the mailing list. > > > > That html reads.... > ERROR > The requested URL could not be retrieved > > While trying to process the request: > > > POST /biomart/martservice? HTTP/1.1 > > Host: www.biomart.org > > Accept: */* > > Proxy-Connection: Keep-Alive > > Content-Length: 483 > > Expect: 100-continue > Content-Type: > multipart/form-data; boundary=----------------------------2224e5531f52 > > > The following error was encountered: > > Invalid Request > > Some aspect of the HTTP Request is invalid. Possible problems: > > Missing or unknown request method > Missing URL > Missing HTTP Identifier (HTTP/1.0) > Request is too large > Content-Length missing for POST or PUT requests > Illegal character in hostname; underscores are not allowed > > Your cache administrator is cacheadmin@udcf.gla.ac.uk. > Generated Thu, 02 Aug 2012 11:12:23 GMT by south (squid/2.7.STABLE9) > > > > sessionInfo() > R version 2.15.1 (2012-06-22) > Platform: x86_64-unknown-linux-gnu (64-bit) > > 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=en_GB.UTF-8 LC_MESSAGES=en_GB.UTF-8 > [7] LC_PAPER=C 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_2.10.0 > > loaded via a namespace (and not attached): > [1] AnnotationDbi_1.16.19 Biobase_2.14.0 Biostrings_2.22.0 > [4] BSgenome_1.22.0 DBI_0.2-5 GenomicFeatures_1.6.9 > [7] GenomicRanges_1.6.7 IRanges_1.12.6 RCurl_1.91-1 > [10] RSQLite_0.11.1 rtracklayer_1.14.4 tools_2.15.1 > [13] XML_3.9-4 zlibbioc_1.0.1 > > > > > > [[alternative HTML version deleted]] > > _______________________________________________ > 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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