Hi, John. The email list to which the message refers is, indeed, the bioconductor email list, but a few of us read both.
The first step is to upgrade your R version to the current version and then reinstall biomaRt. If you still have problems, let us know on the bioconductor mailing list. Thanks, Sean On Thu, Aug 2, 2012 at 6:48 AM, John Coulthard <[email protected]> wrote: > Hi > > When following the instructions in the biomaRt.pdf I get the error below > which ends 'Please report this to the mailing list' (I hope it means the > biomart mailing list rather than R or bioconductor lists). > > 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 2.14.1 (2011-12-22) > Copyright (C) 2011 The R Foundation for Statistical Computing > ISBN 3-900051-07-0 > Platform: x86_64-pc-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 <!DOCTYPE HTML PUBLIC -//W3C//DTD HTML 4.01 > Transitional//EN 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; > <TITLE>ERROR: The requested URL could not be retrieved</TITLE> > 4 <STYLE > type=text/css><!--BODY{background-color:#ffffff;font-family:verdana,sans-serif}PRE{font-family:sans-serif}--></STYLE> > 5 > & nbsp; </HEAD><BODY> > 6 > <H1>ERROR</H1> > 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. > > > > > > > sessionInfo() > R version 2.14.1 (2011-12-22) > Platform: x86_64-pc-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 &nb s p; 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] RCurl_1.91-1 XML_3.9-4 > > > > > > > > source("http://bioconductor.org/biocLite.R";) > BiocInstaller version 1.2.1, ?biocLite for help > > biocLite("org.Hs.eg.db") > BioC_mirror: 'http://www.bioconductor.org' > Using R version 2.14, BiocInstaller version 1.2.1. > Installing package(s) 'org.Hs.eg.db' > Installing package(s) into \u2018/usr/local/lib/R/site-library\u2019 > (as \u2018lib\u2019 is unspecified) > Warning in install.packages(pkgs = pkgs, repos = repos, ...) : > 'lib = "/usr/local/lib/R/site-library"' is not writable > Would you like to create a personal library > ~/R/x86_64-pc-linux-gnu-library/2.14 > to install packages into? (y/n) y > trying URL ' > http://www.bioconductor.org/packages/2.9/data/annotation/src/contrib/org.Hs.eg.db_2.6.4.tar.gz > ' > Content type 'application/x-gzip' length 46530609 bytes (44.4 Mb) > opened URL > ================================================== > downloaded 44.4 Mb > > * installing *source* package \u2018org.Hs.eg.db\u2019 ... > ** R > ** inst > etc, etc. > >
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