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
>  <!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>
>

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I note below in sessionInfo() that you are using an outdated version of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><!--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.
>
>
>
> 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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