Martin Morgan | 3 Oct 01:26 2012

Re: biomaRt error in scan file

On 10/02/2012 04:05 PM, Matthew McCormack wrote:
> When I run the following in biomaRt:
> getBM(attributes=c('affy_ath1_121501', 'tair_locus', 'chromosome_name',
> 'start_position', 'end_position', 'strand', 'transcript_count', 'go_accession'),
> filters = 'affy_ath1_121501', values = affyids, mart = ensemartplants)
>
> I get the following error:
> Error in scan(file, what, nmax, sep, dec, quote, skip, nlines, na.strings,  :
>    line 156 did not have 8 elements
>
>     I seems that the file coming back has a value that does not have all 8
> attributes, but I don't know how I could fix that.

The latest versions of RCurl 1.95.0 / 1.95-0.1 are broken.

OTHER BIOCONDUCTOR USERS SHOULD NOT UPDATE TO THIS VERSION!

The solution is to use an earlier version of RCurl, or for the experienced user, 
download the source

   download.packages("RCurl", repos=biocinstallRepos(), destination="~/tmp")

and make the following change in the RCurl/R/form.S file (delete the single line 
that is prefixed by '-' below)

--- a/R/form.S
+++ b/R/form.S
 <at>  <at>  -140,7 +140,6  <at>  <at>  function(uri, ...,
    } else if(noCurlOptions && .checkParams)
      testCurlOptionsInFormParameters(.params)

-  status = .Call("R_post_form", curl, .opts, .params, TRUE, as.integer(style), 
  PACKAGE = "RCurl")
    status = .postForm(curl, .opts, .params, style)

    if(any(!isProtected)) {

and then install from source R CMD INSTALL RCurl

Installing from source requires appropriate tools and libraries (libcurl-dev) 
and will be very challenging on Windows.

Hopefully a fix from the RCurl maintainer will be forthcoming.

Martin

>
> Matthew
>
>
> The information in this e-mail is intended only for th...{{dropped:18}}

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