Dan Tenenbaum | 3 Oct 02:26 2012

Re: biomaRt error in scan file

On Tue, Oct 2, 2012 at 4:26 PM, Martin Morgan <mtmorgan@...> wrote:
> 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.
>

We have temporarily placed a fixed version of RCurl in our extra
repository, so now it can be installed (with Bioconductor 2.10 or
later) with these commands:

source("http://bioconductor.org/biocLite.R")
biocLite("RCurl")

This should install RCurl 1.95-0.1.2.

The real, long-term solution is still forthcoming from the RCurl
maintainer, at which time we will remove this package from the extra
repository.

Dan

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