[BioC] biomaRt error in scan file

[Matthew McCormack]

Thank you very much, Dan and Martin. I was able to get it working with 
the fixed version of RCurl.

Matthew

On 10/2/2012 8:26 PM, Dan Tenenbaum wrote:
> On Tue, Oct 2, 2012 at 4:26 PM, Martin Morgan<mtmorgan at fhcrc.org>  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
>> @@ -140,7 +140,6 @@ 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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