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