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}} >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor at r-project.org >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: >> http://news.gmane.org/gmane.science.biology.informatics.conductor The information in this e-mail is intended only for the ...{{dropped:11}}