Couple of things to try.  May have an extra quote, so put:

quote = ''

as one of the parameters.  Also, might have comments, so try:

comment.char = ""

Take alook at your file and determine what line was the last complete one
and see if there might be a problem in that line, or preceeding ones.

On Mon, Aug 5, 2013 at 7:11 AM, Asis Hallab <asis.hallab@gmail.com> wrote:

> Dear R experts,
>
> I have a large table saved in a file called "plant_genome.gff". The
> file has 481848 lines in nine columns, which are TAB delimited, and is
> 53 MegaBytes large.
> For anyone who might know the GFF3 format: The table holds a plant
> genome's annotation.
>
> If I read in the table with
> read.table( "plant_genome.gff" )
> I get the following error
> "line 2 did not have 12 elements".
>
> If I read in the table with
> read.table( "plant_genome.gff", sep="\t" )
> no error or warning is given, but my resulting table has only 193547
> instead of the expected 481848 rows! 60% of the lines are omitted.
>
> Also passing in the arguments
> as.is = TRUE
> or setting the columns' classes with
> colClasses = c( "character", …, "integer", "integer", "numeric",
> "character", … )
>    # columns 4, and 5 are integers, column 6 is numeric, all others
> are characters
> does not resolve the problem.
>
> If I read in the file with readLines and then manually split them using
> strplit(…)
> and combine them into a data.frame with
> as.data.frame( do.call( "rbind", splitted.lines ), colClasses=…)
> I get the expected and correct data.frame, representing my GFF3 data.
>
> My questions are:
> 1) Am I using read.table wrong, or did I miss something in the
> documentation?
> 2) Or is this is known problem with large TAB delimited tables, whose
> columns contain white-spaces and are not surrounded by quotes?
>
> Unfortunately due to the unpublished nature of the plant genome I am
> not allowed to give access to the GFF table that causes this problem.
>
> Any ideas, hints, help - or comments on my stupidity having missed
> something important - will be much appreciated!
>
> Cheers!
>
> ______________________________________________
> R-help@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide
> http://www.R-project.org/posting-guide.html<http://www.r-project.org/posting-guide.html>
> and provide commented, minimal, self-contained, reproducible code.
>



-- 
Jim Holtman
Data Munger Guru

What is the problem that you are trying to solve?
Tell me what you want to do, not how you want to do it.

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