It does look like you've got a memory issue. perhaps using
as.is=TRUE, and/or stringsAsFactors=FALSE will help as optional arguments
to read.table
if you don't specify these sorts of things, R can have to look through the
file and figure out which columns are characters/factors etc and so the
larger files cause more of a headache for R I'm guess. Hopefully someone
else can comment further on this? I'd true toggling TRUE/FALSE for as.is and
stringsAsFactors.
do you have other objects loaded in memory as well? this file by itself
might not be the problem - but it's a cumulative issue.
have you checked the file structure in any other manner?
how large (Mb/kb) is the file that you're trying to read?
if you just read in parts of the file, is it okay?
read.table(filename,header=FALSE,sep="\t",nrows=100)
read.table(filename,header=FALSE,sep="\t",skip=20000,nrows=100)
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