From ncbi2r at googlemail.com  Fri Aug 26 21:41:37 2011
From: ncbi2r at googlemail.com (Scott)
Date: Fri, 26 Aug 2011 12:41:37 -0700 (PDT)
Subject: [Rd] read.table segfaults
In-Reply-To: <CAJxcB8mtJ_B=vLm5FSGLpqaN0V1ttKFzLaiBw+mUijBP0wzEyA@mail.gmail.com>
References: <CAJxcB8mtJ_B=vLm5FSGLpqaN0V1ttKFzLaiBw+mUijBP0wzEyA@mail.gmail.com>
Message-ID: <1314387697378-3771817.post@n4.nabble.com>

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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[Rd] read.table segfaults
Scott