Re: [Rd] read.table segfaults

From: Scott <ncbi2r_at_googlemail.com>
Date: Fri, 26 Aug 2011 12:41:37 -0700 (PDT)

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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