Re: [Rd] read.table segfaults

From: Göran Broström <goran.brostrom_at_gmail.com>
Date: Sat, 27 Aug 2011 11:49:21 +0200

On Fri, Aug 26, 2011 at 9:41 PM, Scott <ncbi2r_at_googlemail.com> wrote:
> 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)

Today, after a night's sleep, there are no segfaults! (The computer also slept, I turned it off.) So what is going on? Maybe I shouldn't bother.... but I installed the latest patched version yesterday, immediately tried to read the file with a segfault as a result, turned the machine off and on, and no problems. Do we need to reboot after a new install (note, this is not Windows)?

Göran

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-- 
Göran Broström

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Received on Sat 27 Aug 2011 - 09:54:29 GMT

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