From goran.brostrom at gmail.com  Sat Aug 27 11:49:21 2011
From: goran.brostrom at gmail.com (=?UTF-8?B?R8O2cmFuIEJyb3N0csO2bQ==?=)
Date: Sat, 27 Aug 2011 11:49:21 +0200
Subject: [Rd] read.table segfaults
In-Reply-To: <1314387697378-3771817.post@n4.nabble.com>
References: <CAJxcB8mtJ_B=vLm5FSGLpqaN0V1ttKFzLaiBw+mUijBP0wzEyA@mail.gmail.com>
	<1314387697378-3771817.post@n4.nabble.com>
Message-ID: <CAJxcB8mDdf0_kN8dOv6e5hYDVRjO6BMzie5bwUtxvBYfHpY6cw@mail.gmail.com>

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)?

G?ran

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-- 
G?ran Brostr?m



[Rd] read.table segfaults
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