[R] /tmp/ gets filled up fast

Alessandro Gagliardi alessandro at gagliardi.name
Fri May 25 20:42:37 CEST 2007

Dear useRs,

I'm running some pretty big R scripts using a PBS that calls upon the
RMySQL library and it's filling up the /tmp/ directory with Rtmp*
files.  I thought the problem might have come from scripts crashing
and therefore not getting around to executing the dbDisconnect()
function, but I just ran a script that exited correctly and it still
left a giant file in /tmp/ without cleaning up after itself.  I'm
running all of my scripts using the --vanilla tag (saving the data I
need either into a separate .RData file or into the MySQL database).
Is there some other tag I should be using or some command I can put at
the end of my script to remove the Rtmp file when it's done?

Thank you,

---------- Forwarded message ----------
From: Yaroslav Halchenko
Date: May 24, 2007 7:42 PM
Subject: Re: mysql> Access denied for user
To: Alessandro Gagliardi

We need to resolve the issue somehow better way... /tmp/ gets filled up
fast with your R tasks...

*$> du -scm RtmpvKEqwr/
804     RtmpvKEqwr/
804     total

root at node26:/tmp
$> ls -ld RtmpvKEqwr/
0 drwx------ 2 eklypse eklypse 80 2007-05-24 15:18 RtmpvKEqwr//

root at node26:/tmp
$> df .
Filesystem           1K-blocks      Used Available Use% Mounted on
/dev/sda6              1052184   1052184         0 100% /tmp

I had to remove it...

check if there is a way to use some other directory may be? or properly
clean up??

On Wed, 23 May 2007, Alessandro Gagliardi wrote:

> Well, this is a real problem then.  Because I'm generating tables that
> R cannot get into MySQL because they are too big and it times out
> before it's done.

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