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<TITLE>RE: [Swift-user] swift and R</TITLE>
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<P><FONT SIZE=2>Hi Marcin!<BR>
<BR>
Could you send out the swift and R files, please?<BR>
<BR>
Thanks,<BR>
Erin<BR>
<BR>
<BR>
Erin M. Hodgess, PhD<BR>
Associate Professor<BR>
Department of Computer and Mathematical Sciences<BR>
University of Houston - Downtown<BR>
mailto: hodgesse@uhd.edu<BR>
<BR>
<BR>
<BR>
-----Original Message-----<BR>
From: swift-user-bounces@ci.uchicago.edu on behalf of Marcin Hitczenko<BR>
Sent: Sun 9/20/2009 10:17 PM<BR>
To: swift-user@ci.uchicago.edu<BR>
Subject: [Swift-user] swift and R<BR>
<BR>
Hi,<BR>
<BR>
I am trying to use swift in order to run an R script on various datasets<BR>
on jazz. For each run, I would like to return some output by writing data<BR>
to a file. I have tried to do this in two ways, and while one works I was<BR>
told this was a potentially risky way of doing things.<BR>
<BR>
What I try to do is to feed all relevant filenames to R (location of data<BR>
and location of output file) through swift as described on<BR>
<A HREF="http://www.ci.uchicago.edu/~erin/rguide/rforswift.php">http://www.ci.uchicago.edu/~erin/rguide/rforswift.php</A>.<BR>
<BR>
However, I run into two problems. Swift won't run because it complains<BR>
that the file to which I want to write the data does not exist (which is<BR>
true, but I would like to not have to create these files beforehand).<BR>
However, even when I create the (empty) file, nothing gets written to it.<BR>
I check the R log file and it seems that the data is written to something,<BR>
but when I check the file I created, it is still empty.<BR>
<BR>
The method that works is for me to just feed the datafile to R via swift<BR>
and within the R program itself declare the location to write to. Like I<BR>
said before, I was told this was not ideal, but I am not sure how to fix<BR>
the problems described above?<BR>
<BR>
Also, I noticed that a directory forms during the running of the swift<BR>
code, which I thought used to automatically be removed (except when there<BR>
was an error) at the completion of the run. This folder has not been<BR>
disappearing at completion (based on .out file). Am I not remembering<BR>
correctly that this should be a temporary directory? or am I doing<BR>
something incorrect?<BR>
<BR>
Sorry for the long email, but I figured I should at least partially detail<BR>
what I am trying to do/having problems with. Thank you for your time and<BR>
effort.<BR>
<BR>
Best,<BR>
<BR>
Marcin<BR>
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