Ah! sorted!
it was NOT running the same code.
We're making a GUI using Perl (Tcl/Tkx) to facilitate a number of
analyses in our lab to other people who don't necessarily want to know
about R (their loss ;-)
I provided the R code to my colleague and he assured me he used it
without changes... but when I've looked into it, there were a number
of changes... (?) I restored the code to what I knew to work and from
the Tcl/Tkx GUI it's *almost* as fast as when I run it from a clean
session from the R console. So that was the problem.
In case I'm still not doing things teh best way, we're invoking R from
Perl like this:
invoking the script from Perl:
@output = qx($R.exe --vanilla --args $list of arguments...)
should I use Rterm.exe or Rcmd.exe instead of R.exe?
Jose
Quoting jim holtman <jholt...@gmail.com>:
What operating system are you running under? You should take a look
at the R process and see how much time it is using to see if there is
a difference in the CPU time. Are you paging? Exactly how are you
invoking the R script? Why are you using the GUI instead of Rterm?
You might try to run Rprof on the code to see if there are
differences. Are you sure you are running exactly the same data in
both cases?
On Thu, Sep 3, 2009 at 11:42 AM, <j.delashe...@ed.ac.uk> wrote:
Hello list,
I use R for microarray analysis.
One procedure I use takes a large matrix, and loops through it looking for
specific rows, does an operation with them, and outputs a result (single
row) as a row of another matrix. The loop goes on about 25000 times.
When I run the loop directly from the R console itself, it takes about 3
minutes in my computer. I'm ok with that.
Now, when that same code is ran from within a GUI we created using Perl
(Tcl/Tkx) it's taking 25-30 minutes to run.
Within the R code I inserted a line so that it writes a little file every
1000th iteration of the loop, so that I can follow the progress. I don't
understand why it takes 10x longer when ran from Perl.
I am not new to R, but I am new to using it within Perl or any other
language. Is there a way to improve performance? What is the reason for the
slower speed?
I'll happily provide the code if somebody wants it.
thank you.
Jose
--
Dr. Jose I. de las Heras Email: j.delashe...@ed.ac.uk
The Wellcome Trust Centre for Cell Biology Phone: +44 (0)131 6513374
Institute for Cell & Molecular Biology Fax: +44 (0)131 6507360
Swann Building, Mayfield Road
University of Edinburgh
Edinburgh EH9 3JR
UK
*********************************************
NEW EMAIL from July'09: nach.mcn...@gmail.com
*********************************************
--
The University of Edinburgh is a charitable body, registered in
Scotland, with registration number SC005336.
______________________________________________
R-help@r-project.org mailing list
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
--
Jim Holtman
Cincinnati, OH
+1 513 646 9390
What is the problem that you are trying to solve?
--
Dr. Jose I. de las Heras Email: j.delashe...@ed.ac.uk
The Wellcome Trust Centre for Cell Biology Phone: +44 (0)131 6513374
Institute for Cell & Molecular Biology Fax: +44 (0)131 6507360
Swann Building, Mayfield Road
University of Edinburgh
Edinburgh EH9 3JR
UK
*********************************************
NEW EMAIL from July'09: nach.mcn...@gmail.com
*********************************************
--
The University of Edinburgh is a charitable body, registered in
Scotland, with registration number SC005336.
______________________________________________
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
