From jmc at research.bell-labs.com  Wed Jun  4 15:34:03 2003
From: jmc at research.bell-labs.com (John Chambers)
Date: Wed Jun  4 20:34:24 2003
Subject: [Rd] Slow ttests in R-devel
References: <Pine.SOL.4.20.0306041415200.2329-100000@santiam.dfci.harvard.edu>
Message-ID: <3EDE3B9B.2E3F0C2@research.bell-labs.com>

There was a bug leading to non-caching of methods, in the r-patched code
from a few days ago.

A branch update would have put the changes into R-devel also.

The problem has been partly fixed in the current code committed to
R-patched (and some further fixes are in the works).

(Sorry, this was discussed on r-core, so didn't yet get to the r-devel
list.)

John

Jeff Gentry wrote:
> 
> Hello ...
> 
> I've noticed that some of our Bioconductor code was running drastically
> slower under current R-devel vs. current R-patched - one example is below
> using a ttest.  I have the following snippet of code that demonstrates the
> problem while avoiding "real" code that takes an extremely long time to
> finish on R-devel:
> 
> library(genefilter)
> data(eset)
> eset$cov1
> z <- ttest(eset$cov1, p=0.01)
> gf <- filterfun(z)
> system.time(genefilter(eset, gf))
> 
> (this requires the genefilter & Biobase packages from Bioconductor)
> 
> Using R-1.7.0p I had the following output:
> > data(eset)
> > eset$cov1
>  [1] 1 1 1 1 1 1 1 1 1 1 1 1 1 2 2 2 2 2 2 2 2 2 2 2 2 2
> > z <- ttest(eset$cov1, p=0.01)
> > gf <- filterfun(z)
> > system.time(genefilter(eset, gf))
> [1] 41.73  2.04 44.45  0.00  0.00
> 
> And using R-devel, I have:
> > data(eset)
> > eset$cov1
>  [1] 1 1 1 1 1 1 1 1 1 1 1 1 1 2 2 2 2 2 2 2 2 2 2 2 2 2
> > z <- ttest(eset$cov1, p=0.01)
> > gf <- filterfun(z)
> > system.time(genefilter(eset, gf))
> [1] 80.56  4.20 85.12  0.00  0.00
> 
> Any ideas what might be causing this?
> 
> Thanks
> -Jeff
> 
> ______________________________________________
> R-devel@stat.math.ethz.ch mailing list
> https://www.stat.math.ethz.ch/mailman/listinfo/r-devel

-- 
John M. Chambers                  jmc@bell-labs.com
Bell Labs, Lucent Technologies    office: (908)582-2681
700 Mountain Avenue, Room 2C-282  fax:    (908)582-3340
Murray Hill, NJ  07974            web: http://www.cs.bell-labs.com/~jmc


[Rd] Slow ttests in R-devel
John Chambers