[Rd] Slow ttests in R-devel
John Chambers
jmc at research.bell-labs.com
Wed Jun 4 15:34:03 MEST 2003
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
>
> ______________________________________________
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> https://www.stat.math.ethz.ch/mailman/listinfo/r-devel
--
John M. Chambers jmc at 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
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