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 > > ______________________________________________ > [EMAIL PROTECTED] mailing list > https://www.stat.math.ethz.ch/mailman/listinfo/r-devel -- John M. Chambers [EMAIL PROTECTED] 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 ______________________________________________ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-devel
