Dear R-help, A colleague of mine was running some code on two of our boxes, and noticed a rather large difference in running time. We've so far isolated the problem to the difference between R 1.7.1 and 1.8.0, but not more than that. The exact same code took 933.5 seconds in 1.7.1, and 3594.4 seconds in 1.8.1, on the same box.
Basically, the code calls boot() to bootstrap fitting mixture models by calling flexmix() (in the flexmix package) with intercept-only models. The code needs to be strip down further, but I thought some of you might be able to tell what's wrong from the info we have so far: I ran R profiling on the code, under both R 1.7.1 and 1.8.1 (but the performance gap is there in 1.8.0 already). Sorted by "self" part of the output, the top 10 lines are: R 1.7.1 % self % total self seconds total seconds name 10.75 100.36 10.75 100.36 ".Fortran" 8.71 81.32 34.27 319.88 "lm.wfit" 5.43 50.66 81.19 757.88 "FLXfit" 4.30 40.16 4.30 40.16 "^" 4.26 39.80 4.26 39.80 "==" 4.15 38.74 4.99 46.62 "names" 3.90 36.38 20.57 191.98 "initialize" 3.51 32.80 5.37 50.14 "dnorm" 2.29 21.34 4.94 46.14 "hclass" 1.83 17.10 5.85 54.64 "inherits" R 1.8.1: % self % total self seconds total seconds name 6.24 224.26 11.69 420.32 "paste" 5.93 213.04 13.21 474.76 "read.dcf" 4.37 157.24 5.17 185.92 "names" 4.18 150.42 5.53 198.66 "exists" 3.71 133.52 14.66 527.00 "lapply" 3.15 113.16 4.43 159.32 "names<-" 2.98 107.26 2.98 107.26 ".Fortran" 2.57 92.46 5.75 206.82 "seq" 2.54 91.42 3.18 114.14 "seq.default" 2.37 85.24 8.93 320.96 "lm.wfit" The ".Fortran" call took about the same amount of time, as does "lm.wfit", so that's a bit comforting. (The code also fits the same model using mclust, and that's probably where the .Fortran call is from.) What puzzled me are: - Several functions took much longer in 1.8.1; e.g., 1.7.1 1.8.1 "paste" 28 224 "names" 38 157 "names<-" 15 113 "exists" 4 150 - The presence of "read.dcf" in 1.8.1. Where could this be from? Any clues as to why we're seeing this? Best, Andy Andy Liaw, PhD Biometrics Research PO Box 2000, RY33-300 Merck Research Labs Rahway, NJ 07065 mailto:[EMAIL PROTECTED] 732-594-0820 ______________________________________________ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help