[Rd] Extreme slowdown with named vectors. A bug?
Duncan Murdoch
murdoch at stats.uwo.ca
Sat Oct 7 05:13:39 CEST 2006
On 10/6/2006 6:20 PM, Henrik Bengtsson wrote:
> Tried the following with R --vanilla on the Rv2.4.0 release (see
> details at the end). I think the script and its comments speaks for
> itself, but the outcome is certainly not wanted.
I think this is fixed now in R-devel and R-patched. Thanks for the
report, and the detailed script to reproduce the bug.
Duncan Murdoch
>
> for (n in 58950:58970) {
> cat("n=", n, "\n", sep="");
>
> # Clean up first
> rm(names, x, y); gc();
>
> # Create a named vector of length n
> # Try with format "%5d" and it works
> names <- sprintf("%05d", 1:n);
> x <- seq(along=names);
> names(x) <- names;
>
> # Extract the first k elements
> k <- 36422;
> t0 <- system.time({
> y <- x[names[1:k]];
> })
> str(y);
>
> # But with one more it takes
> # for ever when n >= 58960
> k <- k + 1;
> t1 <- system.time({
> y <- x[names[1:k]];
> })
> # ...then t1/t0 ~= 300-500 and growing!
> print(t1/t0);
> str(y);
> }
>
>
> The interesting this is that if you replace
>
> y <- x[names[1:k]];
>
> with
>
> idxs <- match(names[1:k], names(x));
> y <- x[idxs];
>
> everything is fine.
>
> (For those working with the Affy 100K SNP chips, the freaky thing is
> that the problem occurs at n = 58960 which is exactly the number of
> SNPs on the Xba array; that's how I found out about the bug/feature it
> the first place).
>
> Tried this on two different systems:
>
>> sessionInfo()
> R version 2.4.0 (2006-10-03)
> i386-pc-mingw32
> locale:
> LC_COLLATE=English_United States.1252;LC_CTYPE=English_United
> States.1252;LC_MONETARY=English_United
> States.1252;LC_NUMERIC=C;LC_TIME=English_United States.1252
> attached base packages:
> [1] "methods" "stats" "graphics" "grDevices" "utils" "datasets"
> [7] "base"
>
>> sessionInfo()
> R version 2.4.0 (2006-10-03)
> x86_64-unknown-linux-gnu
> locale:
> C
> attached base packages:
> [1] "methods" "stats" "graphics" "grDevices" "utils" "datasets"
> [7] "base"
>
> Cheers
>
> /Henrik
>
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