[Rd] Memory leakage/violation?
Thomas Lumley
tlumley at u.washington.edu
Fri Aug 26 20:47:45 CEST 2005
I can't reproduce this on R2.2.0dev on Windows XP (in a few hundred
tries), or running under Valgrind on AMD64 Linux (in four or five tries).
-thomas
On Fri, 26 Aug 2005, Henrik Bengtsson wrote:
> Hi,
>
> I've spotted a possible memory leakage/violation in the latest R v2.1.1
> patched and R v2.2.0dev on Windows XP Pro SP2 Eng.
>
> I first caught it deep down in a nested svd algorithm when subtracting a
> double 'c' from a integer vector 'a' where both had finite values but
> when assigning 'a <- a - c' would report NaNs whereas (a-c) alone would
> not. Different runs with the identical data would introduce NaNs at
> random positions, but not all the time.
>
> Troubleshooting is after a couple of hours still at v0.5, but here is a
> script that generates the strange behavior on the above R setups. I let
> the script speak for itself. Note that both the script 'strange.R' and
> the data 'strange.RData' is online too, see code below.
>
> People on other systems (but also on Windows), could you please try it
> and see if you can reproduce what I get.
>
> Cheers
>
> Henrik
>
>
> # The following was tested on: Windows XP Pro SP2 Eng with
> # i) R Version 2.1.1 Patched (2005-08-25)
> # ii) R 2.2.0 Under development (unstable) (2005-08-25 r35394M)
>
> # Start 'R --vanilla' and source() this script, i.e.
> # source("http://www.maths.lth.se/help/R/strange.R")
> # If you do not get any errors, retry a few times.
>
> foo <- function(x) {
> print(list(
> name=as.character(substitute(x)),
> storage.mode=storage.mode(x),
> na=any(is.na(x)),
> nan=any(is.nan(x)),
> inf=any(is.infinite(x)),
> ok=all(is.finite(a))
> ))
> print(length(x))
> print(summary(x))
> }
>
> # Load data from a complicated "non-reproducible" algorithm.
> # The below errors occur also when data is not
> # saved and then reloaded from file. Data was generated in
> # R v2.1.1 patched (see above).
> if (file.exists("strange.RData")) {
> load("strange.RData")
> } else {
> load(url("http://www.maths.lth.se/help/R/strange.RData"))
> }
>
> # First glance at data...
> foo(a)
> foo(c)
>
> ## $name
> ## [1] "a"
> ##
> ## $storage.mode
> ## [1] "integer"
> ##
> ## $na
> ## [1] FALSE
> ##
> ## $nan
> ## [1] FALSE
> ##
> ## $inf
> ## [1] FALSE
> ##
> ## $ok
> ## [1] TRUE
> ##
> ## [1] 15000
> ## Min. 1st Qu. Median Mean 3rd Qu. Max.
> ## 41.0 51.0 63.0 292.2 111.0 65170.0
> ## $name
> ## [1] "c"
> ##
> ## $storage.mode
> ## [1] "double"
> ##
> ## $na
> ## [1] FALSE
> ##
> ## $nan
> ## [1] FALSE
> ##
> ## $inf
> ## [1] FALSE
> ##
> ## $ok
> ## [1] TRUE
> ##
> ## [1] 1
> ## Min. 1st Qu. Median Mean 3rd Qu. Max.
> ## 53.43 53.43 53.43 53.43 53.43 53.43
> ##
>
> # But, trying the following, will result in
> # no-reproducible error messages. Sometimes
> # it errors at kk==1, sometimes at kk >> 1.
> # Also, look at the different output for
> # different kk:s.
> for (kk in 1:100) {
> cat("kk=",kk, "\n")
> print(summary(a-c))
> }
>
> ## kk= 1
> ## Min. 1st Qu. Median Mean 3rd Qu. Max.
> ## -7.741e+307 -2.431e+00 9.569e+00 5.757e+01
> ## kk= 2
> ## Min. 1st Qu. Median Mean 3rd Qu. Max.
> ## -12.430 -2.431 9.569 238.700 57.570 65120.000
> ## kk= 3
> ## Min. 1st Qu. Median Mean 3rd Qu. Max.
> ## -12.430 -2.431 9.569 57.570 65120.000
> ## kk= 4
> ## Min. 1st Qu. Median Mean 3rd Qu. Max.
> ## -12.430 -2.431 9.569 238.700 57.570 65120.000
> ## kk= 5
> ## Min. 1st Qu. Median Mean 3rd Qu. Max.
> ## -12.430 -2.431 9.569 238.700 57.570 65120.000
> ## kk= 6
> ## Error in quantile.default(object) : missing values and NaN's
> ## not allowed if 'na.rm' is FALSE
>
>
> ## Comments: If you shorten down 'a', the bug occurs less frequently.
>
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>
Thomas Lumley Assoc. Professor, Biostatistics
tlumley at u.washington.edu University of Washington, Seattle
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