maechler@stat.math.ethz.ch
2002-Jun-13 06:22 UTC
fisher.test FEXACT memory bug "should not occur" (PR#1662)
This is a bad bug as reported by Robin Hankin,
it is still in "R-patched" ...
##- From: Robin Hankin <r.hankin@auckland.ac.nz>
##- To: r-help@stat.math.ethz.ch
##- Subject: [R] possum sleeping: thanks and fisher.test() FEXACT error
##- Date: Thu, 13 Jun 2002 16:46:26 +1200
## .....
## Example slighlty modified (MM)
d4 <- matrix(c(0, 0, 0, 0, 0, 0, 3, 0, 1, 0, 0, 0, 0, 0, 0,
1, 0, 0, 0, 0, 1, 0, 0, 2, 0, 0, 0, 1, 0, 0,
0, 1, 0, 1, 0, 4, 0, 2, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0,
0, 1, 0, 0, 2, 0, 0, 0, 2, 2, 0, 1, 0, 0, 0,
0, 0, 1, 1, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0,
1, 0, 0, 0, 2, 0, 0, 0, 3, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0,
2, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 1,
0, 0, 0, 0, 2, 0, 0, 0, 0, 8, 0, 0, 0, 3, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1,
0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 2, 0, 0, 1, 0,
0, 2, 0, 0, 0, 0, 2, 0, 0, 1, 3, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 1, 0, 0, 4, 0, 0, 0, 0),
nr=50)
fisher.test(d4)
##- Error in fisher.test(alldata[, 2:5]) : FEXACT error 30.
##- Stack length exceeded in f3xact.
##- This problem should not occur.
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ligges@statistik.uni-dortmund.de
2002-Jun-13 06:59 UTC
fisher.test FEXACT memory bug "should not occur" (PR#1662)
maechler@stat.math.ethz.ch wrote:> > This is a bad bug as reported by Robin Hankin, > it is still in "R-patched" ... > > ##- From: Robin Hankin <r.hankin@auckland.ac.nz> > ##- To: r-help@stat.math.ethz.ch > ##- Subject: [R] possum sleeping: thanks and fisher.test() FEXACT error > ##- Date: Thu, 13 Jun 2002 16:46:26 +1200 > > ## ..... > > ## Example slighlty modified (MM) > > d4 <- matrix(c(0, 0, 0, 0, 0, 0, 3, 0, 1, 0, 0, 0, 0, 0, 0, > 1, 0, 0, 0, 0, 1, 0, 0, 2, 0, 0, 0, 1, 0, 0, > 0, 1, 0, 1, 0, 4, 0, 2, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, > 0, 1, 0, 0, 2, 0, 0, 0, 2, 2, 0, 1, 0, 0, 0, > 0, 0, 1, 1, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, > 1, 0, 0, 0, 2, 0, 0, 0, 3, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, > 2, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 1, > 0, 0, 0, 0, 2, 0, 0, 0, 0, 8, 0, 0, 0, 3, 0, > 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, > 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 2, 0, 0, 1, 0, > 0, 2, 0, 0, 0, 0, 2, 0, 0, 1, 3, 0, 0, 0, 0, > 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 1, 0, 0, 4, 0, 0, 0, 0), > nr=50) > > fisher.test(d4) > ##- Error in fisher.test(alldata[, 2:5]) : FEXACT error 30. > ##- Stack length exceeded in f3xact. > ##- This problem should not occur.Just for the record: repeat try(fisher.test(d4)) results in a crash after a few iterations (R-1.5.0 patched on WinNT 4.0). Uwe Ligges -.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.- r-devel mailing list -- Read http://www.ci.tuwien.ac.at/~hornik/R/R-FAQ.html Send "info", "help", or "[un]subscribe" (in the "body", not the subject !) To: r-devel-request@stat.math.ethz.ch _._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._
ripley@stats.ox.ac.uk
2002-Jun-13 11:16 UTC
fisher.test FEXACT memory bug "should not occur" (PR#1662)
This occurred because integer overflow was giving negative keys.
Append the following line at line 1083 of fexact.c
if (ipn < 1) ipn += ldst; /* because key might be negative */
> fisher.test(d4)
Fisher's Exact Test for Count Data
data: d4
p-value = < 2.2e-16
alternative hypothesis: two.sided
On Thu, 13 Jun 2002 maechler@stat.math.ethz.ch wrote:
> This is a bad bug as reported by Robin Hankin,
> it is still in "R-patched" ...
>
> ##- From: Robin Hankin <r.hankin@auckland.ac.nz>
> ##- To: r-help@stat.math.ethz.ch
> ##- Subject: [R] possum sleeping: thanks and fisher.test() FEXACT error
> ##- Date: Thu, 13 Jun 2002 16:46:26 +1200
>
> ## .....
>
> ## Example slighlty modified (MM)
>
> d4 <- matrix(c(0, 0, 0, 0, 0, 0, 3, 0, 1, 0, 0, 0, 0, 0, 0,
> 1, 0, 0, 0, 0, 1, 0, 0, 2, 0, 0, 0, 1, 0, 0,
> 0, 1, 0, 1, 0, 4, 0, 2, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0,
0,
> 0, 1, 0, 0, 2, 0, 0, 0, 2, 2, 0, 1, 0, 0, 0,
> 0, 0, 1, 1, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0,
> 1, 0, 0, 0, 2, 0, 0, 0, 3, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0,
0,
> 2, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 1,
> 0, 0, 0, 0, 2, 0, 0, 0, 0, 8, 0, 0, 0, 3, 0,
> 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
1,
> 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 2, 0, 0, 1, 0,
> 0, 2, 0, 0, 0, 0, 2, 0, 0, 1, 3, 0, 0, 0, 0,
> 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 1, 0, 0, 4, 0, 0, 0,
0),
> nr=50)
>
> fisher.test(d4)
> ##- Error in fisher.test(alldata[, 2:5]) : FEXACT error 30.
> ##- Stack length exceeded in f3xact.
> ##- This problem should not occur.
>
>
>
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--
Brian D. Ripley, ripley@stats.ox.ac.uk
Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/
University of Oxford, Tel: +44 1865 272861 (self)
1 South Parks Road, +44 1865 272860 (secr)
Oxford OX1 3TG, UK Fax: +44 1865 272595
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