Dear R-devel,
Can anyone give me some hints on how to go about debugging a strange
segfault in my randomForest package? Here's the scoop:
A user reported segfault when running predict() in the randomForest package.
I asked for the data and code. The combination runs fine under WinXPPro,
but does give segfault on one of our Linux boxes running R (1.7.0 through
R-devel_2004-01-08) on Mandrake 9.0.
The predict.randomForest() function calls a C function "runforest" via
.C(..., DUP=FALSE, ...), which in turns calls a Fortran subroutine
"testreebag" within a for loop. The segfault seems to occur right after
finishing the runforest() function in C and returning to R. I inserted the
line:
Rprintf("Done!\n");
as the last line of the runforest() function and got the following output:
> library(randomForest, lib.loc="~/rlibs")
> arabid <- read.table('arabidopsis.out', sep=' ', header=T)
> arabid <- arabid[,-which(names(arabid) == "X0")]
> set.seed(1)
> fit <- randomForest(arabid[,-1], arabid[,1], ntree=100)
> predict(fit, arabid[,-1])
Done!
Program received signal SIGSEGV, Segmentation fault.
0x40152a48 in malloc () from /lib/libc.so.6
[If I change the DUP=FALSE in the .C() call to TRUE, I get the following:
Program received signal SIGSEGV, Segmentation fault.
0x080b412b in Rf_duplicate (s=0x1) at duplicate.c:75
75 switch (TYPEOF(s)) {
]
At this point I'm clueless as to what to do next, and would very much
appreciate any help!
Best,
Andy
Andy Liaw, PhD
Biometrics Research PO Box 2000, RY33-300
Merck Research Labs Rahway, NJ 07065
mailto:[EMAIL PROTECTED] 732-594-0820
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