Dear subscribers of R-devel
I am experiencing that R crashes (further details are given below) in
some complex matrix calculations when EISPACK=TRUE has been specified in
eigen().
I discovered the behaviour some months ago just after the
release of R-2.2.0, and it has been lying on my desk since.
I apologise for not having nailed the problem down to a simple function
call, but I thought I should better report the problem now
instead of waiting.
My hope is that someone will either spot the cause
of the crash in a minute, or otherwise provide some help for me to
investigate further.
## The code :
source("http://www.daimi.au.dk/~olefc/TEST/fct.R";)
source("http://www.daimi.au.dk/~olefc/TEST/parm.crash.R";)
for(l.v in 1:4){
for(r.v in 1:4){
for(l.x in 1:4){
for(r.x in 1:4){
hvad <-
inhomoWmat.complex(subst.ratematrix(parm.same.str.sym$Gamma[,,l.v,r.v]),subst.ratematrix(parm.same.str.sym$Gamma[,,l.x,r.x]),
EISPACK=TRUE)
print(c(l.v,r.v,l.x,r.x))
}
}
}
}
## gives
[1] 1 1 1 1
[1] 1 1 1 2
[1] 1 1 1 3
[1] 1 1 1 4
[1] 1 1 2 1
Segmentation fault
### whereas the code seems to work fine when EISPACK=FALSE :
source("http://www.daimi.au.dk/~olefc/TEST/fct.R";)
source("http://www.daimi.au.dk/~olefc/TEST/parm.crash.R";)
for(l.v in 1:4){
for(r.v in 1:4){
for(l.x in 1:4){
for(r.x in 1:4){
hvad <-
inhomoWmat.complex(subst.ratematrix(parm.same.str.sym$Gamma[,,l.v,r.v]),subst.ratematrix(parm.same.str.sym$Gamma[,,l.x,r.x]),
EISPACK=FALSE)
print(c(l.v,r.v,l.x,r.x))
}
}
}
}
## works fine.
## There is some randomness in how and when the crash happens.
## The crash is either :
Segmentation fault
#
*** glibc detected *** double free or corruption (!prev): 0x08aa7298
***
# or
*** glibc detected *** free(): invalid pointer: 0x082bfd20 ***
## Seen on R-2.2-1 and R-2.2-0 .
## Not seen in R-2.1.1 !
## I haven't investiated whether it happens on Windows also.
### A few details on the matrix calculations :
The eigenvalue decomposition is done on 4 * 4 matrices where the rows
sum to 0.
The matrices may be on the edge of not being complex diagonalizable.
version
_
platform i686-pc-linux-gnu
arch i686
os linux-gnu
system i686, linux-gnu
status
major 2
minor 2.1
year 2005
month 12
day 20
svn rev 36812
language R
Thanks in advance of any help.
Ole Christensen
--
Ole F. Christensen
BiRC - Bioinformatics Research Center
University of Aarhus
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