Brain, Thank you very much for your help.
Using gctorture I was able to produce a simple function call showing the
problem.
Gm <- rbind(c(-0.3194373786, 0.2444066686, 0.0428108831, 3.221983e-02),
c(0.0002071301, -0.0003282719, 0.0001211418,
5.128830e-12),
c(0.0621332005, 0.0545850010, -0.2098487035,
9.313050e-02),
c(0.0280936142, 0.0586642184, 0.1658310277,
-2.525889e-01)
)
print(Gm)
temp <- eigen(Gm)
print(temp)
gctorture(TRUE)
temp <- eigen(Gm, EISPACK = TRUE)
###
# On my computer I get :
##
[,1] [,2] [,3] [,4]
[1,] -0.3194373786 0.2444066686 0.0428108831 3.221983e-02
[2,] 0.0002071301 -0.0003282719 0.0001211418 5.128830e-12
[3,] 0.0621332005 0.0545850010 -0.2098487035 9.313050e-02
[4,] 0.0280936142 0.0586642184 0.1658310277 -2.525889e-01
temp <- eigen(Gm)
print(temp)
$values
[1] -3.464342e-01+1.3161e-03i -3.464342e-01-1.3161e-03i
[3] -8.933476e-02+0.0000e+00i 9.052031e-19+0.0000e+00i
$vectors
[,1] [,2] [,3]
[1,] -0.3419128709-0.03748199i -0.3419128709+0.03748199i -0.222056433+0i
[2,] 0.0003508445+0.00001921i 0.0003508445-0.00001921i 0.001421758+0i
[3,] -0.4179745717+0.01301547i -0.4179745717-0.01301547i -0.664932225+0i
[4,] 0.8407249376+0.00000000i 0.8407249376+0.00000000i -0.713129761+0i
[,4]
[1,] -0.5+0i
[2,] -0.5+0i
[3,] -0.5+0i
[4,] -0.5+0i
temp <- eigen(Gm, EISPACK = TRUE)
*** glibc detected *** free(): invalid pointer: 0x08c4e778 ***
Aborted
# Should I submit this as a bug report also ?
Best
Ole
Prof Brian Ripley wrote:
Try valgrind. That is reporting use outside arrays in rg, that is the
non-complex case of eigen().
Otherwise, using gctorture(TRUE) will help precipitate the error.
On Mon, 2 Jan 2006, Ole F. Christensen wrote:
Dear subscribers of R-devel
I am experiencing that R crashes (further details are given below) in
some complex matrix calculations when EISPACK=TRUE has been specified in
eigen().
I discovered the behaviour some months ago just after the
release of R-2.2.0, and it has been lying on my desk since.
I apologise for not having nailed the problem down to a simple function
call, but I thought I should better report the problem now
instead of waiting.
My hope is that someone will either spot the cause
of the crash in a minute, or otherwise provide some help for me to
investigate further.
## The code :
source("http://www.daimi.au.dk/~olefc/TEST/fct.R")
source("http://www.daimi.au.dk/~olefc/TEST/parm.crash.R")
for(l.v in 1:4){
for(r.v in 1:4){
for(l.x in 1:4){
for(r.x in 1:4){
hvad <-
inhomoWmat.complex(subst.ratematrix(parm.same.str.sym$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