R crash with complex matrix algebra when using EISPACK=TRUE

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 :
##

gctorture(TRUE)

source("http://www.daimi.au.dk/~olefc/TEST/Gm.R")
print(Gm)

             [,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

-- 
Ole F. Christensen
BiRC - Bioinformatics Research Center
University of Aarhus