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
>>
>> ______________________________________________
>> R-devel@r-project.org mailing list
>> https://stat.ethz.ch/mailman/listinfo/r-devel
>>
>>
>
--
Ole F. Christensen
BiRC - Bioinformatics Research Center
University of Aarhus
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