[R] Crash when running functions from contributed packages

[Carel, Roland]

"Prof Brian D Ripley" <ripley at stats.ox.ac.uk> wrote:

>Yes, to use princomp was going to be my advice. (The quotes in example()  
>are optional). But, I have R 0.65.1 on Solaris, so I ran

>R INSTALL multiv_1.0-3.tar.gz 
>R
>
>R : Copyright 1999, The R Development Core Team
>Version 0.65.1 Release (October 07, 1999)
>...
>> library(mva)
>> library(multiv)
>> x <- rbind(cbind(rnorm(200,0,8), rnorm(200,0,8)),
>+  cbind(rnorm(300,50,8), rnorm(300,50,8)))
>> pcax <- pca(x)
>
>which seems to indicate that the problem is somewhere in how you installed
>multiv.  Have you run `make check' on your build of R to check that the
>standard packages do work?

Thanks to the suggestions from several people, I made incremental progress
in resolving the issue I am having with R. However, the mystery now seems
even thicker. The crashes seem to occur when some fortran code is invoked by
the function being run. I am not seeing any problem with princomp() for
example, but clara() or pam() trigger the crash. The behavior is not library
specific and they occur with both cluster and multiv. Below is the ouput
from the debugger for clara() and is typical of what I am seeing. 

Based on the line number generated from the debugger, the error occurs for
the line:
KRAN=RNN+*RAN+1.
which does not make sense.

I am not too familiar with g77 or fortran in general, but is there a chance
that the problem is with the fortran compiler?

Any input would be much appreciated.

-Roland Carel


> library(mva)
> library(cluster)
> example(clara)

clara> x <- rbind(cbind(rnorm(200, 0, 8), rnorm(200, 0, 8)), 
    cbind(rnorm(300, 50, 8), rnorm(300, 50, 8)))

clara> clarax <- clara(x, 2)

Program received signal SIGBUS, Bus error.
0xef420fc4 in clara_ (nn=0xc10c40, jpp=0xc10c38, kk=0xc10c30, x=0xc0ecf0,
nran=0xc0ece8, nsam=0xc0ece0, dys=0xc0cf48, mdata=0xc0cf40, 
    valmd=0xc0cf30, jtmd=0xc0cf28, ndyst=0xc0cf20, nrepr=0xc0ce70,
nsel=0xc0cdc0, nbest=0xc0cd10, nr=0xc0cd08, nrx=0xc0cd00, 
    radus=0xc0ccf0, ttd=0xc0cce0, ratt=0xc0ccd0, ttbes=0xc0ccc0,
rdbes=0xc0ccb0, rabes=0xc0cca0, mtt=0xc0cc98, azba=0xc0cc90, 
    avsyl=0xc0cc80, ttsyl=0xc0cc78, sylinf=0xc0c6f8, jstop=0xc0c6f0,
tmp1=0xc0c590, tmp2=0xc0c430, tmp3=0xc0c2d0, ntmp1=0xc0c220, 
    ntmp2=0xc0c170, ntmp3=0xc0c0c0, ntmp4=0xc0c010, ntmp5=0xc0bf60,
ntmp6=0xc0beb0) at clara.f:86
clara.f:86: No such file or directory.
Current language:  auto; currently fortran
(gdb) bt
#0  0xef420fc4 in clara_ (nn=0xc10c40, jpp=0xc10c38, kk=0xc10c30,
x=0xc0ecf0, nran=0xc0ece8, nsam=0xc0ece0, dys=0xc0cf48, mdata=0xc0cf40, 
    valmd=0xc0cf30, jtmd=0xc0cf28, ndyst=0xc0cf20, nrepr=0xc0ce70,
nsel=0xc0cdc0, nbest=0xc0cd10, nr=0xc0cd08, nrx=0xc0cd00, 
    radus=0xc0ccf0, ttd=0xc0cce0, ratt=0xc0ccd0, ttbes=0xc0ccc0,
rdbes=0xc0ccb0, rabes=0xc0cca0, mtt=0xc0cc98, azba=0xc0cc90, 
    avsyl=0xc0cc80, ttsyl=0xc0cc78, sylinf=0xc0c6f8, jstop=0xc0c6f0,
tmp1=0xc0c590, tmp2=0xc0c430, tmp3=0xc0c2d0, ntmp1=0xc0c220, 
    ntmp2=0xc0c170, ntmp3=0xc0c0c0, ntmp4=0xc0c010, ntmp5=0xc0bf60,
ntmp6=0xc0beb0) at clara.f:86
#1  0x46568 in do_dotCode (call=0x5690a8, op=0x65e2a5, args=0x52eae8,
env=0x5f8a50) at dotcode.c:1379
#2  0x4d7b0 in eval (e=0x5690a8, rho=0x5f8a50) at eval.c:186
#3  0x4ee5c in do_set (call=0x5690e4, op=0x14ca4c, args=0x5690d0,
rho=0x5f8a50) at eval.c:844
#4  0x4d7b0 in eval (e=0x5690e4, rho=0x5f8a50) at eval.c:186
#5  0x4e898 in do_begin (call=0x564c38, op=0x14caec, args=0x5690f8,
rho=0x5f8a50) at eval.c:644
#6  0x4d7b0 in eval (e=0x564c38, rho=0x5f8a50) at eval.c:186
#7  0x4dce4 in applyClosure (call=0x5f6d7c, op=0x5c7504, arglist=0x5f899c,
rho=0x154ea4, suppliedenv=0x14c1a0) at eval.c:347
#8  0x4d824 in eval (e=0x5f6d7c, rho=0x154ea4) at eval.c:195
#9  0x4ee5c in do_set (call=0x5f6d40, op=0x14ca4c, args=0x5f6d54,
rho=0x154ea4) at eval.c:844
#10 0x4d7b0 in eval (e=0x5f6d40, rho=0x154ea4) at eval.c:186
#11 0x4f710 in do_eval (call=0x1, op=0x152cd0, args=0x5f88ac, rho=0x5f8870)
at eval.c:1115
#12 0x69ee0 in do_internal (call=0x10cdac, op=0x152ca8, args=0x5f88ac,
env=0x5f8870) at names.c:853
#13 0x4d7b0 in eval (e=0x46c150, rho=0x5f8870) at eval.c:186
#14 0x4dce4 in applyClosure (call=0x46ea7c, op=0x5ec2dc, arglist=0x5f87f8,
rho=0x5ec28c, suppliedenv=0x14c1a0) at eval.c:347
#15 0x4d824 in eval (e=0x46ea7c, rho=0x5ec28c) at eval.c:195
#16 0x4ee5c in do_set (call=0x46eab8, op=0x14ca4c, args=0x46eaa4,
rho=0x5ec28c) at eval.c:844
#17 0x4d7b0 in eval (e=0x46eab8, rho=0x5ec28c) at eval.c:186
#18 0x4e898 in do_begin (call=0x46dc44, op=0x14caec, args=0x46eacc,
rho=0x5ec28c) at eval.c:644
#19 0x4d7b0 in eval (e=0x46dc44, rho=0x5ec28c) at eval.c:186
#20 0x4e394 in do_for (call=0x46f88c, op=0x14c72c, args=0x46f878,
rho=0x5ec28c) at eval.c:519
#21 0x4d7b0 in eval (e=0x46f88c, rho=0x5ec28c) at eval.c:186
#22 0x4e898 in do_begin (call=0x46c1f0, op=0x14caec, args=0x46f8a0,
rho=0x5ec28c) at eval.c:644
#23 0x4d7b0 in eval (e=0x46c1f0, rho=0x5ec28c) at eval.c:186
#24 0x4dce4 in applyClosure (call=0x474c38, op=0x46f9b8, arglist=0x5ec138,
rho=0x5dd674, suppliedenv=0x14c1a0) at eval.c:347
#25 0x4d824 in eval (e=0x474c38, rho=0x5dd674) at eval.c:195
#26 0x4e898 in do_begin (call=0x4731a8, op=0x14caec, args=0x474c4c,
rho=0x5dd674) at eval.c:644
#27 0x4d7b0 in eval (e=0x4731a8, rho=0x5dd674) at eval.c:186
#28 0x4dce4 in applyClosure (call=0x5dd5ac, op=0x474cec, arglist=0x5dd5e8,
rho=0x154ea4, suppliedenv=0x14c1a0) at eval.c:347
#29 0x4d824 in eval (e=0x5dd5ac, rho=0x154ea4) at eval.c:195
#30 0x62778 in R_ReplConsole (rho=0x154ea4, savestack=0, browselevel=0) at
main.c:173
#31 0x62e70 in run_Rmainloop () at main.c:442
#32 0x62eac in mainloop () at main.c:456
#33 0xacec0 in main (ac=0, av=0xeffff64c) at system.c:490

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