From gb at stat.umu.se  Fri Oct  3 11:32:03 2008
From: gb at stat.umu.se (=?ISO-8859-1?Q?G=F6ran_Brostr=F6m?=)
Date: Fri, 03 Oct 2008 11:32:03 +0200
Subject: [Rd] Memory crash
Message-ID: <48E5E693.7050301@stat.umu.se>

Hello,

I get a segfault when running glmmboot in my own package glmmML. Has 
happened many time before, but this time I get no hint of where in my C 
functions the error might be. I give the output below. Can this be an R 
bug? I suspect it has to do with repeated calls to 'vmmin' like this:

            for (...){
                 vmax = vmaxget();
		vmmin(*p, b, &Fmin,
		      bfun, bfun_gr, *maxit, *trace,
		      mask, abstol, reltol, nREPORT,
		      ext, &fncount, &grcount, &fail);
		vmaxset(vmax);
                 ...
            }

but I am only guessing. Any suggestions?

Ubuntu 8.04, R-2.7.2.

G?ran
-------------------------------------------------------------------
  > glmmboot(y ~ x, cluster = cluster, data = res$dat, family = 
binomial, boot = 400)

Program received signal SIGSEGV, Segmentation fault.
0x000000000041a817 in R_gc_internal (size_needed=3000) at memory.c:1317
1317	    PROCESS_NODES();
(gdb) where
#0  0x000000000041a817 in R_gc_internal (size_needed=3000) at memory.c:1317
#1  0x000000000041c31c in Rf_allocVector (type=14, length=3000)
     at memory.c:1968
#2  0x000000000052a647 in duplicate1 (s=0x20cb4a0) at duplicate.c:214
#3  0x00000000004e1775 in do_makelist (call=<value optimized out>,
     op=<value optimized out>, args=0x1e18238, rho=<value optimized out>)
     at builtin.c:645
#4  0x000000000054697a in Rf_eval (e=0x10685a0, rho=0x1c557e0) at eval.c:492
#5  0x000000000054a7ef in do_set (call=0x10684f8, op=0x936188, 
args=0x1068530,
     rho=0x1c557e0) at eval.c:1424
#6  0x0000000000546896 in Rf_eval (e=0x10684f8, rho=0x1c557e0) at eval.c:463
#7  0x00000000005474c0 in do_begin (call=0x1089ab0, op=0x936ef8,
     args=0x10684c0, rho=0x1c557e0) at eval.c:1176
#8  0x0000000000546896 in Rf_eval (e=0x1089ab0, rho=0x1c557e0) at eval.c:463
#9  0x0000000000546896 in Rf_eval (e=0x1089960, rho=0x1c557e0) at eval.c:463
#10 0x00000000005474c0 in do_begin (call=0x10fa1c0, op=0x936ef8,
     args=0x10898f0, rho=0x1c557e0) at eval.c:1176
#11 0x0000000000546896 in Rf_eval (e=0x10fa1c0, rho=0x1c557e0) at eval.c:463
#12 0x0000000000548a4c in Rf_applyClosure (call=0x13714e8, op=0x10fa4e8,
     arglist=0x1c551c0, rho=0x1e06538, suppliedenv=0x959c50) at eval.c:669
#13 0x00000000005467b8 in Rf_eval (e=0x13714e8, rho=0x1e06538) at eval.c:507
#14 0x000000000054a7ef in do_set (call=0x1371440, op=0x936188, 
args=0x1371478,
     rho=0x1e06538) at eval.c:1424
#15 0x0000000000546896 in Rf_eval (e=0x1371440, rho=0x1e06538) at eval.c:463
#16 0x00000000005474c0 in do_begin (call=0x137e938, op=0x936ef8,
     args=0x1371408, rho=0x1e06538) at eval.c:1176
#17 0x0000000000546896 in Rf_eval (e=0x137e938, rho=0x1e06538) at eval.c:463
#18 0x0000000000548a4c in Rf_applyClosure (call=0x1e05ff8, op=0x137ef08,
     arglist=0x1e060a0, rho=0x959c18, suppliedenv=0x959c50) at eval.c:669
#19 0x00000000005467b8 in Rf_eval (e=0x1e05ff8, rho=0x959c18) at eval.c:507
#20 0x0000000000416b95 in Rf_ReplIteration (rho=0x959c18, savestack=0,
     browselevel=0, state=0x7fffca277fa0) at main.c:257
#21 0x0000000000416e60 in R_ReplConsole (rho=0x959c18, savestack=0,
     browselevel=0) at main.c:306
#22 0x0000000000417140 in run_Rmainloop () at main.c:967
#23 0x0000000000414c08 in main (ac=<value optimized out>,
     av=<value optimized out>) at Rmain.c:35
#24 0x00007f10c116a1c4 in __libc_start_main () from /lib/libc.so.6
#25 0x0000000000414b29 in _start ()

-- 
G?ran Brostr?m               phone: 46 90 786 5223; 46 705 197 507
Department of Statistics     fax: 46 90 786 6614
Ume? University              email: gb at stat.umu.se
SE-90187 Ume?, Sweden        http://www.stat.umu.se/personal/goran.brostrom



[Rd] Memory crash
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