Wolfgang Viechtbauer
?Department of Methodology and Statistics
?University of Maastricht, The Netherlands
?http://www.wvbauer.com/
----Original Message----
From: William Dunlap [mailto:wdunlap at tibco.com]
Sent: Monday, September 29, 2008 21:03
To: Martin Maechler; Viechtbauer Wolfgang (STAT)
Cc: r-sig-mixed-models at r-project.org; R-devel at stat.math.ethz.ch
Subject: RE: [Rd] seg.fault from nlme::gnls() {was "[R-sig-ME] GNLS
Crash"}
> When I run this under valgrind with gctorture(TRUE) I see memory
> misuse in mat_mult (matrix.c, line 82): % R-2.8.0-dev
> --debugger=valgrind --debugger-args=--db-attach=yes ... copyright
> blah blah ...
>> data(Orange)
>> gctorture(TRUE)
>> gnls(circumference ~ Asym/(1 + exp(-(age-xmid)/scal)) ,
> + data = Orange, correlation = corExp(form = ~1 | Tree),
> + start = c(Asym=150, xmid=750, scal=300))
> r==5894== Invalid read of size 4
> ==5894== at 0x580268F: mult_mat (matrix.c:82)
> ==5894== by 0x57FF1B0: corStruct_recalc (corStruct.c:70)
> ==5894== by 0x5801F89: gnls_objective (gnls.c:100)
> ==5894== by 0x58020FE: fit_gnls (gnls.c:152)
> ==5894== by 0x81439A2: do_dotCode (dotcode.c:1758)
> ==5894== by 0x8161C56: Rf_eval (eval.c:487)
> ==5894== by 0x81637D5: do_set (eval.c:1422)
> ==5894== by 0x8161B3B: Rf_eval (eval.c:461)
> ==5894== by 0x816384B: do_begin (eval.c:1174)
> ==5894== by 0x8161B3B: Rf_eval (eval.c:461)
> ==5894== by 0x816397B: do_repeat (eval.c:1137)
> ==5894== by 0x8161B3B: Rf_eval (eval.c:461)
> ==5894== Address 0x4E4A8CC is 12 bytes inside a block of size 864
> free'd ==5894== at 0x40052A3: free (vg_replace_malloc.c:233)
> ==5894== by 0x805ACFD: R_gc_internal (memory.c:767)
> ==5894== by 0x805B933: Rf_cons (memory.c:1755)
> ==5894== by 0x805B98E: Rf_allocList (memory.c:2094)
> ==5894== by 0x815AB4C: replaceCall (Rinlinedfuns.h:84)
> ==5894== by 0x8163476: applydefine (eval.c:919)
> ==5894== by 0x8161B3B: Rf_eval (eval.c:461)
> ==5894== by 0x816384B: do_begin (eval.c:1174)
> ==5894== by 0x8161B3B: Rf_eval (eval.c:461)
> ==5894== by 0x8161B3B: Rf_eval (eval.c:461)
> ==5894== by 0x816384B: do_begin (eval.c:1174)
> ==5894== by 0x8161B3B: Rf_eval (eval.c:461)
>
> My copy of valgrind doesn't get along with my copy of gdb,
> so when it pops into gdb the debugger doesn't get any information
> from *.so files. I don't have the time now to put printf statements
> into mat_mult.
>
> Bill Dunlap
> wdunlap tibco.com
>
> -----Original Message-----
> From: r-devel-bounces at r-project.org
> [mailto:r-devel-bounces at r-project.org] On Behalf Of Martin Maechler
> Sent: Saturday, September 27, 2008 2:20 AM
> To: Viechtbauer Wolfgang (STAT)
> Cc: r-sig-mixed-models at r-project.org; R-devel at stat.math.ethz.ch
> Subject: [Rd] seg.fault from nlme::gnls() {was "[R-sig-ME] GNLS
> Crash"}
>
>>>>>> "VW" == Viechtbauer Wolfgang (STAT)
>>>>>> <Wolfgang.Viechtbauer at STAT.unimaas.nl> on Fri, 26 Sep 2008
>>>>>> 18:00:19 +0200 writes:
>
>> Hi all, I'm trying to fit a marginal (longitudinal)
>> model with an exponential serial correlation function to
>> the Orange tree data set. However, R crashes frequently
>> when using the gnls() function. With the following
>> simple example, I was able to reproduce the problem.
>
>
>> gnls.exp <- gnls(circumference ~ Asym/(1 + exp(-(age-xmid)/scal)) ,
>> data = Orange, correlation = corExp(form = ~1 | Tree),
>> start = c(Asym=150, xmid=750, scal=300))
>
> Yes, I can reproduce it (on a Linux (RHEL 5) 64bit server), using R
> 2.8.0 alpha : Use this
>
> for(i in 1:20)# for MM: ca. 8 to 10 times --> seg.fault try( gnls.exp
> <- gnls(circumference ~ Asym/(1 +
> exp(-(age-xmid)/scal)) , data = Orange, correlation =
> corExp(form = ~1 | Tree), start = c(Asym=150, xmid=750, scal=300)) )
>
> If I run it in the debugger and then do a backtrace I see
>
> Error in gnls(circumference ~ Asym/(1 + exp(-(age - xmid)/scal)),
> data = Orange, : Step halving factor reduced below minimum in NLS
> step
>
> [............................................................]
> [...................the same about 6 times...................]
> [............................................................]
>
> Error in gnls(circumference ~ Asym/(1 + exp(-(age - xmid)/scal)),
> data = Orange, : Step halving factor reduced below minimum in NLS
> step Error in .makeMessage(..., domain = domain) : incorrect number
> of arguments to "<-"
> Error in .makeMessage(..., domain = domain) :
> incorrect number of arguments to "<-"
>
> Program received signal SIGABRT, Aborted.
> 0x0000003294e30155 in raise () from /lib64/libc.so.6
> (gdb) bt
> #0 0x0000003294e30155 in raise () from /lib64/libc.so.6
> #1 0x0000003294e31bf0 in abort () from /lib64/libc.so.6
> #2 0x00000000004184f5 in R_gc_internal (size_needed=0)
> at ../../../R/src/main/memory.c:761
> #3 0x000000000041b121 in Rf_cons (car=0x1b2ec088, cdr=0x1a3436d8)
> at ../../../R/src/main/memory.c:1755
> #4 0x0000000000578472 in applydefine (call=<value optimized out>,
> op=0x1a3617a8, args=0x1ad47590, rho=0x1b2ea428)
> at ../../../R/src/include/Rinlinedfuns.h:153
> #5 0x0000000000575a42 in Rf_eval (e=0x1ad47558, rho=0x1b2ea428)
> at ../../../R/src/main/eval.c:461
> #6 0x0000000000576d50 in do_begin (call=0x1ad48450, op=0x1a362518,
> args=0x1ad47520, rho=0x1b2ea428) at
> ../../../R/src/main/eval.c:1174 #7 0x0000000000575a42 in Rf_eval
> (e=0x1ad48450, rho=0x1b2ea428) at ../../../R/src/main/eval.c:461 #8
> 0x0000000000578f9c in Rf_applyClosure (call=0x1b2e9958,
> op=0x1ad48370, arglist=0x1b2e9a70, rho=0x1b690298,
> suppliedenv=0x1b2e99c8) at ../../../R/src/main/eval.c:667 #9
> 0x00000000004285b9 in Rf_usemethod (generic=0x67e8d7 "[",
> obj=<value optimized out>, call=<value optimized out>,
> args=<value optimized out>, rho=0xffffffffffffffff,
> callrho=0x1b690298, defrho=0x1a384f28, ans=0x7fffcaa8d5a8) at
> ../../../R/src/main/objects.c:311 #10 0x0000000000576a25 in
> Rf_DispatchOrEval (call=0x1a81d8d0, op=0x1a3622e8,
> generic=0x67e8d7 "[", args=0x1a81d908, rho=0x1b690298,
> ans=0x7fffcaa8d5a8, dropmissing=0, argsevald=0) at
> ../../../R/src/main/eval.c:1930 #11 0x00000000004afc40 in
> do_subset (call=0x7716, op=0x7716, args=0xffffffffffffffff,
> rho=0x1b690298) at ../../../R/src/main/subset.c:577 #12
> 0x0000000000575a42 in Rf_eval (e=0x1a81d8d0, rho=0x1b690298) at
> ../../../R/src/main/eval.c:461 #13 0x00000000005780c7 in applydefine
> (call=0x1a81d748, op=0x1a3617a8, args=0x6,
> rho=0xffffffffffffffff) at ../../../R/src/main/eval.c:1318 #14
> 0x0000000000575a42 in Rf_eval (e=0x1a81d748, rho=0x1b690298) at
> ../../../R/src/main/eval.c:461 #15 0x00000000005775de in do_for
> (call=0x1a81d668, op=0x1a360180, args=0x1a81d6a0, rho=0x1b690298) at
> ../../../R/src/main/eval.c:1073
>
> ..... and more (downto #155 for R's main(...)
>
> This is a bug, probably in the C code of package nlme which I guess
> corrupts memory somehere earlier, and we are seeing the effect only
> later. I'll leave this to the (memory-)debugging experts...
>
> Martin
>
>> On my and one other computer, R usually crashes when calling the
>> gnls() function with this code three times in a row. I stumbled
>> across this when trying to fit this model with different starting
>> values.
>
>> Version information:
>
>> platform i386-pc-mingw32
> ......
>> version.string R version 2.7.2 (2008-08-25)
>
>> Can anybody help figure out what causes this problem?
>
>> Best,
>
>> --
>> Wolfgang Viechtbauer
>> ?Department of Methodology and Statistics
>> ?University of Maastricht, The Netherlands
>> ?http://www.wvbauer.com/