[R] R 1.6.1: help with debugging error in RunGenCollect(), R_gc_internal

[Timothy H. Keitt]

Maybe try electric fence. (See docs for LD_PRELOAD trick.)

Tim 

On Mon, 2002-11-11 at 10:18, Stephen Eglen wrote:
> Hi,
> 
> [System info: R 1.6.1 compiled from source (no args to configure) on
> Redhat 7.1 Linux i/386]
> 
> I have some spatial statistics programs that recently (since R 1.6.1)
> have generated SIGSEGV.  These R programs use the splancs library as
> well as some C code of my own for Voronoi analysis.
> 
> The program has a big loop to fit various model parameters against a
> spatial distribution of biological cells.  At some point, varying from
> run to run, it generates the Segmentation fault:
> 
> Program received signal SIGSEGV, Segmentation fault.
> 0xffffffdc in ?? ()
> (gdb) where
> #0  0xffffffdc in ?? ()
> #1  0x080bcae7 in RunGenCollect (size_needed=6777) at memory.c:1286
> #2  0x080bdaa0 in R_gc_internal (size_needed=6777) at memory.c:1859
> #3  0x080bd729 in Rf_allocVector (type=13, length=13554) at memory.c:1722
> #4  0x08090a71 in CPtrToRObj (p=0x98db958, arg=0x98b29f8, Fort=1, type=13)
>     at dotcode.c:209
> #5  0x080933cb in do_dotCode (call=0x89f3880, op=0x8222154, args=0x833b380, 
>     env=0x8346e90) at dotcode.c:1907
> #6  0x080a035d in Rf_eval (e=0x89f3880, rho=0x8346e90) at eval.c:427
> #7  0x080a195a in do_set (call=0x89f390c, op=0x8218610, args=0x89f38b8, 
>     rho=0x8346e90) at eval.c:1102
> #8  0x080a01e1 in Rf_eval (e=0x89f390c, rho=0x8346e90) at eval.c:404
> #9  0x080a12e6 in do_begin (call=0x89f94f0, op=0x8218514, args=0x89f950c, 
>     rho=0x8346e90) at eval.c:891
> #10 0x080a01e1 in Rf_eval (e=0x89f94f0, rho=0x8346e90) at eval.c:404
> 
> [... The whole backtrace in this case goes to #64 frames, with many calls
> to Rf_eval, do_begin, do_for, cut here for space...]
> 
> #59 0x080a03d5 in Rf_eval (e=0x8ba4b6c, rho=0x8228498) at eval.c:439
> #60 0x080b8b56 in Rf_ReplIteration (rho=0x8228498, savestack=0, browselevel=0, 
>     state=0xbfffefe0) at main.c:232
> #61 0x080b8c95 in R_ReplConsole (rho=0x8228498, savestack=0, browselevel=0)
>     at main.c:280
> #62 0x080b9333 in run_Rmainloop () at main.c:579
> #63 0x08118fb2 in main (ac=1, av=0xbffff4c4) at system.c:99
> #64 0x4010a657 in __libc_start_main (main=0x8118f9c <main>, argc=1, 
>     ubp_av=0xbffff4c4, init=0x805cdcc <_init>, fini=0x81a3810 <_fini>, 
>     rtld_fini=0x4000dcd4 <_dl_fini>, stack_end=0xbffff4bc)
>     at ../sysdeps/generic/libc-start.c:129
> 
> I'm sorry that I cannot report a consise example here that reproduces
> the bug, but I am working on that.  My question for now is there a way
> to find out what R command was being executed when the program
> errored?
> 
> I tried running a recent unstable version of R (1.7.0, 2002-11-08),
> and this time didn't get the SIGSEGV.  The only relevant NEWS item in
> 1.7.0 seems to be:
> 
>     o   The code underlying polygon drawing contained a memory leak.
> 	This showed up in persp, but did not affect other graphics
> 	functions.  It is now possible to draw big DEMs.
> 
> 
> However, I think that is not the cause of this problem, I'm not using
> persp in my code.  Also, the R process seems stable at about 30Mb.
> 
> Also, are ChangeLogs available for the unstable branch of R, or is it
> just the NEWS file?
> 
> Any pointers to debugging this appreciated.
> 
> best wishes,
> Stephen Eglen
> 
> -- 
> Stephen Eglen					
> Department of Anatomy and Neurobiology		eglen at thalamus.wustl.edu
> Washington University School of Medicine        Tel: +1 314 362 4870    
> St. Louis MO 63110  USA.			Fax: +1 314 747 1150
> 
> -.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-
> r-help mailing list -- Read http://www.ci.tuwien.ac.at/~hornik/R/R-FAQ.html
> Send "info", "help", or "[un]subscribe"
> (in the "body", not the subject !)  To: r-help-request at stat.math.ethz.ch
> _._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._
-- 
Timothy H. Keitt
The University of Texas at Austin
Section of Integrative Biology
1 University Station C0930
Austin, Texas 78712-0253 USA

-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-
r-help mailing list -- Read http://www.ci.tuwien.ac.at/~hornik/R/R-FAQ.html
Send "info", "help", or "[un]subscribe"
(in the "body", not the subject !)  To: r-help-request at stat.math.ethz.ch
_._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._