Re: [Rd] bus error on calling nmmin

From: Prof Brian Ripley <ripley_at_stats.ox.ac.uk>
Date: Fri 14 Apr 2006 - 06:37:57 GMT

You appear to be trying to call nmmin from a standalone program. You linked against -lR, but failed to initialize R, hence the segfault.

nmmin is not a part of R that is made available except to a running R process: it is documented in `Writing R Extensions' for use in R packages.

On Thu, 13 Apr 2006, David Faden wrote:

> Hi,
>
> I'm trying to get a toy program making use of nmmin to run
> successfully. I've gotten to the point of compiling. However, when I
> attempt to run my executable, I guess a bus error. I see that someone
> else has asked about using nmmin before
> <http://tolstoy.newcastle.edu.au/R/help/06/03/23944.html>, but I
> haven't come across any replies.

In both his case and yours, the problem is that what you are trying to do is well-documented in Writing R Extensions, and people are reluctant both to write manuals out here.

> Is there some documentation on how to call nmmin apart the optim help
> page and the page in the R extensions manual giving the declaration?
> What do I need to change in the below to get it to work? (I also get a
> bus error with trace set to 0.)
>
> The source code and an example session:
>
> nmminDemo.c:
> #include <R_ext/Applic.h>
> #include <stdio.h>
>
> double parabola(int n, double *par, void *ex) {
> double xm = par[0] - 1;
> return xm * xm + 13;
> }
>
> int main()
> {
> double initial[1] = {1.5};
> double result[1];
> double value;
> int convergenceCode;
> const double abstol = 1e-16;
> const double reltol = 1e-8;
> const double alpha = 1.0; /* reflection factor */
> const double beta = 0.5; /* contraction factor */
> const double gamm = 2.0; /* expansion factor */
> const int trace = 4; /* tracing on */
> int fncount;
> const int maxit = 10000;
> nmmin(1, initial, result, &value,
> parabola, &convergenceCode,
> abstol, reltol,
> NULL,
> alpha, beta, gamm,
> trace, &fncount, maxit);
> printf("fncount: %d\n", fncount);
> printf("convergence code: %d\n", convergenceCode);
> printf("min of %f at x = %f\n", value, result[0]);
> return 0;
> }
>
> ------
>
> $ gcc nmminDemo.c -g
> -I/Library/Frameworks/R.framework/Versions/2.1.1/Resources/include
> -L/Library/Frameworks/R.framework/Versions/2.1.1/Resources/lib -lR
> $ ./a.out Bus error
> $ gdb a.out
> GNU gdb 5.3-20030128 (Apple version gdb-330.1) (Fri Jul 16 21:42:28 GMT 2004)
> ...
> (gdb) run
> Starting program: /Users/dfaden/Desktop/R/a.out
> Reading symbols for shared libraries +......... done
>
> Program received signal EXC_BAD_ACCESS, Could not access memory.
> 0x00000000 in ?? ()
> (gdb) bt
> #0 0x00000000 in ?? ()
> Cannot access memory at address 0x0
> Cannot access memory at address 0x0
> #1 0x0054dd5c in REvprintf (format=0x5f0dc8 "%s", arg=0xbfffb5fc "")
> at ../../../../R-2.1.1/src/main/printutils.c:541
> #2 0x0054dab0 in REprintf (format=0xbfff9570 "Error: invalid
> connection\n") at ../../../../R-2.1.1/src/main/printutils.c:458
> #3 0x004de8c4 in verrorcall_dflt (call=0x0, format=0x5f0dc8 "%s",
> ap=0xbfffda30 "???P") at ../../../../R-2.1.1/src/main/errors.c:470
> #4 0x004dea1c in Rf_errorcall (call=0x5f0dc8, format=0xbfffb5fc "")
> at ../../../../R-2.1.1/src/main/errors.c:514
> #5 0x004deb38 in Rf_error (format=0xbfff9570 "Error: invalid
> connection\n") at ../../../../R-2.1.1/src/main/errors.c:538
> #6 0x004acc18 in getConnection (n=-1073769104) at
> ../../../../R-2.1.1/src/main/connections.c:95
> #7 0x0054dc04 in Rvprintf (format=0x5fe004 " Nelder-Mead direct
> search function minimizer\n", arg=0xbffffb7c "???P???X???`") at
> ../../../../R-2.1.1/src/main/printutils.c:494
> #8 0x0054da70 in Rprintf (format=0xbfff9570 "Error: invalid
> connection\n") at ../../../../R-2.1.1/src/main/printutils.c:445
> #9 0x0051bcec in nmmin (n=6575856, Bvec=0x5f0dc8, X=0xbffffd58,
> Fmin=0xbffffd60, fminfn=0x2b8c <parabola>, fail=0xbffffd68,
> abstol=9.9999999999999998e-17, intol=1e-08, ex=0x0, alpha=1, bet=0.5,
> gamm=2, trace=4, fncount=0xbffffd9c, maxit=1000) at
> ../../../../R-2.1.1/src/main/optim.c:667
> #10 0x00002ce0 in main () at nmminDemo.c:30
>
> -----
>
> I'm working under Mac OS X 10.3.9 with gcc 3.3 and R
> platform powerpc-apple-darwin7.9.0
> arch powerpc
> os darwin7.9.0
> system powerpc, darwin7.9.0
> status
> major 2
> minor 1.1
> year 2005
> month 06
> day 20
> language R
>
> Thank you.
>
> David
>
> ______________________________________________
> R-devel@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-devel
>
>

-- 
Brian D. Ripley,                  ripley@stats.ox.ac.uk
Professor of Applied Statistics,  http://www.stats.ox.ac.uk/~ripley/
University of Oxford,             Tel:  +44 1865 272861 (self)
1 South Parks Road,                     +44 1865 272866 (PA)
Oxford OX1 3TG, UK                Fax:  +44 1865 272595

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Received on Fri Apr 14 17:06:54 2006

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