[Rd] Makefile for embedding OpenBUGS in R package
Prof Brian Ripley
ripley at stats.ox.ac.uk
Mon Aug 6 21:37:14 CEST 2007
On Mon, 6 Aug 2007, Tobias Verbeke wrote:
>> ----- Oorspronkelijk bericht -----
>> Van: Prof Brian Ripley [mailto:ripley at stats.ox.ac.uk]
>> Verzonden: maandag, augustus 6, 2007 03:46 PM
>> Aan: 'Tobias Verbeke'
>> CC: r-devel at r-project.org
>> Onderwerp: Re: [Rd] Makefile for embedding OpenBUGS in R package
>> On Mon, 6 Aug 2007, Tobias Verbeke wrote:
>>> Dear list,
>>> I'm trying to embed OpenBUGS in an R package for use of it
>>> on 64-bit Linux. In order to get the CLI working one has to
>>> compile C code contained in $OpenBUGS/Manuals/CBugs.html
>> same as
>> I presume.
> Actually, these files appear to differ. The file I referred to
> was the file ./Manuals/CBugs.html contained in the current OpenBUGS
I am baffled by that C file: why not just link an even simpler stub
against brugs.so rather than play around with dlopen?
>>> (copied to say CBugs.c) using
>>> gcc -m32 -o bugs CBugs.c -ldl
>>> I put the OpenBUGS distribution in the ./inst subdirectory of
>>> the package root. Where should I now put the CBugs.c and how
>> Why do you want to install CBugs.c?
> The CBugs.c file itself is indeed not needed in the built package.
>>> should the Makefile look like in order to be able to call
>>> $PKG_ROOT/OpenBUGS/bugs afterwards ?
>>> Naively putting the following Makefile in ./src does not work
>> What does 'does not work' mean? It's hard to know whether this is just
>> not doing what you wanted, or something else is wrong.
> Apologies. This is the error message when putting the Makefile
> in ./src and launching the package checker:
> $ R.250 CMD check CGHmix
> * checking for working latex ... OK
> * using log directory '/home/tverbek1/pkg/CGHmix.Rcheck'
> * using R version 2.5.0 (2007-04-23)
> * checking for file 'CGHmix/DESCRIPTION' ... OK
> * checking extension type ... Package
> * this is package 'CGHmix' version '0.1-2'
> * checking package dependencies ... OK
> * checking if this is a source package ... OK
> * checking whether package 'CGHmix' can be installed ... ERROR
> Installation failed.
> See '/home/tverbek1/pkg/CGHmix.Rcheck/00install.out' for details.
> The file 00install.out contains:
> * Installing *source* package 'CGHmix' ...
> ** libs
> ** arch -
> gcc -m32 -o ../inst/OpenBUGS/bugs ../inst/OpenBUGS/CBugs.c -ldl
> cp: cannot stat `*.so': No such file or directory
> ERROR: compilation failed for package 'CGHmix'
Ah, so you need to circumvent the installation mechanism as you do not
have a DLL in your package. See package Rserve for a workaround.
[rest not needed for the reply.]
> ** Removing '/home/tverbek1/pkg/CGHmix.Rcheck/CGHmix'
>>> bugs: ../inst/OpenBUGS/CBugs.c
>>> gcc -m32 -o bugs ../inst/OpenBUGS/CBugs.c -ldl
>>> The objective is to use something along the following
>>> execfile <- system.file("OpenBUGS", "bugs", package = mypkg)
>>> system(paste(execfile, "< somescript.script > somefile.out"))
>>> This system call to the CLI is currently the only (non-WINE)
>>> way of using OpenBUGS on Linux in batch mode.
>> I think you need to make ../inst/OpenBUGS/bugs, not src/bugs. So
>> something like
>> all: ../inst/OpenBUGS/bugs
>> ../inst/OpenBUGS/bugs: ../inst/OpenBUGS/CBugs.c
>> gcc -m32 -o ../inst/OpenBUGS/bugs ../inst/OpenBUGS/CBugs.c -ldl
> Thank you.
>> However, -m32 builds a 32-bit executable on 64-bit linux. Is that what you
> Yes. The shared object (brugs.so) comes with the OpenBUGS distribution
> and currently can only be cross-compiled by the main OpenBUGS developer
> (Andrew Thomas) who knows all secrets of the Windows only BlackBox
> (nomen omen) Component Pascal compiler.
> $ file brugs.so
> brugs.so: ELF 32-bit LSB shared object, Intel 80386, version 1 (SYSV), stripped
> Many thanks for your ever instructive answer.
> P.S. Contents of CBugs.c from OpenBUGS distribution (3.0.1)
> /* GNU General Public Licence
> This small C program loads the brugs.so ELF shared library and calls the CLI function.
> Save it as a .c file and then compile it on Linux using gcc -o bugs CBugs.c -ldl
> #include <dlfcn.h>
> #include <stdio.h>
> #include <string.h>
> int main (int argc, char **argv)
> void * handle;
> void (*cli)(void);
> handle = dlopen("./brugs.so", RTLD_LAZY);
> if (!handle)
> return 1;
> * (void **) (&cli) = dlsym(handle, "CLI");
> return 0;
Brian D. Ripley, ripley at 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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