[Rd] Makefile for embedding OpenBUGS in R package

[Uwe Ligges]

As the BRugs maintainer, as far as I can tell, the most recent OpenBUGS 
brugs.so is not compatible with (at least) my system and I do not have 
the compilers to try it myself. Hence we still only ship BRugs for 
Windows, but if anybody else has ideas how to get the BRugs.so compiled 
(or just running without "traps", I'd be happy to hear about it.

Uwe Ligges








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
>>
>> http://mathstat.helsinki.fi/openbugs/data/Docu/CBugs.html
>>
>> I presume.
> 
> Actually, these files appear to differ. The file I referred to
> was the file ./Manuals/CBugs.html contained in the current OpenBUGS 
> release:
> 
> http://mathstat.helsinki.fi/openbugs/OpenBUGS.zip
> 
>>>   (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
> DISPLAY=localhost:10.0
> * 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'
> ** 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 
>> wanted?
> 
> 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.
> 
> Tobias
> 
> 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");
>   (*cli)();
>   dlclose(handle);
> 
>   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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