From ernest.turro at ic.ac.uk  Tue Mar 20 01:41:33 2007
From: ernest.turro at ic.ac.uk (Ernest Turro)
Date: Tue, 20 Mar 2007 00:41:33 +0000
Subject: [Rd] Rinternals.h and undefined symbols
In-Reply-To: <45FF2866.7060705@stats.uwo.ca>
References: <9001E5A6-9080-4224-92ED-4867C858C637@ic.ac.uk>
	<45FF016B.3060505@stats.uwo.ca>
	<4E0FCC76-D2E2-40E3-A2F7-C15519D286C1@ic.ac.uk>
	<45FF2866.7060705@stats.uwo.ca>
Message-ID: <B97996F0-05E3-424E-B79F-BA9C9EE125FE@ic.ac.uk>


On 20 Mar 2007, at 00:18, Duncan Murdoch wrote:

> On 3/19/2007 7:41 PM, Ernest Turro wrote:
>> On 19 Mar 2007, at 21:32, Duncan Murdoch wrote:
>>> On 3/19/2007 5:23 PM, Ernest Turro wrote:
>>>> Hi,
>>>> I'm trying to register my native routines using  
>>>> R_registerRoutines  (...). I can compile the code, but the  
>>>> loader cannot resolve the  symbol:
>>>> undefined symbol:    
>>>> _Z18R_registerRoutinesP8_DllInfoPK12R_CMethodDefPK15R_CallMethodDef 
>>>> S3 _S6 _
>>>> $ nm bgx.Rcheck/bgx/libs/bgx.so | grep R_registerRoutines
>>>>                   U    
>>>> _Z18R_registerRoutinesP8_DllInfoPK12R_CMethodDefPK15R_CallMethodDef 
>>>> S3 _S6 _
>>>> Why does it have this funny name? If I look at libR.so, I get  
>>>> an   ordinary symbol name:
>>> That looks like C++ name mangling.  Are you wrapping your   
>>> declarations in
>>>
>>> extern "C" { }
>>>
>>> ?
>> Yeah, the routine is literally just:
>> extern "C"
>>    void R_init_bgx(DllInfo *info) {
>>      R_registerRoutines(info, cMethods,NULL,NULL,NULL);
>>    }
>> with cMethods declared outside as a static const R_CMethodDef.
>
> I'm no C++ expert, but that looks like it declares R_init_bgx to be  
> a "C" routine, but not R_registerRoutines (which is what the error  
> was about).  Its declaration is in Rdynload.h:
>
> #ifdef __cplusplus
> extern "C" {
> #endif
> int R_registerRoutines(DllInfo *info, const R_CMethodDef * const  
> croutines,
> 		       const R_CallMethodDef * const callRoutines,
> 		       const R_FortranMethodDef * const fortranRoutines,
>                        const R_ExternalMethodDef * const  
> externalRoutines);
>
> Rboolean R_useDynamicSymbols(DllInfo *info, Rboolean value);
> #ifdef __cplusplus
> }
> #endif
>
> so maybe your compiler doesn't define __cplusplus, or you didn't  
> include R_ext/Rdynload.h?

Thanks for the reply.

__cplusplus is defined and I do #include <R_ext/Rdynload.h> (after  
all, it does compile)...

I've tried this on two different machines, so it's not a problem  
specific to my setup either...  ):

Ernest


>
> Duncan Murdoch
>
>
>> The two routines that I am registering are also wrapped in extern  
>> "C".
>> Ernest
>>> Duncan Murdoch
>>>
>>>
>>>> $ nm ~/lib64/R/lib/libR.so | grep R_registerRoutines
>>>> 0000000000032f80 T R_registerRoutines
>>>> I get normal symbol names for R functions not in Rinternals.h  
>>>> and   there is no problem there. For example:
>>>> nm bgx.Rcheck/bgx/libs/bgx.so | grep Rprintf
>>>>                   U Rprintf
>>>> $ nm ~/lib64/R/lib/libR.so  | grep Rprintf
>>>> 0000000000129690 T Rprintf
>>>> The shared library dependencies are also fine:
>>>> $ ldd bgx.Rcheck/bgx/libs/bgx.so
>>>>          libR.so => /home/et04/lib64/R/lib/libR.so   
>>>> (0x0000002a95676000)
>>>>          libstdc++.so.6 => /usr/lib64/libstdc++.so.6    
>>>> (0x0000002a95a80000)
>>>>          libm.so.6 => /lib64/tls/libm.so.6 (0x0000002a95c70000)
>>>>          libgcc_s.so.1 => /lib64/libgcc_s.so.1 (0x0000002a95df7000)
>>>>          libc.so.6 => /lib64/tls/libc.so.6 (0x0000002a95f02000)
>>>>          libRblas.so => /home/et04/lib64/R/lib/libRblas.so    
>>>> (0x0000002a96136000)
>>>>          libg2c.so.0 => /usr/lib64/libg2c.so.0 (0x0000002a96262000)
>>>>          libreadline.so.4 => /usr/lib64/libreadline.so.4    
>>>> (0x0000002a96383000)
>>>>          libncurses.so.5 => /usr/lib64/libncurses.so.5    
>>>> (0x0000002a964bc000)
>>>>          libdl.so.2 => /lib64/libdl.so.2 (0x0000002a96618000)
>>>>          /lib64/ld-linux-x86-64.so.2 (0x000000552aaaa000)
>>>> My LD_LIBRARY_PATH environmental variable is set appropriately.
>>>> Any ideas?
>>>> Thanks,
>>>> E
>>>> ______________________________________________
>>>> R-devel at r-project.org mailing list
>>>> https://stat.ethz.ch/mailman/listinfo/r-devel
>



[Rd] Rinternals.h and undefined symbols
Ernest Turro