namespace and undefined symbols on OSX

[Randy Heiland]

On OSX 10.14.5, I've installed libsbml-5.18.0-libxml2-macosx-mojave.dmg from
https://sourceforge.net/projects/sbml/files/libsbml/5.18.0/stable/Mac%20OS%20X/

and I'm using:
$ g++-9 --version
g++-9 (Homebrew GCC 9.1.0) 9.1.0


I would like to compile my code using the "libsbml" namespace, e.g.:

#include <iostream>
#include <sbml/SBMLTypes.h>
using namespace std;

int main (int argc, char* argv[])
{
libsbml::SBMLDocument* document = libsbml::readSBML(argv[1]);
cout << " error(s): " << document->getNumErrors() << endl;
}

However, I get:
$ g++-9 -DLIBSBML_USE_CPP_NAMESPACE -I/usr/local/include -std=c++11 -L/usr/local/lib -lsbml sbml_test.cpp
Undefined symbols for architecture x86_64:
"libsbml::SBMLDocument::getNumErrors() const", referenced from:
_main in cctircnZ.o
ld: symbol(s) not found for architecture x86_64

FYI:
$ ls -l /usr/local/lib/libsbml*
-rw-r--r-- 1 heiland staff 17352504 Apr 15 10:54 /usr/local/lib/libsbml-static.a
-rwxr-xr-x 1 heiland staff 7763352 Apr 15 10:54 /usr/local/lib/libsbml.5.18.0.dylib*
lrwxr-xr-x 1 heiland staff 20 Jun 23 20:03 /usr/local/lib/libsbml.5.dylib@ -> libsbml.5.18.0.dylib
lrwxr-xr-x 1 heiland staff 15 Jun 23 20:03 /usr/local/lib/libsbml.dylib@ -> libsbml.5.dylib

$ file /usr/local/lib/libsbml.5.18.0.dylib
/usr/local/lib/libsbml.5.18.0.dylib: Mach-O 64-bit dynamically linked shared library x86_64

------------------

If I remove the two "libsbml::" namespace prefixes on the first line (and remove the -D compile flag), it compiles/runs as expected:
$ g++-9 -I/usr/local/include -std=c++11 -L/usr/local/lib -lsbml sbml_test_no_ns.cpp

Can someone explain what I'm doing wrong? I've done a verbose compile on the former, but don't see anything obvious.

thanks, Randy

[Frank T. Bergmann]

Hello, the issue is with adding 'LIBSBML_USE_CPP_NAMESPACE ' to the compile command line, rather then placing it into the source code file. This definition will expand to a using statement, if libSBML is compiled with C++ namespaces, or nothing otherwise. In your case it has to expand to 'using namespace libsbml', however you preclude that with your override on the command line. 

best

Frank

[Randy Heiland]

Frank, thanks for the reply, but I'm still confused - sorry. Are you suggesting that I need to add:

#define LIBSBML_USE_CPP_NAMESPACE

into the top of my test program, rather than use the "-DLIBSBML_USE_CPP_NAMESPACE" on the compile command? If so, I did that, but get the same error (as I would have expected).

$ g++-9 -I/usr/local/include -march=native -fomit-frame-pointer -mfpmath=both -m64 -std=c++11 -L/usr/local/lib -lsbml sbml_test.cpp -o sbml_test

Undefined symbols for architecture x86_64:
"libsbml::SBMLDocument::getNumErrors() const", referenced from:

_main in ccTEEvPB.o

ld: symbol(s) not found for architecture x86_64

To be clear, I *want* to explicitly specify the "libsbml::" namespace on functions in my program.

-Randy

[Frank T. Bergmann]

Sorry, no ... i meant to just include it verbatim in the source code the following will compile whether libSBML has been compiled with namespaces or without. the definition comes from (<sbml/common/libsbml-namespace.h>): 

"""

#include <iostream>
#include <sbml/SBMLTypes.h>
using namespace std; 

LIBSBML_USE_CPP_NAMESPACE

int main (int argc, char* argv[])
{
  libsbml::SBMLDocument* document = libsbml::readSBML(argv[1]);
  cout << "  error(s): " << document->getNumErrors()  << endl;
}

"""

Reading your initial email again, if you downloaded our precompiled binaries, this will not work for you, as the precopiled binaries do not use the c++ namespace. You will have to compile libSBML from source, setting the CMake option WITH_CPP_NAMESPACE=ON. 

best

Frank

[Randy Heiland]

Ah, your last two sentences explain everything. 

thanks, Randy

[Michael Hucka]

On 12 Jul 2019, at 4:29, Frank T. Bergmann wrote:
> Reading your initial email again, if you downloaded our precompiled
> binaries, this will not work for you, as the precopiled binaries do
> not use
> the c++ namespace. You will have to compile libSBML from source,
> setting
> the CMake option WITH_CPP_NAMESPACE=ON.

Where would be a good place to put a note about this? The download page
at http://sbml.org/Software/libSBML/Downloading_libSBML is already very
long, so I hesitate adding more text there.

MH