[Xplor-nih] problems with swig files

Gary Thompson Mon, 10 Jun 2013 03:10:33 -0700


Dear All (most probably charles!)

I am trying to generate a swig wrapper for a c++ class using thefollowing command line (I am doing this outside xplor currently)

swig -python -classptr -c++ -keyword -shadow -I/usr/include/python2.7-I/home/garyt/programs/xplor-nih/2.31.0/CDSlib-I/home/garyt/programs/xplor-nih/2.31.0/common-I/home/garyt/programs/xplor-nih/2.31.0/intVar-I/home/garyt/programs/xplor-nih/2.31.0/nmrPot-I/home/garyt/programs/xplor-nih/2.31.0/vmd-I/home/garyt/programs/xplor-nih/2.31.0/surfD-I/home/garyt/programs/xplor-nih/2.31.0/cminpack-I/home/garyt/programs/xplor-nih/2.31.0/sparta-I/home/garyt/programs/xplor-nih/2.31.0/devel-I/home/garyt/programs/xplor-nih/2.31.0/fortlib -I.-I/home/garyt/programs/xplor-nih/2.31.0/python -opyEnsemblePotProxy_wrap.cpp pyEnsemblePotProxy.i


where  pyEnsemblePotProxy.i contains an empty(ish) potential class

// -*- c++ -*-
#ifndef PY_ENSEMBLE_POT_PROXY_H
#define PY_ENSEMBLE_POT_PROXY_H 1

#include "ensemblePot.hh"

struct _object;
typedef _object PyObject;



class PyEnsemblePotProxy : public EnsemblePot {
public:
   PyObject *m_obj;

PyEnsemblePotProxy(const String&, const String&, Simulation*,PyObject *obj);

   virtual ~PyEnsemblePotProxy();
   void doRun();
   virtual void run();

   float_type rms();
   int violations();
   int numRestraints();
};

#endif // !PY_ENSEMBLE_POT_PROXY_H

however when I compile the resulting swig wrapper I get messages aboutmissing declarations for ‘SWIGPY_POINTER_EXCEPTION’, ‘SWIGPY_ConvertPtr’and ‘SWIGPY_fail'

gcc -pthread -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall-Wstrict-prototypes -fPIC -DCPLUSPLUS=1 -DUSE_CDS_NAMESPACE=1-I/home/garyt/programs/xplor-nih/2.31.0/common-I/home/garyt/programs/xplor-nih/2.31.0/CDSlib-I/home/garyt/programs/xplor-nih/2.31.0/arch/Linux_i686/include-I/usr/include/python2.7 -I/home/garyt/programs/xplor-nih/2.31.0/CDSlib-I/home/garyt/programs/xplor-nih/2.31.0/common-I/home/garyt/programs/xplor-nih/2.31.0/intVar-I/home/garyt/programs/xplor-nih/2.31.0/nmrPot-I/home/garyt/programs/xplor-nih/2.31.0/vmd-I/home/garyt/programs/xplor-nih/2.31.0/surfD-I/home/garyt/programs/xplor-nih/2.31.0/cminpack-I/home/garyt/programs/xplor-nih/2.31.0/sparta-I/home/garyt/programs/xplor-nih/2.31.0/devel-I/home/garyt/programs/xplor-nih/2.31.0/fortlib -I.-I/home/garyt/programs/xplor-nih/2.31.0/python-I/home/garyt/programs/xplor-nih/2.31.0/python/bin.Linux_i686/include/python2.6-c pyEnsemblePotProxy_wrap.cpp -obuild/temp.linux-i686-2.6/pyEnsemblePotProxy_wrap.occ1plus: warning: command line option ‘-Wstrict-prototypes’ is valid forAda/C/ObjC but not for C++ [enabled by default]

pyEnsemblePotProxy_wrap.cpp: In function ‘PyObject* wrapPot(rc_Pot&)’:

pyEnsemblePotProxy_wrap.cpp:3269:45: warning: deprecated conversion fromstring constant to ‘char*’ [-Wwrite-strings]pyEnsemblePotProxy_wrap.cpp: In function ‘PyObject*_wrap_new_PyEnsemblePotProxy__SWIG_0(PyObject*, PyObject*)’:pyEnsemblePotProxy_wrap.cpp:4164:11: error: ‘SWIGPY_POINTER_EXCEPTION’was not declared in this scopepyEnsemblePotProxy_wrap.cpp:4165:31: error: ‘SWIGPY_ConvertPtr’ was notdeclared in this scopepyEnsemblePotProxy_wrap.cpp:4166:7: error: ‘SWIGPY_fail’ was notdeclared in this scopepyEnsemblePotProxy_wrap.cpp: In function ‘PyObject*_wrap_PyEnsemblePotProxy_setEnsWeights(PyObject*, PyObject*, PyObject*)’:pyEnsemblePotProxy_wrap.cpp:5911:43: error: ‘SWIGPY_ConvertPtr’ was notdeclared in this scopepyEnsemblePotProxy_wrap.cpp: In function ‘PyObject*_wrap_PyEnsemblePotProxy_setUseSimEnsWeights(PyObject*, PyObject*,PyObject*)’:pyEnsemblePotProxy_wrap.cpp:6065:27: error: ‘SWIGPY_ConvertPtr’ was notdeclared in this scopepyEnsemblePotProxy_wrap.cpp: In function ‘PyObject*_wrap_PyEnsemblePotProxy_setScale(PyObject*, PyObject*, PyObject*)’:pyEnsemblePotProxy_wrap.cpp:6383:29: error: ‘SWIGPY_ConvertPtr’ was notdeclared in this scopepyEnsemblePotProxy_wrap.cpp: In function ‘PyObject*_wrap_PyEnsemblePotProxy_setThreshold(PyObject*, PyObject*, PyObject*)’:pyEnsemblePotProxy_wrap.cpp:6537:29: error: ‘SWIGPY_ConvertPtr’ was notdeclared in this scopepyEnsemblePotProxy_wrap.cpp: In function ‘PyObject*_wrap_new_PyEnsemblePotProxy_LetterClass(PyObject*, PyObject*, PyObject*)’:pyEnsemblePotProxy_wrap.cpp:7383:29: error: ‘SWIGPY_ConvertPtr’ was notdeclared in this scopepyEnsemblePotProxy_wrap.cpp:7427:29: error: ‘SWIGPY_ConvertPtr’ was notdeclared in this scope

/home/garyt/programs/xplor-nih/2.31.0/CDSlib/cdsString.hh: At global scope:

/home/garyt/programs/xplor-nih/2.31.0/CDSlib/cdsString.hh:222:12:warning: ‘int cdsMapConvertToInt(const String&)’ declared ‘static’ butnever defined [-Wunused-function]/home/garyt/programs/xplor-nih/2.31.0/CDSlib/cdsMap.hh:134:12: warning:‘int cdsMapConvertToInt(int)’ declared ‘static’ but never defined[-Wunused-function]/home/garyt/programs/xplor-nih/2.31.0/CDSlib/cdsMap.hh:135:12: warning:‘int cdsMapConvertToInt(double)’ declared ‘static’ but never defined[-Wunused-function]pyEnsemblePotProxy_wrap.cpp:3283:15: warning: ‘StringPyEnsemblePotProxy_help(PyEnsemblePotProxy*)’ declared ‘static’ butnever defined [-Wunused-function]



I presume  the problem is that I need to do

1. sed 's/SWIG_/SWIGPY_/g' pyEnsemblePotProxy_wrap.cpp >pyEnsemblePotProxy_wrap_new.cpp2. ~/programs/xplor-nih/2.31.0/bin/includeCCpyEnsemblePotProxy_wrap_new.cpp --template-dir/home/garyt/programs/xplor-nih/2.31.0_test_swig/CDSlib --cc 'c++'-DX_MMAP_FLAGS=0 -DFORTRAN_INIT -O3 -DLINUX -D_REENTRANT -DNDEBUG-I/home/garyt/programs/xplor-nih/2.31.0_test_swig/python/-I/home/garyt/programs/xplor-nih/2.31.0_test_swig/arch/Linux_i686/include -DSWIG_VERSION=20004-I/usr/share/swig2.0/python -DCPLUSPLUS -DUSE_CDS_NAMESPACE-I/home/garyt/programs/xplor-nih/2.31.0_test_swig/python/-I/home/garyt/programs/xplor-nih/2.31.0_test_swig/arch/Linux_i686/include -DSWIGPY_GLOBAL-I. -I/usr/include/python2.7-I/home/garyt/programs/xplor-nih/2.31.0_test_swig/CDSlib-I/home/garyt/programs/xplor-nih/2.31.0_test_swig/common-I/home/garyt/programs/xplor-nih/2.31.0_test_swig/intVar-I/home/garyt/programs/xplor-nih/2.31.0_test_swig/nmrPot-I/home/garyt/programs/xplor-nih/2.31.0_test_swig/vmd-I/home/garyt/programs/xplor-nih/2.31.0_test_swig/surfD-I/home/garyt/programs/xplor-nih/2.31.0_test_swig/cminpack-I/home/garyt/programs/xplor-nih/2.31.0_test_swig/sparta-I/home/garyt/programs/xplor-nih/2.31.0_test_swig/devel-I/home/garyt/programs/xplor-nih/2.31.0_test_swig/fortlib-DNIHXPLOR_VERSION='"2.31-custom"' -DPYTHON_VERSION='"2.7"'-DSWIGPY_PYTHON_SILENT_MEMLEAK > pyEnsemblePotProxy_wrap_new_2.cpp

3. c++ -c pyEnsemblePotProxy_wrap_new_2.cpp -DX_MMAP_FLAGS=0-DFORTRAN_INIT -O3 -DLINUX -D_REENTRANT -DNDEBUG-I/home/garyt/programs/xplor-nih/2.31.0_test_swig/python/-I/home/garyt/programs/xplor-nih/2.31.0_test_swig/arch/Linux_i686/include -DSWIG_VERSION=20004-I/usr/share/swig2.0/python -DCPLUSPLUS -DUSE_CDS_NAMESPACE-I/home/garyt/programs/xplor-nih/2.31.0_test_swig/python/-I/home/garyt/programs/xplor-nih/2.31.0_test_swig/arch/Linux_i686/include -DSWIGPY_GLOBAL-I. -I/usr/include/python2.7-I/home/garyt/programs/xplor-nih/2.31.0_test_swig/CDSlib-I/home/garyt/programs/xplor-nih/2.31.0_test_swig/common-I/home/garyt/programs/xplor-nih/2.31.0_test_swig/intVar-I/home/garyt/programs/xplor-nih/2.31.0_test_swig/nmrPot-I/home/garyt/programs/xplor-nih/2.31.0_test_swig/vmd-I/home/garyt/programs/xplor-nih/2.31.0_test_swig/surfD-I/home/garyt/programs/xplor-nih/2.31.0_test_swig/cminpack-I/home/garyt/programs/xplor-nih/2.31.0_test_swig/sparta-I/home/garyt/programs/xplor-nih/2.31.0_test_swig/devel-I/home/garyt/programs/xplor-nih/2.31.0_test_swig/fortlib-DNIHXPLOR_VERSION='"2.31-custom"' -DPYTHON_VERSION='"2.7"'-DSWIGPY_PYTHON_SILENT_MEMLEAK -DSWIGPY_NOINCLUDE


are these all the step I need to do?

nb swig -version gives me


SWIG Version 2.0.4

Compiled with g++ [i686-pc-linux-gnu]

Configured options: +pcre

Please see http://www.swig.org for reporting bugs and further information


regards
gary



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[Xplor-nih] problems with swig files

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