Hi Noel,
I tried Openbabel - 2.4.1 with updated version of SWIG - 3.0.12. But it didn’t
help in getting my issue resolved.
I have used Python-3.6.3, CMake-3.7.2, libxml2-2.9.1, Eigen-3.2.8, zlib-1.2.11
and Java-1.8.0.
Please see the output of cmake and error message of make :
-- The C compiler identification is GNU 6.3.0
-- The CXX compiler identification is GNU 6.3.0
-- Check for working C compiler: /opt/scp/software/GCCcore/6.3.0/bin/cc
-- Check for working C compiler: /opt/scp/software/GCCcore/6.3.0/bin/cc -- works
-- Detecting C compiler ABI info
-- Detecting C compiler ABI info - done
-- Detecting C compile features
-- Detecting C compile features - done
-- Check for working CXX compiler: /opt/scp/software/GCCcore/6.3.0/bin/c++
-- Check for working CXX compiler: /opt/scp/software/GCCcore/6.3.0/bin/c++ --
works
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- Detecting CXX compile features
-- Detecting CXX compile features - done
-- Using included inchi library.
-- Found LibXml2: /opt/scp/software/libxml2/2.9.1-foss-2017a/lib/libxml2.so
(found version "2.9.1")
-- Could NOT find ZLIB (missing: ZLIB_LIBRARY ZLIB_INCLUDE_DIR)
-- Could NOT find wxWidgets (missing: wxWidgets_LIBRARIES
wxWidgets_INCLUDE_DIRS)
-- Looking for conio.h
-- Looking for conio.h - not found
-- Looking for sys/time.h
-- Looking for sys/time.h - found
-- Looking for time.h
-- Looking for time.h - found
-- Looking for strings.h
-- Looking for strings.h - found
-- Looking for rpc/xdr.h
-- Looking for rpc/xdr.h - found
-- Looking for regex.h
-- Looking for regex.h - found
-- Looking for C++ include sstream
-- Looking for C++ include sstream - found
-- Looking for rint
-- Looking for rint - not found
-- Looking for snprintf
-- Looking for snprintf - found
-- Looking for sranddev
-- Looking for sranddev - not found
-- Looking for strcasecmp
-- Looking for strcasecmp - found
-- Looking for strncasecmp
-- Looking for strncasecmp - found
-- Looking for dlopen in dl
-- Looking for dlopen in dl - found
-- Looking for sys/types.h
-- Looking for sys/types.h - found
-- Looking for stdint.h
-- Looking for stdint.h - found
-- Looking for stddef.h
-- Looking for stddef.h - found
-- Check size of clock_t
-- Check size of clock_t - done
-- Performing Test SCANDIR_NEEDS_CONST
-- Performing Test SCANDIR_NEEDS_CONST - Failed
-- Performing Test HAVE_GCC_VISIBILITY
-- Performing Test HAVE_GCC_VISIBILITY - Success
-- Checking available shared pointer...
-- Performing Test HAVE_STD_SHARED_PTR
-- Performing Test HAVE_STD_SHARED_PTR - Success
-- Performing Test HAVE_STD_TR1_SHARED_PTR
-- Performing Test HAVE_STD_TR1_SHARED_PTR - Failed
-- Performing Test HAVE_STD_TR1_SHARED_PTR_IN_TR1_HEADER
-- Performing Test HAVE_STD_TR1_SHARED_PTR_IN_TR1_HEADER - Success
-- Use std::shared_ptr in memory
-- Could NOT find Eigen3 (missing: EIGEN3_INCLUDE_DIR EIGEN3_VERSION_OK)
(Required is at least version "2.91.0")
-- Could NOT find Eigen2 (missing: EIGEN2_INCLUDE_DIR EIGEN2_VERSION_OK)
(Required is at least version "2.0.0")
-- Found PkgConfig: /usr/bin/pkg-config (found version "0.27.1")
-- Checking for module 'cairo'
-- No package 'cairo' found
-- Could NOT find Cairo (missing: CAIRO_LIBRARIES CAIRO_INCLUDE_DIRS)
-- Could NOT find Cairo. PNG output will NOT be supported.
-- Looking for getopt
-- Looking for getopt - found
-- Attempting to build the GUI
-- wxWidgets not found => GUI will not be built
-- Found PythonInterp: /opt/scp/software/Python/3.6.3-foss-2017a/bin/python
(found version "3.6.3")
-- Found SWIG: /home/kzgm200/test/swig/bin/swig (found version "3.0.12")
-- Found SWIG: /home/kzgm200/test/swig/bin/swig (found suitable version
"3.0.12", minimum required is "2.0")
-- Found PythonLibs:
/opt/scp/software/Python/3.6.3-foss-2017a/lib/libpython3.6m.so (found version
"3.6.3")
-- Python bindings will be compiled
-- Found JNI: /opt/scp/software/Java/1.8.0_102/jre/lib/amd64/libjawt.so
-- Found Java: /opt/scp/software/Java/1.8.0_102/bin/java (found version
"1.8.0.102")
-- Java bindings will be compiled
-- Configuring done
-- Generating done
-- Build files have been written to: /home/kzgm200/test/openbabel/build
------------------- Error message of make
[ 99%] Building CXX object
scripts/CMakeFiles/bindings_python.dir/python/openbabel-python.cpp.o
/home/kzgm200/test/openbabel/openbabel-2.4.1/scripts/python/openbabel-python.cpp:
In function ‘PyObject* _wrap_OBForceField_DiverseConfGen__SWIG_0(PyObject*,
int, PyObject**)’:
/home/kzgm200/test/openbabel/openbabel-2.4.1/scripts/python/openbabel-python.cpp:34521:61:
error: ‘class OpenBabel::OBForceField’ has no member named ‘DiverseConfGen’
arg5 = static_cast< bool >(val5); result =
(int)(arg1)->DiverseConfGen(arg2,arg3,arg4,arg5);
^~~~~~~~~~~~~~
/home/kzgm200/test/openbabel/openbabel-2.4.1/scripts/python/openbabel-python.cpp:
In function ‘PyObject* _wrap_OBForceField_DiverseConfGen__SWIG_1(PyObject*,
int, PyObject**)’:
/home/kzgm200/test/openbabel/openbabel-2.4.1/scripts/python/openbabel-python.cpp:34536:63:
error: ‘class OpenBabel::OBForceField’ has no member named ‘DiverseConfGen’
arg4 = static_cast< double >(val4); result =
(int)(arg1)->DiverseConfGen(arg2,arg3,arg4);
^~~~~~~~~~~~~~
/home/kzgm200/test/openbabel/openbabel-2.4.1/scripts/python/openbabel-python.cpp:
In function ‘PyObject* _wrap_OBForceField_DiverseConfGen__SWIG_2(PyObject*,
int, PyObject**)’:
/home/kzgm200/test/openbabel/openbabel-2.4.1/scripts/python/openbabel-python.cpp:34549:69:
error: ‘class OpenBabel::OBForceField’ has no member named ‘DiverseConfGen’
arg3 = static_cast< unsigned int >(val3); result =
(int)(arg1)->DiverseConfGen(arg2,arg3);
^~~~~~~~~~~~~~
/home/kzgm200/test/openbabel/openbabel-2.4.1/scripts/python/openbabel-python.cpp:
In function ‘PyObject* _wrap_OBForceField_DiverseConfGen__SWIG_3(PyObject*,
int, PyObject**)’:
/home/kzgm200/test/openbabel/openbabel-2.4.1/scripts/python/openbabel-python.cpp:34559:63:
error: ‘class OpenBabel::OBForceField’ has no member named ‘DiverseConfGen’
arg2 = static_cast< double >(val2); result =
(int)(arg1)->DiverseConfGen(arg2);
^~~~~~~~~~~~~~
make[2]: ***
[scripts/CMakeFiles/bindings_python.dir/python/openbabel-python.cpp.o] Error 1
make[1]: *** [scripts/CMakeFiles/bindings_python.dir/all] Error 2
make: *** [all] Error 2
Thanks & Regards,
Pankaj Jha
From: Kumar Jha, Pankaj
Sent: 05 April 2018 19:25
To: Noel O'Boyle <baoille...@gmail.com>
Cc: openbabel-disc...@lists.sf.net
Subject: RE: [Open Babel] Openbabel - 2.4.1 - Compilation error for Python
Binding
Hi Noel,
Thanks for your response and suggestion.
Sorry my bad, that’s a typing mistake, I have been using Python 3.6.3.
As per your suggestion I will try with updated version of SWIG and let you know
whether it succeeds or not.
Thanks & Regards,
Pankaj Jha
From: Noel O'Boyle [mailto:baoille...@gmail.com]
Sent: 05 April 2018 19:13
To: Kumar Jha, Pankaj
<pankaj.kumar...@astrazeneca.com<mailto:pankaj.kumar...@astrazeneca.com>>
Cc: openbabel-disc...@lists.sf.net<mailto:openbabel-disc...@lists.sf.net>
Subject: Re: [Open Babel] Openbabel - 2.4.1 - Compilation error for Python
Binding
Hi Pankaj Jha,
We will need a little more information to help.
1. Python 3.6 or Python 2.7? You list both in your email.
2. On a clean build, can you provide the output from running cmake.
A potential problem is the old version of SWIG. If I were you I would download
and compile the latest one (you can install it locally), and use
-DSWIG_EXECUTABLE=whatever to point to the install location.
Regards,
- Noel
On 3 April 2018 at 06:05, Kumar Jha, Pankaj
<pankaj.kumar...@astrazeneca.com<mailto:pankaj.kumar...@astrazeneca.com>> wrote:
Hi,
I am trying to compile Openbabel – 2.4.1 with Python-3.6.3
I have configured this with CMake-3.7.2, Python-2.7.13, libxml2-2.9.1,
Eigen-3.2.8, zlib-1.2.11, SWIG-2.0.12, Java-1.8.0 and GCC-6.3.0.
I have used cmake with following options:
cmake ../openbabel-2.4.1 -DCMAKE_INSTALL_PREFIX=~/openbabel/2.4.1 -DRUN_SWIG=ON
-DPYTHON_BINDINGS=ON -DJAVA_BINDINGS=ON
I am getting error while compiling it as following:
[ 99%] Built target test_runner
Scanning dependencies of target bindings_python
[ 99%] Building CXX object
scripts/CMakeFiles/bindings_python.dir/python/openbabel-python.cpp.o
/home/pkj/test/openbabel/openbabel-2.4.1/scripts/python/openbabel-python.cpp:
In function ‘PyObject* _wrap_OBForceField_DiverseConfGen__SWIG_0(PyObject*,
int, PyObject**)’:
/home/pkj/test/openbabel/openbabel-2.4.1/scripts/python/openbabel-python.cpp:34521:61:
error: ‘class OpenBabel::OBForceField’ has no member named ‘DiverseConfGen’
arg5 = static_cast< bool >(val5); result =
(int)(arg1)->DiverseConfGen(arg2,arg3,arg4,arg5);
^~~~~~~~~~~~~~
/home/pkj/test/openbabel/openbabel-2.4.1/scripts/python/openbabel-python.cpp:
In function ‘PyObject* _wrap_OBForceField_DiverseConfGen__SWIG_1(PyObject*,
int, PyObject**)’:
/home/pkj/test/openbabel/openbabel-2.4.1/scripts/python/openbabel-python.cpp:34536:63:
error: ‘class OpenBabel::OBForceField’ has no member named ‘DiverseConfGen’
arg4 = static_cast< double >(val4); result =
(int)(arg1)->DiverseConfGen(arg2,arg3,arg4);
^~~~~~~~~~~~~~
/home/pkj/test/openbabel/openbabel-2.4.1/scripts/python/openbabel-python.cpp:
In function ‘PyObject* _wrap_OBForceField_DiverseConfGen__SWIG_2(PyObject*,
int, PyObject**)’:
/home/pkj/test/openbabel/openbabel-2.4.1/scripts/python/openbabel-python.cpp:34549:69:
error: ‘class OpenBabel::OBForceField’ has no member named ‘DiverseConfGen’
arg3 = static_cast< unsigned int >(val3); result =
(int)(arg1)->DiverseConfGen(arg2,arg3);
^~~~~~~~~~~~~~
/home/pkj/test/openbabel/openbabel-2.4.1/scripts/python/openbabel-python.cpp:
In function ‘PyObject* _wrap_OBForceField_DiverseConfGen__SWIG_3(PyObject*,
int, PyObject**)’:
/home/pkj/test/openbabel/openbabel-2.4.1/scripts/python/openbabel-python.cpp:34559:63:
error: ‘class OpenBabel::OBForceField’ has no member named ‘DiverseConfGen’
arg2 = static_cast< double >(val2); result =
(int)(arg1)->DiverseConfGen(arg2);
^~~~~~~~~~~~~~
make[2]: ***
[scripts/CMakeFiles/bindings_python.dir/python/openbabel-python.cpp.o] Error 1
make[1]: *** [scripts/CMakeFiles/bindings_python.dir/all] Error 2
make: *** [all] Error 2
I don’t get any error if I remove -DPYTHON_BINDINGS=ON but then I don’t get 2
executables generated including obrms.
Could anyone please let me know what could be the possible reason for this
python binding failure.
Thanks & Regards,
Pankaj Jha
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