openbabel-scripting

[OpenBabel-scripting] Building Python Bindings from SVN

[A. H. <ab...@cs...>]

Hi OpenBabelers,

I'm trying to build Python bindings against the OpenBabel trunk.  I'd like
to follow the instructions for SVN building (
http://openbabel.org/wiki/Install_%28source_code%29) and the Python binding
building instructions (http://openbabel.org/wiki/Install_Python_bindings)
but the Python instructions reference a "Step A2" which doesn't exist when
installing from source.  In particular, it doesn't look like the trunk uses
"configure" anymore.

Instead, I set the CMake options listed at the end of this email and
received the following error.  It looks like everything except the Python
bindings is working.  Any suggestions for how to get the Python built?

Cheers,
Abe


The Python-related CMake options:
  // Enable Python bindings
  ENABLE_PYTHON:BOOL=ON
  // Path to a program.
  PYTHON_EXECUTABLE:FILEPATH=/usr/bin/python2.5
  // Path to a file.
  PYTHON_INCLUDE_PATH:PATH=/usr/include/python2.5
  // Path to a library.
  PYTHON_LIBRARY:FILEPATH=/usr/lib64/python2.5/config/libpython2.5.so
  // No help, variable specified on the command line.
  SWIG_DIR:PATH=/home/myself/swig-1.3.40/build/share/swig/1.3.40
  // No help, variable specified on the command line.
  SWIG_EXECUTABLE:FILEPATH=/home/myself/swig-1.3.40/build/bin/swig


The error:
[myself@yoyodyne openbabel-svn]$ make
[ 34%] Built target openbabel
[ 52%] Built target inchi
...etc...
[ 99%] Built target obrotate
[ 99%] Building CXX object
scripts/CMakeFiles/_openbabel.dir/openbabel-pythonC++_wrap.cxx.o
/home/myself/openbabel-svn/scripts/openbabel-pythonC++_wrap.cxx: In function
‘PyObject* _wrap_OBBuilder_IsSpiroAtom(PyObject*, PyObject*)’:
/home/myself/openbabel-svn/scripts/openbabel-pythonC++_wrap.cxx:27731:
error: ‘OBStereo’ has not been declared
/home/myself/openbabel-svn/scripts/openbabel-pythonC++_wrap.cxx:27731:
error: expected `;' before ‘arg1’
/home/myself/openbabel-svn/scripts/openbabel-pythonC++_wrap.cxx:27737:
error: ‘OBStereo’ has not been declared
/home/myself/openbabel-svn/scripts/openbabel-pythonC++_wrap.cxx:27737:
error: ‘temp’ was not declared in this scope
/home/myself/openbabel-svn/scripts/openbabel-pythonC++_wrap.cxx:27737:
error: expected type-specifier before ‘OBStereo’
/home/myself/openbabel-svn/scripts/openbabel-pythonC++_wrap.cxx:27737:
error: expected `>' before ‘OBStereo’
/home/myself/openbabel-svn/scripts/openbabel-pythonC++_wrap.cxx:27737:
error: expected `(' before ‘OBStereo’
/home/myself/openbabel-svn/scripts/openbabel-pythonC++_wrap.cxx:27737:
error: ‘OBStereo’ has not been declared
/home/myself/openbabel-svn/scripts/openbabel-pythonC++_wrap.cxx:27737:
error: expected primary-expression before ‘>’ token
/home/myself/openbabel-svn/scripts/openbabel-pythonC++_wrap.cxx:27737:
error: expected `)' before ‘;’ token
/home/myself/openbabel-svn/scripts/openbabel-pythonC++_wrap.cxx:27737:
error: ‘arg1’ was not declared in this scope
/home/myself/openbabel-svn/scripts/openbabel-pythonC++_wrap.cxx:27738:
error: type ‘<type error>’ argument given to ‘delete’, expected pointer
/home/myself/openbabel-svn/scripts/openbabel-pythonC++_wrap.cxx:27743:
error: ‘arg1’ was not declared in this scope
make[2]: ***
[scripts/CMakeFiles/_openbabel.dir/openbabel-pythonC++_wrap.cxx.o] Error 1
make[1]: *** [scripts/CMakeFiles/_openbabel.dir/all] Error 2
make: *** [all] Error 2

-- 
A. Heifets
http://www.cs.toronto.edu/~aheifets/

Re: [OpenBabel-scripting] Building Python Bindings from SVN

[Geoffrey H. <ge...@ge...>]

> the Python instructions reference a "Step A2" which doesn't exist when installing from source.  In particular, it doesn't look like the trunk uses "configure" anymore.

No, the problem with trunk is that CMake does things "a little different" from configure. In particular, it thinks it can build the Python bindings itself, when it's probably better to generate the SWIG code, and then let Python build everything.

I should have some time to address this today -- it's been on my TODO list for a while.

Thanks for the reminder,
-Geoff

Re: [OpenBabel-scripting] Building Python Bindings from SVN

[Noel O'B. <bao...@gm...>]

Fixed in r3513. As Geoff says, more work to be done but at least it's
compiling again now - thanks for reporting.

- Noel

On 4 February 2010 15:28, Geoffrey Hutchison <ge...@ge...> wrote:
>> the Python instructions reference a "Step A2" which doesn't exist when installing from source.  In particular, it doesn't look like the trunk uses "configure" anymore.
>
> No, the problem with trunk is that CMake does things "a little different" from configure. In particular, it thinks it can build the Python bindings itself, when it's probably better to generate the SWIG code, and then let Python build everything.
>
> I should have some time to address this today -- it's been on my TODO list for a while.
>
> Thanks for the reminder,
> -Geoff
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