latest SVN doesn't compile Python extensions

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latest SVN doesn't compile Python extensions

Rajarshi Guha-4
Hi, I just updated to the latest SVN and recompiled OpenBabel which
seems towork, but then I also tried to compile the Python extensions
and I get the following:

$: cmake -DCMAKE_INSTALL_PREFIX=/usr/local/openbabel
-DPYTHON_BINDINGS=ON -DRUN_SWIG=ON
-DSWIG_EXECUTABLE=/opt/local/bin/swig ~/src/openbabel

[ 98%] Generating python/openbabel-python.cpp, python/openbabel.py
:3: Error: Unable to find 'python.swg'
/Users/guhar/src/openbabel/scripts/openbabel-python.i:53: Error:
Unable to find 'std_list.i'
/Users/guhar/src/openbabel/scripts/openbabel-python.i:54: Error:
Unable to find 'std_map.i'
/Users/guhar/src/openbabel/scripts/openbabel-python.i:55: Error:
Unable to find 'std_vector.i'
/Users/guhar/src/openbabel/scripts/openbabel-python.i:56: Error:
Unable to find 'std_string.i'
make[2]: *** [scripts/python/openbabel-python.cpp] Error 1
make[1]: *** [scripts/CMakeFiles/_openbabel.dir/all] Error 2
make: *** [all] Error 2


As far as I can tell, python.swg is not in the source tree.

Any pointers would be appreciated

--
Rajarshi Guha
NIH Chemical Genomics Center

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Re: latest SVN doesn't compile Python extensions

Noel O'Boyle
Administrator
Hi Rajarshi

It seems that the problem was in generating the SWIG bindings. Is
there something non-standard about your swig install? It seems that
swig cannot find its own include files.

I've never had to specify this but there is an additional option,
"-DSWIG_DIR" which on my Windows system points to "swigwin-2.0.0/Lib",
which hopefully will do the trick.

- Noel

On 28 August 2010 23:17, Rajarshi Guha <[hidden email]> wrote:

> Hi, I just updated to the latest SVN and recompiled OpenBabel which
> seems towork, but then I also tried to compile the Python extensions
> and I get the following:
>
> $: cmake -DCMAKE_INSTALL_PREFIX=/usr/local/openbabel
> -DPYTHON_BINDINGS=ON -DRUN_SWIG=ON
> -DSWIG_EXECUTABLE=/opt/local/bin/swig ~/src/openbabel
>
> [ 98%] Generating python/openbabel-python.cpp, python/openbabel.py
> :3: Error: Unable to find 'python.swg'
> /Users/guhar/src/openbabel/scripts/openbabel-python.i:53: Error:
> Unable to find 'std_list.i'
> /Users/guhar/src/openbabel/scripts/openbabel-python.i:54: Error:
> Unable to find 'std_map.i'
> /Users/guhar/src/openbabel/scripts/openbabel-python.i:55: Error:
> Unable to find 'std_vector.i'
> /Users/guhar/src/openbabel/scripts/openbabel-python.i:56: Error:
> Unable to find 'std_string.i'
> make[2]: *** [scripts/python/openbabel-python.cpp] Error 1
> make[1]: *** [scripts/CMakeFiles/_openbabel.dir/all] Error 2
> make: *** [all] Error 2
>
>
> As far as I can tell, python.swg is not in the source tree.
>
> Any pointers would be appreciated
>
> --
> Rajarshi Guha
> NIH Chemical Genomics Center
>
> ------------------------------------------------------------------------------
> Sell apps to millions through the Intel(R) Atom(Tm) Developer Program
> Be part of this innovative community and reach millions of netbook users
> worldwide. Take advantage of special opportunities to increase revenue and
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> _______________________________________________
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> [hidden email]
> https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
>

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Re: latest SVN doesn't compile Python extensions

Rajarshi Guha-4

On Aug 29, 2010, at 5:31 AM, Noel O'Boyle wrote:

> Hi Rajarshi
>
> It seems that the problem was in generating the SWIG bindings. Is
> there something non-standard about your swig install? It seems that
> swig cannot find its own include files.

Hmm, I had installed SWIG from mac ports

>
> I've never had to specify this but there is an additional option,
> "-DSWIG_DIR" which on my Windows system points to "swigwin-2.0.0/Lib",
> which hopefully will do the trick.

I'll try this out

thanks

----------------------------------------------------
Rajarshi Guha        | NIH Chemical Genomics Center
http://www.rguha.net | http://ncgc.nih.gov
----------------------------------------------------
A mouse is an elephant built by the Japanese.



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Re: latest SVN doesn't compile Python extensions

Noel O'Boyle
Administrator
On 29 August 2010 21:49, Rajarshi Guha <[hidden email]> wrote:

>
> On Aug 29, 2010, at 5:31 AM, Noel O'Boyle wrote:
>
>> Hi Rajarshi
>>
>> It seems that the problem was in generating the SWIG bindings. Is
>> there something non-standard about your swig install? It seems that
>> swig cannot find its own include files.
>
> Hmm, I had installed SWIG from mac ports

Perhaps you need to install swig-python, etc. I don't know why they've
split it up into different parts.

>> I've never had to specify this but there is an additional option,
>> "-DSWIG_DIR" which on my Windows system points to "swigwin-2.0.0/Lib",
>> which hopefully will do the trick.
>
> I'll try this out
>
> thanks
>
> ----------------------------------------------------
> Rajarshi Guha        | NIH Chemical Genomics Center
> http://www.rguha.net | http://ncgc.nih.gov
> ----------------------------------------------------
> A mouse is an elephant built by the Japanese.
>
>
>

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Re: latest SVN doesn't compile Python extensions

Rajarshi Guha-4

On Aug 29, 2010, at 5:25 PM, Noel O'Boyle wrote:

> On 29 August 2010 21:49, Rajarshi Guha <[hidden email]>  
> wrote:
>>
>> On Aug 29, 2010, at 5:31 AM, Noel O'Boyle wrote:
>>
>>> Hi Rajarshi
>>>
>>> It seems that the problem was in generating the SWIG bindings. Is
>>> there something non-standard about your swig install? It seems that
>>> swig cannot find its own include files.
>>
>> Hmm, I had installed SWIG from mac ports
>
> Perhaps you need to install swig-python, etc. I don't know why they've
> split it up into different parts.


Indeed that did the trick. However after installing swig-python and  
swig-java the compilation proceeds till it tries the Perl bindings -  
this fails, even though I have swig-perl installed

But specifying -DPERL_BINDINGS=OFF doesn't seem to skip compilation of  
the perl bindings

----------------------------------------------------
Rajarshi Guha        | NIH Chemical Genomics Center
http://www.rguha.net | http://ncgc.nih.gov
----------------------------------------------------
Q:  What's polite and works for the phone company?
A:  A deferential operator.



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Re: latest SVN doesn't compile Python extensions

Noel O'Boyle
Administrator
On 29 August 2010 23:08, Rajarshi Guha <[hidden email]> wrote:

>
> On Aug 29, 2010, at 5:25 PM, Noel O'Boyle wrote:
>
>> On 29 August 2010 21:49, Rajarshi Guha <[hidden email]> wrote:
>>>
>>> On Aug 29, 2010, at 5:31 AM, Noel O'Boyle wrote:
>>>
>>>> Hi Rajarshi
>>>>
>>>> It seems that the problem was in generating the SWIG bindings. Is
>>>> there something non-standard about your swig install? It seems that
>>>> swig cannot find its own include files.
>>>
>>> Hmm, I had installed SWIG from mac ports
>>
>> Perhaps you need to install swig-python, etc. I don't know why they've
>> split it up into different parts.
>
>
> Indeed that did the trick. However after installing swig-python and
> swig-java the compilation proceeds till it tries the Perl bindings - this
> fails, even though I have swig-perl installed

It fails for me too on Ubuntu - I think this must be a bug in swig's
FindPerl module. I had to specify the perl libs and so forth.

> But specifying -DPERL_BINDINGS=OFF doesn't seem to skip compilation of the
> perl bindings

A recent change meant that -DRUN_SWIG=ON sets all of the bindings to
on. A quick workaround is to edit the top level CMakeLists.txt (search
for RUN_SWIG). I'll change the build system to avoid this in future.
(Maybe a -DALL_BINDINGS=ON instead, Geoff?)

> ----------------------------------------------------
> Rajarshi Guha        | NIH Chemical Genomics Center
> http://www.rguha.net | http://ncgc.nih.gov
> ----------------------------------------------------
> Q:  What's polite and works for the phone company?
> A:  A deferential operator.
>
>
>

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