Re: [Rdkit-discuss] Problems importing rdkit on Windows

[Greg L. <gre...@gm...>]

Hi Noel,

On Wed, Mar 30, 2011 at 10:59 PM, Noel O'Boyle <bao...@gm...> wrote:
> Hi all,
>
> I'm updating cinfony and using the latest RDKit Release
> (RDKit_2010_12_1, the binary Python 2.6 release), but "from rdkit
> import Chem" is causing Python to crash (on Windows 7) as below. I've
> tried with and without RDBASE defined.
>
> Can someone confirm that it works for them?

As long as I be sure that my PATH is set properly, things work fine.
Here's what I see using a newly downloaded copy of the 2010_12_1
release on my win7 box:
$ python
Python 2.6.6 (r266:84297, Aug 24 2010, 18:46:32) [MSC v.1500 32 bit
(Intel)] on win32
Type "help", "copyright", "credits" or "license" for more information.
>>> from rdkit import Chem
>>> from rdkit import rdBase
>>> rdBase.rdkitVersion
'2010.12.1'
>>>

I mention the PATH setting thing because I normally use python2.7 and
when I first tried testing my freshly downloaded copy of the 2010_12_1
release I also got a crash (ah! panic!), but it turns out that was
caused by me having a boost python dll built for python2.7 somewhere
else in my PATH.

looks like something else is happening for you:

>
> C:\Tools\rdkit\RDKit_2010_12_1>echo %PATH%
> C:\Tools\rdkit\RDKit_2010_12_1\lib
>
> C:\Tools\rdkit\RDKit_2010_12_1>echo %PYTHONPATH%
> %PYTHONPATH%

looks ok so far

> C:\Tools\rdkit\RDKit_2010_12_1>python
> 'python' is not recognized as an internal or external command,
> operable program or batch file.
>
> C:\Tools\rdkit\RDKit_2010_12_1>C:\Python26\python
> Python 2.6.4 (r264:75708, Oct 26 2009, 08:23:19) [MSC v.1500 32 bit (Intel)] on
> win32
> Type "help", "copyright", "credits" or "license" for more information.
>>>> from rdkit import Chem
>
> CRASH!!!

This is, in my experience, always a PATH or PYTHONPATH problem, but it
does look like you have that stuff set correctly.

Can you please try:
C:\Python26\python -v -c 'from rdkit import rdBase'
and see if you get the same crash? If so, take a look at the output
and make sure it really is using the right rdkit.

If that still has problems, the easiest way to diagnose what's going
on is to grab a copy of dependency walker (one of the most useful
windows tools: http://www.dependencywalker.com/), invoking that from
the shell you are running python in (so that it has the same
environment), and then opening either $RDBASE/rdkit/rdBase.pyd or
$RDBASE/rdkit/Chem/rdchem.pyd. Take a look at the what libraries are
being used and see if you can identify anything suspicious.

Best,
-greg