I can't seem to reproduce this; it works well for me using scipy. Could you perhaps post some sample code (a small, simple, complete program including module imports) that produces the error?
I wonder if it's something that's been fixed in the version of scipy that I'm using (0.5.2 on Python 2.5).
First of all, you shouldn't be having to compile pygtk. You can just use "sudo apt-get install python-gtk2". In Ubuntu Feisty, at least, this will get you pygtk 2.10.4. If you really want to compile it, though, or you want that version and you're on too old a version of Ubuntu, fix the error...
I assume you're using Windows. Use Start --> Run... and type cmd in the box. Then navigate to the directory your script is in and type C:\Python24\python yourscript.py into the prompt. Replace C:\Python24 with the appropriate path to Python.
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