Hi,
this looks like bug with hook-sysconfig.
See my gist for details: https://gist.github.com/m1keil/b4914568c8a0e88136b9

Using the latest version of hook-sysconfig (which you can find on github) 
seems to solve this issue:
https://github.com/pyinstaller/pyinstaller/blob/1e38dcb5916f3fc22089e169ff1ea61c05d66ad0/PyInstaller/hooks/hook-sysconfig.py



On Wednesday, January 29, 2014 2:07:51 AM UTC+2, Bogdan Popa wrote:
>
> Hey,
>
> I'm trying to use PyInstaller to bundle a very simple app that contains 
> Flask. I'm on ubuntu 13.10 x86. What I've done is install PyInstaller in 
> the same virtualenv as my project.
>
> My problem is that when I try to run pyinstaller myscript.py I get the 
> following error: "Security-Alert: try to store file outside of 
> dist-directory. Aborting. 
> '../../../../../../usr/lib/python2.7/config-x86_64-linux-gnu/Makefile'"
>
> I don't understand why it needs to write to that location. Furthermore 
> I've tried this on OS X and there it worked fine.
>
> I've attached both the output and the warning logs.
>
> Thanks,
>
>

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