Pyinstaller --onefile warning pyconfig.h when importing scipy or scipy.signal

Question

This is very simple to recreate. If my script foo.py is:

import scipy

Then run:

python pyinstaller.py --onefile foo.py

When I launch foo.exe I get:

WARNING: file already exists but should not: C:\Users\username\AppData\Local\Temp\_MEI86402\Include\pyconfig.h

I've tested a few versions but the latest I've confirmed is 2.1dev-e958e02 running on Win7, Python 2.7.5 (32 bit), Scipy version 0.12.0

I've submitted a ticket with the Pyinstaller folks but haven't heard anything yet. Any clues how to debug this further?

Answer 1

You can hack the spec file to remove the second instance by adding these lines after a=Analysis:

for d in a.datas:
    if 'pyconfig' in d[0]: 
        a.datas.remove(d)
        break

Answer 2

The answer by wtobia@ worked for me. See https://github.com/pyinstaller/pyinstaller/issues/783

1. Go to C:\Python27\Lib\site-packages\PyInstaller\build.py
2. Find the def append(self, tpl): function.
3. Change if tpl[2] == "BINARY": to if tpl[2] in ["BINARY", "DATA"]:

Answer 3

Expanding upon Ilya's solution, I think this is a little bit more robust solution to modifying the spec file (again place after the a=Analysis... statement).

a.datas = list({tuple(map(str.upper, t)) for t in a.datas})

I only tested this on a small test program (one with a single import and print statement), but it seems to work. a.datas is a list of tuples of strings which contain the pyconfig.h paths. I convert them all to lowercase and then dedup. I actually found that converting all of them all to lowercase was sufficient to get it to work, which suggests to me that pyinstaller does case-sensitive deduping when it should be case-insensitive on Windows. However, I did the deduping myself for good measure.

Answer 4

I realized that the problem is that Windows is case-insensitive and these 2 statements are source directories are "duplicates: include\pyconfig.h Include\pyconfig.h

My solution is to manually tweak the .spec file with after the a=Analysis() call:

import platform
if platform.system().find("Windows")>= 0:
    a.datas = [i for i in a.datas if i[0].find('Include') < 0]

This worked in my 2 tests.

A more flexible solution would be to check ALL items for case-insensitive collisions.

Answer 5

I ran the archive_viewer.py utility (from PyInstaller) on one of my own --onefile executables that has the same error and found that pyconfig.h is included twice:

 (31374007, 6521, 21529, 1, 'x', 'include\\pyconfig.h'),
 (31380528, 6521, 21529, 1, 'x', 'Include\\pyconfig.h'),
 (31387049, 984, 2102, 1, 'x', 'pytz\\zoneinfo\\CET'),

Sadly though, I don't know how to fix it.

PyInstaller Manual link: http://www.pyinstaller.org/export/d3398dd79b68901ae1edd761f3fe0f4ff19cfb1a/project/doc/Manual.html#archiveviewer