math/py-numpy + databases/py-MySQLdb compatibility issues

[Sergey Akhmatov]

Hello,

I've experienced very strange problem with two pyhon modules in one script:

Steps to reproduce:

Clean 11.1 amd64 installation.

pkg repo set to pkg+http://pkg.FreeBSD.org/${ABI}/latest

# pkg install py27-numpy py27-MySQLdb

$ python2.7
Python 2.7.14 (default, Mar 15 2018, 01:13:31)
[GCC 4.2.1 Compatible FreeBSD Clang 4.0.0 (tags/RELEASE_400/final 
297347)] on freebsd11
Type "help", "copyright", "credits" or "license" for more information.
 >>> import MySQLdb
 >>> import numpy
Traceback (most recent call last):
   File "<stdin>", line 1, in <module>
   File "/usr/local/lib/python2.7/site-packages/numpy/__init__.py", line 
142, in <module>
     from . import add_newdocs
   File "/usr/local/lib/python2.7/site-packages/numpy/add_newdocs.py", 
line 13, in <module>
     from numpy.lib import add_newdoc
   File "/usr/local/lib/python2.7/site-packages/numpy/lib/__init__.py", 
line 8, in <module>
     from .type_check import *
   File 
"/usr/local/lib/python2.7/site-packages/numpy/lib/type_check.py", line 
11, in <module>
     import numpy.core.numeric as _nx
   File "/usr/local/lib/python2.7/site-packages/numpy/core/__init__.py", 
line 26, in <module>
     raise ImportError(msg)
ImportError:
Importing the multiarray numpy extension module failed.  Most
likely you are trying to import a failed build of numpy.
If you're working with a numpy git repo, try `git clean -xdf` (removes all
files not under version control).  Otherwise reinstall numpy.

Original error was: /lib/libgcc_s.so.1: version GCC_4.6.0 required by 
/usr/local/lib/gcc6/libgfortran.so.3 not found

---------

BUT, when i import modules in reverse order, it works fine:

Python 2.7.14 (default, Mar 15 2018, 01:13:31)
[GCC 4.2.1 Compatible FreeBSD Clang 4.0.0 (tags/RELEASE_400/final 
297347)] on freebsd11
Type "help", "copyright", "credits" or "license" for more information.
 >>> import numpy
 >>> import MySQLdb
 >>>

----------

I've tried to investigate dependencies and found out that 
libgfortran.so.3 from gcc6, used by numpy is linked, with libgcc_s.so.1 
from gcc6

$ ldd /usr/local/lib/gcc6/libgfortran.so.3
/usr/local/lib/gcc6/libgfortran.so.3:
         libquadmath.so.0 => /usr/local/lib/gcc6/libquadmath.so.0 
(0x801327000)
         libm.so.5 => /lib/libm.so.5 (0x801566000)
         libgcc_s.so.1 => /usr/local/lib/gcc6/libgcc_s.so.1 (0x801791000)
         libc.so.7 => /lib/libc.so.7 (0x800824000)

And _mysql.so from py-MySQLdb is linked with libgcc_s.so.1 from base system:

$ ldd /usr/local/lib/python2.7/site-packages/_mysql.so
/usr/local/lib/python2.7/site-packages/_mysql.so:
...

     libgcc_s.so.1 => /lib/libgcc_s.so.1 (0x803572000)


I have no clue if this could actually cause problem.

Could someone please reproduce this behavior and/or give some hints how 
to investigate further?