python/py-numpy @1.8.0_0: Symbol not found: __gfortran_compare_string

[skymoo (Adam Mercer)]

I updated one of my machines yesterday and py27-numpy @1.8.0_0 was installed, now whenever I try import numpy I get the following error:

[ram@cizin ~]$ python
Python 2.7.6 (default, Nov 14 2013, 00:48:33)
[GCC 4.2.1 Compatible Apple LLVM 5.0 (clang-500.2.79)] on darwin
Type "help", "copyright", "credits" or "license" for more information.
>>> import numpy
Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
  File "/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/numpy/__init__.py", line 153, in <module>
    from . import add_newdocs
  File "/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/numpy/add_newdocs.py", line 13, in <module>
    from numpy.lib import add_newdoc
  File "/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/numpy/lib/__init__.py", line 18, in <module>
    from .polynomial import *
  File "/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/numpy/lib/polynomial.py", line 19, in <module>
    from numpy.linalg import eigvals, lstsq, inv
  File "/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/numpy/linalg/__init__.py", line 50, in <module>
    from .linalg import *
  File "/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/numpy/linalg/linalg.py", line 29, in <module>
    from numpy.linalg import lapack_lite, _umath_linalg
ImportError: dlopen(/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/numpy/linalg/lapack_lite.so, 2): Symbol not found: __gfortran_compare_string
  Referenced from: /opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/numpy/linalg/lapack_lite.so
  Expected in: flat namespace
 in /opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/numpy/linalg/lapack_lite.so
>>>

The build succeeds if I revert to `py27-numpy @1.7.1_1`

[seanfarley (Sean Farley)]

Replying to ram@…:

I'm looking into it now.

[seanfarley (Sean Farley)]

Replying to ram@…:

I updated one of my machines yesterday and py27-numpy @1.8.0_0 was installed, now whenever I try import numpy I get the following error:

[ram@cizin ~]$ python
Python 2.7.6 (default, Nov 14 2013, 00:48:33)
[GCC 4.2.1 Compatible Apple LLVM 5.0 (clang-500.2.79)] on darwin
Type "help", "copyright", "credits" or "license" for more information.
>>> import numpy
Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
  File "/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/numpy/__init__.py", line 153, in <module>
    from . import add_newdocs
  File "/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/numpy/add_newdocs.py", line 13, in <module>
    from numpy.lib import add_newdoc
  File "/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/numpy/lib/__init__.py", line 18, in <module>
    from .polynomial import *
  File "/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/numpy/lib/polynomial.py", line 19, in <module>
    from numpy.linalg import eigvals, lstsq, inv
  File "/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/numpy/linalg/__init__.py", line 50, in <module>
    from .linalg import *
  File "/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/numpy/linalg/linalg.py", line 29, in <module>
    from numpy.linalg import lapack_lite, _umath_linalg
ImportError: dlopen(/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/numpy/linalg/lapack_lite.so, 2): Symbol not found: __gfortran_compare_string
  Referenced from: /opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/numpy/linalg/lapack_lite.so
  Expected in: flat namespace
 in /opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/numpy/linalg/lapack_lite.so
>>>

The build succeeds if I revert to `py27-numpy @1.7.1_1`

Can you send the log file as well? At the very least, could you tell me if you have atlas installed? Which gcc installed?

[skymoo (Adam Mercer)]

The log file was deleted after as it was a "successful" install, I'll try run another build and see if I can capture the log. I'm using the following version of @3.10.1_5+gcc48 (active).

[skymoo (Adam Mercer)]

log file attached.

[cooljeanius (Eric Gallager)]

Cc Me!

[seanfarley (Sean Farley)]

Ok, I think I finally got this fixed. It was due to the same error as in ticket #41397, namely, linking to ATLAS accidentally.

[petrrr]

Cc Me!