[MacPorts] #41445: python/py-numpy @1.8.0_0: Symbol not found: __gfortran_compare_string
#41445: python/py-numpy @1.8.0_0: Symbol not found: __gfortran_compare_string --------------------+---------------------- Reporter: ram@… | Owner: dh@… Type: defect | Status: new Priority: Normal | Milestone: Component: ports | Version: 2.2.1 Keywords: | Port: py-numpy --------------------+---------------------- 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` -- Ticket URL: <https://trac.macports.org/ticket/41445> MacPorts <http://www.macports.org/> Ports system for OS X
#41445: python/py-numpy @1.8.0_0: Symbol not found: __gfortran_compare_string -----------------------+------------------- Reporter: ram@… | Owner: dh@… Type: defect | Status: new Priority: Normal | Milestone: Component: ports | Version: 2.2.1 Resolution: | Keywords: Port: py-numpy | -----------------------+------------------- Changes (by ram@…): * cc: michaelld@… (added) * owner: dh@… => dh@… -- Ticket URL: <https://trac.macports.org/ticket/41445#comment:1> MacPorts <http://www.macports.org/> Ports system for OS X
#41445: python/py-numpy @1.8.0_0: Symbol not found: __gfortran_compare_string -----------------------+------------------- Reporter: ram@… | Owner: dh@… Type: defect | Status: new Priority: Normal | Milestone: Component: ports | Version: 2.2.1 Resolution: | Keywords: Port: py-numpy | -----------------------+------------------- Comment (by sean@…): Replying to [comment:1 ram@…]: I'm looking into it now. -- Ticket URL: <https://trac.macports.org/ticket/41445#comment:2> MacPorts <http://www.macports.org/> Ports system for OS X
#41445: python/py-numpy @1.8.0_0: Symbol not found: __gfortran_compare_string -----------------------+------------------- Reporter: ram@… | Owner: dh@… Type: defect | Status: new Priority: Normal | Milestone: Component: ports | Version: 2.2.1 Resolution: | Keywords: Port: py-numpy | -----------------------+------------------- Comment (by sean@…): Replying to [ticket:41445 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? -- Ticket URL: <https://trac.macports.org/ticket/41445#comment:3> MacPorts <http://www.macports.org/> Ports system for OS X
#41445: python/py-numpy @1.8.0_0: Symbol not found: __gfortran_compare_string -----------------------+------------------- Reporter: ram@… | Owner: dh@… Type: defect | Status: new Priority: Normal | Milestone: Component: ports | Version: 2.2.1 Resolution: | Keywords: Port: py-numpy | -----------------------+------------------- Comment (by ram@…): 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)`. -- Ticket URL: <https://trac.macports.org/ticket/41445#comment:4> MacPorts <http://www.macports.org/> Ports system for OS X
#41445: python/py-numpy @1.8.0_0: Symbol not found: __gfortran_compare_string -----------------------+------------------- Reporter: ram@… | Owner: dh@… Type: defect | Status: new Priority: Normal | Milestone: Component: ports | Version: 2.2.1 Resolution: | Keywords: Port: py-numpy | -----------------------+------------------- Comment (by ram@…): log file attached. -- Ticket URL: <https://trac.macports.org/ticket/41445#comment:5> MacPorts <http://www.macports.org/> Ports system for OS X
#41445: python/py-numpy @1.8.0_0: Symbol not found: __gfortran_compare_string -----------------------+------------------- Reporter: ram@… | Owner: dh@… Type: defect | Status: new Priority: Normal | Milestone: Component: ports | Version: 2.2.1 Resolution: | Keywords: Port: py-numpy | -----------------------+------------------- Comment (by sean@…): Ok, I think I finally got this fixed. It was due to the same error as in ticket #41397, namely, linking to ATLAS accidentally. -- Ticket URL: <https://trac.macports.org/ticket/41445#comment:7> MacPorts <http://www.macports.org/> Ports system for OS X
#41445: python/py-numpy @1.8.0_0: Symbol not found: __gfortran_compare_string ------------------------+-------------------- Reporter: ram@… | Owner: dh@… Type: defect | Status: closed Priority: Normal | Milestone: Component: ports | Version: 2.2.1 Resolution: duplicate | Keywords: Port: py-numpy | ------------------------+-------------------- Changes (by sean@…): * status: new => closed * resolution: => duplicate -- Ticket URL: <https://trac.macports.org/ticket/41445#comment:9> MacPorts <http://www.macports.org/> Ports system for OS X
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