py27-scipy "broken files"

[wimmer@…]

When installing scipy in a clean macports install (v2.2), macports complains about linking errors:

--->  Scanning binaries for linking errors
Could not open /opt/local/lib/gcc48/libgcc_s.1.dylib: Error opening or reading file (referenced from /opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/scipy/fftpack/_fftpack.so)
DEBUG: Marking /opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/scipy/fftpack/_fftpack.so as broken
DEBUG: Marking /opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/scipy/fftpack/convolve.so as broken
DEBUG: Marking /opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/scipy/integrate/_dop.so as broken
DEBUG: Marking /opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/scipy/integrate/_odepack.so as broken
DEBUG: Marking /opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/scipy/integrate/_quadpack.so as broken
DEBUG: Marking /opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/scipy/integrate/lsoda.so as broken
DEBUG: Marking /opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/scipy/integrate/vode.so as broken
DEBUG: Marking /opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/scipy/interpolate/_fitpack.so as broken
DEBUG: Marking /opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/scipy/interpolate/dfitpack.so as broken
DEBUG: Marking /opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/scipy/lib/blas/fblas.so as broken
DEBUG: Marking /opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/scipy/lib/lapack/calc_lwork.so as broken
DEBUG: Marking /opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/scipy/linalg/_fblas.so as broken
DEBUG: Marking /opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/scipy/linalg/_flapack.so as broken
DEBUG: Marking /opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/scipy/linalg/_flinalg.so as broken
DEBUG: Marking /opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/scipy/linalg/calc_lwork.so as broken
DEBUG: Marking /opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/scipy/odr/__odrpack.so as broken
DEBUG: Marking /opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/scipy/optimize/_cobyla.so as broken
DEBUG: Marking /opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/scipy/optimize/_lbfgsb.so as broken
DEBUG: Marking /opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/scipy/optimize/_minpack.so as broken
DEBUG: Marking /opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/scipy/optimize/_nnls.so as broken
DEBUG: Marking /opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/scipy/optimize/_slsqp.so as broken
DEBUG: Marking /opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/scipy/optimize/minpack2.so as broken
DEBUG: Marking /opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/scipy/sparse/linalg/eigen/arpack/_arpack.so as broken
DEBUG: Marking /opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/scipy/sparse/linalg/isolve/_iterative.so as broken
DEBUG: Marking /opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/scipy/special/_ufuncs.so as broken
DEBUG: Marking /opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/scipy/special/specfun.so as broken
DEBUG: Marking /opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/scipy/stats/futil.so as broken
DEBUG: Marking /opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/scipy/stats/mvn.so as broken
DEBUG: Marking /opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/scipy/stats/statlib.so as broken

This only happens when the precompiled version is installed. Installing from source does not have these problems.

After finding the linking errors, macports then continues to recompile gcc48 from source which takes ages. So, it does work in principle, but the behavior is rather uncomfortable.

[mf2k (Frank Schima)]

In the future, please fill in the Port field and use complete email addresses.

[petrrr]

Cc Me!

[petrrr]

No problem here! sudo port -v install -b py27-scipy works for me, no recompilation.

• OS X 10.8.5;
• MacPorts 2.2.1;
• Version: py27-scipy @0.13.0_1;
• Binary file: py27-scipy-0.13.0_1+gcc48.darwin_12.x86_64.tbz2;

You probably should specify your OS X version as well, to make this reproducible!