Opened 11 years ago

Closed 11 years ago

#40428 closed defect (worksforme)

py27-scipy "broken files"

Reported by: wimmer@… Owned by: seanfarley (Sean Farley)
Priority: Normal Milestone:
Component: ports Version: 2.2.0
Keywords: Cc: petrrr
Port: py-scipy

Description

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.

Change History (4)

comment:1 Changed 11 years ago by mf2k (Frank Schima)

Cc: sean jeremyhu removed
Owner: changed from macports-tickets@… to sean@…
Port: py-scipy added

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

comment:2 Changed 11 years ago by petrrr

Cc: Peter.Danecek@… added

Cc Me!

comment:3 Changed 11 years ago by 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!

comment:4 Changed 11 years ago by seanfarley (Sean Farley)

Resolution: worksforme
Status: newclosed
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