[MacPorts] #36696: py27-scikits-learn: Missing ATLAS symbol on sklearn.cluster import

[MacPorts]

#36696: py27-scikits-learn: Missing ATLAS symbol on sklearn.cluster import
------------------------------+--------------------------------
 Reporter:  Deil.Christoph@…  |      Owner:  macports-tickets@…
     Type:  defect            |     Status:  new
 Priority:  Normal            |  Milestone:
Component:  ports             |    Version:  2.1.2
 Keywords:                    |       Port:  py27-scikits-learn
------------------------------+--------------------------------
 This issue might be a consequence of #36694 or a separate issue.

 I can't use py27-scikit-learn because I get missing ATLAS symbol errors on
 import of sklearn sub-packages.

 This is with OS X 10.8.2 (12C60) and XCode 4.5.1 (4G1004) and Accelerate
 Framework 1.8.

 {{{
 ChristophMacbook:tmp deil$ python -c 'import sklearn.cluster'
 Traceback (most recent call last):
   File "<string>", line 1, in <module>
   File "/Users/deil/Library/Python/2.7/lib/python/site-
 packages/sklearn/cluster/__init__.py", line 6, in <module>
     from .spectral import spectral_clustering, SpectralClustering
   File "/Users/deil/Library/Python/2.7/lib/python/site-
 packages/sklearn/cluster/spectral.py", line 15, in <module>
     from .k_means_ import k_means
   File "/Users/deil/Library/Python/2.7/lib/python/site-
 packages/sklearn/cluster/k_means_.py", line 29, in <module>
     from . import _k_means
 ImportError: dlopen(/Users/deil/Library/Python/2.7/lib/python/site-
 packages/sklearn/cluster/_k_means.so, 2): Symbol not found: _ATL_ddot
   Referenced from: /Users/deil/Library/Python/2.7/lib/python/site-
 packages/sklearn/cluster/_k_means.so
   Expected in: flat namespace
  in /Users/deil/Library/Python/2.7/lib/python/site-
 packages/sklearn/cluster/_k_means.so
 $ python -c 'import sklearn.decomposition'
 Traceback (most recent call last):
   File "<string>", line 1, in <module>
   File
 "/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7
 /site-packages/sklearn/decomposition/__init__.py", line 10, in <module>
     from .sparse_pca import SparsePCA, MiniBatchSparsePCA
   File
 "/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7
 /site-packages/sklearn/decomposition/sparse_pca.py", line 8, in <module>
     from ..linear_model import ridge_regression
   File
 "/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7
 /site-packages/sklearn/linear_model/__init__.py", line 12, in <module>
     from .base import LinearRegression
   File
 "/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7
 /site-packages/sklearn/linear_model/base.py", line 28, in <module>
     from cd_fast import sparse_std
 ImportError:
 dlopen(/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7
 /site-packages/sklearn/linear_model/cd_fast.so, 2): Symbol not found:
 _ATL_daxpy
   Referenced from:
 /opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7
 /site-packages/sklearn/linear_model/cd_fast.so
   Expected in: flat namespace
  in
 /opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7
 /site-packages/sklearn/linear_model/cd_fast.so
 }}}

 The problem is that some ATLAS symbols are not found in Apple's Accelerate
 library.
 Here is some info that I think shows that numpy, scipy and sklearn were
 linked against the Accelerate library:

 {{{
 $ otool -L
 /opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7
 /site-packages/sklearn/cluster/_k_means.so
 /opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7
 /site-packages/sklearn/cluster/_k_means.so:
         /usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current
 version 169.3.0)
 /System/Library/Frameworks/Accelerate.framework/Versions/A/Accelerate
 (compatibility version 1.0.0, current version 4.0.0)

 $ otool -L
 /opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7
 /site-packages/scipy/sparse/linalg/eigen/arpack/_arpack.so
 /opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7
 /site-packages/scipy/sparse/linalg/eigen/arpack/_arpack.so:
         /opt/local/lib/gcc45/libgfortran.3.dylib (compatibility version
 4.0.0, current version 4.0.0)
 /System/Library/Frameworks/Accelerate.framework/Versions/A/Accelerate
 (compatibility version 1.0.0, current version 4.0.0)
         /usr/lib/libgcc_s.1.dylib (compatibility version 1.0.0, current
 version 1669.0.0)
         /opt/local/lib/gcc45/libgcc_s.1.dylib (compatibility version
 1.0.0, current version 1.0.0)
         /usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current
 version 169.3.0)

 $ otool -L /Users/deil/Library/Python/2.7/lib/python/site-
 packages/numpy/core/_dotblas.so
 /Users/deil/Library/Python/2.7/lib/python/site-
 packages/numpy/core/_dotblas.so:
 /System/Library/Frameworks/Accelerate.framework/Versions/A/Accelerate
 (compatibility version 1.0.0, current version 4.0.0)
         /usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current
 version 169.3.0)

 $ otool -L
 /System/Library/Frameworks/Accelerate.framework/Versions/A/Accelerate
 /System/Library/Frameworks/Accelerate.framework/Versions/A/Accelerate:
 /System/Library/Frameworks/Accelerate.framework/Versions/A/Accelerate
 (compatibility version 1.0.0, current version 4.0.0)
 /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vImage.framework/Versions/A/vImage
 (compatibility version 1.0.0, current version 204.5.0)
 /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/vecLib
 (compatibility version 1.0.0, current version 380.6.0)
 /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libvDSP.dylib
 (compatibility version 1.0.0, current version 380.6.0)
         /usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current
 version 169.3.0)

 }}}

 This shows the existing variants and the ones I have installed:
 {{{
 $ port variants py27-numpy
 py27-numpy has the variants:
    atlas: Use the MacPorts' ATLAS libraries  instead of Apple's Accelerate
 framework
    universal: Build for multiple architectures
 $ port variants py27-scipy
 py27-scipy has the variants:
    atlas: Use MacPorts ATLAS libraries
    gcc43: Use gcc 4.3 tool chain for building
      * conflicts with gcc44 gcc45 gcc46 gcc47
    gcc44: Use gfortran-mp-4.4 as fortran compiler
      * conflicts with gcc43 gcc45 gcc46 gcc47
 [+]gcc45: Use gfortran-mp-4.5 as fortran compiler
      * conflicts with gcc43 gcc44 gcc46 gcc47
    gcc46: Use gfortran-mp-4.6 as fortran compiler
      * conflicts with gcc43 gcc44 gcc45 gcc47
    gcc47: Use gfortran-mp-4.7 as fortran compiler
      * conflicts with gcc43 gcc44 gcc45 gcc46
 $ port variants py27-scikits-learn
 py27-scikits-learn has the variants:
    universal: Build for multiple architectures
 $ port installed py27-numpy
 The following ports are currently installed:
   py27-numpy @1.6.2_0 (active)
 $ port installed py27-scipy
 The following ports are currently installed:
   py27-scipy @0.11.0_0+gcc45 (active)
 $ port installed py27-scikits-learn
 The following ports are currently installed:
   py27-scikits-learn @0.12.1_0 (active)
 }}}

 The problem of missing ATLAS symbols has been discussed before, see e.g.
 https://github.com/scikit-learn/scikit-learn/issues/1247

-- 
Ticket URL: <https://trac.macports.org/ticket/36696>
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