pip install numpy 1.15 from wheel: numpy.dtype size changed Expected 96, got 88

After pip install numpy 1.15 from a wheel,

print "np.dtype.__basicsize__:", np.dtype.__basicsize__  # 96
print "scipy.dtype.__basicsize__:", scipy.dtype.__basicsize__  # 96
from scipy import stats
~ 20 RuntimeWarning: numpy.dtype size   changed, may indicate binary incompatibility. Expected 96, got 88

(Please add labels, don’t see them; is there a label “strange” ?)

A shell script to reproduce this:

#!/bin/bash
# re-install numpy scipy: https://github.com/numpy/numpy/issues/11537  denis 27july

( cd $site;  rm -r tmp;  mkdir tmp;  mv numpy* scipy* tmp )
rm -r ~/Library/Caches/pip

#...............................................................................
pip2 install --user numpy scipy

python2 -c '
import sys
import numpy as np
import scipy

print "versions: numpy %s  scipy %s  python %s  " % (
		np.__version__, scipy.__version__ , sys.version )
print "np.dtype.__basicsize__:", np.dtype.__basicsize__
print "scipy.dtype.__basicsize__:", scipy.dtype.__basicsize__

from scipy import stats
'

pip2 --version
ls -l $site/scipy/*/*cython*.so
otool -L $site/scipy/*/*cython*.so  # mac

and the logfile:

Collecting numpy
  Downloading https://files.pythonhosted.org/packages/3c/bf/e36756c562f7386be78c6942f0a8a647ee4eb374cdf219bece7054832b14/numpy-1.15.0-cp27-cp27m-macosx_10_6_intel.macosx_10_9_intel.macosx_10_9_x86_64.macosx_10_10_intel.macosx_10_10_x86_64.whl (24.5MB)
Collecting scipy
  Downloading https://files.pythonhosted.org/packages/d1/d6/3eac96ffcf7cbeb37ed72982cf3fdd3138472cb04ab32cdce1f444d765f2/scipy-1.1.0-cp27-cp27m-macosx_10_6_intel.macosx_10_9_intel.macosx_10_9_x86_64.macosx_10_10_intel.macosx_10_10_x86_64.whl (16.8MB)
Installing collected packages: numpy, scipy
  The scripts conv-template, f2py and from-template are installed in '/Users/bz/Library/Python/2.7/bin' which is not on PATH.
  Consider adding this directory to PATH or, if you prefer to suppress this warning, use --no-warn-script-location.
Successfully installed numpy-1.15.0 scipy-1.1.0
versions: numpy 1.15.0  scipy 1.1.0  python 2.7.15 (v2.7.15:ca079a3ea3, Apr 29 2018, 20:59:26) 
[GCC 4.2.1 Compatible Apple LLVM 6.0 (clang-600.0.57)]  
np.dtype.__basicsize__: 96
scipy.dtype.__basicsize__: 96
/Library/Python/2.7/site-packages/scipy/special/__init__.py:640: RuntimeWarning: numpy.dtype size changed, may indicate binary incompatibility. Expected 96, got 88
  from ._ufuncs import *
/Library/Python/2.7/site-packages/scipy/linalg/basic.py:17: RuntimeWarning: numpy.dtype size changed, may indicate binary incompatibility. Expected 96, got 88
  from ._solve_toeplitz import levinson
/Library/Python/2.7/site-packages/scipy/linalg/__init__.py:207: RuntimeWarning: numpy.dtype size changed, may indicate binary incompatibility. Expected 96, got 88
  from ._decomp_update import *
/Library/Python/2.7/site-packages/scipy/special/_ellip_harm.py:7: RuntimeWarning: numpy.dtype size changed, may indicate binary incompatibility. Expected 96, got 88
  from ._ellip_harm_2 import _ellipsoid, _ellipsoid_norm
/Library/Python/2.7/site-packages/scipy/interpolate/_bsplines.py:10: RuntimeWarning: numpy.dtype size changed, may indicate binary incompatibility. Expected 96, got 88
  from . import _bspl
/Library/Python/2.7/site-packages/scipy/sparse/lil.py:19: RuntimeWarning: numpy.dtype size changed, may indicate binary incompatibility. Expected 96, got 88
  from . import _csparsetools
/Library/Python/2.7/site-packages/scipy/sparse/csgraph/__init__.py:165: RuntimeWarning: numpy.dtype size changed, may indicate binary incompatibility. Expected 96, got 88
  from ._shortest_path import shortest_path, floyd_warshall, dijkstra,\
/Library/Python/2.7/site-packages/scipy/sparse/csgraph/_validation.py:5: RuntimeWarning: numpy.dtype size changed, may indicate binary incompatibility. Expected 96, got 88
  from ._tools import csgraph_to_dense, csgraph_from_dense,\
/Library/Python/2.7/site-packages/scipy/sparse/csgraph/__init__.py:167: RuntimeWarning: numpy.dtype size changed, may indicate binary incompatibility. Expected 96, got 88
  from ._traversal import breadth_first_order, depth_first_order, \
/Library/Python/2.7/site-packages/scipy/sparse/csgraph/__init__.py:169: RuntimeWarning: numpy.dtype size changed, may indicate binary incompatibility. Expected 96, got 88
  from ._min_spanning_tree import minimum_spanning_tree
/Library/Python/2.7/site-packages/scipy/sparse/csgraph/__init__.py:170: RuntimeWarning: numpy.dtype size changed, may indicate binary incompatibility. Expected 96, got 88
  from ._reordering import reverse_cuthill_mckee, maximum_bipartite_matching, \
/Library/Python/2.7/site-packages/scipy/spatial/__init__.py:95: RuntimeWarning: numpy.dtype size changed, may indicate binary incompatibility. Expected 96, got 88
  from .ckdtree import *
/Library/Python/2.7/site-packages/scipy/spatial/__init__.py:96: RuntimeWarning: numpy.dtype size changed, may indicate binary incompatibility. Expected 96, got 88
  from .qhull import *
/Library/Python/2.7/site-packages/scipy/spatial/_spherical_voronoi.py:18: RuntimeWarning: numpy.dtype size changed, may indicate binary incompatibility. Expected 96, got 88
  from . import _voronoi
/Library/Python/2.7/site-packages/scipy/spatial/distance.py:122: RuntimeWarning: numpy.dtype size changed, may indicate binary incompatibility. Expected 96, got 88
  from . import _hausdorff
/Library/Python/2.7/site-packages/scipy/optimize/_trlib/__init__.py:1: RuntimeWarning: numpy.dtype size changed, may indicate binary incompatibility. Expected 96, got 88
  from ._trlib import TRLIBQuadraticSubproblem
/Library/Python/2.7/site-packages/scipy/optimize/_numdiff.py:10: RuntimeWarning: numpy.dtype size changed, may indicate binary incompatibility. Expected 96, got 88
  from ._group_columns import group_dense, group_sparse
/Library/Python/2.7/site-packages/scipy/stats/_continuous_distns.py:18: RuntimeWarning: numpy.dtype size changed, may indicate binary incompatibility. Expected 96, got 88
  from . import _stats
pip 18.0 from /Library/Python/2.7/site-packages/pip (python 2.7)
-rwxr-xr-x 1 bz admin  306652 Jul 27 11:34 /Library/Python/2.7/site-packages/scipy/linalg/cython_blas.so
-rwxr-xr-x 1 bz admin  817100 Jul 27 11:34 /Library/Python/2.7/site-packages/scipy/linalg/cython_lapack.so
-rwxr-xr-x 1 bz admin 2738116 Jul 27 11:34 /Library/Python/2.7/site-packages/scipy/special/cython_special.so
/Library/Python/2.7/site-packages/scipy/linalg/cython_blas.so:
	@loader_path/../.dylibs/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/libSystem.B.dylib (compatibility version 1.0.0, current version 1238.60.2)
	@loader_path/../.dylibs/libgcc_s.1.dylib (compatibility version 1.0.0, current version 1.0.0)
	@loader_path/../.dylibs/libquadmath.0.dylib (compatibility version 1.0.0, current version 1.0.0)
/Library/Python/2.7/site-packages/scipy/linalg/cython_lapack.so:
	@loader_path/../.dylibs/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/libSystem.B.dylib (compatibility version 1.0.0, current version 1238.60.2)
	@loader_path/../.dylibs/libgcc_s.1.dylib (compatibility version 1.0.0, current version 1.0.0)
	@loader_path/../.dylibs/libquadmath.0.dylib (compatibility version 1.0.0, current version 1.0.0)
/Library/Python/2.7/site-packages/scipy/special/cython_special.so:
	@loader_path/../.dylibs/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/libSystem.B.dylib (compatibility version 1.0.0, current version 1238.60.2)
	@loader_path/../.dylibs/libgcc_s.1.dylib (compatibility version 1.0.0, current version 1.0.0)
	@loader_path/../.dylibs/libquadmath.0.dylib (compatibility version 1.0.0, current version 1.0.0)

[alexiswl]

For now, rolling back to numpy 1.14.5 through conda, will resolve this conda install numpy==1.14.5 --yes

[denis-bz]

Sure, filter. But where’s the size 88 in numpy 1.15 coming from – what changed, if not numpy.dtype: the wheel build chain, .dylibs ?

#!/bin/bash
# https://github.com/numpy/numpy/issues/11628
# scipy 1.1.0, numpy 1.14.5: no warning
# scipy 1.1.0, numpy 1.15.0: RuntimeWarning: numpy.dtype size changed Expected 96, got 88

set -v

PYTHONPATH=/Library/Python/2.7/site-packages \
PYTHONSTARTUP="" \
\
python2 -c '
import numpy
print "numpy", numpy.__version__, numpy.__path__

import scipy
print "scipy", scipy.__version__, scipy.__path__

from scipy.linalg import solve_toeplitz  # 2 RuntimeWarnings
'