[SciPy-Dev] Symbol not found: __ZNSt8ios_base4InitD1Ev for scipy.sparse

[Matthew Brett]

Hi,

I am trying to install scipy master on OSX 10.9.

I'm using

export CC=clang
export CXX=clang
export FFLAGS=--ff2c

from http://www.scipy.org/scipylib/building/macosx.html

I built and installed numpy with these flags, then scipy.

scipy installs:

>>> scipy.__version__
'0.14.0.dev-6b18a3b'

but then:

>>> import scipy.sparse
Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
  File "/Users/mb312/.virtualenvs/py33-sp-devel/lib/python3.3/site-packages/scipy/sparse/__init__.py",
line 206, in <module>
    from .csr import *
  File "/Users/mb312/.virtualenvs/py33-sp-devel/lib/python3.3/site-packages/scipy/sparse/csr.py",
line 13, in <module>
    from .sparsetools import csr_tocsc, csr_tobsr, csr_count_blocks, \
  File "/Users/mb312/.virtualenvs/py33-sp-devel/lib/python3.3/site-packages/scipy/sparse/sparsetools/__init__.py",
line 5, in <module>
    from .csr import *
  File "/Users/mb312/.virtualenvs/py33-sp-devel/lib/python3.3/site-packages/scipy/sparse/sparsetools/csr.py",
line 26, in <module>
    _csr = swig_import_helper()
  File "/Users/mb312/.virtualenvs/py33-sp-devel/lib/python3.3/site-packages/scipy/sparse/sparsetools/csr.py",
line 22, in swig_import_helper
    _mod = imp.load_module('_csr', fp, pathname, description)
  File "/Users/mb312/.virtualenvs/py33-sp-devel/lib/python3.3/imp.py",
line 183, in load_module
    return load_dynamic(name, filename, file)
ImportError: dlopen(/Users/mb312/.virtualenvs/py33-sp-devel/lib/python3.3/site-packages/scipy/sparse/sparsetools/_csr.so,
2): Symbol not found: __ZNSt8ios_base4InitD1Ev
  Referenced from:
/Users/mb312/.virtualenvs/py33-sp-devel/lib/python3.3/site-packages/scipy/sparse/sparsetools/_csr.so
  Expected in: flat namespace
 in /Users/mb312/.virtualenvs/py33-sp-devel/lib/python3.3/site-packages/scipy/sparse/sparsetools/_csr.so

Here's clang version info:

$ clang -v
Apple LLVM version 5.0 (clang-500.2.79) (based on LLVM 3.3svn)
Target: x86_64-apple-darwin13.0.0
Thread model: posix

I noticed a similar issue here:

https://github.com/scipy/scipy/issues/3053

but I think I have clean install (into a virtualenv).

Any hints as to where to look next?

Cheers,

Matthew