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

[Ralf Gommers]

On Mon, Jan 20, 2014 at 1:24 PM, Matthew Brett <matthew.brett at gmail.com>wrote:

> 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?
>

I can't reproduce this with the same OS and Clang versions, XCode 5.0.1 and
Homebrew Python 2.7.

Do you get the same without a virtualenv? Maybe try ``git clean -xdf``
followed by an in-place build. Do you get this for Python 2.7 as well? And
which XCode and Python (version + how installed)?

Ralf



> Cheers,
>
> Matthew
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> SciPy-Dev at scipy.org
> http://mail.scipy.org/mailman/listinfo/scipy-dev
>
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