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

Sun Feb 2 20:16:48 EST 2014

On Sun, Feb 2, 2014 at 9:14 PM, Matthew Brett <matthew.brett at gmail.com>wrote:

> Hi,
>
> On Sun, Feb 2, 2014 at 7:54 AM, Ralf Gommers <ralf.gommers at gmail.com>
> wrote:
> >
> >
> >
> > On Fri, Jan 31, 2014 at 5:09 AM, Matthew Brett <matthew.brett at gmail.com>
> > wrote:
> >>
> >> Hi,
> >>
> >> On Wed, Jan 22, 2014 at 4:59 PM, Matthew Brett <matthew.brett at gmail.com
> >
> >> wrote:
> >> > Hi,
> >> >
> >> > On Wed, Jan 22, 2014 at 11:33 AM, Ralf Gommers <
> ralf.gommers at gmail.com>
> >> > wrote:
> >> >>
> >> >>
> >> >>
> >> >> 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)?
> >> >
> >> > Thanks for checking.
> >> >
> >> > I do get the same with an in-place python 2.7 build, after git clean
> >> > -fxd, and I get the same in a virtualenv with python 2.7.
> >> >
> >> > For both python 3.3 and python 2.7 I'm using the python.org binaries
> >> > installed from the binary dmg installers.
> >> >
> >> > [mb312 at Kerbin ~]$ python2.7 --version
> >> > Python 2.7.6
> >> > [mb312 at Kerbin ~]$ python3.3 --version
> >> > Python 3.3.2
> >> > [mb312 at Kerbin ~]$ xcodebuild -version
> >> > Xcode 5.0.2
> >> > Build version 5A3005
> >>
> >> Just as a data point - the build works fine for system python.
> >
> >
> > Probably the issue is that more recent XCode ignores __STDC_FORMAT_MACROS
> > defined here:
> >
> https://github.com/scipy/scipy/blob/master/scipy/sparse/sparsetools/setup.py#L15
> .
> > At least that's what's claimed here:
> > http://software.intel.com/en-us/forums/topic/498727. Workaround
> suggested
> > there, can you try that out?
> >
> > That still doesn't explain why only the python.org binaries fail, but
> that
> > should have something to do with the different build flags coming from
> > distutils for the different Pythons.
>
> Sorry to be dumb - but I wasn't sure what the workaround should be,
> from that page. Is it:
>
> export CLANG_CXX_LIBRARY=libstdc++
>

Sorry, yes that should do it. Or otherwise somehow get distutils to link
against /usr/lib/libstdc++.dylib. Or try if Bento works better for you. I
don't have the python.org Python installed right now, so I don't have a
more definite answer.

Ralf

> before `python setup.py build` ?
>
> Thanks for keeping going on this one,
>
> Matthew
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