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

[Matthew Brett]

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++

before `python setup.py build` ?

Thanks for keeping going on this one,

Matthew