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

[Ralf Gommers]

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.

Ralf
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