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libstdc++.so.6

A C++ miniconda package is build on conda-build-env-0.1.0 box.

Trying to use the package on Ubuntu 12.04 yield to the error:

/usr/lib/x86_64-linux-gnu/libstdc++.so.6: version `GLIBCXX_3.4.21' not found (required by /home/vagrant/miniconda/lib/python2.7/site-packages/_dfndarray.so)

Edit

There is actually the same problem when trying to use the package on conda-build-env-.0.1.0 box (where the package was built):

ImportError: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.21' not found (required by /home/vagrant/miniconda/lib/python2.7/site-packages/_dfndarray.so)

0.2.0 gcc version too old

gcc 4.4.7 (of centos 6) is too old to build ITK. If fails when linking hdf5_cxx:

$ /usr/bin/c++  -fPIC   -Wall -Wno-long-double -Wcast-align -Wdisabled-optimization -Wextra -Wformat=2 -Winvalid-pch -Wno-format-nonliteral -Wpointer-arith -Wshadow -Wunused -Wwrite-strings -funit-at-a-time -Wno-strict-overflow -Wno-deprecated -Wno-invalid-offsetof -Woverloaded-virtual -Wstrict-null-sentinel  -O3 -DNDEBUG   -shared -Wl,-soname,libITKIOHDF5-4.8.so.1 -o ../../../../lib/libITKIOHDF5-4.8.so.1 CMakeFiles/ITKIOHDF5.dir/itkHDF5ImageIOFactory.cxx.o CMakeFiles/ITKIOHDF5.dir/itkHDF5ImageIO.cxx.o -L/home/vagrant/miniconda/envs/_build/lib /home/vagrant/miniconda/envs/_build/lib/libhdf5.so -lrt /home/vagrant/miniconda/envs/_build/lib/libz.so -ldl -lm /home/vagrant/miniconda/envs/_build/lib/libhdf5_cpp.so /home/vagrant/miniconda/envs/_build/lib/libhdf5.so -lrt /home/vagrant/miniconda/envs/_build/lib/libz.so -ldl -lm ../../../../lib/libITKIOImageBase-4.8.so.1 /home/vagrant/miniconda/envs/_build/lib/libhdf5.so -lrt /home/vagrant/miniconda/envs/_build/lib/libz.so -ldl -lm /home/vagrant/miniconda/envs/_build/lib/libhdf5_cpp.so /home/vagrant/miniconda/envs/_build/lib/libhdf5.so -lrt /home/vagrant/miniconda/envs/_build/lib/libz.so -ldl -lm /home/vagrant/miniconda/envs/_build/lib/libhdf5_cpp.so /home/vagrant/miniconda/envs/_build/lib/libhdf5.so -lrt /home/vagrant/miniconda/envs/_build/lib/libz.so -ldl -lm /home/vagrant/miniconda/envs/_build/lib/libhdf5_cpp.so ../../../../lib/libITKCommon-4.8.so.1 ../../../../lib/libitksys-4.8.so.1 ../../../../lib/libITKVNLInstantiation-4.8.so.1 ../../../../lib/libitkvnl_algo-4.8.so.1 ../../../../lib/libitkv3p_lsqr-4.8.so.1 ../../../../lib/libitkvnl-4.8.so.1 ../../../../lib/libitkvcl-4.8.so.1 ../../../../lib/libitkv3p_netlib-4.8.so.1 -lm ../../../../lib/libitkdouble-conversion-4.8.so.1 -lpthread -ldl -lm -Wl,-rpath,/home/vagrant/miniconda/envs/_build/lib:/home/vagrant/miniconda/conda-bld/work/build/lib

/usr/bin/ld: CMakeFiles/ITKIOHDF5.dir/itkHDF5ImageIO.cxx.o: relocation R_X86_64_PC32 against undefined symbol `H5::DataType::fromClass() const' can not be used when making a shared object; recompile with -fPIC

Note that .o files and hdf5 libraryes are compiled with -fPIC

The symbol that caue problem is:

$ nm CMakeFiles/ITKIOHDF5.dir/itkHDF5ImageIO.cxx.o | grep fromClass
                 U _ZNK2H58DataType9fromClassEv

Just to confirm:

$ c++filt _ZNK2H58DataType9fromClassEv
H5::DataType::fromClass() const

It is a weak symbol:

$ nm -D /home/vagrant/miniconda/envs/_build/lib/libhdf5_cpp.so | grep
_ZNK2H58DataType9fromClassEv
000000000003c514 W _ZNK2H58DataType9fromClassEv

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