[BioPython] Installation problem---c++ os x

[Michiel Jan Laurens de Hoon]

Several people have run into C++ compilation errors when installing 
Biopython. The good news is that there are currently only two 
C++-dependent packages in Biopython (Bio.KDTree and Bio.Affy), and 
neither of them are essential to the rest of biopython. So if you don't 
plan on using Bio.KDTree or Bio.Affy, the simplest way may be to edit 
setup.py and remove those two packages.

In future versions of Biopython, compilation of Bio.KDTree will be 
switched off by default. For Bio.Affy, I am working with Harry Zuzan to 
replace the C++-dependent parts of Bio.Affy by pure python code. 
Hopefully, that will be done by the time Biopython 1.31 will come out 
later this month.

--Michiel.


Arnaout, Ramy wrote:
> I'm having a problem installing biopython (see excerpt below). I am 
> definitely no expert, but I have troubleshot installation problems with 
> other packages; however, here, I can't figure out what's resulting in 
> the error.
> 
> When I run what appears to be the offending command
> 
> c++ -L/sw/lib -bundle -flat_namespace -undefined suppress 
> build/temp.darwin-7.7.0-PowerMacintosh-2.3/Bio/KDTree/KDTree.o 
> build/temp.darwin-7.7.0-PowerMacintosh-2.3/Bio/KDTree/KDTree.swig.o 
> -lstdc++ -o 
> build/lib.darwin-7.7.0-PowerMacintosh-2.3/Bio/KDTree/_CKDTree.so
> 
> at the prompt it returns the same "multiple definitions" flags, but 
> exits without error. I have searched online without success. Does 
> anybody have any ideas?
> 
> I am using python2.3 on a Mac G4 running OS 10.3.7. I have the numpy 
> and numeric modules installed, as well as pygsl. I installed the egenix 
> and reportlab modules with no problems.
> 
> Thanks,
> 
> R
> 
> —————————————
> Ramy Arnaout, MD, DPhil
> Department of Pathology
> Brigham and Women's Hospital
> Harvard Medical School
> 
> ramy$ python2.3 setup.py install
> running install
> running build
> running build_py
> running build_ext
> building 'Bio.KDTree._CKDTree' extension
> creating build/temp.darwin-7.7.0-PowerMacintosh-2.3
> creating build/temp.darwin-7.7.0-PowerMacintosh-2.3/Bio
> creating build/temp.darwin-7.7.0-PowerMacintosh-2.3/Bio/KDTree
> c++ -I/sw/include/python2.3 -c Bio/KDTree/KDTree.cpp -o 
> build/temp.darwin-7.7.0-PowerMacintosh-2.3/Bio/KDTree/KDTree.o
> c++ -I/sw/include/python2.3 -c Bio/KDTree/KDTree.swig.cpp -o 
> build/temp.darwin-7.7.0-PowerMacintosh-2.3/Bio/KDTree/KDTree.swig.o
> In file included from /sw/include/python2.3/Python.h:70,
>                   from Bio/KDTree/KDTree.swig.cpp:26:
> /sw/include/python2.3/objimpl.h:255: warning: use of `long double' 
> type; its
>     size may change in a future release
> /sw/include/python2.3/objimpl.h:255: warning: (Long double usage is 
> reported
>     only once for each file.
> /sw/include/python2.3/objimpl.h:255: warning: To disable this warning, 
> use
>     -Wno-long-double.)
> c++ -L/sw/lib -bundle -flat_namespace -undefined suppress 
> build/temp.darwin-7.7.0-PowerMacintosh-2.3/Bio/KDTree/KDTree.o 
> build/temp.darwin-7.7.0-PowerMacintosh-2.3/Bio/KDTree/KDTree.swig.o 
> -lstdc++ -o 
> build/lib.darwin-7.7.0-PowerMacintosh-2.3/Bio/KDTree/_CKDTree.so
> ld: multiple definitions of symbol __Unwind_SetIP
> /usr/lib/gcc/darwin/3.3/libgcc.a(unwind-dw2.o) private external 
> definition of __Unwind_SetIP in section (__TEXT,__text)
> /usr/local/lib/libgcc_s.1.0.dylib(unwind-dw2.o) definition of 
> __Unwind_SetIP
> ld: multiple definitions of symbol ___frame_state_for
> /usr/lib/gcc/darwin/3.3/libgcc.a(unwind-dw2.o) private external 
> definition of ___frame_state_for in section (__TEXT,__text)
> /usr/local/lib/libgcc_s.1.0.dylib(unwind-dw2.o) definition of 
> ___frame_state_for
> ld: multiple definitions of symbol __Unwind_RaiseException
> /usr/lib/gcc/darwin/3.3/libgcc.a(unwind-dw2.o) private external 
> definition of __Unwind_RaiseException in section (__TEXT,__text)
> /usr/local/lib/libgcc_s.1.0.dylib(unwind-dw2.o) definition of 
> __Unwind_RaiseException
> ld: multiple definitions of symbol __Unwind_DeleteException
> /usr/lib/gcc/darwin/3.3/libgcc.a(unwind-dw2.o) private external 
> definition of __Unwind_DeleteException in section (__TEXT,__text)
> /usr/local/lib/libgcc_s.1.0.dylib(unwind-dw2.o) definition of 
> __Unwind_DeleteException
> ld: multiple definitions of symbol __Unwind_FindEnclosingFunction
> /usr/lib/gcc/darwin/3.3/libgcc.a(unwind-dw2.o) private external 
> definition of __Unwind_FindEnclosingFunction in section (__TEXT,__text)
> /usr/local/lib/libgcc_s.1.0.dylib(unwind-dw2.o) definition of 
> __Unwind_FindEnclosingFunction
> ld: multiple definitions of symbol __Unwind_ForcedUnwind
> /usr/lib/gcc/darwin/3.3/libgcc.a(unwind-dw2.o) private external 
> definition of __Unwind_ForcedUnwind in section (__TEXT,__text)
> /usr/local/lib/libgcc_s.1.0.dylib(unwind-dw2.o) definition of 
> __Unwind_ForcedUnwind
> ld: multiple definitions of symbol __Unwind_GetDataRelBase
> /usr/lib/gcc/darwin/3.3/libgcc.a(unwind-dw2.o) private external 
> definition of __Unwind_GetDataRelBase in section (__TEXT,__text)
> /usr/local/lib/libgcc_s.1.0.dylib(unwind-dw2.o) definition of 
> __Unwind_GetDataRelBase
> ld: multiple definitions of symbol __Unwind_GetGR
> /usr/lib/gcc/darwin/3.3/libgcc.a(unwind-dw2.o) private external 
> definition of __Unwind_GetGR in section (__TEXT,__text)
> /usr/local/lib/libgcc_s.1.0.dylib(unwind-dw2.o) definition of 
> __Unwind_GetGR
> ld: multiple definitions of symbol __Unwind_GetIP
> /usr/lib/gcc/darwin/3.3/libgcc.a(unwind-dw2.o) private external 
> definition of __Unwind_GetIP in section (__TEXT,__text)
> /usr/local/lib/libgcc_s.1.0.dylib(unwind-dw2.o) definition of 
> __Unwind_GetIP
> ld: multiple definitions of symbol __Unwind_GetLanguageSpecificData
> /usr/lib/gcc/darwin/3.3/libgcc.a(unwind-dw2.o) private external 
> definition of __Unwind_GetLanguageSpecificData in section 
> (__TEXT,__text)
> /usr/local/lib/libgcc_s.1.0.dylib(unwind-dw2.o) definition of 
> __Unwind_GetLanguageSpecificData
> ld: multiple definitions of symbol __Unwind_GetRegionStart
> /usr/lib/gcc/darwin/3.3/libgcc.a(unwind-dw2.o) private external 
> definition of __Unwind_GetRegionStart in section (__TEXT,__text)
> /usr/local/lib/libgcc_s.1.0.dylib(unwind-dw2.o) definition of 
> __Unwind_GetRegionStart
> ld: multiple definitions of symbol __Unwind_GetTextRelBase
> /usr/lib/gcc/darwin/3.3/libgcc.a(unwind-dw2.o) private external 
> definition of __Unwind_GetTextRelBase in section (__TEXT,__text)
> /usr/local/lib/libgcc_s.1.0.dylib(unwind-dw2.o) definition of 
> __Unwind_GetTextRelBase
> ld: multiple definitions of symbol __Unwind_Resume
> /usr/lib/gcc/darwin/3.3/libgcc.a(unwind-dw2.o) private external 
> definition of __Unwind_Resume in section (__TEXT,__text)
> /usr/local/lib/libgcc_s.1.0.dylib(unwind-dw2.o) definition of 
> __Unwind_Resume
> ld: multiple definitions of symbol __Unwind_SetGR
> /usr/lib/gcc/darwin/3.3/libgcc.a(unwind-dw2.o) private external 
> definition of __Unwind_SetGR in section (__TEXT,__text)
> /usr/local/lib/libgcc_s.1.0.dylib(unwind-dw2.o) definition of 
> __Unwind_SetGR
> error: command 'c++' failed with exit status 1
> ramy$
> 
> 
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