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khmer Mac OSX gcc installation compile error
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Here's the error I am getting with khmer install on Mac OSX Mavericks (OS X 10.9.4 (13E28)) install | |
``` | |
./setup.py build_ext --inplace | |
running build_ext | |
bash -c cd third-party/zlib && ( test Makefile -nt configure || bash ./configure --static ) && make -f Makefile.pic PIC | |
make[1]: Nothing to be done for `PIC'. | |
bash -c cd third-party/bzip2 && make -f Makefile-libbz2_so all | |
#gcc -shared -Wl,-soname -Wl,libbz2.so.1.0 -o libbz2.so.1.0.6 blocksort.o huffman.o crctable.o randtable.o compress.o decompress.o bzlib.o | |
#gcc -fpic -fPIC -Wall -Winline -O2 -g -D_FILE_OFFSET_BITS=64 -o bzip2-shared bzip2.c libbz2.so.1.0.6 | |
#rm -f libbz2.so.1.0 | |
#ln -s libbz2.so.1.0.6 libbz2.so.1.0 | |
building 'khmer._khmermodule' extension | |
gcc-4.2 -fno-strict-aliasing -I/Users/josh/anaconda/include -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -DVERSION=1.1-88-g51bf29f -UNO_UNIQUE_RC -Ilib -Ithird-party/zlib -Ithird-party/bzip2 -I/Users/josh/anaconda/include/python2.7 -c khmer/_khmermodule.cc -o build/temp.macosx-10.5-x86_64-2.7/khmer/_khmermodule.o -O3 -arch x86_64 | |
cc1plus: warning: command line option "-Wstrict-prototypes" is valid for C/ObjC but not for C++ | |
lib/read_parsers.hh: In instantiation of ‘std::basic_ostream<_CharT, _Traits>& std::operator<<(std::basic_ostream<_CharT, _Traits>&, const std::basic_string<_CharT, _Traits, _Alloc>&) [with _CharT = char, _Traits = std::char_traits<char>, _Alloc = std::allocator<char>]’: | |
lib/read_parsers.hh:550: instantiated from here | |
lib/read_parsers.hh:550: error: explicit instantiation of ‘std::basic_ostream<_CharT, _Traits>& std::operator<<(std::basic_ostream<_CharT, _Traits>&, const std::basic_string<_CharT, _Traits, _Alloc>&) [with _CharT = char, _Traits = std::char_traits<char>, _Alloc = std::allocator<char>]’ but no definition available | |
lib/read_parsers.hh: In instantiation of ‘std::basic_ostream<_CharT, _Traits>& std::operator<<(std::basic_ostream<_CharT, _Traits>&, const std::basic_string<_CharT, _Traits, _Alloc>&) [with _CharT = char, _Traits = std::char_traits<char>, _Alloc = std::allocator<char>]’: | |
lib/read_parsers.hh:550: instantiated from here | |
lib/read_parsers.hh:550: error: explicit instantiation of ‘std::basic_ostream<_CharT, _Traits>& std::operator<<(std::basic_ostream<_CharT, _Traits>&, const std::basic_string<_CharT, _Traits, _Alloc>&) [with _CharT = char, _Traits = std::char_traits<char>, _Alloc = std::allocator<char>]’ but no definition available | |
lib/read_parsers.hh: In instantiation of ‘std::basic_ostream<_CharT, _Traits>& std::operator<<(std::basic_ostream<_CharT, _Traits>&, const std::basic_string<_CharT, _Traits, _Alloc>&) [with _CharT = char, _Traits = std::char_traits<char>, _Alloc = std::allocator<char>]’: | |
lib/read_parsers.hh:550: instantiated from here | |
lib/read_parsers.hh:550: error: explicit instantiation of ‘std::basic_ostream<_CharT, _Traits>& std::operator<<(std::basic_ostream<_CharT, _Traits>&, const std::basic_string<_CharT, _Traits, _Alloc>&) [with _CharT = char, _Traits = std::char_traits<char>, _Alloc = std::allocator<char>]’ but no definition available | |
lib/read_parsers.hh: In instantiation of ‘std::basic_ostream<_CharT, _Traits>& std::operator<<(std::basic_ostream<_CharT, _Traits>&, const std::basic_string<_CharT, _Traits, _Alloc>&) [with _CharT = char, _Traits = std::char_traits<char>, _Alloc = std::allocator<char>]’: | |
lib/read_parsers.hh:550: instantiated from here | |
lib/read_parsers.hh:550: error: explicit instantiation of ‘std::basic_ostream<_CharT, _Traits>& std::operator<<(std::basic_ostream<_CharT, _Traits>&, const std::basic_string<_CharT, _Traits, _Alloc>&) [with _CharT = char, _Traits = std::char_traits<char>, _Alloc = std::allocator<char>]’ but no definition available | |
error: command 'gcc-4.2' failed with exit status 1 | |
make: *** [khmer/_khmermodule.so] Error 1 | |
``` |
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