kmher-install.sh

$ make clean
cd lib && make clean
rm -f *.o zlib-1.2.3/*.o zlib-1.2.3/libz.1.2.3.dylib
cd python && rm -fr build khmer/*.so

$ make all
cd lib && make
cd zlib-1.2.3; ./configure --shared; make; rm minigzip.o; rm example.o
Checking for gcc...
Checking for shared library support...
Building shared library libz.1.2.3.dylib with gcc.
Checking for unistd.h... Yes.
Checking whether to use vs[n]printf() or s[n]printf()... using vs[n]printf()
Checking for vsnprintf() in stdio.h... Yes.
Checking for return value of vsnprintf()... Yes.
Checking for errno.h... Yes.
Checking for mmap support... Yes.
gcc -O3 -fPIC -DUSE_MMAP   -c -o example.o example.c
gcc -O3 -fPIC -DUSE_MMAP   -c -o adler32.o adler32.c
gcc -O3 -fPIC -DUSE_MMAP   -c -o compress.o compress.c
gcc -O3 -fPIC -DUSE_MMAP   -c -o crc32.o crc32.c
gcc -O3 -fPIC -DUSE_MMAP   -c -o gzio.o gzio.c
gcc -O3 -fPIC -DUSE_MMAP   -c -o uncompr.o uncompr.c
gcc -O3 -fPIC -DUSE_MMAP   -c -o deflate.o deflate.c
gcc -O3 -fPIC -DUSE_MMAP   -c -o trees.o trees.c
gcc -O3 -fPIC -DUSE_MMAP   -c -o zutil.o zutil.c
gcc -O3 -fPIC -DUSE_MMAP   -c -o inflate.o inflate.c
gcc -O3 -fPIC -DUSE_MMAP   -c -o infback.o infback.c
gcc -O3 -fPIC -DUSE_MMAP   -c -o inftrees.o inftrees.c
gcc -O3 -fPIC -DUSE_MMAP   -c -o inffast.o inffast.c
gcc -dynamiclib -install_name /usr/local/lib/libz.1.dylib -compatibility_version 1 -current_version 1.2.3 -o libz.1.2.3.dylib adler32.o compress.o crc32.o gzio.o uncompr.o deflate.o trees.o zutil.o inflate.o infback.o inftrees.o inffast.o
rm -f libz.dylib libz.1.dylib
ln -s libz.1.2.3.dylib libz.dylib
ln -s libz.1.2.3.dylib libz.1.dylib
gcc -O3 -fPIC -DUSE_MMAP -o example example.o -L. libz.1.2.3.dylib
gcc -O3 -fPIC -DUSE_MMAP   -c -o minigzip.o minigzip.c
gcc -O3 -fPIC -DUSE_MMAP -o minigzip minigzip.o -L. libz.1.2.3.dylib
c++ -g -fPIC -Wall -O2 -arch x86_64 -DNO_UNIQUE_RC=0   -c -o parsers.o parsers.cc
c++ -g -fPIC -Wall -O2 -arch x86_64 -DNO_UNIQUE_RC=0   -c -o ktable.o ktable.cc
c++ -g -fPIC -Wall -O2 -arch x86_64 -DNO_UNIQUE_RC=0   -c -o hashtable.o hashtable.cc
c++ -g -fPIC -Wall -O2 -arch x86_64 -DNO_UNIQUE_RC=0   -c -o hashbits.o hashbits.cc
c++ -g -fPIC -Wall -O2 -arch x86_64 -DNO_UNIQUE_RC=0   -c -o subset.o subset.cc
subset.cc:544:28: warning: unused variable 'pi' [-Wunused-variable]
    PartitionMap::iterator pi = partition_map.find(kmer);
                           ^
1 warning generated.
c++ -g -fPIC -Wall -O2 -arch x86_64 -DNO_UNIQUE_RC=0   -c -o counting.o counting.cc
cd python && python setup.py build_ext -i
running build_ext
building 'khmer._khmermodule' extension
creating build
creating build/temp.macosx-10.5-i386-2.7
gcc -fno-strict-aliasing -fno-common -dynamic -arch i386 -DNDEBUG -g -O3 -arch i386 -I../lib -I/Library/Frameworks/Python.framework/Versions/7.3/include/python2.7 -c _khmermodule.cc -o build/temp.macosx-10.5-i386-2.7/_khmermodule.o -g
g++ -bundle -undefined dynamic_lookup -g -arch i386 build/temp.macosx-10.5-i386-2.7/_khmermodule.o ../lib/ktable.o ../lib/hashtable.o ../lib/parsers.o ../lib/hashbits.o ../lib/counting.o ../lib/subset.o ../lib/zlib-1.2.3/adler32.o ../lib/zlib-1.2.3/compress.o ../lib/zlib-1.2.3/crc32.o ../lib/zlib-1.2.3/deflate.o ../lib/zlib-1.2.3/gzio.o ../lib/zlib-1.2.3/infback.o ../lib/zlib-1.2.3/inffast.o ../lib/zlib-1.2.3/inflate.o ../lib/zlib-1.2.3/inftrees.o ../lib/zlib-1.2.3/trees.o ../lib/zlib-1.2.3/uncompr.o ../lib/zlib-1.2.3/zutil.o -L../lib -o /Users/arq5x/Documents/SourceCode/other/khmer/python/khmer/_khmermodule.so
ld: warning: ld: warning: ignoring file ../lib/ktable.o, file was built for unsupported file format ( 0xcf 0xfa 0xed 0xfe 0x 7 0x 0 0x 0 0x 1 0x 3 0x 0 0x 0 0x 0 0x 1 0x 0 0x 0 0x 0 ) which is not the architecture being linked (i386): ../lib/ktable.oignoring file ../lib/hashtable.o, file was built for unsupported file format ( 0xcf 0xfa 0xed 0xfe 0x 7 0x 0 0x 0 0x 1 0x 3 0x 0 0x 0 0x 0 0x 1 0x 0 0x 0 0x 0 ) which is not the architecture being linked (i386): ../lib/hashtable.o

ld: warning: ld: warning: ignoring file ../lib/parsers.o, file was built for unsupported file format ( 0xcf 0xfa 0xed 0xfe 0x 7 0x 0 0x 0 0x 1 0x 3 0x 0 0x 0 0x 0 0x 1 0x 0 0x 0 0x 0 ) which is not the architecture being linked (i386): ../lib/parsers.oignoring file ../lib/hashbits.o, file was built for unsupported file format ( 0xcf 0xfa 0xed 0xfe 0x 7 0x 0 0x 0 0x 1 0x 3 0x 0 0x 0 0x 0 0x 1 0x 0 0x 0 0x 0 ) which is not the architecture being linked (i386): ../lib/hashbits.o

ld: warning: ld: warning: ignoring file ../lib/zlib-1.2.3/adler32.o, file was built for unsupported file format ( 0xcf 0xfa 0xed 0xfe 0x 7 0x 0 0x 0 0x 1 0x 3 0x 0 0x 0 0x 0 0x 1 0x 0 0x 0 0x 0 ) which is not the architecture being linked (i386): ../lib/zlib-1.2.3/adler32.oignoring file ../lib/counting.o, file was built for unsupported file format ( 0xcf 0xfa 0xed 0xfe 0x 7 0x 0 0x 0 0x 1 0x 3 0x 0 0x 0 0x 0 0x 1 0x 0 0x 0 0x 0 ) which is not the architecture being linked (i386): ../lib/counting.o
ld: warning: 
ld: warning: ignoring file ../lib/zlib-1.2.3/compress.o, file was built for unsupported file format ( 0xcf 0xfa 0xed 0xfe 0x 7 0x 0 0x 0 0x 1 0x 3 0x 0 0x 0 0x 0 0x 1 0x 0 0x 0 0x 0 ) which is not the architecture being linked (i386): ../lib/zlib-1.2.3/compress.oignoring file ../lib/subset.o, file was built for unsupported file format ( 0xcf 0xfa 0xed 0xfe 0x 7 0x 0 0x 0 0x 1 0x 3 0x 0 0x 0 0x 0 0x 1 0x 0 0x 0 0x 0 ) which is not the architecture being linked (i386): ../lib/subset.o

ld: warning: ignoring file ../lib/zlib-1.2.3/crc32.o, file was built for unsupported file format ( 0xcf 0xfa 0xed 0xfe 0x 7 0x 0 0x 0 0x 1 0x 3 0x 0 0x 0 0x 0 0x 1 0x 0 0x 0 0x 0 ) which is not the architecture being linked (i386): ../lib/zlib-1.2.3/crc32.o
ld: warning: ld: warning: ignoring file ../lib/zlib-1.2.3/gzio.o, file was built for unsupported file format ( 0xcf 0xfa 0xed 0xfe 0x 7 0x 0 0x 0 0x 1 0x 3 0x 0 0x 0 0x 0 0x 1 0x 0 0x 0 0x 0 ) which is not the architecture being linked (i386): ../lib/zlib-1.2.3/gzio.oignoring file ../lib/zlib-1.2.3/deflate.o, file was built for unsupported file format ( 0xcf 0xfa 0xed 0xfe 0x 7 0x 0 0x 0 0x 1 0x 3 0x 0 0x 0 0x 0 0x 1 0x 0 0x 0 0x 0 ) which is not the architecture being linked (i386): ../lib/zlib-1.2.3/deflate.o
ld: warning: 
ld: warning: ld: warning: ld: warning: ld: warning: ignoring file ../lib/zlib-1.2.3/infback.o, file was built for unsupported file format ( 0xcf 0xfa 0xed 0xfe 0x 7 0x 0 0x 0 0x 1 0x 3 0x 0 0x 0 0x 0 0x 1 0x 0 0x 0 0x 0 ) which is not the architecture being linked (i386): ../lib/zlib-1.2.3/infback.old: warning: ignoring file ../lib/zlib-1.2.3/inflate.o, file was built for unsupported file format ( 0xcf 0xfa 0xed 0xfe 0x 7 0x 0 0x 0 0x 1 0x 3 0x 0 0x 0 0x 0 0x 1 0x 0 0x 0 0x 0 ) which is not the architecture being linked (i386): ../lib/zlib-1.2.3/inflate.oignoring file ../lib/zlib-1.2.3/inftrees.o, file was built for unsupported file format ( 0xcf 0xfa 0xed 0xfe 0x 7 0x 0 0x 0 0x 1 0x 3 0x 0 0x 0 0x 0 0x 1 0x 0 0x 0 0x 0 ) which is not the architecture being linked (i386): ../lib/zlib-1.2.3/inftrees.old: warning: ignoring file ../lib/zlib-1.2.3/inffast.o, file was built for unsupported file format ( 0xcf 0xfa 0xed 0xfe 0x 7 0x 0 0x 0 0x 1 0x 3 0x 0 0x 0 0x 0 0x 1 0x 0 0x 0 0x 0 ) which is not the architecture being linked (i386): ../lib/zlib-1.2.3/inffast.oignoring file ../lib/zlib-1.2.3/trees.o, file was built for unsupported file format ( 0xcf 0xfa 0xed 0xfe 0x 7 0x 0 0x 0 0x 1 0x 3 0x 0 0x 0 0x 0 0x 1 0x 0 0x 0 0x 0 ) which is not the architecture being linked (i386): ../lib/zlib-1.2.3/trees.o
ignoring file ../lib/zlib-1.2.3/uncompr.o, file was built for unsupported file format ( 0xcf 0xfa 0xed 0xfe 0x 7 0x 0 0x 0 0x 1 0x 3 0x 0 0x 0 0x 0 0x 1 0x 0 0x 0 0x 0 ) which is not the architecture being linked (i386): ../lib/zlib-1.2.3/uncompr.o

ignoring file ../lib/zlib-1.2.3/zutil.o, file was built for unsupported file format ( 0xcf 0xfa 0xed 0xfe 0x 7 0x 0 0x 0 0x 1 0x 3 0x 0 0x 0 0x 0 0x 1 0x 0 0x 0 0x 0 ) which is not the architecture being linked (i386): ../lib/zlib-1.2.3/zutil.o

$ make test
python setup.py build_ext -i
running build_ext
nosetests
E
======================================================================
ERROR: Failure: ImportError (dlopen(/Users/arq5x/Documents/SourceCode/other/khmer/python/khmer/_khmermodule.so, 2): Symbol not found: __ZTVN5khmer12CountingHashE
  Referenced from: /Users/arq5x/Documents/SourceCode/other/khmer/python/khmer/_khmermodule.so
  Expected in: dynamic lookup
)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/Library/Frameworks/Python.framework/Versions/7.3/lib/python2.7/site-packages/nose/loader.py", line 390, in loadTestsFromName
    addr.filename, addr.module)
  File "/Library/Frameworks/Python.framework/Versions/7.3/lib/python2.7/site-packages/nose/importer.py", line 39, in importFromPath
    return self.importFromDir(dir_path, fqname)
  File "/Library/Frameworks/Python.framework/Versions/7.3/lib/python2.7/site-packages/nose/importer.py", line 86, in importFromDir
    mod = load_module(part_fqname, fh, filename, desc)
  File "/Users/arq5x/Documents/SourceCode/other/khmer/python/khmer/__init__.py", line 3, in <module>
    import _khmer
ImportError: dlopen(/Users/arq5x/Documents/SourceCode/other/khmer/python/khmer/_khmermodule.so, 2): Symbol not found: __ZTVN5khmer12CountingHashE
  Referenced from: /Users/arq5x/Documents/SourceCode/other/khmer/python/khmer/_khmermodule.so
  Expected in: dynamic lookup


----------------------------------------------------------------------
Ran 1 test in 0.002s

FAILED (errors=1)
make: *** [test] Error 1

$ file lib/zlib-1.2.3/*.o
lib/zlib-1.2.3/adler32.o:  Mach-O 64-bit object x86_64
lib/zlib-1.2.3/compress.o: Mach-O 64-bit object x86_64
lib/zlib-1.2.3/crc32.o:    Mach-O 64-bit object x86_64
lib/zlib-1.2.3/deflate.o:  Mach-O 64-bit object x86_64
lib/zlib-1.2.3/gzio.o:     Mach-O 64-bit object x86_64
lib/zlib-1.2.3/infback.o:  Mach-O 64-bit object x86_64
lib/zlib-1.2.3/inffast.o:  Mach-O 64-bit object x86_64
lib/zlib-1.2.3/inflate.o:  Mach-O 64-bit object x86_64
lib/zlib-1.2.3/inftrees.o: Mach-O 64-bit object x86_64
lib/zlib-1.2.3/trees.o:    Mach-O 64-bit object x86_64
lib/zlib-1.2.3/uncompr.o:  Mach-O 64-bit object x86_64
lib/zlib-1.2.3/zutil.o:    Mach-O 64-bit object x86_64

$ file python/khmer/_khmermodule.so 
python/khmer/_khmermodule.so: Mach-O bundle i386