[khmer] Problem installing khmer

[C. Titus Brown]

On Fri, Aug 30, 2013 at 12:58:34AM +0000, Cooper, Joshua T. wrote:
> I've been recently using Khmer for digital normalization, and successfully installed it once (the master version) two months ago and it works great. Then today, python kept unexpectedly failing, and while using khmer. So I reinstalled, this time the bleeding-edge version. However, now this is what it says.
> 
> Screed installed perfectly with easy_install screed within the virtualenv, following the instructions of the website khmer.readthedocs.

Despite all the messages, this compilation is successful :).  What does
'make test' say?

cheers,
--titus

> The screen:
> 
> khmer USER$ make clean all
> cd lib && make clean
> rm -f *.o zlib-1.2.3/*.o zlib-1.2.3/libz.a
> cd python && rm -fr build khmer/*.so
> cd lib && make
> cd zlib-1.2.3; ./configure --shared; make libz.a
> 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 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
> ar rc libz.a adler32.o compress.o crc32.o gzio.o uncompr.o deflate.o trees.o zutil.o inflate.o infback.o inftrees.o inffast.o
> c++ -g -fPIC -Wall -O2 -DNO_UNIQUE_RC=0   -c -o parsers.o parsers.cc
> c++ -g -fPIC -Wall -O2 -DNO_UNIQUE_RC=0   -c -o ktable.o ktable.cc
> c++ -g -fPIC -Wall -O2 -DNO_UNIQUE_RC=0   -c -o hashtable.o hashtable.cc
> c++ -g -fPIC -Wall -O2 -DNO_UNIQUE_RC=0   -c -o hashbits.o hashbits.cc
> hashbits.cc: In member function ?unsigned int khmer::Hashbits::traverse_from_kmer(khmer::HashIntoType, unsigned int, khmer::SeenSet&) const?:
> hashbits.cc:1278:16: warning: variable ?kmer? set but not used [-Wunused-but-set-variable]
>    HashIntoType kmer, kmer_f, kmer_r;
>                 ^
> c++ -g -fPIC -Wall -O2 -DNO_UNIQUE_RC=0   -c -o subset.o subset.cc
> c++ -g -fPIC -Wall -O2 -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-10.6-intel-2.7
> /usr/bin/clang -fno-strict-aliasing -fno-common -dynamic -arch i386 -arch x86_64 -g -O2 -DNDEBUG -g -O3 -I../lib -I/Library/Frameworks/Python.framework/Versions/2.7/include/python2.7 -c _khmermodule.cc -o build/temp.macosx-10.6-intel-2.7/_khmermodule.o -g
> /usr/bin/clang++ -bundle -undefined dynamic_lookup -arch i386 -arch x86_64 -g build/temp.macosx-10.6-intel-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/amycallaghan/programs/khmer/python/khmer/_khmermodule.so
> 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.o
> ld: warning: ignoring 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: 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.o
> ld: warning: ignoring 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: ignoring 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: ignoring 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/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.o
> 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.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: ignoring 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: 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.o
> 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.o
> ld: 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.o
> ld: 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.o
> ld: warning: ignoring 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.o
> ld: warning: ignoring 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
> ld: warning: 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
> ld: warning: 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
> 
> I'm not sure what changed, between when I installed it the first time, and now can't seem to install it at all. I'm running a Intel iMac with Lion 10.7.5. and using Python 2.7.5.
> 
> Thank you for any help, advice or recommendations!
> 
> Cheers,
> 
> Josh

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-- 
C. Titus Brown, ctb at msu.edu