[khmer] Problem installing khmer

C. Titus Brown ctb at msu.edu
Fri Aug 30 11:09:24 PDT 2013


On Fri, Aug 30, 2013 at 04:13:54PM +0000, Cooper, Joshua T. wrote:
> Ha, I would not have expected that. Here is the make test out put:
> 
> Thank you so much for the fast response!

Ahh, I was wrong -- I didn't fully read the original error message.

Can you try:

make CC=gcc CXX=g++ clean all test

?

cheers,
--titus

> Last login: Thu Aug 29 19:44:55 on ttys000
> d-ip-129-15-161-69:~ amycallaghan$ cd ~/programs/khmer/
> d-ip-129-15-161-69:khmer amycallaghan$ ls
> IDEAS		data		lib		sandbox
> Makefile	doc		novelty		scripts
> README.txt	examples	plots		templatem
> TODO		figuregen	python		tests
> d-ip-129-15-161-69:khmer amycallaghan$ make test
> cd lib && make
> make[1]: Nothing to be done for `all'.
> cd python && python setup.py build_ext -i
> running build_ext
> nosetests
> EEEEEEEEEEEEEEE
> ======================================================================
> ERROR: Failure: ImportError (dlopen(/Users/amycallaghan/programs/khmer/python/khmer/_khmermodule.so, 2): Symbol not found: __ZNKSt5ctypeIcE13_M_widen_initEv
>   Referenced from: /Users/amycallaghan/programs/khmer/python/khmer/_khmermodule.so
>   Expected in: flat namespace
>  in /Users/amycallaghan/programs/khmer/python/khmer/_khmermodule.so)
> ----------------------------------------------------------------------
> Traceback (most recent call last):
>   File "/Library/Python/2.7/site-packages/nose-1.3.0-py2.7.egg/nose/loader.py", line 413, in loadTestsFromName
>     addr.filename, addr.module)
>   File "/Library/Python/2.7/site-packages/nose-1.3.0-py2.7.egg/nose/importer.py", line 47, in importFromPath
>     return self.importFromDir(dir_path, fqname)
>   File "/Library/Python/2.7/site-packages/nose-1.3.0-py2.7.egg/nose/importer.py", line 94, in importFromDir
>     mod = load_module(part_fqname, fh, filename, desc)
>   File "/Users/amycallaghan/programs/khmer/tests/test_c_wrapper.py", line 2, in <module>
>     import khmer
>   File "/Users/amycallaghan/programs/khmer/python/khmer/__init__.py", line 3, in <module>
>     import _khmer
> ImportError: dlopen(/Users/amycallaghan/programs/khmer/python/khmer/_khmermodule.so, 2): Symbol not found: __ZNKSt5ctypeIcE13_M_widen_initEv
>   Referenced from: /Users/amycallaghan/programs/khmer/python/khmer/_khmermodule.so
>   Expected in: flat namespace
>  in /Users/amycallaghan/programs/khmer/python/khmer/_khmermodule.so
> 
> ======================================================================
> ERROR: Failure: ImportError (dlopen(/Users/amycallaghan/programs/khmer/python/khmer/_khmermodule.so, 2): Symbol not found: __ZNKSt5ctypeIcE13_M_widen_initEv
>   Referenced from: /Users/amycallaghan/programs/khmer/python/khmer/_khmermodule.so
>   Expected in: flat namespace
>  in /Users/amycallaghan/programs/khmer/python/khmer/_khmermodule.so)
> ----------------------------------------------------------------------
> Traceback (most recent call last):
>   File "/Library/Python/2.7/site-packages/nose-1.3.0-py2.7.egg/nose/loader.py", line 413, in loadTestsFromName
>     addr.filename, addr.module)
>   File "/Library/Python/2.7/site-packages/nose-1.3.0-py2.7.egg/nose/importer.py", line 47, in importFromPath
>     return self.importFromDir(dir_path, fqname)
>   File "/Library/Python/2.7/site-packages/nose-1.3.0-py2.7.egg/nose/importer.py", line 94, in importFromDir
>     mod = load_module(part_fqname, fh, filename, desc)
>   File "/Users/amycallaghan/programs/khmer/tests/test_counting_hash.py", line 4, in <module>
>     import khmer
>   File "/Users/amycallaghan/programs/khmer/python/khmer/__init__.py", line 3, in <module>
>     import _khmer
> ImportError: dlopen(/Users/amycallaghan/programs/khmer/python/khmer/_khmermodule.so, 2): Symbol not found: __ZNKSt5ctypeIcE13_M_widen_initEv
>   Referenced from: /Users/amycallaghan/programs/khmer/python/khmer/_khmermodule.so
>   Expected in: flat namespace
>  in /Users/amycallaghan/programs/khmer/python/khmer/_khmermodule.so
> 
> ======================================================================
> ERROR: Failure: ImportError (dlopen(/Users/amycallaghan/programs/khmer/python/khmer/_khmermodule.so, 2): Symbol not found: __ZNKSt5ctypeIcE13_M_widen_initEv
>   Referenced from: /Users/amycallaghan/programs/khmer/python/khmer/_khmermodule.so
>   Expected in: flat namespace
>  in /Users/amycallaghan/programs/khmer/python/khmer/_khmermodule.so)
> ----------------------------------------------------------------------
> Traceback (most recent call last):
>   File "/Library/Python/2.7/site-packages/nose-1.3.0-py2.7.egg/nose/loader.py", line 413, in loadTestsFromName
>     addr.filename, addr.module)
>   File "/Library/Python/2.7/site-packages/nose-1.3.0-py2.7.egg/nose/importer.py", line 47, in importFromPath
>     return self.importFromDir(dir_path, fqname)
>   File "/Library/Python/2.7/site-packages/nose-1.3.0-py2.7.egg/nose/importer.py", line 94, in importFromDir
>     mod = load_module(part_fqname, fh, filename, desc)
>   File "/Users/amycallaghan/programs/khmer/tests/test_counting_single.py", line 1, in <module>
>     import khmer
>   File "/Users/amycallaghan/programs/khmer/python/khmer/__init__.py", line 3, in <module>
>     import _khmer
> ImportError: dlopen(/Users/amycallaghan/programs/khmer/python/khmer/_khmermodule.so, 2): Symbol not found: __ZNKSt5ctypeIcE13_M_widen_initEv
>   Referenced from: /Users/amycallaghan/programs/khmer/python/khmer/_khmermodule.so
>   Expected in: flat namespace
>  in /Users/amycallaghan/programs/khmer/python/khmer/_khmermodule.so
> 
> ======================================================================
> ERROR: Failure: ImportError (dlopen(/Users/amycallaghan/programs/khmer/python/khmer/_khmermodule.so, 2): Symbol not found: __ZNKSt5ctypeIcE13_M_widen_initEv
>   Referenced from: /Users/amycallaghan/programs/khmer/python/khmer/_khmermodule.so
>   Expected in: flat namespace
>  in /Users/amycallaghan/programs/khmer/python/khmer/_khmermodule.so)
> ----------------------------------------------------------------------
> Traceback (most recent call last):
>   File "/Library/Python/2.7/site-packages/nose-1.3.0-py2.7.egg/nose/loader.py", line 413, in loadTestsFromName
>     addr.filename, addr.module)
>   File "/Library/Python/2.7/site-packages/nose-1.3.0-py2.7.egg/nose/importer.py", line 47, in importFromPath
>     return self.importFromDir(dir_path, fqname)
>   File "/Library/Python/2.7/site-packages/nose-1.3.0-py2.7.egg/nose/importer.py", line 94, in importFromDir
>     mod = load_module(part_fqname, fh, filename, desc)
>   File "/Users/amycallaghan/programs/khmer/tests/test_filter.py", line 1, in <module>
>     import khmer
>   File "/Users/amycallaghan/programs/khmer/python/khmer/__init__.py", line 3, in <module>
>     import _khmer
> ImportError: dlopen(/Users/amycallaghan/programs/khmer/python/khmer/_khmermodule.so, 2): Symbol not found: __ZNKSt5ctypeIcE13_M_widen_initEv
>   Referenced from: /Users/amycallaghan/programs/khmer/python/khmer/_khmermodule.so
>   Expected in: flat namespace
>  in /Users/amycallaghan/programs/khmer/python/khmer/_khmermodule.so
> 
> ======================================================================
> ERROR: Failure: ImportError (dlopen(/Users/amycallaghan/programs/khmer/python/khmer/_khmermodule.so, 2): Symbol not found: __ZNKSt5ctypeIcE13_M_widen_initEv
>   Referenced from: /Users/amycallaghan/programs/khmer/python/khmer/_khmermodule.so
>   Expected in: flat namespace
>  in /Users/amycallaghan/programs/khmer/python/khmer/_khmermodule.so)
> ----------------------------------------------------------------------
> Traceback (most recent call last):
>   File "/Library/Python/2.7/site-packages/nose-1.3.0-py2.7.egg/nose/loader.py", line 413, in loadTestsFromName
>     addr.filename, addr.module)
>   File "/Library/Python/2.7/site-packages/nose-1.3.0-py2.7.egg/nose/importer.py", line 47, in importFromPath
>     return self.importFromDir(dir_path, fqname)
>   File "/Library/Python/2.7/site-packages/nose-1.3.0-py2.7.egg/nose/importer.py", line 94, in importFromDir
>     mod = load_module(part_fqname, fh, filename, desc)
>   File "/Users/amycallaghan/programs/khmer/tests/test_functions.py", line 1, in <module>
>     import khmer
>   File "/Users/amycallaghan/programs/khmer/python/khmer/__init__.py", line 3, in <module>
>     import _khmer
> ImportError: dlopen(/Users/amycallaghan/programs/khmer/python/khmer/_khmermodule.so, 2): Symbol not found: __ZNKSt5ctypeIcE13_M_widen_initEv
>   Referenced from: /Users/amycallaghan/programs/khmer/python/khmer/_khmermodule.so
>   Expected in: flat namespace
>  in /Users/amycallaghan/programs/khmer/python/khmer/_khmermodule.so
> 
> ======================================================================
> ERROR: Failure: ImportError (dlopen(/Users/amycallaghan/programs/khmer/python/khmer/_khmermodule.so, 2): Symbol not found: __ZNKSt5ctypeIcE13_M_widen_initEv
>   Referenced from: /Users/amycallaghan/programs/khmer/python/khmer/_khmermodule.so
>   Expected in: flat namespace
>  in /Users/amycallaghan/programs/khmer/python/khmer/_khmermodule.so)
> ----------------------------------------------------------------------
> Traceback (most recent call last):
>   File "/Library/Python/2.7/site-packages/nose-1.3.0-py2.7.egg/nose/loader.py", line 413, in loadTestsFromName
>     addr.filename, addr.module)
>   File "/Library/Python/2.7/site-packages/nose-1.3.0-py2.7.egg/nose/importer.py", line 47, in importFromPath
>     return self.importFromDir(dir_path, fqname)
>   File "/Library/Python/2.7/site-packages/nose-1.3.0-py2.7.egg/nose/importer.py", line 94, in importFromDir
>     mod = load_module(part_fqname, fh, filename, desc)
>   File "/Users/amycallaghan/programs/khmer/tests/test_graph.py", line 1, in <module>
>     import khmer
>   File "/Users/amycallaghan/programs/khmer/python/khmer/__init__.py", line 3, in <module>
>     import _khmer
> ImportError: dlopen(/Users/amycallaghan/programs/khmer/python/khmer/_khmermodule.so, 2): Symbol not found: __ZNKSt5ctypeIcE13_M_widen_initEv
>   Referenced from: /Users/amycallaghan/programs/khmer/python/khmer/_khmermodule.so
>   Expected in: flat namespace
>  in /Users/amycallaghan/programs/khmer/python/khmer/_khmermodule.so
> 
> ======================================================================
> ERROR: Failure: ImportError (dlopen(/Users/amycallaghan/programs/khmer/python/khmer/_khmermodule.so, 2): Symbol not found: __ZNKSt5ctypeIcE13_M_widen_initEv
>   Referenced from: /Users/amycallaghan/programs/khmer/python/khmer/_khmermodule.so
>   Expected in: flat namespace
>  in /Users/amycallaghan/programs/khmer/python/khmer/_khmermodule.so)
> ----------------------------------------------------------------------
> Traceback (most recent call last):
>   File "/Library/Python/2.7/site-packages/nose-1.3.0-py2.7.egg/nose/loader.py", line 413, in loadTestsFromName
>     addr.filename, addr.module)
>   File "/Library/Python/2.7/site-packages/nose-1.3.0-py2.7.egg/nose/importer.py", line 47, in importFromPath
>     return self.importFromDir(dir_path, fqname)
>   File "/Library/Python/2.7/site-packages/nose-1.3.0-py2.7.egg/nose/importer.py", line 94, in importFromDir
>     mod = load_module(part_fqname, fh, filename, desc)
>   File "/Users/amycallaghan/programs/khmer/tests/test_hashbits.py", line 1, in <module>
>     import khmer
>   File "/Users/amycallaghan/programs/khmer/python/khmer/__init__.py", line 3, in <module>
>     import _khmer
> ImportError: dlopen(/Users/amycallaghan/programs/khmer/python/khmer/_khmermodule.so, 2): Symbol not found: __ZNKSt5ctypeIcE13_M_widen_initEv
>   Referenced from: /Users/amycallaghan/programs/khmer/python/khmer/_khmermodule.so
>   Expected in: flat namespace
>  in /Users/amycallaghan/programs/khmer/python/khmer/_khmermodule.so
> 
> ======================================================================
> ERROR: Failure: ImportError (dlopen(/Users/amycallaghan/programs/khmer/python/khmer/_khmermodule.so, 2): Symbol not found: __ZNKSt5ctypeIcE13_M_widen_initEv
>   Referenced from: /Users/amycallaghan/programs/khmer/python/khmer/_khmermodule.so
>   Expected in: flat namespace
>  in /Users/amycallaghan/programs/khmer/python/khmer/_khmermodule.so)
> ----------------------------------------------------------------------
> Traceback (most recent call last):
>   File "/Library/Python/2.7/site-packages/nose-1.3.0-py2.7.egg/nose/loader.py", line 413, in loadTestsFromName
>     addr.filename, addr.module)
>   File "/Library/Python/2.7/site-packages/nose-1.3.0-py2.7.egg/nose/importer.py", line 47, in importFromPath
>     return self.importFromDir(dir_path, fqname)
>   File "/Library/Python/2.7/site-packages/nose-1.3.0-py2.7.egg/nose/importer.py", line 94, in importFromDir
>     mod = load_module(part_fqname, fh, filename, desc)
>   File "/Users/amycallaghan/programs/khmer/tests/test_ktable.py", line 2, in <module>
>     import khmer
>   File "/Users/amycallaghan/programs/khmer/python/khmer/__init__.py", line 3, in <module>
>     import _khmer
> ImportError: dlopen(/Users/amycallaghan/programs/khmer/python/khmer/_khmermodule.so, 2): Symbol not found: __ZNKSt5ctypeIcE13_M_widen_initEv
>   Referenced from: /Users/amycallaghan/programs/khmer/python/khmer/_khmermodule.so
>   Expected in: flat namespace
>  in /Users/amycallaghan/programs/khmer/python/khmer/_khmermodule.so
> 
> ======================================================================
> ERROR: Failure: ImportError (dlopen(/Users/amycallaghan/programs/khmer/python/khmer/_khmermodule.so, 2): Symbol not found: __ZNKSt5ctypeIcE13_M_widen_initEv
>   Referenced from: /Users/amycallaghan/programs/khmer/python/khmer/_khmermodule.so
>   Expected in: flat namespace
>  in /Users/amycallaghan/programs/khmer/python/khmer/_khmermodule.so)
> ----------------------------------------------------------------------
> Traceback (most recent call last):
>   File "/Library/Python/2.7/site-packages/nose-1.3.0-py2.7.egg/nose/loader.py", line 413, in loadTestsFromName
>     addr.filename, addr.module)
>   File "/Library/Python/2.7/site-packages/nose-1.3.0-py2.7.egg/nose/importer.py", line 47, in importFromPath
>     return self.importFromDir(dir_path, fqname)
>   File "/Library/Python/2.7/site-packages/nose-1.3.0-py2.7.egg/nose/importer.py", line 94, in importFromDir
>     mod = load_module(part_fqname, fh, filename, desc)
>   File "/Users/amycallaghan/programs/khmer/tests/test_lump.py", line 1, in <module>
>     import khmer
>   File "/Users/amycallaghan/programs/khmer/python/khmer/__init__.py", line 3, in <module>
>     import _khmer
> ImportError: dlopen(/Users/amycallaghan/programs/khmer/python/khmer/_khmermodule.so, 2): Symbol not found: __ZNKSt5ctypeIcE13_M_widen_initEv
>   Referenced from: /Users/amycallaghan/programs/khmer/python/khmer/_khmermodule.so
>   Expected in: flat namespace
>  in /Users/amycallaghan/programs/khmer/python/khmer/_khmermodule.so
> 
> ======================================================================
> ERROR: Failure: ImportError (dlopen(/Users/amycallaghan/programs/khmer/python/khmer/_khmermodule.so, 2): Symbol not found: __ZNKSt5ctypeIcE13_M_widen_initEv
>   Referenced from: /Users/amycallaghan/programs/khmer/python/khmer/_khmermodule.so
>   Expected in: flat namespace
>  in /Users/amycallaghan/programs/khmer/python/khmer/_khmermodule.so)
> ----------------------------------------------------------------------
> Traceback (most recent call last):
>   File "/Library/Python/2.7/site-packages/nose-1.3.0-py2.7.egg/nose/loader.py", line 413, in loadTestsFromName
>     addr.filename, addr.module)
>   File "/Library/Python/2.7/site-packages/nose-1.3.0-py2.7.egg/nose/importer.py", line 47, in importFromPath
>     return self.importFromDir(dir_path, fqname)
>   File "/Library/Python/2.7/site-packages/nose-1.3.0-py2.7.egg/nose/importer.py", line 94, in importFromDir
>     mod = load_module(part_fqname, fh, filename, desc)
>   File "/Users/amycallaghan/programs/khmer/tests/test_minmax.py", line 1, in <module>
>     import khmer
>   File "/Users/amycallaghan/programs/khmer/python/khmer/__init__.py", line 3, in <module>
>     import _khmer
> ImportError: dlopen(/Users/amycallaghan/programs/khmer/python/khmer/_khmermodule.so, 2): Symbol not found: __ZNKSt5ctypeIcE13_M_widen_initEv
>   Referenced from: /Users/amycallaghan/programs/khmer/python/khmer/_khmermodule.so
>   Expected in: flat namespace
>  in /Users/amycallaghan/programs/khmer/python/khmer/_khmermodule.so
> 
> ======================================================================
> ERROR: Failure: ImportError (dlopen(/Users/amycallaghan/programs/khmer/python/khmer/_khmermodule.so, 2): Symbol not found: __ZNKSt5ctypeIcE13_M_widen_initEv
>   Referenced from: /Users/amycallaghan/programs/khmer/python/khmer/_khmermodule.so
>   Expected in: flat namespace
>  in /Users/amycallaghan/programs/khmer/python/khmer/_khmermodule.so)
> ----------------------------------------------------------------------
> Traceback (most recent call last):
>   File "/Library/Python/2.7/site-packages/nose-1.3.0-py2.7.egg/nose/loader.py", line 413, in loadTestsFromName
>     addr.filename, addr.module)
>   File "/Library/Python/2.7/site-packages/nose-1.3.0-py2.7.egg/nose/importer.py", line 47, in importFromPath
>     return self.importFromDir(dir_path, fqname)
>   File "/Library/Python/2.7/site-packages/nose-1.3.0-py2.7.egg/nose/importer.py", line 94, in importFromDir
>     mod = load_module(part_fqname, fh, filename, desc)
>   File "/Users/amycallaghan/programs/khmer/tests/test_readmask.py", line 1, in <module>
>     import khmer
>   File "/Users/amycallaghan/programs/khmer/python/khmer/__init__.py", line 3, in <module>
>     import _khmer
> ImportError: dlopen(/Users/amycallaghan/programs/khmer/python/khmer/_khmermodule.so, 2): Symbol not found: __ZNKSt5ctypeIcE13_M_widen_initEv
>   Referenced from: /Users/amycallaghan/programs/khmer/python/khmer/_khmermodule.so
>   Expected in: flat namespace
>  in /Users/amycallaghan/programs/khmer/python/khmer/_khmermodule.so
> 
> ======================================================================
> ERROR: Failure: ImportError (dlopen(/Users/amycallaghan/programs/khmer/python/khmer/_khmermodule.so, 2): Symbol not found: __ZNKSt5ctypeIcE13_M_widen_initEv
>   Referenced from: /Users/amycallaghan/programs/khmer/python/khmer/_khmermodule.so
>   Expected in: flat namespace
>  in /Users/amycallaghan/programs/khmer/python/khmer/_khmermodule.so)
> ----------------------------------------------------------------------
> Traceback (most recent call last):
>   File "/Library/Python/2.7/site-packages/nose-1.3.0-py2.7.egg/nose/loader.py", line 413, in loadTestsFromName
>     addr.filename, addr.module)
>   File "/Library/Python/2.7/site-packages/nose-1.3.0-py2.7.egg/nose/importer.py", line 47, in importFromPath
>     return self.importFromDir(dir_path, fqname)
>   File "/Library/Python/2.7/site-packages/nose-1.3.0-py2.7.egg/nose/importer.py", line 94, in importFromDir
>     mod = load_module(part_fqname, fh, filename, desc)
>   File "/Users/amycallaghan/programs/khmer/tests/test_scripts.py", line 6, in <module>
>     import khmer
>   File "/Users/amycallaghan/programs/khmer/python/khmer/__init__.py", line 3, in <module>
>     import _khmer
> ImportError: dlopen(/Users/amycallaghan/programs/khmer/python/khmer/_khmermodule.so, 2): Symbol not found: __ZNKSt5ctypeIcE13_M_widen_initEv
>   Referenced from: /Users/amycallaghan/programs/khmer/python/khmer/_khmermodule.so
>   Expected in: flat namespace
>  in /Users/amycallaghan/programs/khmer/python/khmer/_khmermodule.so
> 
> ======================================================================
> ERROR: Failure: ImportError (dlopen(/Users/amycallaghan/programs/khmer/python/khmer/_khmermodule.so, 2): Symbol not found: __ZNKSt5ctypeIcE13_M_widen_initEv
>   Referenced from: /Users/amycallaghan/programs/khmer/python/khmer/_khmermodule.so
>   Expected in: flat namespace
>  in /Users/amycallaghan/programs/khmer/python/khmer/_khmermodule.so)
> ----------------------------------------------------------------------
> Traceback (most recent call last):
>   File "/Library/Python/2.7/site-packages/nose-1.3.0-py2.7.egg/nose/loader.py", line 413, in loadTestsFromName
>     addr.filename, addr.module)
>   File "/Library/Python/2.7/site-packages/nose-1.3.0-py2.7.egg/nose/importer.py", line 47, in importFromPath
>     return self.importFromDir(dir_path, fqname)
>   File "/Library/Python/2.7/site-packages/nose-1.3.0-py2.7.egg/nose/importer.py", line 94, in importFromDir
>     mod = load_module(part_fqname, fh, filename, desc)
>   File "/Users/amycallaghan/programs/khmer/tests/test_split.py", line 1, in <module>
>     import khmer
>   File "/Users/amycallaghan/programs/khmer/python/khmer/__init__.py", line 3, in <module>
>     import _khmer
> ImportError: dlopen(/Users/amycallaghan/programs/khmer/python/khmer/_khmermodule.so, 2): Symbol not found: __ZNKSt5ctypeIcE13_M_widen_initEv
>   Referenced from: /Users/amycallaghan/programs/khmer/python/khmer/_khmermodule.so
>   Expected in: flat namespace
>  in /Users/amycallaghan/programs/khmer/python/khmer/_khmermodule.so
> 
> ======================================================================
> ERROR: Failure: ImportError (dlopen(/Users/amycallaghan/programs/khmer/python/khmer/_khmermodule.so, 2): Symbol not found: __ZNKSt5ctypeIcE13_M_widen_initEv
>   Referenced from: /Users/amycallaghan/programs/khmer/python/khmer/_khmermodule.so
>   Expected in: flat namespace
>  in /Users/amycallaghan/programs/khmer/python/khmer/_khmermodule.so)
> ----------------------------------------------------------------------
> Traceback (most recent call last):
>   File "/Library/Python/2.7/site-packages/nose-1.3.0-py2.7.egg/nose/loader.py", line 413, in loadTestsFromName
>     addr.filename, addr.module)
>   File "/Library/Python/2.7/site-packages/nose-1.3.0-py2.7.egg/nose/importer.py", line 47, in importFromPath
>     return self.importFromDir(dir_path, fqname)
>   File "/Library/Python/2.7/site-packages/nose-1.3.0-py2.7.egg/nose/importer.py", line 94, in importFromDir
>     mod = load_module(part_fqname, fh, filename, desc)
>   File "/Users/amycallaghan/programs/khmer/tests/test_subset_graph.py", line 1, in <module>
>     import khmer
>   File "/Users/amycallaghan/programs/khmer/python/khmer/__init__.py", line 3, in <module>
>     import _khmer
> ImportError: dlopen(/Users/amycallaghan/programs/khmer/python/khmer/_khmermodule.so, 2): Symbol not found: __ZNKSt5ctypeIcE13_M_widen_initEv
>   Referenced from: /Users/amycallaghan/programs/khmer/python/khmer/_khmermodule.so
>   Expected in: flat namespace
>  in /Users/amycallaghan/programs/khmer/python/khmer/_khmermodule.so
> 
> ======================================================================
> ERROR: Failure: ImportError (dlopen(/Users/amycallaghan/programs/khmer/python/khmer/_khmermodule.so, 2): Symbol not found: __ZNKSt5ctypeIcE13_M_widen_initEv
>   Referenced from: /Users/amycallaghan/programs/khmer/python/khmer/_khmermodule.so
>   Expected in: flat namespace
>  in /Users/amycallaghan/programs/khmer/python/khmer/_khmermodule.so)
> ----------------------------------------------------------------------
> Traceback (most recent call last):
>   File "/Library/Python/2.7/site-packages/nose-1.3.0-py2.7.egg/nose/loader.py", line 413, in loadTestsFromName
>     addr.filename, addr.module)
>   File "/Library/Python/2.7/site-packages/nose-1.3.0-py2.7.egg/nose/importer.py", line 47, in importFromPath
>     return self.importFromDir(dir_path, fqname)
>   File "/Library/Python/2.7/site-packages/nose-1.3.0-py2.7.egg/nose/importer.py", line 94, in importFromDir
>     mod = load_module(part_fqname, fh, filename, desc)
>   File "/Users/amycallaghan/programs/khmer/tests/test_threaded_sequence_processor.py", line 2, in <module>
>     from khmer.thread_utils import ThreadedSequenceProcessor, SequenceGroup
>   File "/Users/amycallaghan/programs/khmer/python/khmer/__init__.py", line 3, in <module>
>     import _khmer
> ImportError: dlopen(/Users/amycallaghan/programs/khmer/python/khmer/_khmermodule.so, 2): Symbol not found: __ZNKSt5ctypeIcE13_M_widen_initEv
>   Referenced from: /Users/amycallaghan/programs/khmer/python/khmer/_khmermodule.so
>   Expected in: flat namespace
>  in /Users/amycallaghan/programs/khmer/python/khmer/_khmermodule.so
> 
> ----------------------------------------------------------------------
> Ran 15 tests in 0.075s
> 
> FAILED (errors=15)
> make: *** [test] Error 1
> d-ip-129-15-161-69:khmer amycallaghan$ 
> ________________________________________
> From: C. Titus Brown [ctb at msu.edu]
> Sent: Friday, August 30, 2013 7:57 AM
> To: Cooper, Joshua T.
> Cc: khmer at lists.idyll.org
> Subject: Re: [khmer] Problem installing khmer
> 
> 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
> 
> > _______________________________________________
> > khmer mailing list
> > khmer at lists.idyll.org
> > http://lists.idyll.org/listinfo/khmer
> 
> 
> --
> C. Titus Brown, ctb at msu.edu

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




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