Wayne,
Was talking with Justin this morning and it seems that this problem is
only cropping up in the pre-compiled versions of analysis. We also
run analysis and use updateAll (via a cron job) and our builds are
doing fine (as of today, 02-10-09). The only difference between our
analysis builds is that our were built against the fink python/tcl/tk
libraries. Just a few more bits of information for you to mull over
in diagnosing the problem.
J
On Feb 10, 2009, at 7:58 AM, Wayne Boucher wrote:
> Well my theory doesn't seem to have held out, at least on the Macs
> here.
> So I put the Tiger (OSX 10.4) pre-compiled 2.0.5.1 Analysis release
> on a
> Leopard (OSX 10.5) box and did bin/updateAll, and it installed and
> compiled 2.0.6 ok and ran ok. (Note, when moving up versions,
> updateAll
> gets the source code release and compiles it. It does not get the
> pre-compiled OSX release.) And as a second check I then did a "make
> clean" in the ccpnmr2.0/c directory and then a "make" and it did it
> ok and
> ran ok. So this is a puzzle.
>
> Anyway, the first thing worth knowing is if you have Leopard. Another
> alternative for you is just to download the 2.0.6 pre-compiled
> release and
> use that (so get it that way rather than via updateAll). But this C
> compilation is bound to come up at some point in the future, so it's
> worth
> trying to figure out why it's gone wrong.
>
> Wayne
>
> On Tue, 10 Feb 2009, Wayne Boucher wrote:
>
>> Right, it's a compiler problem. So the message
>>
>> ld warning: in /Applications/ccpnmr/python2.5/bin/python2.5, file
>> is not
>> of required architecture
>>
>> is definitely a problem. Can you run
>> /Applications/ccpnmr/python2.5/bin/python2.5? I assume so, since
>> this was
>> working for you, no? Which would mean your Mac is happy with the
>> executable but not happy re-compiling against it (or the other stuff
>> there). Is your Mac Leopard (10.5)? The code was compiled on
>> Tiger. So
>> if the above is correct (namely that Leopard is happy to run Tiger
>> code
>> but not compile against it) then it looks like I'll have to provide a
>> Leopard pre-compiled release as well as the Tiger one.
>>
>> Wayne
>>
>> On Mon, 9 Feb 2009, Justin Douglas wrote:
>>
>>> Hi Wayne
>>>
>>>> So in the /Applications/ccpnmr/bin/analysis script is the
>>>> PYTHONPATH set
>>>> to /Applications/ccpnmr/ccpnmr2.0/python? I guess another thing
>>>> to check
>>>> is if bin/formatConverter is working.
>>>>
>>>
>>> FormatConverter works.
>>>
>>>
>>>> If those are both ok, then cd into /Applications/ccpnmr/ccpnmr2.0/
>>>> c and
>>>> type "make" and see if you get an error (but it might whizz past
>>>> quickly).
>>>> Now the main change recently to the C code was to try and get the
>>>> > 2 Gb
>>>> files to work, so perhaps that is causing problems. But that's
>>>> just a
>>>> possibility.
>>>>
>>>
>>> When I recompile the code I get the following error message:
>>>
>>> cd memops/global; make
>>> cc -L/Applications/ccpnmr/python2.5/lib -bundle -bundle_loader
>>> /Applications/ccp
>>> nmr/python2.5/bin/python2.5 -o BlockFile.so utility.o python_util.o
>>> hash_list.o
>>> hash_table.o mem_cache.o mutex.o py_mem_cache.o block_file.o
>>> shape_file.o
>>> int_a
>>> rray.o py_block_file.o py_shape_file.o
>>> ld warning: in /Applications/ccpnmr/python2.5/bin/python2.5, file
>>> is not of
>>> requ
>>> ired architecture
>>> Undefined symbols:
>>> "_PyInt_Type", referenced from:
>>> _PyInt_Type$non_lazy_ptr in python_util.o
>>> "_PyTuple_Size", referenced from:
>>> _get_python_list_size in python_util.o
>>> _get_python_int_array in python_util.o
>>> _get_python_int_alloc_array in python_util.o
>>> _get_python_float_array in python_util.o
>>> _get_python_float_alloc_array in python_util.o
>>> _get_python_float_alloc_matrix in python_util.o
>>> _get_python_float_alloc_cube in python_util.o
>>> _get_python_double_array in python_util.o
>>> _get_python_double_alloc_array in python_util.o
>>> _get_python_double_alloc_matrix in python_util.o
>>> _set_python_float_matrix in python_util.o
>>> _set_python_double_matrix in python_util.o
>>> _set_python_float_cube in python_util.o
>>> "_PyList_New", referenced from:
>>> _get_python_int_list in python_util.o
>>> _get_python_float_list in python_util.o
>>> _get_python_double_list in python_util.o
>>> _get_python_float_matrix in python_util.o
>>> _get_python_float_matrix in python_util.o
>>> _create_python_float_array in python_util.o
>>> "_PyFloat_Type", referenced from:
>>> _PyFloat_Type$non_lazy_ptr in python_util.o
>>> "_PyInt_FromLong", referenced from:
>>> _get_python_int_list in python_util.o
>>> "_PyInt_AsLong", referenced from:
>>> _get_python_int_array in python_util.o
>>> _get_python_int_alloc_array in python_util.o
>>> _get_python_float_array in python_util.o
>>> _get_python_float_alloc_array in python_util.o
>>> _get_python_double_array in python_util.o
>>> _get_python_double_alloc_array in python_util.o
>>> "_PyErr_Occurred", referenced from:
>>> _initMemCache in py_mem_cache.o
>>> _initBlockFile in py_block_file.o
>>> _initShapeFile in py_shape_file.o
>>> "_PyList_GetItem", referenced from:
>>> _get_python_object_by_index in python_util.o
>>> _get_python_int_array in python_util.o
>>> _get_python_int_alloc_array in python_util.o
>>> _get_python_float_array in python_util.o
>>> _get_python_float_alloc_array in python_util.o
>>> _get_python_float_alloc_matrix in python_util.o
>>> _get_python_float_alloc_cube in python_util.o
>>> _get_python_double_array in python_util.o
>>> _get_python_double_alloc_array in python_util.o
>>> _get_python_double_alloc_matrix in python_util.o
>>> _set_python_float_matrix in python_util.o
>>> _set_python_double_matrix in python_util.o
>>> _set_python_float_cube in python_util.o
>>> "_PyList_SetItem", referenced from:
>>> _get_python_int_list in python_util.o
>>> _get_python_float_list in python_util.o
>>> _get_python_double_list in python_util.o
>>> _get_python_float_matrix in python_util.o
>>> _get_python_float_matrix in python_util.o
>>> _set_python_float_array in python_util.o
>>> _set_python_double_array in python_util.o
>>> "_PyFloat_AsDouble", referenced from:
>>> _get_python_float_array in python_util.o
>>> _get_python_float_alloc_array in python_util.o
>>> _get_python_double_array in python_util.o
>>> _get_python_double_alloc_array in python_util.o
>>> "__Py_NoneStruct", referenced from:
>>> __Py_NoneStruct$non_lazy_ptr in py_mem_cache.o
>>> __Py_NoneStruct$non_lazy_ptr in py_block_file.o
>>> __Py_NoneStruct$non_lazy_ptr in py_shape_file.o
>>> "_PyTuple_Type", referenced from:
>>> _PyTuple_Type$non_lazy_ptr in python_util.o
>>> "_PyObject_Init", referenced from:
>>> _init_Py_Mem_cache in py_mem_cache.o
>>> _init_Py_Block_file in py_block_file.o
>>> _init_Py_Shape_block_file in py_block_file.o
>>> _init_Py_Shape_file in py_shape_file.o
>>> "_PyType_IsSubtype", referenced from:
>>> _get_python_list_size in python_util.o
>>> _get_python_list_size in python_util.o
>>> _get_python_object_by_index in python_util.o
>>> _get_python_object_by_index in python_util.o
>>> _get_python_object_by_index in python_util.o
>>> _get_python_int_array in python_util.o
>>> _get_python_int_array in python_util.o
>>> _get_python_int_array in python_util.o
>>> _get_python_int_alloc_array in python_util.o
>>> _get_python_int_alloc_array in python_util.o
>>> _get_python_int_alloc_array in python_util.o
>>> _get_python_float_array in python_util.o
>>> _get_python_float_array in python_util.o
>>> _get_python_float_array in python_util.o
>>> _get_python_float_array in python_util.o
>>> _get_python_float_array in python_util.o
>>> _get_python_float_alloc_array in python_util.o
>>> _get_python_float_alloc_array in python_util.o
>>> _get_python_float_alloc_array in python_util.o
>>> _get_python_float_alloc_array in python_util.o
>>> _get_python_float_alloc_array in python_util.o
>>> _get_python_float_alloc_matrix in python_util.o
>>> _get_python_float_alloc_matrix in python_util.o
>>> _get_python_float_alloc_cube in python_util.o
>>> _get_python_float_alloc_cube in python_util.o
>>> _get_python_double_array in python_util.o
>>> _get_python_double_array in python_util.o
>>> _get_python_double_array in python_util.o
>>> _get_python_double_array in python_util.o
>>> _get_python_double_array in python_util.o
>>> _get_python_double_alloc_array in python_util.o
>>> _get_python_double_alloc_array in python_util.o
>>> _get_python_double_alloc_array in python_util.o
>>> _get_python_double_alloc_array in python_util.o
>>> _get_python_double_alloc_array in python_util.o
>>> _get_python_double_alloc_matrix in python_util.o
>>> _get_python_double_alloc_matrix in python_util.o
>>> _set_python_float_array in python_util.o
>>> _set_python_double_array in python_util.o
>>> _set_python_float_matrix in python_util.o
>>> _set_python_float_matrix in python_util.o
>>> _set_python_double_matrix in python_util.o
>>> _set_python_double_matrix in python_util.o
>>> _set_python_float_cube in python_util.o
>>> _set_python_float_cube in python_util.o
>>> "_Py_BuildValue", referenced from:
>>> _havePeak in py_block_file.o
>>> _maxValue in py_block_file.o
>>> _minValue in py_block_file.o
>>> _getValue in py_block_file.o
>>> _getPointValue in py_block_file.o
>>> _getattr_py_block_file in py_block_file.o
>>> _compareSlices in py_block_file.o
>>> _getattr_py_shape_file in py_shape_file.o
>>> _getattr_py_shape_file in py_shape_file.o
>>> "_Py_FatalError", referenced from:
>>> _initMemCache in py_mem_cache.o
>>> _initBlockFile in py_block_file.o
>>> _initShapeFile in py_shape_file.o
>>> "_PyTuple_GetItem", referenced from:
>>> _get_python_object_by_index in python_util.o
>>> _get_python_int_array in python_util.o
>>> _get_python_int_alloc_array in python_util.o
>>> _get_python_float_array in python_util.o
>>> _get_python_float_alloc_array in python_util.o
>>> _get_python_float_alloc_matrix in python_util.o
>>> _get_python_float_alloc_cube in python_util.o
>>> _get_python_double_array in python_util.o
>>> _get_python_double_alloc_array in python_util.o
>>> _get_python_double_alloc_matrix in python_util.o
>>> _set_python_float_matrix in python_util.o
>>> _set_python_double_matrix in python_util.o
>>> _set_python_float_cube in python_util.o
>>> "_PyObject_Free", referenced from:
>>> _delete_py_mem_cache in py_mem_cache.o
>>> _delete_py_block_file in py_block_file.o
>>> _delete_py_shape_file in py_shape_file.o
>>> "_PyList_Size", referenced from:
>>> _get_python_list_size in python_util.o
>>> _get_python_int_array in python_util.o
>>> _get_python_int_alloc_array in python_util.o
>>> _get_python_float_array in python_util.o
>>> _get_python_float_alloc_array in python_util.o
>>> _get_python_float_alloc_matrix in python_util.o
>>> _get_python_float_alloc_cube in python_util.o
>>> _get_python_double_array in python_util.o
>>> _get_python_double_alloc_array in python_util.o
>>> _get_python_double_alloc_matrix in python_util.o
>>> _set_python_float_array in python_util.o
>>> _set_python_double_array in python_util.o
>>> _set_python_float_matrix in python_util.o
>>> _set_python_double_matrix in python_util.o
>>> _set_python_float_cube in python_util.o
>>> "_PyType_Type", referenced from:
>>> _Mem_cache_type in py_mem_cache.o
>>> _Shape_block_file_type in py_block_file.o
>>> _Block_file_type in py_block_file.o
>>> _Shape_file_type in py_shape_file.o
>>> "_PyErr_NewException", referenced from:
>>> _initMemCache in py_mem_cache.o
>>> _initBlockFile in py_block_file.o
>>> _initShapeFile in py_shape_file.o
>>> "_PyFloat_FromDouble", referenced from:
>>> _get_python_float_list in python_util.o
>>> _get_python_double_list in python_util.o
>>> _get_python_float_matrix in python_util.o
>>> _set_python_float_array in python_util.o
>>> _set_python_double_array in python_util.o
>>> "_PyArg_ParseTuple", referenced from:
>>> _resize in py_mem_cache.o
>>> _init_Py_Mem_cache in py_mem_cache.o
>>> _maxValue in py_block_file.o
>>> _minValue in py_block_file.o
>>> _getValue in py_block_file.o
>>> _getPointValue in py_block_file.o
>>> _getValues in py_block_file.o
>>> _setValue in py_block_file.o
>>> _setValues in py_block_file.o
>>> _save in py_block_file.o
>>> _planeProduct in py_block_file.o
>>> _planeProduct in py_block_file.o
>>> _init_Py_Block_file in py_block_file.o
>>> _init_Py_Shape_block_file in py_block_file.o
>>> _compareSlices in py_block_file.o
>>> _setComponentAmplitude in py_shape_file.o
>>> _setShapeData in py_shape_file.o
>>> _init_Py_Shape_file in py_shape_file.o
>>> "_Py_FindMethod", referenced from:
>>> _getattr_py_mem_cache in py_mem_cache.o
>>> _getattr_py_block_file in py_block_file.o
>>> _getattr_py_shape_file in py_shape_file.o
>>> "_PyErr_SetString", referenced from:
>>> _resize in py_mem_cache.o
>>> _resize in py_mem_cache.o
>>> _init_Py_Mem_cache in py_mem_cache.o
>>> _init_Py_Mem_cache in py_mem_cache.o
>>> _init_Py_Mem_cache in py_mem_cache.o
>>> _openFile in py_block_file.o
>>> _havePeak in py_block_file.o
>>> _havePeak in py_block_file.o
>>> _havePeak in py_block_file.o
>>> _havePeak in py_block_file.o
>>> _maxValue in py_block_file.o
>>> _maxValue in py_block_file.o
>>> _maxValue in py_block_file.o
>>> _maxValue in py_block_file.o
>>> _minValue in py_block_file.o
>>> _minValue in py_block_file.o
>>> _minValue in py_block_file.o
>>> _minValue in py_block_file.o
>>> _getValue in py_block_file.o
>>> _getValue in py_block_file.o
>>> _getValue in py_block_file.o
>>> _getPointValue in py_block_file.o
>>> _getPointValue in py_block_file.o
>>> _getPointValue in py_block_file.o
>>> _getValues in py_block_file.o
>>> _getValues in py_block_file.o
>>> _getValues in py_block_file.o
>>> _getValues in py_block_file.o
>>> _getValues in py_block_file.o
>>> _setValue in py_block_file.o
>>> _setValue in py_block_file.o
>>> _setValue in py_block_file.o
>>> _setValues in py_block_file.o
>>> _setValues in py_block_file.o
>>> _setValues in py_block_file.o
>>> _setValues in py_block_file.o
>>> _setValues in py_block_file.o
>>> _save in py_block_file.o
>>> _save in py_block_file.o
>>> _check in py_block_file.o
>>> _planeProduct in py_block_file.o
>>> _planeProduct in py_block_file.o
>>> _planeProduct in py_block_file.o
>>> _planeProduct in py_block_file.o
>>> _planeProduct in py_block_file.o
>>> _planeProduct in py_block_file.o
>>> _planeProduct in py_block_file.o
>>> _planeProduct in py_block_file.o
>>> _init_Py_Block_file in py_block_file.o
>>> _init_Py_Block_file in py_block_file.o
>>> _init_Py_Block_file in py_block_file.o
>>> _init_Py_Block_file in py_block_file.o
>>> _init_Py_Block_file in py_block_file.o
>>> _init_Py_Block_file in py_block_file.o
>>> _init_Py_Block_file in py_block_file.o
>>> _init_Py_Shape_block_file in py_block_file.o
>>> _init_Py_Shape_block_file in py_block_file.o
>>> _init_Py_Shape_block_file in py_block_file.o
>>> _init_Py_Shape_block_file in py_block_file.o
>>> _init_Py_Shape_block_file in py_block_file.o
>>> _init_Py_Shape_block_file in py_block_file.o
>>> _init_Py_Shape_block_file in py_block_file.o
>>> _compareSlices in py_block_file.o
>>> _compareSlices in py_block_file.o
>>> _compareSlices in py_block_file.o
>>> _compareSlices in py_block_file.o
>>> _compareSlices in py_block_file.o
>>> _compareSlices in py_block_file.o
>>> _setComponentAmplitude in py_shape_file.o
>>> _setComponentAmplitude in py_shape_file.o
>>> _setShapeData in py_shape_file.o
>>> _setShapeData in py_shape_file.o
>>> _setShapeData in py_shape_file.o
>>> _init_Py_Shape_file in py_shape_file.o
>>> _init_Py_Shape_file in py_shape_file.o
>>> _init_Py_Shape_file in py_shape_file.o
>>> _init_Py_Shape_file in py_shape_file.o
>>> "_PyList_Type", referenced from:
>>> _PyList_Type$non_lazy_ptr in python_util.o
>>> "_Py_InitModule4", referenced from:
>>> _initMemCache in py_mem_cache.o
>>> _initBlockFile in py_block_file.o
>>> _initShapeFile in py_shape_file.o
>>> "_PyObject_Malloc", referenced from:
>>> _init_Py_Mem_cache in py_mem_cache.o
>>> _init_Py_Block_file in py_block_file.o
>>> _init_Py_Shape_block_file in py_block_file.o
>>> _init_Py_Shape_file in py_shape_file.o
>>> "_PyArg_ParseTupleAndKeywords", referenced from:
>>> _havePeak in py_block_file.o
>>> "_PyModule_AddObject", referenced from:
>>> _initMemCache in py_mem_cache.o
>>> _initBlockFile in py_block_file.o
>>> _initShapeFile in py_shape_file.o
>>> ld: symbol(s) not found
>>> collect2: ld returned 1 exit status
>>> make[1]: *** [BlockFile.so] Error 1
>>> make: *** [global] Error 2
>>>
>>> Thanks,
>>>
>>> Justin
>>>
>>
|