Wayne,
Okay, things seem to be really screwed up. I updated my fink
environment and with it came python 2.6. Now when I try and recompile
analysis, I get the following error.
Messages will be logged in "log_Analysis_2.txt"
Assuming your platform is darwin
Found X11 include match: /usr/X11R6/include/X11/Xlib.h
Found X11 lib match: /usr/X11R6/lib/libX11.6.2.0.dylib
Need to know where X11 directory is, in order to compile Analysis
This directory should contain [include/*/X11/Xlib.h, lib*/*/libX11.*],
and as seen, /usr/X11R6 does
Guess X11 dir = "/usr/X11R6", is this correct (y or n)? y
CCPN Tcl gzipped tar file not found, assuming using existing Tcl
Found Tcl include match: /sw/include/tcl.h
Found Tcl lib match: /sw/lib/tclConfig.sh
Need to know where Tcl directory is, in order to compile Analysis
This directory should contain [include/*/tcl.h, lib*/*/tclConfig.sh],
and as seen, /sw does
Guess Tcl dir = "/sw", is this correct (y or n)? y
Guess Tcl version = 8.4 (by looking), is this ok (y or n) (reply y
unless sure otherwise)? y
CCPN Tk gzipped tar file not found, assuming using existing Tk
Found Tk include match: /sw/include/tk.h
Found Tk lib match: /sw/lib/tkConfig.sh
Need to know where Tk directory is, in order to compile Analysis
This directory should contain [include/*/tk.h, lib*/*/tkConfig.sh],
and as seen, /sw does
Guess Tk dir = "/sw", is this correct (y or n)? y
Assuming Tk version is also 8.4
CCPN Python gzipped tar file not found, assuming using existing Python
Found Python include match: /sw/include/python2.5
Found Python lib match: /sw/lib/python2.5
Need to know where Python directory is, in order to compile Analysis
This directory should contain [include/*/python2.*, lib*/*/python2.*],
and as seen, /sw does
Guess Python dir = "/sw", is this correct (y or n)? y
Guess Python version = 2.6 (by looking), is this ok (y or n) (reply y
unless sure otherwise)? y
Do you want OpenGL used in Analysis (y or n) (n means only get Tk)? n
Compile and install Analysis code (y or n)? y
You can create environment file from scratch (this does not copy it
from environment_default.txt)
If you have already created it and edited it by hand you probably do
not want to create it again here.
Create environment file (y or n) (answer y unless you know otherwise)? y
Use -fPIC compiler flag (y or n) (if gcc compiler y, otherwise n;
answer y unless you know otherwise)? y
Backing up ccpnmr2.0/c/environment.txt to ccpnmr2.0/c/environment.bak
cd memops/global; make
cc -L/sw/lib -bundle -bundle_loader /sw/bin/python2.6 -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_array.o py_block_file.o
py_shape_file.o
Undefined symbols:
"_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$non_lazy_ptr in python_util.o
"_PyModule_GetDict", referenced from:
_initMemCache in py_mem_cache.o
_initBlockFile in py_block_file.o
_initShapeFile in py_shape_file.o
"_PyInt_FromLong", referenced from:
_get_python_int_list in python_util.o
"_PyInt_AsLong", referenced from:
_get_python_int_array in python_util.o
_get_python_int_alloc_array in python_util.o
_get_python_float_array in python_util.o
_get_python_float_alloc_array in python_util.o
_get_python_double_array in python_util.o
_get_python_double_alloc_array in python_util.o
"_PyErr_Occurred", referenced from:
_initMemCache in py_mem_cache.o
_initBlockFile in py_block_file.o
_initShapeFile in py_shape_file.o
"_PyList_GetItem", referenced from:
_get_python_object_by_index in python_util.o
_get_python_int_array in python_util.o
_get_python_int_alloc_array in python_util.o
_get_python_float_array in python_util.o
_get_python_float_alloc_array in python_util.o
_get_python_float_alloc_matrix in python_util.o
_get_python_float_alloc_cube in python_util.o
_get_python_double_array in python_util.o
_get_python_double_alloc_array in python_util.o
_get_python_double_alloc_matrix in python_util.o
_set_python_float_matrix in python_util.o
_set_python_double_matrix in python_util.o
_set_python_float_cube in python_util.o
"_PyList_SetItem", referenced from:
_get_python_int_list in python_util.o
_get_python_float_list in python_util.o
_get_python_double_list in python_util.o
_get_python_float_matrix in python_util.o
_get_python_float_matrix in python_util.o
_set_python_float_array in python_util.o
_set_python_double_array in python_util.o
"_PyFloat_AsDouble", referenced from:
_get_python_float_array in python_util.o
_get_python_float_alloc_array in python_util.o
_get_python_double_array in python_util.o
_get_python_double_alloc_array in python_util.o
"__Py_NoneStruct", referenced from:
__Py_NoneStruct$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
"_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_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_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
"_Py_BuildValue", referenced from:
_initMemCache in py_mem_cache.o
_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
_initBlockFile in py_block_file.o
_getattr_py_shape_file in py_shape_file.o
_getattr_py_shape_file in py_shape_file.o
_initShapeFile 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
"_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
"_PyDict_SetItemString", referenced from:
_initMemCache in py_mem_cache.o
_initBlockFile in py_block_file.o
_initShapeFile 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
"_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
ld: symbol(s) not found
collect2: ld returned 1 exit status
make[1]: *** [BlockFile.so] Error 1
make: *** [global] Error 2
Uncommenting future import in Converters.py
Uncommenting future import in part2/Converters2.py
Any ideas.
J
On Nov 5, 2008, at 11:13 AM, Wayne Boucher wrote:
> Right, it turns out the string wasn't "" but " " so I needed to add
> something extra to strip the string before it is checked. So that
> should
> work now (it opened your project ok here, anyway). (With the latest
> update.)
>
> Wayne
>
> On Wed, 5 Nov 2008, Johnny Croy wrote:
>
>> Wayne,
>>
>> Here's a bit more information on what I did to screw things up. I
>> opened up my converted project and I got errors telling me that it
>> couldn't find certain spectra. However, analysis fired up and I
>> didn't have any problems. I then saved the project in 2.0 and tried
>> to reopen. Then I got a pop-p window saying "edit project data
>> paths". The missing spectra are highlighted in orange. I then click
>> on the red x at the bottom of the pop-up window and then the error
>> pops up. I cant attach the tarball (16 MB). Its a big project that
>> contains all of my collected NMR data. Anyway to send it via FTP/
>> SFTP
>> to you?
>>
>> J
>>
>>
>> On Nov 5, 2008, at 10:34 AM, Wayne Boucher wrote:
>>
>>> Hmmm, that error message doesn't make sense to me now. The "if
>>> level"
>>> should explictly stop empty strings getting to the float(). Can you
>>> send
>>> me your project directory (not the spectra), and I'll look at that.
>>>
>>> Thanks, Wayne
>>>
>>> On Wed, 5 Nov 2008, Johnny Croy wrote:
>>>
>>>> Wayne,
>>>>
>>>> Still getting the same error. Here is the traceback after I have
>>>> upgraded.
>>>>
>>>>>>> Warning: spectrum (T1_b_0, nmrPipe): data file None not
>>>>>>> accessible
>>>> ValueError: empty string for float()
>>>> File "/Applications/ccpnmr/ccpnmr2.0/python/memops/editor/
>>>> OpenProjectPopup.py", line 204, in apply
>>>> self.callback(self.project)
>>>> File "/Applications/ccpnmr/ccpnmr2.0/python/ccpnmr/analysis/
>>>> AnalysisPopup.py", line 997, in initProject
>>>> Analysis.initProject(self, project)
>>>> File "/Applications/ccpnmr/ccpnmr2.0/python/ccpnmr/analysis/
>>>> Analysis.py", line 264, in initProject
>>>> self.initSpectra()
>>>> File "/Applications/ccpnmr/ccpnmr2.0/python/ccpnmr/analysis/
>>>> Analysis.py", line 900, in initSpectra
>>>> self.initPeakList(peakList, initialising=True)
>>>> File "/Applications/ccpnmr/ccpnmr2.0/python/ccpnmr/analysis/
>>>> Analysis.py", line 1679, in initPeakList
>>>> view = WindowBasic.getSpectrumWindowView(window, spectrum)
>>>> File "/Applications/ccpnmr/ccpnmr2.0/python/ccpnmr/analysis/core/
>>>> WindowBasic.py", line 384, in getSpectrumWindowView
>>>> analysisSpectrum = Util.getAnalysisSpectrum(spectrum)
>>>> File "/Applications/ccpnmr/ccpnmr2.0/python/ccpnmr/analysis/core/
>>>> Util.py", line 161, in getAnalysisSpectrum
>>>> setupAnalysisSpectrum(analysisSpectrum)
>>>> File "/Applications/ccpnmr/ccpnmr2.0/python/ccpnmr/analysis/core/
>>>> Util.py", line 174, in setupAnalysisSpectrum
>>>> levels = getSpectrumContourLevels(spectrum)
>>>> File "/Applications/ccpnmr/ccpnmr2.0/python/ccpnmr/analysis/core/
>>>> Util.py", line 739, in getSpectrumContourLevels
>>>> levels = [float(level) for level in
>>>> levels.split(spectrum_contour_separator) if level]
>>>> logout
>>>>
>>>> On Nov 5, 2008, at 1:59 AM, Wayne Boucher wrote:
>>>>
>>>>> Right, hopefully that is fixed now.
>>>>>
>>>>> This error was finally picked up because of fixing that problem
>>>>> for
>>>>> Vicky
>>>>> yesterday. There might be other similar problems now cropping up.
>>>>> Also,
>>>>> I forgot to metion that I have now set it up so that old appData
>>>>> that is
>>>>> v1 specific and not needed in v2 should now be deleted if it is
>>>>> accessed
>>>>> (but that might not happen if you've already saved a project in
>>>>> v2).
>>>>> This might also start to pick up some new bugs.
>>>>>
>>>>> Wayne
>>>>>
>>>>> On Tue, 4 Nov 2008, Johnny Croy wrote:
>>>>>
>>>>>> Hello all.
>>>>>>
>>>>>> Just saved my project in Analysis 2.0.5. I had some spectra that
>>>>>> couldn't be found (this wasn't a problem in 1.0) and now when I
>>>>>> try
>>>>>> and open my project I get the following error:
>>>>>>
>>>>>> Project invalid, please quit, fix and re-start: ValueError:
>>>>>> empty
>>>>>> string for float()
>>>>>>
>>>>>> Here is the traceback
>>>>>>
>>>>>>>>> Warning: spectrum (T1_b_0, nmrPipe): data file None not
>>>>>>>>> accessible
>>>>>> ValueError: empty string for float()
>>>>>> File "/Applications/ccpnmr/ccpnmr2.0/python/memops/editor/
>>>>>> OpenProjectPopup.py", line 204, in apply
>>>>>> self.callback(self.project)
>>>>>> File "/Applications/ccpnmr/ccpnmr2.0/python/ccpnmr/analysis/
>>>>>> AnalysisPopup.py", line 997, in initProject
>>>>>> Analysis.initProject(self, project)
>>>>>> File "/Applications/ccpnmr/ccpnmr2.0/python/ccpnmr/analysis/
>>>>>> Analysis.py", line 264, in initProject
>>>>>> self.initSpectra()
>>>>>> File "/Applications/ccpnmr/ccpnmr2.0/python/ccpnmr/analysis/
>>>>>> Analysis.py", line 900, in initSpectra
>>>>>> self.initPeakList(peakList, initialising=True)
>>>>>> File "/Applications/ccpnmr/ccpnmr2.0/python/ccpnmr/analysis/
>>>>>> Analysis.py", line 1679, in initPeakList
>>>>>> view = WindowBasic.getSpectrumWindowView(window, spectrum)
>>>>>> File "/Applications/ccpnmr/ccpnmr2.0/python/ccpnmr/analysis/core/
>>>>>> WindowBasic.py", line 384, in getSpectrumWindowView
>>>>>> analysisSpectrum = Util.getAnalysisSpectrum(spectrum)
>>>>>> File "/Applications/ccpnmr/ccpnmr2.0/python/ccpnmr/analysis/core/
>>>>>> Util.py", line 161, in getAnalysisSpectrum
>>>>>> setupAnalysisSpectrum(analysisSpectrum)
>>>>>> File "/Applications/ccpnmr/ccpnmr2.0/python/ccpnmr/analysis/core/
>>>>>> Util.py", line 174, in setupAnalysisSpectrum
>>>>>> levels = getSpectrumContourLevels(spectrum)
>>>>>> File "/Applications/ccpnmr/ccpnmr2.0/python/ccpnmr/analysis/core/
>>>>>> Util.py", line 739, in getSpectrumContourLevels
>>>>>> levels = [float(level) for level in
>>>>>> levels.split(spectrum_contour_separator)]
>>>>>>
>>>>>> Any ideas on how to fix this.
>>>>>>
>>>>>> Johnny
>>>>>> ------------------------------------------------------------
>>>>>> Johnny Eugene Croy, Ph.D.
>>>>>> Research Associate
>>>>>> Wuttke Lab
>>>>>>
>>>>>> University of Colorado, Boulder
>>>>>> Department of Chemistry and Biochemistry
>>>>>> UCB 215
>>>>>> Boulder, CO 80309-0215
>>>>>>
>>>>>> Lab: (303) 492-2369
>>>>>> Mobile: (303) 304-6069
>>>>>> ------------------------------------------------------------
>>>>>>
>>>>
>>>> ------------------------------------------------------------
>>>> Johnny Eugene Croy, Ph.D.
>>>> Research Associate
>>>> Wuttke Lab
>>>>
>>>> University of Colorado, Boulder
>>>> Department of Chemistry and Biochemistry
>>>> UCB 215
>>>> Boulder, CO 80309-0215
>>>>
>>>> Lab: (303) 492-2369
>>>> Mobile: (303) 304-6069
>>>> ------------------------------------------------------------
>>>>
>>
>> ------------------------------------------------------------
>> Johnny Eugene Croy, Ph.D.
>> Research Associate
>> Wuttke Lab
>>
>> University of Colorado, Boulder
>> Department of Chemistry and Biochemistry
>> UCB 215
>> Boulder, CO 80309-0215
>>
>> Lab: (303) 492-2369
>> Mobile: (303) 304-6069
>> ------------------------------------------------------------
>>
------------------------------------------------------------
Johnny Eugene Croy, Ph.D.
Research Associate
Wuttke Lab
University of Colorado, Boulder
Department of Chemistry and Biochemistry
UCB 215
Boulder, CO 80309-0215
Lab: (303) 492-2369
Mobile: (303) 304-6069
------------------------------------------------------------
|
