JISCMail - CCPNMR Archives

Wayne,

Ended up removing Python26, reinstalling analysis with python25.  I  
needed to edit the environment.txt file as it was pointing to /sw/bin/ 
python24 for some reason even though the installer said that it found  
version 2.5 on my computer.  Fixed that mistake, compiled analysis.   
All files opened up after upgrading.  Then installed python26 and  
everything seems to be working normally.

On a side note.  I compiled analysis2.0 on my hybrid G5 powerpc/linux  
64-bit machine (Ubuntu 8.10) with no problems, even after upgrading to  
python26.  Must be an odd issue with fink, perhaps?

J

On Nov 6, 2008, at 5:52 AM, Wayne Boucher wrote:

> Hello,
>
> Well that error message below is a bug in our code (it turns out not  
> all
> exceptions are classes, including our internal C-world generated  
> ones).
> That should be fixed now.
>
> But the first line (the Warning) looks worrying.
>
> So I just compiled Python 2.6 on one of our Linux boxes (with Dan's
> Tkinter patch, although as he said that's not likely to be the issue  
> here)
> and installed Analysis using that Python.  And it seems to work.  I  
> can't
> test it on the project you sent me because I don't have the data  
> files and
> that BlockFile error message only comes up if you have the data files.
>
> My guess is that it must still be picking up some mismatched C  
> compiled
> code.  So it's worth us seeing your environment.txt.  But also, it  
> might
> be worth doing a "make clean" and a "make" in ccpnmr2.0/c again.
>
> Wayne
>
> On Wed, 5 Nov 2008, Johnny Croy wrote:
>
>> Dan and Wayne,
>>
>> I just ended up removing python 2.6.  Analysis complies fine and will
>> start but when I try to load any project I get the following  
>> traceback.
>>
>>>>> Warning, BlockFile error: points must be list or tuple of size 2
>> AttributeError: 'str' object has no attribute '__name__'
>>   File "/Users/jec/Desktop/ccpnmr/ccpnmr2.0/python/memops/editor/
>> OpenProjectPopup.py", line 204, in apply
>>     self.callback(self.project)
>>   File "/Users/jec/Desktop/ccpnmr/ccpnmr2.0/python/ccpnmr/analysis/
>> AnalysisPopup.py", line 1006, in initProject
>>     error_msg = '%s: %s' % (exc[0].__name__, exc[1])
>>
>> Blah...this is all a bit depressing.  Darn updates.
>>
>> J
>>
>> On Nov 5, 2008, at 2:47 PM, Daniel O'Donovan wrote:
>>
>>> Hi All,
>>>
>>> I've been using 2.6 for some time and I haven't had too many
>>> problems. There is a patch that you need to apply (I've hopefully
>>> attached it) to get Tkinter working, this has been fixed in later
>>> 2.6 releases but my patch wasn't accepted for the first  2.6
>>> release! :-( The win32 release is built on 2.6 and seems to work  
>>> fine.
>>>
>>> Unfortunately your problem isn't related to the patch issue. It
>>> looks like your libpython2.6.so isn't getting picked up - in you
>>> can, have a look at environment.txt and make sure that the your
>>> PYTHON_DIR and PYTHON_LIB are set correctly. I use
>>>
>>> PYTHON_LIB = -L/usr/local/lib/python2.6/config -lpython2.6
>>>
>>> and I would imagine that yours should be
>>>
>>> PYTHON_LIB = -L/sw/lib/python2.6/config -lpython2.6
>>>
>>> and then as Wayne says, either run the script again or try a 'make
>>> clean && make && make links'
>>>
>>> Oh yeah, patch! To apply, find yout Tkinter.py file - it should be  
>>> in
>>>
>>> /sw/lib/python2.5/lib-tk/Tkinter.py
>>>
>>> cd into there
>>>
>>> $ cd /sw/lib/python2.5/lib-tk/Tkinter.py
>>>
>>> and apply the patch
>>>
>>> $ patch  < broken2.6_tkinter_patch.diff
>>>
>>> <broken2.6_tkinter_patch.diff>
>>>
>>>
>>> I've just seen your next mail. Again, it looks like the wrong python
>>> libraries are some how being picked up. Would it be possible for you
>>> to email one of us the relevant (PYTHON) parts of your
>>> environment.txt file so we can have a look to see what's going on?
>>>
>>> Thanks,
>>>
>>> Dan
>>>
>>>
>>> On 5 Nov 2008, at 21:25, Wayne Boucher wrote:
>>>
>>>> I just downloaded and checked the 2.6 source code and the first
>>>> couple of
>>>> functions that it's complaining about still exist.  It looks like  
>>>> you
>>>> might have tried to run the installation script on an existing <  
>>>> 2.6
>>>> compiled version??  If so then do
>>>>
>>>> cd ccpnmr2.0/c
>>>> make clean
>>>> cd ../..
>>>>
>>>> and then run the installation script again.
>>>>
>>>> Note that there are 2.6 compatibility issues that Dan discovered
>>>> (because
>>>> he downloaded 2.6 awhile ago).  I forget if they have all been
>>>> sorted out
>>>> in the Analysis code that is released.  (The one problem I remember
>>>> is
>>>> that the variable name "as", e.g. short-hand for atomSet, is no
>>>> longer
>>>> allowed in 2.6 because it's now a Python keyword.)
>>>>
>>>> Wayne
>>>>
>>>> On Wed, 5 Nov 2008, Johnny Croy wrote:
>>>>
>>>>> 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
>>>>> ------------------------------------------------------------
>>>>>
>>>
>>> Daniel O'Donovan
>>> [log in to unmask]
>>>
>>>
>>>
>>
>> ------------------------------------------------------------
>> 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
------------------------------------------------------------