Closed GoogleCodeExporter closed 9 years ago
Ideally, I would like to be able to run the unit test at:
http://code.google.com/p/cing/source/browse/trunk/cing/python/cing/PluginCode/te
st/test_Analysis.py
Original comment by jurge...@gmail.com
on 17 Jun 2010 at 11:48
The unit test output:
==> Importing data from Ccpn project "1brv_cs_pk_2mdl"
Non-standard (residues and their) atoms added:
GLU : [ 189]
DEBUG: Residue.addDihedralD1: skipping residue <Residue HISH159> because of
missing atoms
DEBUG: Residue.addDihedralD1: skipping residue <Residue GLN160> because of
missing atoms
DEBUG: and so on for a total of 13 messages
==> Molecule 1brv: No potential disulfide bridged residues found
Calculating rmsd's (residues: 158-189, models: 0-1)
==> Ccpn molecule '1brv' imported
==> CCPN ShiftList 'brsvg.prot' imported from CCPN Nmr project '1brv'
==> CING (pseudo-)atom with resonances updated numbering 149
WARNING: CCPN peak '<ccp.nmr.Nmr.Peak ['1brv', 3, 1, 11, 546]>' missing both
volume and height
==> PeakList 'NOESY_brsvg_sparky_11' imported from CCPN Nmr project '1brv'
==> Ccpn project imported
CcpNmr Analysis Version 2.1. Release 3 (Copyright 2003-2009 CCPN)
Distribution created Tue Feb 16 17:09:23 2010
If you use CcpNmr Analysis, please quote the following reference:
Wim F. Vranken, Wayne Boucher, Tim J. Stevens, Rasmus H. Fogh, Anne
Pajon, Miguel Llinas, Eldon L. Ulrich, John L. Markley, John Ionides
and Ernest D. Laue (2005). The CCPN Data Model for NMR Spectroscopy:
Development of a Software Pipeline. Proteins 59, 687 - 696.
For program documentation the CCPN wiki site is located at:
http://sites.google.com/site/ccpnwiki/Home/documentation/ccpnmr-software
For help and support visit the mailing list at:
http://www.jiscmail.ac.uk/ccpnmr
For Python API documentation, tutorials and CCPN web applications visit:
http://www.ccpn.ac.uk/
EXCEPTION CAUGHT: Traceback (most recent call last):
File "/Users/jd/workspace35/cing/python/cing/PluginCode/Analysis.py", line 42, in initAnalysis
self.app.initProject(self.project)
File "/Users/jd/workspace35/ccpnmr/ccpnmr2.1/python/ccpnmr/analysis/Analysis.py", line 287, in initProject
self.initTopObjects(project)
File "/Users/jd/workspace35/ccpnmr/ccpnmr2.1/python/ccpnmr/analysis/Analysis.py", line 222, in initTopObjects
if not project.currentInstrumentStore:
File "/Users/jd/workspace35/cing/python/cing/Libs/NTutils.py", line 1269, in __getattr__
raise AttributeError( '"%s" not found.' % attr )
AttributeError: "currentInstrumentStore" not found.
ERROR: Analysis crashed when starting the non-GUI version
Starting cing.PluginCode.Analysis#runRpf
Peaklists: [[<ccp.nmr.Nmr.PeakList ['1brv', 3, 1, 11]>]]
DEBUG: Using ensemble: <ccp.molecule.MolStructure.StructureEnsemble
[<ccp.molecule.MolSystem.MolSystem ['1brv']>, 2]>
DEBUG: Using peakList.dataSource.name: brsvg_sparky with tolerance:
[[<ccp.nmr.Nmr.FreqDataDim ['1brv', 3, 1, 1]>, 0.050000000000000003, 1,
0.050000000000000003], [<ccp.nmr.Nmr.FreqDataDim ['1brv', 3, 1, 2]>,
0.050000000000000003, 1, 0.050000000000000003]]
Getting resonance-resonance possible peak assignments within tolerances
Peak List NOESY:brsvg_sparky:11
Peak <ccp.nmr.Nmr.Peak ['1brv', 3, 1, 11, 546]> does not have a peakDim1.value
Time taken: 0.345909118652
Getting resonance-resonance NOE distances
Ensemble 2
Time taken: 0.161898851395
Calculating scores and making CCPN validation objects
E
======================================================================
ERROR: Skip until project has been improved; looks like peaks without CS are
found.
----------------------------------------------------------------------
Traceback (most recent call last):
File "/Users/jd/workspace35/cing/python/cing/PluginCode/test/test_Analysis.py", line 64, in testAnalysisRpf
diagonalExclusion=DEFAULT_DIAGONAL_EXCLUSION_SHIFT
File "/Users/jd/workspace35/cing/python/cing/PluginCode/Analysis.py", line 115, in runRpf
verbose=cing.verbosity==cing.verbosityDebug)
File "/Users/jd/workspace35/cing/python/cing/Scripts/Analysis/PyRPF.py", line 1769, in calcRPF
peakListM = predictMissingPeaks(peakList, shiftsMissingPeaks, progressBar)
File "/Users/jd/workspace35/cing/python/cing/Scripts/Analysis/PyRPF.py", line 1931, in predictMissingPeaks
syntheticPeakList = getSyntheticMissingPeaksList(peakList)
File "/Users/jd/workspace35/cing/python/cing/Scripts/Analysis/PyRPF.py", line 1908, in getSyntheticMissingPeaksList
analysisPeakList = getAnalysisPeakList(syntheticPeakList)
File "/Users/jd/workspace35/ccpnmr/ccpnmr2.1/python/ccpnmr/analysis/core/Util.py", line 339, in getAnalysisPeakList
symbol = getPeakListSymbol(peakList)
File "/Users/jd/workspace35/ccpnmr/ccpnmr2.1/python/ccpnmr/analysis/core/Util.py", line 848, in getPeakListSymbol
application = peakList.root.application
AttributeError: 'MemopsRoot' object has no attribute 'application'
----------------------------------------------------------------------
Ran 1 test in 10.251s
FAILED (errors=1)
Original comment by jurge...@gmail.com
on 17 Jun 2010 at 11:51
Oeps, sorry, I should have shown how far I got with the compile.
Alan, do you have Analysis under macport's python?
jd:stella/~/ cdf
/Users/jd/workspace35/ccpnmr/ccpnmr2.1/c
jd:stella/c/ make realclean
cd memops/global && make realclean
rm -f *.o
rm -f *.so
cd ccp/structure && make realclean
rm -f *.o
rm -f *.so
cd ccpnmr/analysis && make realclean
rm -f *.o
rm -f *.so
cd ccpnmr/clouds && make realclean
rm -f *.o
rm -f *.so
cd ccpnmr/dynamics && make realclean
/bin/sh: line 0: cd: ccpnmr/dynamics: No such file or directory
make: *** [dynamics_realclean] Error 1
jd:stella/c/ make
cd memops/global && make
cc -O -fPIC -DDO_NOT_HAVE_MALLOC -c utility.c
cc -O -fPIC -DDO_NOT_HAVE_MALLOC
-I/opt/local/Library/Frameworks/Python.framework/Versions/2.6/include/python2.6
-c python_util.c
python_util.c: In function ‘valid_py_object’:
python_util.c:54: warning: passing argument 1 of ‘equal_strings’ discards
qualifiers from pointer target type
python_util.c:54: warning: passing argument 2 of ‘equal_strings’ discards
qualifiers from pointer target type
cc -O -fPIC -DDO_NOT_HAVE_MALLOC -c hash_list.c
cc -O -fPIC -DDO_NOT_HAVE_MALLOC -c hash_table.c
cc -O -fPIC -DDO_NOT_HAVE_MALLOC -c mem_cache.c
cc -O -fPIC -DDO_NOT_HAVE_MALLOC -c mutex.c
cc -O -fPIC -DDO_NOT_HAVE_MALLOC
-I/opt/local/Library/Frameworks/Python.framework/Versions/2.6/include/python2.6
-c py_mem_cache.c
cc -O -fPIC -DDO_NOT_HAVE_MALLOC -c block_file.c
cc -O -fPIC -DDO_NOT_HAVE_MALLOC -c shape_file.c
cc -O -fPIC -DDO_NOT_HAVE_MALLOC -c int_array.c
cc -O -fPIC -DDO_NOT_HAVE_MALLOC
-I/opt/local/Library/Frameworks/Python.framework/Versions/2.6/include/python2.6
-c py_block_file.c
cc -O -fPIC -DDO_NOT_HAVE_MALLOC
-I/opt/local/Library/Frameworks/Python.framework/Versions/2.6/include/python2.6
-c py_shape_file.c
cc -O -fPIC -L/opt/local/Library/Frameworks/Python.framework/Versions/2.6/lib
-bundle -bundle_loader
/opt/local/Library/Frameworks/Python.framework/Versions/2.6/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
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_get_python_float_array in python_util.o
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ld: symbol(s) not found
collect2: ld returned 1 exit status
make[1]: *** [BlockFile.so] Error 1
make: *** [global] Error 2
Original comment by jurge...@gmail.com
on 17 Jun 2010 at 12:00
Well, I see the problem. What you may try is to compare with my
environment.txt, done for Fink.
Original comment by alanwil...@gmail.com
on 29 Jun 2010 at 10:48
Attachments:
Original comment by jurge...@gmail.com
on 10 Nov 2010 at 1:13
Original issue reported on code.google.com by
jurge...@gmail.com
on 17 Jun 2010 at 11:46