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Earlier this year Apr 10, 2009 GeneTrack-1.0.3.zip (GeneTrack source distribution) file uploaded by istvan.albert - Labels: Featured Type-Source OpSys-All Labels: Featured Type-Source OpSys-All Apr 10, 2009 r33 (Fix for change in the HDF libraries. Report and patch by Ian...) committed by istvan.albert - Fix for change in the HDF libraries. Report and patch by Ian Schenck. Fix for change in the HDF libraries. Report and patch by Ian Schenck. Mar 17, 2009 issue 1 (All tests fail) Status changed by istvan.albert - It appears that an internal method of the hdf library has been changed between releases. A quick fix is to modify hdf.py at line 162 and change text = '%s' % node._v_hdf5name to: text = '%s' % node._v_name I will fix this in the svn soon. Status: Fixed It appears that an internal method of the hdf library has been changed between releases. A quick fix is to modify hdf.py at line 162 and change text = '%s' % node._v_hdf5name to: text = '%s' % node._v_name I will fix this in the svn soon. Status: Fixed Mar 17, 2009 issue 1 (All tests fail) reported by daweonline - What steps will reproduce the problem? 1. python run.py test 2. [or] python run.py execute dmel.dmel_dataconf What is the expected output? What do you see instead? Running on Drosophila test set I have: $ python run.py execute dmel.dmel_dataconf INFO sql.load_features: loading features from /home/dcittaro/GeneTrack- 1.0.1/library/dmel/data/dmel-ORF-features.txt WARNING sql.load_features: feature insert aborted label ORF exists, set clobber to True to override INFO __init__.module_import: imported dmel.dmel_dataconf INFO run.execute: executing dmel.dmel_dataconf INFO commands.execute: * LOADER * INFO loader.loader: data label=H2AZ INFO loader.loader: data_file='/home/dcittaro/GeneTrack-1.0.1/library/dmel/data/dmel- genetrack-input.txt' INFO loader.loader: hdf_database='/home/dcittaro/GeneTrack-1.0.1/library/dmel/db/dmel- data.hdf' ERROR in loader: group ``/H2AZ`` does not have a child named ``_v_hdf5name`` Closing remaining open files: /home/dcittaro/GeneTrack-1.0.1/library/dmel/db/dmel- data.hdf... done The last error is also the first error I get running the test (among several others): $ python run.py test WARNING const.<module>: chartdir license NOT found INFO run.execute: self testing mode INFO test_all.execute: running doctests for module atlas INFO __init__.module_import: imported os.path INFO test_all.execute: running doctests for module atlas.sql INFO sql.make_label: label TEST-LABEL exists, bulk deleting INFO sql.bulk_delete: deleting 0 rows INFO test_all.execute: running doctests for module atlas.hdf ******************************************************************** File "/home/dcittaro/GeneTrack-1.0.1/atlas/hdf.py", line 24, in atlas.hdf Failed example: bar1 = create_table( db=db, name='bar1', where=group, schema=Schema, clobber=True ) Exception raised: Traceback (most recent call last): File "/opt/ActivePython-2.5/lib/python2.5/doctest.py", line 1228, in __run compileflags, 1) in test.globs File "<doctest atlas.hdf[8]>", line 1, in <module> bar1 = create_table( db=db, name='bar1', where=group, schema=Schema, clobber=True ) File "/home/dcittaro/GeneTrack-1.0.1/atlas/hdf.py", line 176, in create_table wtext = as_string( where ) File "/home/dcittaro/GeneTrack-1.0.1/atlas/hdf.py", line 162, in as_string text = '%s' % node._v_hdf5name File "/opt/ActivePython-2.5/lib/python2.5/site-packages/tables-2.1.1-py2.5-linux- x86_64.egg/tables/group.py", line 799, in __getattr__ return self._f_getChild(name) File "/opt/ActivePython-2.5/lib/python2.5/site-packages/tables-2.1.1-py2.5-linux- x86_64.egg/tables/group.py", line 676, in _f_getChild self._g_checkHasChild(childname) File "/opt/ActivePython-2.5/lib/python2.5/site-packages/tables-2.1.1-py2.5-linux- x86_64.egg/tables/group.py", line 423, in _g_checkHasChild % (self._v_pathname, name)) NoSuchNodeError: group ``/foo`` does not have a child named ``_v_hdf5name`` ****************************************************************** What version of the product are you using? On what operating system? Python 2.5.2 hdf5 1.8.0 pytables 2.2.1 numpy 1.2.1 CentOS 5.2 x86_64 Please provide any additional information below. What steps will reproduce the problem? 1. python run.py test 2. [or] python run.py execute dmel.dmel_dataconf What is the expected output? What do you see instead? Running on Drosophila test set I have: $ python run.py execute dmel.dmel_dataconf INFO sql.load_features: loading features from /home/dcittaro/GeneTrack- 1.0.1/library/dmel/data/dmel-ORF-features.txt WARNING sql.load_features: feature insert aborted label ORF exists, set clobber to True to override INFO __init__.module_import: imported dmel.dmel_dataconf INFO run.execute: executing dmel.dmel_dataconf INFO commands.execute: * LOADER * INFO loader.loader: data label=H2AZ INFO loader.loader: data_file='/home/dcittaro/GeneTrack-1.0.1/library/dmel/data/dmel- genetrack-input.txt' INFO loader.loader: hdf_database='/home/dcittaro/GeneTrack-1.0.1/library/dmel/db/dmel- data.hdf' ERROR in loader: group ``/H2AZ`` does not have a child named ``_v_hdf5name`` Closing remaining open files: /home/dcittaro/GeneTrack-1.0.1/library/dmel/db/dmel- data.hdf... done The last error is also the first error I get running the test (among several others): $ python run.py test WARNING const.<module>: chartdir license NOT found INFO run.execute: self testing mode INFO test_all.execute: running doctests for module atlas INFO __init__.module_import: imported os.path INFO test_all.execute: running doctests for module atlas.sql INFO sql.make_label: label TEST-LABEL exists, bulk deleting INFO sql.bulk_delete: deleting 0 rows INFO test_all.execute: running doctests for module atlas.hdf ****************************************************************** File "/home/dcittaro/GeneTrack-1.0.1/atlas/hdf.py", line 24, in atlas.hdf Failed example: bar1 = create_table( db=db, name='bar1', where=group, schema=Schema, clobber=True ) Exception raised: Traceback (most recent call last): File "/opt/ActivePython-2.5/lib/python2.5/doctest.py", line 1228, in __run compileflags, 1) in test.globs File "<doctest atlas.hdf[8]>", line 1, in <module> bar1 = create_table( db=db, name='bar1', where=group, schema=Schema, clobber=True ) File "/home/dcittaro/GeneTrack-1.0.1/atlas/hdf.py", line 176, in create_table wtext = as_string( where ) File "/home/dcittaro/GeneTrack-1.0.1/atlas/hdf.py", line 162, in as_string text = '%s' % node._v_hdf5name File "/opt/ActivePython-2.5/lib/python2.5/site-packages/tables-2.1.1-py2.5-linux- x86_64.egg/tables/group.py", line 799, in __getattr__ return self._f_getChild(name) File "/opt/ActivePython-2.5/lib/python2.5/site-packages/tables-2.1.1-py2.5-linux- x86_64.egg/tables/group.py", line 676, in _f_getChild self._g_checkHasChild(childname) File "/opt/ActivePython-2.5/lib/python2.5/site-packages/tables-2.1.1-py2.5-linux- x86_64.egg/tables/group.py", line 423, in _g_checkHasChild % (self._v_pathname, name)) NoSuchNodeError: group ``/foo`` does not have a child named ``_v_hdf5name`` ******************************************************************** What version of the product are you using? On what operating system? Python 2.5.2 hdf5 1.8.0 pytables 2.2.1 numpy 1.2.1 CentOS 5.2 x86_64 Please provide any additional information below.

issue 1 (All tests fail) reported by daweonline - What steps will reproduce the problem? 1. python run.py test 2. [or] python run.py execute dmel.dmel_dataconf What is the expected output? What do you see instead? Running on Drosophila test set I have: $ python run.py execute dmel.dmel_dataconf INFO sql.load_features: loading features from /home/dcittaro/GeneTrack- 1.0.1/library/dmel/data/dmel-ORF-features.txt WARNING sql.load_features: feature insert aborted label ORF exists, set clobber to True to override INFO __init__.module_import: imported dmel.dmel_dataconf INFO run.execute: executing dmel.dmel_dataconf INFO commands.execute: *** LOADER *** INFO loader.loader: data label=H2AZ INFO loader.loader: data_file='/home/dcittaro/GeneTrack-1.0.1/library/dmel/data/dmel- genetrack-input.txt' INFO loader.loader: hdf_database='/home/dcittaro/GeneTrack-1.0.1/library/dmel/db/dmel- data.hdf' ERROR in loader: group ``/H2AZ`` does not have a child named ``_v_hdf5name`` Closing remaining open files: /home/dcittaro/GeneTrack-1.0.1/library/dmel/db/dmel- data.hdf... done The last error is also the first error I get running the test (among several others): $ python run.py test WARNING const.<module>: chartdir license NOT found INFO run.execute: self testing mode INFO test_all.execute: running doctests for module atlas INFO __init__.module_import: imported os.path INFO test_all.execute: running doctests for module atlas.sql INFO sql.make_label: label TEST-LABEL exists, bulk deleting INFO sql.bulk_delete: deleting 0 rows INFO test_all.execute: running doctests for module atlas.hdf ********************************************************************** File "/home/dcittaro/GeneTrack-1.0.1/atlas/hdf.py", line 24, in atlas.hdf Failed example: bar1 = create_table( db=db, name='bar1', where=group, schema=Schema, clobber=True ) Exception raised: Traceback (most recent call last): File "/opt/ActivePython-2.5/lib/python2.5/doctest.py", line 1228, in __run compileflags, 1) in test.globs File "<doctest atlas.hdf[8]>", line 1, in <module> bar1 = create_table( db=db, name='bar1', where=group, schema=Schema, clobber=True ) File "/home/dcittaro/GeneTrack-1.0.1/atlas/hdf.py", line 176, in create_table wtext = as_string( where ) File "/home/dcittaro/GeneTrack-1.0.1/atlas/hdf.py", line 162, in as_string text = '%s' % node._v_hdf5name File "/opt/ActivePython-2.5/lib/python2.5/site-packages/tables-2.1.1-py2.5-linux- x86_64.egg/tables/group.py", line 799, in __getattr__ return self._f_getChild(name) File "/opt/ActivePython-2.5/lib/python2.5/site-packages/tables-2.1.1-py2.5-linux- x86_64.egg/tables/group.py", line 676, in _f_getChild self._g_checkHasChild(childname) File "/opt/ActivePython-2.5/lib/python2.5/site-packages/tables-2.1.1-py2.5-linux- x86_64.egg/tables/group.py", line 423, in _g_checkHasChild % (self._v_pathname, name)) NoSuchNodeError: group ``/foo`` does not have a child named ``_v_hdf5name`` ********************************************************************** What version of the product are you using? On what operating system? Python 2.5.2 hdf5 1.8.0 pytables 2.2.1 numpy 1.2.1 CentOS 5.2 x86_64 Please provide any additional information below.

What steps will reproduce the problem? 1. python run.py test 2. [or] python run.py execute dmel.dmel_dataconf What is the expected output? What do you see instead? Running on Drosophila test set I have: $ python run.py execute dmel.dmel_dataconf INFO sql.load_features: loading features from /home/dcittaro/GeneTrack- 1.0.1/library/dmel/data/dmel-ORF-features.txt WARNING sql.load_features: feature insert aborted label ORF exists, set clobber to True to override INFO __init__.module_import: imported dmel.dmel_dataconf INFO run.execute: executing dmel.dmel_dataconf INFO commands.execute: *** LOADER *** INFO loader.loader: data label=H2AZ INFO loader.loader: data_file='/home/dcittaro/GeneTrack-1.0.1/library/dmel/data/dmel- genetrack-input.txt' INFO loader.loader: hdf_database='/home/dcittaro/GeneTrack-1.0.1/library/dmel/db/dmel- data.hdf' ERROR in loader: group ``/H2AZ`` does not have a child named ``_v_hdf5name`` Closing remaining open files: /home/dcittaro/GeneTrack-1.0.1/library/dmel/db/dmel- data.hdf... done The last error is also the first error I get running the test (among several others): $ python run.py test WARNING const.<module>: chartdir license NOT found INFO run.execute: self testing mode INFO test_all.execute: running doctests for module atlas INFO __init__.module_import: imported os.path INFO test_all.execute: running doctests for module atlas.sql INFO sql.make_label: label TEST-LABEL exists, bulk deleting INFO sql.bulk_delete: deleting 0 rows INFO test_all.execute: running doctests for module atlas.hdf ********************************************************************** File "/home/dcittaro/GeneTrack-1.0.1/atlas/hdf.py", line 24, in atlas.hdf Failed example: bar1 = create_table( db=db, name='bar1', where=group, schema=Schema, clobber=True ) Exception raised: Traceback (most recent call last): File "/opt/ActivePython-2.5/lib/python2.5/doctest.py", line 1228, in __run compileflags, 1) in test.globs File "<doctest atlas.hdf[8]>", line 1, in <module> bar1 = create_table( db=db, name='bar1', where=group, schema=Schema, clobber=True ) File "/home/dcittaro/GeneTrack-1.0.1/atlas/hdf.py", line 176, in create_table wtext = as_string( where ) File "/home/dcittaro/GeneTrack-1.0.1/atlas/hdf.py", line 162, in as_string text = '%s' % node._v_hdf5name File "/opt/ActivePython-2.5/lib/python2.5/site-packages/tables-2.1.1-py2.5-linux- x86_64.egg/tables/group.py", line 799, in __getattr__ return self._f_getChild(name) File "/opt/ActivePython-2.5/lib/python2.5/site-packages/tables-2.1.1-py2.5-linux- x86_64.egg/tables/group.py", line 676, in _f_getChild self._g_checkHasChild(childname) File "/opt/ActivePython-2.5/lib/python2.5/site-packages/tables-2.1.1-py2.5-linux- x86_64.egg/tables/group.py", line 423, in _g_checkHasChild % (self._v_pathname, name)) NoSuchNodeError: group ``/foo`` does not have a child named ``_v_hdf5name`` ********************************************************************** What version of the product are you using? On what operating system? Python 2.5.2 hdf5 1.8.0 pytables 2.2.1 numpy 1.2.1 CentOS 5.2 x86_64 Please provide any additional information below.

Earlier this year