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jeetsukumaran / DendroPy

A Python library for phylogenetic scripting, simulation, data processing and manipulation.
https://pypi.org/project/DendroPy/.
BSD 3-Clause "New" or "Revised" License
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Probelms with DendroPy compiled with other software. #50

Closed Lily-WL closed 8 years ago

Lily-WL commented 8 years ago

Thank you for your platform to support the use of DendroPy.

I installed a software called CheckM . And DendroPy was also installed. But seems there are some errors. The details are as follows:

[root@student ~]# python -m dendropy DendroPy version : DendroPy 4.1.0 DendroPy location : /usr/local/lib/python2.7/site-packages/dendropy Python version : 2.7 (r27:82500, Apr 29 2016, 10:17:23) [GCC 4.4.6 20120305 (Red Hat 4.4.6-4)] Python executable : /usr/local/bin/python Python site packages : ['/usr/local/lib/python2.7/site-packages', '/usr/local/lib/site-python'] Exception AttributeError: "'NoneType' object has no attribute 'ImmutableTypeError'" in <bound method FrozenOrderedDict.del of FrozenOrderedDict([('1', <StateIdentity at 0x1ed8490: '1'>), ('0', <StateIdentity at 0x1ed84d0: '0'>)])> ignored Exception AttributeError: "'NoneType' object has no attribute 'ImmutableTypeError'" in <bound method FrozenOrderedDict.del of FrozenOrderedDict([('1', <StateIdentity at 0x1ed8490: '1'>), ('0', <StateIdentity at 0x1ed84d0: '0'>)])> ignored Exception AttributeError: "'NoneType' object has no attribute 'ImmutableTypeError'" in <bound method FrozenOrderedDict.del of FrozenOrderedDict()> ignored Exception AttributeError: "'NoneType' object has no attribute 'ImmutableTypeError'" in <bound method FrozenOrderedDict.del of FrozenOrderedDict([(0, <StateIdentity at 0x1ed8490: '1'>), (1, <StateIdentity at 0x1ed84d0: '0'>)])> ignored Exception AttributeError: "'NoneType' object has no attribute 'ImmutableTypeError'" in <bound method FrozenOrderedDict.del of FrozenOrderedDict()> ignored

jeetsukumaran commented 8 years ago

Hi,

This is a tricky one. I cannot replicate the error, and I am not sure what might be going on to cause this on your end. Best thing I can suggest is to try a clean install of DendroPy:

$ pip install --upgrade dendropy
Lily-WL commented 8 years ago

Dear Sir,

Thank you for your reply.

New installation is successful. As the discription:

Installing collected packages: setuptools Found existing installation: setuptools 20.10.1 Uninstalling setuptools-20.10.1: Successfully uninstalled setuptools-20.10.1 Successfully installed setuptools-21.0.0

However, it seems the error still exit. IS it the matter with FrozenOrderedDict?

_[root@student ~]# python -m dendropy DendroPy version : DendroPy 4.1.0 DendroPy location : /usr/local/lib/python2.7/site-packages/dendropy Python version : 2.7 (r27:82500, Apr 29 2016, 10:17:23) [GCC 4.4.6 20120305 (Red Hat 4.4.6-4)] Python executable : /usr/local/bin/python Python site packages : ['/usr/local/lib/python2.7/site-packages', '/usr/local/lib/site-python'] Exception AttributeError: "'NoneType' object has no attribute 'ImmutableTypeError'" in <bound method FrozenOrderedDict.del of FrozenOrderedDict([('1', <StateIdentity at 0x21a74d0: '1'>), ('0', <StateIdentity at 0x21a7510: '0'>)])> ignored Exception AttributeError: "'NoneType' object has no attribute 'ImmutableTypeError'" in <bound method FrozenOrderedDict.del of FrozenOrderedDict([('1', <StateIdentity at 0x21a74d0: '1'>), ('0', <StateIdentity at 0x21a7510: '0'>)])> ignored Exception AttributeError: "'NoneType' object has no attribute 'ImmutableTypeError'" in <bound method FrozenOrderedDict.del of FrozenOrderedDict()> ignored Exception AttributeError: "'NoneType' object has no attribute 'ImmutableTypeError'" in <bound method FrozenOrderedDict.del of FrozenOrderedDict([(0, <StateIdentity at 0x21a74d0: '1'>), (1, <StateIdentity at 0x21a7510: '0'>)])> ignored Exception AttributeError: "'NoneType' object has no attribute 'ImmutableTypeError'" in <bound method FrozenOrderedDict.del of FrozenOrderedDict()> ignored_

jeetsukumaran commented 8 years ago

It is, but I cannot tell from what you have give here what the issue is.

Have you tried running the tests:

$ python setup.py test
jeetsukumaran commented 8 years ago

Can also try using the verbose ("-v") flag: python -vm dendropy.

jeetsukumaran commented 8 years ago

Googling the message it appears possible (by no means certain) that the issue might be related garbage collection on exiting the program:

https://answers.atlassian.com/questions/24661360/exception-on-exit-after-upgrading-to-python2.7.10 https://groups.google.com/forum/#!topic/theano-users/U6PEg-i-Qu4 http://stackoverflow.com/questions/18163697/exception-typeerror-warning-sometimes-shown-sometimes-not-when-using-throw-meth

Except that we only use del in a couple of places, not related to this code.

Lily-WL commented 8 years ago

Dear sir，

Thank you for your immediatedly reply.

I executed "python -vm dendropy". Seen from the feedback, it seems the error came from the dendropy.datamodel.charstatemodel. As follows.

................. _cleanup[2] dendropy.datamodel.charstatemodel Exception AttributeError: "'NoneType' object has no attribute 'ImmutableTypeError'" in <bound method FrozenOrderedDict.del of FrozenOrderedDict([('1', <StateIdentity at 0x151d4d0: '1'>), ('0', <StateIdentity at 0x151d510: '0'>)])> ignored Exception AttributeError: "'NoneType' object has no attribute 'ImmutableTypeError'" in <bound method FrozenOrderedDict.del of FrozenOrderedDict([('1', <StateIdentity at 0x151d4d0: '1'>), ('0', <StateIdentity at 0x151d510: '0'>)])> ignored _Exception AttributeError: "'NoneType' object has no attribute 'ImmutableTypeError'" in <bound method FrozenOrderedDict.del of FrozenOrderedDict()> ignored Exception AttributeError: "'NoneType' object has no attribute 'ImmutableTypeError'" in <bound method FrozenOrderedDict.del of FrozenOrderedDict([(0, <StateIdentity at 0x151d4d0: '1'>), (1, <StateIdentity at 0x151d510: '0'>)])> ignored Exception AttributeError: "'NoneType' object has no attribute 'ImmutableTypeError'" in <bound method FrozenOrderedDict.del of FrozenOrderedDict()> ignored

Lily-WL commented 8 years ago

Furthermore, I executed "python setup.py test" and fail.

[root@student DendroPy-4.0.3]# python setup.py test

......................

ERROR: test_copy (dendropy.test.test_container_frozen_ordered_dict.FrozenOrderedDictTest)

Traceback (most recent call last): File "/opt/DendroPy-4.0.3/dendropy/test/test_container_frozen_ordered_dict.py", line 79, in test_copy d2 = copy.copy(self.d) File "/usr/local/lib/python2.7/copy.py", line 80, in copy return copier(x) File "/opt/DendroPy-4.0.3/dendropy/utility/container.py", line 672, in copy temp = FrozenOrderedDict() File "/opt/DendroPy-4.0.3/dendropy/utility/container.py", line 613, in init super(FrozenOrderedDict, self).init(_args, _kwargs) File "/usr/local/lib/python2.7/collections.py", line 48, in init self.update(_args, _kwds) TypeError: update() takes exactly 2 arguments (1 given)

ERROR: test_deepcopy (dendropy.test.test_container_frozen_ordered_dict.FrozenOrderedDictTest)

Traceback (most recent call last): File "/opt/DendroPy-4.0.3/dendropy/test/test_container_frozen_ordered_dict.py", line 70, in test_deepcopy d2 = copy.deepcopy(self.d) File "/usr/local/lib/python2.7/copy.py", line 174, in deepcopy y = copier(memo) File "/opt/DendroPy-4.0.3/dendropy/utility/container.py", line 659, in deepcopy temp = FrozenOrderedDict() File "/opt/DendroPy-4.0.3/dendropy/utility/container.py", line 613, in init super(FrozenOrderedDict, self).init(_args, _kwargs) File "/usr/local/lib/python2.7/collections.py", line 48, in init self.update(_args, _kwds) TypeError: update() takes exactly 2 arguments (1 given)

ERROR: runTest (dendropy.test.test_container_normalized_bitmask_dict.TestNormalizedBitmaskDict)

Testing NormalizedBitmaskDict

Traceback (most recent call last): File "/opt/DendroPy-4.0.3/dendropy/test/test_container_normalized_bitmask_dict.py", line 38, in runTest d = container.NormalizedBitmaskDict(fill_bitmask=fill_bitmask) File "/opt/DendroPy-4.0.3/dendropy/utility/container.py", line 258, in init collections.OrderedDict.init(self) File "/usr/local/lib/python2.7/collections.py", line 48, in init self.update(_args, *_kwds) TypeError: update() takes exactly 2 arguments (1 given)

FAIL: test_collection_comments_and_annotations (dendropy.test.test_dataio_nexml_reader_tree_list.NexmlStandardTreeParsingTestCase)

Traceback (most recent call last): File "/opt/DendroPy-4.0.3/dendropy/test/test_dataio_nexml_reader_tree_list.py", line 60, in test_collection_comments_and_annotations expected_metadata) File "/opt/DendroPy-4.0.3/dendropy/test/support/standard_file_test_trees.py", line 127, in compare_annotations_to_json_metadata_dict self.assertEqual(item_annotations_as_dict, expectedmetadata) AssertionError: {'Merycoidodon%_$_permeant': 'envyingly247994 wagonload130853 ganglioneuron4665 [truncated]... != {'$demivotary#_monumentlike': '31', '!_missuggestionfrondivorous#': 'False', [truncated]... Diff is 676 characters long. Set self.maxDiff to None to see it.

Ran 785 tests in 502.328s

FAILED (failures=1, errors=3) Exception dendropy.utility.container.ImmutableTypeError: ImmutableTypeError('FrozenOrderedDict is immutable',) in <bound method FrozenOrderedDict.del of FrozenOrderedDict([('a', 1), ('b', 2), ('c', 3)])> ignored Exception dendropy.utility.container.ImmutableTypeError: ImmutableTypeError('FrozenOrderedDict is immutable',) in <bound method FrozenOrderedDict.del of FrozenOrderedDict([('a', 1), ('b', 2), ('c', 3)])> ignored Exception dendropy.utility.container.ImmutableTypeError: ImmutableTypeError('FrozenOrderedDict is immutable',) in <bound method FrozenOrderedDict.del of FrozenOrderedDict([('a', 1), ('b', 2), ('c', 3)])> ignored Exception dendropy.utility.container.ImmutableTypeError: ImmutableTypeError('FrozenOrderedDict is immutable',) in <bound method FrozenOrderedDict.del of FrozenOrderedDict([('a', 1), ('b', 2), ('c', 3)])> ignored Exception dendropy.utility.container.ImmutableTypeError: ImmutableTypeError('FrozenOrderedDict is immutable',) in <bound method FrozenOrderedDict.del of FrozenOrderedDict([('a', 1), ('b', 2), ('c', 3)])> ignored Exception dendropy.utility.container.ImmutableTypeError: ImmutableTypeError('FrozenOrderedDict is immutable',) in <bound method FrozenOrderedDict.del of FrozenOrderedDict([('a', 1), ('b', 2), ('c', 3)])> ignored Exception dendropy.utility.container.ImmutableTypeError: ImmutableTypeError('FrozenOrderedDict is immutable',) in <bound method FrozenOrderedDict.del of FrozenOrderedDict([('a', 1), ('b', 2), ('c', 3)])> ignored Exception dendropy.utility.container.ImmutableTypeError: ImmutableTypeError('FrozenOrderedDict is immutable',) in <bound method FrozenOrderedDict.del of FrozenOrderedDict([('0', <StateIdentity at 0x3c7ae8d0: '0'>), ('1', <StateIdentity at 0x3c7ae910: '1'>), ('2', <StateIdentity at 0x3c7ae950: '2'>), ('3', <StateIdentity at 0x3c7ae990: '3'>), ('4', <StateIdentity at 0x3c7ae9d0: '4'>), ('-', <StateIdentity at 0x3c7ae890: '-'>), ('?', <StateIdentity at 0x3c7aea10: '?'>)])> ignored Exception dendropy.utility.container.ImmutableTypeError: ImmutableTypeError('FrozenOrderedDict is immutable',) in <bound method FrozenOrderedDict.del of FrozenOrderedDict([(None, <StateIdentity at 0x3c7aea10: '?'>), ('0', <StateIdentity at 0x3c7ae8d0: '0'>), ('1', <StateIdentity at 0x3c7ae910: '1'>), ('2', <StateIdentity at 0x3c7ae950: '2'>), ('3', <StateIdentity at 0x3c7ae990: '3'>), ('4', <StateIdentity at 0x3c7ae9d0: '4'>), ('-', <StateIdentity at 0x3c7ae890: '-'>), ('?', <StateIdentity at 0x3c7aea10: '?'>)])> ignored Exception dendropy.utility.container.ImmutableTypeError: ImmutableTypeError('FrozenOrderedDict is immutable',) in <bound method FrozenOrderedDict.del of FrozenOrderedDict()> ignored Exception dendropy.utility.container.ImmutableTypeError: ImmutableTypeError('FrozenOrderedDict is immutable',) in <bound method FrozenOrderedDict.del of FrozenOrderedDict([(0, <StateIdentity at 0x3c7ae8d0: '0'>), (1, <StateIdentity at 0x3c7ae910: '1'>), (2, <StateIdentity at 0x3c7ae950: '2'>), (3, <StateIdentity at 0x3c7ae990: '3'>), (4, <StateIdentity at 0x3c7ae9d0: '4'>), (5, <StateIdentity at 0x3c7ae890: '-'>), (6, <StateIdentity at 0x3c7aea10: '?'>)])> ignored Exception dendropy.utility.container.ImmutableTypeError: ImmutableTypeError('FrozenOrderedDict is immutable',) in <bound method FrozenOrderedDict.del of FrozenOrderedDict([(frozenset([<StateIdentity at 0x3c7ae910: '1'>, <StateIdentity at 0x3c7ae890: '-'>, <StateIdentity at 0x3c7ae950: '2'>, <StateIdentity at 0x3c7ae8d0: '0'>, <StateIdentity at 0x3c7ae990: '3'>, <StateIdentity at 0x3c7ae9d0: '4'>]), <StateIdentity at 0x3c7aea10: '?'>)])> ignored Exception dendropy.utility.container.ImmutableTypeError: ImmutableTypeError('FrozenOrderedDict is immutable',) in <bound method FrozenOrderedDict.del of FrozenOrderedDict([('1', <StateIdentity at 0xdebc50: '1'>), ('0', <StateIdentity at 0xdebc90: '0'>)])> ignored Exception dendropy.utility.container.ImmutableTypeError: ImmutableTypeError('FrozenOrderedDict is immutable',) in <bound method FrozenOrderedDict.del of FrozenOrderedDict([('1', <StateIdentity at 0xdebc50: '1'>), ('0', <StateIdentity at 0xdebc90: '0'>)])> ignored Exception dendropy.utility.container.ImmutableTypeError: ImmutableTypeError('FrozenOrderedDict is immutable',) in <bound method FrozenOrderedDict.del of FrozenOrderedDict()> ignored Exception dendropy.utility.container.ImmutableTypeError: ImmutableTypeError('FrozenOrderedDict is immutable',) in <bound method FrozenOrderedDict.del of FrozenOrderedDict([(0, <StateIdentity at 0xdebc50: '1'>), (1, <StateIdentity at 0xdebc90: '0'>)])> ignored Exception dendropy.utility.container.ImmutableTypeError: ImmutableTypeError('FrozenOrderedDict is immutable',) in <bound method FrozenOrderedDict.del of FrozenOrderedDict()> ignored

jeetsukumaran commented 8 years ago

Can you replicate the problem with a minimal fragment like the following?

 python -c "from dendropy.utility.container import

FrozenOrderedDict; q = FrozenOrderedDict()"

On 5/6/16 1:31 AM, Lily-WL wrote:

  Furthermore, I executed "python setup.py test" and fail.

[root@student DendroPy-4.0.3]# python setup.py test

......................

ERROR: test_copy
(dendropy.test.test_container_frozen_ordered_dict.FrozenOrderedDictTest)

Traceback (most recent call last): File "/opt/DendroPy-4.0.3/dendropy/test/test_container_frozen_ordered_dict.py", line 79, in test_copy d2 = copy.copy(self.d) File "/usr/local/lib/python2.7/copy.py", line 80, in copy return copier(x) File "/opt/DendroPy-4.0.3/dendropy/utility/container.py", line 672, in copy temp = FrozenOrderedDict() File "/opt/DendroPy-4.0.3/dendropy/utility/container.py", line 613, in init super(FrozenOrderedDict, self).init(/args, /kwargs) File "/usr/local/lib/python2.7/collections.py", line 48, in *init self.update(/args, */kwds) TypeError: update() takes exactly 2 arguments (1 given)

ERROR: test_deepcopy
(dendropy.test.test_container_frozen_ordered_dict.FrozenOrderedDictTest)

Traceback (most recent call last): File "/opt/DendroPy-4.0.3/dendropy/test/test_container_frozen_ordered_dict.py", line 70, in test_deepcopy d2 = copy.deepcopy(self.d) File "/usr/local/lib/python2.7/copy.py", line 174, in deepcopy y = copier(memo) File "/opt/DendroPy-4.0.3/dendropy/utility/container.py", line 659, in deepcopy temp = FrozenOrderedDict() File "/opt/DendroPy-4.0.3/dendropy/utility/container.py", line 613, in init super(FrozenOrderedDict, self).init(/args, /kwargs) File "/usr/local/lib/python2.7/collections.py", line 48, in *init self.update(/args, */kwds) TypeError: update() takes exactly 2 arguments (1 given)

ERROR: runTest (dendropy.test.test_container_normalized_bitmask_dict.TestNormalizedBitmaskDict)

Testing NormalizedBitmaskDict

Traceback (most recent call last): File "/opt/DendroPy-4.0.3/dendropy/test/test_container_normalized_bitmask_dict.py", line 38, in runTest d = container.NormalizedBitmaskDict(fill_bitmask=fill_bitmask) File "/opt/DendroPy-4.0.3/dendropy/utility/container.py", line 258, in init collections.OrderedDict.init(self) File "/usr/local/lib/python2.7/collections.py", line 48, in init self.update(/args, */kwds) TypeError: update() takes exactly 2 arguments (1 given)

FAIL: test_collection_comments_and_annotations
(dendropy.test.test_dataio_nexml_reader_tree_list.NexmlStandardTreeParsingTestCase)

Traceback (most recent call last): File "/opt/DendroPy-4.0.3/dendropy/test/test_dataio_nexml_reader_tree_list.py", line 60, in test_collection_comments_and_annotations expected_metadata) File "/opt/DendroPy-4.0.3/dendropy/test/support/standard_file_test_trees.py", line 127, in compare_annotations_to_json_metadata_dict self.assertEqual(item_annotations_as_dict, expectedmetadata) AssertionError: {'Merycoidodon%/$_permeant': 'envyingly247994 wagonload130853 ganglioneuron4665 [truncated]... != {'$_demivotary/#/monumentlike': '31', '!_missuggestion_frondivorous/#': 'False', [truncated]... Diff is 676 characters long. Set self.maxDiff to None to see it.

Ran 785 tests in 502.328s

FAILED (failures=1, errors=3) Exception dendropy.utility.container.ImmutableTypeError: ImmutableTypeError('FrozenOrderedDict is immutable',) in ignored Exception dendropy.utility.container.ImmutableTypeError: ImmutableTypeError('FrozenOrderedDict is immutable',) in ignored Exception dendropy.utility.container.ImmutableTypeError: ImmutableTypeError('FrozenOrderedDict is immutable',) in ignored Exception dendropy.utility.container.ImmutableTypeError: ImmutableTypeError('FrozenOrderedDict is immutable',) in ignored Exception dendropy.utility.container.ImmutableTypeError: ImmutableTypeError('FrozenOrderedDict is immutable',) in ignored Exception dendropy.utility.container.ImmutableTypeError: ImmutableTypeError('FrozenOrderedDict is immutable',) in ignored Exception dendropy.utility.container.ImmutableTypeError: ImmutableTypeError('FrozenOrderedDict is immutable',) in ignored Exception dendropy.utility.container.ImmutableTypeError: ImmutableTypeError('FrozenOrderedDict is immutable',) in ), ('1', ), ('2', ), ('3', ), ('4', ), ('-', ), ('?', )])> ignored Exception dendropy.utility.container.ImmutableTypeError: ImmutableTypeError('FrozenOrderedDict is immutable',) in ), ('0', ), ('1', ), ('2', ), ('3', ), ('4', ), ('-', ), ('?', )])> ignored Exception dendropy.utility.container.ImmutableTypeError: ImmutableTypeError('FrozenOrderedDict is immutable',) in ignored Exception dendropy.utility.container.ImmutableTypeError: ImmutableTypeError('FrozenOrderedDict is immutable',) in ), (1, ), (2, ), (3, ), (4, ), (5, ), (6, )])> ignored Exception dendropy.utility.container.ImmutableTypeError: ImmutableTypeError('FrozenOrderedDict is immutable',) in , , , , , ]), )])> ignored Exception dendropy.utility.container.ImmutableTypeError: ImmutableTypeError('FrozenOrderedDict is immutable',) in ), ('0', )])> ignored Exception dendropy.utility.container.ImmutableTypeError: ImmutableTypeError('FrozenOrderedDict is immutable',) in ), ('0', )])> ignored Exception dendropy.utility.container.ImmutableTypeError: ImmutableTypeError('FrozenOrderedDict is immutable',) in ignored Exception dendropy.utility.container.ImmutableTypeError: ImmutableTypeError('FrozenOrderedDict is immutable',) in ), (1, )])> ignored Exception dendropy.utility.container.ImmutableTypeError: ImmutableTypeError('FrozenOrderedDict is immutable',) in ignored

— You are receiving this because you commented. Reply to this email directly or view it on GitHub https://github.com/jeetsukumaran/DendroPy/issues/50#issuecomment-217351467

Jeet Sukumaran

jeetsukumaran@gmail.com

Blog/Personal Pages: http://jeetworks.org/ GitHub Repositories: http://github.com/jeetsukumaran Photographs (as stream): http://www.flickr.com/photos/jeetsukumaran/ Photographs (by galleries):

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Lily-WL commented 8 years ago

[root@student DendroPy-4.0.3]# python -c "from dendropy.utility.container import FrozenOrderedDict; q = FrozenOrderedDict()" Traceback (most recent call last): File "", line 1, in File "dendropy/utility/container.py", line 613, in init super(FrozenOrderedDict, self).init(_args, _kwargs) File "/usr/local/lib/python2.7/collections.py", line 48, in init self.update(_args, _kwds) TypeError: update() takes exactly 2 arguments (1 given) Exception AttributeError: "'NoneType' object has no attribute 'ImmutableTypeError'" in <bound method FrozenOrderedDict.del of FrozenOrderedDict([('1', <StateIdentity at 0x1a96d90: '1'>), ('0', <StateIdentity at 0x1a96dd0: '0'>)])> ignored Exception AttributeError: "'NoneType' object has no attribute 'ImmutableTypeError'" in <bound method FrozenOrderedDict.del of FrozenOrderedDict([('1', <StateIdentity at 0x1a96d90: '1'>), ('0', <StateIdentity at 0x1a96dd0: '0'>)])> ignored Exception AttributeError: "'NoneType' object has no attribute 'ImmutableTypeError'" in <bound method FrozenOrderedDict.del of FrozenOrderedDict()> ignored Exception AttributeError: "'NoneType' object has no attribute 'ImmutableTypeError'" in <bound method FrozenOrderedDict.del of FrozenOrderedDict([(0, <StateIdentity at 0x1a96d90: '1'>), (1, <StateIdentity at 0x1a96dd0: '0'>)])> ignored Exception AttributeError: "'NoneType' object has no attribute 'ImmutableTypeError'" in <bound method FrozenOrderedDict.del of FrozenOrderedDict()> ignored

jeetsukumaran commented 8 years ago

What version of Python are you running?

-- jeet

On 5/8/16 9:33 PM, Lily-WL wrote:

python -c "from dendropy.utility.container import FrozenOrderedDict; q = FrozenOrderedDict()"

Jeet Sukumaran

jeetsukumaran@gmail.com

Blog/Personal Pages: http://jeetworks.org/ GitHub Repositories: http://github.com/jeetsukumaran Photographs (as stream): http://www.flickr.com/photos/jeetsukumaran/ Photographs (by galleries):

http://www.flickr.com/photos/jeetsukumaran/sets/

Lily-WL commented 8 years ago

I am using DendroPy-4.0.3 now.

jeetsukumaran commented 8 years ago

I mean Python. I see it is 2.7. But what is its minor version.

Also, why are you using DendroPy 4.0.3?

Lily-WL commented 8 years ago

The version of Python is 2.7. Maybe meaning the 2.7.0, but "0" is omitted.

Previously I installed DendroPy-4.0.1 through pip installation. Later, because I want to execute "python setup.py test", I downloaded the 4.0.3 version and reinstalled.

jeetsukumaran commented 8 years ago

I don't think the issues you are facing having to do with the DendroPy version, but there have been lots of fixes and improvements since 4.0.3, and, just to be sure we are on the same page, maybe you should upgrade to the latest DendroPy.

 $ pip install --upgrade DendroPy

Is there any way you can try this in a new version of Python? The current version is 2.7.11. If you are indeed running 2.7.0, then that's a LOT of fixes. I am running 2.7.10, and cannot reproduce this error.

On 5/8/16 10:52 PM, Lily-WL wrote:

The version of Python is 2.7. Maybe meaning the 2.7.0, but "0" is omitted.

Previously I installed DendroPy-4.0.1 through pip installation. Later, because I want to execute "python setup.py test", I downloaded the 4.0.3 version and reinstalled.

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Jeet Sukumaran

jeetsukumaran@gmail.com

Blog/Personal Pages: http://jeetworks.org/ GitHub Repositories: http://github.com/jeetsukumaran Photographs (as stream): http://www.flickr.com/photos/jeetsukumaran/ Photographs (by galleries):

http://www.flickr.com/photos/jeetsukumaran/sets/

Lily-WL commented 8 years ago

Dear Sir,

Seems the error was gone after installation of Python2.7.10 and DendroPy-4.0.3.

Thank you very much for your support.