Probelms with DendroPy compiled with other software. about dendropy

[jeetsukumaran]

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]

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]

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]

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

[jeetsukumaran]

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]

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]

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, expected_metadata)
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 <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]

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, expected_metadata)
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
#50 (comment)

---

Jeet Sukumaran

[email protected]

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]

[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]

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

[email protected]

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]

I am using DendroPy-4.0.3 now.

[jeetsukumaran]

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]

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]

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.

—
You are receiving this because you commented.
Reply to this email directly or view it on GitHub
#50 (comment)

---

Jeet Sukumaran

[email protected]

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]

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.