[MacPorts] #25510: Python Crash

[MacPorts]

#25510: Python Crash
--------------------------------+-------------------------------------------
 Reporter:  raramayo@…          |       Owner:  mmoll@…           
     Type:  defect              |      Status:  new               
 Priority:  Normal              |   Milestone:                    
Component:  ports               |     Version:  1.9.1             
 Keywords:                      |        Port:  py26-biopython    
--------------------------------+-------------------------------------------

Comment(by raramayo@…):

 Obviously, I no longer have my 10.5 installation.[[BR]]

 Also, since this ticket was filed, what we believed to be the culprit,
 Biopython has been updated several times.[[BR]]
 Same can be said for Python 2.6.
 Testing for this bug using:[[BR]]
 MacPorts Python Version: Python 2.6.6[[BR]]

 Apple Python Version: Python 2.6.1[[BR]]
 I get the following:[[BR]]

 MacPorts Python[[BR]]
 /opt/local/bin/python[[BR]]

 38$ python
 Python 2.6.6 (r266:84292, May  5 2011, 11:21:18) [[BR]]
 [GCC 4.2.1 (Apple Inc. build 5664)] on darwin[[BR]]
 Type "help", "copyright", "credits" or "license" for more
 information.[[BR]]
 >>> help()[[BR]]

 Welcome to Python 2.6!  This is the online help utility.[[BR]]

 If this is your first time using Python, you should definitely check
 out[[BR]]
 the tutorial on the Internet at http://docs.python.org/tutorial/.[[BR]]

 Enter the name of any module, keyword, or topic to get help on
 writing[[BR]]
 Python programs and using Python modules.  To quit this help utility
 and[[BR]]
 return to the interpreter, just type "quit".[[BR]]

 To get a list of available modules, keywords, or topics, type
 "modules",[[BR]]
 "keywords", or "topics".  Each module also comes with a one-line
 summary[[BR]]
 of what it does; to list the modules whose summaries contain a given
 word[[BR]]
 such as "spam", type "modules spam".[[BR]]

 help> modules[[BR]]

 Please wait a moment while I gather a list of all available
 modules...[[BR]]

 /opt/local/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6
 /site-packages/Bio/Clustalw/__init__.py:34: [[BR]]
 BiopythonDeprecationWarning: Bio.Clustalw is deprecated. Please use the
 Bio.AlignIO framework for alignment parsing, and the ClustalW command
 [[BR]]
 line wrapper in Bio.Align.Applications for calling the tool. These are
 both described in the current version of the Biopython Tutorial and [[BR]]
 Cookbook.[[BR]]

   warnings.warn("Bio.Clustalw is deprecated. Please use the Bio.AlignIO
 framework for alignment parsing, and the ClustalW command line wrapper
 [[BR]]
 in Bio.Align.Applications for calling the tool. These are both described
 in the current version of the Biopython Tutorial and Cookbook.", [[BR]]
 Bio.BiopythonDeprecationWarning)[[BR]]

 /opt/local/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6
 /site-packages/Bio/InterPro/__init__.py:25: [[BR]]
 BiopythonDeprecationWarning: Bio.InterPro is deprecated, and will be
 removed in a future release of Biopython. Please get in contact via the
 [[BR]]
 mailing lists if this is a problem for you.[[BR]]
   "lists if this is a problem for you.",
 Bio.BiopythonDeprecationWarning)[[BR]]

 /opt/local/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6
 /site-packages/Bio/Parsers/__init__.py:11: BiopythonDeprecationWarning:
 [[BR]]
 Bio.Parsers (including our copy of SPARK) and the only part of Biopython
 which used it, Bio.GenBank.LocationParser, are now deprecated and will
 [[BR]]
 be removed in a future release of Biopython. If you want to continue to
 use any of this code, please get in contact with the Biopython [[BR]]
 developers via the mailing lists to avoid its permanent removal from
 Biopython.
   "Biopython.", Bio.BiopythonDeprecationWarning)[[BR]]

 ArgImagePlugin      WalImageFile        cmath
 pickletools[[BR]]
 ArrayPrinter        WmfImagePlugin      cmd                 pimp[[BR]]
 Audio_mac           XVThumbImagePlugin  code                pipes[[BR]]
 BaseHTTPServer      XbmImagePlugin      codecs
 pkg_resources[[BR]]
 ..........
 ..........[[BR]]

 IF HOWEVER I DO THIS IN[[BR]]
 Apple Python [[BR]]
 /usr/bin/python[[BR]]

 I get the following:[[BR]]
 blackeagle01:galaxy-python babieca$ python[[BR]]
 Python 2.6.1 (r261:67515, Jun 24 2010, 21:47:49) [[BR]]
 [GCC 4.2.1 (Apple Inc. build 5646)] on darwin[[BR]]
 Type "help", "copyright", "credits" or "license" for more
 information.[[BR]]
 >>> help()[[BR]]

 Welcome to Python 2.6!  This is the online help utility.[[BR]]

 If this is your first time using Python, you should definitely check
 out[[BR]]
 the tutorial on the Internet at http://docs.python.org/tutorial/.[[BR]]

 Enter the name of any module, keyword, or topic to get help on
 writing[[BR]]
 Python programs and using Python modules.  To quit this help utility
 and[[BR]]
 return to the interpreter, just type "quit".[[BR]]

 To get a list of available modules, keywords, or topics, type
 "modules",[[BR]]
 "keywords", or "topics".  Each module also comes with a one-line
 summary[[BR]]
 of what it does; to list the modules whose summaries contain a given
 word[[BR]]
 such as "spam", type "modules spam".[[BR]]

 help> modules[[BR]]

 Please wait a moment while I gather a list of all available
 modules...[[BR]]

 Audio_mac           _hashlib            formatter           quopri[[BR]]
 BaseHTTPServer      _heapq              fpformat            random[[BR]]
 ....[[BR]]
 ....[[BR]]

 Obviously this speaks bu itself...

 Thanks

-- 
Ticket URL: <https://trac.macports.org/ticket/25510#comment:8>
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