#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> MacPorts <http://www.macports.org/> Ports system for Mac OS