[MacPorts] #25510: Python Crash running 'modules' with py26-biopython installed
MacPorts
noreply at macports.org
Wed Jul 6 09:05:37 PDT 2011
#25510: Python Crash running 'modules' with py26-biopython installed
--------------------------------+-------------------------------------------
Reporter: raramayo@… | Owner: mmoll@…
Type: defect | Status: new
Priority: Normal | Milestone:
Component: ports | Version: 1.9.1
Keywords: | Port: py26-biopython
--------------------------------+-------------------------------------------
Comment(by raramayo@…):
I have now tested two computers:
Computer A : MacPorts Python 2.6.7, py26-biopython @1.57_0
Computer B : Apple Python 2.6.1, biopython-1.57
I have attached the copy of the logs for each test
Both computers passed the test
Python did not crashed as before
Close the ticket
----
Computer A
64$ python --version
Python 2.6.7
65$ which python
/opt/local/bin/python
66$ python --version
Python 2.6.7
67$ python
Python 2.6.7 (r267:88850, Jul 5 2011, 12:47:20)
[GCC 4.2.1 (Apple Inc. build 5666) (dot 3)] on darwin
Type "help", "copyright", "credits" or "license" for more information.
>>> help()
Welcome to Python 2.6! This is the online help utility.
If this is your first time using Python, you should definitely check out
the tutorial on the Internet at http://docs.python.org/tutorial/.
Enter the name of any module, keyword, or topic to get help on writing
Python programs and using Python modules. To quit this help utility and
return to the interpreter, just type "quit".
To get a list of available modules, keywords, or topics, type "modules",
"keywords", or "topics". Each module also comes with a one-line summary
of what it does; to list the modules whose summaries contain a given word
such as "spam", type "modules spam".
help> modules
Please wait a moment while I gather a list of all available modules...
/opt/local/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6
/site-packages/Bio/Clustalw/__init__.py:34: BiopythonDeprecationWarning:
Bio.Clustalw is deprecated. Please use the Bio.AlignIO framework for
alignment parsing, and the ClustalW command line wrapper in
Bio.Align.Applications for calling the tool. These are both described in
the current version of the Biopython Tutorial and Cookbook.
warnings.warn("Bio.Clustalw is deprecated. Please use the Bio.AlignIO
framework for alignment parsing, and the ClustalW command line wrapper in
Bio.Align.Applications for calling the tool. These are both described in
the current version of the Biopython Tutorial and Cookbook.",
Bio.BiopythonDeprecationWarning)
/opt/local/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6
/site-packages/Bio/InterPro/__init__.py:25: BiopythonDeprecationWarning:
Bio.InterPro is deprecated, and will be removed in a future release of
Biopython. Please get in contact via the mailing lists if this is a
problem for you.
"lists if this is a problem for you.", Bio.BiopythonDeprecationWarning)
/opt/local/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6
/site-packages/Bio/Parsers/__init__.py:11: BiopythonDeprecationWarning:
Bio.Parsers (including our copy of SPARK) and the only part of Biopython
which used it, Bio.GenBank.LocationParser, are now deprecated and will 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 developers via
the mailing lists to avoid its permanent removal from Biopython.
"Biopython.", Bio.BiopythonDeprecationWarning)
ArgImagePlugin XVThumbImagePlugin collections pimp
ArrayPrinter XbmImagePlugin colorsys pipes
Audio_mac XpmImagePlugin commands pkg_resources
BaseHTTPServer _AE compileall pkgutil
Bastion _AH compiler platform
BdfFontFile _App contextlib plistlib
Bio _CF cookielib popen2
BioSQL _CG copy poplib
BmpImagePlugin _CarbonEvt copy_reg posix
BufrStubImagePlugin _Cm crypt posixfile
CGIHTTPServer _Ctl csv posixpath
Canvas _Dlg ctypes pprint
Carbon _Drag curses profile
CodeWarrior _Evt datetime pstats
ColorPicker _File dbhash psyco_full
ConfigParser _Fm dbm pty
ContainerIO _Folder decimal pwd
Cookie _Help decorator py
CurImagePlugin _IBCarbon difflib py7zlib
DcxImagePlugin _Icn dircache pyHnj
Dialog _LWPCookieJar dis py_compile
DocXMLRPCServer _Launch distutils pyclbr
EasyDialogs _List doctest pydoc
EpsImagePlugin _Menu dotblas pydoc_topics
ExifTags _Mlte drv_libxml2 pyexpat
Explorer _MozillaCookieJar dumbdbm pygraphviz
FFT _OSA dummy_thread pylzma
FileDialog _Qd dummy_threading quopri
Finder _Qdoffs easy_install random
FitsStubImagePlugin _Qt elementtree ranlib
FixTk _Res email re
FliImagePlugin _Scrap encodings readline
FontFile _Snd errno reportlab
FpxImagePlugin _TE exceptions repr
FrameWork _Win fcntl resource
GbrImagePlugin __builtin__ filecmp rexec
GdImageFile __future__ fileinput rfc822
GifImagePlugin _abcoll findertools rlcompleter
GimpGradientFile _ast fnmatch robotparser
GimpPaletteFile _bisect formatter routes
Gnuplot _bsddb fpconst rpy2
GribStubImagePlugin _builtinSuites fpformat runpy
HTMLParser _bytesio fractions sched
Hdf5StubImagePlugin _codecs ftplib scipy
IN _codecs_cn functools select
IcnsImagePlugin _codecs_hk future_builtins sets
IcoImagePlugin _codecs_iso2022 galaxy setuptools
ImImagePlugin _codecs_jp galaxy_utils sgmllib
Image _codecs_kr gc sgmlop
ImageChops _codecs_tw gdbm sha
ImageCms _collections genericpath shelve
ImageColor _csv gensuitemodule shlex
ImageDraw _ctypes gestalt shutil
ImageDraw2 _ctypes_test getopt signal
ImageEnhance _curses getpass simplejson
ImageFile _curses_panel gettext site
ImageFileIO _dotblas glob smtpd
ImageFilter _elementtree grp smtplib
ImageFont _fileio gt sndhdr
ImageGL _functools gzip socket
ImageGrab _hashlib hashlib sqlalchemy
ImageMath _heapq heapq sqlite3
ImageMode _hotshot hgext sre
ImageOps _imaging hgsvn sre_compile
ImagePalette _imagingcms hmac sre_constants
ImagePath _imagingft hotshot sre_parse
ImageQt _imagingmath htmlentitydefs ssl
ImageSequence _imagingtk htmllib stat
ImageShow _json httplib statvfs
ImageStat _locale ic string
ImageTk _lsprof icglue stringold
ImageTransform _multibytecodec icopen stringprep
ImageWin _multiprocessing idlelib strop
ImtImagePlugin _numpy ihooks struct
IptcImagePlugin _random imaplib subprocess
JpegImagePlugin _renderPM imghdr sunau
LinearAlgebra _rl_accel imp sunaudio
MA _scproxy imputil symbol
MLab _socket inspect symtable
MacOS _sqlite3 io sys
Matrix _sre itertools syslog
McIdasImagePlugin _ssl json tabnanny
MicImagePlugin _strptime keyword tarfile
MimeWriter _struct lapack_lite telnetlib
MiniAEFrame _symtable lib2to3 tempfile
MpegImagePlugin _testcapi liblzma
terminalcommand
MspImagePlugin _threading_local libxml2 termios
Nav _tkinter libxml2mod test
Netscape _warnings linecache textwrap
Numeric _weakref locale this
Numeric_headers _xmlplus log_tempfile thread
OSATerminology abc logging threading
OleFileIO aepack lxml time
PIL aetools lzma timeit
PSDraw aetypes macerrors tkColorChooser
PaletteFile aifc macostools tkCommonDialog
PalmImagePlugin anydbm macpath tkFileDialog
PcdImagePlugin applesingle macresource tkFont
PcfFontFile appletrawmain macurl2path tkMessageBox
PcxImagePlugin appletrunner mailbox tkSimpleDialog
PdfImagePlugin argvemulator mailcap toaiff
PixMapWrapper array markupbase token
PixarImagePlugin arrayfns marshal tokenize
PngImagePlugin ast math trace
PpmImagePlugin asynchat md5 traceback
Precision asyncore mercurial tty
PsdImagePlugin atexit mhlib turtle
Queue audiodev mimeparse types
RNG audioop mimetools umath
RandomArray autoGIL mimetypes unicodedata
ScrolledText base64 mimify unittest
SgiImagePlugin bdb mmap urllib
SimpleDialog beaker modulefinder urllib2
SimpleHTTPServer bgenlocations multiarray urlparse
SimpleXMLRPCServer binascii multifile user
SocketServer binhex multiprocessing uu
SpiderImagePlugin bisect mutex uuid
StdSuites bsddb netrc videoreader
StringIO buildtools new warnings
SunImagePlugin bundlebuilder nis wave
SystemEvents bz2 nntplib weakref
TarIO cElementTree nose webbrowser
Terminal cPickle ntpath whichdb
TgaImagePlugin cProfile nturl2path wsgiref
TiffImagePlugin cStringIO numbers xdrlib
TiffTags cairo numeric_version xml
Tix calendar numpy xmllib
Tkconstants cfmfile opcode xmlrpclib
Tkdnd cgi operator xxsubtype
Tkinter cgitb optparse yaml
UserArray chunk os zipfile
UserDict cmath os2emxpath zipimport
UserList cmd parser zlib
UserString code pdb
WalImageFile codecs pickle
WmfImagePlugin codeop pickletools
Enter any module name to get more help. Or, type "modules spam" to search
for modules whose descriptions contain the word "spam".
help>
----
Computer B
genomics03:~ admin$ which python
/usr/bin/python
genomics03:~ admin$ python --version
Python 2.6.1
genomics03:~ admin$ python
Python 2.6.1 (r261:67515, Jun 24 2010, 21:47:49)
[GCC 4.2.1 (Apple Inc. build 5646)] on darwin
Type "help", "copyright", "credits" or "license" for more information.
>>> help()
Welcome to Python 2.6! This is the online help utility.
If this is your first time using Python, you should definitely check out
the tutorial on the Internet at http://docs.python.org/tutorial/.
Enter the name of any module, keyword, or topic to get help on writing
Python programs and using Python modules. To quit this help utility and
return to the interpreter, just type "quit".
To get a list of available modules, keywords, or topics, type "modules",
"keywords", or "topics". Each module also comes with a one-line summary
of what it does; to list the modules whose summaries contain a given word
such as "spam", type "modules spam".
help> modules
Please wait a moment while I gather a list of all available modules...
/System/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/pkgutil.py:110:
DeprecationWarning: twisted.flow is unmaintained.
__import__(name)
/System/Library/Frameworks/Python.framework/Versions/2.6/Extras/lib/python/twisted/python/filepath.py:12:
DeprecationWarning: the sha module is deprecated; use the hashlib module
instead
import sha
/System/Library/Frameworks/Python.framework/Versions/2.6/Extras/lib/python/twisted/words/im/__init__.py:8:
UserWarning: twisted.im will be undergoing a rewrite at some point in the
future.
warnings.warn("twisted.im will be undergoing a rewrite at some point in
the future.")
/Library/Python/2.6/site-packages/Bio/Clustalw/__init__.py:34:
BiopythonDeprecationWarning: Bio.Clustalw is deprecated. Please use the
Bio.AlignIO framework for alignment parsing, and the ClustalW command line
wrapper in Bio.Align.Applications for calling the tool. These are both
described in the current version of the Biopython Tutorial and Cookbook.
warnings.warn("Bio.Clustalw is deprecated. Please use the Bio.AlignIO
framework for alignment parsing, and the ClustalW command line wrapper in
Bio.Align.Applications for calling the tool. These are both described in
the current version of the Biopython Tutorial and Cookbook.",
Bio.BiopythonDeprecationWarning)
/Library/Python/2.6/site-packages/Bio/InterPro/__init__.py:25:
BiopythonDeprecationWarning: Bio.InterPro is deprecated, and will be
removed in a future release of Biopython. Please get in contact via the
mailing lists if this is a problem for you.
"lists if this is a problem for you.", Bio.BiopythonDeprecationWarning)
/Library/Python/2.6/site-packages/Bio/Parsers/__init__.py:11:
BiopythonDeprecationWarning: Bio.Parsers (including our copy of SPARK) and
the only part of Biopython which used it, Bio.GenBank.LocationParser, are
now deprecated and will 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 developers via the mailing lists to avoid its permanent
removal from Biopython.
"Biopython.", Bio.BiopythonDeprecationWarning)
2011-07-06 10:47:46.382 Python[23018:d07] Error loading
/Developer/Library/Frameworks/InterfaceBuilderKit.framework/InterfaceBuilderKit:
dlopen(/Developer/Library/Frameworks/InterfaceBuilderKit.framework/InterfaceBuilderKit,
265): Library not loaded:
@rpath/DevToolsRemoteClient.framework/Versions/A/DevToolsRemoteClient
Referenced from:
/Developer/Library/Frameworks/InterfaceBuilderKit.framework/InterfaceBuilderKit
Reason: image not found
/System/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/pkgutil.py:110:
DeprecationWarning: The wxPython compatibility package is no longer
automatically generated or actively maintained. Please switch to the wx
package as soon as possible.
__import__(name)
AddressBook _Win dumbdbm pwd
AppKit __builtin__ dummy_thread py2app
AppleScriptKit __future__ dummy_threading py_compile
Audio_mac _abcoll easy_install pyclbr
Automator _ast email pydoc
BaseHTTPServer _bisect encodings pydoc_topics
Bastion _builtinSuites errno pyexpat
Bio _bytesio exceptions quopri
BioSQL _codecs ez_setup random
CFNetwork _codecs_cn fcntl re
CGIHTTPServer _codecs_hk fetchmailconf readline
CalendarStore _codecs_iso2022 filecmp repr
Canvas _codecs_jp fileinput resource
Carbon _codecs_kr findertools rexec
Cocoa _codecs_tw fnmatch rfc822
CodeWarrior _collections formatter rlcompleter
Collaboration _csv fpformat robotparser
ColorPicker _ctypes fractions runpy
ConfigParser _ctypes_test ftplib sched
Cookie _curses functools select
CoreData _curses_panel future_builtins sets
CoreFoundation _elementtree gc setuptools
CoreGraphics _fileio genericpath sgmllib
CoreText _functools gensuitemodule sha
Dialog _hashlib gestalt shelve
DictionaryServices _heapq getopt shlex
DocXMLRPCServer _hotshot getpass shutil
EasyDialogs _json gettext signal
ExceptionHandling _locale glob site
Explorer _lsprof grp smtpd
FSEvents _multibytecodec gt smtplib
FileDialog _multiprocessing gzip sndhdr
Finder _random hashlib socket
FixTk _socket heapq sqlite3
Foundation _sqlite3 hmac sre
FrameWork _sre hotshot sre_compile
HTMLParser _ssl htmlentitydefs sre_constants
IN _strptime htmllib sre_parse
InputMethodKit _struct httplib ssl
InstallerPlugins _symtable ic stat
InstantMessage _testcapi icglue statvfs
InterfaceBuilderKit _threading_local icopen string
JavaScriptCore _tkinter idlelib stringold
LatentSemanticMapping _warnings ihooks stringprep
LaunchServices _weakref imageop strop
MacOS abc imaplib struct
Message aepack imghdr subprocess
MimeWriter aetools imp sunau
MiniAEFrame aetypes imputil sunaudio
Nav aifc inspect svn
Netscape altgraph io symbol
OSATerminology anydbm itertools symtable
OpenSSL applesingle json sys
PixMapWrapper appletrawmain keyword syslog
PreferencePanes appletrunner lib2to3 tabnanny
PubSub argvemulator libsvn tarfile
PyObjCTools array linecache telnetlib
PyRSS2Gen ast locale tempfile
QTKit asynchat logging
terminalcommand
Quartz asyncore macerrors termios
Queue atexit macholib test
ScreenSaver audiodev macostools textwrap
ScriptingBridge audioop macpath this
ScrolledText autoGIL macresource thread
SearchKit base64 macurl2path threading
SimpleDialog bdb mailbox time
SimpleHTTPServer bdist_mpkg mailcap timeit
SimpleXMLRPCServer bgenlocations markupbase tkColorChooser
SocketServer binascii marshal tkCommonDialog
StdSuites binhex math tkFileDialog
StringIO bisect md5 tkFont
SyncServices bonjour mhlib tkMessageBox
SystemConfiguration bsddb mimetools tkSimpleDialog
SystemEvents bsddb185 mimetypes toaiff
Tix buildtools mimify token
Tkconstants bundlebuilder mmap tokenize
Tkdnd bz2 modulefinder trace
Tkinter cPickle modulegraph traceback
UserDict cProfile multifile tty
UserList cStringIO multiprocessing turtle
UserString calendar mutex twisted
WebKit cfmfile netrc types
XgridFoundation cgi new unicodedata
_AE cgitb nis unittest
_AH chunk nntplib urllib
_App cmath ntpath urllib2
_CF cmd nturl2path urlparse
_CG code numbers user
_CarbonEvt codecs numpy uu
_Cm codeop objc uuid
_Ctl collections opcode videoreader
_Dlg colorsys operator warnings
_Drag commands optparse wave
_Evt compileall os weakref
_File compiler os2emxpath webbrowser
_Fm contextlib parser whichdb
_Folder cookielib pdb wsgiref
_Help copy pickle wx
_IBCarbon copy_reg pickletools wxPython
_Icn crypt pimp wxaddons
_LWPCookieJar csv pipes wxversion
_Launch ctypes pkg_resources xattr
_List curses pkgutil xdrlib
_Menu datetime platform xml
_Mlte dateutil plistlib xmllib
_MozillaCookieJar dbhash popen2 xmlrpclib
_OSA dbm poplib xxsubtype
_Qd decimal posix zipfile
_Qdoffs difflib posixfile zipimport
_Qt dircache posixpath zlib
_Res dis pprint zope
_Scrap distutils profile
_Snd dl pstats
_TE doctest pty
Enter any module name to get more help. Or, type "modules spam" to search
for modules whose descriptions contain the word "spam".
help>
--
Ticket URL: <https://trac.macports.org/ticket/25510#comment:12>
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