Hi,
Chris was right --- when I built my Python 2.6 distribution on my iMac, it
didn't build bsddb nor gdbm. There is a file Modules/Setup in which you can
enable Python to be built with these modules.
The problem, however, is that these modules depend on other libraries on
your system, and I have great difficulties building these libraries from
scratch.
Has any of you tried using MacPorts for building and maintaining your open
source packages? Does it work well? I am hesitant to use fink because I keep
reading that fink breaks a lot of things.
Thanks,
Jenny
On Sun, May 3, 2009 at 12:54 PM, Christopher Lee <l...@chem.ucla.edu> wrote:
> Hi Jenny,
> this is a shelve problem, not a pygr.Data problem or a MySQLdb problem.
> The error message indicates that the shelve's iterator method failed, which
> caused Pygr to try a fall-back iterator method for gdbm (which handles the
> case where your Python install lacks a working bsddb module). But your
> shelve's dict is clearly not a gdbm index either (thus the attribute error).
> There are a couple possibilities here:
>
> - the question is why your shelve's iterator method fails. Please test
> creating a shelve, inserting a bunch of items, closing, re-opening, and
> trying iterating over the items (using iter(), e.g. for k in
> iter(myshelve):).
>
> - perhaps your Python 2.6 lacks a working bsddb? Sometimes it fails to
> compile right on Mac... try the following:
> import _bsddb
>
> - perhaps in the location that it is trying to open you have an old shelve
> file from an earlier version of python, which shelve is trying to open, and
> failing due to a version mismatch? Look for a file .pygr_data in that
> directory and delete it.
>
> -- Chris
>
>
>
>
> On May 2, 2009, at 11:54 PM, Jenny Qing Qian wrote:
>
> Hi Chris,
>>
>> I finally had MySQLdb installed on my new Mac. But, I ran into the
>> following pygr.Data problem:
>>
>> Python 2.6.2 (r262:71600, Apr 29 2009, 23:07:46)
>> [GCC 4.0.1 (Apple Inc. build 5490)] on darwin
>> Type "help", "copyright", "credits" or "license" for more information.
>> >>> import pygr.Data
>> >>> pygr.Data.dir('Bio')
>> Traceback (most recent call last):
>> File "<stdin>", line 1, in <module>
>> File "pygr/metabase.py", line 954, in dir
>> download=download))
>> File "pygr/metabase.py", line 821, in dir
>> download=download)
>> File "pygr/metabase.py", line 538, in dir
>> for name in self.db:
>> File "pygr/dbfile.py", line 81, in iter_gdbm
>> k = db.firstkey()
>> AttributeError: firstkey
>>
>> I thought it might have something to do with the MySQLdb, so I did the
>> following test:
>>
>> [bigmac:~/pygr/pygr] qing% python -i
>> Python 2.6.2 (r262:71600, Apr 29 2009, 23:07:46)
>> [GCC 4.0.1 (Apple Inc. build 5490)] on darwin
>> Type "help", "copyright", "credits" or "license" for more information.
>> >>> import MySQLdb
>> /Library/Frameworks/Python64.framework/Versions/2.6/lib/python2.6/site-packages/MySQL_python-1.2.2-py2.6-macosx-10.5-universal.egg/MySQLdb/__init__.py:34:
>> DeprecationWarning: the sets module is deprecated
>> from sets import ImmutableSet
>> >>> mydb = MySQLdb.Connect(db='test')
>> cursor = mydb.cursor()
>> >>> >>> stmt = "DROP TABLE IF EXISTS COLORS"
>> cursor.execute(stmt)>>>
>> __main__:1: Warning: Unknown table 'colors'
>> 0L
>> >>> stmt = """CREATE TABLE COLORS (
>> COLOR varchar(32) DEFAULT '' NOT NULL,
>> NCOLOR INT UNSIGNED NOT NULL AUTO_INCREMENT,
>> PRIMARY KEY (NCOLOR)
>> )"""... ... ... ...
>> >>> cursor.execute(stmt)
>> 0L
>> >>> colors = ( ('red',), ('blue',), ('yellow',), )
>> stmt = "INSERT INTO COLORS (COLOR) VALUES (%s)"
>> cursor.executemany(stmt, colors)
>> >>> >>> 3L
>> >>>
>> >>> stmt = "select NCOLOR, COLOR from COLORS"
>> cursor.execute(stmt)
>> resultSet = cursor.fetchall()
>> >>> 3L
>> >>> >>> for i, color in resultSet:
>> print "Color number",i,"is", color
>>
>> mydb.close()... ... Color number 1 is red
>> Color number 2 is blue
>> Color number 3 is yellow
>>
>> So, the MySQLdb module works fine.
>>
>> Have you seen this AttributeError:firstkey before?
>>
>> Thanks,
>> Jenny
>>
>
>
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