Question: Pysqlite Problem At Installation
0
Ross Lazarus • 30 wrote:
Apologies if I missed this (I searched the trac...)
Centos 4.3, AMD 64 bit sun x4200 hardware.
Python 2.4.3
sqlite-3.3.8 (latest available)
pysqlite 2.3.2 (latest available at
http://initd.org/pub/software/pysqlite/releases/)
Short story - I get the following error when trying to build galaxy on
the above
system:
from pysqlite2._sqlite import *
ImportError: /usr/local/lib/python2.4/site-
packages/pysqlite2/_sqlite.so:
undefined symbol: sqlite3_enable_shared_cache
Longer story: that symbol appears to be in that _sqlite.so according
to grep:
[root@godzilla pysqlite-2.3.2]# grep _enable_shared_cache
/usr/local/lib/python2.4/site-packages/pysqlite2/_sqlite.so
Binary file /usr/local/lib/python2.4/site-
packages/pysqlite2/_sqlite.so matches
BUT, I get the same error if I use the python2.4 shell to try the same
from..import.
Any suggestions welcomed...
Full install log in case it helps follows below
[root@godzilla galaxy_dist]# sh run.sh
Architecture appears to be linux-x86_64
python path:
/home/rerla/src/galaxy_dist/modules:/home/rerla/src/galaxy_dist/eggs:/
home/rerla/src/galaxy_dist/arch/linux-x86_64/lib/python
Traceback (most recent call last):
File "paster.py", line 7, in ?
command.run()
File
"/home/rerla/src/galaxy_dist/eggs/PasteScript-1.0-py2.4.egg/paste/scri
pt/command.py",
line 76, in run
File
"/home/rerla/src/galaxy_dist/eggs/PasteScript-1.0-py2.4.egg/paste/scri
pt/command.py",
line 115, in invoke
File
"/home/rerla/src/galaxy_dist/eggs/PasteScript-1.0-py2.4.egg/paste/scri
pt/command.py",
line 210, in run
File
"/home/rerla/src/galaxy_dist/eggs/PasteScript-1.0-py2.4.egg/paste/scri
pt/serve.py",
line 184, in command
File
"/home/rerla/src/galaxy_dist/eggs/PasteScript-1.0-py2.4.egg/paste/scri
pt/serve.py",
line 204, in loadapp
File
"/home/rerla/src/galaxy_dist/eggs/PasteDeploy-1.0-py2.4.egg/paste/depl
oy/loadwsgi.py",
line 193, in loadapp
File
"/home/rerla/src/galaxy_dist/eggs/PasteDeploy-1.0-py2.4.egg/paste/depl
oy/loadwsgi.py",
line 214, in loadobj
File
"/home/rerla/src/galaxy_dist/eggs/PasteDeploy-1.0-py2.4.egg/paste/depl
oy/loadwsgi.py",
line 596, in create
File
"/home/rerla/src/galaxy_dist/eggs/PasteDeploy-1.0-py2.4.egg/paste/depl
oy/loadwsgi.py",
line 96, in invoke
File
"/home/rerla/src/galaxy_dist/eggs/PasteDeploy-1.0-py2.4.egg/paste/depl
oy/util/fixtypeerror.py",
line 57, in fix_call
File "/home/rerla/src/galaxy_dist/eggs/Paste-1.0-py2.4.egg/paste/ur
lmap.py",
line 24, in urlmap_factory
File
"/home/rerla/src/galaxy_dist/eggs/PasteDeploy-1.0-py2.4.egg/paste/depl
oy/loadwsgi.py",
line 281, in get_app
File
"/home/rerla/src/galaxy_dist/eggs/PasteDeploy-1.0-py2.4.egg/paste/depl
oy/loadwsgi.py",
line 596, in create
File
"/home/rerla/src/galaxy_dist/eggs/PasteDeploy-1.0-py2.4.egg/paste/depl
oy/loadwsgi.py",
line 99, in invoke
File
"/home/rerla/src/galaxy_dist/eggs/PasteDeploy-1.0-py2.4.egg/paste/depl
oy/util/fixtypeerror.py",
line 57, in fix_call
File "/home/rerla/src/galaxy_dist/universe_wsgi.py", line 17, in
app_factory
app = UniverseApplication( **kwargs )
File "/home/rerla/src/galaxy_dist/galaxy/app.py", line 19, in
__init__
create_tables = True )
File "/home/rerla/src/galaxy_dist/galaxy/model/mapping.py", line
81, in init
from pysqlite2 import dbapi2 as sqlite
File "/usr/local/lib/python2.4/site-packages/pysqlite2/dbapi2.py",
line 27, in ?
from pysqlite2._sqlite import *
ImportError: /usr/local/lib/python2.4/site-
packages/pysqlite2/_sqlite.so:
undefined symbol: sqlite3_enable_shared_cache
--
Ross Lazarus MBBS MPH, Director of Bioinformatics
Channing Laboratory, 181 Longwood Ave., Boston MA 02115, USA.
Voice: +617 525 2730 Fax: +617 525 0958
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modified 12.0 years ago
by
James Taylor • 320
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written
12.0 years ago by
Ross Lazarus • 30
