Question: Pysqlite Problem At Installation
0
gravatar for Ross Lazarus
10.3 years ago by
Ross Lazarus30
Ross Lazarus30 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
galaxy • 929 views
ADD COMMENTlink modified 10.3 years ago by James Taylor320 • written 10.3 years ago by Ross Lazarus30
0
gravatar for James Taylor
10.3 years ago by
James Taylor320
United States
James Taylor320 wrote:
Hi Ross, Did you install pysqlite and sqlite in /usr/local yourself? This definitely looks like a linking problem. It appears in the python module, but the python module is trying to load that symbol from the sqlite library. Is that library being found? Try something like: james% ldd /usr/lib/python2.4/site-packages/_sqlite.so libsqlite.so.0 => /usr/lib/libsqlite.so.0 (0x00002aaaaabc2000) libpthread.so.0 => /lib/libpthread.so.0 (0x00002aaaaad1c000) libc.so.6 => /lib/libc.so.6 (0x00002aaaaae31000) /lib64/ld-linux-x86-64.so.2 (0x0000555555554000) Does it find a target for libsqlite.so? "sqlite3_enable_shared_cache" is only defined in sqlite 3.3.3 and later.
ADD COMMENTlink written 10.3 years ago by James Taylor320
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