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yum error "ImportError: No module named cElementTree" after proposed update

SchattenzeitAug 30 2013 — edited Sep 2 2013

Hello from Berlin!

I  have a problem after setting up a new machine, installing the database I made  an update (please scroll down for the updates I made).

Maybe "ImportError: No module named cElementTree" is the reason why  I can not use yum

anymore. New installation of the machine is the last option, cause the database is installed and 1,4 TB loaded.

I hope one of the specialists can help me  Thanks a lot!!

[oracle@hive01 unix]$ python --version

Python 2.6.6

[oracle@hive01 unix]$ uname -r
2.6.39-200.24.1.el6uek.x86_64


I got this error:

[root@stat89 oracle]# yum -y install ant

Plugin "refresh-packagekit" can't be imported

Loaded plugins: security

Traceback (most recent call last):

  File "/usr/bin/yum", line 29, in <module>

yummain.user_main(sys.argv[1:], exit_code=True)

  File "/usr/share/yum-cli/yummain.py", line 285, in user_main

errcode = main(args)

  File "/usr/share/yum-cli/yummain.py", line 136, in main

result, resultmsgs = base.doCommands()

  File "/usr/share/yum-cli/cli.py", line 434, in doCommands

self._getTs(needTsRemove)

  File "/usr/lib/python2.6/site-packages/yum/depsolve.py", line 99, in _getTs

self._getTsInfo(remove_only)

  File "/usr/lib/python2.6/site-packages/yum/depsolve.py", line 110, in _getTsInfo

pkgSack = self.pkgSack

  File "/usr/lib/python2.6/site-packages/yum/__init__.py", line 887, in <lambda>

pkgSack = property(fget=lambda self: self._getSacks(),

  File "/usr/lib/python2.6/site-packages/yum/__init__.py", line 669, in _getSacks

self.repos.populateSack(which=repos)

  File "/usr/lib/python2.6/site-packages/yum/repos.py", line 309, in populateSack

sack.populate(repo, mdtype, callback, cacheonly)

  File "/usr/lib/python2.6/site-packages/yum/yumRepo.py", line 165, in populate

if self._check_db_version(repo, mydbtype):

  File "/usr/lib/python2.6/site-packages/yum/yumRepo.py", line 223, in _check_db_version

return repo._check_db_version(mdtype)

  File "/usr/lib/python2.6/site-packages/yum/yumRepo.py", line 1256, in _check_db_version

repoXML = self.repoXML

  File "/usr/lib/python2.6/site-packages/yum/yumRepo.py", line 1455, in <lambda>

repoXML = property(fget=lambda self: self._getRepoXML(),

  File "/usr/lib/python2.6/site-packages/yum/yumRepo.py", line 1447, in _getRepoXML

self._loadRepoXML(text=self)

  File "/usr/lib/python2.6/site-packages/yum/yumRepo.py", line 1437, in _loadRepoXML

return self._groupLoadRepoXML(text, self._mdpolicy2mdtypes())

  File "/usr/lib/python2.6/site-packages/yum/yumRepo.py", line 1412, in _groupLoadRepoXML

if self._commonLoadRepoXML(text):

  File "/usr/lib/python2.6/site-packages/yum/yumRepo.py", line 1240, in _commonLoadRepoXML

self._repoXML = self._parseRepoXML(result)

  File "/usr/lib/python2.6/site-packages/yum/yumRepo.py", line 1036, in _parseRepoXML

return repoMDObject.RepoMD(self.id, local)

  File "/usr/lib/python2.6/site-packages/yum/repoMDObject.py", line 124, in __init__

self.parse(srcfile)

  File "/usr/lib/python2.6/site-packages/yum/repoMDObject.py", line 140, in parse

parser = iterparse(infile)

  File "/usr/lib/python2.6/site-packages/yum/misc.py", line 1141, in cElementTree_iterparse

_cElementTree_import()

  File "/usr/lib/python2.6/site-packages/yum/misc.py", line 1136, in _cElementTree_import

import cElementTree

ImportError: No module named cElementTree

[root@stat89 oracle]#

Changes I made:

[root@stat89 ~]# yum history

Plugin "refresh-packagekit" can't be imported

Loaded plugins: security

ID     | Login user               | Date and time    | Action(s)      | Altered

-------------------------------------------------------------------------------

     4 | System <unset>           | 2013-08-29 10:42 | Update         | 14

     3 | root <root>              | 2013-08-29 07:39 | I, U           | 19

     2 | root <root>              | 2013-08-29 07:36 | Install        | 1

     1 | System <unset>           | 2013-08-28 22:48 | Install        | 1199

Warning: RPMDB altered outside of yum.

history list

[root@stat89 ~]#

The last  change ,  I think change ID 4 is the reason why  I can not use yum anymore for Install:

[root@stat89 ~]# yum history info 4

Plugin "refresh-packagekit" can't be imported

Loaded plugins: security

Transaction ID : 4

Begin time     : Thu Aug 29 10:42:04 2013

Begin rpmdb    : 1212:0d0b575cedceac38df1b923bccaca9d0219b0fe0

End time       :            10:42:07 2013 (3 seconds)

End rpmdb      : 1212:15f89a764b5413ee12323e760aac7bc6d7b1b9a4 **

User           : System <unset>

Return-Code    : Success

Transaction performed with:

    Updated       rpm-4.8.0-27.el6.x86_64 @anaconda-OracleLinuxServer-201206261930.x86_64/6.3

    Updated       yum-3.2.29-30.0.1.el6.noarch @anaconda-OracleLinuxServer-201206261930.x86_64/6.3

    Installed     yum-metadata-parser-1.1.2-16.el6.x86_64 @anaconda-OracleLinuxServer-201206261930.x86_64/6.3

Packages Altered:

    Updated PackageKit-0.5.8-20.0.1.el6.x86_64 @anaconda-OracleLinuxServer-201206261930.x86_64/6.3

    Update             0.5.8-21.0.1.el6.x86_64                  @ol6_latest

    Updated PackageKit-device-rebind-0.5.8-20.0.1.el6.x86_64 @anaconda-OracleLinuxServer-201206261930.x86_64/6.3

    Update 0.5.8-21.0.1.el6.x86_64 @ol6_latest

    Updated PackageKit-glib-0.5.8-20.0.1.el6.x86_64 @anaconda-OracleLinuxServer-201206261930.x86_64/6.3

    Update                  0.5.8-21.0.1.el6.x86_64             @ol6_latest

    Updated PackageKit-gstreamer-plugin-0.5.8-20.0.1.el6.x86_64 @anaconda-OracleLinuxServer-201206261930.x86_64/6.3

    Update 0.5.8-21.0.1.el6.x86_64 @ol6_latest

    Updated PackageKit-gtk-module-0.5.8-20.0.1.el6.x86_64 @anaconda-OracleLinuxServer-201206261930.x86_64/6.3

    Update                        0.5.8-21.0.1.el6.x86_64       @ol6_latest

    Updated PackageKit-yum-0.5.8-20.0.1.el6.x86_64 @anaconda-OracleLinuxServer-201206261930.x86_64/6.3

    Update                 0.5.8-21.0.1.el6.x86_64              @ol6_latest

    Updated PackageKit-yum-plugin-0.5.8-20.0.1.el6.x86_64 @anaconda-OracleLinuxServer-201206261930.x86_64/6.3

    Update 0.5.8-21.0.1.el6.x86_64 @ol6_latest

    Updated rpm-4.8.0-27.el6.x86_64 @anaconda-OracleLinuxServer-201206261930.x86_64/6.3

    Update 4.8.0-32.el6.x86_64                             @ol6_latest

    Updated rpm-libs-4.8.0-27.el6.x86_64 @anaconda-OracleLinuxServer-201206261930.x86_64/6.3

    Update           4.8.0-32.el6.x86_64                        @ol6_latest

    Updated rpm-python-4.8.0-27.el6.x86_64 @anaconda-OracleLinuxServer-201206261930.x86_64/6.3

    Update             4.8.0-32.el6.x86_64                      @ol6_latest

    Updated yum-3.2.29-30.0.1.el6.noarch @anaconda-OracleLinuxServer-201206261930.x86_64/6.3

    Update 3.2.29-40.0.1.el6.noarch                        @ol6_latest

    Updated yum-plugin-security-1.1.30-14.el6.noarch @anaconda-OracleLinuxServer-201206261930.x86_64/6.3

    Update 1.1.30-14.0.1.el6.noarch @ol6_latest

    Updated yum-rhn-plugin-0.9.1-40.0.1.el6.noarch              @anaconda-OracleLinuxServer-201206261930.x86_64/6.3

    Update                 0.9.1-43.0.1.el6.noarch              @ol6_latest

    Updated yum-utils-1.1.30-14.el6.noarch @anaconda-OracleLinuxServer-201206261930.x86_64/6.3

    Update 1.1.30-14.0.1.el6.noarch                  @ol6_latest

history info

[root@stat89 ~]#
This post has been answered by LenzGrimmer on Aug 30 2013
Jump to Answer

Comments

dsurber-Oracle
Turn on logging at Level.FINE and get a trace of the exact JDBC methods called. Then see if you can create a pure JDBC test case. That will make it much easier to figure out what is going on. There's a JDBC logging white paper on the OTN JDBC/SQLJ home page.

Douglas
KeithWilliams
So this happened yesterday. All I did was start up tomcat and then try to execute this process and I got these errors. So today, for some unknown reason to me, I decided to repeat my steps. It worked today. Nothing has changed except the weather. So until I get a reproducible case I am going to move on.
14736
I've encountered the same issue with the 11g driver. It turned out the bug is a function of the size of the batch and the number of rows in the table being inserted into. A patch can be found in metalink with the id of 6396242.

-Mark
KeithWilliams
Yes, Oracle support just sent me the patch information on MetaLink.

Thanks, all.
KeithWilliams
I get the following error when applying the patch. Anyone know what causes this?

11:56:22.51>opatch apply
File Not Found
Invoking OPatch 11.1.0.6.0

Oracle Interim Patch Installer version 11.1.0.6.0
Copyright (c) 2007, Oracle Corporation. All rights reserved.


Oracle Home : F:\oracle\product\11.1.0\db_1
Central Inventory : C:\Program Files\Oracle\Inventory
from : n/a
OPatch version : 11.1.0.6.0
OUI version : 11.1.0.6.0
OUI location : F:\oracle\product\11.1.0\db_1\oui
Log file location : F:\oracle\product\11.1.0\db_1\cfgtoollogs\opatch\opatch2007-12-18_11-57-21AM.log

ApplySession applying interim patch '6396242' to OH 'F:\oracle\product\11.1.0\db_1'

Running prerequisite checks...
Prerequisite check "CheckActiveFilesAndExecutables" failed.
The details are:

Following files are active :
F:\oracle\product\11.1.0\db_1\jdbc\lib\ojdbc5.jar
F:\oracle\product\11.1.0\db_1\jdbc\lib\ojdbc5.jar
ApplySession failed during prerequisite checks: Prerequisite check "CheckActiveFilesAndExecutables" failed.
System intact, OPatch will not attempt to restore the system

OPatch failed with error code = 74
14736
Not sure if this is supported but you could just unpack the ojdbc5.jar and replace the class files with those that are included in the patch and then package it back up. I did it this way since I was patching the jar on a host that didn't have opatch/db installed.

Good luck,

-Mark
KeithWilliams
Lol, that's what I ended up doing also. :-)
199713
I can't get access to metalink.

Is a fixed version not available for download?

Thanks.
586088
I hit this same error when using the 11g jdbc driver against a 10g or 11g database.
If I use a 10g jdbc driver I don't get the error.

If I search the patch number, there is a patch supplied for the database server side.

Why isn't the patch for the jdbc driver that would be deployed at the client?
585768
Is there any way to get the patch if I do not have any account at MetaLink?
585768
I tried to apply the patch but am getting the following error:

mymc:/oracle/patch/6396242# su - oracle -bash-3.00$ /u01/oracle/product/11.1/OPatch/opatch apply Invoking OPatch 11.1.0.6.0

Oracle Interim Patch Installer version 11.1.0.6.0 Copyright (c) 2007, Oracle Corporation. All rights reserved.


Oracle Home : /u01/oracle/product/11.1
Central Inventory : /u01/oraInventory
from : /var/opt/oracle/oraInst.loc
OPatch version : 11.1.0.6.0
OUI version : 11.1.0.6.0
OUI location : /u01/oracle/product/11.1/oui
Log file location :
/u01/oracle/product/11.1/cfgtoollogs/opatch/opatch2008-04-21_11-10-36AM.log

ApplySession applying interim patch '6396242' to OH '/u01/oracle/product/11.1'

Running prerequisite checks...
Prerequisite check "CheckApplicable" failed.
The details are:
Patch 6396242: Required component(s) missing : [ oracle.dbjava.rsf, 10.2.0.4.0 ] ApplySession failed during prerequisite checks: Prerequisite check "CheckApplicable" failed.
System intact, OPatch will not attempt to restore the system

OPatch failed with error code 74

Can anyone help me in this regard?

Thanks in advance.
656666
I found that if I throw a random comment in the sql statement to force the driver to use a new statement for each batch it goes away.

Something along these lines...

StringBuilder builder = new StringBuilder("INSERT INTO /* ).append(Math.random()).append(" */ ( columns...) VALUES( values..)");

conn.prepareStatement(builder.toString());
668022
Does anyone know if there's a patch for the 10 driver series? I see this error on 10.2.0.4.0 and do not see a new driver version available.

Thanks,

Eric
674498
Hi all,

I'm getting the same (or similar) error:

java.lang.ArrayIndexOutOfBoundsException: -32403
at oracle.jdbc.driver.OraclePreparedStatement.setupBindBuffers(OraclePreparedStatement.java:2673)
at oracle.jdbc.driver.OraclePreparedStatement.executeBatch(OraclePreparedStatement.java:10723)

My driver is ojdbc14.jar, version is 10.2.0.4.0, just like the previous poster.

I'm also looking for a patch. Any pointers would be greatly appreciated.

Regards,
Erik
14736
Have you tried the latest 11.1.0.7 driver? http://www.oracle.com/technology/software/tech/java/sqlj_jdbc/htdocs/jdbc_111060.html

The readme indicates the patch was included for BUG-6396242.

http://www.oracle.com/technology/software/tech/java/sqlj_jdbc/htdocs/111070_readme.html

-Mark
705912
Hi I experience the same problem than Erik and the other.
I use the jdbc 10.2.0.4.0 to load data (actually serialised objects) from java to my oracle database.

Every times I go beyond 200 objects (which is nothing) I receive the same Exception, following a short version

ERROR [Thread-1] (LoaderTuplesNodes.java:345) - Error in thread: -32713
java.lang.ArrayIndexOutOfBoundsException: -32713
at oracle.jdbc.driver.OraclePreparedStatement.setupBindBuffers(OraclePreparedStatement.java:2673)
at oracle.jdbc.driver.OraclePreparedStatement.executeBatch(OraclePreparedStatement.java:10689)
at com.hp.hpl.jena.sdb.layout2.TupleLoaderBase.flush(TupleLoaderBase.java:200)
at com.hp.hpl.jena.sdb.layout2.TupleLoaderBase.finish(TupleLoaderBase.java:155)
at com.hp.hpl.jena.sdb.layout2.LoaderTuplesNodes.commitTuples(LoaderTuplesNodes.java:283)
at com.hp.hpl.jena.sdb.layout2.LoaderTuplesNodes.access$100(LoaderTuplesNodes.java:31)
at com.hp.hpl.jena.sdb.layout2.LoaderTuplesNodes$Commiter.run(LoaderTuplesNodes.java:318)
at java.lang.Thread.run(Unknown Source)
2009.06.09 14:59:27 Source1Wrapper extract ------
java.lang.ArrayIndexOutOfBoundsException: -32713
at oracle.jdbc.driver.OraclePreparedStatement.setupBindBuffers(OraclePreparedStatement.java:2673)
at oracle.jdbc.driver.OraclePreparedStatement.executeBatch(OraclePreparedStatement.java:10689)
at com.hp.hpl.jena.sdb.layout2.TupleLoaderBase.flush(TupleLoaderBase.java:200)
at com.hp.hpl.jena.sdb.layout2.TupleLoaderBase.finish(TupleLoaderBase.java:155)
at com.hp.hpl.jena.sdb.layout2.LoaderTuplesNodes.commitTuples(LoaderTuplesNodes.java:283)
at com.hp.hpl.jena.sdb.layout2.LoaderTuplesNodes.access$100(LoaderTuplesNodes.java:31)
at com.hp.hpl.jena.sdb.layout2.LoaderTuplesNodes$Commiter.run(LoaderTuplesNodes.java:318)
at java.lang.Thread.run(Unknown Source)
------

Is there any patch ? What should we (users of jdbc 1.4) do ?
thanks
142612
The 10g driver apparently keeps a global serial number for all parameters in the entire batch, with a "short" variable. So you can have at most 32768 parameters in the batch. I was having the same exception because I have a INSERT statement with 42 parameters and my batches can be as big as 1000 records, so 42000 > 32768 and this overflows to a negative index. I reduced the batch factor to 100 to be safe, and all is well. I guess your update DML should have a larger number of parameters per record, right? (My diagnostic of the bug is just deduction from the symptoms)
734271
I downloaded and installed Oracle 10g release 2 from the official website. The JDBC version is 10.2.0.1.0 which contains BUG-6396242. I want to upgrade the JDBC to version 11.1.0.7.0. However, it's from Oracle Database 11g Release 1. And I don't have the Metalink account. How can I upgrade it?
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Locked on Sep 30 2013
Added on Aug 30 2013
#linux, #oracle, #oracle-linux
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