Bug In Yum When Attempting To Update

[BobCochran]

Hi,

Is this a big in yum? Does anyone recognize the cause and know how to fix it? The problem for me started yesterday when I logged in and noticed the automatic package update process was complaining it can't check for packages and I should check my network connections. So I tried running 'yum update' manually. I'm running CentOS 5.2, x86_64 as a Vmware virtual machine.

Here is the output:

# yum update
Loading "fastestmirror" plugin
Loading mirror speeds from cached hostfile
* base: mirrors.serveraxis.net
* updates: yum.singlehop.com
* addons: mirrors.liquidweb.com
* extras: wuarchive.wustl.edu

(process:4048): GLib-CRITICAL **: g_timer_stop: assertion `timer != NULL' failed

(process:4048): GLib-CRITICAL **: g_timer_destroy: assertion `timer != NULL' failed
Traceback (most recent call last):
File "/usr/bin/yum", line 29, in ?
yummain.main(sys.argv[1:])
File "/usr/share/yum-cli/yummain.py", line 105, in main
result, resultmsgs = base.doCommands()
File "/usr/share/yum-cli/cli.py", line 289, in doCommands
self._getTs()
File "/usr/lib/python2.4/site-packages/yum/depsolve.py", line 85, in _getTs
self._getTsInfo()
File "/usr/lib/python2.4/site-packages/yum/depsolve.py", line 91, in _getTsInfo
self._tsInfo.setDatabases(self.rpmdb, self.pkgSack)
File "/usr/lib/python2.4/site-packages/yum/__init__.py", line 537, in
pkgSack = property(fget=lambda self: self._getSacks(),
File "/usr/lib/python2.4/site-packages/yum/__init__.py", line 392, in _getSacks
self.repos.populateSack(which=repos)
File "/usr/lib/python2.4/site-packages/yum/repos.py", line 242, in populateSack
sack.populate(repo, mdtype, callback, cacheonly)
File "/usr/lib/python2.4/site-packages/yum/yumRepo.py", line 168, in populate
dobj = repo_cache_function(xml, csum)
File "/usr/lib64/python2.4/site-packages/sqlitecachec.py", line 42, in getPrimary
self.repoid))
TypeError: Can not create packages table: near "release": syntax error

My Yum version:

# rpm -q yum
yum-3.2.8-9.el5.centos.2.1

Help is much appreciated.

Thanks

Bob Cochran

[AlanBartlett]

Please try [b]yum --enablerepo=\* --disablerepo=c5-media clean all[/b].

If the above command executes without error, then try a [b]yum --disablerepo=\* --enablerepo=base --enablerepo=updates update[/b] command.

If an error is obtained with the second command, please post the error message and also the output from [b]yum repolist all[/b].

[BobCochran]

Thanks for your help! Unfortunately the second command didn't work. As a note, I recently compiled sqlite version 3.6.10 (installed into /usr/local/sqlite-3.6.10), but I've been installing sqlite versions in CentOS for a long time without ill effect. Also, I've been working with a Perl MVC framework named Catalyst. I recently installed Catalyst-Runtime-5.7015 and a large number of Perl dependencies through the CPAN archive.

# yum --enablerepo=\* --disablerepo=c5-media clean all
Loading "fastestmirror" plugin
Loading mirror speeds from cached hostfile
* base: mirrors.liquidweb.com
* updates: yum.singlehop.com
* centosplus: mirror.trouble-free.net
* addons: centos.luhost.info
* extras: wuarchive.wustl.edu
Cleaning up Everything
Cleaning up list of fastest mirrors
# yum --disablerepo=\* --enablerepo=base --enablerepo=updates update
Loading "fastestmirror" plugin
Determining fastest mirrors
* base: centos.cs.wisc.edu
* updates: centos.omnispring.com
base 100% |=========================| 1.1 kB 00:00
primary.xml.gz 100% |=========================| 1.1 MB 00:03

(process:4120): GLib-CRITICAL **: g_timer_stop: assertion `timer != NULL' failed

(process:4120): GLib-CRITICAL **: g_timer_destroy: assertion `timer != NULL' failed
Traceback (most recent call last):
File "/usr/bin/yum", line 29, in ?
yummain.main(sys.argv[1:])
File "/usr/share/yum-cli/yummain.py", line 105, in main
result, resultmsgs = base.doCommands()
File "/usr/share/yum-cli/cli.py", line 289, in doCommands
self._getTs()
File "/usr/lib/python2.4/site-packages/yum/depsolve.py", line 85, in _getTs
self._getTsInfo()
File "/usr/lib/python2.4/site-packages/yum/depsolve.py", line 91, in _getTsInfo
self._tsInfo.setDatabases(self.rpmdb, self.pkgSack)
File "/usr/lib/python2.4/site-packages/yum/__init__.py", line 537, in
pkgSack = property(fget=lambda self: self._getSacks(),
File "/usr/lib/python2.4/site-packages/yum/__init__.py", line 392, in _getSacks
self.repos.populateSack(which=repos)
File "/usr/lib/python2.4/site-packages/yum/repos.py", line 242, in populateSack
sack.populate(repo, mdtype, callback, cacheonly)
File "/usr/lib/python2.4/site-packages/yum/yumRepo.py", line 168, in populate
dobj = repo_cache_function(xml, csum)
File "/usr/lib64/python2.4/site-packages/sqlitecachec.py", line 42, in getPrimary
self.repoid))
TypeError: Can not create packages table: near "release": syntax error

Any suggestions?

Bob Cochran

[AlanBartlett]

[quote]I recently installed [i][/i] a large number of Perl dependencies through the CPAN archive.[/quote]
Ouch!

I'm sorry to say this but I suspect that your use of [i]CPAN[/i] has brought on this problem. The only advice I can offer is to suggest that you revert those additions and re-install the [i]CentOS[/i] perl packages from your installation medium . . .

I wonder if [b]toracat[/b] has a bright idea?

[Evolution]

This one is pretty clearly an sqlite issue. It's almost certainly due to having a newer version of sqlite interacting with the query structure or other bits.

The notable entries in the error which show this are here ->
TypeError: Can not create packages table: near "release": syntax error

Mostly that says that it can't create a table for the packages, and that the query syntax is wrong.
I'd guess that you've gotten away with doing this for a while now, but you were finally bitten by a change in sqlite.

It's not a bug in yum so much as it's a query structure conflict between two versions. The only way out of this I see for you is to nuke yum's cache, and remove the sqlite install that you built into /usr/local from your path. You can still use it, just call it directly when you need to. You'll have to maintain your install and the distro specific install.

[AlanBartlett]

Thanks for those words of wisdom and spotting the bit I missed [b]Jim[/b].

[ot]Did you get a new broom at Christmas? :-P [/ot]

[toracat]

[quote]
AlanJBartlett wrote:

[ot]Did you get a new broom at Christmas? :-P [/ot][/quote]
Yes, I sent him a bunch. CentOS floors should stay clean for a while. :-D

[AlanBartlett]

[quote]
toracat wrote:
[quote]
AlanJBartlett wrote:

[ot]Did you get a new broom at Christmas? :-P [/ot][/quote]
Yes, I sent him a bunch. CentOS floors should stay clean for a while. :-D[/quote]
[b][i]:roll: Egad![/i][/b]

[Evolution]

[quote]
AlanJBartlett wrote:
Thanks for those words of wisdom and spotting the bit I missed [b]Jim[/b].

[ot]Did you get a new broom at Christmas? :-P [/ot][/quote]

I'm all stocked up on brooms now. I've moved on to mops

I <3 mop!

[BobCochran]

[quote]
Evolution wrote:
This one is pretty clearly an sqlite issue. It's almost certainly due to having a newer version of sqlite interacting with the query structure or other bits.

The notable entries in the error which show this are here ->
TypeError: Can not create packages table: near "release": syntax error

Mostly that says that it can't create a table for the packages, and that the query syntax is wrong.
I'd guess that you've gotten away with doing this for a while now, but you were finally bitten by a change in sqlite.

It's not a bug in yum so much as it's a query structure conflict between two versions. The only way out of this I see for you is to nuke yum's cache, and remove the sqlite install that you built into /usr/local from your path. You can still use it, just call it directly when you need to. You'll have to maintain your install and the distro specific install.[/quote]

I'm not totally sure of what is happening but there seems to be a difference between sqlite-3.6.7 (installed on January 9) and sqlite-3.6.10 (installed on January 15) which is causing the problem. My habit is to install them to /usr/local/sqlite-x.x.xx where x is the version number, then edit /etc/ld.so.conf to point to the latest module. The version of sqlite installed by CentOS is 3.3.6 but I guess that even though /usr/local/sqlite-3.6.10 is not on the system's path, that code must be getting executed if I have ld.so.conf pointing to it?

In any case, changing ld.so.conf to point to /usr/local/sqlite-3.6.7 and then running `ldconfig` and then running `yum update` will allow yum to complete normally. Changing it back to /usr/local/sqlite-3.6.10 causes yum to break with the error I've been citing. See the output I'm getting below:

ls -al /usr/local
total 132
drwxr-xr-x 21 root root 4096 Jan 15 20:09 .
drwxr-xr-x 16 root root 4096 Feb 23 2008 ..
drwxr-xr-x 2 root root 4096 Mar 29 2007 bin
drwxr-xr-x 2 root root 4096 Mar 29 2007 etc
drwxr-xr-x 2 root root 4096 Mar 29 2007 games
drwxr-xr-x 2 root root 4096 Mar 29 2007 include
drwxr-xr-x 2 root root 4096 Mar 29 2007 lib
drwxr-xr-x 2 root root 4096 Mar 29 2007 lib64
drwxr-xr-x 2 root root 4096 Mar 29 2007 libexec
drwxr-xr-x 2 root root 4096 Mar 29 2007 sbin
drwxr-xr-x 4 root root 4096 Jul 22 2007 share
drwxr-xr-x 5 root root 4096 Jul 23 2007 sqlite-3.4.1
drwxr-xr-x 5 root root 4096 Nov 30 2007 sqlite-3.5.3
drwxr-xr-x 5 root root 4096 Dec 15 2007 sqlite-3.5.4
drwxr-xr-x 5 root root 4096 Feb 8 2008 sqlite-3.5.6
drwxr-xr-x 5 root root 4096 Apr 3 2008 sqlite-3.5.7
drwxr-xr-x 5 root root 4096 Apr 16 2008 sqlite-3.5.8
drwxr-xr-x 5 root root 4096 Jan 15 20:09 sqlite-3.6.10
drwxr-xr-x 5 root root 4096 Jan 9 19:45 sqlite-3.6.7
drwxr-xr-x 2 root root 4096 Mar 29 2007 src
drwxr-xr-x 6 root root 4096 Jan 10 2008 tt2
su -
Password:
]# gedit /etc/ld.so.conf

[Editorial note: change /etc/ld.so.conf to point to /usr/local/sqlite-3.6.7 here]

# ldconfig

[Editorial note: show SQLite version installed by CentOS]

# sqlite3
SQLite version 3.3.6
Enter ".help" for instructions
sqlite> .quit
# rpm -q sqlite
sqlite-3.3.6-2
sqlite-3.3.6-2

[Editorial note: try a yum update now]

# yum update
Loading "fastestmirror" plugin
Loading mirror speeds from cached hostfile
* base: mirror.skiplink.com
* updates: centos.omnispring.com
* addons: mirrors.unbornmedia.com
* extras: mirror.skiplink.com
base : ################################################## 3223/3223
updates 100% |=========================| 951 B 00:00
primary.xml.gz 100% |=========================| 427 kB 00:41
updates : ################################################## 944/944
addons 100% |=========================| 951 B 00:00
primary.xml.gz 100% |=========================| 157 B 00:00
extras 100% |=========================| 1.1 kB 00:00
primary.xml.gz 100% |=========================| 97 kB 00:00
extras : ################################################## 263/263
Setting up Update Process
No Packages marked for Update

Editorial note: change /etc/ld.so.conf to point to /usr/local/sqlite-3.6.10 here]

# gedit /etc/ld.so.conf
# ldconfig
# yum update
Loading "fastestmirror" plugin
Loading mirror speeds from cached hostfile
* base: centos.omnispring.com
* updates: centos.omnispring.com
* addons: mirrors.serveraxis.net
* extras: pubmirrors.reflected.net

(process:4434): GLib-CRITICAL **: g_timer_stop: assertion `timer != NULL' failed

(process:4434): GLib-CRITICAL **: g_timer_destroy: assertion `timer != NULL' failed
Traceback (most recent call last):
File "/usr/bin/yum", line 29, in ?
yummain.main(sys.argv[1:])
File "/usr/share/yum-cli/yummain.py", line 105, in main
result, resultmsgs = base.doCommands()
File "/usr/share/yum-cli/cli.py", line 289, in doCommands
self._getTs()
File "/usr/lib/python2.4/site-packages/yum/depsolve.py", line 85, in _getTs
self._getTsInfo()
File "/usr/lib/python2.4/site-packages/yum/depsolve.py", line 91, in _getTsInfo
self._tsInfo.setDatabases(self.rpmdb, self.pkgSack)
File "/usr/lib/python2.4/site-packages/yum/__init__.py", line 537, in
pkgSack = property(fget=lambda self: self._getSacks(),
File "/usr/lib/python2.4/site-packages/yum/__init__.py", line 392, in _getSacks
self.repos.populateSack(which=repos)
File "/usr/lib/python2.4/site-packages/yum/repos.py", line 242, in populateSack
sack.populate(repo, mdtype, callback, cacheonly)
File "/usr/lib/python2.4/site-packages/yum/yumRepo.py", line 168, in populate
dobj = repo_cache_function(xml, csum)
File "/usr/lib64/python2.4/site-packages/sqlitecachec.py", line 42, in getPrimary
self.repoid))
TypeError: Can not create packages table: near "release": syntax error

Editorial note: change /etc/ld.so.conf to point to /usr/local/sqlite-3.6.7 again]

# gedit /etc/ld.so.conf
# ldconfig
# yum update
Loading "fastestmirror" plugin
Loading mirror speeds from cached hostfile
* base: centos.omnispring.com
* updates: centos.omnispring.com
* addons: mirrors.serveraxis.net
* extras: pubmirrors.reflected.net
base : ################################################## 3223/3223
Setting up Update Process
No Packages marked for Update
#

Please feel free to set me straight if my practices are not accepted methods here. I can always learn more. I'm also going to post this information to the sqlite-users mailing list to see what they say.

Thanks again, everyone, for all your help!