CentOS - Jul 2013 - Yum errors

Hi,

I have a machine that recently had some file system corruption. fsck was able
repair the file system but I am getting the following error when I try to
do yum update:

[Errno 21] Is a directory:
'/var/lib/yum/yumdb/e/2f883c08e3b596b66fcc19c6b4d73b11c9aaa43e-e2fsprogs-1.41.12-14.el6_4.2-x86_64/checksum_type'

In searching Google, some suggested renaming the yumdb but that just results
in a traceback when I run yum.

There are some files in lost+found but I am not sure what the above file
should look like and inode numbers are not useful to me.

Anyone have an idea how to fix this without reloading the machine?

Regards,

-- 
Tom			me at tdiehl.org		Spamtrap address	 		me123 at tdiehl.org

On 07/01/2013 03:36 PM, me at tdiehl.org wrote:
> Hi,
>
> I have a machine that recently had some file system corruption. fsck was
able
> repair the file system but I am getting the following error when I try to
> do yum update:
>
> [Errno 21] Is a directory:
'/var/lib/yum/yumdb/e/2f883c08e3b596b66fcc19c6b4d73b11c9aaa43e-e2fsprogs-1.41.12-14.el6_4.2-x86_64/checksum_type'
>
> In searching Google, some suggested renaming the yumdb but that just
results
> in a traceback when I run yum.
>
> There are some files in lost+found but I am not sure what the above file
> should look like and inode numbers are not useful to me.
>
> Anyone have an idea how to fix this without reloading the machine?
>
> Regards,
>
You can delete that file without too much problems, according to 
http://yum.baseurl.org/wiki/YumDB

-- 
Ljubomir Ljubojevic
(Love is in the Air)
PL Computers
Serbia, Europe

StarOS, Mikrotik and CentOS/RHEL/Linux consultant

On Mon, 1 Jul 2013, Reindl Harald wrote:
>
>
> Am 01.07.2013 15:36, schrieb me at tdiehl.org:
>> I have a c6.4 machine that recently had some file system corruption.
fsck was able
>> repair the file system but I am getting the following error when I try
to
>> do yum update:
>>
>> [Errno 21] Is a directory:
'/var/lib/yum/yumdb/e/2f883c08e3b596b66fcc19c6b4d73b11c9aaa43e-e2fsprogs-1.41.12-14.el6_4.2-x86_64/checksum_type'
>>
>> In searching Google, some suggested renaming the yumdb but that just
results
>> in a traceback when I run yum
>
> you can do *without any issue*
>
> rm -rf /var/lib/yum/yumdb/*
> rm -rf /var/lib/yum/history/*
>
> and after *twice* "yum history new" there are no longer
tracebacks
> been there, done that on a *lot* of machines multiple times to
> get rid of this tons of old metadata with no benefit
Ok, I am still getting a traceback, obviously, the first traceback is expected
but the last one os not. Below is what I did:

(router pts4) # cd /var/lib/yum/
(router pts4) # rm -r history/ yumdb/
(router pts4) # ll
total 12
drwxr-xr-x. 3 root root 4096 May  6 11:31 repos
drwxr-xr-x. 3 root root 4096 Jun 29 14:14 rpmdb-indexes
-rw-r--r--. 1 root root   36 May  6 11:31 uuid
(router pts4) # yum history new
Loaded plugins: downloadonly, fastestmirror, 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 438, in doCommands
     return self.yum_cli_commands[self.basecmd].doCommand(self, self.basecmd,
self.extcmds)
   File "/usr/share/yum-cli/yumcommands.py", line 1503, in doCommand
     ret = self._hcmd_new(base, extcmds)
   File "/usr/share/yum-cli/yumcommands.py", line 1423, in _hcmd_new
     base.history._create_db_file()
   File "/usr/lib/python2.6/site-packages/yum/history.py", line 1645,
in _create_db_file
     cur.execute(op)
sqlite3.OperationalError: table trans_beg already exists
(router pts4) # yum history new
Loaded plugins: downloadonly, fastestmirror, security
history new
(router pts4) # yum update
Loaded plugins: downloadonly, fastestmirror, security
Loading mirror speeds from cached hostfile
  * elrepo: elrepo.org
Setting up Update Process
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 438, in doCommands
     return self.yum_cli_commands[self.basecmd].doCommand(self, self.basecmd,
self.extcmds)
File "/usr/share/yum-cli/yumcommands.py", line 232, in doCommand
     return base.updatePkgs(extcmds, update_to=(basecmd == 'update-to'))
   File "/usr/share/yum-cli/cli.py", line 725, in updatePkgs
     self.update()
   File "/usr/lib/python2.6/site-packages/yum/__init__.py", line 3735,
in update
     updates = self.up.getUpdatesTuples()
   File "/usr/lib/python2.6/site-packages/yum/__init__.py", line 906,
in <lambda>
     up = property(fget=lambda self: self._getUpdates(),
   File "/usr/lib/python2.6/site-packages/yum/__init__.py", line 726,
in _getUpdates
     self._up = rpmUtils.updates.Updates(self.rpmdb.simplePkgList(),
self.pkgSack.simplePkgList())
   File "/usr/lib/python2.6/site-packages/yum/rpmsack.py", line 502,
in simplePkgList
     return self.pkglist
   File "/usr/lib/python2.6/site-packages/yum/rpmsack.py", line 232,
in _get_pkglist
     csumpkgtups = self.preloadPackageChecksums(load_packages=False)
   File "/usr/lib/python2.6/site-packages/yum/rpmsack.py", line 979,
in preloadPackageChecksums
     rpmdbv = self.simpleVersion(main_only=True)[0]
   File "/usr/lib/python2.6/site-packages/yum/rpmsack.py", line 1163,
in simpleVersion
     self._put_cached_simpleVersion_main(main)
   File "/usr/lib/python2.6/site-packages/yum/rpmsack.py", line 1112,
in _put_cached_simpleVersion_main
     os.rename(rpmdbvfname + ".tmp", rpmdbvfname)
OSError: [Errno 21] Is a directory
(router pts4) #

As you can see, I am still getting the traceback.

I also ran the following to be sure I was not missing something else:
(router pts4) # rpm -qf /var/lib/yum
yum-3.2.29-40.el6.centos.noarch
(router pts4) # rpm -V yum
(router pts4) #

Any ideas what I am missing?

Regards,

-- 
Tom			me at tdiehl.org		Spamtrap address	 		me123 at tdiehl.org

On Mon, 1 Jul 2013, Reindl Harald wrote:
>
>
> Am 01.07.2013 15:36, schrieb me at tdiehl.org:
>> I have a machine that recently had some file system corruption. fsck
was able
>> repair the file system but I am getting the following error when I try
to
>> do yum update:
>>
>> [Errno 21] Is a directory:
'/var/lib/yum/yumdb/e/2f883c08e3b596b66fcc19c6b4d73b11c9aaa43e-e2fsprogs-1.41.12-14.el6_4.2-x86_64/checksum_type'
>>
>> In searching Google, some suggested renaming the yumdb but that just
results
>> in a traceback when I run yum
>
> you can do *without any issue*
>
> rm -rf /var/lib/yum/yumdb/*
> rm -rf /var/lib/yum/history/*
>
> and after *twice* "yum history new" there are no longer
tracebacks
> been there, done that on a *lot* of machines mutiple times to
> get rid of this tons of old metadata with no benefit
>
>
After doing a little more poking around, I moved /var/lib/yum/rpmdb-indexes
out of the way and the issue seems to be solved. Yum seems to have recreated
that directory and appears happy now.

Does anyone know of a downside to doing this?

Regards,

-- 
Tom			me at tdiehl.org		Spamtrap address	 		me123 at tdiehl.org