I have the same experience. After patch rebuilding the repo everything 
works for me using Larry's suggestion of clean all then update.

  Thanks for the help.
  Joe

On 4/23/16 8:00 PM, P. Larry Nelson wrote:
> Forgot to say that one should do a 'yum clean all' and then
> 'yum update' works.
>
> - Larry
>
> P. Larry Nelson wrote on 4/23/16 9:49 PM:
>> Fixed!  Thanks Pat!
>>
>> - Larry
>>
>> Pat Riehecky wrote on 4/23/16 5:52 PM:
>>> Weird, the only change to the on April 21 was a security errata that 
>>> was
>>> published just like the rest.
>>>
>>> I'll rebuild the metadata across the board just to be safe.
>>>
>>> Pat
>>>
>>> On 04/23/2016 05:38 PM, P. Larry Nelson wrote:
>>>> I am having same problem with 3 of my SL5.x systems. One is 5.1 and 
>>>> two are 5.4.
>>>> All my other SL 5.x are 5.5 and have had no problems, nor have I 
>>>> seen this
>>>> problem with any of my SL6.x systems.
>>>>
>>>> The problem seems to be with sl-security repo.
>>>> If I do a 'yum update --disablerepo=sl-security' on the 5.1 and 5.4 
>>>> systems
>>>> I do NOT get the:
>>>>
>>>> Error: file is encrypted or is not a database
>>>>
>>>> This just started happening with the early morning auto yum update 
>>>> on 4/22/16.
>>>>
>>>> - Larry
>>>>
>>>> Joseph Areeda wrote on 4/23/16 4:35 PM:
>>>>> I see people are having the same problem with some of the version 
>>>>> 7 repos.
>>>>> But I
>>>>> don't understand how to figure out which repo is causing the 
>>>>> problem. Are
>>>>> people
>>>>> disabling star and enabling one at a time?
>>>>>
>>>>>  Thanks,
>>>>>  Joe
>>>>>
>>>>> On 4/23/16 1:53 PM, Joseph Areeda wrote:
>>>>>> We started getting this error couple of days ago machine that has 
>>>>>> been auto
>>>>>> updating for years. I would assume that it was a corruption of a 
>>>>>> local
>>>>>> database but it happened on two systems simultaneously.
>>>>>>
>>>>>>  Googling for that error message produces nothing on yum but 
>>>>>> several hits on's
>>>>>> SQLite.
>>>>>>
>>>>>>  I'd appreciate any insight into what the error means and how to 
>>>>>> track down
>>>>>> exactly which repo or file on my system is causing it the problem.
>>>>>>
>>>>>>  Below is what I see, yum update also produces the same error 
>>>>>> message.
>>>>>>
>>>>>>  Thanks,
>>>>>>  Joe
>>>>>>
>>>>>> [root@mavraki yum.repos.d]# yum clean all
>>>>>> Loaded plugins: fastestmirror, refresh-packagekit, security
>>>>>> Cleaning repos: CONDOR-stable VDT-Production-sl6 elrepo lscsoft-epel
>>>>>> lscsoft-pegasus lscsoft-production sl sl-security
>>>>>> Cleaning up Everything
>>>>>> Cleaning up list of fastest mirrors
>>>>>> [root@mavraki yum.repos.d]# yum repolist
>>>>>> Loaded plugins: fastestmirror, refresh-packagekit, security
>>>>>> Determining fastest mirrors
>>>>>>  * elrepo: elrepo.org
>>>>>>  * sl: ftp1.scientificlinux.org
>>>>>>  * sl-security: ftp1.scientificlinux.org
>>>>>> CONDOR-stable | 2.9 kB     00:00
>>>>>> CONDOR-stable/primary_db | 427 kB     00:00
>>>>>> VDT-Production-sl6 | 1.3 kB     00:00
>>>>>> VDT-Production-sl6/primary |  35 kB     00:00
>>>>>> VDT-Production-sl6 11/11
>>>>>> elrepo | 2.9 kB     00:00
>>>>>> elrepo/primary_db | 732 kB     00:00
>>>>>> lscsoft-epel | 2.7 kB     00:00
>>>>>> lscsoft-epel/primary_db | 4.2 MB     00:02
>>>>>> lscsoft-pegasus | 2.6 kB     00:00
>>>>>> lscsoft-pegasus/primary_db | 5.8 kB     00:00
>>>>>> lscsoft-production | 2.9 kB     00:00
>>>>>> lscsoft-production/primary_db | 301 kB     00:00
>>>>>> sl | 3.5 kB     00:00
>>>>>> sl/primary_db | 4.2 MB     00:03
>>>>>> sl-security | 3.0 kB     00:00
>>>>>> sl-security/primary_db |  12 MB     00:06
>>>>>> Error: file is encrypted or is not a database
>>>>>> [root@mavraki yum.repos.d]#
>>>>
>>>>
>>>
>>
>>
>
>