Damaged database?

[Adam Dershowitz]

On Feb 22, 2013, at 3:55 PM, Rainer Müller wrote:

> Hello,
> 
> On 2013-02-22 19:18, Adam Dershowitz wrote:
>> Error: org.macports.deactivate for port gst-plugins-base returned:
>> sqlite error: database disk image is malformed (11) while executing
>> query: SELECT actual_path FROM registry.files WHERE id=? AND active
>> ORDER BY actual_path
> 
> Your SQLite DB was probably in an inconsistent state when your computer
> had a problem. This means the data on disk is damaged and SQLite is
> unable to recover from this by itself.
> 
> Although it might require some time to rebuild some ports, the easiest
> of your options would be to wipe the installation and start from scratch.
> 
> First check the list of requested ports to get an idea what you have
> installed and write down anything important to you:
> 
>  port echo requested and active
> 
> Then follow the instructions given in the guide for uninstalling [1].
> Ignore the first step as you cannot properly run 'port uninstall' with a
> damaged database. Afterwards reinstall from the disk image [2] and
> reinstall any ports noted down previously.
> 
> Rainer
> 
> [1] http://guide.macports.org/#installing.macports.uninstalling
> [2] https://www.macports.org/install.php
> 

I just tried to restore my full /opt/local directory using timemachine from about two weeks ago.  If I then do a sync and try to upgrade gst-plugins-base, the same thing happens.  It first successfully upgrades a bunch of different things.  Finally, it gets to gst-plugins-base and gives the same error.  I also restored from about a month ago, and get the identical results.  I have done many upgrades during that time period.  So, it seems that there is something wrong in the sqlite database that just relates to gst-plugins-base.  And that it has been there for a while.  
Short of doing a full reinstall of all my ports, any other thoughts about how to repair that single entry?  I would think that all I really want to do is to delete the appropriate entries from the database and to do a corresponding forced uninstall of gst-plugins-base.  But, I am not sure how to get that to work.  
Any suggestions?  

Thanks much,

--Adam