Damaged database?

[Adam Dershowitz]

I had a computer problem, and did a restore of my harddrive.  I then reinstalled xcode and macports and all seemed fine.  Since then I have done a few upgrades of my ports with no problems.

Now, I started getting a sqlite error.  Any suggestions for what I can do about it?  Here is the error:


$port outdated
The following installed ports are outdated:
gst-plugins-base               0.10.36_2 < 0_0  (epoch 0 < 1)  
webkit-gtk                     1.10.2_1 < 1.10.2_2       
wine-devel                     1.5.24_0 < 1.5.24_1   


$sudo port -u upgrade outdated
--->  gst-plugins-base is replaced by gstreamer010-gst-plugins-base
--->  Deactivating gst-plugins-base @0.10.36_2+universal
--->  Unable to deactivate gst-plugins-base @0.10.36_2+universal, the following ports depend on it:
--->  	webkit-gtk @1.10.2_1+video
--->  	wine-devel @1.5.24_0
Warning: Deactivate forced.  Proceeding despite dependencies.
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
Please see the log file for port gst-plugins-base for details:
    /opt/local/var/macports/logs/_opt_local_var_macports_registry_portfiles_gst-plugins-base_0.10.36_2+universal/gst-plugins-base/main.log
Warning: Failed to execute portfile from registry for gst-plugins-base @0.10.36_2+universal
--->  Deactivating gst-plugins-base @0.10.36_2+universal
--->  Unable to deactivate gst-plugins-base @0.10.36_2+universal, the following ports depend on it:
--->  	webkit-gtk @1.10.2_1+video
--->  	wine-devel @1.5.24_0
Warning: Deactivate forced.  Proceeding despite dependencies.
Error: Deactivating gst-plugins-base @0.10.36_2+universal failed: 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
To report a bug, follow the instructions in the guide:
    http://guide.macports.org/#project.tickets


And here is what is in the log file:
version:1
:debug:main Executing org.macports.main (gst-plugins-base)
:debug:deactivate deactivate phase started at Fri Feb 22 10:11:33 PST 2013
:debug:deactivate Executing org.macports.deactivate (gst-plugins-base)
:msg:deactivate --->  Deactivating gst-plugins-base @0.10.36_2+universal
:msg:deactivate --->  Unable to deactivate gst-plugins-base @0.10.36_2+universal, the following ports depend on it:
:msg:deactivate --->    webkit-gtk @1.10.2_1+video
:msg:deactivate --->    wine-devel @1.5.24_0
:warn:deactivate Deactivate forced.  Proceeding despite dependencies.
:error:deactivate 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
:debug:deactivate Error code: registry::sqlite-error
:debug:deactivate Backtrace: 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
    while executing
"$requested files"
    (procedure "portimage::deactivate" line 54)
    invoked from within
"registry_deactivate $subport $version $revision $portvariants [array get user_options]"
    (procedure "portdeactivate::deactivate_main" line 3)
    invoked from within
"$procedure $targetname"
:info:deactivate Warning: targets not executed for gst-plugins-base: org.macports.deactivate
:notice:deactivate Please see the log file for port gst-plugins-base for details:
    /opt/local/var/macports/logs/_opt_local_var_macports_registry_portfiles_gst-plugins-base_0.10.36_2+universal/gst-plugins-base/main.log



--Adam