Cannot deactivate port: this entry does not own the given file

[reuben@…]

I have upgraded from Mountain Lion to El Capitan and am migrating following the instructions at Migration. The one snag is that I cannot deactivate the old version of boost:

--->  Deactivating boost @1.58.0_3+no_single+no_static+python27
Error: org.macports.deactivate for port boost returned: this entry does not own the given file
Please see the log file for port boost for details:
    /opt/local/var/macports/logs/_opt_local_var_macports_registry_portfiles_boost-1.58.0_3_371b161d218eb8a2e929ef6264e243ab3f3b452084f057f14bbe95beb2d06919-12796/boost/main.log
Warning: Failed to execute portfile from registry for boost @1.58.0_3+no_single+no_static+python27

[reuben@…]

boost main.log

[ryandesign (Ryan Carsten Schmidt)]

Others have reported this error before, e.g. in #32700 and ​https://lists.macosforge.org/pipermail/macports-dev/2012-February/017837.html. In that mailing list post, the error was determined to be the result of a single-bit corruption.

[reuben@…]

This doesn't appear to be identical to the Feb 2012 mailing list post, which listed a specific file that could not be uninstalled because its name had been corrupted by one character. In this case there's no file name listed in the console output or the log file, and instead there is a complaint of an invalid registry entry.

It could be related to ticked #32700, although that ticket doesn't identify a cause or a solution.

[reuben@…]

In this case, I have checked that all the registry entries in "files" do exist.