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  • Reproduce it and check what process is holding it open. Commented Jun 16 at 7:19
  • Added detail above. Commented Jun 18 at 4:27
  • Have you changed your hostname lately? If so, this was reported to GnuPG and dismissed as not-a-bug, sadly; it triggers what you're seeing after a hostname change. I can reproduce it too, and I'm testing some non-destructive fixes here. Will post an answer if it works. Commented Aug 9 at 22:15
  • I won't be able to test this anymore as I had to change the distro, but I'll describe what I've attempted as a fix. First of all, kill existing processes with gpgconf --kill all. Now, inside ~/.gnupg/public-keys.d you may find, in addition to the zombie lock-file, a few hidden files with strange names. If you read their filenames closer, you'll see that each of them has a hostname — your hostname — near the end of it. Some of them reference your current hostname, but others reference the old one. My suggestion is to delete the files containing your old hostname, and the lock-file. Commented Aug 11 at 1:40