/usr/local/src/xemacs/packages/src/xemacs-base-1.29-pkg.tar.gz ends up installing the package in that ../packages/src/ directory instead of ../xemacs-21.2.9/packages/ making the installed package unreachable. I believe ../packages/src/ was the current working directory when the package-admin-add-binary-package was executed but the command should have used a package hierarchy. The same thing happens when trying to use the package-ui. I had to install all of the packages by hand using tar.