In my experience there are 4 step you may need to take to avoid this annoying message:
Remove the org package source in your emacs config.
Just remove the line
(add-to-list ' package-archives '("org" . "https://orgmode.org/elpa/") t)
org-* packages which status is
installed in your
You can use
/ s installed to filter all the installed packages in
list-package page. Careful, don't delete the
org package which status is
builtin, or you need to reinstall it later.
Delete the package cache in elpa cache directory, the default location is
~/.emacs.d/elpa/. Delete all files started with
If you are using native lisp compilation, delete the compiled caches, the default location is
After the 4 step, restart your emacs, the message should disappeared.
Additionally, if your install you package using
use-package you may want to pin the
org package to your GNU source like follow, then
use-package would try to download
org package only from the GNU source.