M-x package-autoremove is blocked by system packages

Question

Emacs doesn't want to autoremove packages from elpa because some of them are system packages.

How can I launch autoremove ignoring system packages?

Error enabling Flyspell mode: (stringp nil)106 packages will be deleted: notmuch, ws-butler, winum, which-key, volatile-highlights, vi-tilde-fringe, uuidgen, use-package, undo-tree, toc-org, spinner, spaceline, smartparens, s, restart-emacs, request, rainbow-delimiters, projectile, powerline, popwin, popup, persp-mode, pcre2el, parent-mode, paradox, packed, org-bullets, open-junk-file, neotree, move-text, macrostep, lorem-ipsum, linum-relative, link-hint, info+, indent-guide, iedit, hydra, hungry-delete, hl-todo, highlight-parentheses, highlight-numbers, highlight-indentation, highlight, hide-comnt, help-fns+, helm-themes, helm-swoop, helm-projectile, helm-mode-manager, helm-make, helm-flx, helm-descbinds, helm-core, helm-ag, helm, goto-chg, google-translate, golden-ratio, flx-ido, flx, fill-column-indicator, fancy-battery, f, eyebrowse, expand-region, exec-path-from-shell, evil-visualstar, evil-visual-mark-mode, evil-unimpaired, evil-tutor, evil-surround, evil-search-highlight-persist, evil-numbers, evil-nerd-commenter, evil-mc, evil-matchit, evil-lisp-state, evil-indent-plus, evil-iedit-state, evil-exchange, evil-escape, evil-ediff, evil-args, evil-anzu, evil, eval-sexp-fu, elisp-slime-nav, dumb-jump, diminish, define-word, column-enforce-mode, clean-aindent-mode, bind-map, bind-key, avy, auto-highlight-symbol, auto-compile, auctex, async, anzu, aggressive-indent, adaptive-wrap, ace-window, ace-link, ace-jump-helm-line, proceed? (y or n) y

package-delete: Package ‘notmuch-0.26.2’ is a system package, not deleting

Answer 1

I would look at these two. Maybe you could modify package-selected-packages before running package-autoremove.

package-autoremove is an interactive autoloaded compiled Lisp function
in ‘package.el’.

(package-autoremove)

Remove packages that are no more needed.

Packages that are no more needed by other packages in
‘package-selected-packages’ and their dependencies
will be deleted.

[back]  [forward]

package-selected-packages is a variable defined in ‘package.el’.
Its value is
(abyss-theme company-irony company-irony-c-headers flycheck flycheck-irony irony rainbow-delimiters gandalf-theme alect-themes basic-mode elpy org-ac vbasense psvn omnisharp)

Original value was nil

Documentation:
Store here packages installed explicitly by user.
This variable is fed automatically by Emacs when installing a new package.
This variable is used by ‘package-autoremove’ to decide
which packages are no longer needed.
You can use it to (re)install packages on other machines
by running ‘package-install-selected-packages’.

To check if a package is contained in this list here, use
‘package--user-selected-p’, as it may populate the variable with
a sane initial value.

You can customize this variable.

This variable was introduced, or its default value was changed, in
version 25.1 of Emacs.

[back]

Here is the function definition in package.el

;;;###autoload
(defun package-autoremove ()
  "Remove packages that are no more needed.

Packages that are no more needed by other packages in
`package-selected-packages' and their dependencies
will be deleted."
  (interactive)
  ;; If `package-selected-packages' is nil, it would make no sense to
  ;; try to populate it here, because then `package-autoremove' will
  ;; do absolutely nothing.
  (when (or package-selected-packages
            (yes-or-no-p
             (format-message
              "`package-selected-packages' is empty! Really remove ALL packages? ")))
    (let ((removable (package--removable-packages)))
      (if removable
          (when (y-or-n-p
                 (format "%s packages will be deleted:\n%s, proceed? "
                   (length removable)
                   (mapconcat #'symbol-name removable ", ")))
            (mapc (lambda (p)
                    (package-delete (cadr (assq p package-alist)) t))
                  removable))
        (message "Nothing to autoremove")))))