Forgot to mention that this problem occurs even without use-package usage.
(package-initialize)
(add-to-list 'package-archives
'("melpa" . "
https://melpa.org/packages/"))
(defun require-package (package)
"Ensures that PACKAGE is installed."
(unless (or (package-installed-p package)
(require package nil 'noerror))
(unless (assoc package package-archive-contents)
(package-refresh-contents))
(package-install package)))
(require-package 'slime)
(setq custom-file (locate-user-emacs-file "custom.el"))
(load custom-file 'noerror)