It does happen anyway. I had that in to get around this issue a while ago (long story, but it is why we still run 8.2.10), and I still get the issue without it.
I think I have figured it out. The order the packages are installed is important. The code below illustrates the issue for me. If I install org-plus-contrib first, the issue goes away. Note the first thing the pydoc package does is:
(require 'org), which I guess interferes with subsequent building of org. (I am using GNU Emacs 25.1.50.1).
Also, you need to have (R . t) in there. that specifically triggers the error.
(setq user-emacs-directory "./sandbox/")
(require 'package)
(setq package-archives
(package-initialize)
(package-refresh-contents)
(package-install 'pydoc)
(package-install 'org-plus-contrib)
(org-babel-do-load-languages
'org-babel-load-languages
'((emacs-lisp . t)
(R . t)
))
(message "done")