Emacs Error: Invalid function: org-babel-header-args-safe-fn

Possible Cause

This problem is highly possible to be caused by this settings in init files:

;;auto load languages
(org-babel-do-load-languages
 'org-babel-load-languages
 '(
   (sh . t)
   (python . t)
   (R . t)
   (ruby . t)
   (ditaa . t)
   (dot . t)
   (octave . t)
   (sqlite . t)
   (perl . t)
   (C . t)
   ))

There are many people who encountered with exactly the same problem because of org and org-plus-contrib. So I thought this could be the root cause. But shortly it was found that I didn’t have org-plus-contrib at all. So the real cause remained unclear. I would appreciate it if you are willing to share what you find about this error in comments.

Solution

You can simply comment this configuration out to get rid of the launch error. The final solution is provided in this email.

The upshot was run M-x byte-compile-file on file ob-R.el.

If you don’t know where the file ob-R.el is, just search in your emacs configuration folder. After compiled, if everything goes fine, the error should have go away.

However, some may encounter new errors while compiling. Refer to this email for a temporary fix. In case the link could be expired, I copied the email contents here:

Unfortunately I now can’t reproduce the problem, so I can’t check if my suggestion to byte compile ob-R.el works or not. When I did observe the issue you describe that seemed to fix it, and at least one other person confirmed that it worked for them as well.

Since it doesn’t work for you I suggest removing org-plus-contrib (or org), starting emacs with emacs -Q and running something like

(require 'package)
(add-to-list 'package-archives
             '("org" . "http://orgmode.org/elpa/";) t)
(package-initialize)
(package-install 'org-plus-contrib)
;; or (package-install 'org)

Best,

Ista