org-ref invalid org-store-link in org babel

[stardiviner]

When I try to org-store-link in an opened org babel src block like this:

#+BEGIN_SRC clojure
(defn ) 
#+END_SRC

It should be work like this:

#+BEGIN_SRC clojure
(defn )                                                             (ref:hello)
#+END_SRC

But it failed with error:

 Debugger entered--Lisp error: (wrong-type-argument stringp nil)
   looking-at(nil)
   org-element-context()
   org-label-store-link()
   org-store-link(nil)
   ...
   funcall-interactively(org-store-link nil)
   call-interactively(org-store-link nil nil)
   command-execute(org-store-link)

I tried to edebug this, found related to org-ref. Then I confirmed with minimal Emacs config emacs -q -l minimal-init.el.

Emacs version: 26.0.50 build from master source code
Org-mode version: 9.0.6 install from MELPA
org-ref version: 1.0.0 (git-commit 10dc99582ba866fb825443d1bd2132920b9db39f)

[jkitchin]

I can't reproduce the error. (org-store-link) in a code block for me stores a reference to the heading the block is in. Where in org-ref did you find the problem to come from?

[stardiviner]

Did you open the src block with [C-c '] then org-store-link? It will create a code ref like (ref:<string you input>), Then you can org-inser-link ([C-c C-l]) to insert link to (ref:<string you input>). Instead of the heading that the block is in.

[stardiviner]

Have not found where the org-ref problem comes from, but I found if I toggle org-ref, then the error will occurs.

[jkitchin]

yes, that works fine for me. below, i opened the block, ran org-store-link and typed in hello. Then closed the block and used C-c C-l to insert the link.

#+BEGIN_SRC python
print(5)                                                            (ref:hello)
#+END_SRC

[[(hello)]]

[jagrg]

I think it's a bug in org-store-link. It works with the change below, but I'm not sure why it works with python, but not clojure. Maybe raise an issue in the Org-mode mailing list.

modified   lisp/org.el
@@ -9730,7 +9730,7 @@ active region."
 	     (setq sfuns
 		   (delq
 		    nil (mapcar (lambda (f)
-				  (let (fs) (if (funcall f) (push f fs))))
+				  (let (fs) (if (and (stringp f) (funcall f)) (push f fs))))
 				(org-store-link-functions)))
 		   sfunsn (mapcar (lambda (fu) (symbol-name (car fu))) sfuns))
 	     (or (and (cdr sfuns)

[stardiviner]

Confirmed, this patch works. @jagrg Can you send this patch to Org-mode Mailing List?

[jagrg]

I'm not on that list. If you are, please do.

…

On 08 May 2017, stardiviner ***@***.***> wrote: Confirmed, this patch works. @jagrg Can you send this patch to Org-mode Mailing List? — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub, or mute the thread.*

-- Jonathan

[stardiviner]

Ok, I will send this patch to mailing list. Thanks for this patch.

[jkitchin]

It was org-ref after all. I think I have pushed a fix for it. That patch should be unnecessary now. Thanks for reporting it and digging into it!

[jagrg]

Problem solved. Thanks. Pretty sure I dug the wrong hole. ;)

…

On 09 May 2017, John Kitchin ***@***.***> wrote: It was org-ref after all. I think I have pushed a fix for it. — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub, or mute the thread.*

-- Jonathan

[jkitchin]

it did eventually confirm org-ref was to blame ;)