Clojure code evaluation in org-mode produces no output

Question

I am trying to run clojure code from my org file in order to do some literate programming.

What is not working:

When I execute the source code block I get No output produced.

Sample src code block

#+begin_src clojure
(+ 2 2)
#+end_src clojure

What is working:

1. cider-jack-in is working and I am able to execute code in the nREPL
2. I am able to execute code from a .clj file

Thanks

Details

Emacs 25.1 using Spacemacs

Org-Mode 9.0.5

Org babel configuration

(defun dotspacemacs/user-config ()
  (require 'ob)
  (require 'ob-clojure)
  (require 'paredit)
  (require 'org-babel-clojure)
  (setq org-babel-clojure-backend 'cider)
  (require 'cider)
  (org-babel-do-load-languages
   'org-babel-load-languages
   '((clojure . t)))
  )

Please let me know if you need any other information

Answer 1

I'm seeing he same issue. In a little digging, I think I've identified the problem. However, not sure who this should be reported to.

The problem is in the org-babel-execute:clojure function. This function has the following bit of code

(setq result
       (nrepl-dict-get
    (nrepl-sync-request:eval
     expanded (cider-current-connection) (cider-current-session))
    (if (or (member "output" result-params)
        (member "pp" result-params))
        "out"
      "value")))

The problem is in the call to nrepl-sync-request:eval. The documentation states for this function

(nrepl-sync-request:eval INPUT CONNECTION &optional NS)

Send the INPUT to the nREPL server synchronously. The request is dispatched via CONNECTION. If NS is non-nil, include it in the request.

Note the last optional argument NS. This is supposed to be a clojure namespace. However, the org-babel-execute:clojure function is calling this function with the output from cider-current-session, which returns a unique ID representing the current session. As a result, the call is returning a data structure with an error and no output (perhaps some error handling is required). The returned result is

(dict status (namespace-not-found done error done state state) id 17 session 43e9fd6c-82ed-49fe-9624-0cfc6f56f8b1 changed-namespaces (dict) repl-type cljclj)

Note the namespace-not-found

Either the argument should be a call to (cider-current-ns) or perhaps it should just be left out as I don't see how you can pass the namespace as part of the block evaluation.

EDIT: here is a simple patch which appears to fix the problem. Generated against current head of org git repo

---
 lisp/ob-clojure.el | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

diff --git a/lisp/ob-clojure.el b/lisp/ob-clojure.el
index d407105..e542a29 100644
--- a/lisp/ob-clojure.el
+++ b/lisp/ob-clojure.el
@@ -44,6 +44,7 @@

 (declare-function cider-current-connection "ext:cider-client" (&optional type))
 (declare-function cider-current-session "ext:cider-client" ())
+(declare-function cider-current-ns "ext:cider-client" ())
 (declare-function nrepl--merge "ext:nrepl-client" (dict1 dict2))
 (declare-function nrepl-dict-get "ext:nrepl-client" (dict key))
 (declare-function nrepl-dict-put "ext:nrepl-client" (dict key value))
@@ -118,7 +119,7 @@ using the :show-process parameter."
                org-babel-clojure-sync-nrepl-timeout))
               (nrepl-sync-request:eval expanded
                        (cider-current-connection)
-                       (cider-current-session))))
+                       (cider-current-ns))))
           (setq result
             (concat
              (nrepl-dict-get response
@@ -153,7 +154,7 @@ using the :show-process parameter."
        ;; Update the status of the nREPL output session.
        (setq status (nrepl-dict-get response "status")))
          (cider-current-connection)
-         (cider-current-session))
+         (cider-current-ns))

         ;; Wait until the nREPL code finished to be processed.
         (while (not (member "done" status))
-- 
2.7.4

Also sent the patch to the emacs-orgmode list

Answer 2

You need to have header arguments in the block telling org-babel what you want to include in the results produced - result of evaluation or output to stdout or both. In your case, there is no output that the evaluation of (+ 1 1) produces. Try (println (+ 1 1)).

#+name: Lazy Sequences in Clojure
#+begin_src clojure
 (def a-lazy-sequence (cons 1 (lazy-seq (cons (+1 2) ()))))
#+end_src

#+name: List comprehensions in Clojure
#+begin_src clojure :results output
 (println (str (for [x (range 3)
                     y #{:a :b :c}]
                 [x y])))

#+end_src

#+RESULTS: List comprehensions in Clojure
 : (c l o j u r e . l a n g . L a z y S e q @ e a a 0 1 c e 7)

Answer 3

Try

#+begin_src clojure :results value
(+ 2 2)
#+end_src clojure

which prints the returned value instead of output.

Answer 4

This problem is not necessarily specific to Spacemacs.

While the OP may have implicitly sought a solution within Spacemacs, this seems like a good place to mention another alternative (esp. for non-Spacemacs users who are experiencing the same problem after updating some piece of their emacs/org-mode configuration, which is what happened to me).

After trying many re-installs of various emacs and org versions, I finally found that Aquamacs (!) and Org 9.0.5 (downloaded as a tar.gz as instructed on http://orgmode.org/) succeeded in getting around the code block produced no output problem this poster also experienced.

While Aquamacs may not be a long-term solution for everybody, it certainly can help others who are highly dependent on using org-babel with clojure get around this problem until the above solution is fully recognized and implemented.

The version of emacs used by Aquamacs as of this March 9 2017 is:

Aquamacs 3.3 GNU Emacs 25.1.1 (x86_64-apple-darwin14.1.0, NS appkit-1344.72 Version 10.10.2 (Build 14C109)) of 2016-09-19 on 24a02dbf6b34ae061ef4df89f15bfbc5d3ed497e