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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

Drew
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Jeel Shah
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4 Answers4

10

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

Tim X
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  • So are you saying we should edit the function and replace it with `(cider-current-ns)`? And if so, where can I find that function? – Jeel Shah Mar 02 '17 at 15:39
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    I'm saying that to make ob-clojure work, either the call to (cider-current-session) needs to be dropped or it needs to be replaced with (cider-current-ns). The (cider-current-ns) is part of the cider library (along with cider-current-connection) and (cider-current-session)). Either you need to edit the function or wait until someone updates it upstream, but as it stands now, it does not work. I have reported this on the emacs-org list, but no response yet. – Tim X Mar 02 '17 at 20:10
  • Your solution is working perfectly. My `ob-clojure` was a bit older so I pulled the newest ones, made the relevant changes and it works! Thank you so much! I wish you had answered a few days before! I would definitely given the bounty to you. :) Thanks! – Jeel Shah Mar 03 '17 at 18:08
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    As of 3 Jun 2017, Emacs 25.1.1, org 9.0.7, spacemacs 0.200.9, this fix is still not in when I did a fresh clone of spacemacs develop branch and a wipe of my elpa directory. I still needed to purge org directories to get any code-block eval to work `find ~/.emacs.d/elpa/org* -name "*elc" -delete`, then manually apply the patch above. The good news is that the patch works today. – Reb.Cabin Jun 03 '17 at 15:20
  • To be honest, I don't understand the structure of the org git branches and how they relate to the org-plus-contrib package. I know the patch was committed into the main org repository because I did a pull and say the commit. No idea how such patches get into the package files. – Tim X Jun 09 '17 at 02:17
  • Not sure exactly what has changed here, but the above patch was added to the main org branch on March 7 2017. The maint branch has not had any changes sine 2016 - at least according to the logs. So if you run org from the master branch, all works. Not sure what the elpa packages are built from. – Tim X Jul 23 '17 at 08:16
  • As of `org-plus-contrib-20170717`, ob-clojure has changed enough that this patch can't be applied automatically--but adding the `(declare-function cider-current-ns "ext:cider-client" ())` at the beginning and string-replacing `cider-current-session` with `cider-current-ns` in `org-babel-execute:clojure` still fixes it. – Archenoth Jul 25 '17 at 16:56
  • Reinstall with the latest version of org mode (org version 20170925 from the "org" archive) fixes the problem without requiring code changes to ob-clojure – shark8me Sep 25 '17 at 05:12
0

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)
narendraj9
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  • Unfortunately, `(println (+ 1 1))` isn't working. I copy-pasted the code you have above and that does not work either. – Jeel Shah Feb 19 '17 at 20:12
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    Seems same problem with mine. http://lists.gnu.org/archive/html/emacs-orgmode/2017-02/msg00429.html – stardiviner Feb 21 '17 at 00:39
0

Try

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

which prints the returned value instead of output.

Compro Prasad
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0

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

Pliny Suetonious
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