Re: [O] ob-clojure evaluate error when Org-mode buffer has ns clojure code

[address@hidden]

After a new evaluation. I found

```org

#+BEGIN_SRC clojure

(ns user

  (:require '[incanter.core :as mm]))

#+END_SRC

#+RESULTS:

: class clojure.lang.Compiler$CompilerExceptionclass clojure.lang.Compiler$CompilerExceptionCompilerException java.lang.Exception: Found lib name 'incanter.core' containing period with prefix 'quote'.  lib names inside prefix lists must not contain periods, compiling:(/home/stardiviner/Code/learning/Emacs/Org-mode/ob-clojure.org:1:1) 

#+BEGIN_SRC clojure :session :results output

(print "hi")

(def kkkk "hello")

#+END_SRC

#+RESULTS:

: hi

```

Both two src blocks works. Because the first src block Clojure namespace `(ns user ..)` is same with CIDER REPL default namespace `user`. So it works.

But when I tried add header argument `:eval no` on first src block like this:

```org

#+BEGIN_SRC clojure :session :eval no

(ns user.kk

  (:require '[incanter.core :as mm]))

#+END_SRC

#+RESULTS:

#+BEGIN_SRC clojure :session :results output

(print "hi")

(def kkkk "hello")

#+END_SRC

#+RESULTS:

```

The second src block failed again. So I think `ob-clojure` will try to evaluate the first src block even I added header argument `:eval no`. So `ob-clojure.el` does not respect header argument `:eval no`. But I think might because `:eval no` is not work for this purpose. I did can't evaluate by pressing `[C-c C-c]` on first block.

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On Sat, Jun 17, 2017 at 8:57 PM, address@hidden <address@hidden> wrote:

I did configure `ob-clojure` with the following settings:

```elisp

(require 'ob-clojure)

;; use CIDER as the Clojure execution backend

(setq org-babel-clojure-backend 'cider)

;; Useful keybindings when using Clojure from Org

;; (org-defkey org-mode-map (kbd "C-x C-e") 'cider-eval-last-sexp)

;; (org-defkey org-mode-map (kbd "C-c C-d") 'cider-doc)

;; No timeout when executing calls on Cider via nrepl

;; (setq org-babel-clojure-sync-nrepl-timeout nil)

;; let `ob-clojure' babel src blocks allow evaluation.

(add-to-list 'org-babel-default-header-args:clojure

             '(:eval . "yes"))

(add-to-list 'org-babel-default-header-args:clojure

             '(:results . "output"))

;; (add-to-list 'org-babel-default-header-args:clojure

;;              '(:show-process . t))

```

I start CIDER REPL session with `cider-jack-in` without project in Emacs.

I changed namespace to `user` in src blocks like this:

```org

#+BEGIN_SRC clojure

(ns user

  (:require '[incanter.core :as kk]))

#+END_SRC

#+RESULTS:

#+BEGIN_SRC clojure :session :results output

(print "hi")

(def kkkk "hello")

#+END_SRC

#+RESULTS:

: hi

```

Then it works.

Seems you're right, might my first src block can't work correctly. That caused second src block evaluation failed.

But I require `incanter` works, I have `incanter` in Leiningen dependencies.

```clojure

(require '[incanter.core :as kk])

```

But include `incanter` in namespace failed:

```clojure

(ns user

  (:require '[incanter.core :as kk]))

```

with the following error.

```

  Show: Clojure Java REPL Tooling Duplicates All  (29 frames hidden)

2. Unhandled clojure.lang.Compiler$CompilerException

   Error compiling Code/learning/Emacs/Org-mode/ob-clojure.org at (1:1)

                  core.clj: 5771  clojure.core/throw-if

                  core.clj: 5835  clojure.core/load-lib

                  core.clj: 5832  clojure.core/load-lib

               RestFn.java:  142  clojure.lang.RestFn/applyTo

                  core.clj:  659  clojure.core/apply

                  core.clj: 5893  clojure.core/load-libs

                  core.clj: 5873  clojure.core/load-libs

               RestFn.java:  137  clojure.lang.RestFn/applyTo

                  core.clj:  659  clojure.core/apply

                  core.clj: 5911  clojure.core/require

                  core.clj: 5911  clojure.core/require

               RestFn.java:  408  clojure.lang.RestFn/invoke

                      REPL:    1  user/eval46259/loading--auto--

                      REPL:    1  user/eval46259

                      REPL:    1  user/eval46259

             Compiler.java: 6977  clojure.lang.Compiler/eval

             Compiler.java: 6966  clojure.lang.Compiler/eval

             Compiler.java: 6940  clojure.lang.Compiler/eval

                  core.clj: 3187  clojure.core/eval

                  core.clj: 3183  clojure.core/eval

                  main.clj:  242  clojure.main/repl/read-eval-print/fn

                  main.clj:  242  clojure.main/repl/read-eval-print

                  main.clj:  260  clojure.main/repl/fn

                  main.clj:  260  clojure.main/repl

                  main.clj:  176  clojure.main/repl

               RestFn.java: 1523  clojure.lang.RestFn/invoke

    interruptible_eval.clj:   87  clojure.tools.nrepl.middleware.interruptible-eval/evaluate/fn

                  AFn.java:  152  clojure.lang.AFn/applyToHelper

                  AFn.java:  144  clojure.lang.AFn/applyTo

                  core.clj:  657  clojure.core/apply

                  core.clj: 1963  clojure.core/with-bindings*

                  core.clj: 1963  clojure.core/with-bindings*

               RestFn.java:  425  clojure.lang.RestFn/invoke

    interruptible_eval.clj:   85  clojure.tools.nrepl.middleware.interruptible-eval/evaluate

    interruptible_eval.clj:   55  clojure.tools.nrepl.middleware.interruptible-eval/evaluate

    interruptible_eval.clj:  222  clojure.tools.nrepl.middleware.interruptible-eval/interruptible-eval/fn/fn

    interruptible_eval.clj:  190  clojure.tools.nrepl.middleware.interruptible-eval/run-next/fn

                  AFn.java:   22  clojure.lang.AFn/run

   ThreadPoolExecutor.java: 1142  java.util.concurrent.ThreadPoolExecutor/runWorker

   ThreadPoolExecutor.java:  617  java.util.concurrent.ThreadPoolExecutor$Worker/run

               Thread.java:  745  java.lang.Thread/run

1. Caused by java.lang.Exception

   Found lib name 'incanter.stats' containing period with prefix 'quote'. lib

   names inside prefix lists must not contain periods

                  core.clj:  659  clojure.core/apply

                  core.clj: 5893  clojure.core/load-libs

                  core.clj: 5873  clojure.core/load-libs

               RestFn.java:  137  clojure.lang.RestFn/applyTo

                  core.clj:  659  clojure.core/apply

                  core.clj: 5911  clojure.core/require

                  core.clj: 5911  clojure.core/require

               RestFn.java:  408  clojure.lang.RestFn/invoke

                      REPL:    1  user/eval46259/loading--auto--

                      REPL:    1  user/eval46259

                      REPL:    1  user/eval46259

             Compiler.java: 6977  clojure.lang.Compiler/eval

             Compiler.java: 6966  clojure.lang.Compiler/eval

             Compiler.java: 6940  clojure.lang.Compiler/eval

                  core.clj: 3187  clojure.core/eval

                  core.clj: 3183  clojure.core/eval

                  main.clj:  242  clojure.main/repl/read-eval-print/fn

                  main.clj:  242  clojure.main/repl/read-eval-print

                  main.clj:  260  clojure.main/repl/fn

                  main.clj:  260  clojure.main/repl

                  main.clj:  176  clojure.main/repl

               RestFn.java: 1523  clojure.lang.RestFn/invoke

    interruptible_eval.clj:   87  clojure.tools.nrepl.middleware.interruptible-eval/evaluate/fn

                  AFn.java:  152  clojure.lang.AFn/applyToHelper

                  AFn.java:  144  clojure.lang.AFn/applyTo

                  core.clj:  657  clojure.core/apply

                  core.clj: 1963  clojure.core/with-bindings*

                  core.clj: 1963  clojure.core/with-bindings*

               RestFn.java:  425  clojure.lang.RestFn/invoke

    interruptible_eval.clj:   85  clojure.tools.nrepl.middleware.interruptible-eval/evaluate

    interruptible_eval.clj:   55  clojure.tools.nrepl.middleware.interruptible-eval/evaluate

    interruptible_eval.clj:  222  clojure.tools.nrepl.middleware.interruptible-eval/interruptible-eval/fn/fn

    interruptible_eval.clj:  190  clojure.tools.nrepl.middleware.interruptible-eval/run-next/fn

                  AFn.java:   22  clojure.lang.AFn/run

   ThreadPoolExecutor.java: 1142  java.util.concurrent.ThreadPoolExecutor/runWorker

   ThreadPoolExecutor.java:  617  java.util.concurrent.ThreadPoolExecutor$Worker/run

               Thread.java:  745  java.lang.Thread/run

```

[stardiviner]           <Hack this world!>      GPG key ID: 47C32433
IRC(freeenode): stardiviner                     Twitter:  @numbchild
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Blog: http://stardiviner.github.io/

On Sat, Jun 17, 2017 at 9:46 AM, Tim Cross <address@hidden> wrote:

My guess is that cider is not finding the incanter package in the
classpath when the first block attempts to evaluate. Another issue is
that your not using any session options, so your two blocks will be
evaluated in separate environments - not a real problem with your
current example, but will be an issue if you expect to access incanter
functions from separate babel blocks.

There are a number of working parts which all need to be lined up
correctly before babel clojure support will work correctly. Getting
things to work when your just using core clojure functions is fairly
trivial, but getting it to work when you have to pull in other
dependencies can be a little tricky.

You might find this article useful to get started

http://fgiasson.com/blog/index.php/2016/06/21/optimal-emacs-settings-for-org-mode-for-literate-programming/

I also notice you have not set the org-babel-clojure-backend, which you
need to do. My recommendation would be to do the following

1. Create a leinegen project to experiment with i.e.
lein new app my-kk

2. Make sure you can edit and evaluate clojure just using clojure-mode
and cider in emacs

3. Add the incanter package to your project.clj dependencies key

4. Modify core.clj (using clojure-mode) to include the code in your
clojure blocks and run with cider to make sure they work as expected.

5. Create the org file you want to experiment with in the root of your
project. This should ensure that when you try to evaluate clojure
blocks, the cider backend will be loaded with the dependencies in the
project.clj file.

6. Copy the code in your core.clj file into ONE babel src block and see
if you can get it to evaluate correctly. Experiment with the block
configuration options like :output etc.

7. Break the code up into different blocks and experiment with block
options, especially session options.

Once you get to that point, you should be across the various moving
parts with sufficient understanding to then look at how you can tweak
things to get exactly the behaviour and workflow you want.

HTH

Tim

address@hidden writes:

> When Org-mode buffer like this:
>
> #+BEGIN_SRC clojure
> (ns my.kk
>   (:require '[incanter.core :as kk]))
> #+END_SRC
>
> #+BEGIN_SRC clojure
> (print "hi")
> (def kkkk "hello")
> #+END_SRC
>
> #+RESULTS:
>
> When I have `(ns ..)` namespace clojure code in buffer, the second `(print
> ..)` clojure result nothing. But when I remove the first src block, the
> `(print ..)` clojure src block works fine.
>
> I'm using Org-mode version from `master` with `use-package` like this:
>
> (use-package org
>   :load-path "~/Code/Emacs/org-mode/lisp/"
>   :pin manual
>   :mode (("\\.org$" . org-mode))
>   :config
>   (use-package org-plus-contrib
>     :load-path "~/Code/Emacs/org-mode/contrib/lisp/"
>     :pin manual)
>   )
>
>
> [stardiviner]           <Hack this world!>      GPG key ID: 47C32433
> IRC(freeenode): stardiviner                     Twitter:  @numbchild
> Key fingerprint = 9BAA 92BC CDDD B9EF 3B36  CB99 B8C4 B8E5 47C3 2433
> Blog: http://stardiviner.github.io/

--
Tim Cross