From: "numbchild@gmail.com" <numbchild@gmail.com>
To: Tim Cross <theophilusx@gmail.com>
Cc: Org-mode <emacs-orgmode@gnu.org>
Subject: Re: ob-clojure evaluate error when Org-mode buffer has ns clojure code
Date: Sat, 17 Jun 2017 20:57:47 +0800 [thread overview]
Message-ID: <CAL1eYu+1XAv5hBMTF_h1jnvRao38TQRRabU_iTT9WWnJ_8EMWQ@mail.gmail.com> (raw)
In-Reply-To: <87zid7bd46.fsf@gmail.com>
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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
Key fingerprint = 9BAA 92BC CDDD B9EF 3B36 CB99 B8C4 B8E5 47C3 2433
Blog: http://stardiviner.github.io/
On Sat, Jun 17, 2017 at 9:46 AM, Tim Cross <theophilusx@gmail.com> 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
>
> numbchild@gmail.com 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
>
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next prev parent reply other threads:[~2017-06-17 12:58 UTC|newest]
Thread overview: 9+ messages / expand[flat|nested] mbox.gz Atom feed top
2017-06-16 15:36 ob-clojure evaluate error when Org-mode buffer has ns clojure code numbchild
2017-06-17 1:46 ` Tim Cross
2017-06-17 12:57 ` numbchild [this message]
2017-06-17 13:26 ` numbchild
2017-06-18 1:10 ` Tim Cross
2017-06-18 5:48 ` numbchild
2017-06-21 5:12 ` numbchild
2017-12-19 9:54 ` [UPDATE] " stardiviner
2017-12-21 10:15 ` numbchild
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