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 21:26:47 +0800 [thread overview]
Message-ID: <CAL1eYu+_UpYidNkQvXARt1gecXvd49DTLDAC-X8W+K2eGBSKew@mail.gmail.com> (raw)
In-Reply-To: <CAL1eYu+1XAv5hBMTF_h1jnvRao38TQRRabU_iTT9WWnJ_8EMWQ@mail.gmail.com>
[-- Attachment #1: Type: text/plain, Size: 12610 bytes --]
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.
[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 8:57 PM, numbchild@gmail.com <numbchild@gmail.com>
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
> 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 13:27 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
2017-06-17 13:26 ` numbchild [this message]
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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