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


From: Tim Cross
Subject: Re: [O] ob-clojure evaluate error when Org-mode buffer has ns clojure code
Date: Sun, 18 Jun 2017 11:10:22 +1000
User-agent: mu4e 0.9.18; emacs 25.2.1

It looks like you have a combination of both clojure errors and possibly
org babel errors. You need to sort out the clojure errors before you can
verify there are any problems with org babel clojure support.

You mention that

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

but then you say

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

However, if you don't have a project, then you don't have a project.clj
file and if you don't have a project.clj file, you don't have a
:dependencies block with incanter as a specified dependency, so incanter
is not in your classpath and therefore will not be found when you try to
require it.

Note also that you have incorrect syntax for your require
statement. Also to be clear, (ns ... (:require ...)) does not define
dependencies. It simply loads the library into the namespace.

The correct syntax for your first block is

(ns my-kk
  (:require [incanter.core :as k]))

There is no quote before the lib spec - this is also what the error
message is telling you. If you call require as a function, then you do
need to use the quote i.e.

(require 'incanter.core :as k)

You appear to have two main problems here and that is making things
'muddy'. I'm guessing your learning clojure as well as using org babel
clojure support. You need to sort out the clojure problems first. Highly
recommend you suspend using org mode to do your clojure until your
across all the clojure specifics and have a good understanding of the
clojure environment. You will need a good understanding of how clojure
works to then be able to work out what you need to do to get it to work
with org mode. Trying to do both at the same time will just cause
confusion.

HTH

Tim

address@hidden writes:

> 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 <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
>>


-- 
Tim Cross



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