|
| From: | address@hidden |
| Subject: | Re: [O] ob-clojure evaluate error when Org-mode buffer has ns clojure code |
| Date: | Wed, 21 Jun 2017 13:12:42 +0800 |
I see, thanks very much.[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 Sun, Jun 18, 2017 at 9:10 AM, Tim Cross <address@hidden> wrote:
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/interrupti ble-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/interrupti ble-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
>> > ..)` 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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