* ob-clojure evaluate error when Org-mode buffer has ns clojure code
@ 2017-06-16 15:36 numbchild
2017-06-17 1:46 ` Tim Cross
0 siblings, 1 reply; 9+ messages in thread
From: numbchild @ 2017-06-16 15:36 UTC (permalink / raw)
To: Org-mode
[-- Attachment #1: Type: text/plain, Size: 918 bytes --]
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/
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^ permalink raw reply [flat|nested] 9+ messages in thread
* Re: ob-clojure evaluate error when Org-mode buffer has ns clojure code
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
0 siblings, 1 reply; 9+ messages in thread
From: Tim Cross @ 2017-06-17 1:46 UTC (permalink / raw)
To: numbchild@gmail.com; +Cc: Org-mode
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
^ permalink raw reply [flat|nested] 9+ messages in thread
* Re: ob-clojure evaluate error when Org-mode buffer has ns clojure code
2017-06-17 1:46 ` Tim Cross
@ 2017-06-17 12:57 ` numbchild
2017-06-17 13:26 ` numbchild
2017-06-18 1:10 ` Tim Cross
0 siblings, 2 replies; 9+ messages in thread
From: numbchild @ 2017-06-17 12:57 UTC (permalink / raw)
To: Tim Cross; +Cc: Org-mode
[-- Attachment #1: Type: text/plain, Size: 10478 bytes --]
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
>
[-- Attachment #2: Type: text/html, Size: 22129 bytes --]
^ permalink raw reply [flat|nested] 9+ messages in thread
* Re: ob-clojure evaluate error when Org-mode buffer has ns clojure code
2017-06-17 12:57 ` numbchild
@ 2017-06-17 13:26 ` numbchild
2017-06-18 1:10 ` Tim Cross
1 sibling, 0 replies; 9+ messages in thread
From: numbchild @ 2017-06-17 13:26 UTC (permalink / raw)
To: Tim Cross; +Cc: Org-mode
[-- 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
>>
>
>
[-- Attachment #2: Type: text/html, Size: 27706 bytes --]
^ permalink raw reply [flat|nested] 9+ messages in thread
* Re: ob-clojure evaluate error when Org-mode buffer has ns clojure code
2017-06-17 12:57 ` numbchild
2017-06-17 13:26 ` numbchild
@ 2017-06-18 1:10 ` Tim Cross
2017-06-18 5:48 ` numbchild
1 sibling, 1 reply; 9+ messages in thread
From: Tim Cross @ 2017-06-18 1:10 UTC (permalink / raw)
To: numbchild@gmail.com; +Cc: Org-mode
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
numbchild@gmail.com 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 <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
>>
--
Tim Cross
^ permalink raw reply [flat|nested] 9+ messages in thread
* Re: ob-clojure evaluate error when Org-mode buffer has ns clojure code
2017-06-18 1:10 ` Tim Cross
@ 2017-06-18 5:48 ` numbchild
2017-06-21 5:12 ` numbchild
0 siblings, 1 reply; 9+ messages in thread
From: numbchild @ 2017-06-18 5:48 UTC (permalink / raw)
To: Tim Cross; +Cc: Org-mode
[-- Attachment #1: Type: text/plain, Size: 13702 bytes --]
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 <theophilusx@gmail.com> 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
>
> numbchild@gmail.com 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 <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
> >>
>
>
> --
> Tim Cross
>
[-- Attachment #2: Type: text/html, Size: 18463 bytes --]
^ permalink raw reply [flat|nested] 9+ messages in thread
* Re: ob-clojure evaluate error when Org-mode buffer has ns clojure code
2017-06-18 5:48 ` numbchild
@ 2017-06-21 5:12 ` numbchild
2017-12-19 9:54 ` [UPDATE] " stardiviner
0 siblings, 1 reply; 9+ messages in thread
From: numbchild @ 2017-06-21 5:12 UTC (permalink / raw)
To: Tim Cross; +Cc: Org-mode
[-- Attachment #1: Type: text/plain, Size: 15157 bytes --]
Hi, Tim,
Excuse my obstinacy, I still think the problem is in `ob-clojure.el`
Because when I:
```org
#+BEGIN_SRC clojure :session
(ns user-kk)
#+END_SRC
#+BEGIN_SRC clojure :session :results output
(print "hi")
(def kkkk "hello")
#+END_SRC
#+RESULTS:
```
The second block does not return result.
when I remove the first block, the second block works.
Why `ob-clojure.el` don't evaluate the first block when I press [C-c C-c]
on the second block, but still respect the first block's Clojure namespace
definition?
If it is the way `ob-clojure.el` works. I think this should have an option
to disable "respecting babel clojure namespace definition". Because I use
"Literate Programming" a lot. I will add some src blcoks with `(ns ...)` as
example in Org-mode file.
[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 1:48 PM, numbchild@gmail.com <numbchild@gmail.com>
wrote:
> 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 <theophilusx@gmail.com> 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
>>
>> numbchild@gmail.com 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 <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
>> >>
>>
>>
>> --
>> Tim Cross
>>
>
>
[-- Attachment #2: Type: text/html, Size: 21987 bytes --]
^ permalink raw reply [flat|nested] 9+ messages in thread
* [UPDATE] Re: ob-clojure evaluate error when Org-mode buffer has ns clojure code
2017-06-21 5:12 ` numbchild
@ 2017-12-19 9:54 ` stardiviner
2017-12-21 10:15 ` numbchild
0 siblings, 1 reply; 9+ messages in thread
From: stardiviner @ 2017-12-19 9:54 UTC (permalink / raw)
To: Tim Cross; +Cc: Org-mode
I got new update on this issue.
I think it is caused by `(clojure-find-ns)`.
Here is my found:
I created a simple clojure project for used by all org-babel-clojure src
blocks.
```elisp
(progn
(find-file (expand-file-name
"~/.emacs.d/Org-mode/ob-clojure/src/ob_clojure/core.clj"))
(cider-jack-in))
```
I edebug the `org-babel-execute:clojure` process,
`org-babel-execute:clojure' has a step: ~(clojure-find-ns)~ .
This is from ~clojure-mode~. It will find current clojure buffer
possible clojure namespace (even in org-mode). When I the following
example org-mode buffer, it will return "namespace-not-found" error in
nrepl response dict. Then src blcok has no error, not results.
```org
#+BEGIN_SRC clojure :session
(in-ns 'user-kk)
or
(ns user-kk)
#+END_SRC
#+BEGIN_SRC clojure :results output
(print "hi")
#+END_SRC
```
Here is a part of function `clojure-find-ns`:
#+begin_src emacs-lisp
(when (or (re-search-backward clojure-namespace-name-regex nil t)
;; Or any form at all.
(and (goto-char (point-min))
(re-search-forward clojure-namespace-name-regex
nil t)))
(match-string-no-properties 4))
#+end_src
So I created an PR to disable find namespace in Org-mode buffer:
https://github.com/clojure-emacs/clojure-mode/pull/465
^ permalink raw reply [flat|nested] 9+ messages in thread
* Re: [UPDATE] Re: ob-clojure evaluate error when Org-mode buffer has ns clojure code
2017-12-19 9:54 ` [UPDATE] " stardiviner
@ 2017-12-21 10:15 ` numbchild
0 siblings, 0 replies; 9+ messages in thread
From: numbchild @ 2017-12-21 10:15 UTC (permalink / raw)
To: Tim Cross; +Cc: Org-mode
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Finally found a solution. really hard. spend a lot of time on this issue.
The discussion is at here:
https://github.com/clojure-emacs/clojure-mode/pull/465 Here is my final
source code. paste here as a copy. Hope can help someone want same thing.
;; auto start CIDER REPL session in a complete Leiningen project
environment for Org-mode Babel by jack-in.
(add-to-list 'org-babel-default-header-args:clojure
'(:session . "*cider-repl ob-clojure*"))
(progn
(find-file (expand-file-name
"~/.emacs.d/Org-mode/ob-clojure/src/ob_clojure/core.clj"))
(cider-jack-in))
(defun ob-clojure-cider-do-not-find-ns ()
"Fix the issue that `cider-current-ns' try to invoke
`clojure-find-ns' to extract ns from buffer."
(with-current-buffer "*cider-repl ob-clojure*"
(defvar ob-clojure-cider-repl-ns cider-buffer-ns)
(setq-local cider-buffer-ns ob-clojuure-cider-repl-ns)))
(add-hook 'org-mode-hook #'ob-clojure-cider-do-not-find-ns)
[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 Tue, Dec 19, 2017 at 5:54 PM, stardiviner <numbchild@gmail.com> wrote:
> I got new update on this issue.
>
> I think it is caused by `(clojure-find-ns)`.
> Here is my found:
>
> I created a simple clojure project for used by all org-babel-clojure src
> blocks.
> ```elisp
> (progn
> (find-file (expand-file-name "~/.emacs.d/Org-mode/ob-clojur
> e/src/ob_clojure/core.clj"))
> (cider-jack-in))
> ```
>
> I edebug the `org-babel-execute:clojure` process,
>
> `org-babel-execute:clojure' has a step: ~(clojure-find-ns)~ .
> This is from ~clojure-mode~. It will find current clojure buffer possible
> clojure namespace (even in org-mode). When I the following example org-mode
> buffer, it will return "namespace-not-found" error in nrepl response dict.
> Then src blcok has no error, not results.
>
> ```org
> #+BEGIN_SRC clojure :session
> (in-ns 'user-kk)
> or
> (ns user-kk)
> #+END_SRC
>
> #+BEGIN_SRC clojure :results output
> (print "hi")
> #+END_SRC
> ```
>
> Here is a part of function `clojure-find-ns`:
>
> #+begin_src emacs-lisp
> (when (or (re-search-backward clojure-namespace-name-regex nil t)
> ;; Or any form at all.
> (and (goto-char (point-min))
> (re-search-forward clojure-namespace-name-regex nil
> t)))
> (match-string-no-properties 4))
> #+end_src
>
> So I created an PR to disable find namespace in Org-mode buffer:
> https://github.com/clojure-emacs/clojure-mode/pull/465
>
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^ permalink raw reply [flat|nested] 9+ messages in thread
end of thread, other threads:[~2017-12-21 10:16 UTC | newest]
Thread overview: 9+ messages (download: mbox.gz follow: Atom feed
-- links below jump to the message on this page --
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
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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