From: "numbchild@gmail.com" <numbchild@gmail.com>
To: Tim Cross <theophilusx@gmail.com>
Cc: Org-mode <emacs-orgmode@gnu.org>
Subject: Re: ob-clojure evaluate error when Org-mode buffer has ns clojure code
Date: Wed, 21 Jun 2017 13:12:42 +0800 [thread overview]
Message-ID: <CAL1eYuKwrDX6cNTnxu-KKoZP6m1Fi7n4sFgfw45gvfLA6w_9LQ@mail.gmail.com> (raw)
In-Reply-To: <CAL1eYu+Q7JRFEDv2y=p23EiEKPptyWTD_eh=2pHKFqOeR2it+g@mail.gmail.com>
[-- 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 --]
next prev parent reply other threads:[~2017-06-21 5:13 UTC|newest]
Thread overview: 9+ messages / expand[flat|nested] mbox.gz Atom feed top
2017-06-16 15:36 ob-clojure evaluate error when Org-mode buffer has ns clojure code numbchild
2017-06-17 1:46 ` Tim Cross
2017-06-17 12:57 ` numbchild
2017-06-17 13:26 ` numbchild
2017-06-18 1:10 ` Tim Cross
2017-06-18 5:48 ` numbchild
2017-06-21 5:12 ` numbchild [this message]
2017-12-19 9:54 ` [UPDATE] " stardiviner
2017-12-21 10:15 ` numbchild
Reply instructions:
You may reply publicly to this message via plain-text email
using any one of the following methods:
* Save the following mbox file, import it into your mail client,
and reply-to-all from there: mbox
Avoid top-posting and favor interleaved quoting:
https://en.wikipedia.org/wiki/Posting_style#Interleaved_style
List information: https://www.orgmode.org/
* Reply using the --to, --cc, and --in-reply-to
switches of git-send-email(1):
git send-email \
--in-reply-to=CAL1eYuKwrDX6cNTnxu-KKoZP6m1Fi7n4sFgfw45gvfLA6w_9LQ@mail.gmail.com \
--to=numbchild@gmail.com \
--cc=emacs-orgmode@gnu.org \
--cc=theophilusx@gmail.com \
/path/to/YOUR_REPLY
https://kernel.org/pub/software/scm/git/docs/git-send-email.html
* If your mail client supports setting the In-Reply-To header
via mailto: links, try the mailto: link
Be sure your reply has a Subject: header at the top and a blank line
before the message body.
Code repositories for project(s) associated with this public inbox
https://git.savannah.gnu.org/cgit/emacs/org-mode.git
This is a public inbox, see mirroring instructions
for how to clone and mirror all data and code used for this inbox;
as well as URLs for read-only IMAP folder(s) and NNTP newsgroup(s).