From: Rainer M Krug <Rainer@krugs.de>
To: Eric Schulte <schulte.eric@gmail.com>
Cc: emacs-orgmode@gnu.org, Charles Berry <ccberry@ucsd.edu>
Subject: Re: [BABEL] BUG Re: Omitting try/catch blocks from tangled R code?
Date: Mon, 31 Mar 2014 09:52:09 +0200 [thread overview]
Message-ID: <m2y4zqiz4m.fsf@krugs.de> (raw)
In-Reply-To: <87fvlzg45i.fsf@gmail.com> (Eric Schulte's message of "Sun, 30 Mar 2014 08:19:37 -0600")
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Eric Schulte <schulte.eric@gmail.com> writes:
>>
>> Apologies - I am still struggling with encryption......
>>
>> So here is my example:
>>
>> --8<---------------cut here---------------start------------->8---
>> #+TITLE: single_to_multi
>> #+DATE: <2013-10-15 Tue>
>> #+AUTHOR: Rainer M. Krug
>> #+EMAIL: Rainer@krugs.de
>>
>> ≈* Load R packages and data
>> #+BEGIN_SRC R
>> cat("Loading Data\n")
>> #+END_SRC
>> --8<---------------cut here---------------end--------------->8---
>>
>> I am using only org loaded and R enabled.
>>
>> C-c C-c on the block produces the error
>>
>> emacs version:
>> GNU Emacs 24.3.1 (x86_64-apple-darwin13.0.0, Carbon Version 1.6.0
>> AppKit 1265) of 2014-02-13 on Rainers-MacBook-Pro-2.local
>>
>> org version:
>> Org-mode version 8.2.5h (release_8.2.5h-837-gb296cc @
>> /Users/rainerkrug/.emacs.d/org-mode/lisp/)
>>
>
> Thanks, a fixed version of the patch is attached. If this works please
> let me know and I'll apply.
Still the same error:
,----
| Debugger entered--Lisp error: (wrong-type-argument sequencep 99)
| Mapconcat(identity "cat(\"YEAR\")" "\n")
| Org-babel-execute:R("cat(\"YEAR\")" ((:comments . "") (:shebang . "") (:cache . "no") (:padline . "") (:noweb . "no") (:tangle . "no") (:exports . "code") (:results . "replace output") (:session . "none") (:hlines . "no") (:result-type . output) (:result-params "output" "replace") (:rowname-names) (:colname-names)))
| org-babel-execute-src-block(nil)
| org-babel-execute-src-block-maybe()
| org-babel-execute-maybe()
| org-babel-execute-safely-maybe()
| run-hook-with-args-until-success(org-babel-execute-safely-maybe)
| org-ctrl-c-ctrl-c(nil)
| call-interactively(org-ctrl-c-ctrl-c nil nil)
`----
Cheers,
Rainer
>
> Best,
>
>
> From d67248db79faf19e1bdcac0230c37670b6115bdd Mon Sep 17 00:00:00 2001
> From: Eric Schulte <schulte.eric@gmail.com>
> Date: Sun, 23 Mar 2014 20:01:37 -0600
> Subject: [PATCH] only wrap R code graphics-file on execution
>
> Move this out of the expand-body function so that it is *never*
> applied to tangled code.
> ---
> lisp/ob-R.el | 40 +++++++++++++++++++++-------------------
> 1 file changed, 21 insertions(+), 19 deletions(-)
>
> diff --git a/lisp/ob-R.el b/lisp/ob-R.el
> index 62aa7f2..780d99f 100644
> --- a/lisp/ob-R.el
> +++ b/lisp/ob-R.el
> @@ -97,24 +97,15 @@ this variable.")
> "Expand BODY according to PARAMS, return the expanded body."
> (let ((graphics-file
> (or graphics-file (org-babel-R-graphical-output-file params))))
> - (mapconcat
> - #'identity
> - (let ((inside
> - (append
> - (when (cdr (assoc :prologue params))
> - (list (cdr (assoc :prologue params))))
> - (org-babel-variable-assignments:R params)
> - (list body)
> - (when (cdr (assoc :epilogue params))
> - (list (cdr (assoc :epilogue params)))))))
> - (if graphics-file
> - (append
> - (list (org-babel-R-construct-graphics-device-call
> - graphics-file params))
> - inside
> - (list "},error=function(e){plot(x=-1:1, y=-1:1, type='n', xlab='', ylab='', axes=FALSE); text(x=0, y=0, labels=e$message, col='red'); paste('ERROR', e$message, sep=' : ')}); dev.off()"))
> - inside))
> - "\n")))
> + (mapconcat #'identity
> + (append
> + (when (cdr (assoc :prologue params))
> + (list (cdr (assoc :prologue params))))
> + (org-babel-variable-assignments:R params)
> + (list body)
> + (when (cdr (assoc :epilogue params))
> + (list (cdr (assoc :epilogue params)))))
> + "\n")))
>
> (defun org-babel-execute:R (body params)
> "Execute a block of R code.
> @@ -127,7 +118,18 @@ This function is called by `org-babel-execute-src-block'."
> (colnames-p (cdr (assoc :colnames params)))
> (rownames-p (cdr (assoc :rownames params)))
> (graphics-file (org-babel-R-graphical-output-file params))
> - (full-body (org-babel-expand-body:R body params graphics-file))
> + (full-body
> + (let ((inside
> + (list (org-babel-expand-body:R body params graphics-file))))
> + (mapconcat #'identity
> + (if graphics-file
> + (append
> + (list (org-babel-R-construct-graphics-device-call
> + graphics-file params))
> + inside
> + (list "},error=function(e){plot(x=-1:1, y=-1:1, type='n', xlab='', ylab='', axes=FALSE); text(x=0, y=0, labels=e$message, col='red'); paste('ERROR', e$message, sep=' : ')}); dev.off()"))
> + inside)
> + "\n")))
> (result
> (org-babel-R-evaluate
> session full-body result-type result-params
> --
> 1.9.1
--
Rainer M. Krug
email: Rainer<at>krugs<dot>de
PGP: 0x0F52F982
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next prev parent reply other threads:[~2014-03-31 7:52 UTC|newest]
Thread overview: 25+ messages / expand[flat|nested] mbox.gz Atom feed top
2014-02-07 6:18 Omitting try/catch blocks from tangled R code? John Hendy
2014-02-07 8:26 ` [BABEL] BUG " Rainer M Krug
2014-02-07 16:47 ` Eric Schulte
2014-02-07 19:22 ` Rainer M Krug
2014-03-12 1:13 ` John Hendy
2014-03-17 15:00 ` Eric Schulte
2014-03-17 17:11 ` John Hendy
2014-03-17 17:44 ` Eric Schulte
2014-03-18 8:44 ` Rainer M Krug
2014-03-18 21:56 ` John Hendy
2014-03-19 19:07 ` Charles Berry
2014-03-20 4:57 ` Eric Schulte
2014-03-20 9:22 ` Rainer M Krug
2014-03-24 2:03 ` Eric Schulte
2014-03-24 10:22 ` Rainer M Krug
2014-03-24 13:16 ` Eric Schulte
2014-03-25 9:37 ` Rainer M Krug
2014-03-26 20:17 ` Eric Schulte
2014-03-28 8:32 ` Rainer M Krug
2014-03-28 8:51 ` Rainer M Krug
2014-03-30 14:19 ` Eric Schulte
2014-03-31 7:52 ` Rainer M Krug [this message]
2014-04-02 23:09 ` Eric Schulte
2014-04-07 7:59 ` Rainer M Krug
2014-04-11 2:35 ` Eric Schulte
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