From: Eric Schulte <schulte.eric@gmail.com>
To: Rainer M Krug <Rainer@krugs.de>
Cc: emacs-orgmode@gnu.org, Charles Berry <ccberry@ucsd.edu>
Subject: Re: [BABEL] BUG Re: Omitting try/catch blocks from tangled R code?
Date: Wed, 02 Apr 2014 17:09:37 -0600 [thread overview]
Message-ID: <87bnwio5x4.fsf@gmail.com> (raw)
In-Reply-To: m2y4zqiz4m.fsf@krugs.de
Rainer M Krug <Rainer@krugs.de> writes:
> 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:
>
Your previous example works as expected for me with the latest patch.
* Load R packages and data
#+BEGIN_SRC R :results output
cat("Loading Data\n")
#+END_SRC
#+RESULTS:
: Loading Data
Please double check that you applied the patch and reloaded Org-mode,
and if the bug persists provide another minimal example.
Thanks,
>
> ,----
> | 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
--
Eric Schulte
https://cs.unm.edu/~eschulte
PGP: 0x614CA05D
next prev parent reply other threads:[~2014-04-03 14:15 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
2014-04-02 23:09 ` Eric Schulte [this message]
2014-04-07 7:59 ` Rainer M Krug
2014-04-11 2:35 ` Eric Schulte
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