Re: [BABEL] BUG Re: Omitting try/catch blocks from tangled R code?

[Eric Schulte <schulte.eric@gmail.com>]

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