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

[Rainer M Krug]

Eric Schulte <address@hidden> 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: address@hidden
>>
>> ≈* 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 <address@hidden>
> 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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