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

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

[-- Attachment #1: Type: text/plain, Size: 2677 bytes --]

Rainer M Krug <Rainer@krugs.de> writes:

> Eric Schulte <schulte.eric@gmail.com> writes:
>
>> Charles Berry <ccberry@ucsd.edu> writes:
>>
>>> John Hendy <jw.hendy <at> gmail.com> writes:
>>>
>>> [deleted]
>>>> >
>>>> > I think the default behavior should be reverted, as tangling and
>>>> > exporting are two different things. When I tangle, I want to see the
>>>> > code blocks as they are in the org document (with possible variables and
>>>> > expansions) but not to create files where I do not put it explicitly
>>>> > into a code block. These wrappers have nothing to do with the code, and
>>>> > are only there for the exported engine. So I would either revert to the
>>>> > original behavior, or, introduce a new header argument,
>>>> > e.g. :include-wrappers, which would, if set to t, include the export
>>>> > wrappers in the tangled file. This might be useful for debugging
>>>> > exporting of code block results, but not for general tangling.
>>>> 
>>>> Thanks for chiming in. This was my gut reaction to the default
>>>> behavior. I guess we're still only a sample size of 2, but
>>>> intuitively, I would think that tangling would be a separate beast in
>>>> most cases from exporting. Just to have it on the record, if I tangle,
>>>> it's usually to take the code I've used in something like a Beamer
>>>> presentation or document and combine it into a single .R file so
>>>> someone can run it without needing Org-mode.
>>>
>>> [deleted]
>>>
>>> Sorry to be late to add my $0.02...
>>>
>>> I never want the try/catch wrappers.
>>>
>>> But noweb is indispensable.
>>>
>>> I use noweb a lot to organize and collect blocks. In some cases, I export
>>> them and in others I just tangle them.
>>>
>>> I hope that the revised code will allow me to turn off try/catch wrapping
>>> and still be able to use noweb when tangling or exporting.
>>>
>>
>> In addition to noweb, there are cases where variable expansion is useful
>> in tangled code.
>>
>> The simplest option is to move things like try/catch blocks out of the
>> code block expansion function, and into the execution function.  Then if
>> other language present similar constructs (which we want to add to
>> execution by default but never want to tangle), we can think about
>> abstracting this out into some new level of code block expansion.
>>
>> Thoughts?
>
> Makes perfect sense to me, and would definitely be the better place to
> add them.
>
> If one wants enclosing code in the tangling, there is always
> the :epilogue and :prologue header arguments, and the try/catch should
> be considered as internal to the execution.
>

Great, how's this patch work?  If it looks good I'll apply it.

Thanks,


[-- Warning: decoded text below may be mangled, UTF-8 assumed --]
[-- Attachment #2: 0001-only-wrap-R-code-graphics-file-on-execution.patch --]
[-- Type: text/x-diff, Size: 2774 bytes --]

From 838f26c35867e7af0dc46698db41d4df13dfb890 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 | 39 ++++++++++++++++++++-------------------
 1 file changed, 20 insertions(+), 19 deletions(-)

diff --git a/lisp/ob-R.el b/lisp/ob-R.el
index 62aa7f2..bf7029c 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 +118,17 @@ 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 (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
-- 
1.9.0


[-- Attachment #3: Type: text/plain, Size: 63 bytes --]


-- 
Eric Schulte
https://cs.unm.edu/~eschulte
PGP: 0x614CA05D