Re: [O] [BABEL] BUG Re: Omitting try/catch blocks from tangled R code?
I applied the patch and it is working. Great, I've just pushed it up. Best, -- Eric Schulte https://cs.unm.edu/~eschulte PGP: 0x614CA05D
Re: [O] [BABEL] BUG Re: Omitting try/catch blocks from tangled R code?
Eric Schulte schulte.e...@gmail.com writes:
Rainer M Krug rai...@krugs.de writes:
Eric Schulte schulte.e...@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: rai...@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.
Sorry - no idea what went wrong, but I assumed I applied the old
patch.
I applied the patch and it is working.
Cheers,
Rainer
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.e...@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,
Re: [O] [BABEL] BUG Re: Omitting try/catch blocks from tangled R code?
Rainer M Krug rai...@krugs.de writes:
Eric Schulte schulte.e...@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: rai...@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.e...@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()))
+
Re: [O] [BABEL] BUG Re: Omitting try/catch blocks from tangled R code?
Eric Schulte schulte.e...@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: rai...@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.e...@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: Raineratkrugsdotde
PGP: 0x0F52F982
pgpI5sDy3A9Yg.pgp
Description: PGP signature
Re: [O] [BABEL] BUG Re: Omitting try/catch blocks from tangled R code?
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: rai...@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.
Best,
From d67248db79faf19e1bdcac0230c37670b6115bdd Mon Sep 17 00:00:00 2001
From: Eric Schulte schulte.e...@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
Re: [O] [BABEL] BUG Re: Omitting try/catch blocks from tangled R code?
bini55Rmu2tZs.bin Description: application/pgp-encrypted binZzbsrmcnDw.bin Description: Binary data
Re: [O] [BABEL] BUG Re: Omitting try/catch blocks from tangled R code?
Eric Schulte schulte.e...@gmail.com writes: Rainer M Krug rai...@krugs.de writes: Eric Schulte schulte.e...@gmail.com writes: Rainer M Krug rai...@krugs.de writes: Eric Schulte schulte.e...@gmail.com writes: Rainer M Krug rai...@krugs.de writes: Eric Schulte schulte.e...@gmail.com writes: Charles Berry ccbe...@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. Git still puzzles me a lot... If you tell me how I can apply this patch (from emacs?) I will try it out. Here are some instructions from the command line. 1. write the patch out to a file on disk, say /tmp/0001-etc...patch 2. cd into the org-mode directory 3. make sure you're up to date with the latest git pull 4. apply the patch git am /tmp/0001-etc...patch and that should do it. OK - managed to apply the patch. Using Org-mode version 8.2.5h (release_8.2.5h-846-geb806d @ /Users/rainerkrug/.emacs.d/org-mode/lisp/) updated this morning, I get the following error: Could you provide a minimal example file generating this error? 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: rai...@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/) Cheers, Rainer Thanks, , | Debugger entered--Lisp error: (wrong-type-argument sequencep 67) | mapconcat(identity COLUMNS - | read.table(\/var/folders/50/wcr5bjwn75q595n6x82gxj28gn/T/babel-21363l1U/R-import-21363S9b\,\n | header=TRUE,\n row.names=1,\n sep=\\\t\,\n | as.is=TRUE)\nCOLS_TO_EVAL - | read.table(\/var/folders/50/wcr5bjwn75q595n6x82gxj28gn/T/babel-21363l1U/R-import-21363fHi\,\n | header=TRUE,\n row.names=1,\n sep=\\\t\,\n as.is=TRUE)\nALLSPECIES | - | read.table(\/var/folders/50/wcr5bjwn75q595n6x82gxj28gn/T/babel-21363l1U/R-import-21363sRo\,\n | header=TRUE,\n row.names=1,\n sep=\\\t\,\n as.is=TRUE)\nSPECIES - | read.table(\/var/folders/50/wcr5bjwn75q595n6x82gxj28gn/T/babel-21363l1U/R-import-213635bu\,\n | header=TRUE,\n row.names=1,\n sep=\\\t\,\n as.is=TRUE)\nYEARS - |
Re: [O] [BABEL] BUG Re: Omitting try/catch blocks from tangled R code?
Rainer M Krug rai...@krugs.de writes: Eric Schulte schulte.e...@gmail.com writes: Rainer M Krug rai...@krugs.de writes: Eric Schulte schulte.e...@gmail.com writes: Rainer M Krug rai...@krugs.de writes: Eric Schulte schulte.e...@gmail.com writes: Charles Berry ccbe...@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. Git still puzzles me a lot... If you tell me how I can apply this patch (from emacs?) I will try it out. Here are some instructions from the command line. 1. write the patch out to a file on disk, say /tmp/0001-etc...patch 2. cd into the org-mode directory 3. make sure you're up to date with the latest git pull 4. apply the patch git am /tmp/0001-etc...patch and that should do it. OK - managed to apply the patch. Using Org-mode version 8.2.5h (release_8.2.5h-846-geb806d @ /Users/rainerkrug/.emacs.d/org-mode/lisp/) updated this morning, I get the following error: Could you provide a minimal example file generating this error? Thanks, , | Debugger entered--Lisp error: (wrong-type-argument sequencep 67) | mapconcat(identity COLUMNS - | read.table(\/var/folders/50/wcr5bjwn75q595n6x82gxj28gn/T/babel-21363l1U/R-import-21363S9b\,\n | header=TRUE,\n row.names=1,\n sep=\\\t\,\n | as.is=TRUE)\nCOLS_TO_EVAL - | read.table(\/var/folders/50/wcr5bjwn75q595n6x82gxj28gn/T/babel-21363l1U/R-import-21363fHi\,\n | header=TRUE,\n row.names=1,\n sep=\\\t\,\n as.is=TRUE)\nALLSPECIES | - | read.table(\/var/folders/50/wcr5bjwn75q595n6x82gxj28gn/T/babel-21363l1U/R-import-21363sRo\,\n | header=TRUE,\n row.names=1,\n sep=\\\t\,\n as.is=TRUE)\nSPECIES - | read.table(\/var/folders/50/wcr5bjwn75q595n6x82gxj28gn/T/babel-21363l1U/R-import-213635bu\,\n | header=TRUE,\n row.names=1,\n sep=\\\t\,\n as.is=TRUE)\nYEARS - | read.table(\/var/folders/50/wcr5bjwn75q595n6x82gxj28gn/T/babel-21363l1U/R-import-21363Gm0\,\n | header=TRUE,\n row.names=1,\n sep=\\\t\,\n as.is=TRUE)\nPRESENT - | 2008\nMINEFFORT - 3\nPROPTRAIN - 0.6\nRNGSEED - 13\nRNGKIND - | \Mersenne-Twister\\nRNGNORMALKIND - \Inversion\\nREFGRID - | \./refGrid_8km.rds\\nIFN - | \./__BOX__/IFN/DB_IFN/rds/tabplot.rds\\nIFNCOUNT - | \./__BOX__/IFN/DB_IFN/rdsRasterized/tabplot.count.8km.rds\\nIFNMEAN | - | \./__BOX__/IFN/DB_IFN/rdsRasterized/tabplot.mean.8km.rds\\nIFNPRES | - | \./__BOX__/IFN/DB_IFN/rdsRasterized/tabplot.pres.8km.rds\\nIFNSD | - | \./__BOX__/IFN/DB_IFN/rdsRasterized/tabplot.sd.8km.rds\\nIFNTABTREE | - \./__BOX__/IFN/DB_IFN/rds/tabtree.rds\\ndata.sources - | list.files(\./data\, pattern=\*.rda$\, | full.names=TRUE)\nR.sources - list.files(\./R\,
Re: [O] [BABEL] BUG Re: Omitting try/catch blocks from tangled R code?
Eric Schulte schulte.e...@gmail.com writes: Rainer M Krug rai...@krugs.de writes: Eric Schulte schulte.e...@gmail.com writes: Rainer M Krug rai...@krugs.de writes: Eric Schulte schulte.e...@gmail.com writes: Charles Berry ccbe...@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. Git still puzzles me a lot... If you tell me how I can apply this patch (from emacs?) I will try it out. Here are some instructions from the command line. 1. write the patch out to a file on disk, say /tmp/0001-etc...patch 2. cd into the org-mode directory 3. make sure you're up to date with the latest git pull 4. apply the patch git am /tmp/0001-etc...patch and that should do it. OK - managed to apply the patch. Using Org-mode version 8.2.5h (release_8.2.5h-846-geb806d @ /Users/rainerkrug/.emacs.d/org-mode/lisp/) updated this morning, I get the following error: , | Debugger entered--Lisp error: (wrong-type-argument sequencep 67) | mapconcat(identity COLUMNS - read.table(\/var/folders/50/wcr5bjwn75q595n6x82gxj28gn/T/babel-21363l1U/R-import-21363S9b\,\n header=TRUE,\n row.names=1,\n sep=\\\t\,\n as.is=TRUE)\nCOLS_TO_EVAL - read.table(\/var/folders/50/wcr5bjwn75q595n6x82gxj28gn/T/babel-21363l1U/R-import-21363fHi\,\n header=TRUE,\n row.names=1,\n sep=\\\t\,\n as.is=TRUE)\nALLSPECIES - read.table(\/var/folders/50/wcr5bjwn75q595n6x82gxj28gn/T/babel-21363l1U/R-import-21363sRo\,\n header=TRUE,\n row.names=1,\n sep=\\\t\,\n as.is=TRUE)\nSPECIES - read.table(\/var/folders/50/wcr5bjwn75q595n6x82gxj28gn/T/babel-21363l1U/R-import-213635bu\,\n header=TRUE,\n row.names=1,\n sep=\\\t\,\n as.is=TRUE)\nYEARS - read.table(\/var/folders/50/wcr5bjwn75q595n6x82gxj28gn/T/babel-21363l1U/R-import-21363Gm0\,\n header=TRUE,\n row.names=1,\n sep=\\\t\,\n as.is=TRUE)\nPRESENT - 2008\nMINEFFORT - 3\nPROPTRAIN - 0.6\nRNGSEED - 13\nRNGKIND - \Mersenne-Twister\\nRNGNORMALKIND - \Inversion\\nREFGRID - \./refGrid_8km.rds\\nIFN - \./__BOX__/IFN/DB_IFN/rds/tabplot.rds\\nIFNCOUNT - \./__BOX__/IFN/DB_IFN/rdsRasterized/tabplot.count.8km.rds\\nIFNMEAN - \./__BOX__/IFN/DB_IFN/rdsRasterized/tabplot.mean.8km.rds\\nIFNPRES -
Re: [O] [BABEL] BUG Re: Omitting try/catch blocks from tangled R code?
Eric Schulte schulte.e...@gmail.com writes: Rainer M Krug rai...@krugs.de writes: Eric Schulte schulte.e...@gmail.com writes: Charles Berry ccbe...@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. Git still puzzles me a lot... If you tell me how I can apply this patch (from emacs?) I will try it out. Thanks, Rainer Thanks, -- Rainer M. Krug email: Raineratkrugsdotde PGP: 0x0F52F982 pgp2vOWpX0Aa5.pgp Description: PGP signature
Re: [O] [BABEL] BUG Re: Omitting try/catch blocks from tangled R code?
Rainer M Krug rai...@krugs.de writes: Eric Schulte schulte.e...@gmail.com writes: Rainer M Krug rai...@krugs.de writes: Eric Schulte schulte.e...@gmail.com writes: Charles Berry ccbe...@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. Git still puzzles me a lot... If you tell me how I can apply this patch (from emacs?) I will try it out. Here are some instructions from the command line. 1. write the patch out to a file on disk, say /tmp/0001-etc...patch 2. cd into the org-mode directory 3. make sure you're up to date with the latest git pull 4. apply the patch git am /tmp/0001-etc...patch and that should do it. Best, Thanks, Rainer Thanks, -- Eric Schulte https://cs.unm.edu/~eschulte PGP: 0x614CA05D
Re: [O] [BABEL] BUG Re: Omitting try/catch blocks from tangled R code?
Rainer M Krug rai...@krugs.de writes:
Eric Schulte schulte.e...@gmail.com writes:
Charles Berry ccbe...@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,
From 838f26c35867e7af0dc46698db41d4df13dfb890 Mon Sep 17 00:00:00 2001
From: Eric Schulte schulte.e...@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='',
Re: [O] [BABEL] BUG Re: Omitting try/catch blocks from tangled R code?
Eric Schulte schulte.e...@gmail.com writes: Charles Berry ccbe...@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. Rainer Best, Chuck -- Rainer M. Krug email: Raineratkrugsdotde PGP: 0x0F52F982 pgpAsJeYJDIhw.pgp Description: PGP signature
Re: [O] [BABEL] BUG Re: Omitting try/catch blocks from tangled R code?
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. Best, Chuck
Re: [O] [BABEL] BUG Re: Omitting try/catch blocks from tangled R code?
Charles Berry ccbe...@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 $0.02... I never want the try/catch wrappers. But noweb is indispensable. I use noweb a lot to organize and collect blocks. In some cases, I export them and in others I just tangle them. I hope that the revised code will allow me to turn off try/catch wrapping and still be able to use noweb when tangling or exporting. In addition to noweb, there are cases where variable expansion is useful in tangled code. The simplest option is to move things like try/catch blocks out of the code block expansion function, and into the execution function. Then if other language present similar constructs (which we want to add to execution by default but never want to tangle), we can think about abstracting this out into some new level of code block expansion. Thoughts? Best, Chuck -- Eric Schulte https://cs.unm.edu/~eschulte PGP: 0x614CA05D
Re: [O] [BABEL] BUG Re: Omitting try/catch blocks from tangled R code?
Eric Schulte schulte.e...@gmail.com writes:
John Hendy jw.he...@gmail.com writes:
On Mon, Mar 17, 2014 at 10:00 AM, Eric Schulte schulte.e...@gmail.com
wrote:
John Hendy jw.he...@gmail.com writes:
On Fri, Feb 7, 2014 at 1:22 PM, Rainer M Krug rai...@krugs.de wrote:
On 02/07/14, 17:47 , Eric Schulte wrote:
Rainer M Krug rai...@krugs.de writes:
On 02/07/14, 07:18 , John Hendy wrote:
Greetings,
I don't usually tangle, but am creating a code file to go along with a
presentation I'm giving this weekend so that attendees can try things
out afterward by cloning my github repo where all the data and
necessary files are stored.
In my presentation (Beamer), I create plots via the R pdf() device,
and noticed that all of the tangled code where plots are generated
contains the following:
pdf(file=file.pdf); tryCatch({
code block contents here
},error=function(e){plot(x=-1:1, y=-1:1, type='n', xlab='', ylab='',
axes=FALSE); text(x=0, y=0, labels=e$message, col='red');
paste('ERROR', e$message, sep=' : ')}); dev.off()
Is there a way to omit this?
This is a bug which must have been introduced some time ago - in the
stock version of emacs (Org-mode version 7.9.3f
(release_7.9.3f-17-g7524ef @
/usr/local/Cellar/emacs/24.3/share/emacs/24.3/lisp/org/)) it does not
tangle the enclosing commands to create graphics, but in 8.2 it does (I
don't have an older version at hand to go further back).
I believe this was introduced by your commit eaa3a761d. Reversion of
which with the following should provide a temporary workaround.
I take this back, the behavior is unrelated to Rainer's commit adding
try/catch blocks to R graphics creation logic.
In fact I don't believe this is a bug, rather the default behavior is to
expand code block bodies on tangling. This behavior may be changed by
using the :no-expand header argument which will inhibit code block body
expansion during tangling.
Got it, and thanks for the new variable tip!
Out of curiosity, is there a consensus that this is the preferred
behavior for tangling by default?
There may have been a consensus in a single thread motivated by a single
use case, which should not necessarily be a global consensus.
I'm guessing at some point it was decided that the need was preferred
to have these bits inserted before/after code blocks, but just trying
to confirm this. It seems odd to me, at least given R's behavior, that
someone would prefer these bits to show up in the tangled file since
they appeared to serve the purpose of having Org not fail during
export vs. benefitting the code in any way (if I wasn't running code
through R, I'd just get the errors directly).
I'd be happy to add :no-expand to the default R header arguments. Or
even to change this behavior globally, if the current behavior is
universally surprising.
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.
Cheers,
Rainer
Best,
John
Best,
--
Eric Schulte
https://cs.unm.edu/~eschulte
PGP: 0x614CA05D
--
Rainer M. Krug
email: RMKrugatgmaildotcom
pgpbTlCE4agPe.pgp
Description: PGP signature
Re: [O] [BABEL] BUG Re: Omitting try/catch blocks from tangled R code?
John Hendy jw.he...@gmail.com writes:
On Fri, Feb 7, 2014 at 1:22 PM, Rainer M Krug rai...@krugs.de wrote:
On 02/07/14, 17:47 , Eric Schulte wrote:
Rainer M Krug rai...@krugs.de writes:
On 02/07/14, 07:18 , John Hendy wrote:
Greetings,
I don't usually tangle, but am creating a code file to go along with a
presentation I'm giving this weekend so that attendees can try things
out afterward by cloning my github repo where all the data and
necessary files are stored.
In my presentation (Beamer), I create plots via the R pdf() device,
and noticed that all of the tangled code where plots are generated
contains the following:
pdf(file=file.pdf); tryCatch({
code block contents here
},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$message, sep=' : ')}); dev.off()
Is there a way to omit this?
This is a bug which must have been introduced some time ago - in the
stock version of emacs (Org-mode version 7.9.3f
(release_7.9.3f-17-g7524ef @
/usr/local/Cellar/emacs/24.3/share/emacs/24.3/lisp/org/)) it does not
tangle the enclosing commands to create graphics, but in 8.2 it does (I
don't have an older version at hand to go further back).
I believe this was introduced by your commit eaa3a761d. Reversion of
which with the following should provide a temporary workaround.
I take this back, the behavior is unrelated to Rainer's commit adding
try/catch blocks to R graphics creation logic.
In fact I don't believe this is a bug, rather the default behavior is to
expand code block bodies on tangling. This behavior may be changed by
using the :no-expand header argument which will inhibit code block body
expansion during tangling.
Best,
--
Eric Schulte
https://cs.unm.edu/~eschulte
PGP: 0x614CA05D
Re: [O] [BABEL] BUG Re: Omitting try/catch blocks from tangled R code?
On Mon, Mar 17, 2014 at 10:00 AM, Eric Schulte schulte.e...@gmail.com wrote:
John Hendy jw.he...@gmail.com writes:
On Fri, Feb 7, 2014 at 1:22 PM, Rainer M Krug rai...@krugs.de wrote:
On 02/07/14, 17:47 , Eric Schulte wrote:
Rainer M Krug rai...@krugs.de writes:
On 02/07/14, 07:18 , John Hendy wrote:
Greetings,
I don't usually tangle, but am creating a code file to go along with a
presentation I'm giving this weekend so that attendees can try things
out afterward by cloning my github repo where all the data and
necessary files are stored.
In my presentation (Beamer), I create plots via the R pdf() device,
and noticed that all of the tangled code where plots are generated
contains the following:
pdf(file=file.pdf); tryCatch({
code block contents here
},error=function(e){plot(x=-1:1, y=-1:1, type='n', xlab='', ylab='',
axes=FALSE); text(x=0, y=0, labels=e$message, col='red');
paste('ERROR', e$message, sep=' : ')}); dev.off()
Is there a way to omit this?
This is a bug which must have been introduced some time ago - in the
stock version of emacs (Org-mode version 7.9.3f
(release_7.9.3f-17-g7524ef @
/usr/local/Cellar/emacs/24.3/share/emacs/24.3/lisp/org/)) it does not
tangle the enclosing commands to create graphics, but in 8.2 it does (I
don't have an older version at hand to go further back).
I believe this was introduced by your commit eaa3a761d. Reversion of
which with the following should provide a temporary workaround.
I take this back, the behavior is unrelated to Rainer's commit adding
try/catch blocks to R graphics creation logic.
In fact I don't believe this is a bug, rather the default behavior is to
expand code block bodies on tangling. This behavior may be changed by
using the :no-expand header argument which will inhibit code block body
expansion during tangling.
Got it, and thanks for the new variable tip!
Out of curiosity, is there a consensus that this is the preferred
behavior for tangling by default? I'm guessing at some point it was
decided that the need was preferred to have these bits inserted
before/after code blocks, but just trying to confirm this. It seems
odd to me, at least given R's behavior, that someone would prefer
these bits to show up in the tangled file since they appeared to serve
the purpose of having Org not fail during export vs. benefitting the
code in any way (if I wasn't running code through R, I'd just get the
errors directly).
John
Best,
--
Eric Schulte
https://cs.unm.edu/~eschulte
PGP: 0x614CA05D
Re: [O] [BABEL] BUG Re: Omitting try/catch blocks from tangled R code?
On Fri, Feb 7, 2014 at 1:22 PM, Rainer M Krug rai...@krugs.de wrote:
On 02/07/14, 17:47 , Eric Schulte wrote:
Rainer M Krug rai...@krugs.de writes:
On 02/07/14, 07:18 , John Hendy wrote:
Greetings,
I don't usually tangle, but am creating a code file to go along with a
presentation I'm giving this weekend so that attendees can try things
out afterward by cloning my github repo where all the data and
necessary files are stored.
In my presentation (Beamer), I create plots via the R pdf() device,
and noticed that all of the tangled code where plots are generated
contains the following:
pdf(file=file.pdf); tryCatch({
code block contents here
},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()
Is there a way to omit this?
This is a bug which must have been introduced some time ago - in the
stock version of emacs (Org-mode version 7.9.3f
(release_7.9.3f-17-g7524ef @
/usr/local/Cellar/emacs/24.3/share/emacs/24.3/lisp/org/)) it does not
tangle the enclosing commands to create graphics, but in 8.2 it does (I
don't have an older version at hand to go further back).
I believe this was introduced by your commit eaa3a761d. Reversion of
which with the following should provide a temporary workaround.
I checked it with version 8.2, which was, as far as I remember, before
my change of the R code to include the error handling, and the pdf(...)
... dev.off() was in the tangled file as well - so the behaviour must
have been introduced earlier. The only change I did was to change the R
code, so no change in the behavior if it is tangled or not.
I will look at it again on Monday to go back through the released
versions to narrow down where this had changed.
Just following up on this to see if the current behavior is desired or
if, indeed, something should/could change.
Thanks!
John
git revert eaa3a761d
I don't think that this actually changes much - only that the enclosing
code will become pdf(...) THE CODE dev.off()
Cheers,
Rainer
Perhaps the try/catch code should be moved from org-babel-expand-body:R
to org-babel-execute:R. Alternately, the code should stay as is and you
should use the no-expand header argument during tangling.
I'm not sure which makes the most sense, but I'd lean towards the
former.
Best,
I'm guessing this is here to create a blank plot with the error as the
output when something goes awry?
Yes.
I checked around variable completions of org-babel-tangle-* and
searched google for terms like org babel tangle try catch but am not
finding anything that looks like what I need.
There is nothing, as it should not be tangled. The enclosing commands
concern the export, but not tangling,
I agree that the :result graphics header argument caused commands should
not be in the tangled file.
Another question is about the :epilogue and :prologue which I think
should be present (haven't checked if they are...).
Cheers,
Rainer
Thanks,
John
--
Rainer M. Krug, PhD (Conservation Ecology, SUN), MSc (Conservation
Biology, UCT), Dipl. Phys. (Germany)
Centre of Excellence for Invasion Biology
Stellenbosch University
South Africa
Tel : +33 - (0)9 53 10 27 44
Cell: +33 - (0)6 85 62 59 98
Fax : +33 - (0)9 58 10 27 44
Fax (D):+49 - (0)3 21 21 25 22 44
email: rai...@krugs.de
Skype: RMkrug
[O] [BABEL] BUG Re: Omitting try/catch blocks from tangled R code?
On 02/07/14, 07:18 , John Hendy wrote:
Greetings,
I don't usually tangle, but am creating a code file to go along with a
presentation I'm giving this weekend so that attendees can try things
out afterward by cloning my github repo where all the data and
necessary files are stored.
In my presentation (Beamer), I create plots via the R pdf() device,
and noticed that all of the tangled code where plots are generated
contains the following:
pdf(file=file.pdf); tryCatch({
code block contents here
},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()
Is there a way to omit this?
This is a bug which must have been introduced some time ago - in the
stock version of emacs (Org-mode version 7.9.3f
(release_7.9.3f-17-g7524ef @
/usr/local/Cellar/emacs/24.3/share/emacs/24.3/lisp/org/)) it does not
tangle the enclosing commands to create graphics, but in 8.2 it does (I
don't have an older version at hand to go further back).
I'm guessing this is here to create a blank plot with the error as the
output when something goes awry?
Yes.
I checked around variable completions of org-babel-tangle-* and
searched google for terms like org babel tangle try catch but am not
finding anything that looks like what I need.
There is nothing, as it should not be tangled. The enclosing commands
concern the export, but not tangling,
I agree that the :result graphics header argument caused commands should
not be in the tangled file.
Another question is about the :epilogue and :prologue which I think
should be present (haven't checked if they are...).
Cheers,
Rainer
Thanks,
John
--
Rainer M. Krug, PhD (Conservation Ecology, SUN), MSc (Conservation
Biology, UCT), Dipl. Phys. (Germany)
Centre of Excellence for Invasion Biology
Stellenbosch University
South Africa
Tel : +33 - (0)9 53 10 27 44
Cell: +33 - (0)6 85 62 59 98
Fax : +33 - (0)9 58 10 27 44
Fax (D):+49 - (0)3 21 21 25 22 44
email: rai...@krugs.de
Skype: RMkrug
signature.asc
Description: OpenPGP digital signature
Re: [O] [BABEL] BUG Re: Omitting try/catch blocks from tangled R code?
Rainer M Krug rai...@krugs.de writes:
On 02/07/14, 07:18 , John Hendy wrote:
Greetings,
I don't usually tangle, but am creating a code file to go along with a
presentation I'm giving this weekend so that attendees can try things
out afterward by cloning my github repo where all the data and
necessary files are stored.
In my presentation (Beamer), I create plots via the R pdf() device,
and noticed that all of the tangled code where plots are generated
contains the following:
pdf(file=file.pdf); tryCatch({
code block contents here
},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()
Is there a way to omit this?
This is a bug which must have been introduced some time ago - in the
stock version of emacs (Org-mode version 7.9.3f
(release_7.9.3f-17-g7524ef @
/usr/local/Cellar/emacs/24.3/share/emacs/24.3/lisp/org/)) it does not
tangle the enclosing commands to create graphics, but in 8.2 it does (I
don't have an older version at hand to go further back).
I believe this was introduced by your commit eaa3a761d. Reversion of
which with the following should provide a temporary workaround.
git revert eaa3a761d
Perhaps the try/catch code should be moved from org-babel-expand-body:R
to org-babel-execute:R. Alternately, the code should stay as is and you
should use the no-expand header argument during tangling.
I'm not sure which makes the most sense, but I'd lean towards the
former.
Best,
I'm guessing this is here to create a blank plot with the error as the
output when something goes awry?
Yes.
I checked around variable completions of org-babel-tangle-* and
searched google for terms like org babel tangle try catch but am not
finding anything that looks like what I need.
There is nothing, as it should not be tangled. The enclosing commands
concern the export, but not tangling,
I agree that the :result graphics header argument caused commands should
not be in the tangled file.
Another question is about the :epilogue and :prologue which I think
should be present (haven't checked if they are...).
Cheers,
Rainer
Thanks,
John
--
Eric Schulte
https://cs.unm.edu/~eschulte
PGP: 0x614CA05D
Re: [O] [BABEL] BUG Re: Omitting try/catch blocks from tangled R code?
On 02/07/14, 17:47 , Eric Schulte wrote:
Rainer M Krug rai...@krugs.de writes:
On 02/07/14, 07:18 , John Hendy wrote:
Greetings,
I don't usually tangle, but am creating a code file to go along with a
presentation I'm giving this weekend so that attendees can try things
out afterward by cloning my github repo where all the data and
necessary files are stored.
In my presentation (Beamer), I create plots via the R pdf() device,
and noticed that all of the tangled code where plots are generated
contains the following:
pdf(file=file.pdf); tryCatch({
code block contents here
},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()
Is there a way to omit this?
This is a bug which must have been introduced some time ago - in the
stock version of emacs (Org-mode version 7.9.3f
(release_7.9.3f-17-g7524ef @
/usr/local/Cellar/emacs/24.3/share/emacs/24.3/lisp/org/)) it does not
tangle the enclosing commands to create graphics, but in 8.2 it does (I
don't have an older version at hand to go further back).
I believe this was introduced by your commit eaa3a761d. Reversion of
which with the following should provide a temporary workaround.
I checked it with version 8.2, which was, as far as I remember, before
my change of the R code to include the error handling, and the pdf(...)
... dev.off() was in the tangled file as well - so the behaviour must
have been introduced earlier. The only change I did was to change the R
code, so no change in the behavior if it is tangled or not.
I will look at it again on Monday to go back through the released
versions to narrow down where this had changed.
git revert eaa3a761d
I don't think that this actually changes much - only that the enclosing
code will become pdf(...) THE CODE dev.off()
Cheers,
Rainer
Perhaps the try/catch code should be moved from org-babel-expand-body:R
to org-babel-execute:R. Alternately, the code should stay as is and you
should use the no-expand header argument during tangling.
I'm not sure which makes the most sense, but I'd lean towards the
former.
Best,
I'm guessing this is here to create a blank plot with the error as the
output when something goes awry?
Yes.
I checked around variable completions of org-babel-tangle-* and
searched google for terms like org babel tangle try catch but am not
finding anything that looks like what I need.
There is nothing, as it should not be tangled. The enclosing commands
concern the export, but not tangling,
I agree that the :result graphics header argument caused commands should
not be in the tangled file.
Another question is about the :epilogue and :prologue which I think
should be present (haven't checked if they are...).
Cheers,
Rainer
Thanks,
John
--
Rainer M. Krug, PhD (Conservation Ecology, SUN), MSc (Conservation
Biology, UCT), Dipl. Phys. (Germany)
Centre of Excellence for Invasion Biology
Stellenbosch University
South Africa
Tel : +33 - (0)9 53 10 27 44
Cell: +33 - (0)6 85 62 59 98
Fax : +33 - (0)9 58 10 27 44
Fax (D):+49 - (0)3 21 21 25 22 44
email: rai...@krugs.de
Skype: RMkrug
signature.asc
Description: OpenPGP digital signature
