Missing newline in R code causes Org-Mode eval to hang

Missing newline in R code causes Org-Mode eval to hang

[Michael Hannon]

Greetings.  The appended R code fragment executes without problem in
an ESS buffer, but it hangs indefinitely when I try to execute it
directly from the Org buffer via C-c C-c.

The solution is to add the trailing newline in the "noteToSelf"
variable:

    noteToSelf <- "Buy low.\nSell high.\n"

Obviously this isn't a big deal from my perspective, but it did
surprise me, and it does seem inconsistent.

BTW, I've appended also the details of my own (linux) configuration,
but I tried the same thing on a different OS (Mac OS 10.6.8) and got
the same results.

-- Mike

###### Org code that exhibits error

#+BABEL: :session *R* :cache yes :results output verbatim :exports both :tangle yes

* This is a test

#+begin_src R

  x <- 42
  noteToSelf <- "Buy low.\nSell high."
  cat(noteToSelf)
  print("All done now")

#+end_src


###### My set-up

Emacs  : GNU Emacs 23.2.1 (x86_64-redhat-linux-gnu, GTK+ Version 2.24.4)
 of 2011-05-23 on x86-12.phx2.fedoraproject.org
Package: Org-mode version 7.7 (release_7.7.328.g1a97)

current state:
==============
(setq
 org-export-latex-after-initial-vars-hook '(org-beamer-after-initial-vars)
 org-structure-template-alist '(("r" "#+begin_src R\n\n#+end_src" "<src lang=\"R\">\n\n</src>")
("S" "#+BEGIN_SRC ?\n\n#+END_SRC" "<src lang=\"?\">\n\n</src>")
("s" "#+begin_src ?\n\n#+end_src" "<src lang=\"?\">\n\n</src>")
("e" "#+begin_example\n?\n#+end_example" "<example>\n?\n</example>")
("q" "#+begin_quote\n?\n#+end_quote" "<quote>\n?\n</quote>")
("v" "#+begin_verse\n?\n#+end_verse" "<verse>\n?\n/verse>")
("c" "#+begin_center\n?\n#+end_center" "<center>\n?\n/center>")
("l" "#+begin_latex\n?\n#+end_latex" "<literal style=\"latex\">\n?\n</literal>")
("L" "#+latex: " "<literal style=\"latex\">?</literal>")
("h" "#+begin_html\n?\n#+end_html" "<literal style=\"html\">\n?\n</literal>")
("H" "#+html: " "<literal style=\"html\">?</literal>") ("a" "#+begin_ascii\n?\n#+end_ascii")
("A" "#+ascii: ") ("i" "#+index: ?" "#+index: ?")
("I" "#+include %file ?" "<include file=%file markup=\"?\">"))
 org-speed-command-hook '(org-speed-command-default-hook org-babel-speed-command-hook)
 org-agenda-files '("~/Documents/scratch.org")
 org-babel-load-languages '((emacs-lisp . t) (R . t) (python . t) (sh . t) (latex . t) (C . t) (octave \.t))
 org-metaup-hook '(org-babel-load-in-session-maybe)
 org-after-todo-state-change-hook '(org-clock-out-if-current)
 org-babel-tangle-lang-exts '(("C++" . "cpp") ("latex" . "tex") ("python" . "py") ("emacs-lisp" . "el"))
 org-export-blocks-postblock-hook '(org-exp-res/src-name-cleanup)
 org-export-latex-format-toc-function 'org-export-latex-format-toc-default
 org-tab-first-hook '(org-hide-block-toggle-maybe org-src-native-tab-command-maybe org-babel-hide-result-toggle-maybe)
 org-src-mode-hook '(org-src-babel-configure-edit-buffer org-src-mode-configure-edit-buffer)
 org-confirm-shell-link-function 'yes-or-no-p
 org-export-first-hook '(org-beamer-initialize-open-trackers)
 org-agenda-before-write-hook '(org-agenda-add-entry-text)
 org-blank-before-new-entry nil
 org-babel-pre-tangle-hook '(save-buffer)
 org-cycle-hook '(org-cycle-hide-archived-subtrees org-cycle-hide-drawers org-cycle-show-empty-lines
 org-optimize-window-after-visibility-change)
 org-export-preprocess-before-normalizing-links-hook '(org-remove-file-link-modifiers)
 org-mode-hook '(#[nil "\300\301\302\303\304$\207" [org-add-hook change-major-mode-hook org-show-block-all append local] 5]
#[nil "\300\301\302\303\304$\207" [org-add-hook change-major-mode-hook org-babel-show-result-all append local] 5]
org-babel-result-hide-spec org-babel-hide-all-hashes)
 org-ctrl-c-ctrl-c-hook '(org-babel-hash-at-point org-babel-execute-safely-maybe)
 org-confirm-elisp-link-function 'yes-or-no-p
 org-export-interblocks '((lob org-babel-exp-lob-one-liners) (src org-babel-exp-inline-src-blocks))
 org-clock-out-hook '(org-clock-remove-empty-clock-drawer)
 org-occur-hook '(org-first-headline-recenter)
 org-from-is-user-regexp "\\<Michael Hannon\\>"
 org-export-preprocess-before-selecting-backend-code-hook '(org-beamer-select-beamer-code)
 org-confirm-babel-evaluate 'my-org-confirm-babel-evaluate
 org-export-latex-final-hook '(org-beamer-amend-header org-beamer-fix-toc org-beamer-auto-fragile-frames
      org-beamer-place-default-actions-for-lists)
 org-metadown-hook '(org-babel-pop-to-session-maybe)
 org-export-blocks '((src org-babel-exp-src-block nil) (comment org-export-blocks-format-comment t)
    (ditaa org-export-blocks-format-ditaa nil) (dot org-export-blocks-format-dot nil))
 )

Re: Missing newline in R code causes Org-Mode eval to hang

[Eric Schulte]

Hi Michael,

I can confirm this problem occurs on my machine locally.  I believe the
issue has something to do with how ESS sends inputs to R and waits for
command prompts from R.  When the lines are pasted into an ESS buffer
one at a time the problem does not occur, however when the lines are
pasted into ESS all at once (without pressing enter between lines) the
ESS comint buffer hangs.

One option could be to explicitly call `inferior-ess-send-input' between
every line of R code, but I'm loath to touch the comint interface as
small changes like this can sometimes have unpredictable effects.

Perhaps this could be fixed on the ESS side?

Best -- Eric

Michael Hannon <jm_hannon@yahoo.com> writes:

> Greetings.  The appended R code fragment executes without problem in
> an ESS buffer, but it hangs indefinitely when I try to execute it
> directly from the Org buffer via C-c C-c.
>
> The solution is to add the trailing newline in the "noteToSelf"
> variable:
>
>     noteToSelf <- "Buy low.\nSell high.\n"
>
> Obviously this isn't a big deal from my perspective, but it did
> surprise me, and it does seem inconsistent.
>
> BTW, I've appended also the details of my own (linux) configuration,
> but I tried the same thing on a different OS (Mac OS 10.6.8) and got
> the same results.
>
> -- Mike
>
> ###### Org code that exhibits error
>
> #+BABEL: :session *R* :cache yes :results output verbatim :exports both :tangle yes
>
> * This is a test
>
> #+begin_src R
>
>  x <- 42
>  noteToSelf <- "Buy low.\nSell high."
>  cat(noteToSelf)
>  print("All done now")
>
> #+end_src
>
>
> ###### My set-up
>
> Emacs  : GNU Emacs 23.2.1 (x86_64-redhat-linux-gnu, GTK+ Version 2.24.4)
>  of 2011-05-23 on x86-12.phx2.fedoraproject.org
> Package: Org-mode version 7.7 (release_7.7.328.g1a97)
>
> current state:
> ==============
> (setq
>  org-export-latex-after-initial-vars-hook '(org-beamer-after-initial-vars)
>  org-structure-template-alist '(("r" "#+begin_src R\n\n#+end_src" "<src lang=\"R\">\n\n</src>")
> ("S" "#+BEGIN_SRC ?\n\n#+END_SRC" "<src lang=\"?\">\n\n</src>")
> ("s" "#+begin_src ?\n\n#+end_src" "<src lang=\"?\">\n\n</src>")
> ("e" "#+begin_example\n?\n#+end_example" "<example>\n?\n</example>")
> ("q" "#+begin_quote\n?\n#+end_quote" "<quote>\n?\n</quote>")
> ("v" "#+begin_verse\n?\n#+end_verse" "<verse>\n?\n/verse>")
> ("c" "#+begin_center\n?\n#+end_center" "<center>\n?\n/center>")
> ("l" "#+begin_latex\n?\n#+end_latex" "<literal style=\"latex\">\n?\n</literal>")
> ("L" "#+latex: " "<literal style=\"latex\">?</literal>")
> ("h" "#+begin_html\n?\n#+end_html" "<literal style=\"html\">\n?\n</literal>")
> ("H" "#+html: " "<literal style=\"html\">?</literal>") ("a" "#+begin_ascii\n?\n#+end_ascii")
> ("A" "#+ascii: ") ("i" "#+index: ?" "#+index: ?")
> ("I" "#+include %file ?" "<include file=%file markup=\"?\">"))
>  org-speed-command-hook '(org-speed-command-default-hook org-babel-speed-command-hook)
>  org-agenda-files '("~/Documents/scratch.org")
>  org-babel-load-languages '((emacs-lisp . t) (R . t) (python . t) (sh . t) (latex . t) (C . t) (octave \.t))
>  org-metaup-hook '(org-babel-load-in-session-maybe)
>  org-after-todo-state-change-hook '(org-clock-out-if-current)
>  org-babel-tangle-lang-exts '(("C++" . "cpp") ("latex" . "tex") ("python" . "py") ("emacs-lisp" . "el"))
>  org-export-blocks-postblock-hook '(org-exp-res/src-name-cleanup)
>  org-export-latex-format-toc-function 'org-export-latex-format-toc-default
>  org-tab-first-hook '(org-hide-block-toggle-maybe org-src-native-tab-command-maybe org-babel-hide-result-toggle-maybe)
>  org-src-mode-hook '(org-src-babel-configure-edit-buffer org-src-mode-configure-edit-buffer)
>  org-confirm-shell-link-function 'yes-or-no-p
>  org-export-first-hook '(org-beamer-initialize-open-trackers)
>  org-agenda-before-write-hook '(org-agenda-add-entry-text)
>  org-blank-before-new-entry nil
>  org-babel-pre-tangle-hook '(save-buffer)
>  org-cycle-hook '(org-cycle-hide-archived-subtrees org-cycle-hide-drawers org-cycle-show-empty-lines
>  org-optimize-window-after-visibility-change)
>  org-export-preprocess-before-normalizing-links-hook '(org-remove-file-link-modifiers)
>  org-mode-hook '(#[nil "\300\301\302\303\304$\207" [org-add-hook change-major-mode-hook org-show-block-all append local] 5]
> #[nil "\300\301\302\303\304$\207" [org-add-hook change-major-mode-hook org-babel-show-result-all append local] 5]
> org-babel-result-hide-spec org-babel-hide-all-hashes)
>  org-ctrl-c-ctrl-c-hook '(org-babel-hash-at-point org-babel-execute-safely-maybe)
>  org-confirm-elisp-link-function 'yes-or-no-p
>  org-export-interblocks '((lob org-babel-exp-lob-one-liners) (src org-babel-exp-inline-src-blocks))
>  org-clock-out-hook '(org-clock-remove-empty-clock-drawer)
>  org-occur-hook '(org-first-headline-recenter)
>  org-from-is-user-regexp "\\<Michael Hannon\\>"
>  org-export-preprocess-before-selecting-backend-code-hook '(org-beamer-select-beamer-code)
>  org-confirm-babel-evaluate 'my-org-confirm-babel-evaluate
>  org-export-latex-final-hook '(org-beamer-amend-header org-beamer-fix-toc org-beamer-auto-fragile-frames
>       org-beamer-place-default-actions-for-lists)
>  org-metadown-hook '(org-babel-pop-to-session-maybe)
>  org-export-blocks '((src org-babel-exp-src-block nil) (comment org-export-blocks-format-comment t)
>     (ditaa org-export-blocks-format-ditaa nil) (dot org-export-blocks-format-dot nil))
>  )
>

-- 
Eric Schulte
http://cs.unm.edu/~eschulte/

Re: Missing newline in R code causes Org-Mode eval to hang

[Sebastien Vauban]

Hi Michael,

Michael Hannon wrote:
> Greetings.  The appended R code fragment executes without problem in
> an ESS buffer, but it hangs indefinitely when I try to execute it
> directly from the Org buffer via C-c C-c.
>
> The solution is to add the trailing newline in the "noteToSelf"
> variable:
>
>     noteToSelf <- "Buy low.\nSell high.\n"

The following code:

--8<---------------cut here---------------start------------->8---
#+BABEL: :cache yes :results output verbatim :exports both :tangle yes

* This is a test

#+begin_src R

x <- 42
noteToSelf <- "Buy low.\nSell high."
cat(noteToSelf)
print("All done now")

#+end_src

#+results[0688b4b765cdd6745f20cffe1e3b6f1b02ab9b46]:
#+begin_example
Buy low.
Sell high.[1] "All done now"
#+end_example
--8<---------------cut here---------------end--------------->8---

*did work* for me (as you can see).

Though, it is not exactly the same config as yours:

- I've removed the `\240' spaces which prefixed your R code (in your posting)
- I've removed the `session' argument, as `Rterm' is not (correctly?)
  installed on my machine
- I'm on Windows XP.

Best regards,
  Seb

-- 
Sebastien Vauban

Re: Missing newline in R code causes Org-Mode eval to hang

[Nick Dokos]

Sebastien Vauban <wxhgmqzgwmuf@spammotel.com> wrote:

> Hi Michael,
> 
> Michael Hannon wrote:
> > Greetings. =C2=A0The appended R code fragment executes without problem in
> > an ESS buffer, but it hangs indefinitely when I try to execute it
> > directly from the Org buffer via C-c C-c.
> >
> > The solution is to add the trailing newline in the "noteToSelf"
> > variable:
> >
> > =C2=A0 =C2=A0 noteToSelf <- "Buy low.\nSell high.\n"
> 
> The following code:
> 
> #+BABEL: :cache yes :results output verbatim :exports both :tangle yes
> 
> * This is a test
> 
> #+begin_src R
> 
> x <- 42
> noteToSelf <- "Buy low.\nSell high."
> cat(noteToSelf)
> print("All done now")
> 
> #+end_src
> 
> #+results[0688b4b765cdd6745f20cffe1e3b6f1b02ab9b46]:
> #+begin_example
> Buy low.
> Sell high.[1] "All done now"
> #+end_example
> 
> *did work* for me (as you can see).
> 
> Though, it is not exactly the same config as yours:
> 
> - I've removed the `\240' spaces which prefixed your R code (in your postin=
> g)
> - I've removed the `session' argument, as `Rterm' is not (correctly?)
>   installed on my machine

The :session argument is necessary to reproduce the behavior, I think.

Nick

> - I'm on Windows XP.
> 
> Best regards,
>   Seb
> 
> --=20
> Sebastien Vauban
> 
> 

Re: Missing newline in R code causes Org-Mode eval to hang

[Michael Hannon]

Thanks, Eric (and Seb and Nick).  FYI, I've passed this issue to the ESS help list.

-- Mike


----- Original Message -----
> From: Eric Schulte <schulte.eric@gmail.com>
> To: Michael Hannon <jm_hannon@yahoo.com>
> Cc: Org-Mode List <emacs-orgmode@gnu.org>
> Sent: Monday, October 17, 2011 1:30 PM
> Subject: Re: [O] Missing newline in R code causes Org-Mode eval to hang
> 
> Hi Michael,
> 
> I can confirm this problem occurs on my machine locally.  I believe the
> issue has something to do with how ESS sends inputs to R and waits for
> command prompts from R.  When the lines are pasted into an ESS buffer
> one at a time the problem does not occur, however when the lines are
> pasted into ESS all at once (without pressing enter between lines) the
> ESS comint buffer hangs.
> 
> One option could be to explicitly call `inferior-ess-send-input' between
> every line of R code, but I'm loath to touch the comint interface as
> small changes like this can sometimes have unpredictable effects.
> 
> Perhaps this could be fixed on the ESS side?
> 
> Best -- Eric
> 
> Michael Hannon <jm_hannon@yahoo.com> writes:
> 
>>  Greetings.  The appended R code fragment executes without problem in
>>  an ESS buffer, but it hangs indefinitely when I try to execute it
>>  directly from the Org buffer via C-c C-c.
>> 
>>  The solution is to add the trailing newline in the "noteToSelf"
>>  variable:
>> 
>>      noteToSelf <- "Buy low.\nSell high.\n"
>> 
>>  Obviously this isn't a big deal from my perspective, but it did
>>  surprise me, and it does seem inconsistent.
>> 
>>  BTW, I've appended also the details of my own (linux) configuration,
>>  but I tried the same thing on a different OS (Mac OS 10.6.8) and got
>>  the same results.
>> 
>>  -- Mike
>> 
>>  ###### Org code that exhibits error
>> 
>>  #+BABEL: :session *R* :cache yes :results output verbatim :exports both 
> :tangle yes
>> 
>>  * This is a test
>> 
>>  #+begin_src R
>> 
>>   x <- 42
>>   noteToSelf <- "Buy low.\nSell high."
>>   cat(noteToSelf)
>>   print("All done now")
>> 
>>  #+end_src
>> 
>> 
>>  ###### My set-up
>> 
>>  Emacs  : GNU Emacs 23.2.1 (x86_64-redhat-linux-gnu, GTK+ Version 2.24.4)
>>   of 2011-05-23 on x86-12.phx2.fedoraproject.org
>>  Package: Org-mode version 7.7 (release_7.7.328.g1a97)
>> 
>>  current state:
>>  ==============
>>  (setq
>>   org-export-latex-after-initial-vars-hook 
> '(org-beamer-after-initial-vars)
>>   org-structure-template-alist '(("r" "#+begin_src 
> R\n\n#+end_src" "<src 
> lang=\"R\">\n\n</src>")
>>  ("S" "#+BEGIN_SRC ?\n\n#+END_SRC" "<src 
> lang=\"?\">\n\n</src>")
>>  ("s" "#+begin_src ?\n\n#+end_src" "<src 
> lang=\"?\">\n\n</src>")
>>  ("e" "#+begin_example\n?\n#+end_example" 
> "<example>\n?\n</example>")
>>  ("q" "#+begin_quote\n?\n#+end_quote" 
> "<quote>\n?\n</quote>")
>>  ("v" "#+begin_verse\n?\n#+end_verse" 
> "<verse>\n?\n/verse>")
>>  ("c" "#+begin_center\n?\n#+end_center" 
> "<center>\n?\n/center>")
>>  ("l" "#+begin_latex\n?\n#+end_latex" 
> "<literal 
> style=\"latex\">\n?\n</literal>")
>>  ("L" "#+latex: " "<literal 
> style=\"latex\">?</literal>")
>>  ("h" "#+begin_html\n?\n#+end_html" 
> "<literal 
> style=\"html\">\n?\n</literal>")
>>  ("H" "#+html: " "<literal 
> style=\"html\">?</literal>") ("a" 
> "#+begin_ascii\n?\n#+end_ascii")
>>  ("A" "#+ascii: ") ("i" "#+index: ?" 
> "#+index: ?")
>>  ("I" "#+include %file ?" "<include file=%file 
> markup=\"?\">"))
>>   org-speed-command-hook '(org-speed-command-default-hook 
> org-babel-speed-command-hook)
>>   org-agenda-files '("~/Documents/scratch.org")
>>   org-babel-load-languages '((emacs-lisp . t) (R . t) (python . t) (sh . 
> t) (latex . t) (C . t) (octave \.t))
>>   org-metaup-hook '(org-babel-load-in-session-maybe)
>>   org-after-todo-state-change-hook '(org-clock-out-if-current)
>>   org-babel-tangle-lang-exts '(("C++" . "cpp") 
> ("latex" . "tex") ("python" . "py") 
> ("emacs-lisp" . "el"))
>>   org-export-blocks-postblock-hook '(org-exp-res/src-name-cleanup)
>>   org-export-latex-format-toc-function 
> 'org-export-latex-format-toc-default
>>   org-tab-first-hook '(org-hide-block-toggle-maybe 
> org-src-native-tab-command-maybe org-babel-hide-result-toggle-maybe)
>>   org-src-mode-hook '(org-src-babel-configure-edit-buffer 
> org-src-mode-configure-edit-buffer)
>>   org-confirm-shell-link-function 'yes-or-no-p
>>   org-export-first-hook '(org-beamer-initialize-open-trackers)
>>   org-agenda-before-write-hook '(org-agenda-add-entry-text)
>>   org-blank-before-new-entry nil
>>   org-babel-pre-tangle-hook '(save-buffer)
>>   org-cycle-hook '(org-cycle-hide-archived-subtrees 
> org-cycle-hide-drawers org-cycle-show-empty-lines
>>   org-optimize-window-after-visibility-change)
>>   org-export-preprocess-before-normalizing-links-hook 
> '(org-remove-file-link-modifiers)
>>   org-mode-hook '(#[nil 
> "\300\301\302\303\304$\207" [org-add-hook 
> change-major-mode-hook org-show-block-all append local] 5]
>>  #[nil "\300\301\302\303\304$\207" 
> [org-add-hook change-major-mode-hook org-babel-show-result-all append local] 5]
>>  org-babel-result-hide-spec org-babel-hide-all-hashes)
>>   org-ctrl-c-ctrl-c-hook '(org-babel-hash-at-point 
> org-babel-execute-safely-maybe)
>>   org-confirm-elisp-link-function 'yes-or-no-p
>>   org-export-interblocks '((lob org-babel-exp-lob-one-liners) (src 
> org-babel-exp-inline-src-blocks))
>>   org-clock-out-hook '(org-clock-remove-empty-clock-drawer)
>>   org-occur-hook '(org-first-headline-recenter)
>>   org-from-is-user-regexp "\\<Michael 
> Hannon\\>"
>>   org-export-preprocess-before-selecting-backend-code-hook 
> '(org-beamer-select-beamer-code)
>>   org-confirm-babel-evaluate 'my-org-confirm-babel-evaluate
>>   org-export-latex-final-hook '(org-beamer-amend-header 
> org-beamer-fix-toc org-beamer-auto-fragile-frames
>>        org-beamer-place-default-actions-for-lists)
>>   org-metadown-hook '(org-babel-pop-to-session-maybe)
>>   org-export-blocks '((src org-babel-exp-src-block nil) (comment 
> org-export-blocks-format-comment t)
>>      (ditaa org-export-blocks-format-ditaa nil) (dot 
> org-export-blocks-format-dot nil))
>>   )
>> 
> 
> -- 
> Eric Schulte
> http://cs.unm.edu/~eschulte/
>