Re: [O] 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 <address@hidden>
> To: Michael Hannon <address@hidden>
> Cc: Org-Mode List <address@hidden>
> 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 <address@hidden> 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/
>