Re: [O] 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 <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/