Re: [O] Missing newline in R code causes Org-Mode eval to hang
Thanks, Eric (and Seb and Nick). FYI, I've passed this issue to the ESS help list. -- Mike - Original Message - From: Eric Schulte schulte.e...@gmail.com To: Michael Hannon jm_han...@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_han...@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
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_han...@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)
Re: [O] Missing newline in R code causes Org-Mode eval to hang
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: [O] Missing newline in R code causes Org-Mode eval to hang
Sebastien Vauban wxhgmqzgw...@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
