From mboxrd@z Thu Jan 1 00:00:00 1970 From: Andreas Kiermeier Subject: R code block produces only partial output Date: Mon, 4 Aug 2014 20:48:47 +0930 Message-ID: Mime-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Return-path: Received: from eggs.gnu.org ([2001:4830:134:3::10]:43924) by lists.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1XEGIe-0005eh-7r for Emacs-orgmode@gnu.org; Mon, 04 Aug 2014 07:19:33 -0400 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) (envelope-from ) id 1XEGIb-0006U9-0w for Emacs-orgmode@gnu.org; Mon, 04 Aug 2014 07:19:32 -0400 Received: from mail-qa0-x232.google.com ([2607:f8b0:400d:c00::232]:40872) by eggs.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1XEGIa-0006Tt-RM for Emacs-orgmode@gnu.org; Mon, 04 Aug 2014 07:19:28 -0400 Received: by mail-qa0-f50.google.com with SMTP id s7so6544946qap.23 for ; Mon, 04 Aug 2014 04:19:28 -0700 (PDT) List-Id: "General discussions about Org-mode." List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: emacs-orgmode-bounces+geo-emacs-orgmode=m.gmane.org@gnu.org Sender: emacs-orgmode-bounces+geo-emacs-orgmode=m.gmane.org@gnu.org To: Emacs-orgmode@gnu.org Hi all, I've been using Org mode (latest version - see my set up below) to perform some data analysis and have come across a problem evaluating R code blocks. I usually use a session when working and when evaluating a code block with describe (R package "rms") and a quantitative variable the results in .org buffer and the *R* buffer (output) differ. However, it's not the describe function, but something about the output of that function. The following is a minimal example (both with and without the describe function) to illustrate the problem. I think it has something to do with a number of spaces followed by a '.' in the output buffer. Any thoughts or guidance would be greatly appreciated. Thanks in advance. Andreas ------- test.org --------------------- #+STARTUP: showall indent hidestars #+PROPERTY: header-args:R :session *R* #+PROPERTY: header-args :results output graphics :exports both #+BEGIN_SRC R require(rms) x <- rnorm(100) describe(x) #+END_SRC #+RESULTS: : 75 .90 .95 : 0.69261 1.38170 1.71468 : : lowest : -2.270 -1.878 -1.705 -1.525 -1.423 : highest: 1.739 2.032 2.061 2.150 2.480 #+BEGIN_SRC R x <- rnorm(100) y <- quantile(x, probs=seq(0,1,0.1)) names(y) <- as.character(c("0",".1",".2",".3",".4",".5",".6",".7",".8",".9","1")) y #+END_SRC #+RESULTS: : 6 .7 .8 .9 1 : 0.31144890 0.63292642 0.87168950 1.17596547 1.96212110 ------- end test.org --------------------- The actual output for the first code block in the *R* buffer was: > describe(x) x n missing unique Mean .05 .10 .25 .50 100 0 100 0.1118 -1.39404 -1.02732 -0.45899 0.03756 .75 .90 .95 0.69261 1.38170 1.71468 lowest : -2.270 -1.878 -1.705 -1.525 -1.423 highest: 1.739 2.032 2.061 2.150 2.480 Similarly, the second code block resulted in: > y 0 .1 .2 .3 .4 .5 -2.23303584 -1.31137871 -0.69424743 -0.48689155 -0.16973865 0.09289862 .6 .7 .8 .9 1 0.31144890 0.63292642 0.87168950 1.17596547 1.96212110 And finally my set up is: Emacs : GNU Emacs 24.3.1 (i386-mingw-nt6.2.9200) of 2013-03-18 on MARVIN Package: Org-mode version 8.2.7c (8.2.7c-elpa @ c:/Users/andre_000/Documents/.emacs.d/elpa/org-20140730/) current state: ============== (setq org-ctrl-c-ctrl-c-hook '(org-babel-hash-at-point org-babel-execute-safely-maybe) org-latex-format-headline-function 'org-latex-format-headline-default-function org-src-fontify-natively t org-html-format-inlinetask-function 'ignore org-completion-use-iswitchb t org-tab-first-hook '(org-hide-block-toggle-maybe org-src-native-tab-command-maybe org-babel-hide-result-toggle-maybe org-babel-header-arg-expand) org-cycle-hook '(org-cycle-hide-archived-subtrees org-cycle-hide-drawers org-cycle-hide-inline-tasks org-cycle-show-empty-lines org-optimize-window-after-visibility-change) org-agenda-before-write-hook '(org-agenda-add-entry-text) org-confirm-babel-evaluate nil org-speed-command-hook '(org-speed-command-default-hook org-babel-speed-command-hook) org-ascii-format-inlinetask-function 'org-ascii-format-inlinetask-default org-babel-pre-tangle-hook '(save-buffer) org-occur-hook '(org-first-headline-recenter) org-src-lang-modes '(("r" . ess-mode) ("ocaml" . tuareg) ("elisp" . emacs-lisp) ("ditaa" . artist) ("asymptote" . asy) ("dot" . fundamental) ("sqlite" . sql) ("calc" . fundamental) ("C" . c) ("cpp" . c++) ("C++" . c++) ("screen" . shell-script)) org-shiftdown-final-hook '(windmove-down) org-html-format-headline-function 'ignore org-log-done 'time org-metaup-hook '(org-babel-load-in-session-maybe) org-confirm-elisp-link-function 'yes-or-no-p org-catch-invisible-edits 'smart org-default-notes-file "~/.org//notes.org" org-latex-format-drawer-function '(lambda (name contents) contents) org-src-tab-acts-natively t org-export-backends '(ascii html icalendar latex md) org-clock-out-hook '(org-clock-remove-empty-clock-drawer) org-completion-use-ido t org-use-speed-commands t 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-mode-reftex-setup (lambda nil (flyspell-mode 1) (auto-fill-mode 1) (local-set-key "\220" (quote outline-previous-visible-heading)) (local-set-key "\225" (quote outline-up-heading)) (local-set-key "\227" (quote org-table-copy-region)) (local-set-key "\231" (quote org-table-paste-rectangle)) (local-set-key "\214" (quote org-table-sort-lines)) (local-set-key "\311" (quote org-toggle-iimage-in-org))) ) org-shiftup-final-hook '(windmove-up) org-ascii-format-drawer-function '(lambda (name contents width) contents) org-directory "~/.org/" org-html-format-drawer-function '(lambda (name contents) contents) org-shiftleft-final-hook '(windmove-left) org-metadown-hook '(org-babel-pop-to-session-maybe) org-agenda-files '("~/.org/agenda.org") org-src-mode-hook '(org-src-babel-configure-edit-buffer org-src-mode-configure-edit-buffer) org-after-todo-state-change-hook '(org-clock-out-if-current) org-todo-keyword-faces '(("WAITING" . ak-org-todo-warning-face)) org-shiftright-final-hook '(windmove-right) org-babel-load-languages '((emacs-lisp) (R . t)) org-babel-R-command "C:/Progra~1/R/R-3.1.1/bin/x64/R --slave --no-save" org-latex-format-inlinetask-function 'ignore org-confirm-shell-link-function 'yes-or-no-p )