From mboxrd@z Thu Jan 1 00:00:00 1970 From: Eric Schulte Subject: Re: R code block produces only partial output Date: Mon, 04 Aug 2014 07:53:07 -0400 Message-ID: <87iom8zd24.fsf@gmail.com> References: Mime-Version: 1.0 Content-Type: text/plain Return-path: Received: from eggs.gnu.org ([2001:4830:134:3::10]:48914) by lists.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1XEGpT-0000R3-UO for Emacs-orgmode@gnu.org; Mon, 04 Aug 2014 07:53:32 -0400 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) (envelope-from ) id 1XEGpP-0007yn-Tv for Emacs-orgmode@gnu.org; Mon, 04 Aug 2014 07:53:27 -0400 Received: from mail-oi0-x232.google.com ([2607:f8b0:4003:c06::232]:38820) by eggs.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1XEGpP-0007yh-NH for Emacs-orgmode@gnu.org; Mon, 04 Aug 2014 07:53:23 -0400 Received: by mail-oi0-f50.google.com with SMTP id a141so4430324oig.37 for ; Mon, 04 Aug 2014 04:53:22 -0700 (PDT) In-Reply-To: (Andreas Kiermeier's message of "Mon, 4 Aug 2014 20:48:47 +0930") 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: Andreas Kiermeier Cc: Emacs-orgmode@gnu.org Hi Andreas, Why are you setting the output type to "graphics" when you are trying to return text? I think that may be the source of your problem. Best, Eric Andreas Kiermeier writes: > 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 > ) > -- Eric Schulte https://cs.unm.edu/~eschulte PGP: 0x614CA05D (see https://u.fsf.org/yw)