From: Eric Schulte <schulte.eric@gmail.com>
To: Andreas Kiermeier <andreas.kiermeier@gmail.com>
Cc: Emacs-orgmode@gnu.org
Subject: Re: R code block produces only partial output
Date: Mon, 04 Aug 2014 07:53:07 -0400 [thread overview]
Message-ID: <87iom8zd24.fsf@gmail.com> (raw)
In-Reply-To: <CAN7vk5R+2DHRajUR8+NdmWSpLhjtodrdjXOO0v027cjHY7gFxw@mail.gmail.com> (Andreas Kiermeier's message of "Mon, 4 Aug 2014 20:48:47 +0930")
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 <andreas.kiermeier@gmail.com> 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)
next prev parent reply other threads:[~2014-08-04 11:53 UTC|newest]
Thread overview: 41+ messages / expand[flat|nested] mbox.gz Atom feed top
2014-08-04 11:18 R code block produces only partial output Andreas Kiermeier
2014-08-04 11:53 ` Eric Schulte [this message]
2014-08-04 12:23 ` Andreas Kiermeier
2014-08-04 13:10 ` Eric Schulte
2014-08-05 0:46 ` Andreas Kiermeier
2014-08-05 4:00 ` John Hendy
2014-08-05 4:31 ` Andreas Kiermeier
2014-08-05 18:05 ` Charles Berry
2014-08-05 19:02 ` Eric Schulte
2014-08-05 19:11 ` John Hendy
2014-08-05 19:57 ` Nick Dokos
2014-08-05 20:10 ` Nick Dokos
2014-08-05 22:21 ` Charles C. Berry
2014-08-06 3:32 ` Aaron Ecay
2014-08-06 11:30 ` Eric Schulte
2014-08-07 6:00 ` Aaron Ecay
2014-08-07 17:42 ` Charles C. Berry
2014-08-07 18:06 ` Aaron Ecay
2014-08-07 18:42 ` Charles C. Berry
2014-08-07 19:06 ` Thomas S. Dye
2014-08-09 8:54 ` Rainer M Krug
2014-08-16 5:05 ` Aaron Ecay
2014-08-16 18:50 ` Charles C. Berry
2014-08-16 20:58 ` Aaron Ecay
2014-08-17 6:03 ` Achim Gratz
2014-08-19 0:13 ` Aaron Ecay
2014-08-19 5:36 ` Achim Gratz
2014-08-23 8:32 ` Aaron Ecay
2014-08-23 9:24 ` Andreas Kiermeier
2014-08-23 17:10 ` Aaron Ecay
2014-08-23 18:35 ` Thomas S. Dye
2014-08-23 19:37 ` Ista Zahn
2014-08-24 0:10 ` Charles C. Berry
2014-08-28 5:24 ` Aaron Ecay
2014-09-01 5:00 ` Aaron Ecay
2014-09-01 16:08 ` Charles C. Berry
2014-08-09 8:48 ` Rainer M Krug
2014-08-06 1:11 ` Andreas Kiermeier
2014-08-06 2:21 ` Charles C. Berry
2014-08-06 3:24 ` Aaron Ecay
2014-08-06 15:59 ` Charles C. Berry
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