[O] R code block produces only partial output

[Andreas Kiermeier]

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
 )