emacs-orgmode@gnu.org archives
 help / color / mirror / code / Atom feed
From: Feiming Chen <feimingchen@yahoo.com>
To: emacs-orgmode@gnu.org
Subject: Bug: Org-Babel Mode R Plot Output to LaTeX File [Babel] [7.5]
Date: Wed, 13 Jul 2011 14:14:11 -0700 (PDT)	[thread overview]
Message-ID: <1310591651.9859.YahooMailClassic@web81704.mail.mud.yahoo.com> (raw)


[-- Attachment #1.1: Type: text/plain, Size: 9237 bytes --]

Hi, I like org-mode and org-babel mode very much, but recently I am  having problems outputting R graphics to LaTeX report with
Org-Babel mode.  Attached is my test file, where I am generating 4
simple plots of different sizes and format (.png or .pdf).  The HTML
export is satisfactory, however, the LaTeX export (C-c C-e l) presents two problems: 

    1.  All 4 plots have the same size (10em) which is different from the
    header specification and is too small.

\includegraphics[width=10em]{a1.png} ...
\includegraphics[width=10em]{a2.png} ...
\includegraphics[width=10em]{a3.pdf} ...
\includegraphics[width=10em]{a4.pdf} ...

    2. While exporting to PDF file, the R code is mysteriously lost in
    the R execution for the PDF output of the plots and the compilation failed correspondingly: 

> pdf(file="a3.pdf",width=5,height=5)
> 
> dev.off()
> pdf(file="a4.pdf",width=10,height=10)
>
> dev.off()


Hopefully you can replicate my errors and help me on this.  Thanks a
lot!

Best regards, 
Feiming Chen

____________________________________________________________


Emacs  : GNU Emacs 23.2.1 (i386-redhat-linux-gnu, GTK+ Version 2.21.4)
 of 2010-07-08 on x86-05.phx2.fedoraproject.org
Package: Org-mode version 7.5

current state:
==============
(setq
 org-file-apps '((auto-mode . emacs) ("\\.mm\\'" . default)
         ("\\.x?html?\\'" . "firefox %s") ("\\.pdf\\'" . "evince %s"))
 org-export-latex-after-initial-vars-hook '(org-beamer-after-initial-vars)
 org-hide-block-startup t
 org-speed-command-hook '(org-speed-command-default-hook
              org-babel-speed-command-hook)
 org-src-fontify-natively t
 org-babel-load-languages '((emacs-lisp . t) (R . t))
 org-metaup-hook '(org-babel-load-in-session-maybe)
 org-after-todo-state-change-hook '(org-clock-out-if-current)
 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)
 outline-regexp "\\*+ "
 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-reveal-start-hook '(org-decrypt-entry)
 org-export-first-hook '(org-beamer-initialize-open-trackers)
 org-format-latex-header "\\documentclass{article}\n\\usepackage[usenames]{color}\n\\usepackage{amsmath}\n\\usepackage[mathscr]{eucal}\n% Feiming's Customization BEGIN\n\\usepackage[colorlinks=true]{hyperref}\n\\input{/home/chen/lib/math.tex}\n% Feiming's Customization END\n\\pagestyle{empty}             % do not remove\n[PACKAGES]\n[DEFAULT-PACKAGES]\n% The settings below are copied from fullpage.sty\n\\setlength{\\textwidth}{\\paperwidth}\n\\addtolength{\\textwidth}{-3cm}\n\\setlength{\\oddsidemargin}{1.5cm}\n\\addtolength{\\oddsidemargin}{-2.54cm}\n\\setlength{\\evensidemargin}{\\oddsidemargin}\n\\setlength{\\textheight}{\\paperheight}\n\\addtolength{\\textheight}{-\\headheight}\n\\addtolength{\\textheight}{-\\headsep}\n\\addtolength{\\textheight}{-\\footskip}\n\\addtolength{\\textheight}{-3cm}\n\\setlength{\\topmargin}{1.5cm}\n\\addtolength{\\topmargin}{-2.54cm}"
 org-startup-indented t
 org-agenda-before-write-hook '(org-agenda-add-entry-text)
 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-use-speed-commands t
 org-mode-hook '(turn-on-org-cdlatex
         (lambda nil
          (setq org-mouse-context-menu-function
           (quote org-mouse-context-menu))
          (when (memq (quote context-menu) org-mouse-features)
           (org-defkey org-mouse-map [mouse-3] nil)
           (org-defkey org-mode-map [mouse-3]
            (quote org-mouse-show-context-menu))
           )
          (org-defkey org-mode-map [down-mouse-1]
           (quote org-mouse-down-mouse))
          (when (memq (quote context-menu) org-mouse-features)
           (org-defkey org-mouse-map [C-drag-mouse-1]
            (quote org-mouse-move-tree))
           (org-defkey org-mouse-map [C-down-mouse-1]
            (quote org-mouse-move-tree-start))
           )
          (when (memq (quote yank-link) org-mouse-features)
           (org-defkey org-mode-map [S-mouse-2]
            (quote org-mouse-yank-link))
           (org-defkey org-mode-map [drag-mouse-3]
            (quote org-mouse-yank-link))
           )
          (when (memq (quote move-tree) org-mouse-features)
           (org-defkey org-mouse-map [drag-mouse-3]
            (quote org-mouse-move-tree))
           (org-defkey org-mouse-map [down-mouse-3]
            (quote org-mouse-move-tree-start))
           )
          (when (memq (quote activate-stars) org-mouse-features)
           (font-lock-add-keywords nil
            (\`
             (((\, outline-regexp) 0
               (\`
            (face org-link mouse-face highlight keymap
             (\, org-mouse-map))
            )
               (quote prepend))
              )
             )
            t)
           )
          (when (memq (quote activate-bullets) org-mouse-features)
           (font-lock-add-keywords nil
            (\`
             (("^[    ]*\\([-+*]\\|[0-9]+[.)]\\) +"
               (1
            (\`
             (face org-link keymap (\, org-mouse-map) mouse-face
              highlight)
             )
            (quote prepend))
               )
              )
             )
            t)
           )
          (when (memq (quote activate-checkboxes) org-mouse-features)
           (font-lock-add-keywords nil
            (\`
             (("^[    ]*\\([-+*]\\|[0-9]+[.)]\\) +\\(\\[[ X]\\]\\)"
               (2
            (\`
             (face bold keymap (\, org-mouse-map) mouse-face
              highlight)
             )
            t)
               )
              )
             )
            t)
           )
          (defadvice org-open-at-point
           (around org-mouse-open-at-point activate)
           (let ((context (org-context)))
            (cond ((assq :headline-stars context) (org-cycle))
             ((assq :checkbox context) (org-toggle-checkbox))
             ((assq :item-bullet context)
              (let ((org-cycle-include-plain-lists t)) (org-cycle)))
             (t ad-do-it))
            )
           )
          )
         #[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-agenda-mode-hook '((lambda nil
             (setq org-mouse-context-menu-function
              (quote org-mouse-agenda-context-menu))
             (org-defkey org-agenda-mode-map [mouse-3]
              (quote org-mouse-show-context-menu))
             (org-defkey org-agenda-mode-map [down-mouse-3]
              (quote org-mouse-move-tree-start))
             (org-defkey org-agenda-mode-map [C-mouse-4]
              (quote org-agenda-earlier))
             (org-defkey org-agenda-mode-map [C-mouse-5]
              (quote org-agenda-later))
             (org-defkey org-agenda-mode-map [drag-mouse-3]
              (quote
               (lambda (event) (interactive "e")
                (case (org-mouse-get-gesture event)
                 (:left (org-agenda-earlier 1))
                 (:right (org-agenda-later 1)))
                )
               )
              )
             )
            )
 org-export-interblocks '((lob org-babel-exp-lob-one-liners)
              (src org-babel-exp-inline-src-blocks))
 org-occur-hook '(org-first-headline-recenter)
 org-export-preprocess-before-selecting-backend-code-hook '(org-beamer-select-beamer-code)
 org-confirm-babel-evaluate nil
 org-infojs-options '((path . "http://bancs.bdx.com/chen/lib/org-info.js")
              (view . "overview") (toc . "nil") (ftoc . "0")
              (tdepth . "max") (sdepth . "max") (mouse . "underline")
              (buttons . "0") (ltoc . "1") (up . :link-up)
              (home . :link-home))
 org-src-tab-acts-natively t
 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)
 org-export-blocks '((src org-babel-exp-src-block nil)
             (comment org-export-blocks-format-comment t)
             (ditaa org-export-blocks-format-ditaa nil)
             (dot org-export-blocks-format-dot nil))
 )


[-- Attachment #1.2: Type: text/html, Size: 16196 bytes --]

[-- Attachment #2: test.org --]
[-- Type: application/vnd.lotus-organizer, Size: 404 bytes --]

             reply	other threads:[~2011-07-13 21:14 UTC|newest]

Thread overview: 9+ messages / expand[flat|nested]  mbox.gz  Atom feed  top
2011-07-13 21:14 Feiming Chen [this message]
2011-07-15 14:32 ` Bug: Org-Babel Mode R Plot Output to LaTeX File [Babel] [7.5] Eric Schulte
2011-07-16  9:05   ` Stephen Eglen
2011-07-16 13:20     ` Eric Schulte
2011-07-16 18:54       ` Sebastien Vauban
2011-07-17  6:30         ` Bastien
2011-07-18 16:19 Feiming Chen
2011-07-18 16:36 ` Eric Schulte
2011-07-18 17:08   ` Feiming Chen

Reply instructions:

You may reply publicly to this message via plain-text email
using any one of the following methods:

* Save the following mbox file, import it into your mail client,
  and reply-to-all from there: mbox

  Avoid top-posting and favor interleaved quoting:
  https://en.wikipedia.org/wiki/Posting_style#Interleaved_style

  List information: https://www.orgmode.org/

* Reply using the --to, --cc, and --in-reply-to
  switches of git-send-email(1):

  git send-email \
    --in-reply-to=1310591651.9859.YahooMailClassic@web81704.mail.mud.yahoo.com \
    --to=feimingchen@yahoo.com \
    --cc=emacs-orgmode@gnu.org \
    /path/to/YOUR_REPLY

  https://kernel.org/pub/software/scm/git/docs/git-send-email.html

* If your mail client supports setting the In-Reply-To header
  via mailto: links, try the mailto: link
Be sure your reply has a Subject: header at the top and a blank line before the message body.
Code repositories for project(s) associated with this public inbox

	https://git.savannah.gnu.org/cgit/emacs/org-mode.git

This is a public inbox, see mirroring instructions
for how to clone and mirror all data and code used for this inbox;
as well as URLs for read-only IMAP folder(s) and NNTP newsgroup(s).