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))
)