Hi Eric: Thanks a lot!   It would be nice if Org-Babel model could automatically add the "#+ATTR_LaTeX" lines (from the hint in the R code header line) during LaTeX export. Somehow I failed to compile the file on my system.  It seems the line: #+ATTR_LaTeX: width=5px has corrupted the PDF file generated in R.   Because after "C-c C-e d",  I get the following error: !pdfTeX error: pdflatex (file ./a3.pdf): PDF inclusion: required page does not exist <0>  ==> Fatal error occurred, no output PDF file produced! and  I could not open the PDF file of the R plot any more (the error message is "Cannot display this page! Maybe because of a conversion failure").   Attached is the simplified org file that failed on "LaTeX transport" on my computer.  Thanks!  Sincerely, Feiming Chen --- On Fri, 7/15/11, Eric Schulte wrote: From: Eric Schulte Subject: Re: [O] Bug: Org-Babel Mode R Plot Output to LaTeX File [Babel] [7.5] To: "Feiming Chen" Cc: emacs-orgmode@gnu.org Date: Friday, July 15, 2011, 9:32 AM Hi Feiming, The "width" and "height" header arguments are passed to R to affect the size of the generated file e.g.,   png(filename="a1.png",width=500,height=500) however they do not affect the generated latex code.  Luckily Org-mode does support passing information like image width to latex figures.  See my attached version of your test file which uses #+ATTR_LaTeX lines to specify the width during LaTeX export. Best -- Eric -----Inline Attachment Follows----- Feiming Chen writes: > 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)) >  ) > > -- Eric Schulte http://cs.unm.edu/~eschulte/