Hi Eric: Thanks a lot for your quick response!  The problem is solved by "adding a headline".  I can now successfully generated the PDF file from LaTeX export. I agree with your point about complexity vs. convenience. Thanks again, and have a good week! Sincerely, Feiming Chen --- On Mon, 7/18/11, 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: "Eric Schulte" , emacs-orgmode@gnu.org Date: Monday, July 18, 2011, 11:36 AM Feiming Chen writes: > 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. > I don't think this will happen at least in the near term, as searching out and creating/changing org export directives would be a major change to the current behavior which inserts code results, and would cross some semantic lines separating parts of Org-mode. In this case I don't think the relatively limited convenience justifies the added complexity. > > 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.  > I believe in this case the problem is caused by the lack of any headline levels.  The LaTeX exporter can be weird about headline levels, try adding a line like * top to the org file before the code block.  That fixes the problem on my system. Also, there is no way that an #+attr_latex line could affect the execution of a code block, precisely because of the simplifying separation of distinct components mentioned earlier. Best -- Eric > > 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/