From mboxrd@z Thu Jan 1 00:00:00 1970 From: Feiming Chen Subject: Bug: Org-Babel Mode R Plot Output to LaTeX File [Babel] [7.5] Date: Wed, 13 Jul 2011 14:14:11 -0700 (PDT) Message-ID: <1310591651.9859.YahooMailClassic@web81704.mail.mud.yahoo.com> Mime-Version: 1.0 Content-Type: multipart/mixed; boundary="0-545963936-1310591651=:9859" Return-path: Received: from eggs.gnu.org ([140.186.70.92]:57171) by lists.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1Qh6lA-0007g2-IB for emacs-orgmode@gnu.org; Wed, 13 Jul 2011 17:14:25 -0400 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) (envelope-from ) id 1Qh6l6-00008E-3R for emacs-orgmode@gnu.org; Wed, 13 Jul 2011 17:14:20 -0400 Received: from nm20-vm0.access.bullet.mail.mud.yahoo.com ([66.94.236.29]:39205) by eggs.gnu.org with smtp (Exim 4.71) (envelope-from ) id 1Qh6l5-00007h-AY for emacs-orgmode@gnu.org; Wed, 13 Jul 2011 17:14:15 -0400 List-Id: "General discussions about Org-mode." List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: emacs-orgmode-bounces+geo-emacs-orgmode=m.gmane.org@gnu.org Sender: emacs-orgmode-bounces+geo-emacs-orgmode=m.gmane.org@gnu.org To: emacs-orgmode@gnu.org --0-545963936-1310591651=:9859 Content-Type: multipart/alternative; boundary="0-309307567-1310591651=:9859" --0-309307567-1310591651=:9859 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: quoted-printable Hi, I like org-mode and org-babel mode very much, but recently I am=A0 havi= ng problems outputting R graphics to LaTeX report with Org-Babel mode.=A0 Attached is my test file, where I am generating 4 simple plots of different sizes and format (.png or .pdf).=A0 The HTML export is satisfactory, however, the LaTeX export (C-c C-e l) presents two = problems:=20 =A0=A0=A0 1.=A0 All 4 plots have the same size (10em) which is different fr= om the =A0=A0=A0 header specification and is too small. \includegraphics[width=3D10em]{a1.png} ... \includegraphics[width=3D10em]{a2.png} ... \includegraphics[width=3D10em]{a3.pdf} ... \includegraphics[width=3D10em]{a4.pdf} ... =A0=A0=A0 2. While exporting to PDF file, the R code is mysteriously lost i= n =A0=A0=A0 the R execution for the PDF output of the plots and the compilati= on failed correspondingly:=20 > pdf(file=3D"a3.pdf",width=3D5,height=3D5) >=20 > dev.off() > pdf(file=3D"a4.pdf",width=3D10,height=3D10) > > dev.off() Hopefully you can replicate my errors and help me on this.=A0 Thanks a lot! Best regards,=20 Feiming Chen ____________________________________________________________ Emacs=A0 : GNU Emacs 23.2.1 (i386-redhat-linux-gnu, GTK+ Version 2.21.4) =A0of 2010-07-08 on x86-05.phx2.fedoraproject.org Package: Org-mode version 7.5 current state: =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D (setq =A0org-file-apps '((auto-mode . emacs) ("\\.mm\\'" . default) =A0=A0 =A0=A0=A0=A0 =A0("\\.x?html?\\'" . "firefox %s") ("\\.pdf\\'" . "evi= nce %s")) =A0org-export-latex-after-initial-vars-hook '(org-beamer-after-initial-vars= ) =A0org-hide-block-startup t =A0org-speed-command-hook '(org-speed-command-default-hook =A0=A0 =A0=A0=A0=A0 =A0=A0=A0 =A0 org-babel-speed-command-hook) =A0org-src-fontify-natively t =A0org-babel-load-languages '((emacs-lisp . t) (R . t)) =A0org-metaup-hook '(org-babel-load-in-session-maybe) =A0org-after-todo-state-change-hook '(org-clock-out-if-current) =A0org-export-blocks-postblock-hook '(org-exp-res/src-name-cleanup) =A0org-export-latex-format-toc-function 'org-export-latex-format-toc-defaul= t =A0org-tab-first-hook '(org-hide-block-toggle-maybe =A0=A0 =A0=A0=A0=A0 =A0=A0=A0=A0=A0 org-src-native-tab-command-maybe =A0=A0 =A0=A0=A0=A0 =A0=A0=A0=A0=A0 org-babel-hide-result-toggle-maybe) =A0outline-regexp "\\*+ " =A0org-src-mode-hook '(org-src-babel-configure-edit-buffer =A0=A0 =A0=A0=A0=A0 =A0=A0=A0=A0 org-src-mode-configure-edit-buffer) =A0org-confirm-shell-link-function 'yes-or-no-p =A0org-reveal-start-hook '(org-decrypt-entry) =A0org-export-first-hook '(org-beamer-initialize-open-trackers) =A0org-format-latex-header "\\documentclass{article}\n\\usepackage[usenames= ]{color}\n\\usepackage{amsmath}\n\\usepackage[mathscr]{eucal}\n% Feiming's = Customization BEGIN\n\\usepackage[colorlinks=3Dtrue]{hyperref}\n\\input{/ho= me/chen/lib/math.tex}\n% Feiming's Customization END\n\\pagestyle{empty}=A0= =A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0 % do not remove\n[PACKAGES]\n[DEFAULT-PAC= KAGES]\n% The settings below are copied from fullpage.sty\n\\setlength{\\te= xtwidth}{\\paperwidth}\n\\addtolength{\\textwidth}{-3cm}\n\\setlength{\\odd= sidemargin}{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{\\texthe= 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"\300\301\302\303\304$\207" =A0=A0 =A0=A0=A0=A0 =A0=A0 [org-add-hook change-major-mode-hook org-show-bl= ock-all append =A0=A0 =A0=A0=A0=A0 =A0=A0=A0 local] =A0=A0 =A0=A0=A0=A0 =A0=A0 5] =A0=A0 =A0=A0=A0=A0 =A0#[nil "\300\301\302\303\304$\207" =A0=A0 =A0=A0=A0=A0 =A0=A0 [org-add-hook change-major-mode-hook org-babel-s= how-result-all =A0=A0 =A0=A0=A0=A0 =A0=A0=A0 append local] =A0=A0 =A0=A0=A0=A0 =A0=A0 5] =A0=A0 =A0=A0=A0=A0 =A0org-babel-result-hide-spec org-babel-hide-all-hashes= ) =A0org-ctrl-c-ctrl-c-hook '(org-babel-hash-at-point org-babel-execute-safel= y-maybe) =A0org-confirm-elisp-link-function 'yes-or-no-p =A0org-agenda-mode-hook '((lambda nil =A0=A0 =A0=A0=A0=A0 =A0=A0=A0 =A0(setq org-mouse-context-menu-function =A0=A0 =A0=A0=A0=A0 =A0=A0=A0 =A0 (quote org-mouse-agenda-context-menu)) =A0=A0 =A0=A0=A0=A0 =A0=A0=A0 =A0(org-defkey org-agenda-mode-map [mouse-3] =A0=A0 =A0=A0=A0=A0 =A0=A0=A0 =A0 (quote org-mouse-show-context-menu)) =A0=A0 =A0=A0=A0=A0 =A0=A0=A0 =A0(org-defkey 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Hi, I like org-mode and org-babel mode very m= uch, 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).&= nbsp; 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=3D10= em]{a1.png} ...
\includegraphics[width=3D10em]{a2.png} ...
\includegr= aphics[width=3D10em]{a3.pdf} ...
\includegraphics[width=3D10em]{a4.pdf} = ...

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

> pdf(file=3D= "a3.pdf",width=3D5,height=3D5)
>
> dev.off()
> pdf(file= =3D"a4.pdf",width=3D10,height=3D10)
>
> dev.off()


Ho= pefully 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 x= 86-05.phx2.fedoraproject.org
Package: Org-mode version 7.5

curren= t state:
=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D
(setq
 or= g-file-apps '((auto-mode . emacs) ("\\.mm\\'" . default)
   &n= bsp;     ("\\.x?html?\\'" . "firefox %s") ("\\.pdf\\'" = . "evince %s"))
 org-export-latex-after-initial-vars-hook '(org-bea= mer-after-initial-vars)
 org-hide-block-startup t
 org-spee= d-command-hook '(org-speed-command-default-hook
        =       org-babel-speed-command-hook)
 org-src-fo= ntify-natively t
 org-babel-load-languages '((emacs-lisp . t) (R . = t))
 org-metaup-hook '(org-babel-load-in-session-maybe)
 or= g-after-todo-state-change-hook '(org-clock-out-if-current)
 org-exp= ort-blocks-postblock-hook '(org-exp-res/src-name-cleanup)
 org-expo= rt-latex-format-toc-function 'org-export-latex-format-toc-default
 = org-tab-first-hook '(org-hide-block-toggle-maybe
    &nbs= p;         org-src-native-tab-command-ma= ybe
             = org-babel-hide-result-toggle-maybe)
 outline-regexp "\\*+ "
&nb= sp;org-src-mode-hook '(org-src-babel-configure-edit-buffer
   =           org-src-mode-configure-edit-buffer)
 org-confirm-shell-link-functi= on 'yes-or-no-p
 org-reveal-start-hook '(org-decrypt-entry)
&nbs= p;org-export-first-hook '(org-beamer-initialize-open-trackers)
 org= -format-latex-header "\\documentclass{article}\n\\usepackage[usenames]{colo= r}\n\\usepackage{amsmath}\n\\usepackage[mathscr]{eucal}\n% Feiming's Custom= ization BEGIN\n\\usepackage[colorlinks=3Dtrue]{hyperref}\n\\input{/home/che= n/lib/math.tex}\n% Feiming's Customization END\n\\pagestyle{empty} &nb= sp;           % do not re= move\n[PACKAGES]\n[DEFAULT-PACKAGES]\n% The settings below are copied from fullpage.sty\n\\setlength{\\textwidth}{\\paperwidth}\n\\addtolength{\\text= width}{-3cm}\n\\setlength{\\oddsidemargin}{1.5cm}\n\\addtolength{\\oddsidem= argin}{-2.54cm}\n\\setlength{\\evensidemargin}{\\oddsidemargin}\n\\setlengt= h{\\textheight}{\\paperheight}\n\\addtolength{\\textheight}{-\\headheight}\= n\\addtolength{\\textheight}{-\\headsep}\n\\addtolength{\\textheight}{-\\fo= otskip}\n\\addtolength{\\textheight}{-3cm}\n\\setlength{\\topmargin}{1.5cm}= \n\\addtolength{\\topmargin}{-2.54cm}"
 org-startup-indented t
&= nbsp;org-agenda-before-write-hook '(org-agenda-add-entry-text)
 org= -babel-pre-tangle-hook '(save-buffer)
 org-cycle-hook '(org-cycle-h= ide-archived-subtrees org-cycle-hide-drawers
     &n= bsp;    org-cycle-show-empty-lines
     &n= bsp;    org-optimize-window-after-visibility-change)
 org= -export-preprocess-before-normalizing-links-hook '(org-remove-file-link-modifiers)
 org-use-speed-commands t
&nb= sp;org-mode-hook '(turn-on-org-cdlatex
      &n= bsp;  (lambda nil
          (set= q org-mouse-context-menu-function
        =    (quote org-mouse-context-menu))
     &n= bsp;    (when (memq (quote context-menu) org-mouse-features)
&= nbsp;          (org-defkey org-mouse-map= [mouse-3] nil)
           (org-= defkey org-mode-map [mouse-3]
        &nbs= p;   (quote org-mouse-show-context-menu))
    &= nbsp;      )
        &= nbsp; (org-defkey org-mode-map [down-mouse-1]
     &= nbsp;     (quote org-mouse-down-mouse))
          (wh= en (memq (quote context-menu) org-mouse-features)
    &nb= sp;      (org-defkey org-mouse-map [C-drag-mouse-1]
=             (quote org-mouse-m= ove-tree))
           (org-defke= y org-mouse-map [C-down-mouse-1]
        &= nbsp;   (quote org-mouse-move-tree-start))
    =        )
        =   (when (memq (quote yank-link) org-mouse-features)
   &n= bsp;       (org-defkey org-mode-map [S-mouse-2]            (quote org-mouse-= yank-link))
           (org-defk= ey org-mode-map [drag-mouse-3]
            (quote org-mouse-yank-link))           )
   &nbs= p;      (when (memq (quote move-tree) org-mouse-feature= s)
           (org-defkey org-mo= use-map [drag-mouse-3]
          = ;  (quote org-mouse-move-tree))
      &nbs= p;    (org-defkey org-mouse-map [down-mouse-3]
   &n= bsp;        (quote org-mouse-move-tree-start)= )
           )
   &= nbsp;      (when (memq (quote activate-stars) org-mouse= -features)
           (font-lock= -add-keywords nil
          &nbs= p; (\`
             (((\, outline-regexp) 0
    &nb= sp;          (\`
   &n= bsp;        (face org-link mouse-face highlig= ht keymap
             = ;(\, org-mouse-map))
          &= nbsp; )
            &n= bsp;  (quote prepend))
         =      )
         &= nbsp;   )
          &n= bsp; t)
           )
 &n= bsp;        (when (memq (quote activate-bullets) o= rg-mouse-features)
           (f= ont-lock-add-keywords nil
            (\`
         &nbs= p;   (("^[    ]*\\([-+*]\\|[0-9]+[.)]\\) +"
&nb= sp;              (1<= br>            (\`
 &n= bsp;           (face org-link keyma= p (\, org-mouse-map) mouse-face
        &n= bsp;     highlight)
       =      )
         =    (quote prepend))
        &nbs= p;      )
       =       )
        =      )
         &= nbsp;  t)
           )
          (when (memq (quote activ= ate-checkboxes) org-mouse-features)
       = ;    (font-lock-add-keywords nil
     &nbs= p;      (\`
        &n= bsp;    (("^[    ]*\\([-+*]\\|[0-9]+[.)]\\) += \\(\\[[ X]\\]\\)"
          &nbs= p;    (2
         &nbs= p;  (\`
            &n= bsp;(face bold keymap (\, org-mouse-map) mouse-face
    &= nbsp;         highlight)
   &nbs= p;         )
     = ;       t)
       = ;        )
              )
   =           )
    &= nbsp;       t)
      &= nbsp;    )
          (defad= vice org-open-at-point
          = ; (around org-mouse-open-at-point activate)
     &nb= sp;     (let ((context (org-context)))
    = ;        (cond ((assq :headline-stars context= ) (org-cycle))
           &= nbsp; ((assq :checkbox context) (org-toggle-checkbox))
   &nbs= p;         ((assq :item-bullet context)<= br>              (le= t ((org-cycle-include-plain-lists t)) (org-cycle)))
             (t ad-do-it))
 &= nbsp;          )
    &= nbsp;      )
        &= nbsp; )
         #[nil "\300\301\302\= 303\304$\207"
           [org-ad= d-hook change-major-mode-hook org-show-block-all append
   &nb= sp;        local]
     = ;      5]
        &nbs= p;#[nil "\300\301\302\303\304$\207"
       = ;    [org-add-hook change-major-mode-hook org-babel-show-result-a= ll
            append local= ]
           5]
   =       org-babel-result-hide-spec org-babel-hide-all-hashes)
 org-ctrl-c-ctrl-c-hook '(org-babel-has= h-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-co= ntext-menu-function
          &n= bsp;   (quote org-mouse-agenda-context-menu))
    &n= bsp;        (org-defkey org-agenda-mode-map [= mouse-3]
             = (quote org-mouse-show-context-menu))
      &nb= sp;      (org-defkey org-agenda-mode-map [down-mouse-3]=
              (quote = org-mouse-move-tree-start))
         =     (org-defkey org-agenda-mode-map [C-mouse-4]
            &n= bsp; (quote org-agenda-earlier))
        &= nbsp;    (org-defkey org-agenda-mode-map [C-mouse-5]
&nbs= p;             (quote org-agen= da-later))
            &nbs= p;(org-defkey org-agenda-mode-map [drag-mouse-3]
    &nbs= p;         (quote
     = ;          (lambda (event) (interactive = "e")
             &nbs= p;  (case (org-mouse-get-gesture event)
     &n= bsp;           (:left (org-agenda-e= arlier 1))
            &nbs= p;    (:right (org-agenda-later 1)))
                )
 =               )
 =              )
  =           )
    =         )
 org-export-interblocks '((= lob org-babel-exp-lob-one-liners)
        =       (src org-babel-exp-inline-src-blocks))
 o= rg-occur-hook '(org-first-headline-recenter)
 org-export-preprocess= -before-selecting-backend-code-hook '(org-beamer-select-beamer-code)
&nb= sp;org-confirm-babel-evaluate nil
 org-infojs-options '((path . "ht= tp://bancs.bdx.com/chen/lib/org-info.js")
      = ;        (view . "overview") (toc . "nil") (f= toc . "0")
              (tdepth . "max") (sdepth . "max") (mouse . = "underline")
           &nb= sp;  (buttons . "0") (ltoc . "1") (up . :link-up)
   &nbs= p;          (home . :link-home)) org-src-tab-acts-natively t
 org-export-latex-final-hook '(o= rg-beamer-amend-header org-beamer-fix-toc
      = ;             org-beamer-= auto-fragile-frames
          &n= bsp;        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-bloc= ks-format-comment t)
             (ditaa org-export-blocks-format-ditaa nil)
&nb= sp;            (dot org-export= -blocks-format-dot nil))
 )

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