* Bug: Org-Babel Mode R Plot Output to LaTeX File [Babel] [7.5]
@ 2011-07-13 21:14 Feiming Chen
2011-07-15 14:32 ` Eric Schulte
0 siblings, 1 reply; 9+ messages in thread
From: Feiming Chen @ 2011-07-13 21:14 UTC (permalink / raw)
To: emacs-orgmode
[-- 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 --]
^ permalink raw reply [flat|nested] 9+ messages in thread* Re: Bug: Org-Babel Mode R Plot Output to LaTeX File [Babel] [7.5]
2011-07-13 21:14 Bug: Org-Babel Mode R Plot Output to LaTeX File [Babel] [7.5] Feiming Chen
@ 2011-07-15 14:32 ` Eric Schulte
2011-07-16 9:05 ` Stephen Eglen
0 siblings, 1 reply; 9+ messages in thread
From: Eric Schulte @ 2011-07-15 14:32 UTC (permalink / raw)
To: Feiming Chen; +Cc: emacs-orgmode
[-- Attachment #1: Type: text/plain, Size: 435 bytes --]
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
[-- Warning: decoded text below may be mangled, UTF-8 assumed --]
[-- Attachment #2: test.org --]
[-- Type: text/x-org, Size: 700 bytes --]
#+TITLE:test
#+BABEL: :session *R* :results output graphics :exports both
#+source: plot1
#+begin_src R :file a1.png :width 500 :height 500
a <- b <- 1:10
plot(a, b)
#+end_src
#+ATTR_LaTeX: width=500px
#+results: plot1
[[file:a1.png]]
#+source: plot2
#+begin_src R :file a2.png :width 1000 :height 1000
plot(a, b)
#+end_src
#+ATTR_LaTeX: width=100px
#+results: plot2
[[file:a2.png]]
#+source: plot3
#+begin_src R :file a3.pdf :width 5 :height 5
a <- b <- 1:10
plot(a, b)
#+end_src
#+ATTR_LaTeX: width=5px
#+results: plot3
[[file:a3.pdf]]
#+source: plot4
#+begin_src R :file a4.pdf :width 10 :height 10
plot(a, b)
#+end_src
#+ATTR_LaTeX: width=10
#+results: plot4
[[file:a4.pdf]]
[-- Attachment #3: Type: text/plain, Size: 11034 bytes --]
Feiming Chen <feimingchen@yahoo.com> 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/
^ permalink raw reply [flat|nested] 9+ messages in thread* Re: Bug: Org-Babel Mode R Plot Output to LaTeX File [Babel] [7.5]
2011-07-15 14:32 ` Eric Schulte
@ 2011-07-16 9:05 ` Stephen Eglen
2011-07-16 13:20 ` Eric Schulte
0 siblings, 1 reply; 9+ messages in thread
From: Stephen Eglen @ 2011-07-16 9:05 UTC (permalink / raw)
To: emacs-orgmode
> 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.
hi Eric,
why is the default width 10em for latex graphics? (Or at least, how can
I change this default?
thanks,
Stephen
^ permalink raw reply [flat|nested] 9+ messages in thread
* Re: Bug: Org-Babel Mode R Plot Output to LaTeX File [Babel] [7.5]
2011-07-16 9:05 ` Stephen Eglen
@ 2011-07-16 13:20 ` Eric Schulte
2011-07-16 18:54 ` Sebastien Vauban
0 siblings, 1 reply; 9+ messages in thread
From: Eric Schulte @ 2011-07-16 13:20 UTC (permalink / raw)
To: Stephen Eglen; +Cc: emacs-orgmode
See the `org-export-latex-image-default-option' variable.
Generally in such situation you can run the `describe-variable' function
and tab-complete your way to the name of the relevant variable. The
`apropos' function is also useful for suss out this sort of information.
Best -- Eric
Stephen Eglen <S.J.Eglen@damtp.cam.ac.uk> writes:
>> 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.
>
> hi Eric,
> why is the default width 10em for latex graphics? (Or at least, how can
> I change this default?
>
> thanks,
> Stephen
>
>
--
Eric Schulte
http://cs.unm.edu/~eschulte/
^ permalink raw reply [flat|nested] 9+ messages in thread
* Re: Bug: Org-Babel Mode R Plot Output to LaTeX File [Babel] [7.5]
2011-07-16 13:20 ` Eric Schulte
@ 2011-07-16 18:54 ` Sebastien Vauban
2011-07-17 6:30 ` Bastien
0 siblings, 1 reply; 9+ messages in thread
From: Sebastien Vauban @ 2011-07-16 18:54 UTC (permalink / raw)
To: emacs-orgmode-mXXj517/zsQ
Hi Eric and Stephen,
Eric Schulte wrote:
>> why is the default width 10em for latex graphics? (Or at least, how can
>> I change this default?
>
> See the `org-export-latex-image-default-option' variable.
>
> Generally in such situation you can run the `describe-variable' function
> and tab-complete your way to the name of the relevant variable. The
> `apropos' function is also useful for suss out this sort of information.
Shouldn't it more appropriate to give that var such a default:
"width=0.9\\linewidth"
10em seems to me much to small in *all* cases, no?
Best regards,
Seb
--
Sebastien Vauban
^ permalink raw reply [flat|nested] 9+ messages in thread
* Re: Bug: Org-Babel Mode R Plot Output to LaTeX File [Babel] [7.5]
@ 2011-07-18 16:19 Feiming Chen
2011-07-18 16:36 ` Eric Schulte
0 siblings, 1 reply; 9+ messages in thread
From: Feiming Chen @ 2011-07-18 16:19 UTC (permalink / raw)
To: Eric Schulte; +Cc: emacs-orgmode
[-- Attachment #1.1: Type: text/plain, Size: 11417 bytes --]
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 <schulte.eric@gmail.com> wrote:
From: Eric Schulte <schulte.eric@gmail.com>
Subject: Re: [O] Bug: Org-Babel Mode R Plot Output to LaTeX File [Babel] [7.5]
To: "Feiming Chen" <feimingchen@yahoo.com>
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 <feimingchen@yahoo.com> 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/
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[-- Attachment #2: test2.org --]
[-- Type: application/vnd.lotus-organizer, Size: 248 bytes --]
^ permalink raw reply [flat|nested] 9+ messages in thread* Re: Bug: Org-Babel Mode R Plot Output to LaTeX File [Babel] [7.5]
2011-07-18 16:19 Feiming Chen
@ 2011-07-18 16:36 ` Eric Schulte
2011-07-18 17:08 ` Feiming Chen
0 siblings, 1 reply; 9+ messages in thread
From: Eric Schulte @ 2011-07-18 16:36 UTC (permalink / raw)
To: Feiming Chen; +Cc: emacs-orgmode
Feiming Chen <feimingchen@yahoo.com> 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 <schulte.eric@gmail.com> wrote:
>
> From: Eric Schulte <schulte.eric@gmail.com>
> Subject: Re: [O] Bug: Org-Babel Mode R Plot Output to LaTeX File [Babel] [7.5]
> To: "Feiming Chen" <feimingchen@yahoo.com>
> 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 <feimingchen@yahoo.com> 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/
^ permalink raw reply [flat|nested] 9+ messages in thread* Re: Bug: Org-Babel Mode R Plot Output to LaTeX File [Babel] [7.5]
2011-07-18 16:36 ` Eric Schulte
@ 2011-07-18 17:08 ` Feiming Chen
0 siblings, 0 replies; 9+ messages in thread
From: Feiming Chen @ 2011-07-18 17:08 UTC (permalink / raw)
To: Eric Schulte; +Cc: emacs-orgmode
[-- Attachment #1: Type: text/plain, Size: 13285 bytes --]
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 <schulte.eric@gmail.com> wrote:
From: Eric Schulte <schulte.eric@gmail.com>
Subject: Re: [O] Bug: Org-Babel Mode R Plot Output to LaTeX File [Babel] [7.5]
To: "Feiming Chen" <feimingchen@yahoo.com>
Cc: "Eric Schulte" <schulte.eric@gmail.com>, emacs-orgmode@gnu.org
Date: Monday, July 18, 2011, 11:36 AM
Feiming Chen <feimingchen@yahoo.com> 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 <schulte.eric@gmail.com> wrote:
>
> From: Eric Schulte <schulte.eric@gmail.com>
> Subject: Re: [O] Bug: Org-Babel Mode R Plot Output to LaTeX File [Babel] [7.5]
> To: "Feiming Chen" <feimingchen@yahoo.com>
> 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 <feimingchen@yahoo.com> 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/
[-- Attachment #2: Type: text/html, Size: 23138 bytes --]
^ permalink raw reply [flat|nested] 9+ messages in thread
end of thread, other threads:[~2011-07-18 17:08 UTC | newest]
Thread overview: 9+ messages (download: mbox.gz follow: Atom feed
-- links below jump to the message on this page --
2011-07-13 21:14 Bug: Org-Babel Mode R Plot Output to LaTeX File [Babel] [7.5] Feiming Chen
2011-07-15 14:32 ` 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
-- strict thread matches above, loose matches on Subject: below --
2011-07-18 16:19 Feiming Chen
2011-07-18 16:36 ` Eric Schulte
2011-07-18 17:08 ` Feiming Chen
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