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POWhy does org-babel export a ggplot graph fine with C-c C-c but not with export or publish?
 

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  1. POWhy does org-babel export a ggplot graph fine with C-c C-c but not with export or publish?
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    <p>I have a code block with a simple command:</p> <pre><code>#+begin_src R :results output graphics :exports results :file a.png print(qplot(a,binwidth=1)+opts(title="graph title")+scale_x_continuous("axis lable")+scale_y_continuous(formatter="comma")) #+end_src </code></pre> <p>I load ggplot2 in an earlier block of this session, and it works fine when I do <code>C-c C-c</code> to execute that block.</p> <p>When I try <code>C-c C-e h</code> or <code>C-c C-e P</code> to export or publish the file, it writes an a.png of length 0.</p> <p>Here are some of the <code>#+</code> lines at the start of this file:</p> <pre><code>#+OPTIONS: H:3 num:t toc:t \n:nil @:t ::t |:t ^:t -:t f:t *:t &lt;:t #+OPTIONS: TeX:t LaTeX:t skip:nil d:nil todo:t pri:nil tags:not-in-toc #+INFOJS_OPT: view:info toc:nil ltoc:t mouse:underline buttons:0 path:http://orgmode.org/org-info.js #+EXPORT_SELECT_TAGS: export #+EXPORT_EXCLUDE_TAGS: noexport #+BABEL: :session *R* :cache yes :exports both :tangle yes </code></pre> <p>I'm running "GNU Emacs 23.3.1 (i386-mingw-nt5.2.3790) of 2011-03-10 on 3249CTO" on an XP64 system and "Org-mode version 7.5".</p> <p>What am I missing? I didn't find the answer in my search of Stack Overflow, the org-mode mailing list, the manuals, or Google.</p> <p>I tried a simple, executable file this morning:</p> <pre><code>#+TITLE: test.org #+AUTHOR: #+EMAIL: me #+DATE: 2012-03-01 Thu #+DESCRIPTION: #+KEYWORDS: #+LANGUAGE: en #+OPTIONS: H:3 num:t toc:t \n:nil @:t ::t |:t ^:t -:t f:t *:t &lt;:t #+OPTIONS: TeX:t LaTeX:t skip:nil d:nil todo:t pri:nil tags:not-in-toc #+INFOJS_OPT: view:nil toc:nil ltoc:t mouse:underline buttons:0 path:http://orgmode.org/org-info.js #+EXPORT_SELECT_TAGS: export #+EXPORT_EXCLUDE_TAGS: noexport #+LINK_UP: #+LINK_HOME: #+XSLT: #+BABEL: :session *R* :cache yes :exports both :tangle yes * Test of R #+begin_src R :results output :export both summary(rnorm(25)) #+end_src #+results: * Test of ggplot2 #+begin_src R :results output graphics :exports results :file testggplot.png library(ggplot2) qplot(runif(25)) #+end_src </code></pre> <p>Each code block executes fine with <code>C-c C-c</code>. Running <code>C-c C-e h</code> or <code>C-c C-e b</code> to export as HTML gives problems with a big clue: it writes the file testggplot.png with the contents </p> <pre><code>stat_bin: binwidth defaulted to range/30. Use 'binwidth = x' to adjust this. </code></pre> <p>My conjecture: I got a 0-length .png file above because it didn't need to write an error message.</p> <p>If I run <code>C-c C-c</code> first, I get a <code>#+results[</code> section in the .org file with a link to <code>testggplot.png</code>. I can see the graph in the .org file, if I turn on iimage-mode.</p> <p>If I then run <code>C-c C-e h</code>, I get a valid HTML file with the graph.</p> <p>Does that (or the ECM) give any clues that might show me what to do (besides running <code>C-c C-c</code> on every code block first)?</p> <p>UPDATE 2: perhaps snippets of the HTML org-mode produces provide insight. </p> <p>If I have run <code>C-c C-c</code> first, such that the graphic file has been written, then I get</p> <pre><code>&lt;div id="outline-container-2" class="outline-2"&gt; &lt;h2 id="sec-2"&gt;&lt;span class="section-number-2"&gt;2&lt;/span&gt; Test of ggplot2 &lt;/h2&gt; &lt;div class="outline-text-2" id="text-2"&gt; &lt;p&gt; &lt;img src="testggplot.png" alt="testggplot.png" /&gt; &lt;/p&gt; &lt;/div&gt; &lt;/div&gt; </code></pre> <p>If I have not created the file first, then I get</p> <pre><code>&lt;div id="outline-container-2" class="outline-2"&gt; &lt;h2 id="sec-2"&gt;&lt;span class="section-number-2"&gt;2&lt;/span&gt; Test of ggplot2 &lt;/h2&gt; &lt;div class="outline-text-2" id="text-2"&gt; &lt;pre class="example"&gt; testggplot.png &lt;/pre&gt; &lt;/div&gt; &lt;/div&gt; </code></pre> <p>The only difference seems to be whether it wraps the file name in a <code>&lt;pre&gt;</code> block as text or whether it wraps it as an image. Of course, in the first case, it also fails to write a .png file.</p>
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