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POknitr has stopped outputting plots
 

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  1. POknitr has stopped outputting plots
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    <p>I recently ran into a problem with knitr in R, where it suddenly stopped making plots. It does not report any problems, issues. It just that chunk that makes a plot (native R or ggplot2) does nothing. The chunk is evaluated, but somehow regarded as a chunk without R code.</p> <p>I've reduced the problem to a minimal example, but have no idea what has gone wrong. The entire file can be found at <a href="http://pastebin.com/pJUYjkxd" rel="nofollow noreferrer">http://pastebin.com/pJUYjkxd</a> and has this single chunk. Should be pretty straightforward?</p> <pre><code>&lt;&lt;mas11,dev='png'&gt;&gt;= plot(x=1:10, y=rnorm(10)) @ </code></pre> <p>But knitting it produces the following output (with R version 2.14.1):</p> <pre><code>Rscript --vanilla -e "library(knitr); knit('test.dev.2.Rnw');" processing file: test.dev.2.Rnw |&gt;&gt;&gt;&gt;&gt;&gt;&gt;&gt;&gt;&gt;&gt;&gt;&gt;&gt;&gt;&gt;&gt;&gt;&gt;&gt;&gt;&gt; | 33% ordinary text without R code |&gt;&gt;&gt;&gt;&gt;&gt;&gt;&gt;&gt;&gt;&gt;&gt;&gt;&gt;&gt;&gt;&gt;&gt;&gt;&gt;&gt;&gt;&gt;&gt;&gt;&gt;&gt;&gt;&gt;&gt;&gt;&gt;&gt;&gt;&gt;&gt;&gt;&gt;&gt;&gt;&gt;&gt;&gt; | 67% label: mas11 (with options) List of 1 $ dev: chr "png" |&gt;&gt;&gt;&gt;&gt;&gt;&gt;&gt;&gt;&gt;&gt;&gt;&gt;&gt;&gt;&gt;&gt;&gt;&gt;&gt;&gt;&gt;&gt;&gt;&gt;&gt;&gt;&gt;&gt;&gt;&gt;&gt;&gt;&gt;&gt;&gt;&gt;&gt;&gt;&gt;&gt;&gt;&gt;&gt;&gt;&gt;&gt;&gt;&gt;&gt;&gt;&gt;&gt;&gt;&gt;&gt;&gt;&gt;&gt;&gt;&gt;&gt;&gt;&gt;&gt;| 100% ordinary text without R code output file: /home/stefan/Repos/manuscript1/datahandling/test.dev.2.tex </code></pre> <p>And the final pdf-file is <img src="https://i.stack.imgur.com/5yX7f.png" alt="enter image description here"> where you can see the chunk has been echoed.</p> <p>I have no idea how to resolve this problem! Kindly help.</p> <p><strong>Update</strong></p> <pre><code>&gt; sessionInfo() R version 2.14.1 (2011-12-22) Platform: i686-pc-linux-gnu (32-bit) locale: [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C [3] LC_TIME=en_DK.UTF-8 LC_COLLATE=en_US.UTF-8 [5] LC_MONETARY=en_DK.UTF-8 LC_MESSAGES=en_US.UTF-8 [7] LC_PAPER=C LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=en_DK.UTF-8 LC_IDENTIFICATION=C attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] knitr_0.8 loaded via a namespace (and not attached): [1] digest_0.5.2 evaluate_0.4.3 formatR_0.6 plyr_1.8 stringr_0.6.1 [6] tools_2.14.1 </code></pre>
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    1. USMrGumble
    1. USMrGumble
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      1. VTUpMod
    2. VO
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      1. VTUpMod
    1. COI cannot reproduce the problem. `library(knitr); sessionInfo()` please!
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      1. USYihui Xie
    2. COTry using `fig=TRUE` and the various options in the chunk options instead of manually inserting the \begin{figure} stuff.
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      1. USDason
    3. CO@Dason - I cannot find any documentation for `fig=TRUE` in http://yihui.name/knitr/options; there are a lot of variants (''fig.align'', etc.).
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      1. USMrGumble
 

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