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### Running command:
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###   /Library/Frameworks/R.framework/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data ReportingTools
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* checking for file ‘ReportingTools/DESCRIPTION’ ... OK
* preparing ‘ReportingTools’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building ‘basicReportingTools.Rnw’ using Sweave
--- finished re-building ‘basicReportingTools.Rnw’

--- re-building ‘microarrayAnalysis.Rnw’ using Sweave
--- finished re-building ‘microarrayAnalysis.Rnw’

--- re-building ‘rnaseqAnalysis.Rnw’ using Sweave
--- finished re-building ‘rnaseqAnalysis.Rnw’

--- re-building ‘shiny.Rnw’ using Sweave
--- finished re-building ‘shiny.Rnw’

--- re-building ‘knitr.Rmd’ using knitr
Warning in file.info(x, extra_cols = FALSE) :
  expanded path length 6335 would be too long for
<!--
%\VignetteEngine{knitr}
%\VignetteIndexEntry{Knitr and ReportingTools}
-->
<h1 id="knitr-and-reportingtools">Knitr and ReportingTools</h1>
<p>Jessica L. Larson and Gabriel Becker</p>
<p>We can use knitr and ReportingTools together, as shown in this very simple example from our basic vignette.</p>
<p>Here we will create a simple report that integrates <code>ReportingTools</code> report capabilities with knitr.</p>
<p>To build this report, simply call the <code>knit2html</code> function from the
knitr package.</p>
<ul>
<li>By default, knitr will write the destination file within the current working directory.</li>
<li>We thus call <code>knit2html</code> from within the
<code>reportDirectory</code>.</li>
<li>Alternatively, we can call <code>knit2html</code> with an
<code>output</code> argument that matches the <code>reportDirectory</code>
argument passed to <code>HTMLReport</code>.</li>
</ul>
<p><strong>Note: the output html file must b [... truncated]
Warning in file(con, "r") :
  cannot open file 'jslib/jquery-1.8.0.min.js': No such file or directory
Error: processing vignette 'knitr.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building ‘knitr.Rmd’

SUMMARY: processing the following file failed:
  ‘knitr.Rmd’

Error: Vignette re-building failed.
Execution halted