<div class="gmail_quote">Hi All,<div><br></div><div>I'm a new user trying to figure out a good pipeline for R/Latek/Sweave. Works great for me, except it crashes TextMate after rendering the PDF! </div><div><br></div>
<div>Lots of information below and attached. It seems like a TextMate problem (and I've sent off a bug report) but thought someone here might have some insight. </div><div><br></div><div>Any thoughts?</div><meta charset="utf-8">
<div><br></div><div>Thanks!Alex</div><div><br></div><div>PS: I noticed a spam ad for payday loans on the wiki, so I deleted it. If any of you guys need payday loans, I apologize!</div><div><br></div><div><br></div><div>
<u>Reproduce:</u></div><div>- Install TextMate,R,Latek,R/Latek/Sweave bundles</div><div>- Use TextMate to render Example.Rnw (below).</div><div>- TextMate does an admirable job, producing the correct PDF.</div>
<div>- After this, the PDF window shows a spinning cursor in the top-right, and crashes after ~10s.</div><div><br></div><div>Both TextMate and the PDF window respond normally during this time. Crash occurs even if I close the PDF window!</div>
<div><br></div><div><u>Attached for diagnostics:</u></div><div>Crash log: </div><blockquote style="margin:0 0 0 40px;border:none;padding:0px"><div>Crash Report.txt</div></blockquote>
<div>Sample of TextMate process from just before executing Example.Rnw until after the crash: </div><blockquote style="margin:0 0 0 40px;border:none;padding:0px"><div>Exited process_6469.FdDN5T.sample</div>
</blockquote>Console Errors<blockquote style="margin:0 0 0 40px;border:none;padding:0px"><div><div>11/19/10 2:24:40 PM<span style="white-space:pre-wrap"> </span>defaults[6774]<span style="white-space:pre-wrap"> </span>The domain/default pair of (com.macromates.textmate.webpreview, SelectedTheme) does not exist</div>
</div><div><div>11/19/10 2:25:09 PM<span style="white-space:pre-wrap"> </span>com.apple.launchd.peruser.1987805519[4483]<span style="white-space:pre-wrap"> </span>([0x0-0x94094].com.macromates.textmate[6629]) Job appears to have crashed: Segmentation fault</div>
</div></blockquote><div><div><br></div><div><u>Example .Rnw file from the Sweave manual</u></div><div>from: <a href="http://cran.r-project.org/web/packages/pgfSweave/vignettes/pgfSweave.pdf" target="_blank">http://cran.r-project.org/web/packages/pgfSweave/vignettes/pgfSweave.pdf</a></div>
<div><div>\documentclass[a4paper]{article}</div><div>\title{Sweave Example 1} </div><div>\author{Friedrich Leisch}</div><div>\begin{document} </div><div>\maketitle</div><div>In this example we embed parts of the examples from the \texttt{kruskal.test} help page into a \LaTeX{} document:</div>
<div><<>>= </div><div>data(airquality) </div><div>kruskal.test(Ozone ~ Month, data = airquality) </div><div>@ </div><div>which shows that the location parameter of the Ozone distribution varies significantly from month to month. Finally we include a boxplot of the data:</div>
<div>\begin{center} </div><div><<fig=TRUE ,echo=FALSE >>= </div><div>boxplot(Ozone ~ Month, data = airquality) </div><div>@ </div><div>\end{center}</div><div>\end{document}</div></div><i>>> note: delete library(ctest) from the original example to run.</i><br>
<div><br></div><div><br></div><div><u>My installation (all of this as of 10.11.19)</u></div><div><div>- Installed: "R version 2.12.0 (2010-10-15)"</div></div><div>- MacTex basic from <a href="http://mirror.unl.edu/ctan/systems/mac/mactex/mactex-basic.pkg.zip" target="_blank">http://mirror.unl.edu/ctan/systems/mac/mactex/mactex-basic.pkg.zip</a><br>
- TexMate from : <a href="http://download.macromates.com/TextMate_1.5.10.zip" target="_blank">http://download.macromates.com/TextMate_1.5.10.zip</a><br>- Installed R,Latex,and Sweave bundles as per: <a href="http://www.r-bloggers.com/setting-up-textmate-to-use-r/" target="_blank">http://www.r-bloggers.com/setting-up-textmate-to-use-r/</a>, ie., <br>
</div><blockquote style="margin:0 0 0 40px;border:none;padding:0px"><div>mkdir -p /Library/Application\ Support/TextMate/Bundles</div><div>cd /Library/Application\ Support/TextMate/Bundles</div>
<div>svn co <a href="http://svn.textmate.org/trunk/Bundles/R.tmbundle" target="_blank">http://svn.textmate.org/trunk/Bundles/R.tmbundle</a></div><div>svn co <a href="http://svn.textmate.org/trunk/Bundles/Latex.tmbundle" target="_blank">http://svn.textmate.org/trunk/Bundles/Latex.tmbundle</a></div>
<div>svn co <a href="http://svn.textmate.org/trunk/Bundles/SWeave.tmbundle" target="_blank">http://svn.textmate.org/trunk/Bundles/SWeave.tmbundle</a></div></blockquote><div>- Got around the Sweave.sty problem by</div><blockquote style="margin:0 0 0 40px;border:none;padding:0px">
<div>mkdir -p ~/Library/texmf/tex/latex </div><div>cd ~/Library/texmf/tex/latex </div><div>ln -s /Library/Frameworks/R.framework/Resources/share/texmf Sweave</div><div>... as per somewhere.</div></blockquote><div><span style="font-family:Consolas, Monaco, 'Lucida Sans Typewriter', 'Courier New', mono-space;font-size:12px;color:rgb(17, 17, 34);line-height:18px;white-space:pre-wrap"><br>
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</span></div><div><br></div><div><br clear="all">---<br>Alex Vaughan<br>HHMI, Janelia Farm Research Center<br>Dept. of Biology, Stanford University<br>Email :: <a href="mailto:avaughan@stanford.edu" target="_blank">avaughan@stanford.edu</a><br>
Phone :: 510 717 6010<br>---<br>
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