Question

I’m following Gregor Gorjanc’s tutorial on LyX & Sweave. Using Ubuntu 10.04 and LyX version 1.6.5 with all of texlive-full installed.

R scraps which result in numerical output produce a valid PDF.

But, when I try to compile simple figures like

<<chunk, fig=T>>=       [ctrl+enter]
hist(rnorm(100))        [ctrl+enter]
@

I get cryptic errors. Either that chunk.temp.Rnw wasn’t found, or that LaTeX encountered an error and I should hit <enter> to ignore.

If I change fig to figure and T to TRUE, then the LyX document compiles but displays no graphics. With pgfsweave I get this error, or sometimes this one.

Am I working with the wrong versions of these programs? Is there a way to elicit better error messages? Can I somehow dive into the LaTeX prompt and hit <enter> myself?

update: I was using the wrong version of LaTeX; Ubuntu’s default is too old. Also I needed to update to LyX 2.0.1 and a newer version of pgf and pgfSweave (the programs are distinct).

The new (nondescript) error message is: An error occurred while running: Rscript '/home/mars/.lyx/scripts/lyx-sweave-exec.R' 'UTF-8' 'pgfSweave' "/home/mars/" "/tmp/lyx_tmpdir.T1663/lyx_tmpbuf2/" "test.sweave.lyx.Rnw" > "test.sweave.Rnw".log 2>&1

Answer 1

According to https://tex.stackexchange.com/questions/27993/can-i-download-ctan-packages-from-the-command-line-ubuntu/27994#27994 there is a perennial problem with TeX in Ubuntu: their packages are way behind. Since many innovations with Sweave have happened in 2010-2011, it seems one must download and install an .iso from http://ftp.ctex.org/mirrors/CTAN/systems/texlive/Images/ rather than use Synaptic. So much for package management!

I’ll accept my own answer only if this actually works.

update: Make sure you disregard anything you read about Noweb.sty because in LyX 2.0.1 there is a “Sweave Module” meaning you should just use regular document classes (article, book, report) — the scraps are replaced by chunks and essentially Sweave is handled natively. Also disregard Brett Collier’s lucid explanation of how to install LyX because it’s now outdated, despite Gregor Gorjanc’s highly-googleable blog post saying it works. That is also outdated, or maybe it only works in Ubuntu 9 and not Ubuntu 10.04.

So the steps to successfully getting Sweave to work in LyX for Ubuntu 10.04 as of August 2011 are:

1. Get the newest texlive from tug.org — not the one from Synaptic. How to do that: https://tex.stackexchange.com/questions/27993/can-i-download-ctan-packages-from-the-command-line-ubuntu/27994
2. Get pgf and kTikz as described here: http://justbloodywork.blogspot.com/2011/07/installing-latex-and-pgf.html
3. Follow Yihue’s instructions here: http://yihui.name/en/2010/10/how-to-start-using-pgfsweave-in-lyx-in-one-minute/#comment-10929. Build lyx-devel from source, apply Yihue’s patch, and configure some LyX preferences.
4. Tools > Reconfigure LyX.
5. Pray.
6. Start LyX and load Yihue’s test file from (3). Hit Ctrl + R, not Ctrl + D to view.