[Rd] R CMD Sweave tmp.tex doesn't create figures with fig=TRUE, include=FALSE

With this file /tmp$ cat tmp.Rnw \documentclass{article} \begin{document} <>= v = seq(0, 60i, length=1000) plot(abs(v)*exp(v), type="l", col="Royalblue") @ \includegraphics{tmp-figureexample} \end{document} This command /tmp$ R --vanilla CMD Sweave tmp.Rnw Output file: tmp.tex does not produc

[Rd] dispatch on "c" method when passing named arguments

Hi, Many S4 objects in Bioconductor support "combining" via a "c" method. A common use case is to combine a collection of S4 objects stored in a list with the following idiom: do.call("c", list_of_objects) For many users this doesn't return what they expect though, because their 'list_of_obje

[Rd] Graphical parameters xaxs/yaxs

The documentation for `plot.window` says: Note that the coordinate ranges will be extended by 4% if the appropriate graphical parameter xaxs or yaxs has value "s" (which is the default). Yet calling `plot.window` with xaxs or yaxs set to "s" yields an error: > plot.window(c(0,1), c(0,1), xaxs="