[Bioc-devel] BioC 2.13 branch created

2013-10-14 Thread Dan Tenenbaum
The BioC 2.13 branch is now ready. Remember, you always have access to 2 versions of your package: the release and the devel versions. Right now the release version of your package (which is not officially released yet but will be in the next 72 hours if everything goes well) is in the 2.13

Re: [Rd] missing documentation entries ... WARNING

2013-10-14 Thread Duncan Murdoch
On 13-10-14 1:54 PM, Luis Rodríguez wrote: Thanks Duncan (and othersin R-devel). I clearly got away from this project, but I am still quite interested in resolving this issue and getting these codes into the CRAN. Some attempts to repair the documentation have occurred in the intervening

[Rd] how to prevent default argument values from being found

2013-10-14 Thread William Dunlap
Here is a problem I ran across in RStudio, which uses masks a number of standard R functions with versions that do a bit more than the original does. The RStudio people have figured out a way to prevent default values of arguments from being found when an argument is missing from a call!

[Rd] Q-Q plot scaling in plot.lm(); bug or thinko?

2013-10-14 Thread Ben Bolker
-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 I've been looking fairly carefully at the Q-Q plots produced by plot.lm() and am having difficulty understanding why plot.lm() is doing what it's doing, specifically scaling the standardized residuals by the prior weights. Can anyone explain this to