[Bioc-devel] non-pdf documents linked from package pages?

2012-11-21 Thread Michael Lawrence
This may already be documented somewhere, but do the package pages on the bioc website link to any file present in inst/doc? Or does it only work for PDF vignettes? It would be neat if people could produce vignettes in any format and have them linked from the package pages. This relates to Sean's

[Rd] S3 generic/method consistency issue with R CMD check

2012-11-21 Thread Drew Schmidt
Hi, I'm having some trouble setting methods for the qr family of functions. I believe I have distilled my misunderstanding in the code snippet below: foo - function(x, ...) UseMethod(foo) foo.default - function(x) { } # foo setGeneric(name = foo, useAsDefault = foo) setMethod(foo,

[Rd] why does do_stop call R_GetTraceback ?

2012-11-21 Thread Andrew Piskorski
I'm using: R 2.15.1 (beta), 2012-06-11, svn.rev 59557, x86_64-unknown-linux-gnu And I normally use: options(error=recover) I recently ran into a problem where when my code called stop(), recover() was incredibly slow (hours) because it was trying to deparse an extremely large call. I worked