Re: [Rd] missing exported methods when compiling vignettes in R 3.0.0 RC

2013-04-02 Thread Richard D. Morey
OK, so I think until we figure this out and/or the fix is on CRAN I can work around it using eval=FALSE with some hidden code blocks to hide the double colon notation. I've installed the latest revision of knitr, and it does fix the problem. On Tuesday, 2 April 2013 at 4:40 AM, Yihui Xie wr

Re: [Rd] missing exported methods when compiling vignettes in R 3.0.0 RC

2013-04-01 Thread Yihui Xie
I do not know much about S4, but I figured out one possible solution on knitr's side, which I do not really understand. In short, your S4 methods need to be evaluated in globalenv(), but knitr uses the parent.frame() by default, which is not the global environment when it is called as the vignette

Re: [Rd] missing exported methods when compiling vignettes in R 3.0.0 RC

2013-04-01 Thread Martin Morgan
On 04/01/2013 05:37 PM, Henrik Bengtsson wrote: Hi, things have indeed changed on how non-Sweave vignettes are built (this happened around R devel 2013-03-05 r62130). However, it's not clear to me what changes would be behind your problems, if any. Build your vignette with the following buildV

Re: [Rd] missing exported methods when compiling vignettes in R 3.0.0 RC

2013-04-01 Thread Henrik Bengtsson
Hi, things have indeed changed on how non-Sweave vignettes are built (this happened around R devel 2013-03-05 r62130). However, it's not clear to me what changes would be behind your problems, if any. Build your vignette with the following buildVignette(), which emulates what R does when it buil

[Rd] missing exported methods when compiling vignettes in R 3.0.0 RC

2013-04-01 Thread Richard D. Morey
A new problem has cropped up with compiling vignettes for my package BayesFactor. I'm not sure when it started, but I can tell you it didn't occur on R 2.15.3, and it does on 3.0.0 RC (2013-03-31 r62463) (session info is at the bottom of this message). I have defined methods for which.min and w