Re: [Rd] Feature request: mixing `...` (three dots) with other formal arguments in S4 methods

2014-11-27 Thread Janko Thyson
Well, the benefit lies in the ability to pass along arguments via `...` to more than one recipient that use *identical argument names* and/or when these recipients are not necessarily located on the same calling stack layer. I'm *not* after a *general* change in the way arguments are dispatched/fu

Re: [Rd] Feature request: mixing `...` (three dots) with other formal arguments in S4 methods

2014-11-27 Thread Gabriel Becker
I think I understand what you're saying now, but I'm still kind of missing the benefit from the approach. As far as I can tell just giving foo formals for the arguments you want it to catch gives you the end result you want, doesn't it? And if the generic has ... in it, you can (if you're very ca

Re: [Rd] Problem understanding behaviour of versionCheck for loadNamespace (and when versions for Imports packages are checked)

2014-11-27 Thread Geoff Lee
Hi Duncan, Many thanks (yet again). With the hint given by your earlier email (viz that currently loadNamespace expects a 3rd component called name in the list that is used for the versionCheck argument) I had another look at what was going on with my toy examples yesterday evening. I'm still wo

Re: [Rd] Feature request: mixing `...` (three dots) with other formal arguments in S4 methods

2014-11-27 Thread Janko Thyson
Hi Gabriel, and thanks for answering. I'm basically just trying to find a way to use the power of `...` in more complex scenarios and I'm well aware that this might not be the best approach ;-) Regarding your actual question: "Are you suggesting methods be dispatched based on the *contents* of ..

Re: [Rd] testing dontrun examples

2014-11-27 Thread Dirk Eddelbuettel
On 27 November 2014 at 11:23, Paul Gilbert wrote: | On 14-11-26 05:49 PM, Duncan Murdoch wrote: | > On 26/11/2014, 1:45 PM, Paul Gilbert wrote: | >> Wishlist: what I would really like is R CMD check --run-dontrun pkg | > | > We have that in R-devel, so everyone will have it next April, but there

Re: [Rd] Feature request: mixing `...` (three dots) with other formal arguments in S4 methods

2014-11-27 Thread Gabriel Becker
Janko, I'm not entirely sure I understand your proposal. Are you suggesting methods be dispatched based on the *contents* of ... (ie which arguments are in there)? This seems like it would be pretty different from how dispatch behaves now, which is entirely class based. Even the dispatching based

[Rd] Feature request: mixing `...` (three dots) with other formal arguments in S4 methods

2014-11-27 Thread Janko Thyson
Dear List, I'm currently investigating if the argument dispatch mechanism based on `...` could somehow be "generalized" to scenarios that involve `r` recipients located across `c` calling stack layers *and* combined with the S4 method mechanism (for those interested see http://stackoverflow.com/qu

Re: [Rd] testing dontrun examples

2014-11-27 Thread Paul Gilbert
On 14-11-26 05:49 PM, Duncan Murdoch wrote: On 26/11/2014, 1:45 PM, Paul Gilbert wrote: Is there a good strategy for testing examples which should not be run by default? For instance, I have examples which get data from the Internet. If I wrap them in try() then they can be skipped if the Inte

Re: [Rd] Problem understanding behaviour of versionCheck for loadNamespace (and when versions for Imports packages are checked)

2014-11-27 Thread Duncan Murdoch
On 26/11/2014, 8:29 PM, Geoff Lee wrote: > Hi Duncan > > The difference is that in your call to loadNamespace, the versionCheck list > has 3 components (name, op and version), whereas the documentation only > mentions 2 (op and version). > loadNamespace 'works' for me provided I add a third compon

[Rd] p.adjust on a vector including NA values

2014-11-27 Thread Johannes Rainer
dear all, I recently came across the following issue and I was not sure whether it is intentionally or not: using p.adjust to adjust p-values for multiple hypothesis testing using the method from Benjamini and Hochberg removes all NA values from the input vector and does not account for them in