Re: [Rd] Re R CMD check checking in development version of R

2014-08-28 Thread Barry Rowlingson
And if, like me, you always forget which of Depends and Imports is the one you are supposed to be using, the mnemonic device is "DEPends is DEPrecated[1], IMPorts is IMPortant." Barry [1] kinda. On Thu, Aug 28, 2014 at 4:33 AM, Gavin Simpson wrote: > On Aug 27, 2014 5:24 PM, "Hadley Wickham"

Re: [Rd] no visible binding for global variable for data sets in a package

2014-08-28 Thread Martin Maechler
> peter dalgaard > on Wed, 27 Aug 2014 21:09:47 +0200 writes: > On 27 Aug 2014, at 16:48 , Hadley Wickham wrote: >>> I think the right answer _is_ to export the lazy data; the question is how to do it. There's nothing particularly strange about exporting non-functions ("le

Re: [Rd] Re R CMD check checking in development version of R

2014-08-28 Thread Martin Morgan
On 08/27/2014 08:33 PM, Gavin Simpson wrote: On Aug 27, 2014 5:24 PM, "Hadley Wickham" I'd say: Depends is a historical artefact from ye old days before package namespaces. Apart from depending on a specific version of R, you should basically never use depends. (The one exception is, as mentio

Re: [Rd] Re R CMD check checking in development version of R

2014-08-28 Thread Hadley Wickham
>>> I'd say: Depends is a historical artefact from ye old days before >>> package namespaces. Apart from depending on a specific version of R, >>> you should basically never use depends. (The one exception is, as >>> mentioned in R-exts, if you're writing something like latticeExtras >>> that does

Re: [Rd] Re R CMD check checking in development version of R

2014-08-28 Thread Martin Morgan
On 08/28/2014 05:52 AM, Hadley Wickham wrote: I'd say: Depends is a historical artefact from ye old days before package namespaces. Apart from depending on a specific version of R, you should basically never use depends. (The one exception is, as mentioned in R-exts, if you're writing something

Re: [Rd] no visible binding for global variable for data sets in a package

2014-08-28 Thread Therneau, Terry M., Ph.D.
Here is one rationale for the change, which was useful for my understanding This arises in the survival package in the survexp function: survexp <- function(formula, data, weights, subset, na.action, ratetable=survexp.us) The argument has been changed to survival::survexp.us, soon to be

Re: [Rd] Re R CMD check checking in development version of R

2014-08-28 Thread Simon Urbanek
On Aug 27, 2014, at 6:01 PM, Gavin Simpson wrote: > On 27 August 2014 15:24, Hadley Wickham wrote: > >>> Is that the cause of these NOTEs? Is the expectation that if I am using a >>> function from a package, even a package that I have in Depends:, that I >>> have to explicitly declare these im

Re: [Rd] Re R CMD check checking in development version of R

2014-08-28 Thread Bert Gunter
This is a nice explanation of the Imports/Depends distinction. It ought to go into the Extensions ref manual imho. Cheers, Bert Bert Gunter Genentech Nonclinical Biostatistics (650) 467-7374 "Data is not information. Information is not knowledge. And knowledge is certainly not wisdom." Clifford

Re: [Rd] Re R CMD check checking in development version of R

2014-08-28 Thread Ravi Varadhan
Hi, I second Bert's comment. I would like to go even farther and suggest that it would be really useful if one of the R gurus (like Simon) wrote a relatively non-technical article in the R journal on this topic of "Depends/Imports/Suggested." Someone like myself would benefit immensely. Thank

Re: [Rd] Re R CMD check checking in development version of R

2014-08-28 Thread Henrik Bengtsson
>From a developers point of view, these days a less ambiguous name for 'Depends' would be 'Attaches'. ...or maybe even 'ImportsAndAttaches' with 'ImportsOnly' (for 'Imports'). I think Simon phrased it very well, and as others already pointed out, having one package attaching additional ones certa

Re: [Rd] Re R CMD check checking in development version of R

2014-08-28 Thread Gavin Simpson
I fully agree. This is how I have come to understand Depends vs Imports and why I currently will not be removing vegan from Depends for my analogue package. This is also why I was pushing back against the notion that was voiced early in this thread that *nothing* should be in Depends. Cheers G

Re: [Rd] Re R CMD check checking in development version of R

2014-08-28 Thread Gabriel Becker
Gavin, I admit to not knowing the details of your package, but do users commonly need to use symbols from other package *in calls to functions exported by your package*? If so, you're in the situation Martin (Morgan) described, which is one I think everyone agrees Depends is appropriate for. If t

Re: [Rd] Re R CMD check checking in development version of R

2014-08-28 Thread Gavin Simpson
Gabriel, That is not my understanding of this at all. I could hide the fact that I was using vegan under the hood, supplying methods for its generics and by exporting the generic I imported from vegan, etc. But you are missing the point that I see users of my package, because I envisioned close in

Re: [Rd] Re R CMD check checking in development version of R

2014-08-28 Thread Gabriel Becker
Gavin, I don't claim to be the arbiter of good package design. The following are my opinions, along with the reasons I hold them. If you are also importing vegan, which I think everyone agreed needs to happen, the only thing putting vegan in Depends does is attach the package. This is something u

Re: [Rd] Re R CMD check checking in development version of R

2014-08-28 Thread Gabor Grothendieck
Yes, Depends certainly has a role. The ability of one package to automatically provide all the facilities of another package to the user is important. There are many situations where the functionality you want to provide to the user is split among multiple packages. For example, 1. xts uses zoo a

Re: [Rd] Re R CMD check checking in development version of R

2014-08-28 Thread Paul Gilbert
(Please correct me if I'm wrong. I thought I mostly understood this, finally, but I've made the mistake of thinking I understood something too many times before.) On 08/28/2014 10:39 AM, Simon Urbanek wrote: On Aug 27, 2014, at 6:01 PM, Gavin Simpson wrote: On 27 August 2014 15:24, Hadley