From pgilbert902 at gmail.com  Thu Sep 12 18:54:35 2013
From: pgilbert902 at gmail.com (Paul Gilbert)
Date: Thu, 12 Sep 2013 12:54:35 -0400
Subject: [Rd] declaring package dependencies
In-Reply-To: <5231C3E3.3050007@yorku.ca>
References: <5231C3E3.3050007@yorku.ca>
Message-ID: <5231F1CB.2080801@gmail.com>

Michael

(Several of us are struggling with these changes, so my comments are 
from the newly initiated point of view, rather than the fully 
knowledgeable.)

On 13-09-12 09:38 AM, Michael Friendly wrote:
> I received the following email note re: the vcdExtra package
>
>> A vcd update has shown that packages TIMP and vcdExtra are not
>> declaring their dependence on colorspace/MASS: see
>>
>> http://cran.r-project.org/web/checks/check_results_vcdExtra.html
> But, I can't see what to do to avoid this, nor understand what has
> changed in R devel.

Lots in this respect.
>
> Sure enough, CRAN now reports errors in examples using MASS::loglm(),
> using R Under development (unstable) (2013-09-11 r63906)
>
>  > Caesar.mod0 <- loglm(~Infection + (Risk*Antibiotics*Planned),
> data=Caesar)
> Error: could not find function "loglm"
>
> In DESCRIPTION I have
> Depends: R (>= 2.10), vcd, gnm (>= 1.0.3)

The "modern" way of thinking about this is that the Depends line should 
not have much in it, only things from other packages that you want 
directly available to the user. (There are a few other exceptions 
necessary for packages that have not themselves embraced the "modern" 
way.) Since you may want users of vcdExtra to automatically have access 
to functions in vcd, without needing to execute library(vcd), this 
classifies as one of the official exceptions and you probably want cvd 
in the Depends line. However, chances are that gnm should be in 
Imports:. If vcd is in the Depends line then it is automatically 
attached and your examples do not need library(vcd) or requires(vcd).

The Note

   Unexported object imported by a ?:::? call: ?vcd:::rootogram.default?

is harder to decide how to deal with. (This is sill just a note, but it 
looks to me like a note that will soon become a warning or error.) The 
simple solution is to export rootogram.default from vcd, but that 
exposes it to all users, and really you may just want to expose it to 
packages like vcdExtra. There was some recent discussion about this on 
R-devel. I suggested one possibility would be some sort of limited 
export. Since that was a suggestion that required work by someone else, 
it probably went the same place as most of those suggestion do. The 
solution I have adopted for the main case where this causes me problems 
is to split the classes, generics, and methods into one package, and the 
user functions into another. For example, if you have rootogram.default 
in a package called vcdClasses and exported it, then both vcd and 
vcdExtra can import it, but if it is not in their Depends line then it 
will not be visible to a user that executes library(vcd) or 
library(vcdExtra).

Beware that there is currently a small gotcha if the generics are S3, 
which was discussed recently and a patch submitted by Henrik Bengtsson 
(See Re: [Rd] "False" warning on "replacing previous import" when 
re-exporting identical object .)


Although there has been much moaning about these changes, including my 
own, I think the general logic is a real improvement. The way I think of 
it, the namespace imports for a package provide the equivalent of a 
search path for functions in the package, which is not changed by what 
packages a user or other packages attach or import. Thus a package 
developer has much more certain control over where the functions used by 
the package will come from. This is a trade-off for safety rather than 
convenience, thus the moaning. I am a complete newbie on this, but there 
seems to be a pretty good unofficial description at 
http://obeautifulcode.com/R/How-R-Searches-And-Finds-Stuff/.

> Suggests:
> ca,gmodels,Fahrmeir,effects,VGAM,plyr,rgl,lmtest,MASS,nnet,ggplot2,Sleuth2,car

If it is only in Suggests you can refer to it in the example by 
MASS::loglm(), or require(MASS)/library(MASS). (I might have that wrong, 
at least one works but I'm not certain of both.)
>
>
> and the vcd DESCRIPTION has
>
> Depends: R (>= 2.4.0), grid, stats
> Suggests: KernSmooth, mvtnorm, kernlab, HSAUR, coin
> Imports: utils, MASS, grDevices, colorspace

Probably grid and stats should be in Imports.

>
> so, in an R 3.0.0 console, library(vcdExtra) loads vcd and its
> dependencies:
>
>  > library(vcdExtra)
> Loading required package: vcd
> Loading required package: MASS
> Loading required package: grid
> Loading required package: colorspace
> Loading required package: gnm
> Warning messages:
> 1: package ?vcd? was built under R version 3.0.1
> 2: package ?MASS? was built under R version 3.0.1
>  >
>
> Note: these CRAN errors do not occur on R-Forge, using R version 3.0.1

Are you actually getting anything to build on R-forge? All my packages 
have been stuck for a couple of weeks, as have many others.

Paul

> Patched (2013-08-21 r63645)
> and the latest devel version (0.5-11) of vcdExtra.
>
> -Michael
>



[Rd] declaring package dependencies
Paul Gilbert