[Bioc-devel] Why can't NAMESPACE be a strict subset of DESCRIPTION Imports?

[Martin Morgan]

On 10/04/2016 05:09 PM, Martin Morgan wrote:
> On 10/04/2016 05:07 PM, McDavid, Andrew wrote:
>> BiocCheck throws a warning when a package is listed as Imports: in
>> DESCRIPTION but not used in the NAMESPACE.  This may happen when a
>> developer uses the fully qualified names of objects within a package.
>> I am unclear as to the rationale for this warning.
>>
>
> agree it's wrong. can you point to an example? Martin

I updated BiocCheck to be smarter about this; I'm not sure when this 
will propagate to the single package builder. It doesn't complain about 
Imports: in the DESCRIPTION file if the package is used in the NAMESPACE 
or :: or :::. The code is kind of fun, using the codetools package:

library(codetools)

.checkEnv <- function(env, walker) {
     ## look at all closures in 'env' using codetools-derived 'walker'
     for (n in ls(env, all.names = TRUE)) {
         v <- get(n, envir = env)
         if (typeof(v) == "closure")
             walkCode(body(v), walker)
     }
     walker
}

.colonWalker <- function() {
     ## record all pkg used as pkg::foo or pkg:::bar
     PKGS <- character()
     collector <- function(e, w)
         PKGS <<- append(PKGS, as.character(e[[2]]))
     list(handler=function(v, w) {
         switch(v, "::"=collector, ":::"=collector, NULL)
     }, call=function(e, w) {
         for (ee in as.list(e)) if (!missing(ee)) walkCode(ee, w)
     }, leaf = function(e, w) {
         NULL
     }, done = function() {
         sort(unique(PKGS))
     })
}

 > library(codetools)
 > .checkEnv(loadNamespace("IRanges"), .colonWalker())$done()
[1] "base"         "BiocGenerics" "S4Vectors"

Martin

>
>> Per Hadley:
>>
>> It's common for packages to be listed in Imports in DESCRIPTION, but
>> not in NAMESPACE. In fact, this is what I recommend: list the package
>> in DESCRIPTION so that it's installed, then always refer to it
>> explicitly with pkg::fun(). Unless there is a strong reason not to,
>> it's better to be explicit. It's a little more work to write, but a
>> lot easier to read when you come back to the code in the future.
>>
>> Per R extensions:
>>
>> If a package only needs a few objects from another package it can use
>> a fully qualified variable reference in the code instead of a formal
>> import. A fully qualified reference to the function f in package foo
>> is of the form foo::f.
>>
>> -Andrew
>>
>>
>>     [[alternative HTML version deleted]]
>>
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>>
>
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