[Rd] advise on Depends

[John Chambers]

Software generated in methods for user classes calls functions in the methods package, as I said.  I don't  know the circumstances (if any) when such calls fail to find functions if  the whole package is  imported.   Perhaps someone on this list may have examples.

But for sure just importing the functions your package calls during installation (setClass(), setMethod(), etc.) won't always be enough.

When the S4 classes and methods were implemented in R in the early 2000s, it was assumed that the methods package would be considered part of the system, as the analogous code was in S.  

It would be nice to either have the package included in Rscript, CMD check, etc. or for some enterprising and very thorough person to go through and bullet-proof the generated code for the absence of the package from the search list.

Absent either of those, the defensive approach is to put methods in Depends.   Or at least, import the package rather than just the obvious functions.

John


On Oct 25, 2013, at 3:46 PM, Paul Gilbert <pgilbert902 at gmail.com> wrote:

> 
> 
> On 13-10-25 05:21 PM, Henrik Bengtsson wrote:
>> On Fri, Oct 25, 2013 at 1:39 PM, John Chambers <jmc at r-project.org>
>> wrote:
>>> One additional point to Michael's summary:
>>> 
>>> The "methods" package itself should stay in Depends:, to be safe.
> 
> It would be nice to have more detail about when this is necessary, rather than suggested as a general workaround. I thought the principle of putting things in Imports was that it is safer. I have methods listed in Imports rather than Depends in 16 of my packages, doing roughly what was the basis for the original question, and I am not aware of a problem, yet.
> 
> Paul
> 
>>> 
>>> There are a number of function calls to the methods package that
>>> may be included in generated methods for user classes.  These have
>>> not been revised to work when the methods package is not attached,
>>> so importing the package only may run into problems.  This has been
>>> an issue, for example, in using Rscript.
>> 
>> To clarify that last sentence for those not aware (and hopefully
>> spare someone having to troubleshoot this), executing R
>> scripts/expressions using 'Rscript' rather than 'R' differs by which
>> packages are attached by default.  Example:
>> 
>> % Rscript -e "search()" [1] ".GlobalEnv"        "package:stats"
>> "package:graphics" [4] "package:grDevices" "package:utils"
>> "package:datasets" [7] "Autoloads"         "package:base"
>> 
>> % R --quiet -e "search()"
>>> search()
>> [1] ".GlobalEnv"        "package:stats"     "package:graphics" [4]
>> "package:grDevices" "package:utils"     "package:datasets" [7]
>> "package:methods"   "Autoloads"         "package:base"
>> 
>> Note how 'methods' is not attached when using Rscript.  This is
>> explained in help("Rscript"), help("options"), and in 'R
>> Installation and Administration'.
>> 
>> /Henrik
>> 
>> 
>>> 
>>> John
>>> 
>>> On Oct 25, 2013, at 11:26 AM, Michael Lawrence
>>> <lawrence.michael at gene.com> wrote:
>>> 
>>>> On Wed, Oct 23, 2013 at 8:33 PM, Kasper Daniel Hansen <
>>>> kasperdanielhansen at gmail.com> wrote:
>>>> 
>>>>> This is about the new note
>>>>> 
>>>>> Depends: includes the non-default packages: ‘BiocGenerics’
>>>>> ‘Biobase’ ‘lattice’ ‘reshape’ ‘GenomicRanges’ ‘Biostrings’
>>>>> ‘bumphunter’ Adding so many packages to the search path is
>>>>> excessive and importing selectively is preferable.
>>>>> 
>>>>> Let us say my package A either uses a class B (by producing an
>>>>> object that has B embedded as a slot) from another package or
>>>>> provides a specific method for a generic defined in another
>>>>> package (both examples using S4). In both case my impression is
>>>>> that best practices is I ought to Depend on such a package, so
>>>>> it is a available at run time to the user.
>>>>> 
>>>>> 
>>>> For classes, you just need to import the class with
>>>> importClassesFrom(). For generics, as long as your package
>>>> exports the method with exportMethods(), the generic will also be
>>>> exported from your package, regardless of whether the defining
>>>> package is attached. And the methods from the
>>>> loaded-but-not-attached packages are available for the generic.
>>>> So neither of these two is really a problem.
>>>> 
>>>> The rationale for Depends is that the user might always want to
>>>> use functions defined by another package with objects
>>>> consumed/produced by your package, such as generics for which
>>>> your package has not defined any methods. For example,
>>>> rtracklayer Depends on GenomicRanges, because it imports objects
>>>> from files as GenomicRanges objects.  So just consider what the
>>>> user sees when looking at your API. What's private, what's
>>>> public?
>>>> 
>>>> Michael
>>>> 
>>>> 
>>>>> Comments?
>>>>> 
>>>>> Best, Kasper
>>>>> 
>>>>> [[alternative HTML version deleted]]
>>>>> 
>>>>> 
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>>>>> 
>>>>> 
>>>> 
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>>>> 
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