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[R-pkg-devel] Should 'methods' be in Imports?

6 messages · Noah Greifer, Duncan Murdoch, Ivan Krylov

Original
Noah Greifer
# 
Hello developers,

I am wondering if base packages whose functions are used in my package need
to be present in Imports in my DESCRIPTION. For example, if I use the
function abline(), which exists in the *graphics* package, do I need to
include *graphics* in Imports? Note I am not asking about whether I need to
import all or any function from the *graphics* package, that is, assume I
am using graphics::abline(), etc. I am solely asking about the DESCRIPTION
file, not the Namespace.

I ask because there seems to be some ambiguity about this. I received a
pull request from someone adding *methods* to my Imports after noticing I
didn't declare it when using a function from *methods* (accessed in my
package using ::). Looking on StackOverflow, there seems to be confusion
about this. The most relevant question I could find was this one
<https://stackoverflow.com/q/39439006/6348551>. The question was marked as
a duplicate despite the linked duplicate being separate from it (i.e.,
asking about the Namespace, not the DESCRIPTION). Similarly, the answer to
the question does not address the question, again referring to the
Namespace and making an irrelevant distinction between Depends and Imports.
Some of the comments reference a CRAN policy, and yet that policy does not
seem to be implemented since many packages (including all of mine) omit the
base packages from the DESCRIPTION.

So, is it optional to include these packages in the DESCRIPTION? I see some
packages do so and some don't. Is including these packages filling the
DESCRIPTION with unnecessary dependencies that are automatically satisfied,
or is it being helpfully explicit about the packages your package relies
on? Thanks.

Noah
Duncan Murdoch
# 
I think the Writing R Extensions manual is pretty clear about this: 
yes, you should include "methods" in Imports or Depends if you are 
calling methods::<fn>.

You say "some packages do so and some don't".  Which ones don't?  It's 
helpful to be specific in your examples.

Duncan Murdoch
On 16/03/2023 11:29 a.m., Noah Greifer wrote:
Noah Greifer
# 
Thank you for your input. *broom*, *mlogit*, *twang*, and *Hmisc*
are examples of major packages that import functions from *stats*, *utils*,
*graphics*, or other base packages but don't include them in the
DESCRIPTION. All of my packages (*cobalt*, *WeightIt*, *MatchIt*) do too,
and I have never had a message from CRAN about it. (None of these are
specifically about *methods*, but as a base package I assume it should work
the same as these others.)

Noah
Duncan Murdoch
#
On 16/03/2023 2:21 p.m., Noah Greifer wrote:
broom doesn't mention stats in DESCRIPTION, but does import from it in 
the NAMESPACE. (I haven't checked the rest of your list.)  I'm a little 
surprised by that, but it's understandable:  the NAMESPACE does declare 
that stats is needed.  WRE says this about Imports:

"Namespaces accessed by the ?::? and ?:::? operators must be listed 
here, or in ?Suggests? or ?Enhances? (see below). Ideally this field 
will include all the standard packages that are used, and it is 
important to include S4-using packages."

So the use of Imports for "standard packages" that are used in NAMESPACE 
appears to be optional but recommended.

However, my understanding was that you were talking about using things 
like graphics::abline without importing any graphics functions via the 
NAMESPACE; in that case, the manual is very explicit that you would need 
to put graphics in Imports.  That doesn't mean "R CMD check" will 
complain if you don't, but it does mean that it might start doing so if 
it doesn't already.

Do you know of any examples of packages that use things like 
graphics::abline without mentioning graphics in either the NAMESPACE or 
DESCRIPTION file?

Duncan Murdoch
Ivan Krylov
# 
On Thu, 16 Mar 2023 11:29:33 -0400
Noah Greifer <noah.greifer at gmail.com> wrote:

            

      
      
      
    

        
Here's a comment from the part of R CMD check that checks for NAMESPACE
dependencies unstated in DESCRIPTION:

            

      
      
      
    

        
So the answer is maybe. Personally, I opt for listing even the base
packages explicitly, but it's a choice. Duncan's quote from WRE hints
that this may be enforced in the future.

I do find it a bit strange that not listing methods as a dependency in
DESCRIPTION doesn't lead to complaints from R CMD check, because it
does seem that the code excludes methods (and stats4) from the list of
packages that are currently okay not to declare in DESCRIPTION.

  
    

      
      
    

  


  


      

    

    

      
      

        


  

        

      Noah Greifer
    

    

      
      #
    

  


  

      
Thank you both for your responses. Based on Ivan's dig into the comments,
it seems there is ambiguity, even by the CRAN team. Still, it looks like it
would be preferable to (and would not cause any harm to) include the base
packages in DESCRIPTION if they are used at all in a package, whether by ::
or imported from in the Namespace. I'll update my packages accordingly.

Noah