[Bioc-devel] depends on packages providing classes

Kasper Daniel Hansen kasperdanielhansen at gmail.com
Tue Oct 28 16:23:23 CET 2014

Well, first I want to make sure that there is not something special
regarding S4 methods and classes. I have a feeling that they are a special

Second, while I agree with Jim's general opinion, it is a little bit
different when I have return objects which are defined in other packages.
If I don't depend on this other package, the user is hosed wrt. the return
object, unless I manually export all classes from this other package, like
  importClassesFrom("GenomicRanges", "GRanges")
Surely that is not intended.

It is important that my package works without being attached to the search
path and I do this by carefully importing what I need, ie. my code does not
require that my dependencies are attached to the search path.  But the end
user will be hosed without it.

My impression is that the NOTE in R CMD check was written by someone who
did not anticipate large-scale use and re-use of classes and methods across
many packages.


On Tue, Oct 28, 2014 at 11:14 AM, James W. MacDonald <jmacdon at uw.edu> wrote:

> I agree with Vince. It's your job as a package developer to make available
> to your package all the functions necessary for the package to work. But I
> am not sure it is your job to load all the packages that your end user
> might need.
> Best,
> Jim
> On Tue, Oct 28, 2014 at 11:04 AM, Vincent Carey <
> stvjc at channing.harvard.edu> wrote:
>> On Tue, Oct 28, 2014 at 10:19 AM, Kasper Daniel Hansen <
>> kasperdanielhansen at gmail.com> wrote:
>> > What is the current best paradigm for using all the classes in
>> > S4Vectors/GenomeInfoDb/GenomicRanges/IRanges
>> >
>> > I obviously import methods and classes from the relevant packages.
>> >
>> > But shouldn't I depend on these packages as well?  Since I basically
>> want
>> > the user to have this functionality at the command line? That is what I
>> do
>> > now.
>> >
>> >
>> I've wondered about this as well.  It seems the principle is that the user
>> should
>> take care of attaching additional packages when needed.  It might be
>> appropriate
>> to give a hint in the package startup message, if having some other
>> package
>> attached
>> would typically be of great utility.
>> Given your list above, I would think that depending on GenomicRanges would
>> often
>> be sufficient, and IRanges/S4Vectors would not require dependency
>> assertion.  I would
>> think that GenomeInfoDb should be a voluntary attachment for a specific
>> session.
>> These are just my guesses -- I doubt there will be complete consensus, but
>> I have
>> started to think very critically about using Depends, and I think it is
>> better when its
>> use is minimized.
>> > That of course leads to the R CMD check NOTE on depending on too many
>> > packages.... I guess I should ignore that one.
>> >
>> > Best,
>> > Kasper
>> >
>> >         [[alternative HTML version deleted]]
>> >
>> > _______________________________________________
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>> > https://stat.ethz.ch/mailman/listinfo/bioc-devel
>> >
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> --
> James W. MacDonald, M.S.
> Biostatistician
> University of Washington
> Environmental and Occupational Health Sciences
> 4225 Roosevelt Way NE, # 100
> Seattle WA 98105-6099

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