[R-pkg-devel] Registering methods conditionally

Sun, Feb 9, 2025 3:03 AM

Hi Ivan,

Thanks for the careful investigation. I didn't notice that tidy was masked!

I expected that a delayed registration could prevent the error. But I think
I made a bad decision when I defined tidy and I will probably change the
method name.

But I'll talk with Bioconductor people, for advice to see what can be done.
I don't think when BiocGenerics depended on generics they accounted for
this kind of breakage or informed their reverse dependencies.

Many thanks for your help.

On Sat, 8 Feb 2025 at 21:07, Ivan Krylov <ikrylov at disroot.org> wrote:

? Sat, 8 Feb 2025 19:18:59 +0100
Llu?s Revilla <lluis.revilla at gmail.com> ?????:

Error in UseMethod("tidy") : no applicable method for 'tidy' applied
to an object of class "GeneSet"

This seems to be a distant consequence of
<https://github.com/Bioconductor/BiocGenerics/issues/20>.

The example for BaseSet::tidy starts with

if (requireNamespace("GSEABase", quietly = TRUE)) {

which produces the following messages:

Loading required package: BiocGenerics
Loading required package: generics
Attaching package: ?generics?
The following objects are masked from ?package:BaseSet?:
   tidy, union                    # <-- BaseSet::tidy now shadowed

Indeed, at the point of the error, 'tidy' is

Browse[1]> tidy
function (x, ...)
{
    UseMethod("tidy")
}
<bytecode: 0x5615feed95c0>
<environment: namespace:generics>

...which is different from your own 'tidy' generic:

Browse[1]> BaseSet::tidy
function (object)
{
    UseMethod("tidy")
}
<bytecode: 0x5615eed320c8>
<environment: namespace:BaseSet>

...and the method is registered for the BaseSet::tidy generic, not the
generics::tidy generic:

Browse[1]> 'tidy.GeneSet' %in% ls(BaseSet:::.__S3MethodsTable__.)
[1] TRUE
Browse[1]> 'tidy.GeneSet' %in% ls(generics:::.__S3MethodsTable__.)
[1] FALSE

The problem only appears on R-devel because only the development
version of 'BiocGenerics' has the Depends: relationship with 'generics'.

This one is easier to diagnose than to cure. The example seems to work
fine if the methods are registered for the other generic at runtime:

library(BaseSet)
# these are undocumented, use .S3method() in more normal circumstances
registerS3method("tidy", "GeneSet", BaseSet:::tidy.GeneSet,
                 loadNamespace("generics"))
registerS3method("tidy", "GeneSetCollection",
                 BaseSet:::tidy.GeneSetCollection,
                 loadNamespace("generics"))
example("tidy") # doesn't crash

Since BaseSet depends on a new enough R version, it could in theory use
delayed S3 method registration in its NAMESPACE file [1] in addition to
registering a method for BaseSet::tidy, but I think that you're now
expected to importFrom(generics, tidy) and export(tidy) to register S3
methods on it. It's unfortunate that generics::tidy has a different
documented purpose. Perhaps the people better-versed in Bioconductor
have a better suggestion?

Not sure where S4 method dispatch comes into play in your example, but
conditional import of S4 classes may be hard to implement. NAMESPACE
files use R syntax but different semantics. Testing for getRversion()
works because that doesn't usually change for the lifetime of the
package library. Testing for requireNamespace() wouldn't have worked
because the results are normally cached at installation time. Maybe
there's a way using load hooks, but we'd need an S4 wizard to implement
that correctly. Thankfully, 'BaseSet' seems to only call setMethod()
for its own classes, so there are no copies of foreign classes creating
binary dependencies in its namespace.

--
Best regards,
Ivan

[1]
https://cran.r-project.org/doc/manuals/R-exts.html#Registering-S3-methods

[R-pkg-devel] Registering methods conditionally

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