codetools wrongly complains about lazy evaluation in S4 methods

I'd argue that at the root of the problem is that your qr.X() generic 
dispatches on all its arguments, including the 'ncol' argument which I 
think the dispatch mechanism needs to evaluate **before** dispatch can 
actually happen.

So yes lazy evaluation is a real feature but it does not play well for 
arguments of a generic that are involved in the dispatch.

If you explicitly defined your generic with:

?? setGeneric("qr.X", signature="qr")

you should be fine.

More generally speaking, it's a good idea to restrict the signature of 
a generic to the arguments "that make sense". For unary operations 
this is usually the 1st argument, for binary operations the first two 
arguments etc... Additional arguments that control the operation like 
modiflers, toggles, flags, rng seed, and other parameters, usually 
have not place in the signature of the generic.

H.

On 6/14/23 20:57, Mikael Jagan wrote:

Thanks all - yes, I think that Simon's diagnosis ("user error") is 
correct:
in this situation one should define a reasonable generic function 
explicitly,
with a call to setGeneric, and not rely on the call inside of 
setMethod ...

But it is still not clear what the way forward should be (for package 
Matrix,
where we would like to export a method for 'qr.X').? If we do 
nothing, then
there is the note, already mentioned:

??? * checking R code for possible problems ... NOTE
??? qr.X: no visible binding for global variable ?R?
??? Undefined global functions or variables:
????? R

If we add the following to our R/AllGenerics.R :

??? setGeneric("qr.X",
?????????????? function(qr, complete = FALSE, ncol, ...)
?????????????????? standardGeneric("qr.X"),
?????????????? useAsDefault = function(qr, complete = FALSE, ncol, 
...) {
?????????????????? if(missing(ncol))
?????????????????????? base::qr.X(qr, complete = complete)
?????????????????? else base::qr.X(qr, complete = complete, ncol = ncol)
?????????????? },
?????????????? signature = "qr")

then we get a startup message, which would be quite disruptive on CRAN :

??? The following object is masked from 'package:base':

??????? qr.X

and if we further add setGenericImplicit("qr.X", restore = (TRUE|FALSE))
to our R/zzz.R, then for either value of 'restore' we encounter :

??? ** testing if installed package can be loaded from temporary 
location
??? Error: package or namespace load failed for 'Matrix':
???? Function found when exporting methods from the namespace 
'Matrix' which is not S4 generic: 'qr.X'

Are there possibilities that I have missed?

It seems to me that the best option might be to define an implicit 
generic
'qr.X' in methods via '.initImplicitGenerics' in 
methods/R/makeBasicFunsList.R,
where I see that an implicit generic 'qr.R' is already defined ... ?

The patch pasted below "solves everything", though we'd still have to 
think
about how to work for versions of R without the patch ...

Mikael

Index: src/library/methods/R/makeBasicFunsList.R
===================================================================
--- src/library/methods/R/makeBasicFunsList.R??? (revision 84541)
+++ src/library/methods/R/makeBasicFunsList.R??? (working copy)
@@ -263,6 +263,17 @@
??????????? signature = "qr", where = where)
???? setGenericImplicit("qr.R", where, FALSE)

+??? setGeneric("qr.X",
+?????????????? function(qr, complete = FALSE, ncol, ...)
+?????????????????? standardGeneric("qr.X"),
+?????????????? useAsDefault = function(qr, complete = FALSE, ncol, 
...) {
+?????????????????? if(missing(ncol))
+?????????????????????? base::qr.X(qr, complete = complete)
+?????????????????? else base::qr.X(qr, complete = complete, ncol = 
ncol)
+?????????????? },
+?????????????? signature = "qr", where = where)
+??? setGenericImplicit("qr.X", where, FALSE)
+
???? ## our toeplitz() only has 'x'; want the generic "here" rather 
than "out there"
???? setGeneric("toeplitz", function(x, ...) 
standardGeneric("toeplitz"),
??????????? useAsDefault= function(x, ...) stats::toeplitz(x),

On 2023-06-13 8:01 pm, Simon Urbanek wrote:

I agree that this is not an R issue, but rather user error of not 
defining a proper generic so the check is right. Obviously, defining 
a generic with implementation-specific ncol default makes no sense 
at all, it should only be part of the method implementation. If one 
was to implement the same default behavior in the generic itself 
(not necessarily a good idea) the default would be ncol = if 
(complete) nrow(qr.R(qr, TRUE)) else min(dim(qr.R(qr, TRUE))) to not 
rely on the internals of the implementation.

Cheers,
Simon

On 14/06/2023, at 6:03 AM, Kasper Daniel Hansen 
<kasperdanielhansen at gmail.com> wrote:

On Sat, Jun 3, 2023 at 11:51?AM Mikael Jagan <jaganmn2 at gmail.com> 
wrote:

The formals of the newly generic 'qr.X' are inherited from the 
non-generic
function in the base namespace.? Notably, the inherited default 
value of
formal argument 'ncol' relies on lazy evaluation:

formals(qr.X)[["ncol"]]

???? if (complete) nrow(R) else min(dim(R))

where 'R' must be defined in the body of any method that might 
evaluate
'ncol'.

Perhaps I am misunderstanding something, but I think Mikael's 
expectations
about the scoping rules of R are wrong.? The enclosing environment 
of ncol
is where it was _defined_ not where it is _called_ (apologies if I am
messing up the computer science terminology here).

This suggests to me that codetools is right.? But a more extended 
example
would be useful. Perhaps there is something special with setOldClass()
which I am no aware of.

Also, Bioconductor has 100s of packages with S4 where codetools 
works well.

Kasper

????[[alternative HTML version deleted]]

-- 
Herv? Pag?s

Bioconductor Core Team
hpages.on.github at gmail.com