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
<[email protected]> wrote:
On Sat, Jun 3, 2023 at 11:51 AM Mikael Jagan <[email protected]>
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
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