Hello:
Is there a recommended way to inform "R CMD check" that a
function like "as.numeric" is NOT a method for the S3 generic function
"as" for objects of class "numeric"?
I ask, because I'm getting "NOTE" messages for many function
names like this (e.g., "density.fd" in the "fda" package): If there
were a way to tell "R CMD check" that a function name is NOT a method
for an S3 generic, it would make it easier for me to see the messages I
should take seriously.
Thanks,
Spencer
S3 methods with full name in documentation?
3 messages · Duncan Murdoch, Spencer Graves
On 12-03-20 4:40 PM, Spencer Graves wrote:
Hello:
Is there a recommended way to inform "R CMD check" that a
function like "as.numeric" is NOT a method for the S3 generic function
"as" for objects of class "numeric"?
I ask, because I'm getting "NOTE" messages for many function
names like this (e.g., "density.fd" in the "fda" package): If there
were a way to tell "R CMD check" that a function name is NOT a method
for an S3 generic, it would make it easier for me to see the messages I
should take seriously.
I don't think so. The problem you are seeing is that "density" is a generic, so density.fd looks like a method for it. In fact, if you define an object of class "fd" and call density() on it while fda is attached, your density.fd function will be called: > x <- structure(1, class="fd") > density(x) Error in inherits(WfdParobj, "fdPar") : argument "WfdParobj" is missing, with no default So in fact, density.fd *is* an S3 method, even though you didn't know it. Nowadays every package has a namespace, and eventually maybe S3 methods that aren't declared in the namespace as S3 methods won't be recognized as S3 methods. But for now, the only real way around these warnings is not to name things in a way that makes them appear to be S3 methods. Duncan Murdoch
Hi, Duncan:
On 3/20/2012 6:43 PM, Duncan Murdoch wrote:
On 12-03-20 4:40 PM, Spencer Graves wrote:
Hello:
Is there a recommended way to inform "R CMD check" that a
function like "as.numeric" is NOT a method for the S3 generic function
"as" for objects of class "numeric"?
I ask, because I'm getting "NOTE" messages for many function
names like this (e.g., "density.fd" in the "fda" package): If there
were a way to tell "R CMD check" that a function name is NOT a method
for an S3 generic, it would make it easier for me to see the messages I
should take seriously.
I don't think so. The problem you are seeing is that "density" is a generic, so density.fd looks like a method for it. In fact, if you define an object of class "fd" and call density() on it while fda is attached, your density.fd function will be called:
x <- structure(1, class="fd") density(x)
Error in inherits(WfdParobj, "fdPar") : argument "WfdParobj" is missing, with no default So in fact, density.fd *is* an S3 method, even though you didn't know it.
Well, yes, I guess I knew that, but I also knew that "density.fd" should not be called with the first argument having class "fd", even more that "as.numeric", which is also recognized as the "numeric" method for the presumed generic function "as". [Yes, I know that "as" does not call methods dispatch such as "UseMethod" called by "density", so "as.numeric" is different from that perspective.]
Nowadays every package has a namespace, and eventually maybe S3 methods that aren't declared in the namespace as S3 methods won't be recognized as S3 methods. But for now, the only real way around these warnings is not to name things in a way that makes them appear to be S3 methods.
Thanks. I asked, because I thought there might be something one
could do in a NAMESPACE to avoid this. "density.fd" has been around for
some time, and picking a different name for it (and similar functions in
the fda package) would break too much existing code and impose an
unacceptable burden on long-time fda users to justify that option --
similar to "as.numeric".
Thanks, again.
Best Wishes,
Spencer
Duncan Murdoch