>>>>> Duncan Murdoch writes:> On 12/06/2015 4:12 AM, Martin Maechler wrote: >> This is a topic ' "apparent S3 methods" note in R CMD check ' >> from R-package-devel >> https://stat.ethz.ch/pipermail/r-package-devel/2015q2/000126.html >> >> which is relevant to here because some of us have been thinking >> about extending R because of the issue. >> >> John Fox, maintainer of the 'effects' package has enquired about >> the following output from 'R CMD check effects' >> >> >> * checking S3 generic/method consistency ... NOTE >> >> Found the following apparent S3 methods exported but not registered: >> >> all.effects >> >> and added >> >> >> The offending function, all.effects(), is deprecated in favour of >> >> allEffects(), but I'd rather not get rid of it for backwards compatibility. >> >> Is there any way to suppress the note without removing all.effects()? >> >> and I had agreed that this was a "False Positive" in this case. >> >> [.......] >> >> and then >> >> > Now I agree .. and have e-talked about this with another R core >> > member .. that it would be desirable for the package author to >> > effectively declare the fact that such a function is not an S3 >> > method even though it "looks like it" at least if looked from far. >> >> > So, ideally, you could have something like >> >> > nonS3method("all.effects") >> >> > somewhere in your package source ( in NAMESPACE or R/*.R ) >> > which would tell the package-checking code -- but *ALSO* all the other S3 >> > method code that all.effects should be treated as a regular R >> > function. >> >> > I would very much like such a feature in R, and for that reason, >> > I'm cross posting this (as one of the famous exceptions that >> > accompany real-life rules!!) to R-devel. >> >> and actually I did *not* cross post, but have now moved the >> relevant part of the thread to R-devel. >>> It sounds like a good idea. It's a nontrivial amount of work, because > of the "all the other S3 method code" part. There's the question of > functions defined outside of packages: presumably they are still S3 > methods, with no way to suppress that.I am not sure this is the right solution: S3 dispatch will still occur because we first look at foo.bar exports and then in the S3 registry, afaicr (the "all the other S3 method code" part). If we could move to only looking at the registry for dispatch, there would be no need to declare situations where we should not dispatch on foo.bar exports. -k
On 12/06/2015 7:16 AM, Kurt Hornik wrote:>>>>>> Duncan Murdoch writes: > >> On 12/06/2015 4:12 AM, Martin Maechler wrote: >>> This is a topic ' "apparent S3 methods" note in R CMD check ' >>> from R-package-devel >>> https://stat.ethz.ch/pipermail/r-package-devel/2015q2/000126.html >>> >>> which is relevant to here because some of us have been thinking >>> about extending R because of the issue. >>> >>> John Fox, maintainer of the 'effects' package has enquired about >>> the following output from 'R CMD check effects' >>> >>>>> * checking S3 generic/method consistency ... NOTE >>>>> Found the following apparent S3 methods exported but not registered: >>>>> all.effects >>> >>> and added >>> >>>>> The offending function, all.effects(), is deprecated in favour of >>>>> allEffects(), but I'd rather not get rid of it for backwards compatibility. >>>>> Is there any way to suppress the note without removing all.effects()? >>> >>> and I had agreed that this was a "False Positive" in this case. >>> >>> [.......] >>> >>> and then >>> >>>> Now I agree .. and have e-talked about this with another R core >>>> member .. that it would be desirable for the package author to >>>> effectively declare the fact that such a function is not an S3 >>>> method even though it "looks like it" at least if looked from far. >>> >>>> So, ideally, you could have something like >>> >>>> nonS3method("all.effects") >>> >>>> somewhere in your package source ( in NAMESPACE or R/*.R ) >>>> which would tell the package-checking code -- but *ALSO* all the other S3 >>>> method code that all.effects should be treated as a regular R >>>> function. >>> >>>> I would very much like such a feature in R, and for that reason, >>>> I'm cross posting this (as one of the famous exceptions that >>>> accompany real-life rules!!) to R-devel. >>> >>> and actually I did *not* cross post, but have now moved the >>> relevant part of the thread to R-devel. >>> > >> It sounds like a good idea. It's a nontrivial amount of work, because >> of the "all the other S3 method code" part. There's the question of >> functions defined outside of packages: presumably they are still S3 >> methods, with no way to suppress that. > > I am not sure this is the right solution: S3 dispatch will still occur > because we first look at foo.bar exports and then in the S3 registry, > afaicr (the "all the other S3 method code" part). > > If we could move to only looking at the registry for dispatch, there > would be no need to declare situations where we should not dispatch on > foo.bar exports. >I think that would break a lot of existing scripts. I think the logic should be something like this. For each class in the class list: Search backwards through the environment chain. If the current location is a package environment or namespace, look only in the registry. If not, look at all functions. If that search failed, try the next class. A variation on the test is: If there's a registry in the current location, look there. But I think the registry is not on the search list, so I'm not sure that would work. This assumes that we keep separate registries in each package; if we merge them into one big registry, it gets harder. I'm not familiar enough with the code to know which way we do it. Duncan Murdoch
>>>>> Duncan Murdoch writes:> On 12/06/2015 7:16 AM, Kurt Hornik wrote: >>>>>>> Duncan Murdoch writes: >> >>> On 12/06/2015 4:12 AM, Martin Maechler wrote: >>>> This is a topic ' "apparent S3 methods" note in R CMD check ' >>>> from R-package-devel >>>> https://stat.ethz.ch/pipermail/r-package-devel/2015q2/000126.html >>>> >>>> which is relevant to here because some of us have been thinking >>>> about extending R because of the issue. >>>> >>>> John Fox, maintainer of the 'effects' package has enquired about >>>> the following output from 'R CMD check effects' >>>> >>>>> * checking S3 generic/method consistency ... NOTE >>>>> Found the following apparent S3 methods exported but not registered: >>>>> all.effects >>>> >>>> and added >>>> >>>>> The offending function, all.effects(), is deprecated in favour of >>>>> allEffects(), but I'd rather not get rid of it for backwards compatibility. >>>>> Is there any way to suppress the note without removing all.effects()? >>>> >>>> and I had agreed that this was a "False Positive" in this case. >>>> >>>> [.......] >>>> >>>> and then >>>> >>>>> Now I agree .. and have e-talked about this with another R core >>>>> member .. that it would be desirable for the package author to >>>>> effectively declare the fact that such a function is not an S3 >>>>> method even though it "looks like it" at least if looked from far. >>>> >>>>> So, ideally, you could have something like >>>> >>>>> nonS3method("all.effects") >>>> >>>>> somewhere in your package source ( in NAMESPACE or R/*.R ) >>>>> which would tell the package-checking code -- but *ALSO* all the other S3 >>>>> method code that all.effects should be treated as a regular R >>>>> function. >>>> >>>>> I would very much like such a feature in R, and for that reason, >>>>> I'm cross posting this (as one of the famous exceptions that >>>>> accompany real-life rules!!) to R-devel. >>>> >>>> and actually I did *not* cross post, but have now moved the >>>> relevant part of the thread to R-devel. >>>> >> >>> It sounds like a good idea. It's a nontrivial amount of work, because >>> of the "all the other S3 method code" part. There's the question of >>> functions defined outside of packages: presumably they are still S3 >>> methods, with no way to suppress that. >> >> I am not sure this is the right solution: S3 dispatch will still occur >> because we first look at foo.bar exports and then in the S3 registry, >> afaicr (the "all the other S3 method code" part). >> >> If we could move to only looking at the registry for dispatch, there >> would be no need to declare situations where we should not dispatch on >> foo.bar exports. >>> I think that would break a lot of existing scripts. I think the logic > should be something like this.> For each class in the class list:> Search backwards through the environment chain. If the current location > is a package environment or namespace, look only in the registry. If > not, look at all functions.> If that search failed, try the next class.Yep---that's what I meant. I forgot to write the "if namespace semantics applies" part :-) Best -k> A variation on the test is: If there's a registry in the current > location, look there. But I think the registry is not on the search > list, so I'm not sure that would work.> This assumes that we keep separate registries in each package; if we > merge them into one big registry, it gets harder. I'm not familiar > enough with the code to know which way we do it.> Duncan Murdoch