# For integer vectors, `as(x, "numeric")` has no effect.

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## For integer vectors, `as(x, "numeric")` has no effect.

 Here's the surprising behavior:    x <- 1L    xx <- as(x, "numeric")    class(xx)    ## [1] "integer" It occurs because the call to `as(x, "numeric")` dispatches the coerce S4 method for the signature `c("integer", "numeric")`, whose body is copied in below.     function (from, to = "numeric", strict = TRUE)     if (strict) {         class(from) <- "numeric"         from     } else from This in turn does nothing, even when strict=TRUE, because that assignment to class "numeric" has no effect:     x <- 10L     class(x) <- "numeric"     class(x)     [1] "integer" Is this the desired behavior for `as(x, "numeric")`? ______________________________________________ [hidden email] mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
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## Re: For integer vectors, `as(x, "numeric")` has no effect.

 Perhaps it is not that surprising, given that      > mode(1L)      [1] "numeric" and      > is.numeric(1L)      [1] TRUE On the other hand, this is curious, to say the least:      > is.double(as(1L, "double"))      [1] FALSE > Here's the surprising behavior: > >     x <- 1L >     xx <- as(x, "numeric") >     class(xx) >     ## [1] "integer" > > It occurs because the call to `as(x, "numeric")` dispatches the coerce > S4 method for the signature `c("integer", "numeric")`, whose body is > copied in below. > >      function (from, to = "numeric", strict = TRUE) >      if (strict) { >          class(from) <- "numeric" >          from >      } else from > > This in turn does nothing, even when strict=TRUE, because that > assignment to class "numeric" has no effect: > >      x <- 10L >      class(x) <- "numeric" >      class(x) >      [1] "integer" > > Is this the desired behavior for `as(x, "numeric")`? ______________________________________________ [hidden email] mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
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## Re: For integer vectors, `as(x, "numeric")` has no effect.

 We do need an explicit method here, I think. The issue is that as() uses methods for the generic function coerce() but cannot use inheritance in the usual way (if it did, you would be immediately back with no change, since "integer" inherits from "numeric"). Copying in the general method for coercing to "numeric" as an explicit method for "integer" gives the expected result: > setMethod("coerce", c("integer", "numeric"), getMethod("coerce", c("ANY", "numeric"))) [1] "coerce" > typeof(as(1L, "numeric")) [1] "double" Seems like a reasonable addition to the code, unless someone sees a problem. John On Dec 7, 2015, at 3:37 PM, Benjamin Tyner <[hidden email]> wrote: > Perhaps it is not that surprising, given that > >    > mode(1L) >    [1] "numeric" > > and > >    > is.numeric(1L) >    [1] TRUE > > On the other hand, this is curious, to say the least: > >    > is.double(as(1L, "double")) >    [1] FALSE > >> Here's the surprising behavior: >> >>    x <- 1L >>    xx <- as(x, "numeric") >>    class(xx) >>    ## [1] "integer" >> >> It occurs because the call to `as(x, "numeric")` dispatches the coerce >> S4 method for the signature `c("integer", "numeric")`, whose body is >> copied in below. >> >>     function (from, to = "numeric", strict = TRUE) >>     if (strict) { >>         class(from) <- "numeric" >>         from >>     } else from >> >> This in turn does nothing, even when strict=TRUE, because that >> assignment to class "numeric" has no effect: >> >>     x <- 10L >>     class(x) <- "numeric" >>     class(x) >>     [1] "integer" >> >> Is this the desired behavior for `as(x, "numeric")`? > > ______________________________________________ > [hidden email] mailing list > https://stat.ethz.ch/mailman/listinfo/r-devel______________________________________________ [hidden email] mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
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## Re: For integer vectors, `as(x, "numeric")` has no effect.

 >>>>> John Chambers <[hidden email]> >>>>>     on Mon, 7 Dec 2015 16:05:59 -0800 writes:     > We do need an explicit method here, I think.     > The issue is that as() uses methods for the generic function coerce() but cannot use inheritance in the usual way (if it did, you would be immediately back with no change, since "integer" inherits from "numeric").     > Copying in the general method for coercing to "numeric" as an explicit method for "integer" gives the expected result:     >> setMethod("coerce", c("integer", "numeric"), getMethod("coerce", c("ANY", "numeric")))     > [1] "coerce"     >> typeof(as(1L, "numeric"))     > [1] "double"     > Seems like a reasonable addition to the code, unless someone sees a problem.     > John I guess that that some package checks (in CRAN + Bioc + ... - land) will break, but I still think we should add such a coercion to R. Martin     > On Dec 7, 2015, at 3:37 PM, Benjamin Tyner <[hidden email]> wrote:     >> Perhaps it is not that surprising, given that     >>     >> > mode(1L)     >> [1] "numeric"     >>     >> and     >>     >> > is.numeric(1L)     >> [1] TRUE     >>     >> On the other hand, this is curious, to say the least:     >>     >> > is.double(as(1L, "double"))     >> [1] FALSE     >>     >>> Here's the surprising behavior:     >>>     >>> x <- 1L     >>> xx <- as(x, "numeric")     >>> class(xx)     >>> ## [1] "integer"     >>>     >>> It occurs because the call to `as(x, "numeric")` dispatches the coerce     >>> S4 method for the signature `c("integer", "numeric")`, whose body is     >>> copied in below.     >>>     >>> function (from, to = "numeric", strict = TRUE)     >>> if (strict) {     >>> class(from) <- "numeric"     >>> from     >>> } else from     >>>     >>> This in turn does nothing, even when strict=TRUE, because that     >>> assignment to class "numeric" has no effect:     >>>     >>> x <- 10L     >>> class(x) <- "numeric"     >>> class(x)     >>> [1] "integer"     >>>     >>> Is this the desired behavior for `as(x, "numeric")`?     >>     >> ______________________________________________     >> [hidden email] mailing list     >> https://stat.ethz.ch/mailman/listinfo/r-devel    > ______________________________________________     > [hidden email] mailing list     > https://stat.ethz.ch/mailman/listinfo/r-devel______________________________________________ [hidden email] mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
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## Re: For integer vectors, `as(x, "numeric")` has no effect.

 >>>>> Martin Maechler <[hidden email]> >>>>>     on Tue, 8 Dec 2015 15:25:21 +0100 writes: >>>>> John Chambers <[hidden email]> >>>>>     on Mon, 7 Dec 2015 16:05:59 -0800 writes:     >> We do need an explicit method here, I think.     >> The issue is that as() uses methods for the generic function coerce() but cannot use inheritance in the usual way (if it did, you would be immediately back with no change, since "integer" inherits from "numeric").     >> Copying in the general method for coercing to "numeric" as an explicit method for "integer" gives the expected result:     >>> setMethod("coerce", c("integer", "numeric"), getMethod("coerce", c("ANY", "numeric")))     >> [1] "coerce"     >>> typeof(as(1L, "numeric"))     >> [1] "double"     >> Seems like a reasonable addition to the code, unless someone sees a problem.     >> John     > I guess that that some package checks (in CRAN + Bioc + ... -     > land) will break,     > but I still think we should add such a coercion to R.     > Martin Hmm...  I've tried to add the above to R and do notice that there are consequences that may be larger than anticipated: Here is example code:    myN   <- setClass("myN",   contains="numeric")    myNid <- setClass("myNid", contains="numeric", representation(id="character"))    NN <-    setClass("NN", representation(x="numeric"))    (m1 <- myN  (1:3))    (m2 <- myNid(1:3, id = "i3"))    tools::assertError(NN (1:3))# in all R versions    ##                     # current R  |  new R    ##                     # -----------|----------    class(getDataPart(m1)) # integer    |  numeric    class(getDataPart(m2)) # integer    |  numeric In other words, with the above setting, the traditional gentleperson's agreement in S and R,   __ "numeric" sometimes conveniently means "integer" or "double"  __ will be slightly less often used ... which of course may be a very good thing. However, it breaks strict back compatibility also in cases where the previous behavior may have been preferable: After all integer vectors need only have the space of doubles. Shall we still go ahead and do apply this change to R-devel and then all package others will be willing to update where necessary? As this may affect the many hundreds of bioconductor packages using S4 classes, I am -- exceptionally -- cross posting to the bioc-devel list. Martin Maechler     >> On Dec 7, 2015, at 3:37 PM, Benjamin Tyner <[hidden email]> wrote:     >>> Perhaps it is not that surprising, given that     >>>     >>> > mode(1L)     >>> [1] "numeric"     >>>     >>> and     >>>     >>> > is.numeric(1L)     >>> [1] TRUE     >>>     >>> On the other hand, this is curious, to say the least:     >>>     >>> > is.double(as(1L, "double"))     >>> [1] FALSE     >>>     >>>> Here's the surprising behavior:     >>>>     >>>> x <- 1L     >>>> xx <- as(x, "numeric")     >>>> class(xx)     >>>> ## [1] "integer"     >>>>     >>>> It occurs because the call to `as(x, "numeric")` dispatches the coerce     >>>> S4 method for the signature `c("integer", "numeric")`, whose body is     >>>> copied in below.     >>>>     >>>> function (from, to = "numeric", strict = TRUE)     >>>> if (strict) {     >>>> class(from) <- "numeric"     >>>> from     >>>> } else from     >>>>     >>>> This in turn does nothing, even when strict=TRUE, because that     >>>> assignment to class "numeric" has no effect:     >>>>     >>>> x <- 10L     >>>> class(x) <- "numeric"     >>>> class(x)     >>>> [1] "integer"     >>>>     >>>> Is this the desired behavior for `as(x, "numeric")`?     >>>     >>> ______________________________________________     >>> [hidden email] mailing list     >>> https://stat.ethz.ch/mailman/listinfo/r-devel    >> ______________________________________________     >> [hidden email] mailing list     >> https://stat.ethz.ch/mailman/listinfo/r-devel    > ______________________________________________     > [hidden email] mailing list     > https://stat.ethz.ch/mailman/listinfo/r-devel______________________________________________ [hidden email] mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
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## Re: For integer vectors, `as(x, "numeric")` has no effect.

 Somehow, the most obvious fixes are always back-incompatible these days. The example intrigued me, so I looked into it a bit (should have been doing something else, but ....) You're right that this is the proverbial thin-edge-of-the-wedge. The problem is in setDataPart(), which will be called whenever a class extends one of the vector types. It does         as(value, dataClass) The key point is that the third argument to as(), strict=TRUE by default.  So, yes, the change will cause all integer vectors to become double when the class extends "numeric".  Generally, strict=TRUE makes sense here and of course changing THAT would open up yet more incompatibilities. For back compatibility, one would have to have some special code in setDataPart() for the case of integer/numeric. John (Historically, the original sin was probably not making a distinction between "numeric" as a virtual class and "double" as a type/class.) On Dec 11, 2015, at 1:25 AM, Martin Maechler <[hidden email]> wrote: >>>>>> Martin Maechler <[hidden email]> >>>>>>    on Tue, 8 Dec 2015 15:25:21 +0100 writes: > >>>>>> John Chambers <[hidden email]> >>>>>>    on Mon, 7 Dec 2015 16:05:59 -0800 writes: > >>> We do need an explicit method here, I think. >>> The issue is that as() uses methods for the generic function coerce() but cannot use inheritance in the usual way (if it did, you would be immediately back with no change, since "integer" inherits from "numeric"). > >>> Copying in the general method for coercing to "numeric" as an explicit method for "integer" gives the expected result: > >>>> setMethod("coerce", c("integer", "numeric"), getMethod("coerce", c("ANY", "numeric"))) >>> [1] "coerce" >>>> typeof(as(1L, "numeric")) >>> [1] "double" > >>> Seems like a reasonable addition to the code, unless someone sees a problem. >>> John > >> I guess that that some package checks (in CRAN + Bioc + ... - >> land) will break, >> but I still think we should add such a coercion to R. > >> Martin > > Hmm...  I've tried to add the above to R > and do notice that there are consequences that may be larger than > anticipated: > > Here is example code: > >   myN   <- setClass("myN",   contains="numeric") >   myNid <- setClass("myNid", contains="numeric", representation(id="character")) >   NN <-    setClass("NN", representation(x="numeric")) > >   (m1 <- myN  (1:3)) >   (m2 <- myNid(1:3, id = "i3")) >   tools::assertError(NN (1:3))# in all R versions > >   ##                     # current R  |  new R >   ##                     # -----------|---------- >   class(getDataPart(m1)) # integer    |  numeric >   class(getDataPart(m2)) # integer    |  numeric > > > In other words, with the above setting, the traditional > gentleperson's agreement in S and R, > >  __ "numeric" sometimes conveniently means "integer" or "double"  __ > > will be slightly less often used ... which of course may be a > very good thing. > > However, it breaks strict back compatibility also in cases where > the previous behavior may have been preferable: > After all integer vectors need only have the space of doubles. > > Shall we still go ahead and do apply this change to R-devel > and then all package others will be willing to update where necessary? > > As this may affect the many hundreds of bioconductor packages > using S4 classes, I am -- exceptionally -- cross posting to the > bioc-devel list. > > Martin Maechler > > >>> On Dec 7, 2015, at 3:37 PM, Benjamin Tyner <[hidden email]> wrote: > >>>> Perhaps it is not that surprising, given that >>>> >>>>> mode(1L) >>>> [1] "numeric" >>>> >>>> and >>>> >>>>> is.numeric(1L) >>>> [1] TRUE >>>> >>>> On the other hand, this is curious, to say the least: >>>> >>>>> is.double(as(1L, "double")) >>>> [1] FALSE >>>> >>>>> Here's the surprising behavior: >>>>> >>>>> x <- 1L >>>>> xx <- as(x, "numeric") >>>>> class(xx) >>>>> ## [1] "integer" >>>>> >>>>> It occurs because the call to `as(x, "numeric")` dispatches the coerce >>>>> S4 method for the signature `c("integer", "numeric")`, whose body is >>>>> copied in below. >>>>> >>>>> function (from, to = "numeric", strict = TRUE) >>>>> if (strict) { >>>>> class(from) <- "numeric" >>>>> from >>>>> } else from >>>>> >>>>> This in turn does nothing, even when strict=TRUE, because that >>>>> assignment to class "numeric" has no effect: >>>>> >>>>> x <- 10L >>>>> class(x) <- "numeric" >>>>> class(x) >>>>> [1] "integer" >>>>> >>>>> Is this the desired behavior for `as(x, "numeric")`? >>>> >>>> ______________________________________________ >>>> [hidden email] mailing list >>>> https://stat.ethz.ch/mailman/listinfo/r-devel> >>> ______________________________________________ >>> [hidden email] mailing list >>> https://stat.ethz.ch/mailman/listinfo/r-devel> >> ______________________________________________ >> [hidden email] mailing list >> https://stat.ethz.ch/mailman/listinfo/r-devel        [[alternative HTML version deleted]] ______________________________________________ [hidden email] mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
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## Re: For integer vectors, `as(x, "numeric")` has no effect.

 In reply to this post by Martin Maechler From the Bioconductor side of things, the general feeling is that this is a step in the right direction and worth the broken packages. Martin Morgan ________________________________________ From: R-devel [[hidden email]] on behalf of Martin Maechler [[hidden email]] Sent: Friday, December 11, 2015 4:25 AM To: John Chambers; [hidden email]; bioc-devel list; Benjamin Tyner Cc: Martin Maechler Subject: Re: [Rd] For integer vectors, `as(x, "numeric")` has no effect. >>>>> Martin Maechler <[hidden email]> >>>>>     on Tue, 8 Dec 2015 15:25:21 +0100 writes: >>>>> John Chambers <[hidden email]> >>>>>     on Mon, 7 Dec 2015 16:05:59 -0800 writes:     >> We do need an explicit method here, I think.     >> The issue is that as() uses methods for the generic function coerce() but cannot use inheritance in the usual way (if it did, you would be immediately back with no change, since "integer" inherits from "numeric").     >> Copying in the general method for coercing to "numeric" as an explicit method for "integer" gives the expected result:     >>> setMethod("coerce", c("integer", "numeric"), getMethod("coerce", c("ANY", "numeric")))     >> [1] "coerce"     >>> typeof(as(1L, "numeric"))     >> [1] "double"     >> Seems like a reasonable addition to the code, unless someone sees a problem.     >> John     > I guess that that some package checks (in CRAN + Bioc + ... -     > land) will break,     > but I still think we should add such a coercion to R.     > Martin Hmm...  I've tried to add the above to R and do notice that there are consequences that may be larger than anticipated: Here is example code:    myN   <- setClass("myN",   contains="numeric")    myNid <- setClass("myNid", contains="numeric", representation(id="character"))    NN <-    setClass("NN", representation(x="numeric"))    (m1 <- myN  (1:3))    (m2 <- myNid(1:3, id = "i3"))    tools::assertError(NN (1:3))# in all R versions    ##                     # current R  |  new R    ##                     # -----------|----------    class(getDataPart(m1)) # integer    |  numeric    class(getDataPart(m2)) # integer    |  numeric In other words, with the above setting, the traditional gentleperson's agreement in S and R,   __ "numeric" sometimes conveniently means "integer" or "double"  __ will be slightly less often used ... which of course may be a very good thing. However, it breaks strict back compatibility also in cases where the previous behavior may have been preferable: After all integer vectors need only have the space of doubles. Shall we still go ahead and do apply this change to R-devel and then all package others will be willing to update where necessary? As this may affect the many hundreds of bioconductor packages using S4 classes, I am -- exceptionally -- cross posting to the bioc-devel list. Martin Maechler     >> On Dec 7, 2015, at 3:37 PM, Benjamin Tyner <[hidden email]> wrote:     >>> Perhaps it is not that surprising, given that     >>>     >>> > mode(1L)     >>> [1] "numeric"     >>>     >>> and     >>>     >>> > is.numeric(1L)     >>> [1] TRUE     >>>     >>> On the other hand, this is curious, to say the least:     >>>     >>> > is.double(as(1L, "double"))     >>> [1] FALSE     >>>     >>>> Here's the surprising behavior:     >>>>     >>>> x <- 1L     >>>> xx <- as(x, "numeric")     >>>> class(xx)     >>>> ## [1] "integer"     >>>>     >>>> It occurs because the call to `as(x, "numeric")` dispatches the coerce     >>>> S4 method for the signature `c("integer", "numeric")`, whose body is     >>>> copied in below.     >>>>     >>>> function (from, to = "numeric", strict = TRUE)     >>>> if (strict) {     >>>> class(from) <- "numeric"     >>>> from     >>>> } else from     >>>>     >>>> This in turn does nothing, even when strict=TRUE, because that     >>>> assignment to class "numeric" has no effect:     >>>>     >>>> x <- 10L     >>>> class(x) <- "numeric"     >>>> class(x)     >>>> [1] "integer"     >>>>     >>>> Is this the desired behavior for `as(x, "numeric")`?     >>>     >>> ______________________________________________     >>> [hidden email] mailing list     >>> https://stat.ethz.ch/mailman/listinfo/r-devel    >> ______________________________________________     >> [hidden email] mailing list     >> https://stat.ethz.ch/mailman/listinfo/r-devel    > ______________________________________________     > [hidden email] mailing list     > https://stat.ethz.ch/mailman/listinfo/r-devel______________________________________________ [hidden email] mailing list https://stat.ethz.ch/mailman/listinfo/r-develThis email message may contain legally privileged and/or confidential information.  If you are not the intended recipient(s), or the employee or agent responsible for the delivery of this message to the intended recipient(s), you are hereby notified that any disclosure, copying, distribution, or use of this email message is prohibited.  If you have received this message in error, please notify the sender immediately by e-mail and delete this email message from your computer. Thank you. ______________________________________________ [hidden email] mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
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## Re: For integer vectors, `as(x, "numeric")` has no effect.

 In reply to this post by John Chambers-2 >>>>> John Chambers <[hidden email]> >>>>>     on Fri, 11 Dec 2015 10:11:05 -0800 writes:     > Somehow, the most obvious fixes are always back-incompatible these days.     > The example intrigued me, so I looked into it a bit (should have been doing something else, but ....)     > You're right that this is the proverbial thin-edge-of-the-wedge.     > The problem is in setDataPart(), which will be called whenever a class extends one of the vector types.     > It does     > as(value, dataClass)     > The key point is that the third argument to as(), strict=TRUE by default.  So, yes, the change will cause all integer vectors to become double when the class extends "numeric".  Generally, strict=TRUE makes sense here and of course changing THAT would open up yet more incompatibilities.     > For back compatibility, one would have to have some special code in setDataPart() for the case of integer/numeric.     > John     > (Historically, the original sin was probably not making a distinction between "numeric" as a virtual class and "double" as a type/class.) Yes, indeed.  In the mean time, I've seen more cases where   "the change will cause all integer vectors to become double when the class  extends "numeric". seems detrimental. OTOH, I still think we could go in the right direction --- hopefully along the wishes of bioconductor S4 development, see Martin Morgan's e-mail: [This is all S4 - only; should not much affect base R / S3] Currently,   "integer" is a subclass of "numeric"  and so the "integer become double" part seems unwanted to me. OTOH,  it would really make sense to more formally have the basic subclasses of  "numeric" to be "integer" and "double", and  to let  as(*, "double") to become different to as(*, "numeric") [Again, this is just for the S4 classes and as() coercions, *not* e.g.  for as.numeric() / as.double() !] In the DEPRECATED part of the NEWS for R 2.7.0 (April 2008) we have had     o The S4 pseudo-classes "single" and double have been removed.         (The S4 class for a REALSXP is "numeric": for back-compatibility         as(x, "double") coerces to "numeric".) I think the removal of "single" was fine, but in hindsight, maybe the removal of "double" -- which was partly broken then -- possibly could rather have been a fixup of "double" along the following    Current "thought experiment proposal" :    1) "numeric" := {"integer", "double"}   { class - subclasses }    2) as(1L, "numeric")  continues to return 1L .. since integer is                          one case of "numeric"    3) as(1L, "double")  newly returns 1.0   {and in fact would be                                              "equivalent" to   as.double(1L)} After the above change,  S4  as(*, "double") would correspond to S3 as.double but  as(*, "numeric")  would continue to differ from as.numeric(*), the former *not* changing integers to double. Martin     > On Dec 11, 2015, at 1:25 AM, Martin Maechler <[hidden email]> wrote:     >>>>>>> Martin Maechler <[hidden email]>     >>>>>>> on Tue, 8 Dec 2015 15:25:21 +0100 writes:     >>     >>>>>>> John Chambers <[hidden email]>     >>>>>>> on Mon, 7 Dec 2015 16:05:59 -0800 writes:     >>     >>>> We do need an explicit method here, I think.     >>>> The issue is that as() uses methods for the generic function coerce() but cannot use inheritance in the usual way (if it did, you would be immediately back with no change, since "integer" inherits from "numeric").     >>     >>>> Copying in the general method for coercing to "numeric" as an explicit method for "integer" gives the expected result:     >>     >>>>> setMethod("coerce", c("integer", "numeric"), getMethod("coerce", c("ANY", "numeric")))     >>>> [1] "coerce"     >>>>> typeof(as(1L, "numeric"))     >>>> [1] "double"     >>     >>>> Seems like a reasonable addition to the code, unless someone sees a problem.     >>>> John     >>     >>> I guess that that some package checks (in CRAN + Bioc + ... -     >>> land) will break,     >>> but I still think we should add such a coercion to R.     >>     >>> Martin     >>     >> Hmm...  I've tried to add the above to R     >> and do notice that there are consequences that may be larger than     >> anticipated:     >>     >> Here is example code:     >>     >> myN   <- setClass("myN",   contains="numeric")     >> myNid <- setClass("myNid", contains="numeric", representation(id="character"))     >> NN <-    setClass("NN", representation(x="numeric"))     >>     >> (m1 <- myN  (1:3))     >> (m2 <- myNid(1:3, id = "i3"))     >> tools::assertError(NN (1:3))# in all R versions     >>     >> ##                     # current R  |  new R     >> ##                     # -----------|----------     >> class(getDataPart(m1)) # integer    |  numeric     >> class(getDataPart(m2)) # integer    |  numeric     >>     >>     >> In other words, with the above setting, the traditional     >> gentleperson's agreement in S and R,     >>     >> __ "numeric" sometimes conveniently means "integer" or "double"  __     >>     >> will be slightly less often used ... which of course may be a     >> very good thing.     >>     >> However, it breaks strict back compatibility also in cases where     >> the previous behavior may have been preferable:     >> After all integer vectors need only have the space of doubles.     >>     >> Shall we still go ahead and do apply this change to R-devel     >> and then all package others will be willing to update where necessary?     >>     >> As this may affect the many hundreds of bioconductor packages     >> using S4 classes, I am -- exceptionally -- cross posting to the     >> bioc-devel list.     >>     >> Martin Maechler     >>     >>     >>>> On Dec 7, 2015, at 3:37 PM, Benjamin Tyner <[hidden email]> wrote:     >>     >>>>> Perhaps it is not that surprising, given that     >>>>> >>>>> mode(1L)     >>>>> [1] "numeric"     >>>>>     >>>>> and     >>>>> >>>>> is.numeric(1L)     >>>>> [1] TRUE     >>>>>     >>>>> On the other hand, this is curious, to say the least:     >>>>> >>>>> is.double(as(1L, "double"))     >>>>> [1] FALSE     >>>>> >>>>> Here's the surprising behavior: >>>>> >>>>> x <- 1L >>>>> xx <- as(x, "numeric") >>>>> class(xx) >>>>> ## [1] "integer" >>>>> >>>>> It occurs because the call to `as(x, "numeric")` dispatches the coerce >>>>> S4 method for the signature `c("integer", "numeric")`, whose body is >>>>> copied in below. >>>>> >>>>> function (from, to = "numeric", strict = TRUE) >>>>> if (strict) { >>>>> class(from) <- "numeric" >>>>> from >>>>> } else from >>>>> >>>>> This in turn does nothing, even when strict=TRUE, because that >>>>> assignment to class "numeric" has no effect: >>>>> >>>>> x <- 10L >>>>> class(x) <- "numeric" >>>>> class(x) >>>>> [1] "integer" >>>>> >>>>> Is this the desired behavior for `as(x, "numeric")`?     >>>>>     >>>>> ______________________________________________     >>>>> [hidden email] mailing list     >>>>> https://stat.ethz.ch/mailman/listinfo/r-devel    >>     >>>> ______________________________________________     >>>> [hidden email] mailing list     >>>> https://stat.ethz.ch/mailman/listinfo/r-devel    >>     >>> ______________________________________________     >>> [hidden email] mailing list     >>> https://stat.ethz.ch/mailman/listinfo/r-devel______________________________________________ [hidden email] mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
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## Re: For integer vectors, `as(x, "numeric")` has no effect.

 >>>>> Martin Maechler <[hidden email]> >>>>>     on Sat, 12 Dec 2015 10:32:51 +0100 writes: >>>>> John Chambers <[hidden email]> >>>>>     on Fri, 11 Dec 2015 10:11:05 -0800 writes:     >> Somehow, the most obvious fixes are always back-incompatible these days.     >> The example intrigued me, so I looked into it a bit (should have been doing something else, but ....)     >> You're right that this is the proverbial thin-edge-of-the-wedge.     >> The problem is in setDataPart(), which will be called whenever a class extends one of the vector types.     >> It does     >> as(value, dataClass)     >> The key point is that the third argument to as(), strict=TRUE by default.  So, yes, the change will cause all integer vectors to become double when the class extends "numeric".  Generally, strict=TRUE makes sense here and of course changing THAT would open up yet more incompatibilities.     >> For back compatibility, one would have to have some special code in setDataPart() for the case of integer/numeric.     >> John     >> (Historically, the original sin was probably not making a distinction between "numeric" as a virtual class and "double" as a type/class.)     > Yes, indeed.  In the mean time, I've seen more cases where     > "the change will cause all integer vectors to become double when the class  extends "numeric".     > seems detrimental.     > OTOH, I still think we could go in the right direction ---     > hopefully along the wishes of bioconductor S4 development, see     > Martin Morgan's e-mail:     > [This is all S4 - only; should not much affect base R / S3]     > Currently,   "integer" is a subclass of "numeric"  and so the     > "integer become double" part seems unwanted to me.     > OTOH,  it would really make sense to more formally     > have the basic subclasses of  "numeric" to be "integer" and "double",     > and  to let  as(*, "double") to become different to as(*, "numeric")     > [Again, this is just for the S4 classes and as() coercions, *not* e.g.     > for as.numeric() / as.double() !]     > In the DEPRECATED part of the NEWS for R 2.7.0 (April 2008) we     > have had     > o The S4 pseudo-classes "single" and double have been removed.     > (The S4 class for a REALSXP is "numeric": for back-compatibility     > as(x, "double") coerces to "numeric".)     > I think the removal of "single" was fine, but in hindsight,     > maybe the removal of "double" -- which was partly broken then --     > possibly could rather have been a fixup of "double" along the     > following     > Current "thought experiment proposal" :     > 1) "numeric" := {"integer", "double"}   { class - subclasses }     > 2) as(1L, "numeric")  continues to return 1L .. since integer is     > one case of "numeric"     > 3) as(1L, "double")  newly returns 1.0   {and in fact would be     > "equivalent" to   as.double(1L)}     > After the above change,  S4  as(*, "double") would correspond to S3 as.double     > but  as(*, "numeric")  would continue to differ from     > as.numeric(*), the former *not* changing integers to double.     > Martin Also note that e.g.     class(pi)    would return "double" instead of "numeric" and this will break all the bad programming style usages of   if(class(x) == "numeric") which I tend to see in gazillions of user and even package codes This bad (aka error prone !)  because "correct" usage would be   if(inherits(x, "numeric")) and that of course would *not* break after the change above. - - - - A week later, I'm still pretty convinced it would be worth going in the direction proposed above. But I was actually hoping for some encouragement or "mental support"... or then to hear why you think the proposition is not good or not viable ...     >> On Dec 11, 2015, at 1:25 AM, Martin Maechler <[hidden email]> wrote:     >>>>>>>> Martin Maechler <[hidden email]>     >>>>>>>> on Tue, 8 Dec 2015 15:25:21 +0100 writes:     >>>     >>>>>>>> John Chambers <[hidden email]>     >>>>>>>> on Mon, 7 Dec 2015 16:05:59 -0800 writes:     >>>     >>>>> We do need an explicit method here, I think.     >>>>> The issue is that as() uses methods for the generic function coerce() but cannot use inheritance in the usual way (if it did, you would be immediately back with no change, since "integer" inherits from "numeric").     >>>     >>>>> Copying in the general method for coercing to "numeric" as an explicit method for "integer" gives the expected result:     >>>     >>>>>> setMethod("coerce", c("integer", "numeric"), getMethod("coerce", c("ANY", "numeric")))     >>>>> [1] "coerce"     >>>>>> typeof(as(1L, "numeric"))     >>>>> [1] "double"     >>>     >>>>> Seems like a reasonable addition to the code, unless someone sees a problem.     >>>>> John     >>>     >>>> I guess that that some package checks (in CRAN + Bioc + ... -     >>>> land) will break,     >>>> but I still think we should add such a coercion to R.     >>>     >>>> Martin     >>>     >>> Hmm...  I've tried to add the above to R     >>> and do notice that there are consequences that may be larger than     >>> anticipated:     >>>     >>> Here is example code:     >>>     >>> myN   <- setClass("myN",   contains="numeric")     >>> myNid <- setClass("myNid", contains="numeric", representation(id="character"))     >>> NN <-    setClass("NN", representation(x="numeric"))     >>>     >>> (m1 <- myN  (1:3))     >>> (m2 <- myNid(1:3, id = "i3"))     >>> tools::assertError(NN (1:3))# in all R versions     >>>     >>> ##                     # current R  |  new R     >>> ##                     # -----------|----------     >>> class(getDataPart(m1)) # integer    |  numeric     >>> class(getDataPart(m2)) # integer    |  numeric     >>>     >>>     >>> In other words, with the above setting, the traditional     >>> gentleperson's agreement in S and R,     >>>     >>> __ "numeric" sometimes conveniently means "integer" or "double"  __     >>>     >>> will be slightly less often used ... which of course may be a     >>> very good thing.     >>>     >>> However, it breaks strict back compatibility also in cases where     >>> the previous behavior may have been preferable:     >>> After all integer vectors need only have the space of doubles.     >>>     >>> Shall we still go ahead and do apply this change to R-devel     >>> and then all package others will be willing to update where necessary?     >>>     >>> As this may affect the many hundreds of bioconductor packages     >>> using S4 classes, I am -- exceptionally -- cross posting to the     >>> bioc-devel list.     >>>     >>> Martin Maechler     >>>     >>>     >>>>> On Dec 7, 2015, at 3:37 PM, Benjamin Tyner <[hidden email]> wrote:     >>>     >>>>>> Perhaps it is not that surprising, given that     >>>>>> >>>>> mode(1L)     >>>>>> [1] "numeric"     >>>>>>     >>>>>> and     >>>>>> >>>>> is.numeric(1L)     >>>>>> [1] TRUE     >>>>>>     >>>>>> On the other hand, this is curious, to say the least:     >>>>>> >>>>> is.double(as(1L, "double"))     >>>>>> [1] FALSE     >>>>>> >>>>> Here's the surprising behavior: >>>>> >>>>> x <- 1L >>>>> xx <- as(x, "numeric") >>>>> class(xx) >>>>> ## [1] "integer" >>>>> >>>>> It occurs because the call to `as(x, "numeric")` dispatches the coerce >>>>> S4 method for the signature `c("integer", "numeric")`, whose body is >>>>> copied in below. >>>>> >>>>> function (from, to = "numeric", strict = TRUE) >>>>> if (strict) { >>>>> class(from) <- "numeric" >>>>> from >>>>> } else from >>>>> >>>>> This in turn does nothing, even when strict=TRUE, because that >>>>> assignment to class "numeric" has no effect: >>>>> >>>>> x <- 10L >>>>> class(x) <- "numeric" >>>>> class(x) >>>>> [1] "integer" >>>>> >>>>> Is this the desired behavior for `as(x, "numeric")`?     >>>>>>     >>>>>> ______________________________________________     >>>>>> [hidden email] mailing list     >>>>>> https://stat.ethz.ch/mailman/listinfo/r-devel    >>>     >>>>> ______________________________________________     >>>>> [hidden email] mailing list     >>>>> https://stat.ethz.ch/mailman/listinfo/r-devel    >>>     >>>> ______________________________________________     >>>> [hidden email] mailing list     >>>> https://stat.ethz.ch/mailman/listinfo/r-devel______________________________________________ [hidden email] mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
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