[Rd] 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")`?
__
R-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] 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")`?
__
R-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] 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 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")`?
>
> __
> R-devel@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-devel
__
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Re: [Rd] For integer vectors, `as(x, "numeric")` has no effect.
> John Chambers
> 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 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")`?
>>
>> __
>> R-devel@r-project.org mailing list
>> https://stat.ethz.ch/mailman/listinfo/r-devel
> __
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> https://stat.ethz.ch/mailman/listinfo/r-devel
__
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Re: [Rd] For integer vectors, `as(x, "numeric")` has no effect.
> Martin Maechler
> on Tue, 8 Dec 2015 15:25:21 +0100 writes:
> John Chambers
> 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 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")`?
>>>
>>> __
>>> R-devel@r-project.org mailing list
>>> https://stat.ethz.ch/mailman/listinfo/r-devel
>> __
>> R-devel@r-project.org mailing list
>> https://stat.ethz.ch/mailman/listinfo/r-devel
> __
> R-devel@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-devel
__
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Re: [Rd] 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 wrote:
>> Martin Maechler
>>on Tue, 8 Dec 2015 15:25:21 +0100 writes:
>
>> John Chambers
>>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 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")`?
__
R-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-devel
>
>>> __
>>> R-devel@r-project.org mailing list
>>> https://stat.ethz.ch/mailman/listinfo/r-devel
>
>> __
>> R-devel@r-project.org mailing list
>> https://stat.ethz.ch/mailman/listinfo/r-devel
[[alternative HTML version deleted]]
__
Re: [Rd] For integer vectors, `as(x, "numeric")` has no effect.
>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 [r-devel-boun...@r-project.org] on behalf of Martin Maechler
[maech...@stat.math.ethz.ch]
Sent: Friday, December 11, 2015 4:25 AM
To: John Chambers; r-devel@r-project.org; bioc-devel list; Benjamin Tyner
Cc: Martin Maechler
Subject: Re: [Rd] For integer vectors, `as(x, "numeric")` has no effect.
>>>>> Martin Maechler
>>>>> on Tue, 8 Dec 2015 15:25:21 +0100 writes:
>>>>> John Chambers
>>>>> 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 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 thi
Re: [Rd] For integer vectors, `as(x, "numeric")` has no effect.
> John Chambers
> 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
wrote:
>>> Martin Maechler
>>> on Tue, 8 Dec 2015 15:25:21 +0100 writes:
>>
>>> John Chambers
>>> 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" __
>>
Re: [Rd] For integer vectors, `as(x, "numeric")` has no effect.
> Martin Maechler
> on Sat, 12 Dec 2015 10:32:51 +0100 writes:
> John Chambers
> 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
wrote:
Martin Maechler
on Tue, 8 Dec 2015 15:25:21 +0100 writes:
>>>
John Chambers
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 consequenc
Re: [Rd] For integer vectors, `as(x, "numeric")` has no effect.
As I tried to say on Dec. 11, there are two levels of "fix":
1. The fix to the complaint in the OP's subject heading is to conform to the
default third argument, strict=TRUE: as(1L, "numeric") == 1.0
This generates some incompatibilities, as for classes that extend "numeric".
But still leaves class(1.0) "numeric" and typeof(1.0) "double".
The workaround for class definitions that really need NOT to coerce integers to
double is to define a class union, say
setClassUnion("Number", c("numeric", "integer"))
and use that for the slot.
2. The "right" concept is arguably that "numeric" is a virtual class with two
subclasses, "double" and "integer". Given a time machine back to < 1998, that
would be my choice. But already in the 1998 S4 book, "numeric" was equated
with "double".
so, there it is, IMO. This is what you get with a successful open-source
language: Much hassle to do the "right thing" after the fact and the more
change, the more hassle.
Fix 1. seems to me an actual bug fix, so my inclination would be to go with
that (on r-devel), advertising that it may change the effective definition of
some classes.
But I can sympathize with choosing 1, 2 or neither.
John
PS: Until Jan. 4, I may be even poorer at replying than usual, while getting
the current book off to the publisher.
On Dec 19, 2015, at 3:32 AM, Martin Maechler wrote:
>> Martin Maechler
>>on Sat, 12 Dec 2015 10:32:51 +0100 writes:
>
>> John Chambers
>>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
>
>> oThe 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
Re: [Rd] For integer vectors, `as(x, "numeric")` has no effect.
On Dec 19, 2015, at 3:32 AM, Martin Maechler wrote:
>> Martin Maechler
>>on Sat, 12 Dec 2015 10:32:51 +0100 writes:
>
>> John Chambers
>>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
>
>> oThe 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 ...
>
>
I really like Martin Maechler's "thought experiment proposal", but (based
partly on the reception its gotten) figure I mustn't be appreciating
the complications
it would introduce..
That said, if it's decided to just make a smaller fix of as(x, "numeric"),
might it be better to make the change at the C level, to R_set_class
in $RHOME/src/main/coerce.c?
Here's the 'offending' bit of R_set_class (the C-code implementing the
R function `class<-`), which treats an INTSXP in the same way as a
REALSXP, breaking before it get coerced to REALSXP:
else if(!strcmp("numeric", valueString)) {
setAttrib(obj, R_ClassSymbol, R_NilValue);
if(IS_S4_OBJECT(obj)) /* NULL class is only valid for S3 objects */
do_unsetS4(obj, value);
switch(TYPEOF(obj)) {
case INTSXP: case REALSXP: break;
default: PROTECT(obj = coerceVector(obj, REALSXP));
nProtect++;
}
}
Simply deleting "case INTSXP: " will let integer vectors pass
through and get converted to REALSXP by coerceVector().
This approach has a couple of advantages that (unless I'm missing
something) make it seem relatively clean:
- It requires no additional explicit S4 "coerce" method for
signature c("integer", "numeric").
- It simultaneously fi
Re: [Rd] For integer vectors, `as(x, "numeric")` has no effect.
> Josh O'Brien
> on Mon, 4 Jan 2016 16:16:51 -0800 writes:
> On Dec 19, 2015, at 3:32 AM, Martin Maechler wrote:
>>> Martin Maechler on
>>> Sat, 12 Dec 2015 10:32:51 +0100 writes:
>>
>>> John Chambers 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 ...
>>
>>
> I really like Martin Maechler's "thought experiment
> proposal", but (based partly on the reception its gotten)
> figure I mustn't be appreciating the complications it
> would introduce..
Actually, I've spent half day implementing it and was very
pleased about it... as matter of fact it passed *all* our checks
also in all recommended packages (*)
To do it cleanly... with very few code changes,
the *only* consequence would be that
class(1.)
(and similar) then returned "double" instead of "numeric".
which *would* be logical consequent, because indeed,
numeric = {integer, double
Re: [Rd] For integer vectors, `as(x, "numeric")` has no effect.
On Tue, Jan 5, 2016 at 1:31 AM, Martin Maechler
wrote:
>> Josh O'Brien
>> on Mon, 4 Jan 2016 16:16:51 -0800 writes:
>
> > On Dec 19, 2015, at 3:32 AM, Martin Maechler stat.math.ethz.ch> wrote:
>
> >>> Martin Maechler on
> >>> Sat, 12 Dec 2015 10:32:51 +0100 writes:
> >>
> >>> John Chambers 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 ...
> >>
> >>
>
> > I really like Martin Maechler's "thought experiment
> > proposal", but (based partly on the reception its gotten)
> > figure I mustn't be appreciating the complications it
> > would introduce..
>
> Actually, I've spent half day implementing it and was very
> pleased about it... as matter of fact it passed *all* our che
