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Pages, Herve

2019-Mar-22 04:52 UTC

[Rd] selectMethod() can fail to find methods in situations of multiple dispatch

Fine with me as long as eliminating the inconveniences associated with it can be
put on the roadmap. The alias instability and the fact that the user has no way
to know if s/he should do ?`foo,numeric-method` or ?`foo,numeric,ANY-method` to
find the method has been a long-standing problem.

H.

On 3/21/19 21:29, Michael Lawrence wrote:
If we started over, I'd try to avoid this sort of complexity, but
"ANY" truncation has been happening since at least 2003.
> matchSignature(c("numeric", "ANY"), foo)        x
"numeric"

So I'm not sure we want to mess with it.

Michael

On Thu, Mar 21, 2019 at 8:14 PM Pages, Herve <hpages at
fredhutch.org<mailto:hpages at fredhutch.org>> wrote:

Hi Michael,

Thanks for looking into this. I suspect that truncation of ANY suffixes from
method signatures is also the culprit behind the sudden breakage of aliases of
the form \alias{foo,numeric-method} when a method without the ANY suffix in its
signature gets added to the ecosystem. See my post about this to the Bioc-devel
mailing list a couple of months ago:
https://stat.ethz.ch/pipermail/bioc-devel/2019-January/014603.html<https://urldefense.proofpoint.com/v2/url?u=https-3A__stat.ethz.ch_pipermail_bioc-2Ddevel_2019-2DJanuary_014603.html&d=DwMFaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=kjmNpPtpGtaMCrw8ubpy0siyz1xl8WY9gONjtL65IxE&s=R9Hi4Rm4nk-izYC8vDCj0NiuFdUMG4vZVbdQgsvxkDM&e=>

So overall isn't this truncation more trouble than it's worth?

H.

On 3/19/19 10:12, Michael Lawrence wrote:
This is due to the intentional truncation of ANY suffixes from method
signatures. I've hacked selectMethod() to be robust to that and will commit
soon. Thanks for the report.

Michael

On Thu, Mar 14, 2019 at 9:32 AM Pages, Herve <hpages at
fredhutch.org<mailto:hpages at fredhutch.org>> wrote:
Here is an example:

  setGeneric("foo", function(x, y) standardGeneric("foo"))

  setMethod("foo", c("numeric", "ANY"),
    function(x, y) cat("I'm the foo#numeric#ANY method\n")
  )

Dispatch works as expected but selectMethod() fails to find the method:

  > foo(1, TRUE)
  I'm the foo#numeric#ANY method

  > selectMethod("foo", c("numeric",
"logical"))
  Error in selectMethod("foo", c("numeric",
"logical")) :
    no method found for signature numeric, logical

Adding an arbitrary method that doesn't have ANY in the signature
"fixes" selectMethod():

  setMethod("foo", c("complex", "integer"),
    function(x, y) cat("I'm the foo#complex#integer method\n")
  )

Then:

  > selectMethod("foo", c("numeric",
"logical"))
  Method Definition:

  function (x, y)
  cat("I'm the foo#numeric#ANY method\n")

  Signatures:
        x         y
  target  "numeric" "logical"
  defined "numeric" "ANY"

Thanks,

H.

--
Herv? Pag?s

Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N, M1-B514
P.O. Box 19024
Seattle, WA 98109-1024

E-mail: hpages at fredhutch.org<mailto:hpages at
fredhutch.org><mailto:hpages at fredhutch.org<mailto:hpages at
fredhutch.org>>
Phone:  (206) 667-5791
Fax:    (206) 667-1319

        [[alternative HTML version deleted]]

______________________________________________
R-devel at r-project.org<mailto:R-devel at r-project.org> mailing list
https://stat.ethz.ch/mailman/listinfo/r-devel<https://urldefense.proofpoint.com/v2/url?u=https-3A__stat.ethz.ch_mailman_listinfo_r-2Ddevel&d=DwMFaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=4e2MsIBoF9YnF3BCkiOk1m2kFgKBe24FwU28c-wuAyc&s=ydXNxAwEa5eG9lTu27sx-8KsT6gU66TbmJLcaYEaleg&e=>

--
Herv? Pag?s

Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N, M1-B514
P.O. Box 19024
Seattle, WA 98109-1024

E-mail: hpages at fredhutch.org<mailto:hpages at fredhutch.org>
Phone:  (206) 667-5791
Fax:    (206) 667-1319

--
Herv? Pag?s

Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N, M1-B514
P.O. Box 19024
Seattle, WA 98109-1024

E-mail: hpages at fredhutch.org<mailto:hpages at fredhutch.org>
Phone:  (206) 667-5791
Fax:    (206) 667-1319

	[[alternative HTML version deleted]]

Michael Lawrence

2019-Mar-22 05:05 UTC

head link

[Rd] selectMethod() can fail to find methods in situations of multiple dispatch

Agreed but I'm not sure we want users accessing documentation with those
types of aliases. One option is the method?foo("numeric") syntax.

On Thu, Mar 21, 2019 at 9:52 PM Pages, Herve <hpages at fredhutch.org>
wrote:
> Fine with me as long as eliminating the inconveniences associated with it
> can be put on the roadmap. The alias instability and the fact that the user
> has no way to know if s/he should do ?`foo,numeric-method` or
> ?`foo,numeric,ANY-method` to find the method has been a long-standing
> problem.
>
> H.
> On 3/21/19 21:29, Michael Lawrence wrote:
>
> If we started over, I'd try to avoid this sort of complexity, but
"ANY"
> truncation has been happening since at least 2003.
>
> > matchSignature(c("numeric", "ANY"), foo)
>         x
> "numeric"
>
> So I'm not sure we want to mess with it.
>
> Michael
>
> On Thu, Mar 21, 2019 at 8:14 PM Pages, Herve <hpages at
fredhutch.org> wrote:
>
>> Hi Michael,
>>
>> Thanks for looking into this. I suspect that truncation of ANY suffixes
>> from method signatures is also the culprit behind the sudden breakage
of
>> aliases of the form \alias{foo,numeric-method} when a method without
the
>> ANY suffix in its signature gets added to the ecosystem. See my post
about
>> this to the Bioc-devel mailing list a couple of months ago:
>> https://stat.ethz.ch/pipermail/bioc-devel/2019-January/014603.html
>>
<https://urldefense.proofpoint.com/v2/url?u=https-3A__stat.ethz.ch_pipermail_bioc-2Ddevel_2019-2DJanuary_014603.html&d=DwMFaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=kjmNpPtpGtaMCrw8ubpy0siyz1xl8WY9gONjtL65IxE&s=R9Hi4Rm4nk-izYC8vDCj0NiuFdUMG4vZVbdQgsvxkDM&e=>
>>
>> So overall isn't this truncation more trouble than it's worth?
>>
>> H.
>> On 3/19/19 10:12, Michael Lawrence wrote:
>>
>> This is due to the intentional truncation of ANY suffixes from method
>> signatures. I've hacked selectMethod() to be robust to that and
will commit
>> soon. Thanks for the report.
>>
>> Michael
>>
>> On Thu, Mar 14, 2019 at 9:32 AM Pages, Herve <hpages at
fredhutch.org>
>> wrote:
>>
>>> Here is an example:
>>>
>>>   setGeneric("foo", function(x, y)
standardGeneric("foo"))
>>>
>>>   setMethod("foo", c("numeric",
"ANY"),
>>>     function(x, y) cat("I'm the foo#numeric#ANY
method\n")
>>>   )
>>>
>>>
>>> Dispatch works as expected but selectMethod() fails to find the
method:
>>>
>>>
>>>   > foo(1, TRUE)
>>>   I'm the foo#numeric#ANY method
>>>
>>>   > selectMethod("foo", c("numeric",
"logical"))
>>>   Error in selectMethod("foo", c("numeric",
"logical")) :
>>>     no method found for signature numeric, logical
>>>
>>> Adding an arbitrary method that doesn't have ANY in the
signature
>>> "fixes" selectMethod():
>>>
>>>   setMethod("foo", c("complex",
"integer"),
>>>     function(x, y) cat("I'm the foo#complex#integer
method\n")
>>>   )
>>>
>>> Then:
>>>
>>>   > selectMethod("foo", c("numeric",
"logical"))
>>>   Method Definition:
>>>
>>>   function (x, y)
>>>   cat("I'm the foo#numeric#ANY method\n")
>>>
>>>   Signatures:
>>>         x         y
>>>   target  "numeric" "logical"
>>>   defined "numeric" "ANY"
>>>
>>>
>>> Thanks,
>>>
>>> H.
>>>
>>>
>>> --
>>> Herv? Pag?s
>>>
>>> Program in Computational Biology
>>> Division of Public Health Sciences
>>> Fred Hutchinson Cancer Research Center
>>> 1100 Fairview Ave. N, M1-B514
>>> P.O. Box 19024
>>> Seattle, WA 98109-1024
>>>
>>> E-mail: hpages at fredhutch.org<mailto:hpages at
fredhutch.org>
>>> Phone:  (206) 667-5791
>>> Fax:    (206) 667-1319
>>>
>>>
>>>         [[alternative HTML version deleted]]
>>>
>>> ______________________________________________
>>> R-devel at r-project.org mailing list
>>> https://stat.ethz.ch/mailman/listinfo/r-devel
>>>
<https://urldefense.proofpoint.com/v2/url?u=https-3A__stat.ethz.ch_mailman_listinfo_r-2Ddevel&d=DwMFaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=4e2MsIBoF9YnF3BCkiOk1m2kFgKBe24FwU28c-wuAyc&s=ydXNxAwEa5eG9lTu27sx-8KsT6gU66TbmJLcaYEaleg&e=>
>>>
>> --
>> Herv? Pag?s
>>
>> Program in Computational Biology
>> Division of Public Health Sciences
>> Fred Hutchinson Cancer Research Center
>> 1100 Fairview Ave. N, M1-B514
>> P.O. Box 19024
>> Seattle, WA 98109-1024
>>
>> E-mail: hpages at fredhutch.org
>> Phone:  (206) 667-5791
>> Fax:    (206) 667-1319
>>
>> --
> Herv? Pag?s
>
> Program in Computational Biology
> Division of Public Health Sciences
> Fred Hutchinson Cancer Research Center
> 1100 Fairview Ave. N, M1-B514
> P.O. Box 19024
> Seattle, WA 98109-1024
>
> E-mail: hpages at fredhutch.org
> Phone:  (206) 667-5791
> Fax:    (206) 667-1319
>
>
	[[alternative HTML version deleted]]

Pages, Herve

2019-Mar-22 05:52 UTC

head link

[Rd] selectMethod() can fail to find methods in situations of multiple dispatch

Good to know about the method?foo("numeric") syntax. And apparently it
knows about inheritance! Thanks for mentioning that. I see it's documented
in ?`?`... Darn! How could I miss it for so many years!

Note however that this syntax doesn't seem to work in case of
"ANY" truncation so I won't be able to fully adopt this syntax for
now:
> library(Matrix)
> showMethods("colSums")Function: colSums (package base)
x="ANY"
x="CsparseMatrix"
x="ddenseMatrix"
x="denseMatrix"
x="dgCMatrix"
x="dgeMatrix"
x="diagonalMatrix"
x="igCMatrix"
x="indMatrix"
x="lgCMatrix"
x="ngCMatrix"
x="RsparseMatrix"
x="TsparseMatrix"
> method?colSums("dgCMatrix")Error in .helpForCall(topicExpr, parent.frame(), FALSE) :
  no documentation for function ?colSums? and signature ?x =
"dgCMatrix", na.rm = "logical", dims = "numeric"?
In addition: Warning message:
In .helpForCall(topicExpr, parent.frame(), FALSE) :
  no method defined for function ?colSums? and signature ?x =
"dgCMatrix", na.rm = "logical", dims = "numeric"?

But maybe it uses selectMethod() behind the seen so will work once
selectMethod() gets fixed?

Thanks,

H.

On 3/21/19 22:05, Michael Lawrence wrote:
Agreed but I'm not sure we want users accessing documentation with those
types of aliases. One option is the method?foo("numeric") syntax.

On Thu, Mar 21, 2019 at 9:52 PM Pages, Herve <hpages at
fredhutch.org<mailto:hpages at fredhutch.org>> wrote:

Fine with me as long as eliminating the inconveniences associated with it can be
put on the roadmap. The alias instability and the fact that the user has no way
to know if s/he should do ?`foo,numeric-method` or ?`foo,numeric,ANY-method` to
find the method has been a long-standing problem.

H.

On 3/21/19 21:29, Michael Lawrence wrote:
If we started over, I'd try to avoid this sort of complexity, but
"ANY" truncation has been happening since at least 2003.
> matchSignature(c("numeric", "ANY"), foo)        x
"numeric"

So I'm not sure we want to mess with it.

Michael

On Thu, Mar 21, 2019 at 8:14 PM Pages, Herve <hpages at
fredhutch.org<mailto:hpages at fredhutch.org>> wrote:

Hi Michael,

Thanks for looking into this. I suspect that truncation of ANY suffixes from
method signatures is also the culprit behind the sudden breakage of aliases of
the form \alias{foo,numeric-method} when a method without the ANY suffix in its
signature gets added to the ecosystem. See my post about this to the Bioc-devel
mailing list a couple of months ago:
https://stat.ethz.ch/pipermail/bioc-devel/2019-January/014603.html<https://urldefense.proofpoint.com/v2/url?u=https-3A__stat.ethz.ch_pipermail_bioc-2Ddevel_2019-2DJanuary_014603.html&d=DwMFaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=kjmNpPtpGtaMCrw8ubpy0siyz1xl8WY9gONjtL65IxE&s=R9Hi4Rm4nk-izYC8vDCj0NiuFdUMG4vZVbdQgsvxkDM&e=>

So overall isn't this truncation more trouble than it's worth?

H.

On 3/19/19 10:12, Michael Lawrence wrote:
This is due to the intentional truncation of ANY suffixes from method
signatures. I've hacked selectMethod() to be robust to that and will commit
soon. Thanks for the report.

Michael

On Thu, Mar 14, 2019 at 9:32 AM Pages, Herve <hpages at
fredhutch.org<mailto:hpages at fredhutch.org>> wrote:
Here is an example:

  setGeneric("foo", function(x, y) standardGeneric("foo"))

  setMethod("foo", c("numeric", "ANY"),
    function(x, y) cat("I'm the foo#numeric#ANY method\n")
  )

Dispatch works as expected but selectMethod() fails to find the method:

  > foo(1, TRUE)
  I'm the foo#numeric#ANY method

  > selectMethod("foo", c("numeric",
"logical"))
  Error in selectMethod("foo", c("numeric",
"logical")) :
    no method found for signature numeric, logical

Adding an arbitrary method that doesn't have ANY in the signature
"fixes" selectMethod():

  setMethod("foo", c("complex", "integer"),
    function(x, y) cat("I'm the foo#complex#integer method\n")
  )

Then:

  > selectMethod("foo", c("numeric",
"logical"))
  Method Definition:

  function (x, y)
  cat("I'm the foo#numeric#ANY method\n")

  Signatures:
        x         y
  target  "numeric" "logical"
  defined "numeric" "ANY"

Thanks,

H.

--
Herv? Pag?s

Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N, M1-B514
P.O. Box 19024
Seattle, WA 98109-1024

E-mail: hpages at fredhutch.org<mailto:hpages at
fredhutch.org><mailto:hpages at fredhutch.org<mailto:hpages at
fredhutch.org>>
Phone:  (206) 667-5791
Fax:    (206) 667-1319

        [[alternative HTML version deleted]]

______________________________________________
R-devel at r-project.org<mailto:R-devel at r-project.org> mailing list
https://stat.ethz.ch/mailman/listinfo/r-devel<https://urldefense.proofpoint.com/v2/url?u=https-3A__stat.ethz.ch_mailman_listinfo_r-2Ddevel&d=DwMFaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=4e2MsIBoF9YnF3BCkiOk1m2kFgKBe24FwU28c-wuAyc&s=ydXNxAwEa5eG9lTu27sx-8KsT6gU66TbmJLcaYEaleg&e=>

--
Herv? Pag?s

Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N, M1-B514
P.O. Box 19024
Seattle, WA 98109-1024

E-mail: hpages at fredhutch.org<mailto:hpages at fredhutch.org>
Phone:  (206) 667-5791
Fax:    (206) 667-1319

--
Herv? Pag?s

Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N, M1-B514
P.O. Box 19024
Seattle, WA 98109-1024

E-mail: hpages at fredhutch.org<mailto:hpages at fredhutch.org>
Phone:  (206) 667-5791
Fax:    (206) 667-1319

--
Herv? Pag?s

Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N, M1-B514
P.O. Box 19024
Seattle, WA 98109-1024

E-mail: hpages at fredhutch.org<mailto:hpages at fredhutch.org>
Phone:  (206) 667-5791
Fax:    (206) 667-1319

	[[alternative HTML version deleted]]

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