R devel - Mar 2019 - selectMethod() can fail to find methods in situations of multiple dispatch

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

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


	[[alternative HTML version deleted]]

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
>
> 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
>
>
	[[alternative HTML version deleted]]

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]]