R devel - Feb 2020 - Possible Regression in setClassUnion between 3.5.0 and 3.6.0

I am trying to create a class union of class unions to facilitate method
dispatch. When I execute code in the global environment, everything acts as
expected, however when I put the same code in the context of a package,
selectMethod can no longer find the correct method. This first block below
puts the code in the context of a package:

fn <- "codefile.R"
writeLines(
    c(
        "setClass('x', slots = list(slot
='character'))",
        "setClass('y', slots = list(slot
='character'))",
        "setClass('a', slots = list(slot
='character'))",
        "setClass('b', slots = list(slot
='character'))",
        "setClassUnion('xy', c('x', 'y'))",
        "setClassUnion('ab', c('a', 'b'))",
        "setClassUnion('xyab', c('xy',
'ab'))",
        "setGeneric('f', function(object, ...)
standardGeneric('f'))",
        "setMethod('f', 'xyab', function(object, ...)
print('hi!'))"
    ),
    con = fn
)
package.skeleton(code_files = "codefile.R")
system("rm -rf anRpackage/man")
system("R CMD INSTALL anRpackage")
library(anRpackage)
## fails in R 3.6.2, but works in R 3.5.0
f(new("a"))

Next, if a fresh R 3.6.2 session is started and I execute the following at
the prompt, method dispatch works as expected.

setClass("x", slots = list(slot ="character"))
setClass("y", slots = list(slot ="character"))
setClass("a", slots = list(slot ="character"))
setClass("b", slots = list(slot ="character"))
setClassUnion("xy", c("x", "y"))
setClassUnion("ab", c("a", "b"))
setClassUnion("xyab", c("xy", "ab"))
setGeneric("f", function(object, ...) standardGeneric("f"))
setMethod("f", "xyab", function(object, ...)
print("hi!"))
## print's "hi!" as expected
f(new("a"))

I have also posted to stack overflow here:
https://stackoverflow.com/questions/60264786/r-s4-class-union-of-class-unions?noredirect=1#comment106627883_60264786,
(the example in this note removes devtools to make the environment
cleaner).

Interestingly, the issue only seems to arise when there are > 1 layer
of the class union. E.g. if I were to setMethod on "ab" instead of
"xyab", method dispatch would work as expected. I am not posting a bug
yet as it is still unclear to me if I am doing something incorrect.

My sessionInfo() is :

R version 3.6.2 (2019-12-12)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 18.04.3 LTS

Matrix products: default
BLAS:   /usr/local/lib/R/lib/libRblas.so
LAPACK: /usr/local/lib/R/lib/libRlapack.so

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C
 [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8
 [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8
 [7] LC_PAPER=en_US.UTF-8       LC_NAME=C
 [9] LC_ADDRESS=C               LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base

other attached packages:
[1] anRpackage_1.0

loaded via a namespace (and not attached):
[1] compiler_3.6.2 tools_3.6.2

Thanks in advance for the help!

	[[alternative HTML version deleted]]

Hi Robert,

This looks like a bug to me (tested in R 3.6.2 on Windows),
f(new("a"))
should return "hi!". I'll add that this DOES work properly in
3.6.1
which leads me to suspect this could be due to the subtle change in the 
way method dispatch was performed to fix a different bug, in 3.6.2. Can 
anybody else confirm that?


On 2/18/2020 9:32 AM, Robert Harlow wrote:
> I am trying to create a class union of class unions to facilitate method
> dispatch. When I execute code in the global environment, everything acts as
> expected, however when I put the same code in the context of a package,
> selectMethod can no longer find the correct method. This first block below
> puts the code in the context of a package:
>
> fn <- "codefile.R"
> writeLines(
>      c(
>          "setClass('x', slots = list(slot
='character'))",
>          "setClass('y', slots = list(slot
='character'))",
>          "setClass('a', slots = list(slot
='character'))",
>          "setClass('b', slots = list(slot
='character'))",
>          "setClassUnion('xy', c('x',
'y'))",
>          "setClassUnion('ab', c('a',
'b'))",
>          "setClassUnion('xyab', c('xy',
'ab'))",
>          "setGeneric('f', function(object, ...)
standardGeneric('f'))",
>          "setMethod('f', 'xyab', function(object, ...)
print('hi!'))"
>      ),
>      con = fn
> )
> package.skeleton(code_files = "codefile.R")
> system("rm -rf anRpackage/man")
> system("R CMD INSTALL anRpackage")
> library(anRpackage)
> ## fails in R 3.6.2, but works in R 3.5.0
> f(new("a"))
>
> Next, if a fresh R 3.6.2 session is started and I execute the following at
> the prompt, method dispatch works as expected.
>
> setClass("x", slots = list(slot ="character"))
> setClass("y", slots = list(slot ="character"))
> setClass("a", slots = list(slot ="character"))
> setClass("b", slots = list(slot ="character"))
> setClassUnion("xy", c("x", "y"))
> setClassUnion("ab", c("a", "b"))
> setClassUnion("xyab", c("xy", "ab"))
> setGeneric("f", function(object, ...)
standardGeneric("f"))
> setMethod("f", "xyab", function(object, ...)
print("hi!"))
> ## print's "hi!" as expected
> f(new("a"))
>
> I have also posted to stack overflow here:
>
https://stackoverflow.com/questions/60264786/r-s4-class-union-of-class-unions?noredirect=1#comment106627883_60264786,
> (the example in this note removes devtools to make the environment
> cleaner).
>
> Interestingly, the issue only seems to arise when there are > 1 layer
> of the class union. E.g. if I were to setMethod on "ab" instead
of
> "xyab", method dispatch would work as expected. I am not posting
a bug
> yet as it is still unclear to me if I am doing something incorrect.
>
> My sessionInfo() is :
>
> R version 3.6.2 (2019-12-12)
> Platform: x86_64-pc-linux-gnu (64-bit)
> Running under: Ubuntu 18.04.3 LTS
>
> Matrix products: default
> BLAS:   /usr/local/lib/R/lib/libRblas.so
> LAPACK: /usr/local/lib/R/lib/libRlapack.so
>
> locale:
>   [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C
>   [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8
>   [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8
>   [7] LC_PAPER=en_US.UTF-8       LC_NAME=C
>   [9] LC_ADDRESS=C               LC_TELEPHONE=C
> [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
>
> attached base packages:
> [1] stats     graphics  grDevices utils     datasets  methods   base
>
> other attached packages:
> [1] anRpackage_1.0
>
> loaded via a namespace (and not attached):
> [1] compiler_3.6.2 tools_3.6.2
>
> Thanks in advance for the help!
>
> 	[[alternative HTML version deleted]]
>
> ______________________________________________
> R-devel at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-devel

Thanks, I'll look into it.

On Tue, Feb 18, 2020 at 8:32 AM Ezra Tucker <ezztucker at gmail.com>
wrote:
>
> Hi Robert,
>
> This looks like a bug to me (tested in R 3.6.2 on Windows),
f(new("a"))
> should return "hi!". I'll add that this DOES work properly in
3.6.1
> which leads me to suspect this could be due to the subtle change in the
> way method dispatch was performed to fix a different bug, in 3.6.2. Can
> anybody else confirm that?
>
>
> On 2/18/2020 9:32 AM, Robert Harlow wrote:
> > I am trying to create a class union of class unions to facilitate
method
> > dispatch. When I execute code in the global environment, everything
acts as
> > expected, however when I put the same code in the context of a
package,
> > selectMethod can no longer find the correct method. This first block
below
> > puts the code in the context of a package:
> >
> > fn <- "codefile.R"
> > writeLines(
> >      c(
> >          "setClass('x', slots = list(slot
='character'))",
> >          "setClass('y', slots = list(slot
='character'))",
> >          "setClass('a', slots = list(slot
='character'))",
> >          "setClass('b', slots = list(slot
='character'))",
> >          "setClassUnion('xy', c('x',
'y'))",
> >          "setClassUnion('ab', c('a',
'b'))",
> >          "setClassUnion('xyab', c('xy',
'ab'))",
> >          "setGeneric('f', function(object, ...)
standardGeneric('f'))",
> >          "setMethod('f', 'xyab', function(object,
...) print('hi!'))"
> >      ),
> >      con = fn
> > )
> > package.skeleton(code_files = "codefile.R")
> > system("rm -rf anRpackage/man")
> > system("R CMD INSTALL anRpackage")
> > library(anRpackage)
> > ## fails in R 3.6.2, but works in R 3.5.0
> > f(new("a"))
> >
> > Next, if a fresh R 3.6.2 session is started and I execute the
following at
> > the prompt, method dispatch works as expected.
> >
> > setClass("x", slots = list(slot ="character"))
> > setClass("y", slots = list(slot ="character"))
> > setClass("a", slots = list(slot ="character"))
> > setClass("b", slots = list(slot ="character"))
> > setClassUnion("xy", c("x", "y"))
> > setClassUnion("ab", c("a", "b"))
> > setClassUnion("xyab", c("xy", "ab"))
> > setGeneric("f", function(object, ...)
standardGeneric("f"))
> > setMethod("f", "xyab", function(object, ...)
print("hi!"))
> > ## print's "hi!" as expected
> > f(new("a"))
> >
> > I have also posted to stack overflow here:
> >
https://stackoverflow.com/questions/60264786/r-s4-class-union-of-class-unions?noredirect=1#comment106627883_60264786,
> > (the example in this note removes devtools to make the environment
> > cleaner).
> >
> > Interestingly, the issue only seems to arise when there are > 1
layer
> > of the class union. E.g. if I were to setMethod on "ab"
instead of
> > "xyab", method dispatch would work as expected. I am not
posting a bug
> > yet as it is still unclear to me if I am doing something incorrect.
> >
> > My sessionInfo() is :
> >
> > R version 3.6.2 (2019-12-12)
> > Platform: x86_64-pc-linux-gnu (64-bit)
> > Running under: Ubuntu 18.04.3 LTS
> >
> > Matrix products: default
> > BLAS:   /usr/local/lib/R/lib/libRblas.so
> > LAPACK: /usr/local/lib/R/lib/libRlapack.so
> >
> > locale:
> >   [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C
> >   [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8
> >   [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8
> >   [7] LC_PAPER=en_US.UTF-8       LC_NAME=C
> >   [9] LC_ADDRESS=C               LC_TELEPHONE=C
> > [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
> >
> > attached base packages:
> > [1] stats     graphics  grDevices utils     datasets  methods   base
> >
> > other attached packages:
> > [1] anRpackage_1.0
> >
> > loaded via a namespace (and not attached):
> > [1] compiler_3.6.2 tools_3.6.2
> >
> > Thanks in advance for the help!
> >
> >       [[alternative HTML version deleted]]
> >
> > ______________________________________________
> > R-devel at r-project.org mailing list
> > https://stat.ethz.ch/mailman/listinfo/r-devel
>
> ______________________________________________
> R-devel at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-devel


-- 
Michael Lawrence
Senior Scientist, Bioinformatics and Computational Biology
Genentech, A Member of the Roche Group
Office +1 (650) 225-7760
michafla at gene.com

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