[Rd] Possible Regression in setClassUnion between 3.5.0 and 3.6.0

[Michael Lawrence]

They're stabilizing. All changes are internal and addressing bugs; not
user-facing.

On Tue, Feb 25, 2020 at 5:34 PM Robert Harlow <rharlow86 using gmail.com> wrote:
>
> Okay - that makes sense and thanks for looking into this! As an aside, from R-devel's perspective would you say methods are stabilizing again or do you foresee a lot of changes coming in the 4.* series?
>
> On Tue, Feb 25, 2020 at 3:39 PM Michael Lawrence via R-devel <r-devel using r-project.org> wrote:
>>
>> This seems to work as expected (returning "hi!") in R-devel, but there
>> have been so many destabilizing changes to methods that it would be
>> tough to port this to release. Probably should just wait for 4.0.
>>
>> Michael
>>
>> On Tue, Feb 18, 2020 at 8:00 PM Michael Lawrence <michafla using gene.com> wrote:
>> >
>> > Thanks, I'll look into it.
>> >
>> > On Tue, Feb 18, 2020 at 8:32 AM Ezra Tucker <ezztucker using 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 using r-project.org mailing list
>> > > > https://stat.ethz.ch/mailman/listinfo/r-devel
>> > >
>> > > ______________________________________________
>> > > R-devel using 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 using gene.com
>> >
>> > Join Genentech on LinkedIn | Twitter | Facebook | Instagram | YouTube
>>
>>
>>
>> --
>> Michael Lawrence
>> Senior Scientist, Bioinformatics and Computational Biology
>> Genentech, A Member of the Roche Group
>> Office +1 (650) 225-7760
>> michafla using gene.com
>>
>> Join Genentech on LinkedIn | Twitter | Facebook | Instagram | YouTube
>>
>> ______________________________________________
>> R-devel using 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 using gene.com

Join Genentech on LinkedIn | Twitter | Facebook | Instagram | YouTube