R devel - May 2015 - S4 method dispatch sometimes leads to incorrect when object loaded from file?

Loading an S4 object from a file without first loading the library sometimes (?,
the example below and actual example involves a virtual base class and the show 
generic) leads to incorrect dispatch (to the base class method).

The attached package reproduces the problem. It has

setClass("A")
setClass("B", contains="A")
setMethod("show", "A", function(object)
cat("A\n"))
setMethod("show", "B", function(object)
cat("B\n"))

with NAMESPACE

import(methods)
exportClasses(A, B)
exportMethods(show)

This creates the object and illustrated expected behavior

   ~/tmp$ R --vanilla --slave -e "library(PkgA); b = new('B');
save(b,
file='b.Rda'); b"
   B

Loading PkgA before the object leads to correct dispatch

   ~/tmp$ R --vanilla --slave -e "library(PkgA);
load(file='b.Rda'); b"
   B

but loading the object without first loading PkgA leads to dispatch to 
show,A-method.

   ~/tmp$ R --vanilla --slave -e "load(file='b.Rda'); b"
   Loading required package: PkgA
   A

Martin Morgan
-- 
Computational Biology / Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N.
PO Box 19024 Seattle, WA 98109

Location: Arnold Building M1 B861
Phone: (206) 667-2793

On 05/10/2015 08:19 AM, Martin Morgan wrote:
> Loading an S4 object from a file without first loading the library
sometimes (?,
> the example below and actual example involves a virtual base class and the
show
> generic) leads to incorrect dispatch (to the base class method).
>
> The attached package reproduces the problem. It has
The package was attached but stripped; a version is at

   https://github.com/mtmorgan/PkgA

FWIW the sent mail was a multi-part MIME with the header on the package part

Content-Type: application/gzip;
  name="PkgA.tar.gz"
Content-Transfer-Encoding: base64
Content-Disposition: attachment;
  filename="PkgA.tar.gz"

 From http://www.r-project.org/mail.html#instructions "we allow
application/pdf,
application/postscript, and image/png (and x-tar and gzip on R-devel)" so I
thought that this mime type would not be stripped?

Martin Morgan
>
> setClass("A")
> setClass("B", contains="A")
> setMethod("show", "A", function(object)
cat("A\n"))
> setMethod("show", "B", function(object)
cat("B\n"))
>
> with NAMESPACE
>
> import(methods)
> exportClasses(A, B)
> exportMethods(show)
>
> This creates the object and illustrated expected behavior
>
>    ~/tmp$ R --vanilla --slave -e "library(PkgA); b = new('B');
save(b,
> file='b.Rda'); b"
>    B
>
> Loading PkgA before the object leads to correct dispatch
>
>    ~/tmp$ R --vanilla --slave -e "library(PkgA);
load(file='b.Rda'); b"
>    B
>
> but loading the object without first loading PkgA leads to dispatch to
> show,A-method.
>
>    ~/tmp$ R --vanilla --slave -e "load(file='b.Rda'); b"
>    Loading required package: PkgA
>    A
>
> Martin Morgan

-- 
Computational Biology / Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N.
PO Box 19024 Seattle, WA 98109

Location: Arnold Building M1 B861
Phone: (206) 667-2793

>>>>> Martin Morgan <mtmorgan at fredhutch.org>
>>>>>     on Mon, 11 May 2015 10:18:07 -0700 writes:
    > On 05/10/2015 08:19 AM, Martin Morgan wrote:
    >> Loading an S4 object from a file without first loading the library
sometimes (?,
    >> the example below and actual example involves a virtual base class
and the show
    >> generic) leads to incorrect dispatch (to the base class method).

"Of course", this is not as desired.

Other code automatically does try and typically succeed to load the package
(yes "package" ! ;-)) when 'needed', right,  so  show() is an
exception here, no ?


    >> The attached package reproduces the problem. It has

    > The package was attached but stripped; a version is at

    > https://github.com/mtmorgan/PkgA

    > FWIW the sent mail was a multi-part MIME with the header on the package
part

    > Content-Type: application/gzip;
    > name="PkgA.tar.gz"
    > Content-Transfer-Encoding: base64
    > Content-Disposition: attachment;
    > filename="PkgA.tar.gz"

    > From http://www.r-project.org/mail.html#instructions "we allow
application/pdf,
    > application/postscript, and image/png (and x-tar and gzip on
R-devel)" so I
    > thought that this mime type would not be stripped?

You were alright in your assumptions -- but unfortunately, the
accepted type has been  application/x-gzip instead of .../gzip.
I now *have* added the 2nd one as well.

Sorry for that.
The other Martin M..

    > Martin Morgan

    >> 
    >> setClass("A")
    >> setClass("B", contains="A")
    >> setMethod("show", "A", function(object)
cat("A\n"))
    >> setMethod("show", "B", function(object)
cat("B\n"))
    >> 
    >> with NAMESPACE
    >> 
    >> import(methods)
    >> exportClasses(A, B)
    >> exportMethods(show)
    >> 
    >> This creates the object and illustrated expected behavior
    >> 
    >> ~/tmp$ R --vanilla --slave -e "library(PkgA); b =
new('B'); save(b,
    >> file='b.Rda'); b"
    >> B
    >> 
    >> Loading PkgA before the object leads to correct dispatch
    >> 
    >> ~/tmp$ R --vanilla --slave -e "library(PkgA);
load(file='b.Rda'); b"
    >> B
    >> 
    >> but loading the object without first loading PkgA leads to dispatch
to
    >> show,A-method.
    >> 
    >> ~/tmp$ R --vanilla --slave -e "load(file='b.Rda');
b"
    >> Loading required package: PkgA
    >> A
    >> 
    >> Martin Morgan


    > -- 
    > Computational Biology / Fred Hutchinson Cancer Research Center
    > 1100 Fairview Ave. N.
    > PO Box 19024 Seattle, WA 98109

    > Location: Arnold Building M1 B861
    > Phone: (206) 667-2793

    > ______________________________________________
    > R-devel at r-project.org mailing list
    > https://stat.ethz.ch/mailman/listinfo/r-devel