[Rd] S4 method dispatch sometimes leads to incorrect when object loaded from file?
maechler at lynne.stat.math.ethz.ch
Tue May 12 14:31:11 CEST 2015
>>>>> 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
> FWIW the sent mail was a multi-part MIME with the header on the package part
> Content-Type: application/gzip;
> Content-Transfer-Encoding: base64
> Content-Disposition: attachment;
> 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("B", contains="A")
>> setMethod("show", "A", function(object) cat("A\n"))
>> setMethod("show", "B", function(object) cat("B\n"))
>> with NAMESPACE
>> exportClasses(A, B)
>> This creates the object and illustrated expected behavior
>> ~/tmp$ R --vanilla --slave -e "library(PkgA); b = new('B'); save(b,
>> file='b.Rda'); b"
>> Loading PkgA before the object leads to correct dispatch
>> ~/tmp$ R --vanilla --slave -e "library(PkgA); load(file='b.Rda'); b"
>> but loading the object without first loading PkgA leads to dispatch to
>> ~/tmp$ R --vanilla --slave -e "load(file='b.Rda'); b"
>> Loading required package: PkgA
>> Martin Morgan
> Computational Biology / Fred Hutchinson Cancer Research Center
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