On 05/12/2015 05:31 AM, Martin Maechler wrote:
Martin Morgan <mtmor...@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 ?
I added dim() methods, which also misbehave (differently)
setMethod("dim", "A", function(x) "A-dim")
setMethod("dim", "B", function(x) "B-dim")
~/tmp$ R --vanilla --slave -e "load('b.Rda'); dim(b)"
Loading required package: PkgA
NULL
~/tmp$ R --vanilla --slave -e "require('PkgA'); load('b.Rda'); dim(b)"
[1] "B-dim"
but sort of auto-heal (versus show, which is corrupted)
~/tmp$ R --vanilla --slave -e "load('b.Rda'); dim(b); dim(b)"
Loading required package: PkgA
NULL
[1] "B-dim"
~/tmp$ R --vanilla --slave -e "load('b.Rda'); b; b"
Loading required package: PkgA
A
A
>> 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
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--
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
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