R devel - Feb 2009 - Unexpected side effect of the ":::" operator on the value of isGeneric

Hi,

when running the following on a fresh R,


  library("IRanges")
  annotation
  showMethods("annotation")
  Biobase:::annotation
  showMethods("annotation")


I get (see the "^^^^^" marked output at the bottom):

> library("IRanges")
Carico il pacchetto richiesto: 'IRanges'

	The following object(s) are masked from package:base :

	 cbind,
	 order,
	 pmax,
	 pmax.int,
	 pmin,
	 pmin.int,
	 rbind,
	 rep.int,
	 table
> annotation
standardGeneric for "annotation" defined from package
"IRanges"

function (x, ...)
standardGeneric("annotation")
<environment: 0x1a302b0>
Methods may be defined for arguments: x
Use  showMethods("annotation")  for currently available ones.
> showMethods("annotation")
Function: annotation (package IRanges)
x="AnnotatedList"
> Biobase:::annotation
standardGeneric for "annotation" defined from package
"Biobase"

function (object)
standardGeneric("annotation")
<environment: 0x205cee0>
Methods may be defined for arguments: object
Use  showMethods("annotation")  for currently available ones.
> showMethods("annotation")
Function "annotation":
 <not a generic function>
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^


It seems that the value of isGeneric("annotation"), when it is called
within showMethods, is FALSE, while it is TRUE when called outside.


> sessionInfo()
R version 2.9.0 Under development (unstable) (2009-02-25 r48007)
x86_64-unknown-linux-gnu

locale:
LC_CTYPE=it_IT.UTF-8;LC_NUMERIC=C;LC_TIME=it_IT.UTF-8;LC_COLLATE=it_IT.UTF-8;LC_MONETARY=C;LC_MESSAGES=it_IT.UTF-8;LC_PAPER=it_IT.UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=it_IT.UTF-8;LC_IDENTIFICATION=C

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

other attached packages:
[1] IRanges_1.1.40

loaded via a namespace (and not attached):
[1] Biobase_2.3.10



Best wishes
 Wolfgang

------------------------------------------------------------------
Wolfgang Huber  EBI/EMBL  Cambridge UK  http://www.ebi.ac.uk/huber

>>>>> "Wolfi" == Wolfgang Huber <huber at
ebi.ac.uk>
>>>>>     on Wed, 25 Feb 2009 18:15:03 +0000 writes:
    Wolfi> Hi,
    Wolfi> when running the following on a fresh R,


    Wolfi> library("IRanges")
    Wolfi> annotation
    Wolfi> showMethods("annotation")
    Wolfi> Biobase:::annotation
    Wolfi> showMethods("annotation")


    Wolfi> I get (see the "^^^^^" marked output at the bottom):


    >> library("IRanges")

    Wolfi> Carico il pacchetto richiesto: 'IRanges'

    Wolfi> The following object(s) are masked from package:base :

    Wolfi> cbind,
    Wolfi> order,
    Wolfi> pmax,
    Wolfi> pmax.int,
    Wolfi> pmin,
    Wolfi> pmin.int,
    Wolfi> rbind,
    Wolfi> rep.int,
    Wolfi> table

    >> annotation
    Wolfi> standardGeneric for "annotation" defined from package
"IRanges"

    Wolfi> function (x, ...)
    Wolfi> standardGeneric("annotation")
    Wolfi> <environment: 0x1a302b0>
    Wolfi> Methods may be defined for arguments: x
    Wolfi> Use  showMethods("annotation")  for currently available
ones.

    >> showMethods("annotation")
    Wolfi> Function: annotation (package IRanges)
    Wolfi> x="AnnotatedList"

    >> Biobase:::annotation
    Wolfi> standardGeneric for "annotation" defined from package
"Biobase"

    Wolfi> function (object)
    Wolfi> standardGeneric("annotation")
    Wolfi> <environment: 0x205cee0>
    Wolfi> Methods may be defined for arguments: object
    Wolfi> Use  showMethods("annotation")  for currently available
ones.

    >> showMethods("annotation")

    Wolfi> Function "annotation":
    Wolfi> <not a generic function>
    Wolfi> ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^


    Wolfi> It seems that the value of isGeneric("annotation"), when
it is called
    Wolfi> within showMethods, is FALSE, while it is TRUE when called
outside.

Hi Wolfgang,

I have looked at the NAMESPACE files of the two packages  
Biobase and IRanges, (the Bioconductor development version in SVN),
and I think the problem might result from the fact
that IRanges  does export the  annotation  generic, does not 
exportMethods( ...  annotation ...).

OTOH,  Biobase  exportMethods(  annotation ) only [but not the generic].
and then both packages do not at all mention each other,
neither in DESCRIPTION nor NAMESPACE.

Either you are talking about conceptually the same generic
annotation(); in that case one package needs to import*() it
from the other, 
or then you have two completely different animals, but then
(masking) problems are unavoidable 
-- in spite of the fact that I vaguely remember that some
   Bioconductor developers repeatedly emphasize that these
   problems are not problems for them
 
Martin

    >> sessionInfo()
    Wolfi> R version 2.9.0 Under development (unstable) (2009-02-25 r48007)
    Wolfi> x86_64-unknown-linux-gnu

    Wolfi> locale:
    Wolfi>
LC_CTYPE=it_IT.UTF-8;LC_NUMERIC=C;LC_TIME=it_IT.UTF-8;LC_COLLATE=it_IT.UTF-8;LC_MONETARY=C;LC_MESSAGES=it_IT.UTF-8;LC_PAPER=it_IT.UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=it_IT.UTF-8;LC_IDENTIFICATION=C

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

    Wolfi> other attached packages:
    Wolfi> [1] IRanges_1.1.40

    Wolfi> loaded via a namespace (and not attached):
    Wolfi> [1] Biobase_2.3.10



    Wolfi> Best wishes
    Wolfi> Wolfgang

    Wolfi> ------------------------------------------------------------------
    Wolfi> Wolfgang Huber  EBI/EMBL  Cambridge UK  http://www.ebi.ac.uk/huber

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