[Rd] Unexpected side effect of the ":::" operator on the value of isGeneric

From: Wolfgang Huber <huber_at_ebi.ac.uk>
Date: Wed, 25 Feb 2009 18:15:03 +0000


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

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