[Bioc-devel] Biobase/IRanges annotation maksing

Wolfgang Huber <huber at ebi.ac.uk> writes:
Hi

of course there is no fundamental reason why the same name should not
be used for different things in different packages, and in many
instances this is the most reasonable solution. However, I think the
user-friendliness of the set of Bioconductor packages would be
improved if authors tried to keep such instances to a minimum.

Since there is considerable overlap and collaboration between the
authors of Biobase and IRange I am optimistic that a (perhaps less
modular but) more integrated solution could be found.

Currently, the generic function Biobase::annotation has exactly one
method, for signature "eSet", and the generic function
IRanges::annotation has exactly one method, for signature
"AnnotatedList". I.e. although they are generic functions in the
S4-technical sense, neither is generic in the common sense of the
word. I think it could be a goal for us that the concepts "S4" and
Hi Wolfgang --

Not exactly sure what you're getting at here (which doesn't bode well
for common sense on my part, I guess); I read this as saying these
functions might be 'regular', and not generic at all. But as you know

* Methods are not restricted to definition in the package of the
generic. So there are two methods on Biobase::annotation after
library(GSEABase), three after library(affyPLM), etc.

* Generics provide type checking that is useful even when there is a
single method (e.g., Biobase::annotation does not operate on, say, a
data.frame).

* Generics help to define an API (e.g., Biobase::annotation's single
method operates on 4 different classes defined in Biobase). The API
can be discovered programmatically, modulo the quirks of showMethod
(the 'where' argument can be useful under the current regime).

* Two identically named regular functions would conflict in the same
way, except perhaps without notifying the user.

Also worth reiterating that the example I mentioned pointed to a bug
(relying on user search path for function discovery) that has been
resolved through use of a name space and 'imports'. 

End users still have to contend with the competing functions (using
Biobase::annotation to disambiguate). This is unfortunate and perhaps
amenable to common sense, but independent of S4 / generics.

Martin
"common sense" be not opposed to each other.

Best wishes
      Wolfgang

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

Martin Morgan wrote:
Laurent Gatto <l.gatto at dnavision.be> writes:

Dear Bioc developeRs,

I noted recently that Biobase's 'annotation' and 'annotation<-'
objects are masked by IRanges. Now calling annotation(AffyBatch),
of annotation(ExpressionSet) throws an 'unable to find an inherited
method for function "annotation", for signature "AffyBatch"' error.
Some of my functions fail because they rely on functions that call
annotation(AffyBatch). 

My questions are (1) is this the expected behaviour and if yes (2)
how am I and/or upstream maintainers supposed to elegantly deal
with it?
Hi Laurent -- I just came across this issue myself -- package A
failed
because it called a function in package B which had a dependency on
package C which, due to changes in package D, now attached IRanges to
the search path. Package B then found IRange::annotation on the search
path, instead of Biobase::annotation.
The solution was easy, in the end -- add
  importMethodsFrom(Biobase, annotation)
to the NAMESPACE of package B, and move Biobase from 'Depends:' to
'Imports:' in package B, which is definitely the Right Thing To Do. It
doesn't matter now that IRanges is on the user search path, package B
always gets the function it wants.
The solution is less elegant for a function that is not in a name
space, e.g., because the user is writing it in the global environment,
as in your example below. Then the solution is to use
  Biobase::annotation(eset)
in place of annotation(eset).
There might be additional technical solutions that Biobase / IRanges
/
Biostrings package authors can explore for this particular case...
Martin

Illustrative code and sessionInfo are given below.

I hope that I am not missing anything obvious here.

Thank you in advance.

Laurent

-- R code ---------------------------------------
source("http://bioconductor.org/biocLite.R")
update.packages(rep=biocinstallRepos(), ask=FALSE)
library(affydata)
Loading required package: affy
Loading required package: Biobase

Welcome to Bioconductor

  Vignettes contain introductory material. To view, type
  'openVignette()'. To cite Bioconductor, see
  'citation("Biobase")' and for packages 'citation(pkgname)'.

data(Dilution)
annotation(Dilution)
[1] "hgu95av2"
library(IRanges)
Attaching package: 'IRanges'

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

	 annotation,
	 annotation<- 

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

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

annotation(Dilution)
Error in function (classes, fdef, mtable)  :   unable to find an
inherited method for function "annotation", for signature
"AffyBatch"
Biobase:::annotation(Dilution)
[1] "hgu95av2"
sessionInfo()
R version 2.9.0 Under development (unstable) (2009-02-12 r47911)
i686-pc-linux-gnu 

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

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

other attached packages:
[1] IRanges_1.1.38  affydata_1.11.3 affy_1.21.7     Biobase_2.3.10 

loaded via a namespace (and not attached):
[1] affyio_1.11.3        preprocessCore_1.5.3 tools_2.9.0

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Martin Morgan
Computational Biology / Fred Hutchinson Cancer Research Center
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[Bioc-devel] Biobase/IRanges annotation maksing

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