[Bioc-devel] Identical methods in two packages

[Laurent Gatto]

Hi Herve,

I understand that there is a clash between the two identical methods.
Both packages seem to have good reasons to implement their own
`Ontology,character`. Such clashes are relatively frequent.

My issue really is that when unloading AnnotationDbi's namespace,
`Ontology,character` is removed from the methods' dispatch table, and
thus becomes unavailable to rols users. What really should happen is
that when AnnotationDbi's namespace is unloaded, the method in rols
works again, similar to what happens for function.

Is this something that is worth raising on R-devel?

Best wishes,

Laurent

On 12 September 2017 16:35, Hervé Pagès wrote:

> Hi Laurent,
>
> The 2 Ontology,character methods defined in AnnotationDbi and
> rols do very different things. The 1st one expects a vector of
> GO IDs and returns the GO sub-ontologies that they belong to:
>
>  > Ontology(c("GO:0000009", "GO:0000012", "GO:0000006"))
> GO:0000009 GO:0000012 GO:0000006
>        "MF"       "BP"       "MF"
>
> The 2nd one takes the name of an ontology and returns a
> summary/description of it:
>
>  > Ontology("efo")
> Ontology: Experimental Factor Ontology (efo)
>    The Experimental Factor Ontology (EFO) provides a systematic
>    description of many experimental variables available in EBI databases,
>    and for external projects such as the NHGRI GWAS catalogue. It combines
>    parts of several biological ontologies, such as anatomy, disease and
>    chemical compounds. The scope of EFO is to support the annotation,
>    analysis and visualization of data handled by many groups at the EBI
>    and as the core ontology for OpenTargets.org
>     Loaded: 2017-08-16 Updated: 2017-09-12 Version: 2.87
>     20063 terms  297 properties  0 individuals
>
> So the problem here is that even though now we have a single Ontology
> generic in BiocGenerics for the 2 methods, we haven't really talked
> about semantics i.e. what Ontology() is actually supposed to do. Having
> a generic without some sort of contract that methods are supposed to
> honor is like having a generic called doSomething() and have people
> start writing a bunch of methods for it ;-)
>
> The right thing to do here would be to use 2 different generics with
> 2 different names e.g. Ontology() in AnnotationDbi and ontologySummary()
> in rols. Or GOontology() in AnnotationDbi and Ontology() in rols.
>
> If we want to keep the current situation and make it work properly, we
> could implement the following hack: have rols depend on AnnotationDbi
> and make the method in rols work on GO ids. The code would just need
> to detect whether the strings in the supplied character vector start
> with the "GO:" prefix and delegate to the code in AnnotationDbi (this
> means that rols would need to be able to call that code so the body
> of the AnnotationDbi method would need to be moved to an helper
> function). An ugly hack though!
>
> What do you want to do?
>
> H.
>
> On 09/03/2017 07:59 AM, Laurent Gatto wrote:
>>
>> Dear all,
>>
>> This is a follow up to a previous email regarding the Ontology generic
>> function, that is now in the BiocGenerics package. It seems that my
>> problem was not only that both rols and AnnotationDbi defined the same
>> generic, but they also both defined Ontology,character.
>>
>>> library("rols")
>>
>> This is 'rols' version 2.5.2
>>
>>> Ontology("go")
>> Ontology: Gene Ontology (go)
>>    An ontology for describing the function of genes and gene products
>>     Loaded: 2017-08-31 Updated: 2017-09-01 Version: 2017-08-30
>>     49075 terms  67 properties  0 individuals
>>> Ontology
>> standardGeneric for "Ontology" defined from package "BiocGenerics"
>>
>> function (object)
>> standardGeneric("Ontology")
>> <environment:0x2da7cf0>
>> Methods may be defined for arguments: object
>> Use  showMethods("Ontology")  for currently available ones.
>>> showMethods("Ontology")
>> Function: Ontology (package BiocGenerics)
>> object="character"
>> object="Ontology"
>>
>>> getMethod("Ontology", "character")
>> Method Definition:
>>
>> function (object)
>> {
>>      url <- ontologyUrl(object)
>>      x <- GET(url)
>>      stop_for_status(x)
>>      cx <- content(x)
>>      makeOntology(cx)
>> }
>> <environment:namespace:rols>
>>
>> Signatures:
>>          object
>> target  "character"
>> defined "character"
>>
>> Until now, everything works as expected. The trouble begins when loading
>> AnnotationDbi.
>>
>>> suppressPackageStartupMessages(library("AnnotationDbi"))
>>> showMethods("Ontology")
>> Function: Ontology (package BiocGenerics)
>> object="character"
>> object="GOTerms"
>> object="GOTermsAnnDbBimap"
>> object="Ontology"
>>
>>> getMethod("Ontology", "character")
>> Method Definition:
>>
>> function (object)
>> .GOid2go_termField(object, "ontology")
>> <environment:namespace:AnnotationDbi>
>>
>> Signatures:
>>          object
>> target  "character"
>> defined "character"
>>> Ontology("go")
>> Loading required package: GO.db
>>
>> <NA>
>>    NA
>>
>> Ok, fair enough, these things happen. The issue is to recover
>> Ontology,character from rols. If I unload AnnotationDbi's namespace (I
>> also neet to unload GO.db, that got loaded automatically), there is no
>> Ontology,character anymore.
>>
>>> unloadNamespace("GO.db")
>>> unloadNamespace("AnnotationDbi")
>>> showMethods("Ontology")
>> Function: Ontology (package BiocGenerics)
>> object="Ontology"
>>
>>> Ontology("go")
>> Error in (function (classes, fdef, mtable)  :
>>    unable to find an inherited method for function ‘Ontology’ for signature ‘"character"’
>>> rols::Ontology("go")
>> Error in (function (classes, fdef, mtable)  :
>>    unable to find an inherited method for function ‘Ontology’ for signature ‘"character"’
>>
>>> getMethod("Ontology", "character")
>> Error in getMethod("Ontology", "character") :
>>    no method found for function 'Ontology' and signature character
>>> getMethod("Ontology", "character", where = "package:rols")
>> Method Definition:
>>
>> function (object)
>> {
>>      url <- ontologyUrl(object)
>>      x <- GET(url)
>>      stop_for_status(x)
>>      cx <- content(x)
>>      makeOntology(cx)
>> }
>> <environment:namespace:rols>
>>
>> Signatures:
>>          object
>> target  "character"
>> defined "character"
>>
>>
>> It is really the expected behaviour? How could I recover rols'
>> Ontology,character?
>>
>> Thank you in advance.
>>
>> Best wishes,
>>
>> Laurent
>>


-- 
Laurent Gatto | @lgatt0
http://cpu.sysbiol.cam.ac.uk/
http://lgatto.github.io/