[Bioc-devel] Warnings from ls() in AnnotationDbi

[Martin Morgan]

On 04/24/2015 09:07 AM, James W. MacDonald wrote:
> A poster on the support site reported some warnings issued when running
> hyperGTest() from GOstats. I tracked this down to the ls() function from
> AnnotationDbi, when it dispatches on AnnDbBimap objects. The method is:
>
> setMethod("ls", signature(name="Bimap"),
>      function(name, pos, envir, all.names, pattern){
>          if (!missing(pos))
>            warning("ignoring 'pos' argument")
>          if (!missing(envir))
>            warning("ignoring 'envir' argument")
>          if (!missing(all.names))
>            warning("ignoring 'all.names' argument")
>          .ls(name, pos, envir, all.names, pattern)
>      }
> )
>
> And as noted, everything but 'name' is ignored in .ls().
>
> This seemingly hasn't changed in years. In R-3.1.1 the method appears as
>
>> showMethods(ls, class = "AnnDbBimap", includeDefs = T)
> Function: ls (package base)
> name="AnnDbBimap"
> function (name, pos = -1L, envir = as.environment(pos), all.names = FALSE,
>      pattern)
> {
>      if (!missing(pos))
>          warning("ignoring 'pos' argument")
>      if (!missing(envir))
>          warning("ignoring 'envir' argument")
>      if (!missing(all.names))
>          warning("ignoring 'all.names' argument")
>      .ls(name, pos, envir, all.names, pattern)
> }
>
> And now in R-3.2.0, the method appears as
>
>> showMethods(ls, class = "Bimap", includeDefs = TRUE)
> Function: ls (package base)
> name="Bimap"
> function (name, pos = -1L, envir = as.environment(pos), all.names = FALSE,
>      pattern, sorted = TRUE)
> {
>      .local <- function (name, pos, envir, all.names, pattern)
>      {
>          if (!missing(pos))
>              warning("ignoring 'pos' argument")
>          if (!missing(envir))
>              warning("ignoring 'envir' argument")
>          if (!missing(all.names))
>              warning("ignoring 'all.names' argument")
>          .ls(name, pos, envir, all.names, pattern)
>      }
>      .local(name, pos, envir, all.names, pattern)
> }
>
> Where everything gets wrapped in a call to .local(). Prior to this, we
> never saw the warnings, but now we do:
>
>   z <- ls(annotate:::getAnnMap("BPPARENTS", chip = "GO"))
> Warning messages:
> 1: In .local(name, pos, envir, all.names, pattern) :
>    ignoring 'pos' argument
> 2: In .local(name, pos, envir, all.names, pattern) :
>    ignoring 'envir' argument
> 3: In .local(name, pos, envir, all.names, pattern) :
>    ignoring 'all.names' argument
>
> This is going to be a consistent issue going forward, so should all those
> warnings be stripped out of the method for ls() in AnnotationDbi?

I changed the signature of the method to match the signature of the generic, so 
the missing-ness of the arguments, and hence warnings, are assessed appropriately.

In devel, I supported sort=..., whereas in release it is ignored.

Thanks for pointing this out.

Martin

>
> Best,
>
> Jim
>
>
>
>
>


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