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

James W. MacDonald 
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
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
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?

Best,

Jim

Thread (2 messages)

James W. MacDonald Warnings from ls() in AnnotationDbi Apr 24 Martin Morgan Warnings from ls() in AnnotationDbi Apr 24