[Bioc-devel] cleaning up obsolete warnings

I'm getting a little tired of this one popping up:

In x %in% other :
    Starting with BioC 2.12, the behavior of %in% on GenomicRanges objects
   has changed to use *equality* instead of *overlap* for comparing
   elements between GenomicRanges objects 'x' and 'table'. Now 'x[i]' and
   'table[j]' are considered to match when they are equal (i.e. 'x[i] ==
   table[j]'), instead of when they overlap. This new behavior is consistent
   with base::`%in%`(). If you need the old behavior, please use:

     query %over% subject

Now that even release is Bioc 2.13, can we remove it? And there might be
others.

Thanks,
Michael

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Great, thanks for updating. I legitimately wanted to use %in%, not %over%.

Michael


On Wed, Nov 6, 2013 at 10:59 AM, Herv? Pag?s <hpages at fhcrc.org
<mailto:hpages at fhcrc.org>> wrote:

    Hi Michael,


    On 11/05/2013 04:30 PM, Michael Lawrence wrote:

        I'm getting a little tired of this one popping up:

        In x %in% other :
             Starting with BioC 2.12, the behavior of %in% on
        GenomicRanges objects
            has changed to use *equality* instead of *overlap* for comparing
            elements between GenomicRanges objects 'x' and 'table'. Now
        'x[i]' and
            'table[j]' are considered to match when they are equal (i.e.
        'x[i] ==
            table[j]'), instead of when they overlap. This new behavior
        is consistent
            with base::`%in%`(). If you need the old behavior, please use:

              query %over% subject

        Now that even release is Bioc 2.13, can we remove it? And there
        might be
        others.


    If you use %over% you don't get the warning ;-)

    Anyway this is gone in BioC 2.14 as part of the normal process of
    removing features that were defunct in BioC 2.13.

    Cheers,
    H.



        Thanks,
        Michael

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