[Bioc-devel] seq*apply deprecation

[Hervé Pagès]

On 01/22/2014 08:15 PM, Michael Lawrence wrote:
> Sounds good. But who is "she"?

we would, she should, she would, we should... that's it! we should...
that's what I meant :-b

H.

>
>
> On Wed, Jan 22, 2014 at 3:48 PM, Hervé Pagès <hpages at fhcrc.org
> <mailto:hpages at fhcrc.org>> wrote:
>
>     On 01/22/2014 03:02 PM, Michael Lawrence wrote:
>
>
>
>
>         On Wed, Jan 22, 2014 at 1:29 PM, Hervé Pagès <hpages at fhcrc.org
>         <mailto:hpages at fhcrc.org>
>         <mailto:hpages at fhcrc.org <mailto:hpages at fhcrc.org>>> wrote:
>
>              Hi Michael,
>
>
>              On 01/12/2014 05:16 AM, Michael Lawrence wrote:
>
>                  Hi,
>
>
>                  It may be time to deprecate the seq*apply family of
>         functions,
>                  including
>                  seqapply, mseqapply, tseqapply, seqby and seqsplit.
>         These are
>                  ancient
>                  functions named in referece to the "Sequence" class,
>         now called
>                  "Vector".
>                  It would seem better for the user to write:
>         asList(lapply(...))
>                  instead of
>                  coming up with an alias for that. For readability, we
>         should
>                  probably
>                  export asList() as an alias for as(x, "List"), which I just
>                  cleaned up.
>
>
>              Sounds good to me.
>
>
>
>                  There is one caveat though: mseqapply has been particularly
>                  useful, because
>                  it delegates to mapply_List, which is smart enough to
>         handle any
>                  vector
>                  argument in "...". The mapply,List method of course
>         restricts
>                  everything to
>                  List. We should probably export mapply_List, probably
>         with a
>                  better name.
>                  Suggestions?
>
>
>              Why do we need all this?
>
>
>         Neat. Presumably due to this patch:
>
>         commit 42139699d91a34c401eedd36db6271__6a607d0b06
>         Author: maechler <maechler at 00db46b3-68df-0310-__9c12-caf00c1e9a41>
>         Date:   Wed Nov 28 10:31:42 2012 +0000
>
>               mapply(F, <S4>) now works thanks to a version of Herve's patch
>
>         We should do away with mapply_List now that this is part of
>         released R.
>
>
>     Furthermore, maybe she should also remove the mapply() S4 generic from
>     the BiocGenerics package. It's not needed anymore. base::mapply() should
>     work out-of-the-box on any object for which length() and [[ are
>     implemented.
>
>     H.
>
>
>
>                 x <- RleList(11:14, 3:1)
>
>              Then:
>
>                 > IRanges:::mapply_List(____function(a, b) {a+b}, x, 10)
>
>                 [[1]]
>                 numeric-Rle of length 4 with 4 runs
>                   Lengths:  1  1  1  1
>                   Values : 21 22 23 24
>
>                 [[2]]
>                 numeric-Rle of length 3 with 3 runs
>                   Lengths:  1  1  1
>                   Values : 13 12 11
>
>              But also:
>
>                 > base::mapply(function(a, b) {a+b}, x, 10)
>                 [[1]]
>                 numeric-Rle of length 4 with 4 runs
>                   Lengths:  1  1  1  1
>                   Values : 21 22 23 24
>
>                 [[2]]
>                 numeric-Rle of length 3 with 3 runs
>                   Lengths:  1  1  1
>                   Values : 13 12 11
>
>              What am I missing?
>
>              Thanks,
>              H.
>
>
>                  Michael
>
>                           [[alternative HTML version deleted]]
>
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>
>
>              --
>              Hervé Pagès
>
>              Program in Computational Biology
>              Division of Public Health Sciences
>              Fred Hutchinson Cancer Research Center
>              1100 Fairview Ave. N, M1-B514
>              P.O. Box 19024
>              Seattle, WA 98109-1024
>
>              E-mail: hpages at fhcrc.org <mailto:hpages at fhcrc.org>
>         <mailto:hpages at fhcrc.org <mailto:hpages at fhcrc.org>>
>              Phone: (206) 667-5791 <tel:%28206%29%20667-5791>
>         <tel:%28206%29%20667-5791>
>              Fax: (206) 667-1319 <tel:%28206%29%20667-1319>
>         <tel:%28206%29%20667-1319>
>
>
>
>     --
>     Hervé Pagès
>
>     Program in Computational Biology
>     Division of Public Health Sciences
>     Fred Hutchinson Cancer Research Center
>     1100 Fairview Ave. N, M1-B514
>     P.O. Box 19024
>     Seattle, WA 98109-1024
>
>     E-mail: hpages at fhcrc.org <mailto:hpages at fhcrc.org>
>     Phone: (206) 667-5791 <tel:%28206%29%20667-5791>
>     Fax: (206) 667-1319 <tel:%28206%29%20667-1319>
>
>

-- 
Hervé Pagès

Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N, M1-B514
P.O. Box 19024
Seattle, WA 98109-1024

E-mail: hpages at fhcrc.org
Phone:  (206) 667-5791
Fax:    (206) 667-1319