[Bioc-devel] as.list of a GRanges

[Bernat Gel]

Hi Hervé and others,

Thanks for the responses.

I woudn't call as.list() of a GRanges an "obscure behaviour" but more a 
"works as expected, even if not clearly documented" behaviour.

In any case I can change the code to as(gr, "GRangesList") as suggested.

Thanks again for the responses and discussion :)

Bernat


*Bernat Gel Moreno*
Bioinformatician

Hereditary Cancer Program
Program of Predictive and Personalized Medicine of Cancer (PMPPC)
Germans Trias i Pujol Research Institute (IGTP)

Campus Can Ruti
Carretera de Can Ruti, Camí de les Escoles s/n
08916 Badalona, Barcelona, Spain

Tel: (+34) 93 554 3068
Fax: (+34) 93 497 8654
08916 Badalona, Barcelona, Spain
bgel at igtp.cat <mailto:bgel at igtp.cat>
www.germanstrias.org <http://www.germanstrias.org/>

<http://www.germanstrias.org/>







El 02/15/2018 a las 11:19 PM, Hervé Pagès escribió:
> On 02/15/2018 01:57 PM, Michael Lawrence wrote:
>>
>>
>> On Thu, Feb 15, 2018 at 1:45 PM, Hervé Pagès <hpages at fredhutch.org 
>> <mailto:hpages at fredhutch.org>> wrote:
>>
>>     On 02/15/2018 11:53 AM, Cook, Malcolm wrote:
>>
>>         Hi,
>>
>>         Can I ask, is this change under discussion in current release or
>>         so far in Bioconductor devel only (my assumption)?
>>
>>
>>     Bioconductor devel only.
>>
>>
>>            > On 02/15/2018 08:37 AM, Michael Lawrence wrote:
>>            > > So is as.list() no longer supported for GRanges objects?
>>         I have found it
>>            > > useful in places.
>>            >
>>            > Very few places. I found a dozen of them in the entire
>>         software repo.
>>
>>         However there are probably more in the wild...
>>
>>
>>     What as.list() was doing on a GRanges object was not documented. 
>> Relying
>>     on some kind of obscure undocumented feature is never a good idea.
>>
>>
>> There's just too much that is documented implicitly through inherited 
>> behaviors, or where we say things like "this data structure behaves 
>> as one would expect given base R". It's not fair to claim that those 
>> features are undocumented. Our documentation is not complete enough 
>> to use it as an excuse.
>
> It's not fair to suggest that this is a widely used feature either.
>
> I've identified all the places in the 1500 software packages where
> this was used, and, as I said, there were very few places. BTW I
> fixed most of them but my plan is to fix all of them. Some of the
> code that is outside the Bioc package corpus might be affected but
> it's fair to assume that this will be a very rare occurence. This can
> be mitigated by temporary restoring as.list() on GRanges, with a
> deprecation message, and wait 1 more devel cycle to replace it with
> the new behavior. I chose to disable it for now, on purpose, so I can
> identify packages that break (the build report is a great tool for
> that) and fix them.
>
> I'm not using the fact that as.list() on a GRanges is not documented
> as an excuse for anything. Only to help those with concerns to
> relativize and relax.
>
> H.
>
>>
>>
>>            > Now you should use as.list(as(gr, "GRangesList")) instead.
>>            > as.list() was behaving inconsistently on IRanges and
>>         GRanges objects,
>>            > which is blocking new developments. It will come back with
>>         a consistent
>>            > behavior. More generally speaking IRanges and GRanges will
>>         behave
>>            > consistently as far as their "list interpretation" is
>>         concerned.
>>
>>         Can we please be assured to be reminded of this prominently in
>>         release notes?
>>
>>
>>     The changes will be announced and described on this list and in the
>>     NEWS files of the IRanges and GenomicRanges packages.
>>
>>     H.
>>
>>
>>         Thanks!
>>
>>         ~malcolm
>>
>>
>>     --     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 fredhutch.org <mailto:hpages at fredhutch.org>
>>     Phone: (206) 667-5791 <tel:%28206%29%20667-5791>
>>     Fax: (206) 667-1319 <tel:%28206%29%20667-1319>
>>
>>
>