[Bioc-devel] as.list of a GRanges

[Nathan Sheffield]

For what it's worth, my package (LOLA) was one that used as.list on a 
GRanges or GRangesList, and those calls were broken by changes to devel. 
Since I was also pushing changes at the time, I assumed the devel build 
errors were due to my updates -- I spent quite a bit of time trying to 
figure out what was wrong before I realized this breakage was not caused 
by my updates, but by upstream changes in GRanges...eventually I tracked 
down errors to as.list (and ultimately, found other errors, which we 
discussed earlier on this list), but my conclusion from this was that, 
from my perspective, using the deployed bioc devel as a way to test for 
what refactoring will break doesn't seem like the ideal way to go -- I 
assumed that generally, other package changes wouldn't typically be 
pushed that would break my package's build, so it devalued the role of 
the dev builds and reduced my confidence in using that (now when I see 
error I may assume it's something else, and wait a few days, instead of 
diving right in to try to solve the problem).

I like the idea of temporarily restoring as.list with a deprecation 
message -- also, as a general development philosophy going forward in 
terms of testing on devel. This would have saved me a lot of time 
troubleshooting in this instance.

Just my 2 cents.

-Nathan


On 02/16/2018 02:57 AM, Bernat Gel wrote:
> 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*
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>
> <http://www.germanstrias.org/>
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>
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>
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>
> 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>
>>>
>>>
>>
>
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