[Bioc-devel] as.list of a GRanges

Michael Lawrence lawrence.michael at gene.com
Mon Feb 19 15:43:50 CET 2018 

On Mon, Feb 19, 2018 at 2:10 AM, Bernat Gel <bgel at igtp.cat> wrote:

> Hi Hervé,
>
> I completely agree with the goal of having the semantics of list-like
> operations standardised and documented to avoid surprises, and if to do so,
> the current use of as.list must be changed I'm pefectly ok with that. I had
> not seen the strange behaviour with IRanges,


Just want to point out that it's important to keep in mind that many of our
users never use IRanges directly, so consistency is not an absolute
requirement.

so I was not aware of the problem.
>
> In any case, thanks for fixing (and simplifying) karyoploteR. In
> retrospective I don't know why I didn't use simple vectorization! So, thanks
>
>
> 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 02/17/2018 a las 04:19 AM, Hervé Pagès escribió:
>
>> Hi Bernat,
>>
>> On 02/15/2018 11:57 PM, 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.
>>>
>>
>> Most users/developers will probably agree that as.list() worked
>> as expected on a GRanges object. But then they'll be surprised
>> and confused when they use it on an IRanges object and discover
>> that it does something completely different. The current effort
>> is to bring more consistency between GRanges and IRanges objects
>> and to have their list-like semantics aligned and documented so
>> there will be no more such surprise.
>>
>>
>>> In any case I can change the code to as(gr, "GRangesList") as suggested.
>>>
>>
>> I went ahead and fixed karyoploteR. This is karyoploteR 1.5.2. Make
>> sure to resync your GitHub repo by following the instructions here:
>>
>>
>> https://bioconductor.org/developers/how-to/git/sync-existing
>> -repositories/
>>
>> Note that the loop on the GRanges object (via the call to Map())
>> was not needed and could be replaced with a solution that uses
>> proper vectorization.
>>
>> Best,
>> H.
>>
>>
>>> 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 <https://urldefense.proofpoint
>>> .com/v2/url?u=http-3A__www.germanstrias.org_&d=DwMDaQ&c=e
>>> RAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJK
>>> aaPhzWA&m=Wwl42dL5uGJa8PR0aAcNnIN0t-uut5R2xLKBhl0ynV8&s=z45_
>>> PX78N6zLu1Bcn-mYQcyRortvXjNyQcWASriwsr0&e=>
>>>
>>> <https://urldefense.proofpoint.com/v2/url?u=http-3A__www.
>>> germanstrias.org_&d=DwMDaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3X
>>> eAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=Wwl42dL5uGJa8PR0aAcN
>>> nIN0t-uut5R2xLKBhl0ynV8&s=z45_PX78N6zLu1Bcn-mYQcyRortvXjNyQcWASriwsr0&e=>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>> 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 a
>>>>> <https://maps.google.com/?q=ribed+on+this+list+a&entry=gmail&source=g>nd
>>>>> 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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