[Bioc-devel] as.list of a GRanges

Hi Herv?,

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, Cam? 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, Herv? Pag?s escribi?:

Hi Bernat,

On 02/15/2018 11:57 PM, Bernat Gel wrote:

Hi Herv? 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, Cam? 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.
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nIN0t-uut5R2xLKBhl0ynV8&s=z45_PX78N6zLu1Bcn-mYQcyRortvXjNyQcWASriwsr0&e=>

El 02/15/2018 a las 11:19 PM, Herv? Pag?s escribi?:

On 02/15/2018 01:57 PM, Michael Lawrence wrote:

On Thu, Feb 15, 2018 at 1:45 PM, Herv? Pag?s <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

    --     Herv? Pag?s

    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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[Bioc-devel] as.list of a GRanges

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