[Bioc-devel] as.list of a GRanges
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 and 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
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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 Phone: (206) 667-5791 Fax: (206) 667-1319