[Bioc-devel] New argument 'use.names' in granges() function

Hervé Pagès hpages at fredhutch.org
Fri Jun 17 11:11:54 CEST 2016

Done in SGSeq 1.6.3 (release) and 1.7.4 (devel).

Also done in SomaticSignatures 2.8.4 (release) and 2.9.4 (devel).

I scanned the entire Rpacks folder and those are the only 2 packages
I found that contain calls to granges() with 2 unnamed arguments.

Sorry for the trouble.


On 06/16/2016 11:55 PM, Hervé Pagès wrote:
> Hi Leonard,
> I really like having 'use.names' before 'use.mcols'. Sorry for breaking
> SGSeq, I'll fix it.
> FWIW I think it's good practice to always name this kind of arguments.
> Not the first argument 'x' or the first 2 arguments 'x' and 'y' of a
> unary or binary function, but the toggles that follow them like
> 'use.names', 'use.mcols', 'ignore.strand' etc..
> That makes the code a lot more readable.
> Cheers,
> H.
> On 06/16/2016 04:46 PM, Leonard Goldstein wrote:
>> Hi Hervé,
>> I noticed a recent change in the release and development version of
>> GenomicRanges, which introduces a new argument 'use.names' for granges()
>> and other functions.
>> The change breaks the SGSeq package, since it uses granges() relying on
>> positional argument matching (and 'use.names' has been added preceding
>> existing arguments). Should GenomicRanges be changed so that newly
>> arguments occur after existing arguments? Otherwise I can fix the problem
>> in SGSeq.
>> Many thanks,
>> Leonard
>>     [[alternative HTML version deleted]]
>> _______________________________________________
>> Bioc-devel at r-project.org mailing list
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Hervé Pagès

Program in Computational Biology
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