[Bioc-devel] Generic for write to BiocGenerics

[Laurent Gatto]

On 21 September 2017 04:15, Hervé Pagès wrote:

> If we want to move export() to BiocGenerics of course import()
> would need to follow.
>
> My rough estimate is that this move would possibly break between
> 20-30 packages or more. The BioC 3.6 release is coming soon and
> it's a bit late to introduce such a disruptive change. So I vote
> for postponing this to BioC 3.7.
>
> @jo: Would you consider making MSnbase depend on rtracklayer in
> the mean time? Alternatively, my suggestion to use a specific
> write* name still stands.

writeMSData is indeed the route we decided to go in the end, so no need
to move export() and import() for us at the moment.

Thanks again for your input.

Best wishes,

Laurent

> H.
>
>
> On 09/18/2017 11:28 PM, Laurent Gatto wrote:
>>
>> Out of curiosity, do you also have an import() function?
>>
>> On 18 September 2017 22:22, Michael Lawrence wrote:
>>
>>> I was also about to suggest that we converge on export() but held back
>>> because I was obviously biased. I also agree with making the target
>>> explicit in the function name. It makes the intent of the code way
>>> more obvious.
>>>
>>> On Mon, Sep 18, 2017 at 3:15 PM, Hervé Pagès <hpages at fredhutch.org> wrote:
>>>> Hi jo,
>>>>
>>>> At the moment probably not much to be gained unless you ran into
>>>> some conflicts with other "write" methods defined in Bioconductor?
>>>>
>>>> Note that the arguments/signature of base::write() don't really
>>>> help making it a clean generic functions (e.g. weird 'file' default,
>>>> 'ncolumns' and 'sep' args that lack generality, no ellipsis). It seems
>>>> to me that instead of trying to force write() into a generic, it might
>>>> be easier/cleaner to define a method for the export() generic defined
>>>> in rtracklayer. Maybe the discussion would be whether we should consider
>>>> moving rtracklayer::export() to BiocGenerics?
>>>>
>>>> Finally, IMO there is nothing wrong in using specific write* names like
>>>> writeMgfData, writeMSData, writeMzTabData, etc... It plays nicely with
>>>> tab-completion, the user can use args() to quickly see all the args and
>>>> their defaults, tab-completion also works on the arguments, and the user
>>>> does not struggle in finding the man page (like s/he does sometimes
>>>> with generic and methods, especially when those are defined in
>>>> different packages).
>>>>
>>>> H.
>>>>
>>>>
>>>> On 09/18/2017 10:21 AM, Rainer Johannes wrote:
>>>>>
>>>>> Dear all!
>>>>>
>>>>> We are currently implementing mzML write support in `MSnbase` and did
>>>>> implement a `write` method for the S4 objects in `MSnbase`. Now, the
>>>>> question is whether it might not be better to define a `write` S4
>>>>> generic in `BiocGenerics`?
>>>>>
>>>>>
>>>>> cheers, jo
>>>>>
>>>>>
>>>>>
>>>>> _______________________________________________
>>>>> Bioc-devel at r-project.org mailing list
>>>>>
>>>>> https://urldefense.proofpoint.com/v2/url?u=https-3A__stat.ethz.ch_mailman_listinfo_bioc-2Ddevel&d=DwICAg&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=10yPFYogq10f-iQf5EwJPYNuEYfi2q0m-34r6ELrqqQ&s=Ukn5OXjj6C3HDU7w5fAKxAeEAhG_9IC3llSKwkgMHCA&e=
>>>>>
>>>>
>>>> --
>>>> 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
>>>> Phone:  (206) 667-5791
>>>> Fax:    (206) 667-1319
>>>>
>>>>
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>>>
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>>
>>


-- 
Laurent Gatto | @lgatt0
http://cpu.sysbiol.cam.ac.uk/
http://lgatto.github.io/