[Bioc-devel] Generic for write to BiocGenerics

[Hervé Pagès]

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.

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
>>>>
>>>>
>>>>
>>>> _______________________________________________
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>>>>
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>>>>
>>>
>>> --
>>> 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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>
>

-- 
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