[Bioc-devel] Generic for write to BiocGenerics

[Hervé Pagès]

On 09/20/2017 09:49 PM, Laurent Gatto wrote:
>
> 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.

Great to hear. Thanks Laurent for the update.

H.

>
> 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
>>>>>
>>>>>
>>>>> _______________________________________________
>>>>> 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=DwIDaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=KNjmRskD426_2APrwfYPNYyyXx80yHG1l8HJKli_1ZI&s=KNPhDjYIj7OsHiT1JRb1cicEc4RqDIZY1E6gjcKbbkQ&e=
>>>>
>>>> _______________________________________________
>>>> 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=DwIDaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=KNjmRskD426_2APrwfYPNYyyXx80yHG1l8HJKli_1ZI&s=KNPhDjYIj7OsHiT1JRb1cicEc4RqDIZY1E6gjcKbbkQ&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