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 <hpa...@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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E-mail: hpa...@fredhutch.org
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