[Bioc-devel] importing (and therefore requiring) one function, vs copying function

James W. MacDonald jmacdon at med.umich.edu
Mon Jan 30 21:57:12 CET 2012

Hi Robert,

On 1/30/2012 3:31 PM, Robert M. Flight wrote:
> Hi Everyone,
> I'm creating my own package, and one use case utilizes gene ontology
> graphs generated based on a user defined set of GO terms. There is a
> function in GOstats, GOGraph that does this, but that would be the
> only function I actually use from GOstats. Instead of putting an
> import for the one function (and therefore adding to the dependency),
> I thought about instead just putting a copy of the function in my own
> package with a note as to the original source.

Putting a copy in your package is much less desirable than importing the 
one function. Yes, people will have to download one more package, but 
GOstats is small and most people aren't that bandwidth-constrained these 

If you put a copy in your package, you will then be responsible for 
ensuring that it is kept in sync with the GOstats version. This might 
not ever be a problem, but then again it might. Importing keeps that 
mess out of your hair.



> My question is which would be the best practice?
> Regards,
> -Robert
> Robert M. Flight, Ph.D.
> University of Louisville Bioinformatics Laboratory
> University of Louisville
> Louisville, KY
> PH 502-852-1809 (HSC)
> PH 502-852-0467 (Belknap)
> EM robert.flight at louisville.edu
> EM rflight79 at gmail.com
> robertmflight.blogspot.com
> bioinformatics.louisville.edu/lab
> The most exciting phrase to hear in science, the one that heralds new
> discoveries, is not "Eureka!" (I found it!) but "That's funny ..." -
> Isaac Asimov
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James W. MacDonald, M.S.
Douglas Lab
University of Michigan
Department of Human Genetics
5912 Buhl
1241 E. Catherine St.
Ann Arbor MI 48109-5618

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