[Bioc-devel] is there such a thing as too much dependency?

Stephanie M. Gogarten sdmorris at u.washington.edu
Fri Feb 22 19:32:33 CET 2013

Following up on the discussion this morning about refining the 
guidelines for using existing classes and generics, I am wondering if 
there is such a thing as too much dependency.  Say there is a package 
that has a useful class, but it depends/imports 10 other packages (none 
of which I would import otherwise), each of which import other packages, 
and so on.  If I wanted to use that class in my package, I am thus 
introducing a dependency tree of, say, 20 additional packages.  If I 
could easily write my own version of the useful class, would it ever be 
worth it to avoid all the dependencies?

I know R and especially Bioconductor is designed so that managing all 
the dependencies should be easy (just use biocLite and everything you 
need is there), but in practice it is not always so easy.  For example, 
I import package A to get a single function, but package A depends on 
package B which gets removed from CRAN, so the installation of my 
package is broken until the author of package A deals with the sudden 
loss of package B.

I known one should always use the "base" Bioconductor classes (GRanges, 
DataFrame, SummarizedExperiment, etc.) if at all possible, but I'm 
curious about the experts' opinion on the limitations of package dependency.


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