[Bioc-devel] affypdnn: Request for moving "Depends" packages to "Suggests"

[Richard Pearson]

Hi

I guess you mean require() here, or is there a request() function that I'm not aware of?

I'm sorry to say I'm still a little confused as to the effects of moving something from Depends to Suggests. I realise that one effect of this is that the package in Suggests won't get loaded until needed, which is generally a good thing. However, isn't a side effect of this that the package in Suggests won't get installed by biocLite()?

Lets say I'm developing a package foop which has a function foo(). foo() uses the function bar() from package barp. Many users use foop without ever using foo(). Therefore it would seem sensible to put barp in Suggests so it doesn't get loaded all the time, but rarely used. However, if a user installs foop on a fresh R installation using biocLite(), they will get an error when trying to use foo(). A non-expert user might at this point simply think that foop is broken and give up. What's the recommended strategy in this scenario? If barp has a namespace, should I put barp in Imports (so it gets installed by biocLite), and then access bar() using barp::bar()? What should I do if barp has no namespace? Should I recommend to the barp maintainer that they add one? More likely, have I completely misunderstood Depends/Suggests/Imports/biocLite...?

No doubt this is covered in documentation someplace, any pointers appreciated!

Thanks

Richard.


Henrik Bengtsson wrote:
> Hi,
> 
> this one is mainly for the maintainer (Laurent Gautier), but I post it
> to bioc-devel also as request to minimize package dependencies in R
> and BioC in general:
> 
> The current DESCRIPTION of 'affypdnn' is:
> 
> Package: affypdnn
> Version: 1.14.3
> Depends: R (>= 2.3.0), affy (>= 1.5), affydata, hgu95av2probe
> 
> Could you please update this to:
> 
> Package: affypdnn
> Version: 1.14.3
> Depends: R (>= 2.3.0), affy (>= 1.5)
> Suggests: affydata, hgu95av2probe
> 
> and use request("affydata") and request("hgu95av2probe") where those
> two are actually needed?
> 
> Cheers
> 
> Henrik
> 
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> https://stat.ethz.ch/mailman/listinfo/bioc-devel
> 

-- 
Richard D. Pearson             richard.pearson at postgrad.manchester.ac.uk
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