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

Laurent Gautier lgautier at gmail.com
Tue Jul 1 12:07:05 CEST 2008

Trying to minimize hard package dependencies is commendable, but there
points to keep in mind.

Just case the mere thought of seeing one day their name between
parenthesis right behind "the maintainer" in an email otherwise
addressed to all is not enough to make innoncent bystanders feel
concerned about their package and what is happening here, I'll make a
short list of what it means to have a package listed in the "Depends"
field, and what are possible reasons for having a package in

The usage of the field "Suggests" came out of the need for a gradation
in dependencies between packages, differing from "Depends" with:
- loading the package not contingent on the presence of dependencies
- the dependencies not being loaded

(I that suspect the feature was used for tcltk-based GUIs causing R
installs without tcltk, and a number of things nor working properly
under Win32 at the time).

In my view, or may be that was the general view at the time the
package incriminated was written, being able to run examples justified
having a dependency listed in "Depends".
I agree that this can be discussed, and the particular case discussed,
the dependencies listed can be moved to "Suggests" (there is a chance
that the pack was written before "Suggests" was in use, or just about
the time it appeared). Still, there are many ways to decide on whether
a package should be in "Depends" or in "Suggests", and all can
probably be justified; there is a need for common/public guidelines
(that I might have missed if they exist).

I'd also like to point that dependencies can be good, and that there
are in my view currently not enough of them and the call for
minimizing them should not be taken to the extreme.
There is a fair amount of duplication in functionalities within
bioconductor packages (count the FASTA parsers, for example), and it
would be good if we could have
more cross-talks between packages.

As an emerging guideline, would it be acceptable to say that "data"
packages used for examples should be in "Suggests" unless there is
good reason ?



PS: I have not found the function "request", I assume that "require" was meant.

PPS: Nothing personal about FASTA, I took the example because I own
one of the parsers ;-)

2008/7/1 Henrik Bengtsson <hb at stat.berkeley.edu>:
> 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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