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

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

Hi Richard,

Richard Pearson wrote:

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()?

 Yes, and so it should only be used if the functionality is for fairly
specialized tasks that are not likely to be carried out by all users. The
network of Dependencies can get very large, and the number of packages a
user has to install that they never use should be minimized if possible
(whence the Lite in biocLite).

 However, a review of Suggests, Depends, and package size is something that
package developers should be carrying out regularly.  There are some
examples where the need for dependencies has essentially gone away but the
package has never been cleaned up to reflect that. Or where Dependencies
would be better handled via imports.

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

  One certainly hopes that even naive users could see and interpret the
corresponding error message. And you as the developer of foop could
intervene directly, by either printing a specific warning, or as some have
done (not always very well) automatically downloading the needed package at
run time (possibly after asking the user).

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...?

 There is also the issue that some packages Depend on foop, when indeed they
really only want to Import from foop.  This is also something that could be
cleaned up. Both Depends and Suggests have the effect of attaching the
package to the searchpath and that can have unwanted effects.  Cleaning up a
number of these instances would also help.

 For namespaces Luke Tierney's R News article is the only real reference I
know of.  Other issues are discussed in the R Extensions manual, and on-line
man pages.

 best wishes
   Robert

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

--
Robert Gentleman, PhD
Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N, M2-B876
PO Box 19024
Seattle, Washington 98109-1024
206-667-7700
rgentlem at fhcrc.org