[BioC] package structure

[Robert M. Flight]

Thank you both very much for the suggestions, I'm sure one or the
other will definitely help me solve this. This should definitely make
the overall package development easier.

-Robert

On Fri, Feb 25, 2011 at 20:26, Vincent Carey <stvjc at channing.harvard.edu> wrote:
> In addition to Valerie's suggestions, you might consider an
> interesting approach to dynamic response to package loading in the
> oligoClasses/oligo stack.  The packageEvent and setHook functions of
> base R are used quite effectively there -- see oligoClasses/R/zzz.R
>
> On Fri, Feb 25, 2011 at 5:43 PM, Valerie Obenchain <vobencha at fhcrc.org> wrote:
>> Hi Robert,
>>
>> I don't think you need to create two packages. You can put Rgraphviz and
>> Cairo in the Suggests field of your package DESCRIPTION file.
>> Using the .onLoad function in a zzz.R file you can include a check if
>> the user has the packages loaded and set a global varaiable.
>> The global variable can be used to dictate if code dependent on
>> Rgarphviz and Ciaro is run.
>>
>> For example,
>>
>> In a zzz.R file, define a global variable
>>
>>    .options <- new.env(parent = emptyenv())
>>
>> Use the .onLoad function to set the global variable,
>>
>>    .onLoad <- function(...) {
>>        .options[["foo.available"]] <- require(foo, quietly = TRUE)
>>    }
>>
>> In your package code, check the value of the global variable to execute
>> code dependent on the graph packages,
>>
>> if(.options[["foo.available"]]) do something ... else do something else ....
>>
>>
>> Valerie
>>
>>
>>
>> On 02/25/2011 12:15 PM, Robert M. Flight wrote:
>>> Hi All,
>>>
>>> I'm looking for some advice on package structure and dependencies.
>>>
>>> I'm working on a package that allows for different types of
>>> meta-analyses between different datasets. As part of the original
>>> development leading up to creating a package, I also generated a
>>> series of functions that do a lot of work to generate navigable
>>> results using HTML imagemaps.
>>>
>>> However, the visualizations depend currently on Rgraphviz (layouts)
>>> and Cairo (PNG figure generation). The results can be summarized in
>>> different ways than the visualizations I have developed (potentially
>>> using Cytoscape, or just as a table), and I want to make the package
>>> as easy to install and use as possible. Therefore, if I can make the
>>> analysis package not require Rgraphviz and Cairo, I think that would
>>> be good.
>>>
>>> Would it be advisable to create a second package containing the
>>> functions necessary for creating the visualizations? Otherwise I
>>> introduce dependencies that may not even be used by the users of the
>>> package. And I don't know of any other proper way (i.e. besides
>>> "require", which I believe is to be avoided in packages) to call other
>>> packages than having them in the DESCRIPTION and NAMESPACE files, and
>>> I believe anything in NAMESPACE requires that the package be
>>> installed.
>>>
>>> I would appreciate others thoughts on this.
>>>
>>> Thanks,
>>>
>>> -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
>>>
>>> Williams and Holland's Law:
>>>        If enough data is collected, anything may be proven by
>>> statistical methods.
>>>
>>> _______________________________________________
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>>> Bioconductor at r-project.org
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>>>
>>
>>
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>