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. >>> >>> _______________________________________________ >>> Bioconductor mailing list >>> Bioconductor at r-project.org >>> https://stat.ethz.ch/mailman/listinfo/bioconductor >>> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor >>> >> >> >> ? ? ? ?[[alternative HTML version deleted]] >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor at r-project.org >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor >> >