Hi All, Eric recently solved an issue he was having with the affy package... On 14 Nov 2005, Eric.Kort at vai.org wrote: > I have solved this issue with expresso. The problem was that I am > a/an <insert preferred="" derogatory="" euphemism="" here=""> and masked the > "normalize" function with the little macro function I wrote to > perform these normalizations. These sorts of name collisions can be nasty. There are, however, some things that package developers can do to make it more difficult for us <pde here=""> users to mess things up. One of them is for more packages to use name spaces. I believe that Eric's helper function would not have confused affy if the affy package was using a name space (it will have one in the next release). So to all those package developers and maintainers on the list: you may want to consider adding a name space to your package. Advantages for your package include: - Your package won't be broken by "helper" functions that your users define in the global name space - Your package won't be bothered by functions in other packages with the same name. - A name space gives you the ability to clearly specify which functions are part of the public interface and which are private. R CMD check won't bother you for documentation on non-exported functions, although it is often still useful to give them some documentation. There are some disadvantages: - You have to maintain the NAMESPACE file - It is less convenient to debug/develop packages with name spaces because you have to run R CMD INSTALL to be sure everything gets updated in the name space properly. Although less convenient, you will be more certain that the behavior is really in your package and not a result of things hiding in your global workspace. Finally, an offer of help: If you would like help adding a name space to your package, let us know and we will provide assistance. A great place to start, would be to send questions to bioc-devel. Best Wishes, + seth PS: You can read more about name spaces in the Writing R Extensions Manual http://cran.fhcrc.org/doc/manuals/R-exts.html#Package-name-spaces