Re: [Bioc-devel] How to extend nonstandardGenericFunction

2018-10-19 Thread Elizabeth Purdom
No, sorry, it was also a problem with `Matrix` package. I was too quick in checking it. I think upgrading my devtools and roxygen2 may have fixed it. Thanks for helping me pinpoint where the problem was. > On Oct 19, 2018, at 12:37 PM, Elizabeth Purdom > wrote: > > Thanks Martin. And of cours

Re: [Bioc-devel] How to extend nonstandardGenericFunction

2018-10-19 Thread Elizabeth Purdom
Thanks Martin. And of course you’re right! The errors I was getting came from devtools functions— I didn’t think to check it outside of there and assumed it was a general problem with my package setup. But it's actually a problem in devtools. When I set up your example (thanks!) with Roxygen a

Re: [Bioc-devel] How to extend nonstandardGenericFunction

2018-10-19 Thread Martin Morgan
That doesn't sound correct. I just created a simple package with DESCRIPTION Package: PkgA Title: What the Package Does (one line, title case) Version: 0.0.0.9000 Authors@R: person("First", "Last", email = "first.l...@example.com", role = c("aut", "cre")) Description: What the package does (one

Re: [Bioc-devel] How to extend nonstandardGenericFunction

2018-10-19 Thread Elizabeth Purdom
Sorry, I copied the wrong code from phylobase (I copied the setMethod code). Their setGeneric calls are in the following format: setGeneric("nNodes", function(x) { standardGeneric("nNodes") }) > On Oct 19, 2018, at 9:07 AM, Elizabeth Purdom > wrote: > > Hello, > > In my package (`cluste

[Bioc-devel] How to extend nonstandardGenericFunction

2018-10-19 Thread Elizabeth Purdom
Hello, In my package (`clusterExperiment`) I want to extend a S4 method from a package `phylobase` for my class. However, in the phylobase package, all of the `setGeneric` calls are in the form of setMethod("nTips", signature(x="phylo"), function(x) { Ntip(x) }) Namely, they use braces