This message could be useful for people fairly new to S4 classes. Therefore r-help and not r-devel.
One use for showMethods(), important to me, is to find all methods that use a particular class in their signatures. This works: showMethods(class="Action", where="package:CTDesignExplorer") It finds the methods in the package. This works: showMethods(class="Action", where=topenv(parent.frame())) in the sense that it finds nothing (looking in .GlobalEnv). "no applicable functions" The default for "where" is where=topenv(parent.frame()), so you'd think this would also give nothing. showMethods(class="Action") Instead, it prints names of hundreds of S4 generics, reporting that they are not. For example, Function "xvcopy": <not an S4 generic function> that come from packages installed even though they are not loaded. Since this was the first thing I tried, getting to the bottom of it derailed me for hours. The problem seems to be from this, in the definition of showMethod: if (length(f) == 0L) { f <- if (missing(.where)) ### This is the problem. It's missing, even though the default value is set. getGenerics() else getGenerics(.where) } I think better would be just f <- getGenerics(.where) Then the default value would apply. This would forestall a vast downpour of reports about generics claiming that they are not generics. Or maybe someone can explain the thinking behind the if clause. Thanks. -Roger Day > sessionInfo() R version 3.0.1 (2013-05-16) Platform: x86_64-apple-darwin10.8.0 (64-bit) locale: [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8 attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] CTDesignExplorer_1.3.9 loaded via a namespace (and not attached): [1] BiocGenerics_0.6.0 Biostrings_2.28.0 grid_3.0.1 IRanges_1.18.1 [5] lattice_0.20-15 parallel_3.0.1 stats4_3.0.1 tools_3.0.1 ______________________________________________ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.