Martin Morgan
2012-Aug-17 20:24 UTC
[Rd] data() documentation ambiguous about loaded versus attached packages?
Under ?data package: a character vector giving the package(s) to look in for data sets, or 'NULL'. By default, all packages in the search path are used, then the 'data' subdirectory (if present) of the current working directory. which I think is accurate -- packages have to be attached for their data to be found; being loaded (as when PkgB Imports: PkgA) is not sufficient. Later we have If 'lib.loc' and 'package' are both 'NULL' (the default), the data sets are searched for in all the currently loaded packages then in the 'data' directory (if any) of the current working directory. which I think is incorrect ('currently attached packages') and If 'lib.loc = NULL' but 'package' is specified as a character vector, the specified package(s) are searched for first amongst loaded packages and then in the default library/ies (see '.libPaths'). which I'm unsure of -- probably 'amongst attached packages'. FWIW most Bioconductor packages that use data() in function calls currently do so without specifying 'package', and without specifying an 'envir' argument (hence overwriting user objects in the global environment). > R.version.string [1] "R Under development (unstable) (2012-08-17 r60296)" Martin -- Computational Biology / Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109 Location: Arnold Building M1 B861 Phone: (206) 667-2793
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