[R] listing all functions in R

Seth Falcon sfalcon at fhcrc.org
Tue Jan 9 16:29:03 CET 2007

"Earl F. Glynn" <efg at stowers-institute.org> writes:
> "Prof Brian Ripley" <ripley at stats.ox.ac.uk> wrote in message 
> news:Pine.LNX.4.64.0701061331420.8651 at gannet.stats.ox.ac.uk...
>> Here is a reasonable shot:
>> findfuns <- function(x) {
>>     if(require(x, character.only=TRUE)) {
>>        env <- paste("package", x, sep=":")
>>        nm <- ls(env, all=TRUE)
>>        nm[unlist(lapply(nm, function(n) exists(n, where=env,
>>                                               mode="function",
>>                                               inherits=FALSE)))]
>>     } else character(0)
>> }
>> pkgs <- dir(.Library)
>> z <-  lapply(pkgs, findfuns)
>> names(z) <- pkgs
> Any recommendations on how to trap problems with "require" when using 
> findfuns?  One bad package and the lapply above doesn't return
> anything.

Are you sure you need to?  I just tried your code above with:

pkgs <- c("Biobase", "GOstats", "flrblr", "bazbaz")

And while I see warning messages about the flrblr and bazbaz packages,
the function completed and I get the expected results in z.

Oh, perhaps you have some broken installs?  Broken in the sense that
you have a package installed but not its dependencies?

How about this:

safeRequire <- function(x) {
    tryCatch(require(x, character.only=TRUE),
             error=function(e) FALSE)

And then replace the call to require in findfuns().

+ seth

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