[R] function coverage [solved?]

Ross Boylan ross at biostat.ucsf.edu
Wed Jan 16 00:05:38 CET 2013

On Mon, 2013-01-14 at 13:08 -0800, Ross Boylan wrote:
> Is there an easy way to identify all the functions called as a result of
> invoking a function?  Getting the calling hierarchy too would be nice,
> but is definitely not essential.
> I'm trying to understand someone else's package, which is in a namespace
> and has some S3 functions.  I could probably live without tracing the S3
> functions.  All the functions I want to trace are in R.  The code passes
> functions around as arguments, so that the function being called is not
> always obvious from inspection of the source immediately around the
> call.
> I can imagine a solution that went something like this:
> 1. identify all functions by searching the sources for xxxx <- function(
> (probably only at the left margin, to avoid attempting to trace
> functions defined inside of functions).
> 2. Write a function that wraps another function to record the fact that
> it has been called.
> 3. Somehow replace all functions with their wrapped equivalents.
> 4. make the top level call.
> 5. inspect the data constructed by the wrapper.
> The code is recursive and iterative; manual stepping does not seem
> feasible.  The package includes a lot of earlier versions of the code,
> and so I suspect that a lot of the code is not active.
> Thanks.
> Ross Boylan

Inspired particularly by Michael Weylandt's suggestion I developed the
following functions, with a typical usage indicated int he comments.
The file is cover.R.  I'm not sure if attachments are allowed, so here
it is inline
# cover.R  determine functions called
# GPL 3.0 license

# Typical use
# mylog <- gzfile("try2.gz", "w")
# monitorNamespace("missreg2", "mylog")
# call one or more functions
# unmonitorNamespace("missreg2")
# close(mylog)

# monitor f (type character, name of function) in environmnet env for calls
# log results to connection con (type character, name of global variable)
monitor <- function(f, con, env=parent.frame()) {
  tin <- parse(text=paste('writeLines("', f, ' in", ', con,")", sep=""))
  tout <- parse(text=paste('writeLines("', f, ' out", ', con,")", sep=""))
  trace(f, tin, tout, print=FALSE, where=env)

unmonitor <- function(f, env=parent.frame()) {
  untrace(f, where=env)

# monitor all functions in ns
# con is a global variable that receives the log
monitorNamespace <- function(ns, con){
  e <- getNamespace(ns)
  invisible(sapply(ls(e), function(nm) if (is.function(get(nm, envir=e, inherits=FALSE)))
                   monitor(nm, con, env=e)))

unmonitorNamespace <- function(ns){
  e <- getNamespace(ns)
  lapply(ls(e), function(nm) unmonitor(nm, env=e))


This mostly seemed to work, but for some reason the outerlevel call I
made is not recorded in the log.  I thought this might be a result of
previous calls to trace or debug, or perhaps my having edited the
function and stuck it in my global namespace.  I tried
detach("missreg2", unload=TRUE") and reloading the library; it didn't
help.  And the function loaation looks like all the others that were
> getAnywhere("rclusbin3")
2 differing objects matching ‘rclusbin3’ were found
in the following places
which is exactly the same as other functions it did trace.

Thanks also to Duncan and Hadley for their ideas.  I figured with the
profiler I'd always wonder if I'd missed something, and so went this low
tech route.  Because of the missing log entry for the outer level
function, I'm still wondering if I got everything (since the reason the
outer level function wasn't traced might apply to others).

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