Interactive debugging

Description

mtrace sets or clears debugging mode for a function; mtrace.off clears debugging mode for all functions; check.for.tracees shows which functions are in debugging mode.

Usage

1
2
3
4
# Usual: mtrace( fname) or mtrace( fname, F) or mtrace( apackage:::afunction)
mtrace( fname, tracing=TRUE, char.fname, from=mvb.sys.parent(), update.tracees=TRUE, return.envs=FALSE)
mtrace.off()
check.for.tracees( where=1)

Arguments

fname

quoted or unquoted function name, or unquoted reference to function in package (via :: or :::) or list/environment (via $)

tracing

TRUE to turn tracing on, FALSE to turn it off

char.fname

(rarely used) if your function name is stored in a character object x, use char.fname=x. If you want to turn off tracing while doing so, mtrace( char=x, F) won't work because of argument matching rules; you need mtrace( char.fname=x, tracing=F).

from

where to start looking for fname (not usually needed)

where

(character or integer) position in search path

update.tracees

don't set this parameter! It's only for use by other functions

return.envs

if TRUE, this will return a list of the environments where the function has been replaced by the mtraced version

Details

mtrace(myfun) modifies the body code of myfun, and also stores debugging information about myfun in tracees$myfun. Next time the function is invoked, the modified debug-ready version will be called instead of the orginal. mtrace does not modify source code (or other) attributes, so myfun will "look" exactly the same afterwards. mtrace(myfun,FALSE) restores myfun to normal. mtrace.off unmtraces all mtraced functions (see below for exceptions).

Because mtrace modifies function bodies (possibly in several places, if namespaced packages are involved), calling save.image or save while functions are still mtraced is probably not a good idea– if the saved image is reloaded in a new R session, the debugger won't know how to handle the previously mtraced functions, and an error message will be given if they are invoked. The Save and Save.pos functions in package mvbutils will get round this without your having to manually untrace and retrace functions.

If you do see a "maybe saved before being un-mtraced?" error message when myfun is invoked, all is not lost; you can restore myfun to health via mtrace(myfun,F), or put it properly into debugging mode via mtrace(myfun). mtrace.off won't work in such cases, because myfun isn't included in tracees.

check.for.tracees checks for functions which have been mtraced, but only in one directory. By contrast, names(tracees) will return all functions that are currently known to be mtraced. However, unlike check.for.tracees, names(tracees) won't show functions that were saved during a previous R session in an mtraced state.

mtrace.off will try to untrace all functions. Specifically, it deals with those returned by names( tracees) and/or check.for.tracees( 1). It doesn't currently deal with methods of reference-class and S4-class objects, for which you'll need to call mtrace(..., tracing=FALSE) manually.

mtrace puts a breakpoint (see bp) at line 1, but clears all other breakpoints.

mtrace can handle mlocal functions, but not (yet) do.in.envir functions– the latter appear as monolithic statements in the code window. See package mvbutils for more details.

If you use fixr to edit functions, mtrace will automatically be re-applied when an updated function file is sourced back in. Otherwise, you'll need to call mtrace manually after updating a function.

Finding functions

mtrace by default looks for a function in the following places: first in the frame stack, then in the search path, then in all namespaces, then in all S3 methods tables. If several copies of a function are found, all will get modified (mtraced) to the same code; ditto when unmtracing.

For functions that live somewhere unusual, you'll need to set the from argument. One case is for functions that live inside a list, such as family-functions like poisson for GLMs. Another case is as follows. Suppose there is a function f which first defines functions g and h, then calls g. Now suppose you have mtraced f and then g from inside f, and that g is currently running. If you now want to mtrace(h), the problem is that h is not visible from the frame of g. To tell mtrace where to find g, call mtrace( h, from=sys.parent()). [You can also replace sys.parent() with the absolute frame number of f, if f has been mtraced and its code window is visible.] mtrace will then look through the enclosing environments of from until it finds a definition of h.

If myfun has been defined in a namespaced package, then there may be several copies of myfun in the system, different ones being used at different times. mtrace will change them all; see fun.locator if you really want to know more.

If mtrace(bar) is called while function foo is being debugged (mtrace(foo) having previously been called), and bar has been redefined within foo or a parent environment of foo, then only the redefined copy of bar will be mtraced.

S4 and reference class methods

S4 methods can be mtraced, but like much about S4 it's clunky; see package?debug. Reference class methods can be mtraced easily after an object has been instantiated. You might call this "object-level" mtracing, because it only works for one object of each class at a time. To mtrace e.g. the edit method in the example for "?ReferenceClasses", just do:

1
2
  mtrace( edit, from=xx) # NB will force a method into existence even if it's not been invoked yet
  mtrace( edit, from=xx, FALSE) # to clear it; mtrace.off() won't work properly

You can also do "class-level" mtracing, so that all subsequently-created objects of that class will use the mtraced version. Just do this:

1
2
3
  mtrace( edit, from=mEditor$def@refMethods)
  xx <- mEditor$new( ...)
  mtrace( edit, from=mEditor$def@refMethods, FALSE) # to clear it; mtrace.off() won't work properly

In the "class-level" case, xx will still have an mtraced version of edit even after the mtrace( from=mEditor..., FALSE). You'll need to use the "object-level" technique to clear it.

As of April 2011, methods are only set up inside a ref-class object when they are first accessed, not when the object is created. mtrace (actually fun.locator) works round this.

Limitations

Probably many; but the main one I'm aware of, is the inability to have mtrace on simultaneously for two functions that have the same name but that have different bodies and live in different places. In theory, the solution is for me to incorporate "location" into the function-level debug info in mtracees, but I've not been able to figure out a good general-purpose way to do so. If this describes your particular debugging hell, you certainly have my sympathy...

Value

mtrace by default returns an invisible copy of the modified function body. If you set return.envs=TRUE, it will instead return a list of the environments in which the function has been modified. This is only intended for "internal use". check.for.tracees returns a character vector of function names.

Examples

 1
 2
 3
 4
 5
 6
 7
 8
 9
10
11
## Not run: 
mtrace(glm) # turns tracing on
names( tracees) # "glm"
check.for.tracees( "package:base") # "glm"
glm(stupid.args) # voila le debugger
qqq() # back to command prompt
mtrace( glm, FALSE)
mtrace.off() # turns it off for all functions
mtrace( debug:::setup.debug.admin) # woe betide ye

## End(Not run)