How to catch warnings sent during S4 method selection

r, r-s4, warnings

Solution

My original guess was that this is because method dispatch muffles warnings

f = function(x) withCallingHandlers(x, warning=function(w) { 
    cat('muffled\n')
    invokeRestart("muffleWarning")
})

and then

> withCallingHandlers(f(warning("f")), warning=function(w) message("caught"))
muffled

Digging deeper, the actual warning call is in this C stack trace

#0  do_warning (call=0x3d4ad50, op=0x9c4bf0, args=0x45b9968, rho=0x45b9c40) at /home/mtmorgan/src/R-devel/src/main/errors.c:1140
#1  0x00000000004b4198 in bcEval (body=<optimized out>, rho=<optimized out>, useCache=<optimized out>) at /home/mtmorgan/src/R-devel/src/main/eval.c:4700
#2  0x00000000004bff40 in Rf_eval (e=0x3d45618, rho=0x45b9c40) at /home/mtmorgan/src/R-devel/src/main/eval.c:554
#3  0x00000000004c4e4d in Rf_applyClosure (call=0x45b8630, op=0x3d45730, arglist=<optimized out>, rho=0x9e7638, suppliedenv=0x9e7670) at /home/mtmorgan/src/R-devel/src/main/eval.c:1033
#4  0x00000000004c0005 in Rf_eval (e=0x45b8630, rho=0x9e7638) at /home/mtmorgan/src/R-devel/src/main/eval.c:670
#5  0x00000000004c0695 in forcePromise (e=0x45b9410) at /home/mtmorgan/src/R-devel/src/main/eval.c:458
#6  0x00000000004c0462 in Rf_eval (e=0xa1d338, rho=0x45b9368) at /home/mtmorgan/src/R-devel/src/main/eval.c:577
#7  0x000000000046fbfb in protectedEval (d=0x7fffffffc7f0) at /home/mtmorgan/src/R-devel/src/main/context.c:750
#8  0x0000000000470d48 in R_ToplevelExec (fun=0x46fbe0 <protectedEval>, data=0x7fffffffc7f0) at /home/mtmorgan/src/R-devel/src/main/context.c:705
#9  0x0000000000470de7 in R_tryEval (e=<optimized out>, env=<optimized out>, ErrorOccurred=0x7fffffffc89c) at /home/mtmorgan/src/R-devel/src/main/context.c:764
#10 0x0000000000470e26 in R_tryEvalSilent (e=<optimized out>, env=<optimized out>, ErrorOccurred=<optimized out>) at /home/mtmorgan/src/R-devel/src/main/context.c:787
#11 0x00007ffff49230b9 in R_dispatchGeneric (fname=0x44b37e8, ev=0x45b9368, fdef=0x45b92f8) at /home/mtmorgan/src/R-devel/src/library/methods/src/methods_list_dispatch.c:993
#12 0x00000000004f5337 in do_standardGeneric (call=<optimized out>, op=<optimized out>, args=<optimized out>, env=0x45b9368) at /home/mtmorgan/src/R-devel/src/main/objects.c:1167
....

where in the C code of `R_dispatchGeneric` method dispatch is trying to figure out the class of the argument by evaluating it

989         if(arg_sym == R_dots) {
990         thisClass = dots_class(ev, &check_err);
991         }
992         else {
993         PROTECT(arg = R_tryEvalSilent(arg_sym, ev, &check_err));
994         if(!check_err)
995             thisClass = R_data_class(arg, TRUE);
996         UNPROTECT(1); /* for arg */
997         }

This seems to be done to implement a C-level error handler:

998         if(check_err)
999         error(_("error in evaluating the argument '%s' in selecting a method for function '%s': %s"),
1000                  CHAR(PRINTNAME(arg_sym)),CHAR(asChar(fname)),
1001                  R_curErrorBuf());

`Rf_tryEvalSilent` evaluates at the top level, something like at the command prompt where there are no calling handlers established; you can see this in the C code, where the handler stack is set to NULL

686 Rboolean R_ToplevelExec(void (*fun)(void *), void *data)
687 {
688     RCNTXT thiscontext;
689     RCNTXT * volatile saveToplevelContext;
690     volatile SEXP topExp, oldHStack;
691     Rboolean result;
692 
693 
694     PROTECT(topExp = R_CurrentExpr);
695     PROTECT(oldHStack = R_HandlerStack);
696     R_HandlerStack = R_NilValue;
697     saveToplevelContext = R_ToplevelContext;

Since argument evaluation starts without handlers, a work-around might be

my_method(withCallingHandlers(warning('arrgh'), warning=function(w) ...))

but that's probably not practical.

Problem

Warnings generated when evaluation arguments of S4 generic functions can not be caught using withCallingHandlers(). Illustration of the normal behaviour of withCallingHandlers: ``` ### simple function that sends a warning send_warning <- function() { warning('send_warning') } send_warning() # Warning message: # In send_warning() : send_warning ### the warning can be caught by withCallingHandlers withCallingHandlers(send_warning(), warning = function(w) { stop('got warning:', w) }) # Error in (function (w) : # got warning:simpleWarning in send_warning(): send_warning ``` Now, let's make the warning be emitted during a S4 dispatch: ``` ### simplest method ever setGeneric('my_method', function(x) standardGeneric('my_method') ) setMethod('my_method', 'ANY', function(x) str(x) ) ### call it with an argument that produces a warning: seems to work my_method(warning('argh')) # chr "argh" # Warning message: # argh ### !!! BUT it is not caught !!!!!!!!!!!!!!!!!!: withCallingHandlers(my_method(warning('argh')), warning = function(w) { stop('got warning:', w) }) # chr "argh" # Warning message: # argh ``` A last example to show that this does not happen during S4 method call: ``` setGeneric('my_method2', function(x) standardGeneric('my_method2') ) setMethod('my_method2', 'ANY', function(x) warning('my_method2') ) my_method2() # Warning message: # In my_method2() : my_method2 ### warning is caught withCallingHandlers(my_method2(), warning = function(w) { stop('got warning:', w) }) # Error in (function (w) : # got warning:simpleWarning in my_method2(): my_method2 ``` From what I understand, there seems to be a special behavior of the warnings emitted during the S4 dispatch. I'd like to know why and how to catch them.

Original source