So, working on my theory that $? and $! are being trashed because of the call to the signal handler, I localised the variables $? and $! which has made a positive difference. Here is the code. 

$SIG{ALRM} = sub {
    local $? = 0;
    local $! = 0;
    print( "Alarm triggered in $$\n" );
    unlink('/doesnt/exist');  # this will definitely fail
};

alarm(2);
my $rt = system("sleep 4");
print "system returned $rt, \$? is $?\n";

[download]

And the output is - 

Alarm triggered in 26346
system returned 0, $? is 0

[download]

Give it a try in your code. Let me know how is goes.

In reply to Re^2: System call + signals = bad return code? by bruceb3
in thread System call + signals = bad return code? by swkronenfeld

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