I suspect you've left PrintError => 1 in DBI (which is its default value). This means DBI is warning, not dying and the eval block doesn't trap warnings -- they'll go to whatever your $SIG{__WARN__} handler is (which is probably the default and is printing to STDERR.) Set RaiseError => 1, PrintError => 0.

I don't know anything about BioPerl but expect it's also warnings.

Thanks: this did indeed fix the DBI-based warnings I was getting.

For that you have to set up a $SIG{__WARN__} handler.

See warn for a brief discussion on how to trap warnings. Also, look at perlvar for info on setting %SIG entries, and the Carp module's POD for a more detailed discussion on error and warning handling.

What you're thinking are errors might, in fact, just be warnings.

Thanks, this was necessary for most of the BioPerl warnings.

$SIG{__DIE__} = sub {
    return if $^S;  # inside eval
    # write to log:
    ...
};
[download]

Either get a properly updated module containing the error handler/log writer, fix the module if it's one of your own, or temporarily clear $SIG{__DIE__} for the eval, like this:

{
    local $SIG{__DIE__};
    eval {
        # your code here
        ...
    };
}
if($@) {
    # oops!
    ... 
}
[download]

You surely mean eval { }; if ($@) { }, don't you? The semicolon is imporant there.

No, bart put his eval, whose block was correctly terminated with a semicolon, within another block so he could localize $SIG{__DIE__}. That block shouldn't get a semicolon and doesn't have one.