gives the line number of the line with the shift command.

I'm not sure what would cause that, but the warning is indeed originating from "$item". $item contains undef, either because the first element of @data was undef before the shift, or because @data was empty before the shift.

By the way, shifting out of @data will not effect @{$hoa{$head}}. You need to shift from @{$hoa{$head}} directly to do that.

$\ = "\n";

{
   my %hoa = ( head => [ 'abc', 'def' ] );
   print shift(@{$hoa{head}});   # abc
   print @{$hoa{head}};          # def    -> ok
}

{
   my %hoa = ( head => [ 'abc', 'def' ] );
   my $data = $hoa{head};
   print shift(@$data);          # abc
   print @{$hoa{head}};          # def    -> ok
}

{
   my %hoa = ( head => [ 'abc', 'def' ] );
   my @data = @{$hoa{head}};
   print shift(@data);           # abc
   print @{$hoa{head}};          # abcdef -> BAD!
}
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