Use of uninitialized value

madM has asked for the wisdom of the Perl Monks concerning the following question:

Hi people! If i run this code i get this error:"Use of uninitialized value in division (/) at aprende2.pl line 64." does anybody knows how to solve it?

my @matrix =(
[0.54, 0.03, 0.03, 0.03, 0.08, 0.04, 0.05, 0.05, 0.02, 0.02, 0.03, 0.0
+4, 0.03, 0.01, 0.06, 0.11, 0.06, 0.01, 0.01,0.06],
[0.02, 0.57, 0.03, 0.01, 0.02, 0.06, 0.03, 0.01, 0.04, 0.01, 0.01, 0.1
+1, 0.02, 0.01, 0.01, 0.02, 0.02, 0.01, 0.01, 0.01],
[0.01, 0.02, 0.48, 0.06, 0.01, 0.03, 0.03, 0.03, 0.05, 0.01, 0.01, 0.0
+3, 0.01, 0.00, 0.01, 0.04, 0.03, 0.00, 0.02, 0.01],
[0.02, 0.01, 0.09, 0.57, 0.01, 0.04, 0.11, 0.02, 0.03, 0.00, 0.00, 0.0
+3, 0.01, 0.00, 0.02, 0.04, 0.02, 0.00, 0.01, 0.00],
[0.01, 0.00, 0.00, 0.00, 0.57, 0.00, 0.00, 0.00, 0.00, 0.00, 0.00, 0.0
+0, 0.00, 0.01, 0.00, 0.01, 0.01, 0.01, 0.01, 0.01],
[0.02, 0.04, 0.03, 0.02, 0.01, 0.42, 0.05, 0.01, 0.04, 0.01, 0.01, 0.0
+5, 0.02, 0.00, 0.01, 0.02, 0.02, 0.01, 0.01, 0.01],
[0.04, 0.04, 0.05, 0.13, 0.01, 0.11, 0.52, 0.02, 0.03, 0.01, 0.01, 0.0
+7, 0.01, 0.00, 0.02, 0.04, 0.04, 0.01, 0.01, 0.01],
[0.05, 0.02, 0.05, 0.03, 0.02, 0.02, 0.02, 0.77, 0.02, 0.00, 0.00, 0.0
+2, 0.01, 0.00, 0.01, 0.04, 0.01, 0.01, 0.00, 0.01],
[0.01, 0.01, 0.02, 0.01, 0.01, 0.02, 0.01, 0.00, 0.54, 0.00, 0.00, 0.0
+1, 0.01, 0.02, 0.01, 0.01, 0.01, 0.02, 0.04, 0.00],
[0.02, 0.01, 0.01, 0.00, 0.03, 0.01, 0.01, 0.00, 0.01, 0.50, 0.10, 0.0
+1, 0.09, 0.04, 0.01, 0.01, 0.03, 0.02, 0.01, 0.18],
[0.03, 0.02, 0.01, 0.01, 0.03, 0.03, 0.01, 0.00, 0.02, 0.13, 0.60, 0.0
+2, 0.19, 0.09, 0.02, 0.02, 0.02, 0.02, 0.03, 0.08],
[0.03, 0.14, 0.06, 0.03, 0.01, 0.09, 0.06, 0.02, 0.05, 0.01, 0.01, 0.5
+0, 0.02, 0.01, 0.02, 0.04, 0.03, 0.01, 0.01, 0.01],
[0.01, 0.01, 0.00, 0.00, 0.01, 0.02, 0.00, 0.00, 0.01, 0.03, 0.05, 0.0
+1, 0.42, 0.02, 0.00, 0.01, 0.01, 0.01, 0.01, 0.02],
[0.01, 0.01, 0.00, 0.00, 0.02, 0.01, 0.00, 0.00, 0.03, 0.02, 0.04, 0.0
+0, 0.04, 0.61, 0.00, 0.01, 0.01, 0.07, 0.14, 0.01],
[0.03, 0.01, 0.01, 0.01, 0.00, 0.01, 0.01, 0.01, 0.02, 0.00, 0.01, 0.0
+1, 0.01, 0.00, 0.72, 0.03, 0.01, 0.00, 0.00, 0.01],
[0.07, 0.03, 0.06, 0.04, 0.05, 0.04, 0.03, 0.03, 0.02, 0.01, 0.01, 0.0
+4, 0.02, 0.01, 0.04, 0.43, 0.09, 0.02, 0.01, 0.01],
[0.04, 0.02, 0.04, 0.02, 0.04, 0.03, 0.03, 0.01, 0.02, 0.02, 0.02, 0.0
+3, 0.03, 0.01, 0.02, 0.09, 0.52, 0.01, 0.01, 0.04],
[0.00, 0.00, 0.00, 0.00, 0.01, 0.00, 0.00, 0.00, 0.01, 0.00, 0.00, 0.0
+0, 0.00, 0.02, 0.00, 0.00, 0.00, 0.71, 0.02, 0.00],
[0.00, 0.01, 0.01, 0.00, 0.01, 0.01, 0.00, 0.00, 0.05, 0.01, 0.01, 0.0
+1, 0.01, 0.10, 0.00, 0.01, 0.01, 0.06, 0.61, 0.01],
[0.05, 0.01, 0.01, 0.01, 0.07, 0.02, 0.02, 0.01, 0.01, 0.20, 0.07, 0.0
+1, 0.06, 0.03, 0.01, 0.02, 0.06, 0.02, 0.02, 0.51]);

my @frequency = ([0.08477395, 0.05103334, 0.03837665, 0.05740129, 0.01
+256165, 0.03471746,
0.06883297, 0.07907659, 0.02077239, 0.06813598, 0.08906677, 0.06501537
+,
0.02318017, 0.03823936, 0.04036729, 0.05668318, 0.05721648, 0.00871765
+,
0.02785317, 0.07797831]);

my $mutrate=0;
my $matrix2={};
my $e;
$e=1;$e/=2 while $e/2+1>1;

my @PAM1= @matrix;

my @lnPAM1=();
LINE: for (my $i=0; $i<20; $i++){
    for (my $j=0; $j<20; $j++){
        if ($matrix[$i][$j] > 0){
            $lnPAM1[$i][$j] = log $matrix[$i][$j];
        }else{ next LINE;
        }
    }
}

for (my $i=0; $i<20; $i++){
    $mutrate += $frequency[0][$i]*(1-$matrix[$i][$i]);
}


my $k=1;
my $iter = 0;

while (($mutrate-0.01) > $e){
    $iter++;
    $k= $k * $mutrate * 100;
    for (my $i=0; $i<20; $i++){
        for (my $j=0; $j<20; $j++){
            $lnPAM1[$i][$j]= ($lnPAM1[$i][$j]) /($mutrate*100);
            $PAM1[$i][$j]=exp($lnPAM1[$i][$j]);
        }
    }
            for (my $i=0; $i<20; $i++){
                $mutrate += $frequency[0][$i]*(1-$PAM1[$i][$i]);
            }
            
    
    
    
    print " iteration: $iter, k: $k, MutationRate:$mutrate\n";
    
}
[download]

Comment on Use of uninitialized value Download Code

Replies are listed 'Best First'.
Re: Use of uninitialized value by farang (Chaplain) on Aug 11, 2013 at 05:14 UTC
I get those warnings (with `use warnings` in effect). The problem comes from this loop. `my @lnPAM1=(); LINE: for (my $i=0; $i<20; $i++){ for (my $j=0; $j<20; $j++){ if ($matrix[$i][$j] > 0){ $lnPAM1[$i][$j] = log $matrix[$i][$j]; }else{ next LINE; } } }` [download] When a matrix element equals zero, that value of @lnPAM1 remains undefined, and that undefined value is being used at line 64. `$lnPAM1[$i][$j]= ($lnPAM1[$i][$j]) /($mutrate*100);` [download] For instance, `$lnPAM1[0][17]` and `$lnPAM1[0][18]` are `undef`. To avoid the warnings, you'll need to either assign some value to all of them or exclude matrix elements which are `undef` from executing line 64.	[reply] [d/l] [select]
Re: Use of uninitialized value by frozenwithjoy (Priest) on Aug 11, 2013 at 04:45 UTC
Assuming line 64 is `$lnPAM1[$i][$j]= ($lnPAM1[$i][$j]) /($mutrate*100);`, you could try troubleshooting with something like this on the line before: `say "$lnPAM1[$i][$j]:$i:$j";` [download] When I do this I see something like this snippet: `-3.91202300542815:3:7 -3.50655789731998:3:8 :3:9 :3:10 :3:11 :3:12 :3:13 :3:14 :3:15 :3:16 :3:17 :3:18 :3:19 -4.60517018598809:4:0 :4:1 :4:2 :4:3` [download] Taking a look at where the matrix is built, it seems that the problem stems from your use of `next` in: `LINE: for (my $i=0; $i<20; $i++){ for (my $j=0; $j<20; $j++){ if ($matrix[$i][$j] > 0){ $lnPAM1[$i][$j] = log $matrix[$i][$j]; }else{ next LINE; } } }` [download] By using `next`, you don't use all 20 iterations of `i` or `j` when building the matrix, but you do later on. You could look to see the dimensions of the matrix before iterating through its dimensions.	[reply] [d/l] [select]
Re: Use of uninitialized value by 5mi11er (Deacon) on Aug 11, 2013 at 03:24 UTC
I downloaded and ran it just fine. Perhaps you didn't post the version of code that you thought you did? -Scott	[reply]
Re^2: Use of uninitialized value by madM (Beadle) on Aug 11, 2013 at 03:37 UTC
Thats strange... Im still getting the same error.. are you using warning and strict?	[reply]
Re: Use of uninitialized value by BillKSmith (Monsignor) on Aug 11, 2013 at 13:29 UTC
Is there a reason you cannot use BrowserUK's suggestion from your previous post? If you can assume that the zero is just the roundoff of a small number, replace the zero with a any small number before you take the log. If you believe that the zero is exact and that its log has no meaning, use my suggestion. Store HUGE_VAL as the value of the log. It will fail if you try to use it, but you will know for sure where it came from. Bill	[reply]