On the basis of what you've provided, you can just use this for loop instead of your current while loop:

    for (my $i = 0; $i <= $#list; $i += $C) {
        push @AoA, [ @list[$i .. $i + $C - 1] ];
    }
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Output (showing "@list remains unaffected"):

[[1 .. 4], [5 .. 8], [9 .. 12]]
[1 .. 12]
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I don't know why you've declared and initialised $R but then didn't use it. It's complete guesswork on my part, but I get the impression you're using a matrix with all elements being used. If that's the case, the code above works if you add a couple of elements to @list; giving this output:

[[1 .. 4], [5 .. 8], [9 .. 12], [13, 14, undef, undef]]
[1 .. 14]
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If my guess was wrong, and that's not what you want, use this code:

    for (my $i = 0; $i <= $#list; $i += $C) {
        my $end = $i + $C - 1;
        $end = $#list if $end > $#list;
        push @AoA, [ @list[$i .. $end] ];
    }
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To get this output:

[[1 .. 4], [5 .. 8], [9 .. 12], [13, 14]]
[1 .. 14]
[download]

With the original @list (holding 12 elements), this code produces the same output as the first code I posted:

[[1 .. 4], [5 .. 8], [9 .. 12]]
[1 .. 12]
[download]