Issue with graphviz never completing

Question

Can someone help me figure out why the following graph never generates in dot? I think the problem has something to do with the headport and tailport. It works if I take those out, but ideally I want those to stay for stylistic reasons.

digraph G {
    nodesep = 0.5;
    0 [width=0.75, height=0.75, fontsize=20];
    1 [width=0.75, height=0.75, fontsize=20, shape=square];
    2 [width=0.75, height=0.75, fontsize=20];
    3 [width=0.75, height=0.75, fontsize=20];
    4 [width=0.75, height=0.75, fontsize=20];
    5 [width=0.75, height=0.75, fontsize=20, shape=square];
    6 [width=0.75, height=0.75, fontsize=20];
    7 [width=0.75, height=0.75, fontsize=20, shape=square];
    8 [width=0.75, height=0.75, fontsize=20, shape=square];
    9 [width=0.75, height=0.75, fontsize=20, shape=square];
    10 [width=0.75, height=0.75, fontsize=20, shape=square];
    11 [width=0.75, height=0.75, fontsize=20, shape=square];
    12 [width=0.75, height=0.75, fontsize=20];
    subgraph directed{
            rankdir= LR;rank= max;
            0->1->2->3->4->5->6->7->8->9->10->11->12;
    }
    subgraph undirected{
            rankdir= LR;rank= min;edge[tailport=n,headport=n];
            0->1[dir=none, color=red];
            0->2[dir=none, color=red];
            1->9[dir=none, color=red];
            2->3[dir=none, color=red];
            2->8[dir=none, color=red];
            3->4[dir=none, color=red];
            4->8[dir=none, color=red];
            7->9[dir=none, color=red];
            8->9[dir=none, color=red];
            9->10[dir=none, color=red];
            9->11[dir=none, color=red];
            10->11[dir=none, color=red];
    }
}

Answer 1

Unfortunately, this is hitting a long-standing bug related to certain edges that have both ports specified:

Warning: Unable to reclaim box space in spline routing for edge "4" -> "8". Something is probably seriously wrong.
Warning: Unable to reclaim box space in spline routing for edge "1" -> "9". Something is probably seriously wrong.

(https://gitlab.com/graphviz/graphviz/-/issues/241).
There are two edges that seem to hit this bug (4->8 & 1->9). The graph is correctly produced if [tailport=""] is set for these two edges.

Answer 2

Difficult to know what you are after. However, the graph has some problems:

• Nodes cannot be part of multiple subgraphs - they're either in the graph or a subgraph, wherever they appear first. Where are yours supposed to appear?
• rankdir is a graph attribute and cannot be applied to a subgraph

Edit

Following up on your comment, here's a version without any subgraphs. However, you won't like the routing of the edges, something which will be difficult to control.

The idea is to align the nodes in a straight line, then add the other edges with constraint=false in order to not have them influence the ranking of the nodes.

digraph G {
    nodesep = 0.5;
    node[width=0.75, height=0.75, fontsize=20];
    rankdir=LR;

    0;
    1 [shape=square];
    2;
    3;
    4;
    5 [shape=square];
    6;
    7 [shape=square];
    8 [shape=square];
    9 [shape=square];
    10 [shape=square];
    11 [shape=square];
    12;

    0->1->2->3->4->5->6->7->8->9->10->11->12;

    edge[constraint=false, tailport=n,headport=n,dir=none, color=red];
    0->1;
    0->2;
    1->9;
    2->3;
    2->8;
    3->4;
    4->8;
    7->9;
    8->9;
    9->10;
    9->11;
    10->11;
}

Answer 3

Without spending a lot of time digging through the sources, it'd be difficult to say why, but you can move the troublesome elements out of the second subgraph to fix the problem:

Remove 1->9 and 2->8 from the undirected subgraph, and add them below it:

digraph G {
    nodesep = 0.5;
    0 [width=0.75, height=0.75, fontsize=20];
    1 [width=0.75, height=0.75, fontsize=20, shape=square];
    2 [width=0.75, height=0.75, fontsize=20];
    3 [width=0.75, height=0.75, fontsize=20];
    4 [width=0.75, height=0.75, fontsize=20];
    5 [width=0.75, height=0.75, fontsize=20, shape=square];
    6 [width=0.75, height=0.75, fontsize=20];
    7 [width=0.75, height=0.75, fontsize=20, shape=square];
    8 [width=0.75, height=0.75, fontsize=20, shape=square];
    9 [width=0.75, height=0.75, fontsize=20, shape=square];
    10 [width=0.75, height=0.75, fontsize=20, shape=square];
    11 [width=0.75, height=0.75, fontsize=20, shape=square];
    12 [width=0.75, height=0.75, fontsize=20];
    subgraph directed{
            rankdir= LR;rank= max;
            0->1->2->3->4->5->6->7->8->9->10->11->12;
    }
    subgraph undirected{
            rankdir= LR;rank= min;edge[tailport=n,headport=n];
            0->1[dir=none, color=red];
            0->2[dir=none, color=red];
            2->3[dir=none, color=red];
            3->4[dir=none, color=red];
            4->8[dir=none, color=red];
            7->9[dir=none, color=red];
            8->9[dir=none, color=red];
            9->10[dir=none, color=red];
            9->11[dir=none, color=red];
            10->11[dir=none, color=red];
    }
    1->9[dir="none", color="red", headport="n"];
    2->8[dir="none", color="red", headport="n"];
}