Subscript out of bounds – general definition and solution?

This is because you try to access an array out of its boundary.

I will show you how you can debug such errors.

  1. I set options(error=recover)
  2. I run reach_full_in <- reachability(krack_full, 'in') I get :reach_full_in <- reachability(krack_full, 'in') Error in reach_mat[i, alter] = 1 : subscript out of bounds Enter a frame number, or 0 to exit 1: reachability(krack_full, "in")
  3. I enter 1 and I get Called from: top level
  4. I type ls() to see my current variables 1] "*tmp*" "alter" "g" "i" "j" "m" "reach_mat" "this_node_reach"

Now, I will see the dimensions of my variables :

Browse[1]> i
[1] 1
Browse[1]> j
[1] 21
Browse[1]> alter
[1] 22
Browse[1]> dim(reach_mat)
[1] 21 21

You see that alter is out of bounds. 22 > 21 . in the line :

  reach_mat[i, alter] = 1

To avoid such error, personally I do this :

  • Try to use applyxx function. They are safer than for
  • I use seq_along and not 1:n (1:0)
  • Try to think in a vectorized solution if you can to avoid mat[i,j] index access.

EDIT vectorize the solution

For example, here I see that you don’t use the fact that set.vertex.attribute is vectorized.

You can replace:

# Set vertex attributes
for (i in V(krack_full)) {
    for (j in names(attributes)) {
        krack_full <- set.vertex.attribute(krack_full, j, index=i, attributes[i+1,j])

by this:

##  set.vertex.attribute is vectorized!
##  no need to loop over vertex!
for (attr in names(attributes))
      krack_full <<- set.vertex.attribute(krack_full, 
                                             attr, value = attributes[,attr])

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