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])

It just means that either alter > ncol( reach_mat ) or i > nrow( reach_mat ), in other words, your indices exceed the array boundary (i is greater than the number of rows, or alter is greater than the number of columns).

Just run the above tests to see what and when is happening.