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Maximilian Kofler

2010-May-06 09:40 UTC

[R] Problem with nested functions - functions nested too deeply in source code

Hi all!

I¹m just implementing the Ullmann¹s algorithm for searching subgraph
isomorphisms in graphNEL objects. The algorithm is running with smaller
graphs, but when I¹m calling it i get an R error message saying that
functions are nested too deeply in source code. I found out that the problem
is in the so called refinement procedure of the algorithm which consists of
10 different functions, returning an adjacency matrix. I¹m calling the
refinement procedure with

M <- refine1(M, A, B, p_A, p_B, FAIL) (note that all parameters in call
refine1 have been defined previosly)

Then the following steps look like this

#####################################
# Refinement process                #
#####################################

refine1 <- function(M, A, B, p_A, p_B, FAIL, elim, i, j, k, sc, h, lst, x){
    
    #print("refine 1")
    
    # elim marks if there was eliminated a 1 (and changed to 0)
    
    lst <- vector(mode = "numeric")
    elim <- 0
    i <- 1
    
    refine2(M, A, B, p_A, p_B, FAIL, elim, i, j, k, sc, h, lst, x)
}

refine2 <- function(M, A, B, p_A, p_B, FAIL, elim, i, j, k, sc, h, lst, x){
    
    #print("refine 2")
    
    k <- 1
    h <- 1
    
    sc <- vector(mode = "numeric", length = p_A)
    
    for (l in 1:p_A){
        
        sc[l] <- 0
    }
    
    sc[1] <- 1
    
    refine3(M, A, B, p_A, p_B, FAIL, elim, i, j, k, sc, h, lst, x)
}

refine3 <- function(M, A, B, p_A, p_B, FAIL, elim, i, j, k, sc, h, lst, x){
    
    #print("refine 3")
    
    # check if there is a 1 in the current row in adjacency matrix of graph1
which is on the same position of the 1 in sc
    # sc is a binary string whith only one 1. The position of the one goes
from the first position of sc to the last position
    # and is used for scanning. First this is done for graph 1, and than for
graph 2. Then it is checked if the following condition
    # is fulfilled: (for all x) ((A[i,x] = 1) => (there exists one ore more
y) (M[x,y] * B[x,j] = 1)). The algorithm terminates if no more
    # 1 can be changed in a 0
    
    if (1 %in% collation(A[i,], sc) == FALSE){
        
        refine4(M, A, B, p_A, p_B, FAIL, elim, i, j, k, sc, h, lst, x)
    }
    
    else {
        
        
        
        lst[k] <- h
        k <- k+1
        
        refine4(M, A, B, p_A, p_B, FAIL, elim, i, j, k, sc, h, lst, x)
    }
}

refine4 <- function(M, A, B, p_A, p_B, FAIL, elim, i, j, k, sc, h, lst, x){
    
    #print("refine 4")
    
    sc <- c(0,sc[-p_A])
    h <- h+1
    
    if (k != (rowSums(A)[i])+1){
        
        refine3(M, A, B, p_A, p_B, FAIL, elim, i, j, k, sc, h, lst, x)
    }
    
    else {
        
        refine5(M, A, B, p_A, p_B, FAIL, elim, i, j, k, sc, h, lst, x)
    }
}

refine5 <- function(M, A, B, p_A, p_B, FAIL, elim, i, j, k, sc, h, lst, x){
    
    #print("refine 5")
    
    j <- 1
    
    sc <- vector(mode = "numeric", length = p_B)
    
    for (l in 1:p_B){
        
        sc[l] <- 0
    }
    
    sc[1] <- 1
    
    refine6(M, A, B, p_A, p_B, FAIL, elim, i, j, k, sc, h, lst, x)
}

refine6 <- function(M, A, B, p_A, p_B, FAIL, elim, i, j, k, sc, h, lst, x){
    
    #print("refine 6")
    
    if (1 %in% collation(M[i,], sc) == FALSE){
        
        refine9(M, A, B, p_A, p_B, FAIL, elim, i, j, k, sc, h, lst, x)
    }
    
    else {
        
        h <- 1
        
        refine7(M, A, B, p_A, p_B, FAIL, elim, i, j, k, sc, h, lst, x)
    }
}

refine7 <- function(M, A, B, p_A, p_B, FAIL, elim, i, j, k, sc, h, lst, x){
    
    #print("refine 7")
    
    x <- lst[h]
    
    if (1 %in% collation(M[x,], B[,j]) == FALSE){
        
        refine8(M, A, B, p_A, p_B, FAIL, elim, i, j, k, sc, h, lst, x)
    }
    
    else {
        
        h <- h+1
        
        if (h != (rowSums(A)[i])+1){
            
            refine7(M, A, B, p_A, p_B, FAIL, elim, i, j, k, sc, h, lst, x)
        }
        
        else {
            
            refine9(M, A, B, p_A, p_B, FAIL, elim, i, j, k, sc, h, lst, x)
        }
    }
}

refine8 <- function(M, A, B, p_A, p_B, FAIL, elim, i, j, k, sc, h, lst, x){
    
    #print("refine 8")
    
    not_sc <- vector(mode = "numeric", length = p_B)
    
    for (n in 1:p_B){
        
        if (sc[n] == 1){
            
            not_sc[n] <- 0
        }
        else {
            
            not_sc[n] <- 1
            
        }
    }
    
    M[i,] <- collation(M[i,], not_sc)
    
    elim <- elim+1
    h <- h+1
    
    refine9(M, A, B, p_A, p_B, FAIL, elim, i, j, k, sc, h, lst, x)
}

refine9 <- function(M, A, B, p_A, p_B, FAIL, elim, i, j, k, sc, h, lst, x){
    
    #print("refine 9")
    
    sc <- c(0,sc[-p_B])
    j <- j+1
    
    if (j != p_B+1){
        
        refine6(M, A, B, p_A, p_B, FAIL, elim, i, j, k, sc, h, lst, x)
    }
    
    else {
        
        refine10(M, A, B, p_A, p_B, FAIL, elim, i, j, k, sc, h, lst, x)
    }
}

refine10 <- function(M, A, B, p_A, p_B, FAIL, elim, i, j, k, sc, h, lst, x){
    
    print("refine 10")
    
    if (1 %in% M[i,] == FALSE){
        
        FAIL <- 1
        print(M)
        return(FAIL)
    }
    
    else {
        
        i <- i+1
        
        if (i != (p_A)+1){
            
            refine2(M, A, B, p_A, p_B, FAIL, elim, i, j, k, sc, h, lst, x)
        }
        
        else {
            
            
            if (elim != 0){
                
                refine1(M, A, B, p_A, p_B, FAIL, elim, i, j, k, sc, h, lst,
x)
            }
            
            else {

                return(M)
            }
        }
    }
}


I really don¹t now where the problem is. Hope that anybody can help me
solving it.



	[[alternative HTML version deleted]]

Maximilian Kofler

2010-May-06 10:18 UTC

head link

[R] Problem with nested functions - functions nested too deeply in source code

Forgot to add that function collation "and"'s two binary vectors.

For example 1 0 0 and 1 0 1 in collation returns 1 0 0. But how already
said, the algorithm itself should work fine because with small graphs I
don't have problems

Duncan Murdoch

2010-May-07 11:19 UTC

head link

[R] Problem with nested functions - functions nested too deeply in source code

Maximilian Kofler wrote:> Hi all!
>
> I?m just implementing the Ullmann?s algorithm for searching subgraph
> isomorphisms in graphNEL objects. The algorithm is running with smaller
> graphs, but when I?m calling it i get an R error message saying that
> functions are nested too deeply in source code. 
I doubt if that was the error message.  More likely you saw

Error: evaluation nested too deeply: infinite recursion / 
options(expressions=)?

(or perhaps a German translation of that).  This isn't a case of the 
source being nested to deeply, but rather of the evaluation being nested 
too deeply.  This happens in recursive algorithms when R runs out of 
stack space, around 5000 calls deep.  Is it likely in your dataset that 
a recursion depth of 5000 is reasonable?  In most cases this indicates a 
programming error that leads to an infinite recursion, but there are 
probably cases where a depth like that is reasonable.

Duncan Murdoch
> I found out that the problem
> is in the so called refinement procedure of the algorithm which consists of
> 10 different functions, returning an adjacency matrix. I?m calling the
> refinement procedure with
>
> M <- refine1(M, A, B, p_A, p_B, FAIL) (note that all parameters in call
> refine1 have been defined previosly)
>
> Then the following steps look like this
>
> #####################################
> # Refinement process                #
> #####################################
>
> refine1 <- function(M, A, B, p_A, p_B, FAIL, elim, i, j, k, sc, h, lst,
x){
>     
>     #print("refine 1")
>     
>     # elim marks if there was eliminated a 1 (and changed to 0)
>     
>     lst <- vector(mode = "numeric")
>     elim <- 0
>     i <- 1
>     
>     refine2(M, A, B, p_A, p_B, FAIL, elim, i, j, k, sc, h, lst, x)
> }
>
> refine2 <- function(M, A, B, p_A, p_B, FAIL, elim, i, j, k, sc, h, lst,
x){
>     
>     #print("refine 2")
>     
>     k <- 1
>     h <- 1
>     
>     sc <- vector(mode = "numeric", length = p_A)
>     
>     for (l in 1:p_A){
>         
>         sc[l] <- 0
>     }
>     
>     sc[1] <- 1
>     
>     refine3(M, A, B, p_A, p_B, FAIL, elim, i, j, k, sc, h, lst, x)
> }
>
> refine3 <- function(M, A, B, p_A, p_B, FAIL, elim, i, j, k, sc, h, lst,
x){
>     
>     #print("refine 3")
>     
>     # check if there is a 1 in the current row in adjacency matrix of
graph1
> which is on the same position of the 1 in sc
>     # sc is a binary string whith only one 1. The position of the one goes
> from the first position of sc to the last position
>     # and is used for scanning. First this is done for graph 1, and than
for
> graph 2. Then it is checked if the following condition
>     # is fulfilled: (for all x) ((A[i,x] = 1) => (there exists one ore
more
> y) (M[x,y] * B[x,j] = 1)). The algorithm terminates if no more
>     # 1 can be changed in a 0
>     
>     if (1 %in% collation(A[i,], sc) == FALSE){
>         
>         refine4(M, A, B, p_A, p_B, FAIL, elim, i, j, k, sc, h, lst, x)
>     }
>     
>     else {
>         
>         
>         
>         lst[k] <- h
>         k <- k+1
>         
>         refine4(M, A, B, p_A, p_B, FAIL, elim, i, j, k, sc, h, lst, x)
>     }
> }
>
> refine4 <- function(M, A, B, p_A, p_B, FAIL, elim, i, j, k, sc, h, lst,
x){
>     
>     #print("refine 4")
>     
>     sc <- c(0,sc[-p_A])
>     h <- h+1
>     
>     if (k != (rowSums(A)[i])+1){
>         
>         refine3(M, A, B, p_A, p_B, FAIL, elim, i, j, k, sc, h, lst, x)
>     }
>     
>     else {
>         
>         refine5(M, A, B, p_A, p_B, FAIL, elim, i, j, k, sc, h, lst, x)
>     }
> }
>
> refine5 <- function(M, A, B, p_A, p_B, FAIL, elim, i, j, k, sc, h, lst,
x){
>     
>     #print("refine 5")
>     
>     j <- 1
>     
>     sc <- vector(mode = "numeric", length = p_B)
>     
>     for (l in 1:p_B){
>         
>         sc[l] <- 0
>     }
>     
>     sc[1] <- 1
>     
>     refine6(M, A, B, p_A, p_B, FAIL, elim, i, j, k, sc, h, lst, x)
> }
>
> refine6 <- function(M, A, B, p_A, p_B, FAIL, elim, i, j, k, sc, h, lst,
x){
>     
>     #print("refine 6")
>     
>     if (1 %in% collation(M[i,], sc) == FALSE){
>         
>         refine9(M, A, B, p_A, p_B, FAIL, elim, i, j, k, sc, h, lst, x)
>     }
>     
>     else {
>         
>         h <- 1
>         
>         refine7(M, A, B, p_A, p_B, FAIL, elim, i, j, k, sc, h, lst, x)
>     }
> }
>
> refine7 <- function(M, A, B, p_A, p_B, FAIL, elim, i, j, k, sc, h, lst,
x){
>     
>     #print("refine 7")
>     
>     x <- lst[h]
>     
>     if (1 %in% collation(M[x,], B[,j]) == FALSE){
>         
>         refine8(M, A, B, p_A, p_B, FAIL, elim, i, j, k, sc, h, lst, x)
>     }
>     
>     else {
>         
>         h <- h+1
>         
>         if (h != (rowSums(A)[i])+1){
>             
>             refine7(M, A, B, p_A, p_B, FAIL, elim, i, j, k, sc, h, lst, x)
>         }
>         
>         else {
>             
>             refine9(M, A, B, p_A, p_B, FAIL, elim, i, j, k, sc, h, lst, x)
>         }
>     }
> }
>
> refine8 <- function(M, A, B, p_A, p_B, FAIL, elim, i, j, k, sc, h, lst,
x){
>     
>     #print("refine 8")
>     
>     not_sc <- vector(mode = "numeric", length = p_B)
>     
>     for (n in 1:p_B){
>         
>         if (sc[n] == 1){
>             
>             not_sc[n] <- 0
>         }
>         else {
>             
>             not_sc[n] <- 1
>             
>         }
>     }
>     
>     M[i,] <- collation(M[i,], not_sc)
>     
>     elim <- elim+1
>     h <- h+1
>     
>     refine9(M, A, B, p_A, p_B, FAIL, elim, i, j, k, sc, h, lst, x)
> }
>
> refine9 <- function(M, A, B, p_A, p_B, FAIL, elim, i, j, k, sc, h, lst,
x){
>     
>     #print("refine 9")
>     
>     sc <- c(0,sc[-p_B])
>     j <- j+1
>     
>     if (j != p_B+1){
>         
>         refine6(M, A, B, p_A, p_B, FAIL, elim, i, j, k, sc, h, lst, x)
>     }
>     
>     else {
>         
>         refine10(M, A, B, p_A, p_B, FAIL, elim, i, j, k, sc, h, lst, x)
>     }
> }
>
> refine10 <- function(M, A, B, p_A, p_B, FAIL, elim, i, j, k, sc, h, lst,
x){
>     
>     print("refine 10")
>     
>     if (1 %in% M[i,] == FALSE){
>         
>         FAIL <- 1
>         print(M)
>         return(FAIL)
>     }
>     
>     else {
>         
>         i <- i+1
>         
>         if (i != (p_A)+1){
>             
>             refine2(M, A, B, p_A, p_B, FAIL, elim, i, j, k, sc, h, lst, x)
>         }
>         
>         else {
>             
>             
>             if (elim != 0){
>                 
>                 refine1(M, A, B, p_A, p_B, FAIL, elim, i, j, k, sc, h, lst,
> x)
>             }
>             
>             else {
>
>                 return(M)
>             }
>         }
>     }
> }
>
>
> I really don?t now where the problem is. Hope that anybody can help me
> solving it.
>
>
>
> 	[[alternative HTML version deleted]]
>
>   
> ------------------------------------------------------------------------
>
> ______________________________________________
> R-help at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide
http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.
>

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