Why do I keep getting a Method Error for Graphs package every time?

Specific Domains Graphs
,
1

Hello there,
I am having a seemingly recurring issue here.
Lets say I am working on a Julia file with graphs for a while and everything is going well. Then I close that file and don’t use it for ages, and then the next time I come back, I get this error related to the Graphs package. Every single time. I don’t know what is causing this, please help.
It has become very frustrating as my work uses network graphs ALOT.
I suspect it’s something I am doing.

But here is the error message I get:

MethodError: no method matching layout(::Spring{2, Float64}, ::SimpleDiGraph{Int64})
Closest candidates are:
  layout(::NetworkLayout.IterativeLayout, ::AbstractMatrix) at \NetworkLayout.jl:75       
  layout(::NetworkLayout.AbstractLayout, ::LightGraphs.AbstractGraph)

Here is a snippet of my code to better explain

import Cairo,Fontconfig 
using Random, Graphs, GraphMakie, GLMakie, CairoMakie, DataFrames, DelimitedFiles, Distributions, MetaGraphs
using GraphMakie.NetworkLayout 
CairoMakie.activate!()

Random.seed!(2409);
system_data = readdlm("PrPm/16 NodeNetwork Adjacency matrix.csv",  ',', header= false, Int);
system_matrix = Matrix(DataFrame(system_data, :auto));
system_graph= DiGraph(system_matrix)
Sources=[1,3,13]; link_reliability=0.9; Node_Priors = 1 #no node failure therefore node reliability = 1
    f, ax, p = graphplot(system_graph, #layout=SquareGrid(),
                arrow_size=[25 for i in 1:ne(system_graph)],
                nlabels= repr.(1:nv(system_graph)),    
                                                            
                node_color=[if i in Sources "blue" else "pink"  end for i in 1:nv(system_graph)  ], #Use colours to identify sink vs source nodes                                      
                node_size=[20 for i in 1:nv(system_graph) ])
                ax.yreversed = true 
                hidedecorations!(ax)  # hides ticks, grid and lables 
                hidespines!(ax)  # hide the frame 
    display(f)

What I have tried:

  1. Running my code line by line to figure out where problem is. I believe the problem line to be: graph plot line here: f, ax, p = graphplot(system_graph, #layout=SquareGrid(),
  2. Killing and restarting julia REPL
  3. Updating Graphs package in package manager
    4.Restarting everything
2

Most likely is due to incompatible packages. The following works just fine

using Graphs, GraphMakie, GLMakie
using NetworkLayout
g = wheel_graph(10)
f, ax, p = graphplot(g, edge_width=[3 for i in 1:ne(g)],
    node_size=[10 for i in 1:nv(g)])

with the following versions:

 Status `~/Documents/FunArt/graphsmakie/Project.toml`
  [e9467ef8] GLMakie v0.5.5
  [1ecd5474] GraphMakie v0.3.4
  [86223c79] Graphs v1.6.0
  [46757867] NetworkLayout v0.4.4
3

Copying and pasting the above on my side gives me the same code. I went back to my julia package manager to check my package versions to compare to yours. My versions are:

GLMakie v0.4.5
GraphMakie v0.2.3
Graphs v1.6.0
NetworkLayout v0.4.0

I wonder if the version mismatch is the cause,.
The problem now is that when I call update to all three non-up-to-date packages in julia, its says no changes and doesn’t seem to find a new version for non of them.

4

Your version of NetworkLayout is looking for LightGraphs - later versions look for Graphs…

1 Like
5

Thank you,
Forcing an update by: NetworkLayout@0.4.0 threw an error about AbstractPlotting package was preventing the update. By removing AbstractPlotting package, I was able to update and now my code is working as normal thank you very much.

For future reference, may I ask how you were able to deduce that the package version was the issue or was it by process of elimination?

Thank you again :slight_smile:

6

:grinning: Your first error message mentions LightGraphs …

1 Like
7

Ohhh yes, that makes sense.
This also gives me a much clearer understanding of these kinds of errors in the future.
Thanks again for taking time to help :+1:t3:

1 Like