Error: MethodError: no method matching validate

New to Julia
, ,
1

Hi! I’m new to Julia and Catalyst.jl. I am trying to follow the tutorial of Introduction to learn how to use catalyst. I install packages, including

Blockquote
Status C:\Users\23954749\.julia\environments\v1.10\Project.toml
⌃ [479239e8] Catalyst v12.1.1
⌃ [0c46a032] DifferentialEquations v6.20.0
[f80590ac] JuliaFEM v0.5.1
⌅ [98e50ef6] JuliaFormatter v0.15.11
⌅ [961ee093] ModelingToolkit v6.4.9
[2774e3e8] NLsolve v4.5.1
⌅ [1dea7af3] OrdinaryDiffEq v5.71.2
[91a5bcdd] Plots v1.40.9
⌅ [47a9eef4] SparseDiffTools v1.21.0
[24249f21] SymPy v2.2.1
Info Packages marked with ⌃ and ⌅ have new versions available. Those with ⌃ may be upgradable, but those with ⌅ are restricted by compatibility constraints from upgrading. To see why use status --outdated

I directly copied the codes in tutorial of constructing the reaction network, as shown below,

Blockquote
using Catalyst
using OrdinaryDiffEq
using Plots
rn = @reaction_network begin
b, 0 → X
d, X → 0
end

Julia returned errors that I can’t solve, which I hope to get helped so I can keep going on.

Blockquote
ERROR: MethodError: no method matching validate(::ReactionSystem{Nothing, Catalyst.NetworkProperties{Int64, Term{Real, Base.ImmutableDict{DataType, Any}}}})

Closest candidates are:
validate(::Equation; info)
@ ModelingToolkit C:\Users\23954749.julia\packages\ModelingToolkit\0dKHa\src\systems\validation.jl:185
validate(::Equation, ::Union{Num, SymbolicUtils.Symbolic, Unitful.Quantity}; info)
@ ModelingToolkit C:\Users\23954749.julia\packages\ModelingToolkit\0dKHa\src\systems\validation.jl:186
validate(::Equation, ::Vector; info)
@ ModelingToolkit C:\Users\23954749.julia\packages\ModelingToolkit\0dKHa\src\systems\validation.jl:187
…

Stacktrace:
[1] ReactionSystem(eqs::Vector{…}, iv::Sym{…}, states::Vector{…}, ps::Vector{…}, var_to_name::Dict{…}, observed::Vector{…}, name::Symbol, systems::Vector{…}, defaults::Dict{…}, connection_type::Nothing, csys::Nothing, nps::Catalyst.NetworkProperties{…}, cls::Bool; checks::Bool)
@ Catalyst C:\Users\23954749.julia\packages\Catalyst\JocXA\src\reactionsystem.jl:460
[2] ReactionSystem(eqs::Vector{…}, iv::Sym{…}, states::Vector{…}, ps::Vector{…}; observed::Vector{…}, systems::Vector{…}, name::Symbol, default_u0::Dict{…}, default_p::Dict{…}, defaults::Dict{…}, connection_type::Nothing, checks::Bool, constraints::Nothing, networkproperties::Nothing, combinatoric_ratelaws::Bool, balanced_bc_check::Bool)
@ Catalyst C:\Users\23954749.julia\packages\Catalyst\JocXA\src\reactionsystem.jl:547
[3] make_ReactionSystem_internal(rxs::Vector{…}, iv::Num, no_sps::Nothing, ps_in::Vector{…}; kwargs::@Kwargs{…})
@ Catalyst C:\Users\23954749.julia\packages\Catalyst\JocXA\src\reactionsystem.jl:597
[4] top-level scope
@ C:\Users\23954749.julia\packages\Catalyst\JocXA\src\reaction_network.jl:282

Thank you!

3

I have been reading the other similar questions in Julia Forum. Their ‘error: no method matching’ is often relevant to the specific function or expression in their codes. That came to my blindside: I didn’t call ‘validate’ function, which I assume should be embedded in the package or somewhere that the experienced developers did. I don’t know if this could be a stupid question, but I would really appreciate it if somebody could help me out. Thanks!

4

You are on Catalyst v12 which is at this point two and a half years old, while the current release is 14.4.1.

Make sure you either read the documentation for v12, or update to v14 if you’re reading the latest docs.

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5

Yes! I noticed and I tried both documentations of catalyst v12 and v14. They returned the same error. I’m using VS Code for Julia. I don’t know if that could be the problem, such as missing packages to support catalyst.jl.

6

I’m not sure where in the docs you get your example from, but in any event here’s what I get on Julia 1.11.1:

(jl_hXzRfb) pkg> st
Status `(...)\Temp\jl_hXzRfb\Project.toml`
  [479239e8] Catalyst v14.4.1
  [1dea7af3] OrdinaryDiffEq v6.90.1

julia> using Catalyst, OrdinaryDiffEq

julia> rn = @reaction_network begin
       b, 0 --> X
       d, X --> 0
       end
Model ##ReactionSystem#250:
Unknowns (1): see unknowns(##ReactionSystem#250)
  X(t)
Parameters (2): see parameters(##ReactionSystem#250)
  b
  d
7

Problem solved~! After reading your comment, I am pretty sure something should go wrong with my Julia. So I uninstalled Julia and deleted all folders, and I re-installed Julia and catalyst. Everything worked out! I guess this problem could be the conflict of my tons of packages.
Such a long day! feels like an ambitious man stumbled down in his first step out because he is too equipped. :joy:

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8

This is very likely, make sure to do your work in minimal project specific environments containing only the packages you really need for the task at hand:

1 Like
9

I will delete this question in 3 days. Thank you for the community! If any newbies met similar problems like I did. Just re-install Julia and Catalyst~ :innocent:

10

No need to delete - you never know who might stumble upon this and find it helpful in future.

3 Likes
11

You are right! I hope my experience could help the other new users of Julia! Thank you Nilshg! :smiling_face_with_three_hearts:

1 Like