Precompilation Errors and UndefVarError in DifferentialEquations.jl (Julia 1.11.3 on macOS)

[hpoit]

Issue Description

I am experiencing persistent issues with DifferentialEquations.jl, Flux.jl, and DiffEqJump.jl on Julia 1.11.3 running on macOS.

When I try:

using DifferentialEquations, Flux, DiffEqJump

I receive multiple precompilation errors, including:

• ERROR: Method overwriting is not permitted during Module precompilation.
• UndefVarError: ODEProblem not defined
• Modules are failing to precompile due to missing dependencies.

Steps to Reproduce

1. Open Julia 1.11.3
2. Run the following:

import Pkg
Pkg.add(["DifferentialEquations", "Flux", "DiffEqJump"])
Pkg.precompile()
using DifferentialEquations, Flux, DiffEqJump

3. Observe errors during precompilation.

System Info

• Julia Version: 1.11.3
• Operating System: macOS (specify version)
• Installed Packages (Pkg.status() output): https://gist.github.com/hpoit/b9d75f503c271f15892a9a069e123b1f

Expected Behavior
The packages should load without precompilation errors.

Observed Behavior

• Precompilation fails for DifferentialEquations.jl and DiffEqJump.jl
• Errors related to SciMLBase.ODEProblem
• UndefVarError: ODEProblem not defined

Additional Notes

• I have tried removing and reinstalling all packages.
• The issue persists in both the Julia REPL and VSCode Jupyter notebook.

[ChrisRackauckas]

Share ]st

[hpoit]

Hi Chris, here are the outputs of the actual notebook that I am trying to run:
Integrated-cell - output issues.pdf

[hpoit]

Hey @ChrisRackauckas, if you try using these packages:
Installed Packages (Pkg.status() output): https://gist.github.com/hpoit/b9d75f503c271f15892a9a069e123b1f

Do you get the same error? If not, should I just try uninstalling Julia completely and installing it again?

I have an important meeting today with the founder of a genomics company and it would be nice to show the packages in action.

[ChrisRackauckas]

Again you need to share ]st to have an idea of how to recreate it

[hpoit]

Chris were you able to open the PDF I shared 2 messages ago? There you will find the complete notebook.

…

On Wed, Feb 5, 2025, 12:32 Christopher Rackauckas ***@***.***> wrote: Again you need to share ]st to have an idea of how to recreate it — Reply to this email directly, view it on GitHub <#1072 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AA4KA7CBMCG2DOA7OP67ZXD2OIVI3AVCNFSM6AAAAABWPK7NQOVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDMMZXGI2TKMZZGA> . You are receiving this because you authored the thread.Message ID: ***@***.***>

[ChrisRackauckas]

But share ]st... because it's not in there...

[hpoit]

Chris, forgive me for my ignorance. Here's ]st:

(@v1.11) pkg> st
Status `~/.julia/environments/v1.11/Project.toml`
⌃ [2b5f629d] DiffEqBase v6.130.1
⌃ [c894b116] DiffEqJump v8.6.2
⌃ [0c46a032] DifferentialEquations v7.11.0
  [31c24e10] Distributions v0.25.117
⌃ [587475ba] Flux v0.14.21
  [7073ff75] IJulia v1.26.0
  [91a5bcdd] Plots v1.40.9
  [f27b6e38] Polynomials v4.0.14
Info Packages marked with ⌃ have new versions available and may be upgradable.

[ChrisRackauckas]

What if you remove Flux and ]up?

[hpoit]

Integrated-cell - output issues 2.pdf

[hpoit]

The second block of the notebook requires Flux, how would I do without it though?

[ChrisRackauckas]

Oh wait, remove DiffEqJump and change that to JumpProcesses. It was renamed years ago so that's why you're on old versions.

[hpoit]

Thanks Chris, notebook working!