Several Compilation errors and continuous recompilation issue

General Usage
1

Hi all,
I have been using (Ordinary)DifferentialEquations.jl for a few years without issues. As of today, after an update, a very long list of errors is generated which there seems to be no way to resolve. I paste only part of it below. I am using julia 1.12.5
I tried to remove ~/.julia and .julia from my current project, re-install everythibg, but the issue with OrdinaryDiffEqDifferentiation, Sundials, BoundaryValueDiffEqMIRK etc. cannot be resolved.

I paste below part of the recursive error. It is the same, just for different packages.

thanks

. ? OrdinaryDiffEqDifferentiation → OrdinaryDiffEqDifferentiationSparseArraysExt
│ This may mean OrdinaryDiffEqSDIRK [2d112036-d095-4a1e-ab9a-08536f3ecdbf] does not support precompilation but is imported by a module that does.
└ @ Base loading.jl:2641
  ? OrdinaryDiffEqDifferentiation
  ? OrdinaryDiffEqDifferentiation → OrdinaryDiffEqDifferentiationSparseArraysExt
  ? OrdinaryDiffEqNonlinearSolve
  ? OrdinaryDiffEqSDIRK
  ? OrdinaryDiffEqBDF
[ Info: Precompiling OrdinaryDiffEqBDF [6ad6398a-0878-4a85-9266-38940aa047c8] (cache misses: incompatible header (4))
┌ Warning: Module OrdinaryDiffEqSDIRK with build ID ffffffff-ffff-ffff-cd6f-11d5ad4c9603 is missing from the cache.
│ This may mean OrdinaryDiffEqSDIRK [2d112036-d095-4a1e-ab9a-08536f3ecdbf] does not support precompilation but is imported by a module that does.
└ @ Base loading.jl:2641
┌ Info: Skipping precompilation due to precompilable error. Importing OrdinaryDiffEqBDF [6ad6398a-0878-4a85-9266-38940aa047c8].
└   exception = Error when precompiling module, potentially caused by a __precompile__(false) declaration in the module.
Info Given OrdinaryDiffEqRosenbrock was explicitly requested, output will be shown live 
WARNING: Method definition rrule(typeof(SciMLBase.numargs), Any) in module SciMLBaseChainRulesCoreExt at /Users/simone/.julia/packages/SciMLBase/3RWdf/ext/SciMLBaseChainRulesCoreExt.jl:12 overwritten in module DiffEqBaseChainRulesCoreExt at /Users/simone/.julia/packages/DiffEqBase/5LeiG/ext/DiffEqBaseChainRulesCoreExt.jl:10.
ERROR: Method overwriting is not permitted during Module precompilation. Use `__precompile__(false)` to opt-out of precompilation.
  ? OrdinaryDiffEqDifferentiation
  ? OrdinaryDiffEqDifferentiation → OrdinaryDiffEqDifferentiationSparseArraysExt
  ? OrdinaryDiffEqRosenbrock
[ Info: Precompiling OrdinaryDiffEqRosenbrock [43230ef6-c299-4910-a778-202eb28ce4ce] (cache misses: incompatible header (4))
WARNING: Method definition rrule(typeof(SciMLBase.numargs), Any) in module SciMLBaseChainRulesCoreExt at /Users/simone/.julia/packages/SciMLBase/3RWdf/ext/SciMLBaseChainRulesCoreExt.jl:12 overwritten in module DiffEqBaseChainRulesCoreExt at /Users/simone/.julia/packages/DiffEqBase/5LeiG/ext/DiffEqBaseChainRulesCoreExt.jl:10.
ERROR: Method overwriting is not permitted during Module precompilation. Use `__precompile__(false)` to opt-out of precompilation.
┌ Info: Skipping precompilation due to precompilable error. Importing OrdinaryDiffEqRosenbrock [43230ef6-c299-4910-a778-202eb28ce4ce].
└   exception = Error when precompiling module, potentially caused by a __precompile__(false) declaration in the module.



Info Given OrdinaryDiffEqDefault was explicitly requested, output will be shown live 
┌ Warning: Module OrdinaryDiffEqRosenbrock with build ID ffffffff-ffff-ffff-690b-38e0a770143e is missing from the cache.dinaryDiffEqDifferentiation → OrdinaryDiffEqDifferentiationSparseArraysExt
│ This may mean OrdinaryDiffEqRosenbrock [43230ef6-c299-4910-a778-202eb28ce4ce] does not support precompilation but is imported by a module that does.
└ @ Base loading.jl:2641
  ? OrdinaryDiffEqDifferentiation
  ? OrdinaryDiffEqDifferentiation → OrdinaryDiffEqDifferentiationSparseArraysExt
  ? OrdinaryDiffEqRosenbrock
  ? OrdinaryDiffEqNonlinearSolve
  ? OrdinaryDiffEqSDIRK
  ? OrdinaryDiffEqBDF
  ? OrdinaryDiffEqDefault
[ Info: Precompiling OrdinaryDiffEqDefault [50262376-6c5a-4cf5-baba-aaf4f84d72d7] (cache misses: incompatible header (4))
┌ Warning: Module OrdinaryDiffEqRosenbrock with build ID ffffffff-ffff-ffff-690b-38e0a770143e is missing from the cache.
│ This may mean OrdinaryDiffEqRosenbrock [43230ef6-c299-4910-a778-202eb28ce4ce] does not support precompilation but is imported by a module that does.
└ @ Base loading.jl:2641
┌ Info: Skipping precompilation due to precompilable error. Importing OrdinaryDiffEqDefault [50262376-6c5a-4cf5-baba-aaf4f84d72d7].
└   exception = Error when precompiling module, potentially caused by a __precompile__(false) declaration in the module.
Info Given OrdinaryDiffEqFIRK was explicitly requested, output will be shown live 
WARNING: Method definition rrule(typeof(SciMLBase.numargs), Any) in module SciMLBaseChainRulesCoreExt at /Users/simone/.julia/packages/SciMLBase/3RWdf/ext/SciMLBaseChainRulesCoreExt.jl:12 overwritten in module DiffEqBaseChainRulesCoreExt at /Users/simone/.julia/packages/DiffEqBase/5LeiG/ext/DiffEqBaseChainRulesCoreExt.jl:10.
ERROR: Method overwriting is not permitted during Module precompilation. Use `__precompile__(false)` to opt-out of precompilation.
  ? OrdinaryDiffEqDifferentiation
  ? OrdinaryDiffEqDifferentiation → OrdinaryDiffEqDifferentiationSparseArraysExt
  ? OrdinaryDiffEqNonlinearSolve
  ? OrdinaryDiffEqFIRK
[ Info: Precompiling OrdinaryDiffEqFIRK [5960d6e9-dd7a-4743-88e7-cf307b64f125] (cache misses: incompatible header (4))
WARNING: Method definition rrule(typeof(SciMLBase.numargs), Any) in module SciMLBaseChainRulesCoreExt at /Users/simone/.julia/packages/SciMLBase/3RWdf/ext/SciMLBaseChainRulesCoreExt.jl:12 overwritten in module DiffEqBaseChainRulesCoreExt at /Users/simone/.julia/packages/DiffEqBase/5LeiG/ext/DiffEqBaseChainRulesCoreExt.jl:10.
ERROR: Method overwriting is not permitted during Module precompilation. Use `__precompile__(false)` to opt-out of precompilation.
┌ Info: Skipping precompilation due to precompilable error. Importing OrdinaryDiffEqFIRK [5960d6e9-dd7a-4743-88e7-cf307b64f125].
└   exception = Error when precompiling module, potentially caused by a __precompile__(false) declaration in the module.
Info Given OrdinaryDiffEqPDIRK was explicitly requested, output will be shown live 
┌ Warning: Module OrdinaryDiffEqDifferentiation with build ID ffffffff-ffff-ffff-9056-85af3b962caf is missing from the cache.yDiffEqDifferentiation → OrdinaryDiffEqDifferentiationSparseArraysExt
│ This may mean OrdinaryDiffEqDifferentiation [4302a76b-040a-498a-8c04-15b101fed76b] does not support precompilation but is imported by a module that does.
└ @ Base loading.jl:2641
  ? OrdinaryDiffEqDifferentiation
  ? OrdinaryDiffEqDifferentiation → OrdinaryDiffEqDifferentiationSparseArraysExt
  ? OrdinaryDiffEqNonlinearSolve
  ? OrdinaryDiffEqPDIRK
[ Info: Precompiling OrdinaryDiffEqPDIRK [5dd0a6cf-3d4b-4314-aa06-06d4e299bc89] (cache misses: incompatible header (4))
┌ Warning: Module OrdinaryDiffEqDifferentiation with build ID ffffffff-ffff-ffff-9056-85af3b962caf is missing from the cache.
│ This may mean OrdinaryDiffEqDifferentiation [4302a76b-040a-498a-8c04-15b101fed76b] does not support precompilation but is imported by a module that does.
└ @ Base loading.jl:2641
┌ Info: Skipping precompilation due to precompilable error. Importing OrdinaryDiffEqPDIRK [5dd0a6cf-3d4b-4314-aa06-06d4e299bc89].
└   exception = Error when precompiling module, potentially caused by a __precompile__(false) declaration in the module.
Info Given OrdinaryDiffEqIMEXMultistep was explicitly requested, output will be shown live 
┌ Warning: Module OrdinaryDiffEqDifferentiation with build ID ffffffff-ffff-ffff-9056-85af3b962caf is missing from the cache.yDiffEqDifferentiation → OrdinaryDiffEqDifferentiationSparseArraysExt
│ This may mean OrdinaryDiffEqDifferentiation [4302a76b-040a-498a-8c04-15b101fed76b] does not support precompilation but is imported by a module that does.
└ @ Base loading.jl:2641
  ? OrdinaryDiffEqDifferentiation
  ? OrdinaryDiffEqDifferentiation → OrdinaryDiffEqDifferentiationSparseArraysExt
  ? OrdinaryDiffEqNonlinearSolve
  ? OrdinaryDiffEqIMEXMultistep
[ Info: Precompiling OrdinaryDiffEqIMEXMultistep [9f002381-b378-40b7-97a6-27a27c83f129] (cache misses: incompatible header (4))
┌ Warning: Module OrdinaryDiffEqDifferentiation with build ID ffffffff-ffff-ffff-9056-85af3b962caf is missing from the cache.
│ This may mean OrdinaryDiffEqDifferentiation [4302a76b-040a-498a-8c04-15b101fed76b] does not support precompilation but is imported by a module that does.
└ @ Base loading.jl:2641
┌ Info: Skipping precompilation due to precompilable error. Importing OrdinaryDiffEqIMEXMultistep [9f002381-b378-40b7-97a6-27a27c83f129].
└   exception = Error when precompiling module, potentially caused by a __precompile__(false) declaration in the module.
Info Given OrdinaryDiffEqExponentialRK was explicitly requested, output will be shown live 
┌ Warning: Module OrdinaryDiffEqDifferentiation with build ID ffffffff-ffff-ffff-9056-85af3b962caf is missing from the cache.yDiffEqDifferentiation → OrdinaryDiffEqDifferentiationSparseArraysExt
│ This may mean OrdinaryDiffEqDifferentiation [4302a76b-040a-498a-8c04-15b101fed76b] does not support precompilation but is imported by a module that does.
└ @ Base loading.jl:2641
  ? OrdinaryDiffEqDifferentiation
  ? OrdinaryDiffEqDifferentiation → OrdinaryDiffEqDifferentiationSparseArraysExt
  ? OrdinaryDiffEqExponentialRK
[ Info: Precompiling OrdinaryDiffEqExponentialRK [e0540318-69ee-4070-8777-9e2de6de23de] (cache misses: incompatible header (4))
┌ Warning: Module OrdinaryDiffEqDifferentiation with build ID ffffffff-ffff-ffff-9056-85af3b962caf is missing from the cache.
│ This may mean OrdinaryDiffEqDifferentiation [4302a76b-040a-498a-8c04-15b101fed76b] does not support precompilation but is imported by a module that does.
└ @ Base loading.jl:2641
┌ Info: Skipping precompilation due to precompilable error. Importing OrdinaryDiffEqExponentialRK [e0540318-69ee-4070-8777-9e2de6de23de].
└   exception = Error when precompiling module, potentially caused by a __precompile__(false) declaration in the module.
2

Sorry we had a bit of a hiccup today cleaning up a type piracy. If you update SciMLBase to the patch version it should be gone.

1 Like
3

I have a similar recursive precompilation error

How exactly do I update to the patched version of SciMLBase?

4

Just do ]up

5

I did that. The continuos recursive error has vanished. But there are these other warnings that are still showing up.

(@v1.12) pkg> up
    Updating registry at `~/.julia/registries/General.toml`
   Installed TiffImages ─ v0.11.8
     Project No packages added to or removed from `~/.julia/environments/v1.12/Project.toml`
    Updating `~/.julia/environments/v1.12/Manifest.toml`
  [731e570b] ↑ TiffImages v0.11.6 ⇒ v0.11.8
Precompiling packages  ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 25/25
  ? BoundaryValueDiffEqCore
  ? BoundaryValueDiffEqCore
  ? OrdinaryDiffEqDifferentiation
  ? OrdinaryDiffEqDifferentiation → OrdinaryDiffEqDifferentiationSparseArra…
  ? BoundaryValueDiffEqAscher
  ? BoundaryValueDiffEqShooting
  ? BoundaryValueDiffEqFIRK
  ? BoundaryValueDiffEqMIRK
  ? BoundaryValueDiffEqMIRKN
  ? OrdinaryDiffEqRosenbrock
  ? OrdinaryDiffEqExponentialRK
  ? OrdinaryDiffEqExtrapolation
  ? OrdinaryDiffEqNonlinearSolve
  ? OrdinaryDiffEqPDIRK
  ? OrdinaryDiffEqStabilizedIRK
  ? OrdinaryDiffEqSDIRK
  ? OrdinaryDiffEqFIRK
  ? OrdinaryDiffEqIMEXMultistep
  ? StochasticDiffEq
  ? OrdinaryDiffEqBDF
  ? BoundaryValueDiffEq
  ? OrdinaryDiffEqDefault
  ? OrdinaryDiffEq
  ? DelayDiffEq
  ? DifferentialEquations
Precompiling packages finished.
  1 dependency successfully precompiled in 42 seconds. 548 already precompiled.
  24 dependencies failed but may be precompilable after restarting julia
  24 dependencies had output during precompilation:
┌ OrdinaryDiffEq
│  WARNING: Method definition rrule(typeof(SciMLBase.checkkwargs), Any) in module SciMLBaseChainRulesCoreExt at /home/user/.julia/packages/SciMLBase/eTBDr/ext/SciMLBaseChainRulesCoreExt.jl:10 overwritten in module DiffEqBaseChainRulesCoreExt at /home/user/.julia/packages/DiffEqBase/cggak/ext/DiffEqBaseChainRulesCoreExt.jl:11.
│  ERROR: Method overwriting is not permitted during Module precompilation. Use `__precompile__(false)` to opt-out of precompilation.
└  
┌ OrdinaryDiffEqNonlinearSolve
│  WARNING: Method definition rrule(typeof(SciMLBase.checkkwargs), Any) in module SciMLBaseChainRulesCoreExt at /home/user/.julia/packages/SciMLBase/eTBDr/ext/SciMLBaseChainRulesCoreExt.jl:10 overwritten in module DiffEqBaseChainRulesCoreExt at /home/user/.julia/packages/DiffEqBase/cggak/ext/DiffEqBaseChainRulesCoreExt.jl:11.
│  ERROR: Method overwriting is not permitted during Module precompilation. Use `__precompile__(false)` to opt-out of precompilation.
└  
┌ BoundaryValueDiffEqMIRKN
│  WARNING: Method definition rrule(typeof(SciMLBase.checkkwargs), Any) in module SciMLBaseChainRulesCoreExt at /home/user/.julia/packages/SciMLBase/eTBDr/ext/SciMLBaseChainRulesCoreExt.jl:10 overwritten in module DiffEqBaseChainRulesCoreExt at /home/user/.julia/packages/DiffEqBase/cggak/ext/DiffEqBaseChainRulesCoreExt.jl:11.
│  ERROR: Method overwriting is not permitted during Module precompilation. Use `__precompile__(false)` to opt-out of precompilation.
└  
┌ OrdinaryDiffEqDifferentiation → OrdinaryDiffEqDifferentiationSparseArraysExt
│  WARNING: Method definition rrule(typeof(SciMLBase.checkkwargs), Any) in module SciMLBaseChainRulesCoreExt at /home/user/.julia/packages/SciMLBase/eTBDr/ext/SciMLBaseChainRulesCoreExt.jl:10 overwritten in module DiffEqBaseChainRulesCoreExt at /home/user/.julia/packages/DiffEqBase/cggak/ext/DiffEqBaseChainRulesCoreExt.jl:11.
│  ERROR: Method overwriting is not permitted during Module precompilation. Use `__precompile__(false)` to opt-out of precompilation.
└  
┌ OrdinaryDiffEqPDIRK
│  WARNING: Method definition rrule(typeof(SciMLBase.checkkwargs), Any) in module SciMLBaseChainRulesCoreExt at /home/user/.julia/packages/SciMLBase/eTBDr/ext/SciMLBaseChainRulesCoreExt.jl:10 overwritten in module DiffEqBaseChainRulesCoreExt at /home/user/.julia/packages/DiffEqBase/cggak/ext/DiffEqBaseChainRulesCoreExt.jl:11.
│  ERROR: Method overwriting is not permitted during Module precompilation. Use `__precompile__(false)` to opt-out of precompilation.
└  
┌ DelayDiffEq
│  WARNING: Method definition rrule(typeof(SciMLBase.checkkwargs), Any) in module SciMLBaseChainRulesCoreExt at /home/user/.julia/packages/SciMLBase/eTBDr/ext/SciMLBaseChainRulesCoreExt.jl:10 overwritten in module DiffEqBaseChainRulesCoreExt at /home/user/.julia/packages/DiffEqBase/cggak/ext/DiffEqBaseChainRulesCoreExt.jl:11.
│  ERROR: Method overwriting is not permitted during Module precompilation. Use `__precompile__(false)` to opt-out of precompilation.
└  
┌ BoundaryValueDiffEqMIRK
│  WARNING: Method definition rrule(typeof(SciMLBase.checkkwargs), Any) in module SciMLBaseChainRulesCoreExt at /home/user/.julia/packages/SciMLBase/eTBDr/ext/SciMLBaseChainRulesCoreExt.jl:10 overwritten in module DiffEqBaseChainRulesCoreExt at /home/user/.julia/packages/DiffEqBase/cggak/ext/DiffEqBaseChainRulesCoreExt.jl:11.
│  ERROR: Method overwriting is not permitted during Module precompilation. Use `__precompile__(false)` to opt-out of precompilation.
└  
┌ BoundaryValueDiffEqShooting
│  WARNING: Method definition rrule(typeof(SciMLBase.checkkwargs), Any) in module SciMLBaseChainRulesCoreExt at /home/user/.julia/packages/SciMLBase/eTBDr/ext/SciMLBaseChainRulesCoreExt.jl:10 overwritten in module DiffEqBaseChainRulesCoreExt at /home/user/.julia/packages/DiffEqBase/cggak/ext/DiffEqBaseChainRulesCoreExt.jl:11.
│  ERROR: Method overwriting is not permitted during Module precompilation. Use `__precompile__(false)` to opt-out of precompilation.
└  
┌ OrdinaryDiffEqIMEXMultistep
│  WARNING: Method definition rrule(typeof(SciMLBase.checkkwargs), Any) in module SciMLBaseChainRulesCoreExt at /home/user/.julia/packages/SciMLBase/eTBDr/ext/SciMLBaseChainRulesCoreExt.jl:10 overwritten in module DiffEqBaseChainRulesCoreExt at /home/user/.julia/packages/DiffEqBase/cggak/ext/DiffEqBaseChainRulesCoreExt.jl:11.
│  ERROR: Method overwriting is not permitted during Module precompilation. Use `__precompile__(false)` to opt-out of precompilation.
└  
┌ BoundaryValueDiffEq
│  WARNING: Method definition rrule(typeof(SciMLBase.checkkwargs), Any) in module SciMLBaseChainRulesCoreExt at /home/user/.julia/packages/SciMLBase/eTBDr/ext/SciMLBaseChainRulesCoreExt.jl:10 overwritten in module DiffEqBaseChainRulesCoreExt at /home/user/.julia/packages/DiffEqBase/cggak/ext/DiffEqBaseChainRulesCoreExt.jl:11.
│  ERROR: Method overwriting is not permitted during Module precompilation. Use `__precompile__(false)` to opt-out of precompilation.
└  
┌ BoundaryValueDiffEqAscher
│  WARNING: Method definition rrule(typeof(SciMLBase.checkkwargs), Any) in module SciMLBaseChainRulesCoreExt at /home/user/.julia/packages/SciMLBase/eTBDr/ext/SciMLBaseChainRulesCoreExt.jl:10 overwritten in module DiffEqBaseChainRulesCoreExt at /home/user/.julia/packages/DiffEqBase/cggak/ext/DiffEqBaseChainRulesCoreExt.jl:11.
│  ERROR: Method overwriting is not permitted during Module precompilation. Use `__precompile__(false)` to opt-out of precompilation.
└  
┌ StochasticDiffEq
│  WARNING: Method definition rrule(typeof(SciMLBase.checkkwargs), Any) in module SciMLBaseChainRulesCoreExt at /home/user/.julia/packages/SciMLBase/eTBDr/ext/SciMLBaseChainRulesCoreExt.jl:10 overwritten in module DiffEqBaseChainRulesCoreExt at /home/user/.julia/packages/DiffEqBase/cggak/ext/DiffEqBaseChainRulesCoreExt.jl:11.
│  ERROR: Method overwriting is not permitted during Module precompilation. Use `__precompile__(false)` to opt-out of precompilation.
└  
┌ OrdinaryDiffEqBDF
│  WARNING: Method definition rrule(typeof(SciMLBase.checkkwargs), Any) in module SciMLBaseChainRulesCoreExt at /home/user/.julia/packages/SciMLBase/eTBDr/ext/SciMLBaseChainRulesCoreExt.jl:10 overwritten in module DiffEqBaseChainRulesCoreExt at /home/user/.julia/packages/DiffEqBase/cggak/ext/DiffEqBaseChainRulesCoreExt.jl:11.
│  ERROR: Method overwriting is not permitted during Module precompilation. Use `__precompile__(false)` to opt-out of precompilation.
└  
┌ OrdinaryDiffEqExtrapolation
│  WARNING: Method definition rrule(typeof(SciMLBase.checkkwargs), Any) in module SciMLBaseChainRulesCoreExt at /home/user/.julia/packages/SciMLBase/eTBDr/ext/SciMLBaseChainRulesCoreExt.jl:10 overwritten in module DiffEqBaseChainRulesCoreExt at /home/user/.julia/packages/DiffEqBase/cggak/ext/DiffEqBaseChainRulesCoreExt.jl:11.
│  ERROR: Method overwriting is not permitted during Module precompilation. Use `__precompile__(false)` to opt-out of precompilation.
└  
┌ OrdinaryDiffEqStabilizedIRK
│  WARNING: Method definition rrule(typeof(SciMLBase.checkkwargs), Any) in module SciMLBaseChainRulesCoreExt at /home/user/.julia/packages/SciMLBase/eTBDr/ext/SciMLBaseChainRulesCoreExt.jl:10 overwritten in module DiffEqBaseChainRulesCoreExt at /home/user/.julia/packages/DiffEqBase/cggak/ext/DiffEqBaseChainRulesCoreExt.jl:11.
│  ERROR: Method overwriting is not permitted during Module precompilation. Use `__precompile__(false)` to opt-out of precompilation.
└  
┌ OrdinaryDiffEqFIRK
│  WARNING: Method definition rrule(typeof(SciMLBase.checkkwargs), Any) in module SciMLBaseChainRulesCoreExt at /home/user/.julia/packages/SciMLBase/eTBDr/ext/SciMLBaseChainRulesCoreExt.jl:10 overwritten in module DiffEqBaseChainRulesCoreExt at /home/user/.julia/packages/DiffEqBase/cggak/ext/DiffEqBaseChainRulesCoreExt.jl:11.
│  ERROR: Method overwriting is not permitted during Module precompilation. Use `__precompile__(false)` to opt-out of precompilation.
└  
┌ DifferentialEquations
│  WARNING: Method definition rrule(typeof(SciMLBase.checkkwargs), Any) in module SciMLBaseChainRulesCoreExt at /home/user/.julia/packages/SciMLBase/eTBDr/ext/SciMLBaseChainRulesCoreExt.jl:10 overwritten in module DiffEqBaseChainRulesCoreExt at /home/user/.julia/packages/DiffEqBase/cggak/ext/DiffEqBaseChainRulesCoreExt.jl:11.
│  ERROR: Method overwriting is not permitted during Module precompilation. Use `__precompile__(false)` to opt-out of precompilation.
└  
┌ OrdinaryDiffEqDifferentiation
│  WARNING: Method definition rrule(typeof(SciMLBase.checkkwargs), Any) in module SciMLBaseChainRulesCoreExt at /home/user/.julia/packages/SciMLBase/eTBDr/ext/SciMLBaseChainRulesCoreExt.jl:10 overwritten in module DiffEqBaseChainRulesCoreExt at /home/user/.julia/packages/DiffEqBase/cggak/ext/DiffEqBaseChainRulesCoreExt.jl:11.
│  ERROR: Method overwriting is not permitted during Module precompilation. Use `__precompile__(false)` to opt-out of precompilation.
└  
┌ OrdinaryDiffEqDefault
│  WARNING: Method definition rrule(typeof(SciMLBase.checkkwargs), Any) in module SciMLBaseChainRulesCoreExt at /home/user/.julia/packages/SciMLBase/eTBDr/ext/SciMLBaseChainRulesCoreExt.jl:10 overwritten in module DiffEqBaseChainRulesCoreExt at /home/user/.julia/packages/DiffEqBase/cggak/ext/DiffEqBaseChainRulesCoreExt.jl:11.
│  ERROR: Method overwriting is not permitted during Module precompilation. Use `__precompile__(false)` to opt-out of precompilation.
└  
┌ BoundaryValueDiffEqCore
│  WARNING: Method definition rrule(typeof(SciMLBase.checkkwargs), Any) in module SciMLBaseChainRulesCoreExt at /home/user/.julia/packages/SciMLBase/eTBDr/ext/SciMLBaseChainRulesCoreExt.jl:10 overwritten in module DiffEqBaseChainRulesCoreExt at /home/user/.julia/packages/DiffEqBase/cggak/ext/DiffEqBaseChainRulesCoreExt.jl:11.
│  ERROR: Method overwriting is not permitted during Module precompilation. Use `__precompile__(false)` to opt-out of precompilation.
└  
┌ OrdinaryDiffEqSDIRK
│  WARNING: Method definition rrule(typeof(SciMLBase.checkkwargs), Any) in module SciMLBaseChainRulesCoreExt at /home/user/.julia/packages/SciMLBase/eTBDr/ext/SciMLBaseChainRulesCoreExt.jl:10 overwritten in module DiffEqBaseChainRulesCoreExt at /home/user/.julia/packages/DiffEqBase/cggak/ext/DiffEqBaseChainRulesCoreExt.jl:11.
│  ERROR: Method overwriting is not permitted during Module precompilation. Use `__precompile__(false)` to opt-out of precompilation.
└  
┌ OrdinaryDiffEqRosenbrock
│  WARNING: Method definition rrule(typeof(SciMLBase.checkkwargs), Any) in module SciMLBaseChainRulesCoreExt at /home/user/.julia/packages/SciMLBase/eTBDr/ext/SciMLBaseChainRulesCoreExt.jl:10 overwritten in module DiffEqBaseChainRulesCoreExt at /home/user/.julia/packages/DiffEqBase/cggak/ext/DiffEqBaseChainRulesCoreExt.jl:11.
│  ERROR: Method overwriting is not permitted during Module precompilation. Use `__precompile__(false)` to opt-out of precompilation.
└  
┌ OrdinaryDiffEqExponentialRK
│  WARNING: Method definition rrule(typeof(SciMLBase.checkkwargs), Any) in module SciMLBaseChainRulesCoreExt at /home/user/.julia/packages/SciMLBase/eTBDr/ext/SciMLBaseChainRulesCoreExt.jl:10 overwritten in module DiffEqBaseChainRulesCoreExt at /home/user/.julia/packages/DiffEqBase/cggak/ext/DiffEqBaseChainRulesCoreExt.jl:11.
│  ERROR: Method overwriting is not permitted during Module precompilation. Use `__precompile__(false)` to opt-out of precompilation.
└  
┌ BoundaryValueDiffEqFIRK
│  WARNING: Method definition rrule(typeof(SciMLBase.checkkwargs), Any) in module SciMLBaseChainRulesCoreExt at /home/user/.julia/packages/SciMLBase/eTBDr/ext/SciMLBaseChainRulesCoreExt.jl:10 overwritten in module DiffEqBaseChainRulesCoreExt at /home/user/.julia/packages/DiffEqBase/cggak/ext/DiffEqBaseChainRulesCoreExt.jl:11.
│  ERROR: Method overwriting is not permitted during Module precompilation. Use `__precompile__(false)` to opt-out of precompilation.

Edit: Nevermind it is still there when I try to import differentialequations.jl
Copying a part of the recursive error:

[ Info: Precompiling OrdinaryDiffEqIMEXMultistep [9f002381-b378-40b7-97a6-27a27c83f129] (cache misses: wrong dep version loaded (4))
┌ Warning: Module OrdinaryDiffEqDifferentiation with build ID ffffffff-ffff-ffff-3e06-9cc9448e1b5f is missing from the cache.
│ This may mean OrdinaryDiffEqDifferentiation [4302a76b-040a-498a-8c04-15b101fed76b] does not support precompilation but is imported by a module that does.
└ @ Base loading.jl:2641
┌ Info: Skipping precompilation due to precompilable error. Importing OrdinaryDiffEqIMEXMultistep [9f002381-b378-40b7-97a6-27a27c83f129].
└   exception = Error when precompiling module, potentially caused by a __precompile__(false) declaration in the module.
Info Given OrdinaryDiffEqExponentialRK was explicitly requested, output will be shown live 
┌ Warning: Module OrdinaryDiffEqDifferentiation with build ID ffffffff-ffff-ffff-3e06-9cc9448e1b5f is missing from the cache.
│ This may mean OrdinaryDiffEqDifferentiation [4302a76b-040a-498a-8c04-15b101fed76b] does not support precompilation but is imported by a module that does.
└ @ Base loading.jl:2641
  ? OrdinaryDiffEqDifferentiation
  ? OrdinaryDiffEqDifferentiation → OrdinaryDiffEqDifferentiationSparseArraysExt
  ? OrdinaryDiffEqExponentialRK
[ Info: Precompiling OrdinaryDiffEqExponentialRK [e0540318-69ee-4070-8777-9e2de6de23de] (cache misses: wrong dep version loaded (4))
┌ Warning: Module OrdinaryDiffEqDifferentiation with build ID ffffffff-ffff-ffff-3e06-9cc9448e1b5f is missing from the cache.
│ This may mean OrdinaryDiffEqDifferentiation [4302a76b-040a-498a-8c04-15b101fed76b] does not support precompilation but is imported by a module that does.
└ @ Base loading.jl:2641
┌ Info: Skipping precompilation due to precompilable error. Importing OrdinaryDiffEqExponentialRK [e0540318-69ee-4070-8777-9e2de6de23de].
└   exception = Error when precompiling module, potentially caused by a __precompile__(false) declaration in the module.
Info Given BoundaryValueDiffEq was explicitly requested, output will be shown live 
WARNING: Method definition rrule(typeof(SciMLBase.checkkwargs), Any) in module SciMLBaseChainRulesCoreExt at /home/azafar/.julia/packages/SciMLBase/eTBDr/ext/SciMLBaseChainRulesCoreExt.jl:10 overwritten in module DiffEqBaseChainRulesCoreExt at /home/azafar/.julia/packages/DiffEqBase/cggak/ext/DiffEqBaseChainRulesCoreExt.jl:11.
ERROR: Method overwriting is not permitted during Module precompilation. Use `__precompile__(false)` to opt-out of precompilation.
  ? BoundaryValueDiffEqCore
  ? BoundaryValueDiffEqAscher
  ? BoundaryValueDiffEqShooting
  ? BoundaryValueDiffEqFIRK
  ? BoundaryValueDiffEqMIRK
  ? BoundaryValueDiffEqMIRKN
  ? BoundaryValueDiffEq
[ Info: Precompiling BoundaryValueDiffEq [764a87c0-6b3e-53db-9096-fe964310641d] (cache misses: wrong dep version loaded (4))
WARNING: Method definition rrule(typeof(SciMLBase.checkkwargs), Any) in module SciMLBaseChainRulesCoreExt at /home/azafar/.julia/packages/SciMLBase/eTBDr/ext/SciMLBaseChainRulesCoreExt.jl:10 overwritten in module DiffEqBaseChainRulesCoreExt at /home/azafar/.julia/packages/DiffEqBase/cggak/ext/DiffEqBaseChainRulesCoreExt.jl:11.
ERROR: Method overwriting is not permitted during Module precompilation. Use `__precompile__(false)` to opt-out of precompilation.
┌ Info: Skipping precompilation due to precompilable error. Importing BoundaryValueDiffEq [764a87c0-6b3e-53db-9096-fe964310641d].
└   exception = Error when precompiling module, potentially caused by a __precompile__(false) declaration in the module.
Info Given BoundaryValueDiffEqAscher was explicitly requested, output will be shown live 
WARNING: Method definition rrule(typeof(SciMLBase.checkkwargs), Any) in module SciMLBaseChainRulesCoreExt at /home/azafar/.julia/packages/SciMLBase/eTBDr/ext/SciMLBaseChainRulesCoreExt.jl:10 overwritten in module DiffEqBaseChainRulesCoreExt at /home/azafar/.julia/packages/DiffEqBase/cggak/ext/DiffEqBaseChainRulesCoreExt.jl:11.
ERROR: Method overwriting is not permitted during Module precompilation. Use `__precompile__(false)` to opt-out of precompilation.
  ? BoundaryValueDiffEqCore
  ? BoundaryValueDiffEqAscher
[ Info: Precompiling BoundaryValueDiffEqAscher [7227322d-7511-4e07-9247-ad6ff830280e] (cache misses: wrong dep version loaded (4))
WARNING: Method definition rrule(typeof(SciMLBase.checkkwargs), Any) in module SciMLBaseChainRulesCoreExt at /home/azafar/.julia/packages/SciMLBase/eTBDr/ext/SciMLBaseChainRulesCoreExt.jl:10 overwritten in module DiffEqBaseChainRulesCoreExt at /home/azafar/.julia/packages/DiffEqBase/cggak/ext/DiffEqBaseChainRulesCoreExt.jl:11.
ERROR: Method overwriting is not permitted during Module precompilation. Use `__precompile__(false)` to opt-out of precompilation.
┌ Info: Skipping precompilation due to precompilable error. Importing BoundaryValueDiffEqAscher [7227322d-7511-4e07-9247-ad6ff830280e].
└   exception = Error when precompiling module, potentially caused by a __precompile__(false) declaration in the module.
Info Given BoundaryValueDiffEqCore was explicitly requested, output will be shown live 
WARNING: Method definition rrule(typeof(SciMLBase.checkkwargs), Any) in module SciMLBaseChainRulesCoreExt at /home/azafar/.julia/packages/SciMLBase/eTBDr/ext/SciMLBaseChainRulesCoreExt.jl:10 overwritten in module DiffEqBaseChainRulesCoreExt at /home/azafar/.julia/packages/DiffEqBase/cggak/ext/DiffEqBaseChainRulesCoreExt.jl:11.
ERROR: Method overwriting is not permitted during Module precompilation. Use `__precompile__(false)` to opt-out of precompilation.
  ? BoundaryValueDiffEqCore
6

That should be harmless, but go away with the DiffEqBase update. Do you have something upper bounding your DiffEqBase version?

7

@atiyabzafar, you may try to remove your Manifest.toml (and even your ~/.julia) and recompile everything from clean. That solved it for me.