Methods overwritten in extensions

[RGonTheNoble]

I'm getting a method-overwrite error when precompiling the package:

WARNING: Method definition getproperty(SciMLBase.AbstractOptimizationCache, Symbol) in module SciMLBase at /home/user/.julia/packages/SciMLBase/JKXkh/src/solutions/optimization_solutions.jl:136 overwritten in module Optimization at /home/user/.julia/packages/Optimization/fPVIW/src/cache.jl:2.
ERROR: Method overwriting is not permitted during Module precompilation. Use __precompile__(false) to opt-out of precompilation.

Environment:

• Output of using Pkg; Pkg.status()

Status `~/Documents/Git Repos/carbon-calculation-engine/Project.toml`
  [7d9f7c33] Accessors v0.1.42
  [7c7805af] Clapeyron v0.6.12
  [76e01b6b] FlexUnits v0.1.3
  [f6369f11] ForwardDiff v1.0.1
  [0f8b85d8] JSON3 v1.14.2
⌃ [7f7a1694] Optimization v3.19.3
  [90137ffa] StaticArrays v1.9.13
  [b543fe20] TimeRecords v2.0.1
  [e88e6eb3] Zygote v0.7.7
  [ade2ca70] Dates v1.11.0
  [37e2e46d] LinearAlgebra v1.11.0
  [2f01184e] SparseArrays v1.11.0
Info Packages marked with ⌃ have new versions available and may be upgradable.

• Output of using Pkg; Pkg.status(; mode = PKGMODE_MANIFEST)

⌅ [47edcb42] ADTypes v0.2.7
  [621f4979] AbstractFFTs v1.5.0
  [1520ce14] AbstractTrees v0.4.5
  [7d9f7c33] Accessors v0.1.42
  [79e6a3ab] Adapt v4.3.0
  [66dad0bd] AliasTables v1.1.3
  [4fba245c] ArrayInterface v7.19.0
  [a134a8b2] BlackBoxOptim v0.6.3
  [a9c8d775] CPUTime v1.0.0
  [336ed68f] CSV v0.10.15
  [082447d4] ChainRules v1.72.3
  [d360d2e6] ChainRulesCore v1.25.1
  [7c7805af] Clapeyron v0.6.12
  [944b1d66] CodecZlib v0.7.8
  [38540f10] CommonSolve v0.2.4
  [bbf7d656] CommonSubexpressions v0.3.1
  [34da2185] Compat v4.16.0
  [a33af91c] CompositionsBase v0.1.2
  [88cd18e8] ConsoleProgressMonitor v0.1.2
  [187b0558] ConstructionBase v1.5.8
  [a8cc5b0e] Crayons v4.1.1
  [9a962f9c] DataAPI v1.16.0
  [864edb3b] DataStructures v0.18.22
  [e2d170a0] DataValueInterfaces v1.0.0
  [163ba53b] DiffResults v1.1.0
  [b552c78f] DiffRules v1.15.1
  [31c24e10] Distributions v0.25.120
  [ffbed154] DocStringExtensions v0.9.4
  [4e289a0a] EnumX v1.0.5
  [e2ba6199] ExprTools v0.1.10
  [55351af7] ExproniconLite v0.10.14
  [48062228] FilePathsBase v0.9.24
  [1a297f60] FillArrays v1.13.0
  [76e01b6b] FlexUnits v0.1.3
  [f6369f11] ForwardDiff v1.0.1
  [069b7b12] FunctionWrappers v1.1.3
  [77dc65aa] FunctionWrappersWrappers v0.1.3
  [46192b85] GPUArraysCore v0.2.0
  [34004b35] HypergeometricFunctions v0.3.28
  [7869d1d1] IRTools v0.4.14
  [842dd82b] InlineStrings v1.4.3
  [3587e190] InverseFunctions v0.1.17
  [92d709cd] IrrationalConstants v0.2.4
  [42fd0dbc] IterativeSolvers v0.9.4
  [82899510] IteratorInterfaceExtensions v1.0.0
  [692b3bcd] JLLWrappers v1.7.0
  [682c06a0] JSON v0.21.4
  [0f8b85d8] JSON3 v1.14.2
  [ae98c720] Jieko v0.2.1
  [b964fa9f] LaTeXStrings v1.4.0
  [1d6d02ad] LeftChildRightSiblingTrees v0.2.0
  [2ab3a3ac] LogExpFunctions v0.3.29
  [e6f89c97] LoggingExtras v1.1.0
  [1914dd2f] MacroTools v0.5.16
  [e1d29d7a] Missings v1.2.0
  [2e0e35c7] Moshi v0.3.5
  [337daf1e] NLSolvers v0.5.0
  [77ba4419] NaNMath v1.1.3
⌃ [7f7a1694] Optimization v3.19.3
  [bac558e1] OrderedCollections v1.8.0
  [90014a1f] PDMats v0.11.35
  [7713531c] PackedVectorsOfVectors v0.1.2
  [69de0a69] Parsers v2.8.3
  [2dfb63ee] PooledArrays v1.4.3
  [85a6dd25] PositiveFactorizations v0.2.4
⌅ [aea7be01] PrecompileTools v1.2.1
  [21216c6a] Preferences v1.4.3
  [08abe8d2] PrettyTables v2.4.0
  [33c8b6b6] ProgressLogging v0.1.4
  [92933f4c] ProgressMeter v1.10.4
  [43287f4e] PtrArrays v1.3.0
  [1fd47b50] QuadGK v2.11.2
  [c1ae055f] RealDot v0.1.0
  [3cdcf5f2] RecipesBase v1.3.4
  [731186ca] RecursiveArrayTools v3.33.0
  [189a3867] Reexport v1.2.2
  [ae029012] Requires v1.3.1
  [79098fc4] Rmath v0.8.0
  [f2b01f46] Roots v2.2.7
  [7e49a35a] RuntimeGeneratedFunctions v0.5.14
  [0bca4576] SciMLBase v2.89.1
  [c0aeaf25] SciMLOperators v0.4.0
  [53ae85a6] SciMLStructures v1.7.0
  [6c6a2e73] Scratch v1.2.1
  [91c51154] SentinelArrays v1.4.8
  [a2af1166] SortingAlgorithms v1.2.1
  [dc90abb0] SparseInverseSubset v0.1.2
  [d4ead438] SpatialIndexing v0.1.6
  [276daf66] SpecialFunctions v2.5.1
  [91464d47] StableTasks v0.1.7
  [90137ffa] StaticArrays v1.9.13
  [1e83bf80] StaticArraysCore v1.4.3
  [10745b16] Statistics v1.11.1
  [82ae8749] StatsAPI v1.7.0
  [2913bbd2] StatsBase v0.34.5
  [4c63d2b9] StatsFuns v1.5.0
  [892a3eda] StringManipulation v0.4.1
  [09ab397b] StructArrays v0.7.1
  [856f2bd8] StructTypes v1.11.0
  [2efcf032] SymbolicIndexingInterface v0.3.40
  [3783bdb8] TableTraits v1.0.1
  [bd369af6] Tables v1.12.0
  [5d786b92] TerminalLoggers v0.1.7
  [b543fe20] TimeRecords v2.0.1
  [3bb67fe8] TranscodingStreams v0.11.3
  [ea10d353] WeakRefStrings v1.4.2
  [76eceee3] WorkerUtilities v1.6.1
  [e88e6eb3] Zygote v0.7.7
  [700de1a5] ZygoteRules v0.2.7
  [efe28fd5] OpenSpecFun_jll v0.5.6+0
  [f50d1b31] Rmath_jll v0.5.1+0
  [0dad84c5] ArgTools v1.1.2
  [56f22d72] Artifacts v1.11.0
  [2a0f44e3] Base64 v1.11.0
  [ade2ca70] Dates v1.11.0
  [8ba89e20] Distributed v1.11.0
  [f43a241f] Downloads v1.6.0
  [7b1f6079] FileWatching v1.11.0
  [9fa8497b] Future v1.11.0
  [b77e0a4c] InteractiveUtils v1.11.0
  [b27032c2] LibCURL v0.6.4
  [76f85450] LibGit2 v1.11.0
  [8f399da3] Libdl v1.11.0
  [37e2e46d] LinearAlgebra v1.11.0
  [56ddb016] Logging v1.11.0
  [d6f4376e] Markdown v1.11.0
  [a63ad114] Mmap v1.11.0
  [ca575930] NetworkOptions v1.2.0
  [44cfe95a] Pkg v1.11.0
  [de0858da] Printf v1.11.0
  [9a3f8284] Random v1.11.0
  [ea8e919c] SHA v0.7.0
  [9e88b42a] Serialization v1.11.0
  [6462fe0b] Sockets v1.11.0
  [2f01184e] SparseArrays v1.11.0
  [4607b0f0] SuiteSparse
  [fa267f1f] TOML v1.0.3
  [a4e569a6] Tar v1.10.0
  [cf7118a7] UUIDs v1.11.0
  [4ec0a83e] Unicode v1.11.0
  [e66e0078] CompilerSupportLibraries_jll v1.1.1+0
  [deac9b47] LibCURL_jll v8.6.0+0
  [e37daf67] LibGit2_jll v1.7.2+0
  [29816b5a] LibSSH2_jll v1.11.0+1
  [c8ffd9c3] MbedTLS_jll v2.28.6+0
  [14a3606d] MozillaCACerts_jll v2023.12.12
  [4536629a] OpenBLAS_jll v0.3.27+1
  [05823500] OpenLibm_jll v0.8.5+0
  [bea87d4a] SuiteSparse_jll v7.7.0+0
  [83775a58] Zlib_jll v1.2.13+1
  [8e850b90] libblastrampoline_jll v5.11.0+0
  [8e850ede] nghttp2_jll v1.59.0+0
  [3f19e933] p7zip_jll v17.4.0+2

• Output of versioninfo()

Julia Version 1.11.5
Commit 760b2e5b739 (2025-04-14 06:53 UTC)
Build Info:
  Official https://julialang.org/ release
Platform Info:
  OS: Linux (x86_64-linux-gnu)
  CPU: 22 × Intel(R) Core(TM) Ultra 7 165H
  WORD_SIZE: 64
  LLVM: libLLVM-16.0.6 (ORCJIT, alderlake)
Threads: 22 default, 0 interactive, 11 GC (on 22 virtual cores)
Environment:
  JULIA_EDITOR = code
  JULIA_VSCODE_REPL = 1

Additional context

Add any other context about the problem here.

[SebastianM-C]

It looks like you have an old version of Optimization. Can you try updating to Optimization@v4.2?
Does ]add Optimization@4.2 work for you?

[RGonTheNoble]

Yes, it does. Although because I was using this inside a package, I had to add a compat entry of 4.0 which solved the issue. This forced a downgrade of ForwardDiff and Zygote I think, which I'm perfectly fine with.

[SebastianM-C]

Yeah, that's expected. Those version bumps are still being worked on in SciML. You probably got the older version because some packages were not strict enough with the compat bounds.

[ChrisRackauckas]

ForwardDiff is still being worked through. I don't think anything is blocking Zygote though?

[SebastianM-C]

Ah, nice. In that case, @RGonTheNoble using ]add Zygote@0.7 should either work or tell you what's holding it back

[RGonTheNoble]

Adding the compat entry
Optimization = "4.0"
Added a second one
Zygote = "0.7.7"
and everything worked afterwards! Thanks! Moreover, thanks for all the hard work you're doing.