Circular dependency precompilation hangs #511
Description
I get circular dependency warning both on julia v1.10.7 and v1.11.1. I am getting this as WARNING and the dependency chain as follows
julia> using OrdinaryDiffEq
┌ Warning: Circular dependency detected. Precompilation will be skipped for:
│ Base.PkgId(Base.UUID("e3ecd195-ca82-5397-9546-f380c1e34951"), "NonlinearSolveBaseSparseMatrixColoringsExt")
│ Base.PkgId(Base.UUID("385e4588-a1a0-5c1d-98fa-d45bf6f8ecf9"), "LinearSolveKernelAbstractionsExt")
│ Base.PkgId(Base.UUID("b00db79b-61e3-50fb-b26f-2d35b2d9e4ed"), "DiffEqBaseChainRulesCoreExt")
│ Base.PkgId(Base.UUID("8913a72c-1f9b-4ce2-8d82-65094dcecaec"), "NonlinearSolve")
│ Base.PkgId(Base.UUID("1dea7af3-3e70-54e6-95c3-0bf5283fa5ed"), "OrdinaryDiffEq")
│ Base.PkgId(Base.UUID("0d7ed370-da01-4f52-bd93-41d350b8b718"), "StaticArrayInterface")
│ Base.PkgId(Base.UUID("63d416d0-6995-5965-81e0-55251226d976"), "NonlinearSolveBaseForwardDiffExt")
│ Base.PkgId(Base.UUID("63c18a36-062a-441e-b654-da1e3ab1ce7c"), "KernelAbstractions")
│ Base.PkgId(Base.UUID("bdcacae8-1622-11e9-2a5c-532679323890"), "LoopVectorization")
│ Base.PkgId(Base.UUID("8d20b31a-8b56-511a-b573-0bef60e8c8c7"), "LineSearchLineSearchesExt")
│ Base.PkgId(Base.UUID("d3585ca7-f5d3-4ba6-8057-292ed1abd90f"), "OrdinaryDiffEqFunctionMap")
│ Base.PkgId(Base.UUID("bb5d69b7-63fc-4a16-80bd-7e42200c7bdb"), "MaybeInplace")
│ Base.PkgId(Base.UUID("133222a9-3015-5ee0-8b28-65fc8ed13c28"), "LinearSolveEnzymeExt")
│ Base.PkgId(Base.UUID("f517fe37-dbe3-4b94-8317-1923a5111588"), "Polyester")
│ Base.PkgId(Base.UUID("521117fe-8c41-49f8-b3b6-30780b3f0fb5"), "OrdinaryDiffEqLinear")
│ Base.PkgId(Base.UUID("d41bc354-129a-5804-8e4c-c37616107c6c"), "NLSolversBase")
│ Base.PkgId(Base.UUID("699899dd-2948-59d9-a4f6-ce210f3f1f61"), "FiniteDiffSparseArraysExt")
│ Base.PkgId(Base.UUID("45f359ea-796d-4f51-95a5-deb1a414c586"), "MLJBalancing")
│ Base.PkgId(Base.UUID("10f19ff3-798f-405d-979b-55457f8fc047"), "LayoutPointers")
│ Base.PkgId(Base.UUID("b1df2697-797e-41e3-8120-5422d3b24e4a"), "OrdinaryDiffEqTsit5")
│ Base.PkgId(Base.UUID("8a688d86-d2bc-5ad3-8ed1-384f9f2c8cc5"), "NNlibCUDAExt")
│ Base.PkgId(Base.UUID("6ad6398a-0878-4a85-9266-38940aa047c8"), "OrdinaryDiffEqBDF")
│ Base.PkgId(Base.UUID("6a86dc24-6348-571c-b903-95158fe2bd41"), "FiniteDiff")
│ Base.PkgId(Base.UUID("499d2952-c3ce-5339-96ee-b197ee6daaa6"), "SpecialFunctionsExt")
│ Base.PkgId(Base.UUID("eae2faf6-b232-58cb-a410-7764fda2830c"), "ChainRulesCoreExt")
│ Base.PkgId(Base.UUID("47a9eef4-7e08-11e9-0b38-333d64bd3804"), "SparseDiffTools")
│ Base.PkgId(Base.UUID("872c559c-99b0-510c-b3b7-b6c96a88d5cd"), "NNlib")
│ Base.PkgId(Base.UUID("5b33eab2-c0f1-4480-b2c3-94bc1e80bda1"), "OrdinaryDiffEqPRK")
│ Base.PkgId(Base.UUID("50262376-6c5a-4cf5-baba-aaf4f84d72d7"), "OrdinaryDiffEqDefault")
│ Base.PkgId(Base.UUID("7d52e85c-72bb-51a3-82f3-f6aed919620f"), "ExponentialUtilitiesStaticArraysExt")
│ Base.PkgId(Base.UUID("bb716554-e89b-5af4-bfb6-0f88eb8bb218"), "BracketingNonlinearSolveForwardDiffExt")
│ Base.PkgId(Base.UUID("a8fab69c-de6f-5f74-aba3-bef19c2d033f"), "StaticArrayInterfaceOffsetArraysExt")
│ Base.PkgId(Base.UUID("43230ef6-c299-4910-a778-202eb28ce4ce"), "OrdinaryDiffEqRosenbrock")
│ Base.PkgId(Base.UUID("9c97de4a-2903-5b9c-add6-4b1aaffe4ab8"), "MaybeInplaceSparseArraysExt")
│ Base.PkgId(Base.UUID("0c5d862f-8b57-4792-8d23-62f2024744c7"), "Symbolics")
│ Base.PkgId(Base.UUID("cd430d6f-1330-5ba3-8763-ae950e38ad4f"), "SparseDiffToolsSymbolicsExt")
│ Base.PkgId(Base.UUID("89bda076-bce5-4f1c-845f-551c83cdda9a"), "OrdinaryDiffEqAdamsBashforthMoulton")
│ Base.PkgId(Base.UUID("75e56524-3a34-51de-85ea-03aa6eac4b64"), "FiniteDiffStaticArraysExt")
│ Base.PkgId(Base.UUID("9286f039-9fbf-40e8-bf65-aa933bdc4db0"), "OrdinaryDiffEqExplicitRK")
│ Base.PkgId(Base.UUID("70df07ce-3d50-431d-a3e7-ca6ddb60ac1e"), "BracketingNonlinearSolve")
│ Base.PkgId(Base.UUID("bbf590c4-e513-4bbe-9b18-05decba2e5d8"), "OrdinaryDiffEqCore")
│ Base.PkgId(Base.UUID("1285c0f1-ff9f-5867-b66e-0f359bcf09ba"), "SpecialFunctionsExt")
│ Base.PkgId(Base.UUID("a19d573c-0a75-4610-95b3-7071388c7541"), "StatisticalMeasures")
│ Base.PkgId(Base.UUID("ca1c724a-f4aa-55ef-b8e4-2f05449449ac"), "OrdinaryDiffEqCoreEnzymeCoreExt")
│ Base.PkgId(Base.UUID("5dd0a6cf-3d4b-4314-aa06-06d4e299bc89"), "OrdinaryDiffEqPDIRK")
│ Base.PkgId(Base.UUID("f04539eb-3b94-5d9d-8be7-45665d72dc4b"), "SymbolicsSymPyExt")
│ Base.PkgId(Base.UUID("7792a7ef-975c-4747-a70f-980b88e8d1da"), "StrideArraysCore")
│ Base.PkgId(Base.UUID("358294b1-0aab-51c3-aafe-ad5ab194a2ad"), "OrdinaryDiffEqStabilizedRK")
│ Base.PkgId(Base.UUID("669c94d9-1f4b-4b64-b377-1aa079aa2388"), "OrdinaryDiffEqSSPRK")
│ Base.PkgId(Base.UUID("03970b2e-30c4-11ea-3135-d1576263f10f"), "MLJTuning")
│ Base.PkgId(Base.UUID("8494477e-8a74-521a-b11a-5a22161b1bc8"), "NonlinearSolveBaseSparseArraysExt")
│ Base.PkgId(Base.UUID("052768ef-5323-5732-b1bb-66c8b64840ba"), "CUDA")
│ Base.PkgId(Base.UUID("8254be44-1295-4e6a-a16d-46603ac705cb"), "SymbolicRegression")
│ Base.PkgId(Base.UUID("85068d23-b5fb-53f1-8204-05c2aba6942f"), "SparseArraysExt")
│ Base.PkgId(Base.UUID("13011619-4c7c-5ef0-948f-5fc81565cd05"), "AtomixCUDAExt")
│ Base.PkgId(Base.UUID("06b0261c-7a9b-5753-9bdf-fd6840237b4a"), "StaticArrayInterfaceStaticArraysExt")
│ Base.PkgId(Base.UUID("d083c4ab-32a5-5342-b289-e118b48fb79d"), "SciMLBasePyCallExt")
│ Base.PkgId(Base.UUID("af6ede74-add8-4cfd-b1df-9a4dbb109d7a"), "OrdinaryDiffEqRKN")
│ Base.PkgId(Base.UUID("26075421-4e9a-44e1-8bd1-420ed7ad02b2"), "NonlinearSolveSpectralMethods")
│ Base.PkgId(Base.UUID("53ae85a6-f571-4167-b2af-e1d143709226"), "SciMLStructures")
│ Base.PkgId(Base.UUID("7ed4a6bd-45f5-4d41-b270-4a48e9bafcae"), "LinearSolve")
│ Base.PkgId(Base.UUID("04162be5-8125-4266-98ed-640baecc6514"), "OrdinaryDiffEqQPRK")
│ Base.PkgId(Base.UUID("14203109-85fb-5f77-af23-1cb7d9032242"), "RecursiveArrayToolsForwardDiffExt")
│ Base.PkgId(Base.UUID("106586fb-0781-5151-be1c-b45c40028622"), "ScientificTypesExt")
│ Base.PkgId(Base.UUID("4131c53f-b1d6-5635-a7a3-57f6f930b644"), "DiffEqBaseSparseArraysExt")
│ Base.PkgId(Base.UUID("a7f614a8-145f-11e9-1d2a-a57a1082229d"), "MLJBase")
│ Base.PkgId(Base.UUID("e24d4dde-ed20-5ee7-b465-f1dd73f9b6ba"), "LinearSolveCUDAExt")
│ Base.PkgId(Base.UUID("5959db7a-ea39-4486-b5fe-2dd0bf03d60d"), "NonlinearSolveFirstOrder")
│ Base.PkgId(Base.UUID("d236fae5-4411-538c-8e31-a6e3d9e00b46"), "PreallocationTools")
│ Base.PkgId(Base.UUID("a2df0a61-553a-563b-aed7-0ce21874eb58"), "SciMLOperatorsStaticArraysCoreExt")
│ Base.PkgId(Base.UUID("42296aa8-c874-5f57-b5c1-8d6f5ebd5400"), "RecursiveArrayToolsFastBroadcastExt")
│ Base.PkgId(Base.UUID("0bca4576-84f4-4d90-8ffe-ffa030f20462"), "SciMLBase")
│ Base.PkgId(Base.UUID("78064ecb-8a7e-51fd-a998-f0197ddca326"), "DiffEqBaseCUDAExt")
│ Base.PkgId(Base.UUID("d28bc4f8-55e1-4f49-af69-84c1a99f0f58"), "OrdinaryDiffEqHighOrderRK")
│ Base.PkgId(Base.UUID("b0944070-b475-4768-8dec-fb6eb410534d"), "OrdinaryDiffEqLowStorageRK")
│ Base.PkgId(Base.UUID("fa646aed-7ef9-47eb-84c4-9443fc8cbfa8"), "OrdinaryDiffEqSymplecticRK")
│ Base.PkgId(Base.UUID("e3e12d00-db14-5390-b879-ac3dd2ef6296"), "OrdinaryDiffEqStabilizedIRK")
│ Base.PkgId(Base.UUID("1344f307-1e59-4825-a18e-ace9aa3fa4c6"), "OrdinaryDiffEqLowOrderRK")
│ Base.PkgId(Base.UUID("e0540318-69ee-4070-8777-9e2de6de23de"), "OrdinaryDiffEqExponentialRK")
│ Base.PkgId(Base.UUID("c8a29c40-e0ac-5e6e-8984-8da3115ac879"), "NNlibEnzymeCoreExt")
│ Base.PkgId(Base.UUID("6044458a-139e-583a-bc2f-a730a9b54282"), "DifferentiationInterfaceFiniteDiffExt")
│ Base.PkgId(Base.UUID("7034ab61-46d4-4ed7-9d0f-46aef9175898"), "FastBroadcast")
│ Base.PkgId(Base.UUID("4302a76b-040a-498a-8c04-15b101fed76b"), "OrdinaryDiffEqDifferentiation")
│ Base.PkgId(Base.UUID("d4d017d3-3776-5f7e-afef-a10c40355c18"), "ExponentialUtilities")
│ Base.PkgId(Base.UUID("127b3ac7-2247-4354-8eb6-78cf4e7c58e8"), "OrdinaryDiffEqNonlinearSolve")
│ Base.PkgId(Base.UUID("9f049cbb-7c7d-5dfe-91f7-cf323d5306ff"), "SparseDiffToolsPolyesterExt")
│ Base.PkgId(Base.UUID("2d112036-d095-4a1e-ab9a-08536f3ecdbf"), "OrdinaryDiffEqSDIRK")
│ Base.PkgId(Base.UUID("87fe0de2-c867-4266-b59a-2f0a94fc965b"), "LineSearch")
│ Base.PkgId(Base.UUID("66d79d19-2cc4-5b0b-ac7a-b340256d1ecd"), "LinearAlgebraExt")
│ Base.PkgId(Base.UUID("6425d1ab-ad86-5f6e-82f1-f5118e0dc800"), "EnzymeExt")
│ Base.PkgId(Base.UUID("4676cac9-c8e0-5d6e-a4e0-e3351593cdf5"), "SciMLBaseChainRulesCoreExt")
│ Base.PkgId(Base.UUID("becaefa8-8ca2-5cf9-886d-c06f3d2bd2c4"), "OrdinaryDiffEqExtrapolation")
│ Base.PkgId(Base.UUID("100afd77-a77b-5381-b1ec-69e200d58033"), "SymbolicRegressionSymbolicUtilsExt")
│ Base.PkgId(Base.UUID("565f26a4-c902-5eae-92ad-e10714a9d9de"), "SciMLBaseMakieExt")
│ Base.PkgId(Base.UUID("79d7bb75-1356-48c1-b8c0-6832512096c2"), "OrdinaryDiffEqVerner")
│ Base.PkgId(Base.UUID("b85ff9ab-f544-5eb2-8eaf-e219a5e7647d"), "DynamicExpressionsSymbolicUtilsExt")
│ Base.PkgId(Base.UUID("e6c02559-e2b6-5021-bc6e-a9f025c2d0c8"), "DifferentiationInterfaceSymbolicsExt")
│ Base.PkgId(Base.UUID("d1185830-fcd6-423d-90d6-eec64667417b"), "SymbolicUtils")
│ Base.PkgId(Base.UUID("073a8d7d-86ee-5d75-9348-f9bf6155b014"), "SimpleNonlinearSolveChainRulesCoreExt")
│ Base.PkgId(Base.UUID("4a213a23-c09c-5cde-9712-b631ad2c72df"), "SymbolicsForwardDiffExt")
│ Base.PkgId(Base.UUID("96386cae-6b62-59ad-b532-a94eae05753e"), "NNlibFFTWExt")
│ Base.PkgId(Base.UUID("24f3332a-0dc5-5d65-94b6-25e75cab9690"), "DiffEqBaseDistributionsExt")
│ Base.PkgId(Base.UUID("c0aeaf25-5076-4817-a8d5-81caf7dfa961"), "SciMLOperators")
│ Base.PkgId(Base.UUID("731186ca-8d62-57ce-b412-fbd966d074cd"), "RecursiveArrayTools")
│ Base.PkgId(Base.UUID("d3d80556-e9d4-5f37-9878-2ab0fcc64255"), "LineSearches")
│ Base.PkgId(Base.UUID("101fe9f7-ebb6-4678-b671-3a81e7194747"), "OrdinaryDiffEqFeagin")
│ Base.PkgId(Base.UUID("2b5f629d-d688-5b77-993f-72d75c75574e"), "DiffEqBase")
│ Base.PkgId(Base.UUID("50ed68f4-41fd-4504-931a-ed422449fee0"), "MLJEnsembles")
│ Base.PkgId(Base.UUID("4b8ca102-9d0f-5df8-84ed-253e0f005ba7"), "ForwardDiffExt")
│ Base.PkgId(Base.UUID("f2c3362d-daeb-58d1-803e-2bc74f2840b4"), "RecursiveFactorization")
│ Base.PkgId(Base.UUID("fe5f6ac0-33d3-5066-8083-2d519bb7c971"), "DefaultMeasuresExt")
│ Base.PkgId(Base.UUID("2bc1baa2-0022-5d69-b2bc-3cdc5d5c3803"), "LossFunctionsExt")
│ Base.PkgId(Base.UUID("9a2c21bd-3a47-402d-9113-8faf9a0ee114"), "NonlinearSolveQuasiNewton")
│ Base.PkgId(Base.UUID("d5829a12-d9aa-46ab-831f-fb7c9ab06edf"), "TriangularSolve")
│ Base.PkgId(Base.UUID("07510ace-05c5-59ac-8535-cc0df8d4a157"), "RecursiveArrayToolsStructArraysExt")
│ Base.PkgId(Base.UUID("73e54eaf-3344-511d-b088-1ac5413eca63"), "RecursiveArrayToolsSparseArraysExt")
│ Base.PkgId(Base.UUID("614be32b-d00c-4edb-bd02-1eb411ab5e55"), "MLJIteration")
│ Base.PkgId(Base.UUID("904f2055-56f7-5591-b06b-453cba458f4b"), "SimpleNonlinearSolveDiffEqBaseExt")
│ Base.PkgId(Base.UUID("f78586ac-ba87-5ec7-b3a5-84bc1b258ee3"), "ArrayInterfaceCUDAExt")
│ Base.PkgId(Base.UUID("7b7b8358-b45c-48ea-a8ef-7ca328ad328f"), "MLJFlow")
│ Base.PkgId(Base.UUID("476501e8-09a2-5ece-8869-fb82de89a1fa"), "SLEEFPirates")
│ Base.PkgId(Base.UUID("429524aa-4258-5aef-a3af-852621145aeb"), "Optim")
│ Base.PkgId(Base.UUID("fb6a15b2-703c-40df-9091-08a04967cfa9"), "CloseOpenIntervals")
│ Base.PkgId(Base.UUID("add582a8-e3ab-11e8-2d5e-e98b27df1bc7"), "MLJ")
│ Base.PkgId(Base.UUID("04950c4b-5bc4-5740-952d-02d2c1eb583a"), "LinearSolveRecursiveArrayToolsExt")
│ Base.PkgId(Base.UUID("19f34311-ddf3-4b8b-af20-060888a46c0e"), "SciMLJacobianOperators")
│ Base.PkgId(Base.UUID("a65b7766-7c26-554a-8b8d-165d7f96f890"), "NonlinearSolveBaseLineSearchExt")
│ Base.PkgId(Base.UUID("3d5dd08c-fd9d-11e8-17fa-ed2836048c2f"), "VectorizationBase")
│ Base.PkgId(Base.UUID("5458d0c1-52ec-57a8-a2ac-7e1b9fb3c3b9"), "DynamicExpressionsOptimExt")
│ Base.PkgId(Base.UUID("aeb06bb4-539b-5a1b-8332-034ed9f8ca66"), "DiffEqBaseUnitfulExt")
│ Base.PkgId(Base.UUID("c062fc1d-0d66-479b-b6ac-8b44719de4cc"), "StatisticalMeasuresBase")
│ Base.PkgId(Base.UUID("19f23fe9-fdab-4a78-91af-e7b7767979c3"), "SymbolicLimits")
│ Base.PkgId(Base.UUID("3d4538b4-647b-544e-b0c2-b52d0495c932"), "NonlinearSolveBaseLinearSolveExt")
│ Base.PkgId(Base.UUID("0d7ce1ac-5836-50ef-99a4-53a3fff820f1"), "DynamicExpressionsLoopVectorizationExt")
│ Base.PkgId(Base.UUID("c9986a66-5c92-4813-8696-a7ec84c806c8"), "OrdinaryDiffEqNordsieck")
│ Base.PkgId(Base.UUID("5960d6e9-dd7a-4743-88e7-cf307b64f125"), "OrdinaryDiffEqFIRK")
│ Base.PkgId(Base.UUID("d479e226-fb54-5ebe-a75e-a7af7f39127f"), "SymbolicsPreallocationToolsExt")
│ Base.PkgId(Base.UUID("c3ed20f3-746d-5a71-99a7-df1cca8c2b90"), "EnzymeCoreExt")
│ Base.PkgId(Base.UUID("e8958739-db86-5f80-9e4c-f7c96aa15038"), "NNlibForwardDiffExt")
│ Base.PkgId(Base.UUID("a0bd8381-04c7-5287-82b0-0bf1e59008be"), "NonlinearSolveBaseDiffEqBaseExt")
│ Base.PkgId(Base.UUID("727e6d20-b764-4bd8-a329-72de5adea6c7"), "SimpleNonlinearSolve")
│ Base.PkgId(Base.UUID("be0214bd-f91f-a760-ac4e-3421ce2b2da0"), "NonlinearSolveBase")
│ Base.PkgId(Base.UUID("9f002381-b378-40b7-97a6-27a27c83f129"), "OrdinaryDiffEqIMEXMultistep")
│ Base.PkgId(Base.UUID("2efcf032-c050-4f8e-a9bb-153293bab1f5"), "SymbolicIndexingInterface")
│ Base.PkgId(Base.UUID("9985400b-97ec-5583-b534-4f70b643bcf7"), "SciMLOperatorsSparseArraysExt")
│ Base.PkgId(Base.UUID("f1d291b0-491e-4a28-83b9-f70985020b54"), "MLUtils")
└ @ Base.Precompilation precompilation.jl:511
[ Info: Precompiling OrdinaryDiffEq [1dea7af3-3e70-54e6-95c3-0bf5283fa5ed]
I file it here because the chain starts with NonlinearSolveBaseSparseMatrixColoringsExt. This warning first happened while upgrading packages and I get the hanging issue in using OrdinaryDiffEq and even keyboard interrupt did not work after that.
Finally, package status
(@v1.11) pkg> status -m --outdated
Status `~/.julia/environments/v1.11/Manifest.toml`
⌅ [3da002f7] ColorTypes v0.11.5 (<v0.12.0): ColorVectorSpace, Colors, ScientificTypes, ShaderAbstractions
⌃ [c3611d14] ColorVectorSpace v0.10.0 (<v0.11.0)
⌅ [5ae59095] Colors v0.12.11 (<v0.13.0): ColorBrewer
⌅ [6b7a57c9] Expronicon v0.8.5 (<v0.10.13): SciMLBase
⌅ [0c68f7d7] GPUArrays v10.3.1 (<v11.1.0): CUDA
⌅ [46192b85] GPUArraysCore v0.1.6 (<v0.2.0): GPUArrays
⌅ [61eb1bfa] GPUCompiler v0.27.8 (<v1.0.1): CUDA
⌅ [5c1252a2] GeometryBasics v0.4.11 (<v0.5.1): CairoMakie, GLMakie, Makie, MakieCore, MeshIO, ShaderAbstractions
⌅ [30fc2ffe] LossFunctions v0.11.2 (<v1.0.0): SymbolicRegression
⌅ [7269a6da] MeshIO v0.4.13 (<v0.5.0): GLMakie
⌅ [65257c39] ShaderAbstractions v0.4.1 (<v0.5.0): GLMakie, Makie
⌅ [09ab397b] StructArrays v0.6.18 (<v0.7.0): GeometryBasics, Makie, ShaderAbstractions
⌅ [b22a6f82] FFMPEG_jll v4.4.4+1 (<v6.1.2+0): FFMPEG
⌅ [e9f186c6] Libffi_jll v3.2.2+1 (<v3.4.6+1): Glib_jll, HarfBuzz_jll, Wayland_jll
⌅ [30392449] Pixman_jll v0.43.4+0 (<v0.44.0+0): Cairo_jll
⌅ [1270edf5] x264_jll v2021.5.5+0 (<v10164.0.0+0): FFMPEG_jll
⌅ [dfaa095f] x265_jll v3.5.0+0 (<v4.0.0+0): FFMPEG_jll
(@v1.11) pkg> status --outdated
Status `~/.julia/environments/v1.11/Project.toml`
(@v1.11) pkg>