v3.2.0 precompiles fail with "Method definition overwritten" #306
Description
Describe the bug 🐞
Many SciML packages fail to precompile following a pkg> update that updates to:
- DiffEqBase v6.144.0 -> v6.144.1
- SciMLBase v2.11.1 -> v2.11.3
- RecursiveArrayTools v3.1.0 -> v3.2.0
- OffsetArrays v1.12.10 -> v1.13.0
Pinning RecursiveArrayTools to v3.1.0 [edit: not v3.2.1 !] allows precompile to work normally
Expected behavior
A clear and concise description of what you expected to happen.
Minimal Reproducible Example 👇
] update
Error & Stacktrace
┌ SciMLBase
│ WARNING: Method definition ldiv!(T, RecursiveArrayTools.ArrayPartition{T, S} where S<:Tuple where T) where {T<:Union{}} in module RecursiveArrayTools at /home/sd336/.julia/packages/RecursiveArrayTools/aXSjX/src/array_partition.jl:431 overwritten on the same line (check for duplicate calls to `include`).
│ ERROR: Method overwriting is not permitted during Module precompilation. Use `__precompile__(false)` to opt-out of precompilation.
└ and many other examples from SciML packages
Environment (please complete the following information):
- Output of
using Pkg; Pkg.status()
- Output of
using Pkg; Pkg.status(; mode = PKGMODE_MANIFEST)
julia> Pkg.status(;mode=Pkg.PKGMODE_MANIFEST)
Project PALEOreactions v0.21.10
Status `~/PALEO/PALEOdev.jl/PALEOreactions/Manifest.toml`
[47edcb42] ADTypes v0.2.5
⌅ [79e6a3ab] Adapt v3.7.2
[ec485272] ArnoldiMethod v0.2.0
[4fba245c] ArrayInterface v7.7.0
[4c555306] ArrayLayouts v1.4.5
⌃ [13072b0f] AxisAlgorithms v1.0.1
[6e4b80f9] BenchmarkTools v1.4.0
[62783981] BitTwiddlingConvenienceFunctions v0.1.5
[e1450e63] BufferedStreams v1.2.1
[179af706] CFTime v0.1.2
[2a0fbf3d] CPUSummary v0.2.4
[336ed68f] CSV v0.10.11
[d360d2e6] ChainRulesCore v1.19.0
[fb6a15b2] CloseOpenIntervals v0.1.12
[da1fd8a2] CodeTracking v1.3.5
[944b1d66] CodecZlib v0.7.3
⌅ [1fbeeb36] CommonDataModel v0.2.5
[38540f10] CommonSolve v0.2.4
[bbf7d656] CommonSubexpressions v0.3.0
[34da2185] Compat v4.10.1
[2569d6c7] ConcreteStructs v0.2.3
[187b0558] ConstructionBase v1.5.4
[adafc99b] CpuId v0.3.1
[a8cc5b0e] Crayons v4.1.1
[9a962f9c] DataAPI v1.15.0
[a93c6f00] DataFrames v1.6.1
[864edb3b] DataStructures v0.18.15
[e2d170a0] DataValueInterfaces v1.0.0
[8bb1440f] DelimitedFiles v1.9.1
[2b5f629d] DiffEqBase v6.144.1
[163ba53b] DiffResults v1.1.0
[b552c78f] DiffRules v1.15.1
[b4f34e82] Distances v0.10.11
[ffbed154] DocStringExtensions v0.9.3
[4e289a0a] EnumX v1.0.4
[f151be2c] EnzymeCore v0.6.4
[d4d017d3] ExponentialUtilities v1.25.0
[e2ba6199] ExprTools v0.1.10
[8f5d6c58] EzXML v1.2.0
[7034ab61] FastBroadcast v0.2.8
[9aa1b823] FastClosures v0.3.2
[29a986be] FastLapackInterface v2.0.0
[48062228] FilePathsBase v0.9.21
[1a297f60] FillArrays v1.9.3
[6a86dc24] FiniteDiff v2.21.1
[f6369f11] ForwardDiff v0.10.36
[069b7b12] FunctionWrappers v1.1.3
[77dc65aa] FunctionWrappersWrappers v0.1.3
⌃ [46192b85] GPUArraysCore v0.1.5
[c145ed77] GenericSchur v0.5.3
[86223c79] Graphs v1.9.0
[f67ccb44] HDF5 v0.17.1
[3e5b6fbb] HostCPUFeatures v0.1.16
[615f187c] IfElse v0.1.1
[5903a43b] Infiltrator v1.6.4
[d25df0c9] Inflate v0.1.4
[842dd82b] InlineStrings v1.4.0
⌅ [a98d9a8b] Interpolations v0.14.7
[41ab1584] InvertedIndices v1.3.0
[92d709cd] IrrationalConstants v0.2.2
[82899510] IteratorInterfaceExtensions v1.0.0
[692b3bcd] JLLWrappers v1.5.0
[682c06a0] JSON v0.21.4
[aa1ae85d] JuliaInterpreter v0.9.27
[ef3ab10e] KLU v0.4.1
[ba0b0d4f] Krylov v0.9.5
[b964fa9f] LaTeXStrings v1.3.1
[10f19ff3] LayoutPointers v0.1.15
[50d2b5c4] Lazy v0.15.1
[5078a376] LazyArrays v1.8.3
[d3d80556] LineSearches v7.2.0
[7ed4a6bd] LinearSolve v2.21.1
[2ab3a3ac] LogExpFunctions v0.3.26
[bdcacae8] LoopVectorization v0.12.166
[6f1432cf] LoweredCodeUtils v2.3.2
[23992714] MAT v0.10.6
[3da0fdf6] MPIPreferences v0.1.10
[1914dd2f] MacroTools v0.5.12
[d125e4d3] ManualMemory v0.1.8
[a3b82374] MatrixFactorizations v2.1.0
[bb5d69b7] MaybeInplace v0.1.1
[e1d29d7a] Missings v1.1.0
[46d2c3a1] MuladdMacro v0.2.4
⌅ [85f8d34a] NCDatasets v0.12.17
[d41bc354] NLSolversBase v7.8.3
[2774e3e8] NLsolve v4.5.1 `https://github.com/PALEOtoolkit/NLsolve.jl#project_region`
[77ba4419] NaNMath v1.0.2
[8913a72c] NonlinearSolve v3.1.1
[6fe1bfb0] OffsetArrays v1.13.0
[bac558e1] OrderedCollections v1.6.3
[1dea7af3] OrdinaryDiffEq v6.63.0
[673cec3b] PALEOaqchem v0.3.1
[804b410e] PALEOboxes v0.21.20
[41de04b1] PALEOocean v0.4.3
[65ce6f38] PackageExtensionCompat v1.0.2
[d96e819e] Parameters v0.12.3
[69de0a69] Parsers v2.8.0
[f517fe37] Polyester v0.7.9
[1d0040c9] PolyesterWeave v0.2.1
[2dfb63ee] PooledArrays v1.4.3
[d236fae5] PreallocationTools v0.4.13
[aea7be01] PrecompileTools v1.2.0
[21216c6a] Preferences v1.4.1
[08abe8d2] PrettyTables v2.3.1
[c84ed2f1] Ratios v0.4.5
[3cdcf5f2] RecipesBase v1.3.4
[731186ca] RecursiveArrayTools v3.2.0
[f2c3362d] RecursiveFactorization v0.2.21
[189a3867] Reexport v1.2.2
[ae029012] Requires v1.3.0
[295af30f] Revise v3.5.10
[f2b01f46] Roots v2.0.22
[7e49a35a] RuntimeGeneratedFunctions v0.5.12
[fdea26ae] SIMD v3.4.6
[94e857df] SIMDTypes v0.1.0
[476501e8] SLEEFPirates v0.6.42
[0bca4576] SciMLBase v2.11.3
[c0aeaf25] SciMLOperators v0.3.7
[91c51154] SentinelArrays v1.4.1
[efcf1570] Setfield v1.1.1
[727e6d20] SimpleNonlinearSolve v1.0.3
[699a6c99] SimpleTraits v0.9.4
[ce78b400] SimpleUnPack v1.1.0
[66db9d55] SnoopPrecompile v1.0.3
[a2af1166] SortingAlgorithms v1.2.0
[47a9eef4] SparseDiffTools v2.15.0
[e56a9233] Sparspak v0.3.9
[276daf66] SpecialFunctions v2.3.1
[aedffcd0] Static v0.8.8
[0d7ed370] StaticArrayInterface v1.5.0
[90137ffa] StaticArrays v1.8.1
[1e83bf80] StaticArraysCore v1.4.2
[82ae8749] StatsAPI v1.7.0
[7792a7ef] StrideArraysCore v0.5.2
[69024149] StringEncodings v0.3.7
[892a3eda] StringManipulation v0.3.4
[09ab397b] StructArrays v0.6.16
[2efcf032] SymbolicIndexingInterface v0.3.0
[3783bdb8] TableTraits v1.0.1
[bd369af6] Tables v1.11.1
[1e6cf692] TestEnv v1.101.1
[8290d209] ThreadingUtilities v0.5.2
[a759f4b9] TimerOutputs v0.5.23
[3bb67fe8] TranscodingStreams v0.10.2
[d5829a12] TriangularSolve v0.1.20
[410a4b4d] Tricks v0.1.8
[781d530d] TruncatedStacktraces v1.4.0
[3a884ed6] UnPack v1.0.2
[3d5dd08c] VectorizationBase v0.21.65
[19fa3120] VertexSafeGraphs v0.2.0
[ea10d353] WeakRefStrings v1.4.2
⌅ [efce3f68] WoodburyMatrices v0.5.6
[76eceee3] WorkerUtilities v1.6.1
[fdbf4ff8] XLSX v0.10.0
[ddb6d928] YAML v0.4.9
[a5390f91] ZipFile v0.10.1
⌅ [0234f1f7] HDF5_jll v1.12.2+2
[1d5cc7b8] IntelOpenMP_jll v2024.0.0+0
[94ce4f54] Libiconv_jll v1.17.0+0
[856f044c] MKL_jll v2024.0.0+0
⌃ [7243133f] NetCDF_jll v400.902.5+1
⌅ [458c3c95] OpenSSL_jll v1.1.23+0
[efe28fd5] OpenSpecFun_jll v0.5.5+0
[63e82ce6] SLEEF_jll v3.5.2+0
[02c8fc9c] XML2_jll v2.12.2+0
[0dad84c5] ArgTools v1.1.1
[56f22d72] Artifacts
[2a0f44e3] Base64
[ade2ca70] Dates
[8ba89e20] Distributed
[f43a241f] Downloads v1.6.0
[7b1f6079] FileWatching
[9fa8497b] Future
[b77e0a4c] InteractiveUtils
[4af54fe1] LazyArtifacts
[b27032c2] LibCURL v0.6.4
[76f85450] LibGit2
[8f399da3] Libdl
[37e2e46d] LinearAlgebra
[56ddb016] Logging
[d6f4376e] Markdown
[a63ad114] Mmap
[ca575930] NetworkOptions v1.2.0
[44cfe95a] Pkg v1.10.0
[de0858da] Printf
[9abbd945] Profile
[3fa0cd96] REPL
[9a3f8284] Random
[ea8e919c] SHA v0.7.0
[9e88b42a] Serialization
[1a1011a3] SharedArrays
[6462fe0b] Sockets
[2f01184e] SparseArrays v1.10.0
[10745b16] Statistics v1.10.0
[4607b0f0] SuiteSparse
[fa267f1f] TOML v1.0.3
[a4e569a6] Tar v1.10.0
[8dfed614] Test
[cf7118a7] UUIDs
[4ec0a83e] Unicode
[e66e0078] CompilerSupportLibraries_jll v1.0.5+1
[781609d7] GMP_jll v6.2.1+6
[deac9b47] LibCURL_jll v8.4.0+0
[e37daf67] LibGit2_jll v1.6.4+0
[29816b5a] LibSSH2_jll v1.11.0+1
[3a97d323] MPFR_jll v4.2.0+1
[c8ffd9c3] MbedTLS_jll v2.28.2+1
[14a3606d] MozillaCACerts_jll v2023.1.10
[4536629a] OpenBLAS_jll v0.3.23+2
[05823500] OpenLibm_jll v0.8.1+2
[bea87d4a] SuiteSparse_jll v7.2.1+1
[83775a58] Zlib_jll v1.2.13+1
[8e850b90] libblastrampoline_jll v5.8.0+1
[8e850ede] nghttp2_jll v1.52.0+1
[3f19e933] p7zip_jll v17.4.0+2
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 -m`
- Output of
versioninfo()
julia> versioninfo()
Julia Version 1.10.0-rc3
Commit ed79752b939 (2023-12-18 09:57 UTC)
Build Info:
Official https://julialang.org/ release
Platform Info:
OS: Linux (x86_64-linux-gnu)
CPU: 12 × AMD Ryzen 5 7600 6-Core Processor
WORD_SIZE: 64
LIBM: libopenlibm
LLVM: libLLVM-15.0.7 (ORCJIT, znver3)
Threads: 1 on 12 virtual coresAdditional context
Not sure if this is actually a problem in RecursiveArrayTools or a symptom of an issue somewhere else, but pinning to v3.1.0 does allow other packages to precompile normally