Precompile warnings for method redefinition in LinearSolveSparseArraysExt in v3.50

[mjowen]

Describe the bug 🐞

Warnings during precompilation of LinearSolveSparseArraysExt due to method overwrites.
Also the extension appears to be loaded with only using LinearSolve

Minimal Reproducible Example 👇

using Pkg; Pkg.activate(; temp=true)
Pkg.add("LinearSolve")
using LinearSolve

Error & Stacktrace ⚠️

julia> using LinearSolve
Precompiling LinearSolveSparseArraysExt...
Info Given LinearSolveSparseArraysExt was explicitly requested, output will be shown live 
WARNING: Method definition init_cacheval(LinearSolve.LUFactorization{P} where P, SciMLOperators.AbstractSciMLOperator{T} where T, Any, Any, Any, Any, Int64, Any, Any, Union{Bool, LinearSolve.LinearVerbosity{__T_default_lu_fallback, __T_no_right_preconditioning, __T_using_IterativeSolvers, __T_IterativeSolvers_iterations, __T_KrylovKit_verbosity, __T_KrylovJL_verbosity, __T_HYPRE_verbosity, __T_pardiso_verbosity, __T_blas_errors, __T_blas_invalid_args, __T_blas_info, __T_blas_success, __T_condition_number, __T_convergence_failure, __T_solver_failure, __T_max_iters} where __T_max_iters where __T_solver_failure where __T_convergence_failure where __T_condition_number where __T_blas_success where __T_blas_info where __T_blas_invalid_args where __T_blas_errors where __T_pardiso_verbosity where __T_HYPRE_verbosity where __T_KrylovJL_verbosity where __T_KrylovKit_verbosity where __T_IterativeSolvers_iterations where __T_using_IterativeSolvers where __T_no_right_preconditioning where __T_default_lu_fallback}, LinearSolve.OperatorAssumptions{T} where T) in module LinearSolve at /Users/qr24461/.julia/packages/LinearSolve/ag6R4/src/factorization.jl:247 overwritten in module LinearSolveSparseArraysExt at /Users/qr24461/.julia/packages/LinearSolve/ag6R4/ext/LinearSolveSparseArraysExt.jl:303.
ERROR: Method overwriting is not permitted during Module precompilation. Use `__precompile__(false)` to opt-out of precompilation.
  ? LinearSolve → LinearSolveSparseArraysExt
[ Info: Precompiling LinearSolveSparseArraysExt [acf9803d-64eb-5f69-b965-a71e3e6e1ed4] (cache misses: wrong dep version loaded (6), mismatched flags (12))
WARNING: Method definition init_cacheval(LinearSolve.LUFactorization{P} where P, SciMLOperators.AbstractSciMLOperator{T} where T, Any, Any, Any, Any, Int64, Any, Any, Union{Bool, LinearSolve.LinearVerbosity{__T_default_lu_fallback, __T_no_right_preconditioning, __T_using_IterativeSolvers, __T_IterativeSolvers_iterations, __T_KrylovKit_verbosity, __T_KrylovJL_verbosity, __T_HYPRE_verbosity, __T_pardiso_verbosity, __T_blas_errors, __T_blas_invalid_args, __T_blas_info, __T_blas_success, __T_condition_number, __T_convergence_failure, __T_solver_failure, __T_max_iters} where __T_max_iters where __T_solver_failure where __T_convergence_failure where __T_condition_number where __T_blas_success where __T_blas_info where __T_blas_invalid_args where __T_blas_errors where __T_pardiso_verbosity where __T_HYPRE_verbosity where __T_KrylovJL_verbosity where __T_KrylovKit_verbosity where __T_IterativeSolvers_iterations where __T_using_IterativeSolvers where __T_no_right_preconditioning where __T_default_lu_fallback}, LinearSolve.OperatorAssumptions{T} where T) in module LinearSolve at /Users/qr24461/.julia/packages/LinearSolve/ag6R4/src/factorization.jl:247 overwritten in module LinearSolveSparseArraysExt at /Users/qr24461/.julia/packages/LinearSolve/ag6R4/ext/LinearSolveSparseArraysExt.jl:303.
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 LinearSolveSparseArraysExt [acf9803d-64eb-5f69-b965-a71e3e6e1ed4].
└   exception = Error when precompiling module, potentially caused by a __precompile__(false) declaration in the module.

Environment (please complete the following information):

• Output of using Pkg; Pkg.status()

Status `/private/var/folders/sq/qg5k_lb90mvgph1ysj0cz4sh0000gp/T/jl_qLgaU1/Project.toml`
  [7ed4a6bd] LinearSolve v3.50.0

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

Status `/private/var/folders/sq/qg5k_lb90mvgph1ysj0cz4sh0000gp/T/jl_qLgaU1/Manifest.toml`
  [47edcb42] ADTypes v1.20.0
  [7d9f7c33] Accessors v0.1.43
  [79e6a3ab] Adapt v4.4.0
  [4fba245c] ArrayInterface v7.22.0
  [4c555306] ArrayLayouts v1.12.2
  [d360d2e6] ChainRulesCore v1.26.0
  [38540f10] CommonSolve v0.2.4
  [34da2185] Compat v4.18.1
  [a33af91c] CompositionsBase v0.1.2
  [2569d6c7] ConcreteStructs v0.2.3
  [187b0558] ConstructionBase v1.6.0
  [ffbed154] DocStringExtensions v0.9.5
  [4e289a0a] EnumX v1.0.5
  [e2ba6199] ExprTools v0.1.10
  [55351af7] ExproniconLite v0.10.14
  [1a297f60] FillArrays v1.15.0
  [069b7b12] FunctionWrappers v1.1.3
  [77dc65aa] FunctionWrappersWrappers v0.1.3
  [46192b85] GPUArraysCore v0.2.0
  [3587e190] InverseFunctions v0.1.17
  [82899510] IteratorInterfaceExtensions v1.0.0
  [692b3bcd] JLLWrappers v1.7.1
  [ae98c720] Jieko v0.2.1
  [ba0b0d4f] Krylov v0.10.3
  [5078a376] LazyArrays v2.9.4
  [7ed4a6bd] LinearSolve v3.50.0
  [e6f89c97] LoggingExtras v1.2.0
  [1914dd2f] MacroTools v0.5.16
  [2e0e35c7] Moshi v0.3.7
  [d236fae5] PreallocationTools v0.4.34
⌅ [aea7be01] PrecompileTools v1.2.1
  [21216c6a] Preferences v1.5.0
  [3cdcf5f2] RecipesBase v1.3.4
  [731186ca] RecursiveArrayTools v3.39.0
  [189a3867] Reexport v1.2.2
  [ae029012] Requires v1.3.1
  [7e49a35a] RuntimeGeneratedFunctions v0.5.16
  [0bca4576] SciMLBase v2.128.0
  [a6db7da4] SciMLLogging v1.7.1
  [c0aeaf25] SciMLOperators v1.14.0
  [431bcebd] SciMLPublic v1.0.0
  [53ae85a6] SciMLStructures v1.7.0
  [efcf1570] Setfield v1.1.2
  [90137ffa] StaticArrays v1.9.15
  [1e83bf80] StaticArraysCore v1.4.4
  [10745b16] Statistics v1.11.1
  [2efcf032] SymbolicIndexingInterface v0.3.46
  [1d5cc7b8] IntelOpenMP_jll v2025.2.0+0
  [856f044c] MKL_jll v2025.2.0+0
  [1317d2d5] oneTBB_jll v2022.0.0+1
  [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
  [4af54fe1] LazyArtifacts 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
  [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
  [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
  [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
Info Packages marked with ⌅ have new versions available but compatibility constraints restrict them from upgrading. To see why use `status --outdated -m`

• Output of versioninfo()

Julia Version 1.11.7
Commit f2b3dbda30a (2025-09-08 12:10 UTC)
Build Info:
  Official https://julialang.org/ release
Platform Info:
  OS: macOS (arm64-apple-darwin24.0.0)
  CPU: 14 × Apple M4 Pro
  WORD_SIZE: 64
  LLVM: libLLVM-16.0.6 (ORCJIT, apple-m1)
Threads: 1 default, 0 interactive, 1 GC (on 10 virtual cores)
Environment:
  JULIA_EDITOR = code
  JULIA_VSCODE_REPL = 1

[DanielDoehring]

We see that issue as well in our CI

https://github.com/trixi-framework/Trixi.jl/actions/runs/20135706261/job/57788325566?pr=2696#step:7:25864

[yuyichao]

The issue doesn't seem to be fully fixed. There's still a redefinition between

LinearSolve.jl/ext/LinearSolveSparseArraysExt.jl

Line 327 in 39b60af

function LinearSolve.init_cacheval(

and

LinearSolve.jl/src/factorization.jl

Line 254 in 39b60af

function init_cacheval(alg::GenericLUFactorization,

[ChrisRackauckas]

How do I make these error? I don't want these as warnings, I've never wanted them as warnings.