Package evaluation to test PEtab on Julia 1.12.7-DEV.42 (6f510b6086*) started at 2026-06-20T10:19:01.298 ################################################################################ # Set-up # Installing PkgEval dependencies (TestEnv)... Activating project at `~/.julia/environments/v1.12` Set-up completed after 8.11s ################################################################################ # Installation # Installing PEtab... Resolving package versions... Updating `~/.julia/environments/v1.12/Project.toml` [48d54b35] + PEtab v5.3.1 Updating `~/.julia/environments/v1.12/Manifest.toml` [47edcb42] + ADTypes v1.22.0 [14f7f29c] + AMD v0.5.3 [6e696c72] + AbstractPlutoDingetjes v1.4.0 [1520ce14] + AbstractTrees v0.4.5 [7d9f7c33] + Accessors v0.1.44 [79e6a3ab] + Adapt v4.6.1 [66dad0bd] + AliasTables v1.1.3 [ec485272] + ArnoldiMethod v0.4.0 [4fba245c] + ArrayInterface v7.25.0 [4c555306] + ArrayLayouts v1.12.2 [aae01518] + BandedMatrices v1.11.0 [e2ed5e7c] + Bijections v0.2.2 [caf10ac8] + BipartiteGraphs v0.1.7 [8e7c35d0] + BlockArrays v1.9.3 [70df07ce] + BracketingNonlinearSolve v1.12.1 [fa961155] + CEnum v0.5.0 [336ed68f] + CSV v0.10.16 [479239e8] + Catalyst v16.2.0 [d360d2e6] + ChainRulesCore v1.26.1 [944b1d66] + CodecZlib v0.7.8 ⌅ [861a8166] + Combinatorics v1.0.2 [38540f10] + CommonSolve v0.2.7 [bbf7d656] + CommonSubexpressions v0.3.1 [f70d9fcc] + CommonWorldInvalidations v1.0.0 [34da2185] + Compat v4.18.1 [b0b7db55] + ComponentArrays v0.15.39 [b152e2b5] + CompositeTypes v0.1.4 [a33af91c] + CompositionsBase v0.1.2 [2569d6c7] + ConcreteStructs v0.2.4 [187b0558] + ConstructionBase v1.6.0 [a8cc5b0e] + Crayons v4.1.1 [9a962f9c] + DataAPI v1.16.0 [a93c6f00] + DataFrames v1.8.2 [864edb3b] + DataStructures v0.19.5 [e2d170a0] + DataValueInterfaces v1.0.0 [8bb1440f] + DelimitedFiles v1.9.1 [2b5f629d] + DiffEqBase v7.5.5 [459566f4] + DiffEqCallbacks v4.18.0 [163ba53b] + DiffResults v1.1.0 [b552c78f] + DiffRules v1.16.0 [a0c0ee7d] + DifferentiationInterface v0.7.18 [8d63f2c5] + DispatchDoctor v0.4.28 [31c24e10] + Distributions v0.25.127 [ffbed154] + DocStringExtensions v0.9.5 [5b8099bc] + DomainSets v0.8.0 [7c1d4256] + DynamicPolynomials v0.6.6 [06fc5a27] + DynamicQuantities v1.13.0 [4e289a0a] + EnumX v1.0.7 [f151be2c] + EnzymeCore v0.8.20 [e2ba6199] + ExprTools v0.1.10 [55351af7] + ExproniconLite v0.10.14 [7034ab61] + FastBroadcast v1.3.2 [9aa1b823] + FastClosures v0.3.2 [a4df4552] + FastPower v1.3.1 [48062228] + FilePathsBase v0.9.24 [1a297f60] + FillArrays v1.16.0 [6a86dc24] + FiniteDiff v2.31.0 [1fa38f19] + Format v1.3.7 [f6369f11] + ForwardDiff v1.4.1 [a85aefff] + FunctionMaps v0.1.2 [069b7b12] + FunctionWrappers v1.1.3 [77dc65aa] + FunctionWrappersWrappers v1.9.1 [d9f16b24] + Functors v0.5.2 [46192b85] + GPUArraysCore v0.2.0 [86223c79] + Graphs v1.14.0 [f67ccb44] + HDF5 v0.17.3 [34004b35] + HypergeometricFunctions v0.3.28 [615f187c] + IfElse v0.1.1 [3263718b] + ImplicitDiscreteSolve v2.1.0 [d25df0c9] + Inflate v0.1.5 [842dd82b] + InlineStrings v1.4.5 [18e54dd8] + IntegerMathUtils v0.1.3 [8197267c] + IntervalSets v0.7.14 [3587e190] + InverseFunctions v0.1.17 [41ab1584] + InvertedIndices v1.3.1 [92d709cd] + IrrationalConstants v0.2.6 [82899510] + IteratorInterfaceExtensions v1.0.0 [692b3bcd] + JLLWrappers v1.8.0 [ae98c720] + Jieko v0.2.1 [ccbc3e58] + JumpProcesses v9.29.0 [ba0b0d4f] + Krylov v0.10.6 [b964fa9f] + LaTeXStrings v1.4.0 [23fbe1c1] + Latexify v0.16.10 [73f95e8e] + LatticeRules v0.0.1 [87fe0de2] + LineSearch v0.1.9 [7ed4a6bd] + LinearSolve v3.86.0 [2ab3a3ac] + LogExpFunctions v1.0.1 [e6f89c97] + LoggingExtras v1.2.0 [3da0fdf6] + MPIPreferences v0.1.12 [1914dd2f] + MacroTools v0.5.16 [bb5d69b7] + MaybeInplace v0.1.4 [e1d29d7a] + Missings v1.2.0 [7771a370] + ModelingToolkitBase v1.44.0 [2e0e35c7] + Moshi v0.3.8 [46d2c3a1] + MuladdMacro v0.2.4 [102ac46a] + MultivariatePolynomials v0.5.19 [d8a4904e] + MutableArithmetics v1.8.0 [77ba4419] + NaNMath v1.1.4 [8913a72c] + NonlinearSolve v4.19.1 [be0214bd] + NonlinearSolveBase v2.31.0 [5959db7a] + NonlinearSolveFirstOrder v2.1.1 [9a2c21bd] + NonlinearSolveQuasiNewton v1.13.1 [26075421] + NonlinearSolveSpectralMethods v1.7.1 [6fe1bfb0] + OffsetArrays v1.17.0 ⌅ [bac558e1] + OrderedCollections v1.8.2 [6ad6398a] + OrdinaryDiffEqBDF v2.2.0 [bbf590c4] + OrdinaryDiffEqCore v4.3.0 [4302a76b] + OrdinaryDiffEqDifferentiation v3.2.0 [127b3ac7] + OrdinaryDiffEqNonlinearSolve v2.0.0 [43230ef6] + OrdinaryDiffEqRosenbrock v2.3.0 [b4bd8bb3] + OrdinaryDiffEqRosenbrockTableaus v2.1.0 [2d112036] + OrdinaryDiffEqSDIRK v2.7.0 [b1df2697] + OrdinaryDiffEqTsit5 v2.0.1 [90014a1f] + PDMats v0.11.37 [48d54b35] + PEtab v5.3.1 ⌅ [d96e819e] + Parameters v0.12.3 [69de0a69] + Parsers v2.8.6 [e409e4f3] + PoissonRandom v0.4.9 [2dfb63ee] + PooledArrays v1.4.3 [d236fae5] + PreallocationTools v1.2.0 [aea7be01] + PrecompileTools v1.3.4 [21216c6a] + Preferences v1.5.2 [08abe8d2] + PrettyTables v3.3.2 [27ebfcd6] + Primes v0.5.7 [43287f4e] + PtrArrays v1.4.0 [0c0d3e7f] + PureKLU v1.0.1 [1fd47b50] + QuadGK v2.11.3 [8a4e6c94] + QuasiMonteCarlo v0.3.5 [988b38a3] + ReadOnlyArrays v0.2.0 [795d4caa] + ReadOnlyDicts v1.0.1 [3cdcf5f2] + RecipesBase v1.3.4 [731186ca] + RecursiveArrayTools v4.3.1 [189a3867] + Reexport v1.2.2 [ae029012] + Requires v1.3.1 [37e2e3b7] + ReverseDiff v1.17.0 [79098fc4] + Rmath v0.9.0 [7e49a35a] + RuntimeGeneratedFunctions v0.5.19 [e5567a89] + SBML v1.6.0 [210efffb] + SBMLImporter v4.1.0 [9dfe8606] + SCCNonlinearSolve v1.13.0 [0bca4576] + SciMLBase v3.21.0 [19f34311] + SciMLJacobianOperators v0.1.13 [a6db7da4] + SciMLLogging v2.0.0 [c0aeaf25] + SciMLOperators v1.22.0 [431bcebd] + SciMLPublic v1.0.1 [53ae85a6] + SciMLStructures v1.10.0 [91c51154] + SentinelArrays v1.4.10 [efcf1570] + Setfield v1.1.2 [727e6d20] + SimpleNonlinearSolve v2.12.0 [699a6c99] + SimpleTraits v0.9.6 [ed01d8cd] + Sobol v1.5.0 [a2af1166] + SortingAlgorithms v1.2.2 [a57abbd0] + SparseColumnPivotedQR v2.1.1 [0a514795] + SparseMatrixColorings v0.4.27 [276daf66] + SpecialFunctions v2.8.0 [0c0c59c1] + StarAlgebras v0.3.0 [aedffcd0] + Static v1.4.0 [0d7ed370] + StaticArrayInterface v1.10.0 [90137ffa] + StaticArrays v1.9.18 [1e83bf80] + StaticArraysCore v1.4.4 [10745b16] + Statistics v1.11.1 [82ae8749] + StatsAPI v1.8.0 [2913bbd2] + StatsBase v0.34.12 [4c63d2b9] + StatsFuns v2.2.0 [69024149] + StringEncodings v0.3.7 [892a3eda] + StringManipulation v0.4.4 [c3572dad] + Sundials v6.2.1 [2efcf032] + SymbolicIndexingInterface v0.3.48 [19f23fe9] + SymbolicLimits v1.1.0 [d1185830] + SymbolicUtils v4.35.3 [0c5d862f] + Symbolics v7.28.1 [3783bdb8] + TableTraits v1.0.1 [bd369af6] + Tables v1.12.1 [ed4db957] + TaskLocalValues v0.1.3 [8ea1fca8] + TermInterface v2.0.0 [1c621080] + TestItems v1.0.0 [a759f4b9] + TimerOutputs v0.5.29 [3bb67fe8] + TranscodingStreams v0.11.3 [410a4b4d] + Tricks v0.1.13 [781d530d] + TruncatedStacktraces v1.4.0 [3a884ed6] + UnPack v1.0.2 [1986cc42] + Unitful v1.28.0 [d30d5f5c] + WeakCacheSets v0.1.0 [ea10d353] + WeakRefStrings v1.4.3 [76eceee3] + WorkerUtilities v1.6.1 [ddb6d928] + YAML v0.4.16 [61579ee1] + Ghostscript_jll v9.55.1+0 [0234f1f7] + HDF5_jll v2.1.2+0 [e33a78d0] + Hwloc_jll v2.14.0+0 [1d5cc7b8] + IntelOpenMP_jll v2025.2.0+0 [aacddb02] + JpegTurbo_jll v3.1.5+0 [94ce4f54] + Libiconv_jll v1.18.0+0 [856f044c] + MKL_jll v2025.2.0+0 [b5ada748] + MPIABI_jll v0.1.5+0 [7cb0a576] + MPICH_jll v5.0.1+0 [f1f71cc9] + MPItrampoline_jll v5.5.6+0 [9237b28f] + MicrosoftMPI_jll v10.1.4+3 [656ef2d0] + OpenBLAS32_jll v0.3.33+1 [fe0851c0] + OpenMPI_jll v5.0.11+0 [efe28fd5] + OpenSpecFun_jll v0.5.6+0 [f50d1b31] + Rmath_jll v0.5.1+0 [bb12108a] + SBML_jll v5.21.0+0 [ca45d3f4] + SuiteSparse32_jll v7.12.1+0 [fb77eaff] + Sundials_jll v7.5.0+0 ⌅ [02c8fc9c] + XML2_jll v2.13.9+0 [a65dc6b1] + Xorg_libpciaccess_jll v0.19.0+0 ⌅ [2b3700d1] + aws_c_auth_jll v0.9.6+0 [70f11efc] + aws_c_cal_jll v0.9.13+0 [73048d1d] + aws_c_common_jll v0.12.6+0 [73a04cd5] + aws_c_compression_jll v0.3.2+0 [3254fc65] + aws_c_http_jll v0.10.13+0 [13c41daa] + aws_c_io_jll v0.26.3+0 ⌅ [bd1f34fb] + aws_c_s3_jll v0.11.5+0 [1282aa60] + aws_c_sdkutils_jll v0.2.4+1 [b2a88e68] + aws_checksums_jll v0.2.10+0 [c4b69c83] + dlfcn_win32_jll v1.4.2+0 [477f73a3] + libaec_jll v1.1.7+0 [9aeb927a] + mpif_jll v0.1.7+0 [1317d2d5] + oneTBB_jll v2022.3.0+0 [cddc5d3d] + s2n_tls_jll v1.7.3+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 v1.7.0 [7b1f6079] + FileWatching v1.11.0 [9fa8497b] + Future v1.11.0 [b77e0a4c] + InteractiveUtils v1.11.0 [ac6e5ff7] + JuliaSyntaxHighlighting v1.12.0 [4af54fe1] + LazyArtifacts v1.11.0 [b27032c2] + LibCURL v0.6.4 [76f85450] + LibGit2 v1.11.0 [8f399da3] + Libdl v1.11.0 [37e2e46d] + LinearAlgebra v1.12.0 [56ddb016] + Logging v1.11.0 [d6f4376e] + Markdown v1.11.0 [a63ad114] + Mmap v1.11.0 [ca575930] + NetworkOptions v1.3.0 [44cfe95a] + Pkg v1.12.1 [de0858da] + Printf v1.11.0 [3fa0cd96] + REPL 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 v1.12.0 [f489334b] + StyledStrings v1.11.0 [4607b0f0] + SuiteSparse [fa267f1f] + TOML v1.0.3 [a4e569a6] + Tar v1.10.0 [8dfed614] + Test v1.11.0 [cf7118a7] + UUIDs v1.11.0 [4ec0a83e] + Unicode v1.11.0 [e66e0078] + CompilerSupportLibraries_jll v1.3.0+1 [deac9b47] + LibCURL_jll v8.15.0+0 [e37daf67] + LibGit2_jll v1.9.0+0 [29816b5a] + LibSSH2_jll v1.11.3+1 [14a3606d] + MozillaCACerts_jll v2025.11.4 [4536629a] + OpenBLAS_jll v0.3.29+0 [05823500] + OpenLibm_jll v0.8.7+0 [458c3c95] + OpenSSL_jll v3.5.6+0 [bea87d4a] + SuiteSparse_jll v7.8.3+2 [83775a58] + Zlib_jll v1.3.1+2 [8e850b90] + libblastrampoline_jll v5.15.0+0 [8e850ede] + nghttp2_jll v1.64.0+1 [3f19e933] + p7zip_jll v17.7.0+0 Info Packages marked with ⌅ have new versions available but compatibility constraints restrict them from upgrading. To see why use `status --outdated -m` Installation completed after 12.66s ################################################################################ # Precompilation # Precompiling PkgEval dependencies... ┌ Warning: Could not use exact versions of packages in manifest, re-resolving └ @ TestEnv ~/.julia/packages/TestEnv/RUPmD/src/julia-1.12/activate_set.jl:78 Precompiling package dependencies... Precompiling packages... 15700.2 ms ✓ HypothesisTests 328869.5 ms ✓ LikelihoodProfiler 67187.0 ms ✓ SimpleNonlinearSolve → SimpleNonlinearSolveTrackerExt 1.2432182e6 ms ✓ SciMLSensitivity 773418.2 ms ✓ ModelingToolkitBase → MTKDiffEqNoiseProcessExt 41193.4 ms ✓ ModelingToolkitBase → MTKDynamicQuantitiesExt ====================================================================================== Information request received. A stacktrace will print followed by a 1.0 second profile ====================================================================================== cmd: /opt/julia/bin/julia 55 running 0 of 1 signal (10): User defined signal 1 epoll_pwait at /lib/x86_64-linux-gnu/libc.so.6 (unknown line) uv__io_poll at /workspace/srcdir/libuv/src/unix/linux.c:1404 uv_run at /workspace/srcdir/libuv/src/unix/core.c:430 ijl_task_get_next at /source/src/scheduler.c:457 poptask at ./task.jl:1216 wait at ./task.jl:1228 #wait#406 at ./condition.jl:141 wait at ./condition.jl:136 [inlined] _trywait at ./asyncevent.jl:185 #653 at ./asyncevent.jl:359 jfptr_YY.653_3180.1 at /opt/julia/lib/julia/sys.so (unknown line) _jl_invoke at /source/src/gf.c:4014 [inlined] ijl_apply_generic at /source/src/gf.c:4214 jl_apply at /source/src/julia.h:2397 [inlined] start_task at /source/src/task.c:1253 unknown function (ip: (nil)) at (unknown file) ============================================================== Profile collected. A report will print at the next yield point ============================================================== ┌ Warning: There were no samples collected in one or more groups. │ This may be due to idle threads, or you may need to run your │ program longer (perhaps by running it multiple times), │ or adjust the delay between samples with `Profile.init()`. └ @ Profile /opt/julia/share/julia/stdlib/v1.12/Profile/src/Profile.jl:1361 Overhead ╎ [+additional indent] Count File:Line Function ========================================================= Thread 1 (default) Task 0x0000755e18e9fd00 Total snapshots: 406. Utilization: 0% ╎406 @Base/asyncevent.jl:359 (::Base.var"#653#654"{FileWatching.Pidfile.var… ╎ 406 @Base/asyncevent.jl:185 _trywait(t::Timer) ╎ 406 @Base/condition.jl:136 wait ╎ 406 @Base/condition.jl:141 wait(c::Base.GenericCondition{Base.Threads.S… ╎ 406 @Base/task.jl:1228 wait() 405╎ 406 @Base/task.jl:1216 poptask(W::Base.IntrusiveLinkedListSynchronize… ====================================================================================== Information request received. A stacktrace will print followed by a 1.0 second profile ====================================================================================== cmd: /opt/julia/bin/julia 1 running 0 of 1 signal (10): User defined signal 1 epoll_pwait at /lib/x86_64-linux-gnu/libc.so.6 (unknown line) uv__io_poll at /workspace/srcdir/libuv/src/unix/linux.c:1404 uv_run at /workspace/srcdir/libuv/src/unix/core.c:430 ijl_task_get_next at /source/src/scheduler.c:457 poptask at ./task.jl:1216 wait at ./task.jl:1228 task_done_hook at ./task.jl:868 jfptr_task_done_hook_43684.1 at /opt/julia/lib/julia/sys.so (unknown line) _jl_invoke at /source/src/gf.c:4014 [inlined] ijl_apply_generic at /source/src/gf.c:4214 jl_apply at /source/src/julia.h:2397 [inlined] jl_finish_task at /source/src/task.c:342 start_task at /source/src/task.c:1264 unknown function (ip: (nil)) at (unknown file) ============================================================== Profile collected. A report will print at the next yield point ============================================================== ┌ Warning: There were no samples collected in one or more groups. │ This may be due to idle threads, or you may need to run your │ program longer (perhaps by running it multiple times), │ or adjust the delay between samples with `Profile.init()`. └ @ Profile /opt/julia/share/julia/stdlib/v1.12/Profile/src/Profile.jl:1361 Overhead ╎ [+additional indent] Count File:Line Function ========================================================= Thread 1 (default) Task 0x0000732f0ccaa3b0 Total snapshots: 368. Utilization: 0% ╎368 @Base/task.jl:868 task_done_hook(t::Task) ╎ 368 @Base/task.jl:1228 wait() 367╎ 368 @Base/task.jl:1216 poptask(W::Base.IntrusiveLinkedListSynchronized{T… [55] signal 15: Terminated in expression starting at /PkgEval.jl/scripts/precompile.jl:34 epoll_pwait at /lib/x86_64-linux-gnu/libc.so.6 (unknown line) uv__io_poll at /workspace/srcdir/libuv/src/unix/linux.c:1404 uv_run at /workspace/srcdir/libuv/src/unix/core.c:430 ijl_task_get_next at /source/src/scheduler.c:457 poptask at ./task.jl:1216 wait at ./task.jl:1228 #wait#406 at ./condition.jl:141 wait at ./condition.jl:136 [inlined] _trywait at ./asyncevent.jl:185 #653 at ./asyncevent.jl:359 jfptr_YY.653_3180.1 at /opt/julia/lib/julia/sys.so (unknown line) _jl_invoke at /source/src/gf.c:4014 [inlined] ijl_apply_generic at /source/src/gf.c:4214 jl_apply at /source/src/julia.h:2397 [inlined] start_task at /source/src/task.c:1253 unknown function (ip: (nil)) at (unknown file) Allocations: 138216633 (Pool: 138215378; Big: 1255); GC: 110 PkgEval terminated after 2755.11s: test duration exceeded the time limit