Package evaluation to test sparseQFCA on Julia 1.14.0-DEV.1730 (9c1e1fa299*) started at 2026-02-18T00:06:53.898 ################################################################################ # Set-up # Installing PkgEval dependencies (TestEnv)... Activating project at `~/.julia/environments/v1.14` Set-up completed after 13.17s ################################################################################ # Installation # Installing sparseQFCA... Resolving package versions... Installed MacroTools ──────────── v0.5.16 Installed DiffResults ─────────── v1.1.0 Installed HiGHS_jll ───────────── v1.13.1+0 Installed ForwardDiff ─────────── v1.3.2 Installed SnoopPrecompile ─────── v1.0.3 Installed DataStructures ──────── v0.18.22 Installed JLD2 ────────────────── v0.5.15 Installed SBML ────────────────── v1.6.0 Installed Bzip2_jll ───────────── v1.0.9+0 Installed HiGHS ───────────────── v1.21.1 Installed ConstructionBase ────── v1.6.0 Installed libaec_jll ──────────── v1.1.5+0 Installed DelimitedFiles ──────── v1.9.1 Installed MPICH_jll ───────────── v4.3.2+0 Installed oneTBB_jll ──────────── v2022.0.0+1 Installed MKL_jll ─────────────── v2024.2.0+0 Installed Clp ─────────────────── v1.3.0 Installed CodecZlib ───────────── v0.7.8 Installed ExprTools ───────────── v0.1.10 Installed Cgl_jll ─────────────── v0.6000.900+0 Installed Cbc_jll ─────────────── v200.1000.1200+0 Installed HSL_jll ─────────────── v4.0.4+0 Installed OrderedCollections ──── v1.8.1 Installed TranscodingStreams ──── v0.11.3 Installed SBMLFBCModels ───────── v1.1.1 Installed MicrosoftMPI_jll ────── v10.1.4+3 Installed HashArrayMappedTries ── v0.2.0 Installed Compat ──────────────── v4.18.1 Installed PrecompileTools ─────── v1.3.3 Installed Clp_jll ─────────────── v100.1700.1000+1 Installed CDDLib ──────────────── v0.10.2 Installed MUMPS_seq_jll ───────── v500.800.100+0 Installed Xorg_libpciaccess_jll ─ v0.18.1+0 Installed Statistics ──────────── v1.11.1 Installed Clarabel ────────────── v0.10.0 Installed ConstraintTrees ─────── v1.11.0 Installed CoinUtils_jll ───────── v200.1100.1200+0 Installed CEnum ───────────────── v0.5.0 Installed TimerOutputs ────────── v0.5.29 Installed IntelOpenMP_jll ─────── v2024.2.1+0 Installed Colors ──────────────── v0.13.1 Installed ASL_jll ─────────────── v0.1.3+0 Installed CommonSubexpressions ── v0.3.1 Installed JuMP ────────────────── v1.29.4 Installed FileIO ──────────────── v1.18.0 Installed StaticArraysCore ────── v1.4.4 Installed IrrationalConstants ─── v0.2.6 Installed NaNMath ─────────────── v1.1.3 Installed CodecBzip2 ──────────── v0.8.5 Installed StaticArrays ────────── v1.9.16 Installed ColorTypes ──────────── v0.12.1 Installed Requires ────────────── v1.3.1 Installed AbstractFBCModels ───── v1.3.0 Installed OpenSpecFun_jll ─────── v0.5.6+0 Installed GenericLinearAlgebra ── v0.3.19 Installed QDLDL ───────────────── v0.4.1 Installed SCS ─────────────────── v2.6.2 Installed HDF5_jll ────────────── v1.14.6+0 Installed LogExpFunctions ─────── v0.3.29 Installed StableRNGs ──────────── v1.0.4 Installed Pardiso ─────────────── v0.5.7 Installed AMD ─────────────────── v0.5.3 Installed DiffRules ───────────── v1.15.1 Installed SBML_jll ────────────── v5.21.0+0 Installed OpenBLAS32_jll ──────── v0.3.30+0 Installed OpenMPI_jll ─────────── v5.0.9+0 Installed Parsers ─────────────── v2.8.3 Installed JSON ────────────────── v0.21.4 Installed Cbc ─────────────────── v1.3.0 Installed Hwloc_jll ───────────── v2.13.0+0 Installed ECOS_jll ────────────── v200.0.800+0 Installed GLPK_jll ────────────── v5.0.1+1 Installed IfElse ──────────────── v0.1.1 Installed ScopedValues ────────── v1.5.0 Installed ECOS ────────────────── v1.1.3 Installed XML2_jll ────────────── v2.13.9+0 Installed Unitful ─────────────── v1.28.0 Installed MathOptIIS ──────────── v0.1.1 Installed SpecialFunctions ────── v2.7.1 Installed PikaParser ──────────── v0.6.1 Installed COBREXA ─────────────── v2.9.1 Installed JSONFBCModels ───────── v1.0.1 Installed Reexport ────────────── v1.2.2 Installed MPIPreferences ──────── v0.1.11 Installed FixedPointNumbers ───── v0.8.5 Installed BenchmarkTools ──────── v1.6.3 Installed Preferences ─────────── v1.5.1 Installed MutableArithmetics ──── v1.6.7 Installed JLLWrappers ─────────── v1.7.1 Installed Libiconv_jll ────────── v1.18.0+0 Installed LLVMOpenMP_jll ──────── v18.1.8+0 Installed cddlib_jll ──────────── v0.94.14+0 Installed MPItrampoline_jll ───── v5.5.5+0 Installed HDF5 ────────────────── v0.17.2 Installed Polyhedra ───────────── v0.8.1 Installed GLPK ────────────────── v1.2.1 Installed SCS_jll ─────────────── v300.200.1100+0 Installed METIS_jll ───────────── v5.1.2+1 Installed DocStringExtensions ─── v0.9.5 Installed Osi_jll ─────────────── v0.10800.1100+0 Installed HSL ─────────────────── v0.4.3 Installed MathOptInterface ────── v1.49.0 Installed sparseQFCA ──────────── v2.3.0 Installing 26 artifacts Installed artifact OpenSpecFun 194.9 KiB Installed artifact LLVMOpenMP 661.6 KiB Installed artifact Clp 1.4 MiB Installed artifact Cgl 656.0 KiB Installed artifact METIS 1.1 MiB Installed artifact ASL 276.3 KiB Installed artifact HiGHS 2.4 MiB Installed artifact MPICH 3.3 MiB Installed artifact ECOS 75.2 KiB Installed artifact Libiconv 1.9 MiB Installed artifact SCS 543.6 KiB Installed artifact Bzip2 503.5 KiB Installed artifact cddlib 1.0 MiB Installed artifact HSL 1.1 MiB Installed artifact libaec 49.6 KiB Installed artifact MUMPS_seq 8.6 MiB Installed artifact CoinUtils 811.6 KiB Installed artifact SBML 6.0 MiB Installed artifact Hwloc 3.5 MiB Installed artifact XML2 2.5 MiB Installed artifact GLPK 3.1 MiB Installed artifact Cbc 1.1 MiB Installed artifact Xorg_libpciaccess 24.8 KiB Installed artifact Osi 443.6 KiB Installed artifact HDF5 5.7 MiB Installed artifact OpenBLAS32 10.0 MiB Updating `~/.julia/environments/v1.14/Project.toml` [077cf62c] + sparseQFCA v2.3.0 Updating `~/.julia/environments/v1.14/Manifest.toml` [14f7f29c] + AMD v0.5.3 [5a4f3dfa] + AbstractFBCModels v1.3.0 [6e4b80f9] + BenchmarkTools v1.6.3 [3391f64e] + CDDLib v0.10.2 [fa961155] + CEnum v0.5.0 [babc4406] + COBREXA v2.9.1 [9961bab8] + Cbc v1.3.0 ⌅ [61c947e1] + Clarabel v0.10.0 [e2554f3b] + Clp v1.3.0 [523fee87] + CodecBzip2 v0.8.5 [944b1d66] + CodecZlib v0.7.8 [3da002f7] + ColorTypes v0.12.1 [5ae59095] + Colors v0.13.1 [bbf7d656] + CommonSubexpressions v0.3.1 [34da2185] + Compat v4.18.1 [5515826b] + ConstraintTrees v1.11.0 [187b0558] + ConstructionBase v1.6.0 ⌅ [864edb3b] + DataStructures v0.18.22 [8bb1440f] + DelimitedFiles v1.9.1 [163ba53b] + DiffResults v1.1.0 [b552c78f] + DiffRules v1.15.1 [ffbed154] + DocStringExtensions v0.9.5 [e2685f51] + ECOS v1.1.3 [e2ba6199] + ExprTools v0.1.10 [5789e2e9] + FileIO v1.18.0 [53c48c17] + FixedPointNumbers v0.8.5 [f6369f11] + ForwardDiff v1.3.2 [60bf3e95] + GLPK v1.2.1 [14197337] + GenericLinearAlgebra v0.3.19 [f67ccb44] + HDF5 v0.17.2 ⌅ [34c5aeac] + HSL v0.4.3 [076d061b] + HashArrayMappedTries v0.2.0 [87dc4568] + HiGHS v1.21.1 [615f187c] + IfElse v0.1.1 [92d709cd] + IrrationalConstants v0.2.6 ⌅ [033835bb] + JLD2 v0.5.15 [692b3bcd] + JLLWrappers v1.7.1 ⌅ [682c06a0] + JSON v0.21.4 [475c1105] + JSONFBCModels v1.0.1 [4076af6c] + JuMP v1.29.4 [2ab3a3ac] + LogExpFunctions v0.3.29 [3da0fdf6] + MPIPreferences v0.1.11 [1914dd2f] + MacroTools v0.5.16 [8c4f8055] + MathOptIIS v0.1.1 [b8f27783] + MathOptInterface v1.49.0 [d8a4904e] + MutableArithmetics v1.6.7 [77ba4419] + NaNMath v1.1.3 [bac558e1] + OrderedCollections v1.8.1 ⌅ [46dd5b70] + Pardiso v0.5.7 [69de0a69] + Parsers v2.8.3 [3bbf5609] + PikaParser v0.6.1 [67491407] + Polyhedra v0.8.1 [aea7be01] + PrecompileTools v1.3.3 [21216c6a] + Preferences v1.5.1 [bfc457fd] + QDLDL v0.4.1 [189a3867] + Reexport v1.2.2 [ae029012] + Requires v1.3.1 [e5567a89] + SBML v1.6.0 [3e8f9d1a] + SBMLFBCModels v1.1.1 [c946c3f1] + SCS v2.6.2 [7e506255] + ScopedValues v1.5.0 [66db9d55] + SnoopPrecompile v1.0.3 [276daf66] + SpecialFunctions v2.7.1 [860ef19b] + StableRNGs v1.0.4 [90137ffa] + StaticArrays v1.9.16 [1e83bf80] + StaticArraysCore v1.4.4 [10745b16] + Statistics v1.11.1 [a759f4b9] + TimerOutputs v0.5.29 [3bb67fe8] + TranscodingStreams v0.11.3 [1986cc42] + Unitful v1.28.0 [077cf62c] + sparseQFCA v2.3.0 [ae81ac8f] + ASL_jll v0.1.3+0 [6e34b625] + Bzip2_jll v1.0.9+0 [38041ee0] + Cbc_jll v200.1000.1200+0 [3830e938] + Cgl_jll v0.6000.900+0 ⌅ [06985876] + Clp_jll v100.1700.1000+1 [be027038] + CoinUtils_jll v200.1100.1200+0 [c2c64177] + ECOS_jll v200.0.800+0 [e8aa6df9] + GLPK_jll v5.0.1+1 ⌅ [0234f1f7] + HDF5_jll v1.14.6+0 [017b0a0e] + HSL_jll v4.0.4+0 [8fd58aa0] + HiGHS_jll v1.13.1+0 [e33a78d0] + Hwloc_jll v2.13.0+0 ⌅ [1d5cc7b8] + IntelOpenMP_jll v2024.2.1+0 [1d63c593] + LLVMOpenMP_jll v18.1.8+0 [94ce4f54] + Libiconv_jll v1.18.0+0 ⌅ [d00139f3] + METIS_jll v5.1.2+1 ⌅ [856f044c] + MKL_jll v2024.2.0+0 ⌅ [7cb0a576] + MPICH_jll v4.3.2+0 [f1f71cc9] + MPItrampoline_jll v5.5.5+0 ⌅ [d7ed1dd3] + MUMPS_seq_jll v500.800.100+0 [9237b28f] + MicrosoftMPI_jll v10.1.4+3 [656ef2d0] + OpenBLAS32_jll v0.3.30+0 [fe0851c0] + OpenMPI_jll v5.0.9+0 [efe28fd5] + OpenSpecFun_jll v0.5.6+0 [7da25872] + Osi_jll v0.10800.1100+0 [bb12108a] + SBML_jll v5.21.0+0 [f4f2fc5b] + SCS_jll v300.200.1100+0 ⌅ [02c8fc9c] + XML2_jll v2.13.9+0 [a65dc6b1] + Xorg_libpciaccess_jll v0.18.1+0 ⌅ [f07e07eb] + cddlib_jll v0.94.14+0 [477f73a3] + libaec_jll v1.1.5+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 v1.7.0 [7b1f6079] + FileWatching v1.11.0 [b77e0a4c] + InteractiveUtils v1.11.0 [ac6e5ff7] + JuliaSyntaxHighlighting v1.13.0 [4af54fe1] + LazyArtifacts v1.11.0 [b27032c2] + LibCURL v1.0.0 [76f85450] + LibGit2 v1.11.0 [8f399da3] + Libdl v1.11.0 [37e2e46d] + LinearAlgebra v1.13.0 [56ddb016] + Logging v1.11.0 [d6f4376e] + Markdown v1.11.0 [a63ad114] + Mmap v1.11.0 [ca575930] + NetworkOptions v1.3.0 [44cfe95a] + Pkg v1.14.0 [de0858da] + Printf v1.11.0 [9abbd945] + Profile v1.11.0 [9a3f8284] + Random v1.11.0 [ea8e919c] + SHA v1.0.0 [9e88b42a] + Serialization v1.11.0 [1a1011a3] + SharedArrays v1.11.0 [6462fe0b] + Sockets v1.11.0 [2f01184e] + SparseArrays v1.13.0 [f489334b] + StyledStrings v1.13.0 [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 [781609d7] + GMP_jll v6.3.0+2 [deac9b47] + LibCURL_jll v8.18.0+0 [e37daf67] + LibGit2_jll v1.9.2+0 [29816b5a] + LibSSH2_jll v1.11.3+1 [14a3606d] + MozillaCACerts_jll v2025.12.2 [4536629a] + OpenBLAS_jll v0.3.30+0 [05823500] + OpenLibm_jll v0.8.7+0 [458c3c95] + OpenSSL_jll v3.5.5+0 [efcefdf7] + PCRE2_jll v10.47.0+0 [bea87d4a] + SuiteSparse_jll v7.10.1+0 [83775a58] + Zlib_jll v1.3.1+2 [3161d3a3] + Zstd_jll v1.5.7+1 [8e850b90] + libblastrampoline_jll v5.15.0+0 [8e850ede] + nghttp2_jll v1.68.0+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` Building Pardiso → `~/.julia/scratchspaces/44cfe95a-1eb2-52ea-b672-e2afdf69b78f/4b618484bf94a52f02595cd73ac8a6417f4c0c70/build.log` Installation completed after 22.23s ################################################################################ # Precompilation # Precompiling PkgEval dependencies... Precompiling packages... 4562.6 ms ✓ TestEnv 1 dependency successfully precompiled in 5 seconds. 27 already precompiled. Precompiling package dependencies... Precompiling packages... 4568.4 ms ✓ MacroTools 796.7 ms ✓ Reexport 1132.5 ms ✓ Statistics 1105.4 ms ✓ ConstructionBase 1918.7 ms ✓ IrrationalConstants 961.8 ms ✓ StaticArraysCore 1137.3 ms ✓ Requires 1234.4 ms ✓ OrderedCollections 895.4 ms ✓ StableRNGs 902.0 ms ✓ HashArrayMappedTries 1139.1 ms ✓ DocStringExtensions 831.2 ms ✓ CEnum 870.8 ms ✓ ExprTools 784.2 ms ✓ IfElse 1210.8 ms ✓ TranscodingStreams 1632.2 ms ✓ AMD 1598.9 ms ✓ GenericLinearAlgebra 1011.1 ms ✓ NaNMath 962.0 ms ✓ DelimitedFiles 33366.6 ms ✓ Unitful 1189.4 ms ✓ Compat 1189.3 ms ✓ Preferences 12341.9 ms ✓ MutableArithmetics 1889.3 ms ✓ CommonSubexpressions 3897.0 ms ✓ FixedPointNumbers 1334.5 ms ✓ Statistics → SparseArraysExt 816.8 ms ✓ ConstructionBase → ConstructionBaseLinearAlgebraExt 877.3 ms ✓ DiffResults 8609.8 ms ✓ FileIO 871.5 ms ✓ ScopedValues 3711.1 ms ✓ AbstractFBCModels 1296.6 ms ✓ LogExpFunctions 1441.4 ms ✓ PikaParser 3565.6 ms ✓ TimerOutputs 974.7 ms ✓ CodecZlib 1424.8 ms ✓ QDLDL 2311.1 ms ✓ Unitful → PrintfExt 2126.1 ms ✓ Unitful → ConstructionBaseUnitfulExt 2176.0 ms ✓ Unitful → NaNMathExt 820.4 ms ✓ Compat → CompatLinearAlgebraExt 1203.8 ms ✓ JLLWrappers 1068.7 ms ✓ SnoopPrecompile 1427.1 ms ✓ MPIPreferences 934.4 ms ✓ PrecompileTools 2773.2 ms ✓ ColorTypes 3853.8 ms ✓ DataStructures 1415.4 ms ✓ METIS_jll 1448.1 ms ✓ libaec_jll 5483.2 ms ✓ IntelOpenMP_jll 1463.2 ms ✓ OpenBLAS32_jll 1359.4 ms ✓ Xorg_libpciaccess_jll 1363.8 ms ✓ Bzip2_jll 1364.0 ms ✓ LLVMOpenMP_jll 1344.2 ms ✓ GLPK_jll 1382.3 ms ✓ Libiconv_jll 1363.4 ms ✓ HiGHS_jll 4544.4 ms ✓ oneTBB_jll 1396.4 ms ✓ ECOS_jll 1456.8 ms ✓ cddlib_jll 1454.7 ms ✓ HSL_jll 1440.9 ms ✓ ASL_jll 1191.5 ms ✓ MicrosoftMPI_jll 1441.9 ms ✓ OpenSpecFun_jll 1491.6 ms ✓ CoinUtils_jll 5533.3 ms ✓ MPItrampoline_jll 14323.1 ms ✓ StaticArrays 18049.5 ms ✓ Parsers 47404.3 ms ✓ JLD2 1358.4 ms ✓ ColorTypes → StyledStringsExt 8209.6 ms ✓ Colors 3618.6 ms ✓ ConstraintTrees 1617.8 ms ✓ MUMPS_seq_jll 1117.2 ms ✓ CodecBzip2 1622.0 ms ✓ SCS_jll 1583.6 ms ✓ XML2_jll  Downloading artifact: IntelOpenMP  Downloading artifact: oneTBB 9677.6 ms ✓ MKL_jll 10156.8 ms ✓ HSL 5320.2 ms ✓ SpecialFunctions 1457.8 ms ✓ Osi_jll 1707.6 ms ✓ StaticArrays → StaticArraysStatisticsExt 1549.0 ms ✓ ConstructionBase → ConstructionBaseStaticArraysExt 3674.3 ms ✓ JSON 1675.2 ms ✓ SBML_jll 1536.5 ms ✓ Hwloc_jll  Downloading artifact: MKL ERROR: LoadError: TypeError: in ccall library name, expected Symbol, got a value of type Expr Stacktrace:  [1] top-level scope  @ ~/.julia/packages/Pardiso/z4YUw/src/mkl_pardiso.jl:41  [2] include(mapexpr::Function, mod::Module, _path::String)  @ Base ./Base.jl:310  [3] top-level scope  @ ~/.julia/packages/Pardiso/z4YUw/src/Pardiso.jl:198  [4] include(mod::Module, _path::String)  @ Base ./Base.jl:309  [5] include_package_for_output(pkg::Base.PkgId, input::String, syntax_version::VersionNumber, depot_path::Vector{String}, dl_load_path::Vector{String}, load_path::Vector{String}, concrete_deps::Vector{Pair{Base.PkgId, UInt128}}, source::Nothing)  @ Base ./loading.jl:3288  [6] top-level scope  @ stdin:5  [7] eval(m::Module, e::Any)  @ Core ./boot.jl:489  [8] include_string(mapexpr::typeof(identity), mod::Module, code::String, filename::String)  @ Base ./loading.jl:3130  [9] include_string  @ ./loading.jl:3140 [inlined]  [10] exec_options(opts::Base.JLOptions)  @ Base ./client.jl:342  [11] _start()  @ Base ./client.jl:585 in expression starting at /home/pkgeval/.julia/packages/Pardiso/z4YUw/src/mkl_pardiso.jl:41 in expression starting at /home/pkgeval/.julia/packages/Pardiso/z4YUw/src/Pardiso.jl:3 in expression starting at stdin:5 ✗ Pardiso 1225.9 ms ✓ DiffRules 1580.9 ms ✓ Clp_jll 3241.2 ms ✓ BenchmarkTools 7281.2 ms ✓ JSONFBCModels 18170.9 ms ✓ SBML 5017.3 ms ✓ MPICH_jll 4521.9 ms ✓ OpenMPI_jll 6495.9 ms ✓ ForwardDiff 1409.4 ms ✓ Cgl_jll 4945.7 ms ✓ SBMLFBCModels 5738.7 ms ✓ HDF5_jll 1763.2 ms ✓ ForwardDiff → ForwardDiffStaticArraysExt 2369.4 ms ✓ Unitful → ForwardDiffExt 75984.4 ms ✓ MathOptInterface 1433.5 ms ✓ Cbc_jll 15001.9 ms ✓ HDF5 5851.9 ms ✓ MathOptIIS 49418.9 ms ✓ SCS 60303.0 ms ✓ JuMP 11715.2 ms ✓ Polyhedra 9079.5 ms ✓ GLPK 8309.2 ms ✓ ECOS 148724.5 ms ✓ Clarabel 30028.4 ms ✓ Clp 8426.1 ms ✓ Cbc 30703.2 ms ✓ HiGHS 19839.4 ms ✓ COBREXA 12448.9 ms ✓ Polyhedra → PolyhedraJuMPExt 8159.8 ms ✓ CDDLib 52393.2 ms ✓ sparseQFCA 114 dependencies successfully precompiled in 928 seconds. 40 already precompiled. 1 dependency had output during precompilation: ┌ MKL_jll │ Downloading artifact: IntelOpenMP │ Downloading artifact: oneTBB └ Precompilation completed after 957.91s ################################################################################ # Testing # Testing sparseQFCA Status `/tmp/jl_FT2O2a/Project.toml` [5a4f3dfa] AbstractFBCModels v1.3.0 [3391f64e] CDDLib v0.10.2 [babc4406] COBREXA v2.9.1 [9961bab8] Cbc v1.3.0 ⌅ [61c947e1] Clarabel v0.10.0 [e2554f3b] Clp v1.3.0 [5ae59095] Colors v0.13.1 [8bb1440f] DelimitedFiles v1.9.1 [e2685f51] ECOS v1.1.3 [60bf3e95] GLPK v1.2.1 [f67ccb44] HDF5 v0.17.2 [87dc4568] HiGHS v1.21.1 ⌅ [033835bb] JLD2 v0.5.15 ⌅ [682c06a0] JSON v0.21.4 [475c1105] JSONFBCModels v1.0.1 [4076af6c] JuMP v1.29.4 [b8f27783] MathOptInterface v1.49.0 [3e8f9d1a] SBMLFBCModels v1.1.1 [c946c3f1] SCS v2.6.2 [077cf62c] sparseQFCA v2.3.0 [8ba89e20] Distributed v1.11.0 [37e2e46d] LinearAlgebra v1.13.0 [1a1011a3] SharedArrays v1.11.0 [2f01184e] SparseArrays v1.13.0 [8dfed614] Test v1.11.0 Status `/tmp/jl_FT2O2a/Manifest.toml` [14f7f29c] AMD v0.5.3 [5a4f3dfa] AbstractFBCModels v1.3.0 [6e4b80f9] BenchmarkTools v1.6.3 [3391f64e] CDDLib v0.10.2 [fa961155] CEnum v0.5.0 [babc4406] COBREXA v2.9.1 [9961bab8] Cbc v1.3.0 ⌅ [61c947e1] Clarabel v0.10.0 [e2554f3b] Clp v1.3.0 [523fee87] CodecBzip2 v0.8.5 [944b1d66] CodecZlib v0.7.8 [3da002f7] ColorTypes v0.12.1 [5ae59095] Colors v0.13.1 [bbf7d656] CommonSubexpressions v0.3.1 [34da2185] Compat v4.18.1 [5515826b] ConstraintTrees v1.11.0 [187b0558] ConstructionBase v1.6.0 ⌅ [864edb3b] DataStructures v0.18.22 [8bb1440f] DelimitedFiles v1.9.1 [163ba53b] DiffResults v1.1.0 [b552c78f] DiffRules v1.15.1 [ffbed154] DocStringExtensions v0.9.5 [e2685f51] ECOS v1.1.3 [e2ba6199] ExprTools v0.1.10 [5789e2e9] FileIO v1.18.0 [53c48c17] FixedPointNumbers v0.8.5 [f6369f11] ForwardDiff v1.3.2 [60bf3e95] GLPK v1.2.1 [14197337] GenericLinearAlgebra v0.3.19 [f67ccb44] HDF5 v0.17.2 ⌅ [34c5aeac] HSL v0.4.3 [076d061b] HashArrayMappedTries v0.2.0 [87dc4568] HiGHS v1.21.1 [615f187c] IfElse v0.1.1 [92d709cd] IrrationalConstants v0.2.6 ⌅ [033835bb] JLD2 v0.5.15 [692b3bcd] JLLWrappers v1.7.1 ⌅ [682c06a0] JSON v0.21.4 [475c1105] JSONFBCModels v1.0.1 [4076af6c] JuMP v1.29.4 [2ab3a3ac] LogExpFunctions v0.3.29 [3da0fdf6] MPIPreferences v0.1.11 [1914dd2f] MacroTools v0.5.16 [8c4f8055] MathOptIIS v0.1.1 [b8f27783] MathOptInterface v1.49.0 [d8a4904e] MutableArithmetics v1.6.7 [77ba4419] NaNMath v1.1.3 [bac558e1] OrderedCollections v1.8.1 ⌅ [46dd5b70] Pardiso v0.5.7 [69de0a69] Parsers v2.8.3 [3bbf5609] PikaParser v0.6.1 [67491407] Polyhedra v0.8.1 [aea7be01] PrecompileTools v1.3.3 [21216c6a] Preferences v1.5.1 [bfc457fd] QDLDL v0.4.1 [189a3867] Reexport v1.2.2 [ae029012] Requires v1.3.1 [e5567a89] SBML v1.6.0 [3e8f9d1a] SBMLFBCModels v1.1.1 [c946c3f1] SCS v2.6.2 [7e506255] ScopedValues v1.5.0 [66db9d55] SnoopPrecompile v1.0.3 [276daf66] SpecialFunctions v2.7.1 [860ef19b] StableRNGs v1.0.4 [90137ffa] StaticArrays v1.9.16 [1e83bf80] StaticArraysCore v1.4.4 [10745b16] Statistics v1.11.1 [a759f4b9] TimerOutputs v0.5.29 [3bb67fe8] TranscodingStreams v0.11.3 [1986cc42] Unitful v1.28.0 [077cf62c] sparseQFCA v2.3.0 [ae81ac8f] ASL_jll v0.1.3+0 [6e34b625] Bzip2_jll v1.0.9+0 [38041ee0] Cbc_jll v200.1000.1200+0 [3830e938] Cgl_jll v0.6000.900+0 ⌅ [06985876] Clp_jll v100.1700.1000+1 [be027038] CoinUtils_jll v200.1100.1200+0 [c2c64177] ECOS_jll v200.0.800+0 [e8aa6df9] GLPK_jll v5.0.1+1 ⌅ [0234f1f7] HDF5_jll v1.14.6+0 [017b0a0e] HSL_jll v4.0.4+0 [8fd58aa0] HiGHS_jll v1.13.1+0 [e33a78d0] Hwloc_jll v2.13.0+0 ⌅ [1d5cc7b8] IntelOpenMP_jll v2024.2.1+0 [1d63c593] LLVMOpenMP_jll v18.1.8+0 [94ce4f54] Libiconv_jll v1.18.0+0 ⌅ [d00139f3] METIS_jll v5.1.2+1 ⌅ [856f044c] MKL_jll v2024.2.0+0 ⌅ [7cb0a576] MPICH_jll v4.3.2+0 [f1f71cc9] MPItrampoline_jll v5.5.5+0 ⌅ [d7ed1dd3] MUMPS_seq_jll v500.800.100+0 [9237b28f] MicrosoftMPI_jll v10.1.4+3 [656ef2d0] OpenBLAS32_jll v0.3.30+0 [fe0851c0] OpenMPI_jll v5.0.9+0 [efe28fd5] OpenSpecFun_jll v0.5.6+0 [7da25872] Osi_jll v0.10800.1100+0 [bb12108a] SBML_jll v5.21.0+0 [f4f2fc5b] SCS_jll v300.200.1100+0 ⌅ [02c8fc9c] XML2_jll v2.13.9+0 [a65dc6b1] Xorg_libpciaccess_jll v0.18.1+0 ⌅ [f07e07eb] cddlib_jll v0.94.14+0 [477f73a3] libaec_jll v1.1.5+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 v1.7.0 [7b1f6079] FileWatching v1.11.0 [b77e0a4c] InteractiveUtils v1.11.0 [ac6e5ff7] JuliaSyntaxHighlighting v1.13.0 [4af54fe1] LazyArtifacts v1.11.0 [b27032c2] LibCURL v1.0.0 [76f85450] LibGit2 v1.11.0 [8f399da3] Libdl v1.11.0 [37e2e46d] LinearAlgebra v1.13.0 [56ddb016] Logging v1.11.0 [d6f4376e] Markdown v1.11.0 [a63ad114] Mmap v1.11.0 [ca575930] NetworkOptions v1.3.0 [44cfe95a] Pkg v1.14.0 [de0858da] Printf v1.11.0 [9abbd945] Profile v1.11.0 [9a3f8284] Random v1.11.0 [ea8e919c] SHA v1.0.0 [9e88b42a] Serialization v1.11.0 [1a1011a3] SharedArrays v1.11.0 [6462fe0b] Sockets v1.11.0 [2f01184e] SparseArrays v1.13.0 [f489334b] StyledStrings v1.13.0 [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 [781609d7] GMP_jll v6.3.0+2 [deac9b47] LibCURL_jll v8.18.0+0 [e37daf67] LibGit2_jll v1.9.2+0 [29816b5a] LibSSH2_jll v1.11.3+1 [14a3606d] MozillaCACerts_jll v2025.12.2 [4536629a] OpenBLAS_jll v0.3.30+0 [05823500] OpenLibm_jll v0.8.7+0 [458c3c95] OpenSSL_jll v3.5.5+0 [efcefdf7] PCRE2_jll v10.47.0+0 [bea87d4a] SuiteSparse_jll v7.10.1+0 [83775a58] Zlib_jll v1.3.1+2 [3161d3a3] Zstd_jll v1.5.7+1 [8e850b90] libblastrampoline_jll v5.15.0+0 [8e850ede] nghttp2_jll v1.68.0+1 [3f19e933] p7zip_jll v17.7.0+0 Info Packages marked with ⌅ have new versions available but compatibility constraints restrict them from upgrading. Testing Running tests... #-------------------------------------------------------------------------------------------# Number of Proccess : 8 Number of Workers : 7 #-------------------------------------------------------------------------------------------# sparseQFCA : iIS312 : Metabolic Network: Number of Metabolites : 606 Number of Reactions : 519 Number of Genes : 312 Stoichiometric matrix : 606 x 519 Homogenization: M = 1.0e6 Reversibility Checking: Number of irreversible reactions : 218 Number of reversible reactions : 301 Consistency_Checking(SwiftCC): Number of Proccess : 8 Number of Workers : 7 Solver = HiGHS Tolerance = 1.0e-9 Number of irreversible blocked reactions : 154 Number of reversible blocked reactions : 133 Number of blocked reactions : 287 Distributed Reversibility Correction: Number of Proccess : 8 Number of Workers : 7 Solver = HiGHS Tolerance = 1.0e-6 Number of reversibe blocked in forward direction : 44 Number of reversibe blocked in backward direction : 51 Number of irreversible reactions after Correction : 313 Number of reversible reactions after Correction : 206 terminate called after throwing an instance of 'std::system_error' what(): Resource temporarily unavailable [663] signal 6 (-6): Aborted in expression starting at timing.jl:395 unknown function (ip: 0x7ad2afda7ebc) at /lib/x86_64-linux-gnu/libc.so.6 gsignal at /lib/x86_64-linux-gnu/libc.so.6 (unknown line) abort at /lib/x86_64-linux-gnu/libc.so.6 (unknown line) __verbose_terminate_handler at /workspace/srcdir/gcc-14.2.0/libstdc++-v3/libsupc++/vterminate.cc:95 __terminate at /workspace/srcdir/gcc-14.2.0/libstdc++-v3/libsupc++/eh_terminate.cc:48 terminate at /workspace/srcdir/gcc-14.2.0/libstdc++-v3/libsupc++/eh_terminate.cc:58 __cxa_throw at /workspace/srcdir/gcc-14.2.0/libstdc++-v3/libsupc++/eh_throw.cc:98 __throw_system_error at /workspace/srcdir/gcc-14.2.0/libstdc++-v3/src/c++11/system_error.cc:595 _M_start_thread at /workspace/srcdir/gcc-14.2.0/libstdc++-v3/src/c++11/thread.cc:176 _ZN17HighsTaskExecutor10initializeEi.part.686 at /home/pkgeval/.julia/artifacts/57846bf52e8d91e2d6dfef3b0e474315208dc524/lib/libhighs.so (unknown line) _ZN5Highs19calledOptimizeModelEv at /home/pkgeval/.julia/artifacts/57846bf52e8d91e2d6dfef3b0e474315208dc524/lib/libhighs.so (unknown line) _ZN5Highs13optimizeModelEv at /home/pkgeval/.julia/artifacts/57846bf52e8d91e2d6dfef3b0e474315208dc524/lib/libhighs.so (unknown line) _ZN5Highs3runEv at /home/pkgeval/.julia/artifacts/57846bf52e8d91e2d6dfef3b0e474315208dc524/lib/libhighs.so (unknown line) Highs_run at /home/pkgeval/.julia/packages/HiGHS/lBNEK/src/gen/libhighs.jl:328 [inlined] _Highs_run_workaround_issue_316 at /home/pkgeval/.julia/packages/HiGHS/lBNEK/src/MOI_wrapper.jl:2229 [inlined] #47 at /home/pkgeval/.julia/packages/HiGHS/lBNEK/src/MOI_wrapper.jl:2276 [inlined] disable_sigint at ./c.jl:167 optimize! at /home/pkgeval/.julia/packages/HiGHS/lBNEK/src/MOI_wrapper.jl:2276 optimize! at /home/pkgeval/.julia/packages/MathOptInterface/Q3V1z/src/Bridges/bridge_optimizer.jl:367 [inlined] optimize! at /home/pkgeval/.julia/packages/MathOptInterface/Q3V1z/src/MathOptInterface.jl:122 [inlined] optimize! at /home/pkgeval/.julia/packages/MathOptInterface/Q3V1z/src/Utilities/cachingoptimizer.jl:370 unknown function (ip: 0x7ad290560a92) at (unknown file) _jl_invoke at /source/src/gf.c:4120 [inlined] ijl_apply_generic at /source/src/gf.c:4317 #optimize!#96 at /home/pkgeval/.julia/packages/JuMP/7eD71/src/optimizer_interface.jl:609 optimize! at /home/pkgeval/.julia/packages/JuMP/7eD71/src/optimizer_interface.jl:560 [inlined] QFCA at /home/pkgeval/.julia/packages/sparseQFCA/VIdqW/src/QFCA/SQFCA.jl:79 QFCA at /home/pkgeval/.julia/packages/sparseQFCA/VIdqW/src/QFCA/SQFCA.jl:61 unknown function (ip: 0x7ad29060f634) at (unknown file) _jl_invoke at /source/src/gf.c:4120 [inlined] ijl_apply_generic at /source/src/gf.c:4317 top-level scope at ./timing.jl:739 _jl_invoke at /source/src/gf.c:4120 [inlined] ijl_invoke at /source/src/gf.c:4127 ijl_eval_thunk at /source/src/toplevel.c:757 jl_toplevel_eval_flex at /source/src/toplevel.c:712 jl_eval_toplevel_stmts at /source/src/toplevel.c:602 jl_toplevel_eval_flex at /source/src/toplevel.c:684 ijl_toplevel_eval at /source/src/toplevel.c:779 ijl_toplevel_eval_in at /source/src/toplevel.c:824 eval at ./boot.jl:489 include_string at ./loading.jl:3130 _jl_invoke at /source/src/gf.c:4120 [inlined] ijl_apply_generic at /source/src/gf.c:4317 _include at ./loading.jl:3190 include at ./Base.jl:310 IncludeInto at ./Base.jl:311 jfptr_IncludeInto_49432.1 at /opt/julia/lib/julia/sys.so (unknown line) _jl_invoke at /source/src/gf.c:4120 [inlined] ijl_apply_generic at /source/src/gf.c:4317 jl_apply at /source/src/julia.h:2285 [inlined] do_call at /source/src/interpreter.c:123 eval_value at /source/src/interpreter.c:243 eval_stmt_value at /source/src/interpreter.c:194 [inlined] eval_body at /source/src/interpreter.c:679 jl_interpret_toplevel_thunk at /source/src/interpreter.c:884 ijl_eval_thunk at /source/src/toplevel.c:765 jl_toplevel_eval_flex at /source/src/toplevel.c:712 jl_eval_toplevel_stmts at /source/src/toplevel.c:602 jl_toplevel_eval_flex at /source/src/toplevel.c:684 ijl_toplevel_eval at /source/src/toplevel.c:779 ijl_toplevel_eval_in at /source/src/toplevel.c:824 eval at ./boot.jl:489 exec_options at ./client.jl:310 _start at ./client.jl:585 jfptr__start_74606.1 at /opt/julia/lib/julia/sys.so (unknown line) _jl_invoke at /source/src/gf.c:4120 [inlined] ijl_apply_generic at /source/src/gf.c:4317 jl_apply at /source/src/julia.h:2285 [inlined] true_main at /source/src/jlapi.c:971 jl_repl_entrypoint at /source/src/jlapi.c:1138 main at /source/cli/loader_exe.c:58 unknown function (ip: 0x7ad2afd44249) at /lib/x86_64-linux-gnu/libc.so.6 __libc_start_main at /lib/x86_64-linux-gnu/libc.so.6 (unknown line) unknown function (ip: 0x4010b8) at /workspace/srcdir/glibc-2.17/csu/../sysdeps/x86_64/start.S Allocations: 68439341 (Pool: 68438168; Big: 1173); GC: 28 Testing failed after 207.28s ERROR: LoadError: Package sparseQFCA errored during testing (received signal: 6) Stacktrace: [1] pkgerror(msg::String) @ Pkg.Types /opt/julia/share/julia/stdlib/v1.14/Pkg/src/Types.jl:68 [2] test(ctx::Pkg.Types.Context, pkgs::Vector{PackageSpec}; coverage::Bool, julia_args::Cmd, test_args::Cmd, test_fn::Nothing, force_latest_compatible_version::Bool, allow_earlier_backwards_compatible_versions::Bool, allow_reresolve::Bool) @ Pkg.Operations /opt/julia/share/julia/stdlib/v1.14/Pkg/src/Operations.jl:3138 [3] test @ /opt/julia/share/julia/stdlib/v1.14/Pkg/src/Operations.jl:3003 [inlined] [4] test(ctx::Pkg.Types.Context, pkgs::Vector{PackageSpec}; coverage::Bool, test_fn::Nothing, julia_args::Cmd, test_args::Cmd, force_latest_compatible_version::Bool, allow_earlier_backwards_compatible_versions::Bool, allow_reresolve::Bool, kwargs::@Kwargs{io::IOContext{IO}}) @ Pkg.API /opt/julia/share/julia/stdlib/v1.14/Pkg/src/API.jl:586 [5] kwcall(::@NamedTuple{julia_args::Cmd, io::IOContext{IO}}, ::typeof(Pkg.API.test), ctx::Pkg.Types.Context, pkgs::Vector{PackageSpec}) @ Pkg.API /opt/julia/share/julia/stdlib/v1.14/Pkg/src/API.jl:562 [6] test(pkgs::Vector{PackageSpec}; io::IOContext{IO}, kwargs::@Kwargs{julia_args::Cmd}) @ Pkg.API /opt/julia/share/julia/stdlib/v1.14/Pkg/src/API.jl:172 [7] kwcall(::@NamedTuple{julia_args::Cmd}, ::typeof(Pkg.API.test), pkgs::Vector{PackageSpec}) @ Pkg.API /opt/julia/share/julia/stdlib/v1.14/Pkg/src/API.jl:161 [8] test(pkgs::Vector{String}; kwargs::@Kwargs{julia_args::Cmd}) @ Pkg.API /opt/julia/share/julia/stdlib/v1.14/Pkg/src/API.jl:160 [9] test @ /opt/julia/share/julia/stdlib/v1.14/Pkg/src/API.jl:160 [inlined] [10] kwcall(::@NamedTuple{julia_args::Cmd}, ::typeof(Pkg.API.test), pkg::String) @ Pkg.API /opt/julia/share/julia/stdlib/v1.14/Pkg/src/API.jl:159 [11] top-level scope @ /PkgEval.jl/scripts/evaluate.jl:223 [12] include(mod::Module, _path::String) @ Base ./Base.jl:309 [13] exec_options(opts::Base.JLOptions) @ Base ./client.jl:344 [14] _start() @ Base ./client.jl:585 in expression starting at /PkgEval.jl/scripts/evaluate.jl:214 PkgEval crashed after 2214.36s: the process was aborted ################################################################################ # Bug reporting # The package crashed during testing (reason=abort), but PkgEval was unable to reproduce the crash under rr (status=kill, reason=time_limit). For debugging, here is the tail end of the rr log: > From worker 2: │ program longer (perhaps by running it multiple times), > From worker 2: │ or adjust the delay between samples with `Profile.init()`. > From worker 2: └ @ Profile /opt/julia/share/julia/stdlib/v1.14/Profile/src/Profile.jl:1361 > From worker 2: Overhead ╎ [+additional indent] Count File:Line Function > From worker 2: ========================================================= > From worker 2: Thread 1 (default) Task 0x00007961f7c27850 Total snapshots: 1. Utilization: 0% > From worker 2: ╎1 @Base/task.jl:1168 wait_forever() > From worker 2: ╎ 1 @Base/task.jl:1246 wait() > From worker 2: > Number of Metabolites : 72 > Number of Reactions : 95 > Number of Genes : 137 > Stoichiometric matrix : 72 x 95 > There is no duplicate reaction. > Homogenization: > M = 1.0e6 > Consistency_Checking(SwiftCC): > Number of Proccess : 8 > Number of Workers : 7 > Solver = HiGHS > Tolerance = 1.0e-9 > Number of irreversible blocked reactions : 8 > Number of reversible blocked reactions : 0 > Number of blocked reactions : 8 > 0.015654 seconds (18.63 k allocations: 1.278 MiB, 8.43% compilation time) > #-------------------------------------------------------------------------------------------# > CC_TheNaiveApproach : > iIS312 : > Metabolic Network: > Number of Metabolites : 606 > Number of Reactions : 519 > Number of Genes : 312 > Stoichiometric matrix : 606 x 519 > Reversibility Checking: > Number of irreversible reactions : 218 > Number of reversible reactions : 301 > Homogenization: > Consistency_Checking(TheNaiveApproch): > Number of Proccess : 8 > Number of Workers : 7 > Solver = HiGHS > Tolerance = 1.0e-9 > Number of irreversible blocked reactions : 154 > Number of reversible blocked reactions : 133 > Number of blocked reactions : 287 > 3.044679 seconds (154.18 k allocations: 48.636 MiB, 2.69% gc time, 0.09% compilation time) > #-------------------------------------------------------------------------------------------# > CC_SwiftCC : > iIS312 : > Metabolic Network: > Number of Metabolites : 606 > Number of Reactions : 519 > Number of Genes : 312 > Stoichiometric matrix : 606 x 519 > There is no duplicate reaction. > Homogenization: > M = 1.0e6 > Consistency_Checking(SwiftCC): > Number of Proccess : 8 > Number of Workers : 7 > Solver = HiGHS > Tolerance = 1.0e-9 > Number of irreversible blocked reactions : 154 > Number of reversible blocked reactions : 133 > Number of blocked reactions : 287 > 0.081889 seconds (67.81 k allocations: 10.794 MiB, 1.78% compilation time) > > [815] signal 15: Terminated > in expression starting at /home/pkgeval/bugreport.jl:13 > 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 > wait at ./task.jl:1246 > wait_forever at ./task.jl:1168 > > [1] signal 15: Terminated > in expression starting at /PkgEval.jl/scripts/evaluate.jl:214 > 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 > wait at ./task.jl:1246 > wait_forever at ./task.jl:1168 > jfptr_wait_forever_53765.1 at /opt/julia/lib/julia/sys.so (unknown line) > _jl_invoke at /source/src/gf.c:4120 [inlined] > ijl_apply_generic at /source/src/gf.c:4317 > jl_apply at /source/src/julia.h:2285 [inlined] > start_task at /source/src/task.c:1275 > unknown function (ip: (nil)) at (unknown file) > Allocations: 27414753 (Pool: 27413641; Big: 1112); GC: 33 > jfptr_wait_forever_53765.1 at /opt/julia/lib/julia/sys.so (unknown line) > _jl_invoke at /source/src/gf.c:4120 [inlined] > ijl_apply_generic at /source/src/gf.c:4317 > jl_apply at /source/src/julia.h:2285 [inlined] > start_task at /source/src/task.c:1275 > unknown function (ip: (nil)) at (unknown file) > Allocations: 4087215 (Pool: 4087119; Big: 96); GC: 5 > > PkgEval terminated after 2804.08s: test duration exceeded the time limit