Package evaluation to test sparseQFCA on Julia 1.14.0-DEV.2186 (48ff18f4cd*) started at 2026-05-15T00:40:13.262 ################################################################################ # Set-up # Installing PkgEval dependencies (TestEnv)... Activating project at `~/.julia/environments/v1.14` Set-up completed after 16.06s ################################################################################ # Installation # Installing sparseQFCA... Resolving package versions... 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 [3391f64e] + CDDLib v0.10.2 [fa961155] + CEnum v0.5.0 [babc4406] + COBREXA v2.9.1 ⌃ [9961bab8] + Cbc v1.2.0 ⌅ [61c947e1] + Clarabel v0.7.1 ⌃ [e2554f3b] + Clp v1.2.2 [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 v1.11.1 [187b0558] + ConstructionBase v1.6.0 [864edb3b] + DataStructures v0.19.4 [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 v1.19.0 [53c48c17] + FixedPointNumbers v0.8.5 [f6369f11] + ForwardDiff v1.3.3 [60bf3e95] + GLPK v1.2.1 ⌅ [14197337] + GenericLinearAlgebra v0.3.19 [f67ccb44] + HDF5 v0.17.3 [076d061b] + HashArrayMappedTries v0.2.0 [87dc4568] + HiGHS v1.23.0 [615f187c] + IfElse v0.1.1 [92d709cd] + IrrationalConstants v0.2.6 ⌅ [033835bb] + JLD2 v0.5.15 [692b3bcd] + JLLWrappers v1.8.0 ⌅ [682c06a0] + JSON v0.21.4 [475c1105] + JSONFBCModels v1.0.1 [4076af6c] + JuMP v1.30.1 [2ab3a3ac] + LogExpFunctions v0.3.29 [3da0fdf6] + MPIPreferences v0.1.12 [1914dd2f] + MacroTools v0.5.16 [8c4f8055] + MathOptIIS v0.2.0 [b8f27783] + MathOptInterface v1.51.0 [d8a4904e] + MutableArithmetics v1.7.1 [77ba4419] + NaNMath v1.1.3 [bac558e1] + OrderedCollections v1.8.1 [69de0a69] + Parsers v2.8.4 [3bbf5609] + PikaParser v0.6.1 [67491407] + Polyhedra v0.8.1 [aea7be01] + PrecompileTools v1.3.4 [21216c6a] + Preferences v1.5.2 [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 v2.6.3 [7e506255] + ScopedValues v1.6.2 [66db9d55] + SnoopPrecompile v1.0.3 [276daf66] + SpecialFunctions v2.7.2 [860ef19b] + StableRNGs v1.0.4 [90137ffa] + StaticArrays v1.9.18 [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 v200.1000.800+0 ⌅ [3830e938] + Cgl_jll v0.6000.600+0 ⌅ [06985876] + Clp_jll v100.1700.700+1 ⌅ [be027038] + CoinUtils_jll v200.1100.600+0 [c2c64177] + ECOS_jll v200.0.800+0 [e8aa6df9] + GLPK_jll v5.0.1+1 [0234f1f7] + HDF5_jll v2.1.2+0 [8fd58aa0] + HiGHS_jll v1.14.0+0 [e33a78d0] + Hwloc_jll v2.13.0+1 [1d63c593] + LLVMOpenMP_jll v18.1.8+0 [94ce4f54] + Libiconv_jll v1.18.0+0 [d00139f3] + METIS_jll v5.1.3+0 [b5ada748] + MPIABI_jll v0.1.5+0 [7cb0a576] + MPICH_jll v5.0.1+0 [f1f71cc9] + MPItrampoline_jll v5.5.6+0 [d7ed1dd3] + MUMPS_seq_jll v500.900.0+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 ⌅ [7da25872] + Osi_jll v0.10800.700+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 v0.19.0+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 ⌅ [f07e07eb] + cddlib_jll v0.94.14+0 [c4b69c83] + dlfcn_win32_jll v1.4.2+0 [477f73a3] + libaec_jll v1.1.6+0 [9aeb927a] + mpif_jll v0.1.7+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 [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 [9a3f8284] + Random v1.11.0 [ea8e919c] + SHA v1.13.0 [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 v1.5.1+0 [781609d7] + GMP_jll v6.3.0+2 [deac9b47] + LibCURL_jll v8.20.0+1 [e37daf67] + LibGit2_jll v1.9.3+0 [29816b5a] + LibSSH2_jll v1.11.101+0 [14a3606d] + MozillaCACerts_jll v2026.3.19 [4536629a] + OpenBLAS_jll v0.3.33+0 [05823500] + OpenLibm_jll v0.8.7+0 [458c3c95] + OpenSSL_jll v3.5.6+0 [efcefdf7] + PCRE2_jll v10.47.0+0 [bea87d4a] + SuiteSparse_jll v7.10.1+0 [83775a58] + Zlib_jll v1.3.2+0 [3161d3a3] + Zstd_jll v1.5.7+1 [8e850b90] + libblastrampoline_jll v5.15.0+0 [8e850ede] + nghttp2_jll v1.69.0+0 [3f19e933] + p7zip_jll v17.8.0+0 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` Installation completed after 12.79s ################################################################################ # Precompilation # Precompiling PkgEval dependencies... Precompiling package dependencies... Precompiling project... 123.1 s ✓ Clarabel 42.8 s ✓ Clp 11.6 s ✓ Cbc 10.7 s ✓ CDDLib 47.6 s ✓ sparseQFCA 5 dependencies successfully precompiled in 238 seconds. 155 already precompiled. Precompilation completed after 274.74s ################################################################################ # Testing # Testing sparseQFCA Status `/tmp/jl_F1Xnah/Project.toml` [5a4f3dfa] AbstractFBCModels v1.3.0 [3391f64e] CDDLib v0.10.2 [babc4406] COBREXA v2.9.1 ⌃ [9961bab8] Cbc v1.2.0 ⌅ [61c947e1] Clarabel v0.7.1 ⌃ [e2554f3b] Clp v1.2.2 [5ae59095] Colors v0.13.1 [8bb1440f] DelimitedFiles v1.9.1 [e2685f51] ECOS v1.1.3 [60bf3e95] GLPK v1.2.1 [f67ccb44] HDF5 v0.17.3 [87dc4568] HiGHS v1.23.0 ⌅ [033835bb] JLD2 v0.5.15 ⌅ [682c06a0] JSON v0.21.4 [475c1105] JSONFBCModels v1.0.1 [4076af6c] JuMP v1.30.1 [b8f27783] MathOptInterface v1.51.0 [3e8f9d1a] SBMLFBCModels v1.1.1 [c946c3f1] SCS v2.6.3 [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_F1Xnah/Manifest.toml` [14f7f29c] AMD v0.5.3 [5a4f3dfa] AbstractFBCModels v1.3.0 [3391f64e] CDDLib v0.10.2 [fa961155] CEnum v0.5.0 [babc4406] COBREXA v2.9.1 ⌃ [9961bab8] Cbc v1.2.0 ⌅ [61c947e1] Clarabel v0.7.1 ⌃ [e2554f3b] Clp v1.2.2 [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 v1.11.1 [187b0558] ConstructionBase v1.6.0 [864edb3b] DataStructures v0.19.4 [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 v1.19.0 [53c48c17] FixedPointNumbers v0.8.5 [f6369f11] ForwardDiff v1.3.3 [60bf3e95] GLPK v1.2.1 ⌅ [14197337] GenericLinearAlgebra v0.3.19 [f67ccb44] HDF5 v0.17.3 [076d061b] HashArrayMappedTries v0.2.0 [87dc4568] HiGHS v1.23.0 [615f187c] IfElse v0.1.1 [92d709cd] IrrationalConstants v0.2.6 ⌅ [033835bb] JLD2 v0.5.15 [692b3bcd] JLLWrappers v1.8.0 ⌅ [682c06a0] JSON v0.21.4 [475c1105] JSONFBCModels v1.0.1 [4076af6c] JuMP v1.30.1 [2ab3a3ac] LogExpFunctions v0.3.29 [3da0fdf6] MPIPreferences v0.1.12 [1914dd2f] MacroTools v0.5.16 [8c4f8055] MathOptIIS v0.2.0 [b8f27783] MathOptInterface v1.51.0 [d8a4904e] MutableArithmetics v1.7.1 [77ba4419] NaNMath v1.1.3 [bac558e1] OrderedCollections v1.8.1 [69de0a69] Parsers v2.8.4 [3bbf5609] PikaParser v0.6.1 [67491407] Polyhedra v0.8.1 [aea7be01] PrecompileTools v1.3.4 [21216c6a] Preferences v1.5.2 [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 v2.6.3 [7e506255] ScopedValues v1.6.2 [66db9d55] SnoopPrecompile v1.0.3 [276daf66] SpecialFunctions v2.7.2 [860ef19b] StableRNGs v1.0.4 [90137ffa] StaticArrays v1.9.18 [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 v200.1000.800+0 ⌅ [3830e938] Cgl_jll v0.6000.600+0 ⌅ [06985876] Clp_jll v100.1700.700+1 ⌅ [be027038] CoinUtils_jll v200.1100.600+0 [c2c64177] ECOS_jll v200.0.800+0 [e8aa6df9] GLPK_jll v5.0.1+1 [0234f1f7] HDF5_jll v2.1.2+0 [8fd58aa0] HiGHS_jll v1.14.0+0 [e33a78d0] Hwloc_jll v2.13.0+1 [1d63c593] LLVMOpenMP_jll v18.1.8+0 [94ce4f54] Libiconv_jll v1.18.0+0 [d00139f3] METIS_jll v5.1.3+0 [b5ada748] MPIABI_jll v0.1.5+0 [7cb0a576] MPICH_jll v5.0.1+0 [f1f71cc9] MPItrampoline_jll v5.5.6+0 [d7ed1dd3] MUMPS_seq_jll v500.900.0+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 ⌅ [7da25872] Osi_jll v0.10800.700+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 v0.19.0+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 ⌅ [f07e07eb] cddlib_jll v0.94.14+0 [c4b69c83] dlfcn_win32_jll v1.4.2+0 [477f73a3] libaec_jll v1.1.6+0 [9aeb927a] mpif_jll v0.1.7+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 [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 [9a3f8284] Random v1.11.0 [ea8e919c] SHA v1.13.0 [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 v1.5.1+0 [781609d7] GMP_jll v6.3.0+2 [deac9b47] LibCURL_jll v8.20.0+1 [e37daf67] LibGit2_jll v1.9.3+0 [29816b5a] LibSSH2_jll v1.11.101+0 [14a3606d] MozillaCACerts_jll v2026.3.19 [4536629a] OpenBLAS_jll v0.3.33+0 [05823500] OpenLibm_jll v0.8.7+0 [458c3c95] OpenSSL_jll v3.5.6+0 [efcefdf7] PCRE2_jll v10.47.0+0 [bea87d4a] SuiteSparse_jll v7.10.1+0 [83775a58] Zlib_jll v1.3.2+0 [3161d3a3] Zstd_jll v1.5.7+1 [8e850b90] libblastrampoline_jll v5.15.0+0 [8e850ede] nghttp2_jll v1.69.0+0 [3f19e933] p7zip_jll v17.8.0+0 Info Packages marked with ⌃ and ⌅ have new versions available. Those with ⌃ may be upgradable, but those with ⌅ are restricted by compatibility constraints 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 [172] signal 6 (-6): Aborted in expression starting at timing.jl:395 unknown function (ip: 0x7a82949eeebc) 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-15.2.0/libstdc++-v3/libsupc++/vterminate.cc:95:10 __terminate at /workspace/srcdir/gcc-15.2.0/libstdc++-v3/libsupc++/eh_terminate.cc:48:15 terminate at /workspace/srcdir/gcc-15.2.0/libstdc++-v3/libsupc++/eh_terminate.cc:58:27 __cxa_throw at /workspace/srcdir/gcc-15.2.0/libstdc++-v3/libsupc++/eh_throw.cc:98:18 __throw_system_error at /workspace/srcdir/gcc-15.2.0/libstdc++-v3/src/c++11/system_error.cc:599:5 _M_start_thread at /workspace/srcdir/gcc-15.2.0/libstdc++-v3/src/c++11/thread.cc:176:27 _ZN17HighsTaskExecutor10initializeEi.part.668 at /home/pkgeval/.julia/artifacts/0f5853b2f0786049f8ae5d642f412a7a73bfad68/lib/libhighs.so (unknown line) _ZN5Highs19calledOptimizeModelEv at /home/pkgeval/.julia/artifacts/0f5853b2f0786049f8ae5d642f412a7a73bfad68/lib/libhighs.so (unknown line) _ZN5Highs13optimizeModelEv at /home/pkgeval/.julia/artifacts/0f5853b2f0786049f8ae5d642f412a7a73bfad68/lib/libhighs.so (unknown line) _ZN5Highs3runEv at /home/pkgeval/.julia/artifacts/0f5853b2f0786049f8ae5d642f412a7a73bfad68/lib/libhighs.so (unknown line) Highs_run at /home/pkgeval/.julia/packages/HiGHS/yPMPW/src/gen/libhighs.jl:328:9 [inlined] _Highs_run_workaround_issue_316 at /home/pkgeval/.julia/packages/HiGHS/yPMPW/src/MOI_wrapper.jl:2253:3 [inlined] #47 at /home/pkgeval/.julia/packages/HiGHS/yPMPW/src/MOI_wrapper.jl:2300:3 [inlined] disable_sigint at ./c.jl:167:3 optimize! at /home/pkgeval/.julia/packages/HiGHS/yPMPW/src/MOI_wrapper.jl:2300:67 optimize! at /home/pkgeval/.julia/packages/MathOptInterface/EMtxt/src/Bridges/bridge_optimizer.jl:367:6 [inlined] optimize! at /home/pkgeval/.julia/packages/MathOptInterface/EMtxt/src/MathOptInterface.jl:122:4 [inlined] optimize! at /home/pkgeval/.julia/packages/MathOptInterface/EMtxt/src/Utilities/cachingoptimizer.jl:370:51 unknown function (ip: 0x7a827575ac52) at (unknown file) _jl_invoke at /source/src/gf.c:4127:23 [inlined] ijl_apply_generic at /source/src/gf.c:4353:12 #optimize!#96 at /home/pkgeval/.julia/packages/JuMP/EHXNP/src/optimizer_interface.jl:610:106 optimize! at /home/pkgeval/.julia/packages/JuMP/EHXNP/src/optimizer_interface.jl:560:12 [inlined] QFCA at /home/pkgeval/.julia/packages/sparseQFCA/VIdqW/src/QFCA/SQFCA.jl:79:419 QFCA at /home/pkgeval/.julia/packages/sparseQFCA/VIdqW/src/QFCA/SQFCA.jl:61:1 unknown function (ip: 0x7a827564a484) at (unknown file) _jl_invoke at /source/src/gf.c:4127:23 [inlined] ijl_apply_generic at /source/src/gf.c:4353:12 top-level scope at ./timing.jl:739:24 jl_invoke_oneshot at /source/src/gf.c:4162:23 ijl_eval_thunk at /source/src/toplevel.c:760:18 jl_toplevel_eval_flex at /source/src/toplevel.c:712:26 jl_eval_toplevel_stmts at /source/src/toplevel.c:602:15 jl_toplevel_eval_flex at /source/src/toplevel.c:684:27 ijl_toplevel_eval at /source/src/toplevel.c:782:12 ijl_toplevel_eval_in at /source/src/toplevel.c:827:13 eval at ./boot.jl:517:3 include_string at ./loading.jl:3113:125 _jl_invoke at /source/src/gf.c:4127:23 [inlined] ijl_apply_generic at /source/src/gf.c:4353:12 _include at ./loading.jl:3173:35 include at ./Base.jl:327:3 IncludeInto at ./Base.jl:328:4 jfptr_IncludeInto_1.1 at /opt/julia/lib/julia/sys.so (unknown line) _jl_invoke at /source/src/gf.c:4127:23 [inlined] ijl_apply_generic at /source/src/gf.c:4353:12 jl_apply at /source/src/julia.h:2328:12 [inlined] do_call at /source/src/interpreter.c:123:26 eval_value at /source/src/interpreter.c:243:16 eval_stmt_value at /source/src/interpreter.c:194:23 [inlined] eval_body at /source/src/interpreter.c:706:13 jl_interpret_toplevel_thunk at /source/src/interpreter.c:897:21 ijl_eval_thunk at /source/src/toplevel.c:768:18 jl_toplevel_eval_flex at /source/src/toplevel.c:712:26 jl_eval_toplevel_stmts at /source/src/toplevel.c:602:15 jl_toplevel_eval_flex at /source/src/toplevel.c:684:27 ijl_toplevel_eval at /source/src/toplevel.c:782:12 ijl_toplevel_eval_in at /source/src/toplevel.c:827:13 eval at ./boot.jl:517:3 exec_options at ./client.jl:318:353 _start at ./client.jl:593:35 jfptr__start_0.1 at /opt/julia/lib/julia/sys.so (unknown line) _jl_invoke at /source/src/gf.c:4127:23 [inlined] ijl_apply_generic at /source/src/gf.c:4353:12 jl_apply at /source/src/julia.h:2328:12 [inlined] true_main at /source/src/jlapi.c:971:29 jl_repl_entrypoint at /source/src/jlapi.c:1138:15 main at /source/cli/loader_exe.c:58:15 unknown function (ip: 0x7a829498b249) 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: 74456269 (Pool: 74455107; Big: 1162); GC: 30 Testing failed after 236.59s 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:3247 [3] Cmd(cmd::Cmd) @ Base /opt/julia/share/julia/stdlib/v1.14/Pkg/src/Operations.jl:3110 [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:587 [5] 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 [6] test(pkgs::Vector{String}; kwargs::@Kwargs{julia_args::Cmd}) @ Pkg.API /opt/julia/share/julia/stdlib/v1.14/Pkg/src/API.jl:160 [7] test @ /opt/julia/share/julia/stdlib/v1.14/Pkg/src/API.jl:160 [inlined] [8] test(pkg::String; kwargs::@Kwargs{julia_args::Cmd}) @ Pkg.API /opt/julia/share/julia/stdlib/v1.14/Pkg/src/API.jl:159 [inlined] [9] top-level scope @ /PkgEval.jl/scripts/evaluate.jl:223 [10] include(mod::Module, _path::String) @ Base ./Base.jl:326 [11] exec_options(opts::Base.JLOptions) @ Base ./client.jl:352 [12] _start() @ Base ./client.jl:593 in expression starting at /PkgEval.jl/scripts/evaluate.jl:214 PkgEval crashed after 1671.19s: the process was aborted ################################################################################ # Bug reporting # The package crashed during testing (reason=abort), but PkgEval was unable to reproduce the crash under rr (status=fail, reason=test_errors). For debugging, here is the tail end of the rr log: > 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 > Distributed Quantitative Flux Coupling Analysis(distributedQFCA): > Number of Proccess : 8 > Number of Workers : 7 > The name of the solver = HiGHS > Tolerance = 1.0e-9 > Final fctable : > Number of 0's (unCoupled) : 49916 > Number of 1's (Fully) : 1782 > Number of 2's (Partialy) : 30 > Number of 3's (DC i-->j) : 1048 > Number of 4's (DC j-->i) : 1048 > 13.858660 seconds (354.55 k allocations: 14.179 MiB) > #-------------------------------------------------------------------------------------------# > ToyModels: > ToyModel1 : > ERROR: LoadError: SystemError: opening file "../test/Models/ToyModel1.json": Permission denied > Stacktrace: > [1] systemerror(p::String, errno::Int32; extrainfo::Nothing) > @ Base ./error.jl:188 > [2] open(fname::String; lock::Bool, read::Nothing, write::Nothing, create::Nothing, truncate::Bool, append::Nothing) > @ Base ./iostream.jl:327 > [3] open > @ ./iostream.jl:306 [inlined] > [4] open(fname::String, mode::String; lock::Bool) > @ Base ./iostream.jl:390 > [5] open(fname::String, mode::String) > @ Base ./iostream.jl:389 > [6] open(::JSONFBCModels.var"#17#18"{JSONFBCModel}, ::String, ::Vararg{String}; kwargs::@Kwargs{}) > @ Base ./io.jl:427 > [7] open > @ ./io.jl:426 [inlined] > [8] save > @ ~/.julia/packages/JSONFBCModels/544sa/src/io.jl:4 [inlined] > [9] save_model(model::JSONFBCModel, path::String) > @ COBREXA ~/.julia/packages/COBREXA/9nHZI/src/io.jl:77 > [10] top-level scope > @ ~/.julia/packages/sparseQFCA/VIdqW/test/runtests.jl:330 > [11] include(mapexpr::Function, mod::Module, _path::String) > @ Base ./Base.jl:327 > [12] top-level scope > @ none:6 > [13] eval(m::Module, e::Any) > @ Core ./boot.jl:517 > [14] exec_options(opts::Base.JLOptions) > @ Base ./client.jl:318 > [15] _start() > @ Base ./client.jl:593 > in expression starting at /home/pkgeval/.julia/packages/sparseQFCA/VIdqW/test/runtests.jl:330 > ┌ Warning: Forcibly interrupting busy workers > │ exception = rmprocs: pids [2, 3, 4, 5, 6, 7, 8] not terminated after 5.0 seconds. > └ @ Distributed /opt/julia/share/julia/stdlib/v1.14/Distributed/src/cluster.jl:1279 > ┌ Warning: rmprocs: process 1 not removed > └ @ Distributed /opt/julia/share/julia/stdlib/v1.14/Distributed/src/cluster.jl:1074 > > Testing failed after 2337.74s > > ERROR: LoadError: Package sparseQFCA errored during testing > 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:3247 > [3] Cmd(cmd::Cmd) > @ Base /opt/julia/share/julia/stdlib/v1.14/Pkg/src/Operations.jl:3110 [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:587 > [5] 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 > [6] test(pkgs::Vector{String}; kwargs::@Kwargs{julia_args::Cmd}) > @ Pkg.API /opt/julia/share/julia/stdlib/v1.14/Pkg/src/API.jl:160 > [7] test > @ /opt/julia/share/julia/stdlib/v1.14/Pkg/src/API.jl:160 [inlined] > [8] test(pkg::String; kwargs::@Kwargs{julia_args::Cmd}) > @ Pkg.API /opt/julia/share/julia/stdlib/v1.14/Pkg/src/API.jl:159 [inlined] > [9] top-level scope > @ /PkgEval.jl/scripts/evaluate.jl:221 > [10] include(mod::Module, _path::String) > @ Base ./Base.jl:326 > [11] exec_options(opts::Base.JLOptions) > @ Base ./client.jl:352 > [12] _start() > @ Base ./client.jl:593 > in expression starting at /PkgEval.jl/scripts/evaluate.jl:214 > > PkgEval failed after 2457.15s: package tests unexpectedly errored