Package evaluation to test COBREXA on Julia 1.13.0-DEV.1319 (9cddfda8ef*) started at 2025-10-16T18:29:17.005 ################################################################################ # Set-up # Installing PkgEval dependencies (TestEnv)... Set-up completed after 10.73s ################################################################################ # Installation # Installing COBREXA... Resolving package versions... Installed Bzip2_jll ──────────── v1.0.9+0 Installed CodecZlib ──────────── v0.7.8 Installed MacroTools ─────────── v0.5.16 Installed DiffResults ────────── v1.1.0 Installed ConstructionBase ───── v1.6.0 Installed DataStructures ─────── v0.18.22 Installed ForwardDiff ────────── v1.2.2 Installed TranscodingStreams ─── v0.11.3 Installed Statistics ─────────── v1.11.1 Installed Compat ─────────────── v4.18.1 Installed OrderedCollections ─── v1.8.1 Installed StaticArraysCore ───── v1.4.3 Installed CommonSubexpressions ─ v0.3.1 Installed PrecompileTools ────── v1.3.3 Installed IrrationalConstants ── v0.2.6 Installed CodecBzip2 ─────────── v0.8.5 Installed NaNMath ────────────── v1.1.3 Installed ConstraintTrees ────── v1.11.0 Installed StructUtils ────────── v2.5.1 Installed AbstractFBCModels ──── v1.3.0 Installed JSON3 ──────────────── v1.14.3 Installed OpenSpecFun_jll ────── v0.5.6+0 Installed StableRNGs ─────────── v1.0.3 Installed DiffRules ──────────── v1.15.1 Installed LogExpFunctions ────── v0.3.29 Installed Parsers ────────────── v2.8.3 Installed JSON ───────────────── v1.1.0 Installed JLLWrappers ────────── v1.7.1 Installed SpecialFunctions ───── v2.6.1 Installed StructTypes ────────── v1.11.0 Installed COBREXA ────────────── v2.9.1 Installed Preferences ────────── v1.5.0 Installed MutableArithmetics ─── v1.6.6 Installed BenchmarkTools ─────── v1.6.1 Installed JuMP ───────────────── v1.29.1 Installed DocStringExtensions ── v0.9.5 Installed MathOptInterface ───── v1.45.0 Installing 2 artifacts Installed artifact OpenSpecFun 194.9 KiB Installed artifact Bzip2 503.5 KiB Updating `~/.julia/environments/v1.13/Project.toml` [babc4406] + COBREXA v2.9.1 Updating `~/.julia/environments/v1.13/Manifest.toml` [5a4f3dfa] + AbstractFBCModels v1.3.0 [6e4b80f9] + BenchmarkTools v1.6.1 [babc4406] + COBREXA v2.9.1 [523fee87] + CodecBzip2 v0.8.5 [944b1d66] + CodecZlib v0.7.8 [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 [163ba53b] + DiffResults v1.1.0 [b552c78f] + DiffRules v1.15.1 [ffbed154] + DocStringExtensions v0.9.5 [f6369f11] + ForwardDiff v1.2.2 [92d709cd] + IrrationalConstants v0.2.6 [692b3bcd] + JLLWrappers v1.7.1 [682c06a0] + JSON v1.1.0 [0f8b85d8] + JSON3 v1.14.3 [4076af6c] + JuMP v1.29.1 [2ab3a3ac] + LogExpFunctions v0.3.29 [1914dd2f] + MacroTools v0.5.16 [b8f27783] + MathOptInterface v1.45.0 [d8a4904e] + MutableArithmetics v1.6.6 [77ba4419] + NaNMath v1.1.3 [bac558e1] + OrderedCollections v1.8.1 [69de0a69] + Parsers v2.8.3 [aea7be01] + PrecompileTools v1.3.3 [21216c6a] + Preferences v1.5.0 [276daf66] + SpecialFunctions v2.6.1 [860ef19b] + StableRNGs v1.0.3 [1e83bf80] + StaticArraysCore v1.4.3 [10745b16] + Statistics v1.11.1 [856f2bd8] + StructTypes v1.11.0 [ec057cc2] + StructUtils v2.5.1 [3bb67fe8] + TranscodingStreams v0.11.3 [6e34b625] + Bzip2_jll v1.0.9+0 [efe28fd5] + OpenSpecFun_jll v0.5.6+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 v1.12.0 [b27032c2] + LibCURL v0.6.4 [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 v1.13.0 [de0858da] + Printf v1.11.0 [9abbd945] + Profile 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 v1.13.0 [f489334b] + StyledStrings v1.11.0 [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 v8.16.0+0 [e37daf67] + LibGit2_jll v1.9.1+0 [29816b5a] + LibSSH2_jll v1.11.3+1 [14a3606d] + MozillaCACerts_jll v2025.9.9 [4536629a] + OpenBLAS_jll v0.3.29+0 [05823500] + OpenLibm_jll v0.8.7+0 [458c3c95] + OpenSSL_jll v3.5.4+0 [efcefdf7] + PCRE2_jll v10.46.0+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 v1.67.1+0 [3f19e933] + p7zip_jll v17.6.0+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 9.71s ################################################################################ # Precompilation # Precompiling PkgEval dependencies... Precompiling packages... 4622.9 ms ✓ TestEnv 1 dependency successfully precompiled in 5 seconds. 27 already precompiled. ┌ Warning: Could not use exact versions of packages in manifest, re-resolving └ @ TestEnv ~/.julia/packages/TestEnv/nGMfF/src/julia-1.11/activate_set.jl:76 Precompiling package dependencies... Precompilation completed after 80.61s ################################################################################ # Testing # Testing COBREXA Test Could not use exact versions of packages in manifest, re-resolving. Note: if you do not check your manifest file into source control, then you can probably ignore this message. However, if you do check your manifest file into source control, then you probably want to pass the `allow_reresolve = false` kwarg when calling the `Pkg.test` function. Updating `/tmp/jl_g0H920/Project.toml` ⌅ [4c88cf16] + Aqua v0.7.4 [babc4406] + COBREXA v2.9.1 [336ed68f] + CSV v0.10.15 ⌅ [61c947e1] + Clarabel v0.6.0 [87dc4568] + HiGHS v1.19.3 [475c1105] + JSONFBCModels v1.0.1 [3e8f9d1a] + SBMLFBCModels v1.1.1 [6dd1b50a] + Tulip v0.9.8 Updating `/tmp/jl_g0H920/Manifest.toml` [14f7f29c] + AMD v0.5.3 ⌅ [4c88cf16] + Aqua v0.7.4 [babc4406] + COBREXA v2.9.1 [336ed68f] + CSV v0.10.15 ⌅ [61c947e1] + Clarabel v0.6.0 [9a962f9c] + DataAPI v1.16.0 [e2d170a0] + DataValueInterfaces v1.0.0 [e2ba6199] + ExprTools v0.1.10 [9aa1b823] + FastClosures v0.3.2 [48062228] + FilePathsBase v0.9.24 [14197337] + GenericLinearAlgebra v0.3.18 [87dc4568] + HiGHS v1.19.3 [615f187c] + IfElse v0.1.1 [842dd82b] + InlineStrings v1.4.5 [82899510] + IteratorInterfaceExtensions v1.0.0 ⌅ [682c06a0] ↓ JSON v1.1.0 ⇒ v0.21.4 [475c1105] + JSONFBCModels v1.0.1 [ba0b0d4f] + Krylov v0.10.2 [40e66cde] + LDLFactorizations v0.10.1 [5c8ed15e] + LinearOperators v2.11.0 [8c4f8055] + MathOptIIS v0.1.1 [3bbf5609] + PikaParser v0.6.1 [2dfb63ee] + PooledArrays v1.4.3 [bfc457fd] + QDLDL v0.4.1 [10f199a5] + QPSReader v0.2.1 [ae029012] + Requires v1.3.1 [e5567a89] + SBML v1.6.0 [3e8f9d1a] + SBMLFBCModels v1.1.1 [91c51154] + SentinelArrays v1.4.8 [66db9d55] + SnoopPrecompile v1.0.3 [90137ffa] + StaticArrays v1.9.15 [ec057cc2] - StructUtils v2.5.1 [3783bdb8] + TableTraits v1.0.1 [bd369af6] + Tables v1.12.1 [a759f4b9] + TimerOutputs v0.5.29 [6dd1b50a] + Tulip v0.9.8 [1986cc42] + Unitful v1.25.0 [ea10d353] + WeakRefStrings v1.4.2 [76eceee3] + WorkerUtilities v1.6.1 [8fd58aa0] + HiGHS_jll v1.11.0+1 [94ce4f54] + Libiconv_jll v1.18.0+0 [bb12108a] + SBML_jll v5.20.1+0 ⌅ [02c8fc9c] + XML2_jll v2.13.9+0 [9fa8497b] + Future v1.11.0 [4607b0f0] + SuiteSparse Info Packages marked with ⌅ have new versions available but compatibility constraints restrict them from upgrading. To see why use `status --outdated -m` Test Successfully re-resolved Status `/tmp/jl_g0H920/Project.toml` [5a4f3dfa] AbstractFBCModels v1.3.0 ⌅ [4c88cf16] Aqua v0.7.4 [babc4406] COBREXA v2.9.1 [336ed68f] CSV v0.10.15 ⌅ [61c947e1] Clarabel v0.6.0 [5515826b] ConstraintTrees v1.11.0 [ffbed154] DocStringExtensions v0.9.5 [87dc4568] HiGHS v1.19.3 [475c1105] JSONFBCModels v1.0.1 [4076af6c] JuMP v1.29.1 [3e8f9d1a] SBMLFBCModels v1.1.1 [860ef19b] StableRNGs v1.0.3 [6dd1b50a] Tulip v0.9.8 [8ba89e20] Distributed v1.11.0 [f43a241f] Downloads v1.7.0 [37e2e46d] LinearAlgebra v1.13.0 [44cfe95a] Pkg v1.13.0 [9a3f8284] Random v1.11.0 [ea8e919c] SHA v0.7.0 [2f01184e] SparseArrays v1.13.0 [8dfed614] Test v1.11.0 Status `/tmp/jl_g0H920/Manifest.toml` [14f7f29c] AMD v0.5.3 [5a4f3dfa] AbstractFBCModels v1.3.0 ⌅ [4c88cf16] Aqua v0.7.4 [6e4b80f9] BenchmarkTools v1.6.1 [babc4406] COBREXA v2.9.1 [336ed68f] CSV v0.10.15 ⌅ [61c947e1] Clarabel v0.6.0 [523fee87] CodecBzip2 v0.8.5 [944b1d66] CodecZlib v0.7.8 [bbf7d656] CommonSubexpressions v0.3.1 [34da2185] Compat v4.18.1 [5515826b] ConstraintTrees v1.11.0 [187b0558] ConstructionBase v1.6.0 [9a962f9c] DataAPI v1.16.0 ⌅ [864edb3b] DataStructures v0.18.22 [e2d170a0] DataValueInterfaces v1.0.0 [163ba53b] DiffResults v1.1.0 [b552c78f] DiffRules v1.15.1 [ffbed154] DocStringExtensions v0.9.5 [e2ba6199] ExprTools v0.1.10 [9aa1b823] FastClosures v0.3.2 [48062228] FilePathsBase v0.9.24 [f6369f11] ForwardDiff v1.2.2 [14197337] GenericLinearAlgebra v0.3.18 [87dc4568] HiGHS v1.19.3 [615f187c] IfElse v0.1.1 [842dd82b] InlineStrings v1.4.5 [92d709cd] IrrationalConstants v0.2.6 [82899510] IteratorInterfaceExtensions v1.0.0 [692b3bcd] JLLWrappers v1.7.1 ⌅ [682c06a0] JSON v0.21.4 [0f8b85d8] JSON3 v1.14.3 [475c1105] JSONFBCModels v1.0.1 [4076af6c] JuMP v1.29.1 [ba0b0d4f] Krylov v0.10.2 [40e66cde] LDLFactorizations v0.10.1 [5c8ed15e] LinearOperators v2.11.0 [2ab3a3ac] LogExpFunctions v0.3.29 [1914dd2f] MacroTools v0.5.16 [8c4f8055] MathOptIIS v0.1.1 [b8f27783] MathOptInterface v1.45.0 [d8a4904e] MutableArithmetics v1.6.6 [77ba4419] NaNMath v1.1.3 [bac558e1] OrderedCollections v1.8.1 [69de0a69] Parsers v2.8.3 [3bbf5609] PikaParser v0.6.1 [2dfb63ee] PooledArrays v1.4.3 [aea7be01] PrecompileTools v1.3.3 [21216c6a] Preferences v1.5.0 [bfc457fd] QDLDL v0.4.1 [10f199a5] QPSReader v0.2.1 [ae029012] Requires v1.3.1 [e5567a89] SBML v1.6.0 [3e8f9d1a] SBMLFBCModels v1.1.1 [91c51154] SentinelArrays v1.4.8 [66db9d55] SnoopPrecompile v1.0.3 [276daf66] SpecialFunctions v2.6.1 [860ef19b] StableRNGs v1.0.3 [90137ffa] StaticArrays v1.9.15 [1e83bf80] StaticArraysCore v1.4.3 [10745b16] Statistics v1.11.1 [856f2bd8] StructTypes v1.11.0 [3783bdb8] TableTraits v1.0.1 [bd369af6] Tables v1.12.1 [a759f4b9] TimerOutputs v0.5.29 [3bb67fe8] TranscodingStreams v0.11.3 [6dd1b50a] Tulip v0.9.8 [1986cc42] Unitful v1.25.0 [ea10d353] WeakRefStrings v1.4.2 [76eceee3] WorkerUtilities v1.6.1 [6e34b625] Bzip2_jll v1.0.9+0 [8fd58aa0] HiGHS_jll v1.11.0+1 [94ce4f54] Libiconv_jll v1.18.0+0 [efe28fd5] OpenSpecFun_jll v0.5.6+0 [bb12108a] SBML_jll v5.20.1+0 ⌅ [02c8fc9c] XML2_jll v2.13.9+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 [b27032c2] LibCURL v0.6.4 [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 v1.13.0 [de0858da] Printf v1.11.0 [9abbd945] Profile 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 v1.13.0 [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 v8.16.0+0 [e37daf67] LibGit2_jll v1.9.1+0 [29816b5a] LibSSH2_jll v1.11.3+1 [14a3606d] MozillaCACerts_jll v2025.9.9 [4536629a] OpenBLAS_jll v0.3.29+0 [05823500] OpenLibm_jll v0.8.7+0 [458c3c95] OpenSSL_jll v3.5.4+0 [efcefdf7] PCRE2_jll v10.46.0+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 v1.67.1+0 [3f19e933] p7zip_jll v17.6.0+0 Info Packages marked with ⌅ have new versions available but compatibility constraints restrict them from upgrading. Testing Running tests... [ Info: misc.jl done in 56.78s docs/01-loading-and-saving.jl: Error During Test at /home/pkgeval/.julia/packages/COBREXA/9nHZI/test/runtests.jl:40 Got exception outside of a @test LoadError: ParseError: # Error @ /home/pkgeval/.julia/packages/Unitful/HCJFR/src/logarithm.jl:127:5 Base. *(::MixedUnits, ::MixedUnits) = # └───────────────────────────────┘ ── extra tokens after end of expression Stacktrace: [1] top-level scope @ ~/.julia/packages/Unitful/HCJFR/src/logarithm.jl:127 [2] include(mapexpr::Function, mod::Module, _path::String) @ Base ./Base.jl:310 [3] top-level scope @ ~/.julia/packages/Unitful/HCJFR/src/Unitful.jl:67 [4] include(mod::Module, _path::String) @ Base ./Base.jl:309 [5] __require_prelocked(pkg::Base.PkgId, env::String) @ Base ./loading.jl:2777 [6] _require_prelocked(uuidkey::Base.PkgId, env::String) @ Base ./loading.jl:2536 [7] macro expansion @ ./loading.jl:2464 [inlined] [8] macro expansion @ ./lock.jl:376 [inlined] [9] __require(into::Module, mod::Symbol) @ Base ./loading.jl:2428 [10] require @ ./loading.jl:2404 [inlined] [11] eval_import_path @ ./module.jl:36 [inlined] [12] eval_import_path_all(at::Module, path::Expr, keyword::String) @ Base ./module.jl:60 [13] _eval_using(to::Module, path::Expr) @ Base ./module.jl:137 [14] top-level scope @ ~/.julia/packages/SBML/mJIpc/src/SBML.jl:11 [15] include(mod::Module, _path::String) @ Base ./Base.jl:309 [16] __require_prelocked(pkg::Base.PkgId, env::String) @ Base ./loading.jl:2777 [17] _require_prelocked(uuidkey::Base.PkgId, env::String) @ Base ./loading.jl:2536 [18] macro expansion @ ./loading.jl:2464 [inlined] [19] macro expansion @ ./lock.jl:376 [inlined] [20] __require(into::Module, mod::Symbol) @ Base ./loading.jl:2428 [21] require @ ./loading.jl:2404 [inlined] [22] eval_import_path @ ./module.jl:36 [inlined] [23] _eval_import(imported::Bool, to::Module, from::Nothing, paths::Expr) @ Base ./module.jl:111 [24] top-level scope @ ~/.julia/packages/SBMLFBCModels/Xntgh/src/SBMLFBCModels.jl:9 [25] include(mod::Module, _path::String) @ Base ./Base.jl:309 [26] __require_prelocked(pkg::Base.PkgId, env::String) @ Base ./loading.jl:2777 [27] _require_prelocked(uuidkey::Base.PkgId, env::String) @ Base ./loading.jl:2536 [28] macro expansion @ ./loading.jl:2464 [inlined] [29] macro expansion @ ./lock.jl:376 [inlined] [30] __require(into::Module, mod::Symbol) @ Base ./loading.jl:2428 [31] require @ ./loading.jl:2404 [inlined] [32] eval_import_path @ ./module.jl:36 [inlined] [33] _eval_import(imported::Bool, to::Module, from::Nothing, paths::Expr) @ Base ./module.jl:111 [34] top-level scope @ ~/.julia/packages/COBREXA/9nHZI/docs/src/examples/01-loading-and-saving.jl:57 [35] include(mapexpr::Function, mod::Module, _path::String) @ Base ./Base.jl:310 [36] IncludeInto @ ./Base.jl:311 [inlined] [37] macro expansion @ ./timing.jl:461 [inlined] [38] run_test_file @ ~/.julia/packages/COBREXA/9nHZI/test/runtests.jl:34 [inlined] [39] macro expansion @ ~/.julia/packages/COBREXA/9nHZI/test/runtests.jl:41 [inlined] [40] macro expansion @ /opt/julia/share/julia/stdlib/v1.13/Test/src/Test.jl:1961 [inlined] [41] run_doc_examples() @ Main ~/.julia/packages/COBREXA/9nHZI/test/runtests.jl:41 [42] top-level scope @ ~/.julia/packages/COBREXA/9nHZI/test/runtests.jl:59 [43] macro expansion @ /opt/julia/share/julia/stdlib/v1.13/Test/src/Test.jl:1961 [inlined] [44] macro expansion @ ~/.julia/packages/COBREXA/9nHZI/test/runtests.jl:62 [inlined] [45] include(mapexpr::Function, mod::Module, _path::String) @ Base ./Base.jl:310 [46] top-level scope @ none:6 [47] eval(m::Module, e::Any) @ Core ./boot.jl:489 [48] exec_options(opts::Base.JLOptions) @ Base ./client.jl:310 [49] _start() @ Base ./client.jl:577 in expression starting at /home/pkgeval/.julia/packages/Unitful/HCJFR/src/logarithm.jl:127 in expression starting at /home/pkgeval/.julia/packages/Unitful/HCJFR/src/Unitful.jl:1 in expression starting at /home/pkgeval/.julia/packages/SBML/mJIpc/src/SBML.jl:1 in expression starting at /home/pkgeval/.julia/packages/SBMLFBCModels/Xntgh/src/SBMLFBCModels.jl:1 in expression starting at /home/pkgeval/.julia/packages/COBREXA/9nHZI/docs/src/examples/01-loading-and-saving.jl:57 [ Info: using cached `e_coli_core.json' [ Info: ../docs/src/examples/02a-flux-balance-analysis.jl done in 17.2s [ Info: using cached `e_coli_core.json' nothing Problem info Name : Constraints : 262 Variables : 95 Non-zeros : 550 Reduced problem info Constraints : 62 (removed 200) Variables : 81 (removed 14) Non-zeros : 325 (removed 225) Presolve time : 0.000s Optimizer info (HSD) Constraints : 62 Variables : 81 RHS : [+0.00e+00, +0.00e+00] Lower bounds : [-2.32e+03, +1.25e+01] Upper bounds : [+0.00e+00, +1.16e+04] Linear solver options Arithmetic : Float64 Backend : CHOLMOD System : Augmented system (K2) Itn PObj DObj PFeas DFeas GFeas Mu Time 0 -0.0000000e+00 +1.7686535e+05 1.16e+04 8.59e-02 1.77e+05 1.0e+00 2.29 Solver exited with status Trm_TimeLimit [ Info: ../docs/src/examples/02b-optimizer-parameters.jl done in 84.06s [ Info: using cached `e_coli_core.json' [ Info: ../docs/src/examples/02c-model-modifications.jl done in 15.83s [ Info: using cached `e_coli_core.json' nothing[ Info: ../docs/src/examples/02d-constraint-modifications.jl done in 0.18s [ Info: using cached `e_coli_core.json' [ Info: ../docs/src/examples/03a-flux-variability-analysis.jl done in 89.97s [ Info: using cached `e_coli_core.json' [ Info: ../docs/src/examples/03b-parsimonious-flux-balance.jl done in 159.66s [ Info: using cached `e_coli_core.json' [ Info: ../docs/src/examples/03c-envelopes.jl done in 14.09s [ Info: using cached `e_coli_core.json' [ Info: ../docs/src/examples/03d-unidirectional.jl done in 7.18s [ Info: using cached `e_coli_core.json' [ Info: ../docs/src/examples/03e-min-exchange.jl done in 12.04s [ Info: using cached `e_coli_core.json' [ Info: ../docs/src/examples/04-community-models.jl done in 88.93s [ Info: using cached `e_coli_core.json' [ Info: ../docs/src/examples/04a-composition-models.jl done in 6.06s [ Info: using cached `e_coli_core.json' [ Info: ../docs/src/examples/05a-minimization-of-metabolic-adjustment.jl done in 3.7s [ Info: using cached `e_coli_core.json' [ Info: ../docs/src/examples/05b-enzyme-constrained-models.jl done in 16.01s [ Info: using cached `e_coli_core.json' [ Info: ../docs/src/examples/05c-mmdf.jl done in 6.65s [ Info: using cached `e_coli_core.json' [ Info: ../docs/src/examples/05d-loopless-models.jl done in 6.96s [ Info: using cached `e_coli_core.json' [ Info: ../docs/src/examples/05e-knockouts.jl done in 27.76s [ Info: using cached `e_coli_core.json' [ Info: ../docs/src/examples/05f-cyclefree.jl done in 41.8s [ Info: using cached `e_coli_core.json' nothing [ Info: ../docs/src/examples/05g-gapfilling.jl done in 6.64s [ Info: using cached `e_coli_core.json' nothing [ Info: ../docs/src/examples/05h-medium.jl done in 2.9s [ Info: using cached `e_coli_core.json' [ Info: ../docs/src/examples/06a-sampling.jl done in 7.98s [ Info: using cached `e_coli_core.json' [ Info: ../docs/src/examples/06b-screening.jl done in 10.66s [ Info: ../docs/src/examples/07a-srba.jl done in 146.62s [ Info: using cached `iML1515.json' [ Info: ../docs/src/examples/07b-community-ecfba.jl done in 17.15s ┌ Warning: `isbindingresolved(m::Module, var::Symbol)` is deprecated, use `true` instead. │ caller = walkmodules(f::Aqua.var"#undefined_exports##0#undefined_exports##1"{Vector{Symbol}}, x::Module) at exports.jl:5 └ @ Core ~/.julia/packages/Aqua/rmHe1/src/exports.jl:5 [ Info: aqua.jl done in 14.76s Test Summary: | Pass Error Total Time COBREXA test suite | 113 1 114 15m02.3s Miscellaneous tests | 39 39 57.1s docs/01-loading-and-saving.jl | 1 1 37.2s docs/02a-flux-balance-analysis.jl | 1 1 17.2s docs/02b-optimizer-parameters.jl | 2 2 1m24.1s docs/02c-model-modifications.jl | 4 4 15.8s docs/02d-constraint-modifications.jl | 2 2 0.2s docs/03a-flux-variability-analysis.jl | 2 2 1m30.0s docs/03b-parsimonious-flux-balance.jl | 6 6 2m39.7s docs/03c-envelopes.jl | 1 1 14.1s docs/03d-unidirectional.jl | 6 6 7.2s docs/03e-min-exchange.jl | 1 1 12.0s docs/04-community-models.jl | 3 3 1m28.9s docs/04a-composition-models.jl | 7 7 6.1s docs/05a-minimization-of-metabolic-adjustment.jl | 7 7 3.7s docs/05b-enzyme-constrained-models.jl | 7 7 16.0s docs/05c-mmdf.jl | 5 5 6.6s docs/05d-loopless-models.jl | 1 1 7.0s docs/05e-knockouts.jl | 5 5 27.8s docs/05f-cyclefree.jl | 0 41.8s docs/05g-gapfilling.jl | 2 2 6.6s docs/05h-medium.jl | 3 3 2.9s docs/06a-sampling.jl | 1 1 8.0s docs/06b-screening.jl | 0 10.7s docs/07a-srba.jl | 1 1 2m29.4s docs/07b-community-ecfba.jl | 1 1 17.2s Automated QUality Assurance | 6 6 14.5s RNG of the outermost testset: Random.Xoshiro(0x37c9b31eaf47c781, 0xa90a76c8a2bb2375, 0x2e4a29fb5f7f2572, 0xdf9eb05908b2021b, 0x37b2bbd0b1d2fbd7) ERROR: LoadError: Some tests did not pass: 113 passed, 0 failed, 1 errored, 0 broken. in expression starting at /home/pkgeval/.julia/packages/COBREXA/9nHZI/test/runtests.jl:58 Testing failed after 1518.95s ERROR: LoadError: Package COBREXA errored during testing Stacktrace: [1] pkgerror(msg::String) @ Pkg.Types /opt/julia/share/julia/stdlib/v1.13/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/v1.13/Pkg/src/Operations.jl:2674 [3] test @ /opt/julia/share/julia/stdlib/v1.13/Pkg/src/Operations.jl:2523 [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/v1.13/Pkg/src/API.jl:548 [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/v1.13/Pkg/src/API.jl:525 [6] test(pkgs::Vector{PackageSpec}; io::IOContext{IO}, kwargs::@Kwargs{julia_args::Cmd}) @ Pkg.API /opt/julia/share/julia/stdlib/v1.13/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/v1.13/Pkg/src/API.jl:161 [8] test(pkgs::Vector{String}; kwargs::@Kwargs{julia_args::Cmd}) @ Pkg.API /opt/julia/share/julia/stdlib/v1.13/Pkg/src/API.jl:160 [9] test @ /opt/julia/share/julia/stdlib/v1.13/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/v1.13/Pkg/src/API.jl:159 [11] top-level scope @ /PkgEval.jl/scripts/evaluate.jl:219 [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:577 in expression starting at /PkgEval.jl/scripts/evaluate.jl:210 PkgEval failed after 1661.03s: package tests unexpectedly errored