Package evaluation to test COBREXA on Julia 1.12.4 (01a2eadb04*) started at 2026-01-29T08:21:05.644 ################################################################################ # Set-up # Installing PkgEval dependencies (TestEnv)... Activating project at `~/.julia/environments/v1.12` Set-up completed after 9.4s ################################################################################ # Installation # Installing COBREXA... Resolving package versions... Installed IrrationalConstants ── v0.2.6 Installed DiffRules ──────────── v1.15.1 Installed JSON3 ──────────────── v1.14.3 Installed StableRNGs ─────────── v1.0.4 Installed Preferences ────────── v1.5.1 Installed MutableArithmetics ─── v1.6.7 Installed JSON ───────────────── v1.4.0 Installed DiffResults ────────── v1.1.0 Installed Bzip2_jll ──────────── v1.0.9+0 Installed CodecBzip2 ─────────── v0.8.5 Installed Parsers ────────────── v2.8.3 Installed SpecialFunctions ───── v2.6.1 Installed BenchmarkTools ─────── v1.6.3 Installed JLLWrappers ────────── v1.7.1 Installed StaticArraysCore ───── v1.4.4 Installed AbstractFBCModels ──── v1.3.0 Installed NaNMath ────────────── v1.1.3 Installed OrderedCollections ─── v1.8.1 Installed ConstructionBase ───── v1.6.0 Installed PrecompileTools ────── v1.3.3 Installed TranscodingStreams ─── v0.11.3 Installed Statistics ─────────── v1.11.1 Installed CommonSubexpressions ─ v0.3.1 Installed DataStructures ─────── v0.18.22 Installed ForwardDiff ────────── v1.3.1 Installed ConstraintTrees ────── v1.11.0 Installed COBREXA ────────────── v2.9.1 Installed LogExpFunctions ────── v0.3.29 Installed JuMP ───────────────── v1.29.4 Installed OpenSpecFun_jll ────── v0.5.6+0 Installed MacroTools ─────────── v0.5.16 Installed CodecZlib ──────────── v0.7.8 Installed Compat ─────────────── v4.18.1 Installed StructTypes ────────── v1.11.0 Installed StructUtils ────────── v2.6.2 Installed DocStringExtensions ── v0.9.5 Installed MathOptInterface ───── v1.48.0 Installing 2 artifacts Installed artifact OpenSpecFun 194.9 KiB Installed artifact Bzip2 503.5 KiB Updating `~/.julia/environments/v1.12/Project.toml` [babc4406] + COBREXA v2.9.1 Updating `~/.julia/environments/v1.12/Manifest.toml` [5a4f3dfa] + AbstractFBCModels v1.3.0 [6e4b80f9] + BenchmarkTools v1.6.3 [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 v1.3.1 [92d709cd] + IrrationalConstants v0.2.6 [692b3bcd] + JLLWrappers v1.7.1 [682c06a0] + JSON v1.4.0 [0f8b85d8] + JSON3 v1.14.3 [4076af6c] + JuMP v1.29.4 [2ab3a3ac] + LogExpFunctions v0.3.29 [1914dd2f] + MacroTools v0.5.16 [b8f27783] + MathOptInterface v1.48.0 [d8a4904e] + MutableArithmetics v1.6.7 [77ba4419] + NaNMath v1.1.3 [bac558e1] + OrderedCollections v1.8.1 [69de0a69] + Parsers v2.8.3 [aea7be01] + PrecompileTools v1.3.3 [21216c6a] + Preferences v1.5.1 [276daf66] + SpecialFunctions v2.6.1 [860ef19b] + StableRNGs v1.0.4 [1e83bf80] + StaticArraysCore v1.4.4 [10745b16] + Statistics v1.11.1 [856f2bd8] + StructTypes v1.11.0 [ec057cc2] + StructUtils v2.6.2 [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 v1.12.0 [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 [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 v1.12.0 [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 v8.15.0+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 v3.5.4+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 9.9s ################################################################################ # Precompilation # Precompiling PkgEval dependencies... Precompiling packages... 4586.3 ms ✓ TestEnv 1 dependency successfully precompiled in 5 seconds. 26 already precompiled. ┌ Warning: Could not use exact versions of packages in manifest, re-resolving └ @ TestEnv ~/.julia/packages/TestEnv/h9a3r/src/julia-1.12/activate_set.jl:78 Precompiling package dependencies... Precompiling packages... 4223.9 ms ✓ OrderedCollections 821.1 ms ✓ DataValueInterfaces 961.9 ms ✓ StableRNGs 1131.3 ms ✓ DocStringExtensions 1849.5 ms ✓ InlineStrings 1116.9 ms ✓ Statistics 841.0 ms ✓ ExprTools 785.0 ms ✓ IfElse 4896.5 ms ✓ IrrationalConstants 3952.6 ms ✓ ConstructionBase 721.8 ms ✓ IteratorInterfaceExtensions 818.8 ms ✓ DataAPI 1036.8 ms ✓ WorkerUtilities 820.1 ms ✓ FastClosures 7643.1 ms ✓ MacroTools 1668.9 ms ✓ GenericLinearAlgebra 982.7 ms ✓ StaticArraysCore 1262.3 ms ✓ TranscodingStreams 3860.1 ms ✓ NaNMath 1186.5 ms ✓ Requires 2175.4 ms ✓ SentinelArrays 4486.9 ms ✓ StructTypes 41172.4 ms ✓ Unitful 1735.1 ms ✓ AMD 15010.1 ms ✓ Krylov 3961.9 ms ✓ Compat 1101.3 ms ✓ Preferences 11185.4 ms ✓ MutableArithmetics 4551.9 ms ✓ QPSReader 1464.2 ms ✓ PikaParser 3834.4 ms ✓ AbstractFBCModels 1307.0 ms ✓ Statistics → SparseArraysExt 6047.6 ms ✓ TimerOutputs 1362.7 ms ✓ LogExpFunctions 788.9 ms ✓ ConstructionBase → ConstructionBaseLinearAlgebraExt 717.4 ms ✓ TableTraits 1015.8 ms ✓ PooledArrays 1541.0 ms ✓ CommonSubexpressions 812.2 ms ✓ DiffResults 891.2 ms ✓ CodecZlib 1726.0 ms ✓ Unitful → ConstructionBaseUnitfulExt 2018.0 ms ✓ Unitful → PrintfExt 2340.0 ms ✓ Unitful → NaNMathExt 1798.1 ms ✓ QDLDL 4029.3 ms ✓ LDLFactorizations 874.0 ms ✓ Compat → CompatLinearAlgebraExt 1088.2 ms ✓ SnoopPrecompile 857.8 ms ✓ PrecompileTools 1181.9 ms ✓ JLLWrappers 4200.2 ms ✓ LinearOperators 4327.7 ms ✓ Tables 4098.6 ms ✓ DataStructures 2504.0 ms ✓ FilePathsBase 6658.1 ms ✓ Aqua 16749.6 ms ✓ StaticArrays 20921.6 ms ✓ Parsers 1392.6 ms ✓ Libiconv_jll 1396.2 ms ✓ Bzip2_jll 1417.4 ms ✓ OpenSpecFun_jll 1405.5 ms ✓ OpenBLAS32_jll 1412.9 ms ✓ METIS_jll 2166.2 ms ✓ LinearOperators → LinearOperatorsLDLFactorizationsExt 4647.9 ms ✓ ConstraintTrees 2945.1 ms ✓ FilePathsBase → FilePathsBaseTestExt 1334.6 ms ✓ FilePathsBase → FilePathsBaseMmapExt 1364.9 ms ✓ StaticArrays → StaticArraysStatisticsExt 1390.7 ms ✓ ConstructionBase → ConstructionBaseStaticArraysExt 15096.9 ms ✓ JSON3 3884.2 ms ✓ JSON 924.7 ms ✓ InlineStrings → ParsersExt 1358.1 ms ✓ XML2_jll 942.7 ms ✓ CodecBzip2 5939.7 ms ✓ SpecialFunctions 1365.5 ms ✓ HiGHS_jll 2943.1 ms ✓ BenchmarkTools 7381.5 ms ✓ JSONFBCModels 2194.6 ms ✓ WeakRefStrings 1385.7 ms ✓ SBML_jll 1278.6 ms ✓ DiffRules 31325.1 ms ✓ CSV 18833.3 ms ✓ SBML 9626.9 ms ✓ ForwardDiff 4663.4 ms ✓ SBMLFBCModels 1575.5 ms ✓ ForwardDiff → ForwardDiffStaticArraysExt 1963.6 ms ✓ Unitful → ForwardDiffExt 79969.9 ms ✓ MathOptInterface 5984.8 ms ✓ MathOptIIS 50848.7 ms ✓ JuMP 135208.0 ms ✓ Clarabel 16031.9 ms ✓ Tulip 35235.9 ms ✓ HiGHS 17002.1 ms ✓ COBREXA 92 dependencies successfully precompiled in 695 seconds. 37 already precompiled. Precompilation completed after 722.25s ################################################################################ # Testing # Testing COBREXA Test Could not use exact versions of packages in manifest. Re-resolving dependencies Updating `/tmp/jl_RqGl2v/Project.toml` ⌅ [4c88cf16] + Aqua v0.7.4 [babc4406] + COBREXA v2.9.1 [336ed68f] + CSV v0.10.15 ⌅ [61c947e1] + Clarabel v0.6.0 [87dc4568] + HiGHS v1.20.1 [475c1105] + JSONFBCModels v1.0.1 [3e8f9d1a] + SBMLFBCModels v1.1.1 [6dd1b50a] + Tulip v0.9.8 Updating `/tmp/jl_RqGl2v/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 v0.3.19 [87dc4568] + HiGHS v1.20.1 [615f187c] + IfElse v0.1.1 [842dd82b] + InlineStrings v1.4.5 [82899510] + IteratorInterfaceExtensions v1.0.0 ⌅ [682c06a0] ↓ JSON v1.4.0 ⇒ v0.21.4 [475c1105] + JSONFBCModels v1.0.1 [ba0b0d4f] + Krylov v0.10.5 [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 v1.4.9 [66db9d55] + SnoopPrecompile v1.0.3 [90137ffa] + StaticArrays v1.9.16 [ec057cc2] - StructUtils v2.6.2 [3783bdb8] + TableTraits v1.0.1 [bd369af6] + Tables v1.12.1 [a759f4b9] + TimerOutputs v0.5.29 [6dd1b50a] + Tulip v0.9.8 [1986cc42] + Unitful v1.27.0 [ea10d353] + WeakRefStrings v1.4.2 [76eceee3] + WorkerUtilities v1.6.1 [8fd58aa0] + HiGHS_jll v1.12.0+0 [94ce4f54] + Libiconv_jll v1.18.0+0 [d00139f3] + METIS_jll v5.1.3+0 [656ef2d0] + OpenBLAS32_jll v0.3.30+0 [bb12108a] + SBML_jll v5.21.0+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_RqGl2v/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 v1.20.1 [475c1105] JSONFBCModels v1.0.1 [4076af6c] JuMP v1.29.4 [3e8f9d1a] SBMLFBCModels v1.1.1 [860ef19b] StableRNGs v1.0.4 [6dd1b50a] Tulip v0.9.8 [8ba89e20] Distributed v1.11.0 [f43a241f] Downloads v1.7.0 [37e2e46d] LinearAlgebra v1.12.0 [44cfe95a] Pkg v1.12.1 [9a3f8284] Random v1.11.0 [ea8e919c] SHA v0.7.0 [2f01184e] SparseArrays v1.12.0 [8dfed614] Test v1.11.0 Status `/tmp/jl_RqGl2v/Manifest.toml` [14f7f29c] AMD v0.5.3 [5a4f3dfa] AbstractFBCModels v1.3.0 ⌅ [4c88cf16] Aqua v0.7.4 [6e4b80f9] BenchmarkTools v1.6.3 [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 v1.3.1 [14197337] GenericLinearAlgebra v0.3.19 [87dc4568] HiGHS v1.20.1 [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 v1.29.4 [ba0b0d4f] Krylov v0.10.5 [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 v1.48.0 [d8a4904e] MutableArithmetics v1.6.7 [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 v1.5.1 [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 v1.4.9 [66db9d55] SnoopPrecompile v1.0.3 [276daf66] SpecialFunctions v2.6.1 [860ef19b] StableRNGs v1.0.4 [90137ffa] StaticArrays v1.9.16 [1e83bf80] StaticArraysCore v1.4.4 [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 v1.27.0 [ea10d353] WeakRefStrings v1.4.2 [76eceee3] WorkerUtilities v1.6.1 [6e34b625] Bzip2_jll v1.0.9+0 [8fd58aa0] HiGHS_jll v1.12.0+0 [94ce4f54] Libiconv_jll v1.18.0+0 [d00139f3] METIS_jll v5.1.3+0 [656ef2d0] OpenBLAS32_jll v0.3.30+0 [efe28fd5] OpenSpecFun_jll v0.5.6+0 [bb12108a] SBML_jll v5.21.0+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 v1.12.0 [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 [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 v1.12.0 [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 v3.5.4+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. Testing Running tests... [ Info: misc.jl done in 63.01s 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: RequestError: Operation too slow. Less than 1 bytes/sec transferred the last 20 seconds while requesting http://bigg.ucsd.edu/static/models/e_coli_core.xml Stacktrace: [1] (::Downloads.var"#26#27"{IOStream, Base.DevNull, Nothing, Vector{Pair{String, String}}, Float64, Nothing, Bool, Nothing, Bool, Nothing, String, Bool, Bool})(easy::Downloads.Curl.Easy) @ Downloads /opt/julia/share/julia/stdlib/v1.12/Downloads/src/Downloads.jl:479 [2] with_handle(f::Downloads.var"#26#27"{IOStream, Base.DevNull, Nothing, Vector{Pair{String, String}}, Float64, Nothing, Bool, Nothing, Bool, Nothing, String, Bool, Bool}, handle::Downloads.Curl.Easy) @ Downloads.Curl /opt/julia/share/julia/stdlib/v1.12/Downloads/src/Curl/Curl.jl:105 [3] #24 @ /opt/julia/share/julia/stdlib/v1.12/Downloads/src/Downloads.jl:390 [inlined] [4] arg_write(f::Downloads.var"#24#25"{Base.DevNull, Nothing, Vector{Pair{String, String}}, Float64, Nothing, Bool, Nothing, Bool, Nothing, String, Bool, Bool}, arg::IOStream) @ ArgTools /opt/julia/share/julia/stdlib/v1.12/ArgTools/src/ArgTools.jl:134 [5] #22 @ /opt/julia/share/julia/stdlib/v1.12/Downloads/src/Downloads.jl:389 [inlined] [6] arg_read @ /opt/julia/share/julia/stdlib/v1.12/ArgTools/src/ArgTools.jl:76 [inlined] [7] request(url::String; input::Nothing, output::IOStream, method::Nothing, headers::Vector{Pair{String, String}}, timeout::Float64, progress::Nothing, verbose::Bool, debug::Nothing, throw::Bool, downloader::Nothing, interrupt::Nothing) @ Downloads /opt/julia/share/julia/stdlib/v1.12/Downloads/src/Downloads.jl:388 [8] request @ /opt/julia/share/julia/stdlib/v1.12/Downloads/src/Downloads.jl:355 [inlined] [9] (::Downloads.var"#7#8"{Nothing, Vector{Pair{String, String}}, Float64, Nothing, Bool, Nothing, Nothing, String})(output::IOStream) @ Downloads /opt/julia/share/julia/stdlib/v1.12/Downloads/src/Downloads.jl:273 [10] open(f::Downloads.var"#7#8"{Nothing, Vector{Pair{String, String}}, Float64, Nothing, Bool, Nothing, Nothing, String}, args::String; kwargs::@Kwargs{write::Bool, lock::Bool}) @ Base ./io.jl:410 [11] open_nolock @ /opt/julia/share/julia/stdlib/v1.12/ArgTools/src/ArgTools.jl:35 [inlined] [12] arg_write(f::Function, arg::String) @ ArgTools /opt/julia/share/julia/stdlib/v1.12/ArgTools/src/ArgTools.jl:103 [13] #download#5 @ /opt/julia/share/julia/stdlib/v1.12/Downloads/src/Downloads.jl:272 [inlined] [14] download @ /opt/julia/share/julia/stdlib/v1.12/Downloads/src/Downloads.jl:252 [inlined] [15] download_data_file(url::String, path::String, hash::String) @ AbstractFBCModels ~/.julia/packages/AbstractFBCModels/bQECn/src/utils.jl:128 [16] download_model(::String, ::Vararg{String}; kwargs::@Kwargs{}) @ COBREXA ~/.julia/packages/COBREXA/9nHZI/src/io.jl:119 [17] top-level scope @ ~/.julia/packages/COBREXA/9nHZI/docs/src/examples/01-loading-and-saving.jl:36 [18] include(mapexpr::Function, mod::Module, _path::String) @ Base ./Base.jl:307 [19] IncludeInto @ ./Base.jl:308 [inlined] [20] macro expansion @ ./timing.jl:461 [inlined] [21] run_test_file @ ~/.julia/packages/COBREXA/9nHZI/test/runtests.jl:34 [inlined] [22] macro expansion @ ~/.julia/packages/COBREXA/9nHZI/test/runtests.jl:41 [inlined] [23] macro expansion @ /opt/julia/share/julia/stdlib/v1.12/Test/src/Test.jl:1776 [inlined] [24] run_doc_examples() @ Main ~/.julia/packages/COBREXA/9nHZI/test/runtests.jl:41 [25] top-level scope @ ~/.julia/packages/COBREXA/9nHZI/test/runtests.jl:59 [26] macro expansion @ /opt/julia/share/julia/stdlib/v1.12/Test/src/Test.jl:1776 [inlined] [27] macro expansion @ ~/.julia/packages/COBREXA/9nHZI/test/runtests.jl:62 [inlined] [28] include(mapexpr::Function, mod::Module, _path::String) @ Base ./Base.jl:307 [29] top-level scope @ none:6 [30] eval(m::Module, e::Any) @ Core ./boot.jl:489 [31] exec_options(opts::Base.JLOptions) @ Base ./client.jl:283 [32] _start() @ Base ./client.jl:550 in expression starting at /home/pkgeval/.julia/packages/COBREXA/9nHZI/docs/src/examples/01-loading-and-saving.jl:36 [ Info: using cached `e_coli_core.json' [ Info: ../docs/src/examples/02a-flux-balance-analysis.jl done in 16.52s [ 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 1.47 Solver exited with status Trm_TimeLimit [ Info: ../docs/src/examples/02b-optimizer-parameters.jl done in 92.11s [ Info: using cached `e_coli_core.json' [ Info: ../docs/src/examples/02c-model-modifications.jl done in 15.2s [ Info: using cached `e_coli_core.json' nothing[ Info: ../docs/src/examples/02d-constraint-modifications.jl done in 0.72s [ Info: using cached `e_coli_core.json' [ Info: ../docs/src/examples/03a-flux-variability-analysis.jl done in 94.0s [ Info: using cached `e_coli_core.json' [ Info: ../docs/src/examples/03b-parsimonious-flux-balance.jl done in 114.59s [ Info: using cached `e_coli_core.json' [ Info: ../docs/src/examples/03c-envelopes.jl done in 17.17s [ Info: using cached `e_coli_core.json' [ Info: ../docs/src/examples/03d-unidirectional.jl done in 8.32s [ Info: using cached `e_coli_core.json' [ Info: ../docs/src/examples/03e-min-exchange.jl done in 12.33s [ Info: using cached `e_coli_core.json' [ Info: ../docs/src/examples/04-community-models.jl done in 95.44s [ Info: using cached `e_coli_core.json' [ Info: ../docs/src/examples/04a-composition-models.jl done in 9.75s [ Info: using cached `e_coli_core.json' [ Info: ../docs/src/examples/05a-minimization-of-metabolic-adjustment.jl done in 4.99s [ Info: using cached `e_coli_core.json' [ Info: ../docs/src/examples/05b-enzyme-constrained-models.jl done in 21.02s [ Info: using cached `e_coli_core.json' [ Info: ../docs/src/examples/05c-mmdf.jl done in 8.66s [ Info: using cached `e_coli_core.json' [ Info: ../docs/src/examples/05d-loopless-models.jl done in 8.6s [ Info: using cached `e_coli_core.json' [ Info: ../docs/src/examples/05e-knockouts.jl done in 30.23s [ Info: using cached `e_coli_core.json' [ Info: ../docs/src/examples/05f-cyclefree.jl done in 43.06s [ Info: using cached `e_coli_core.json' nothing [ Info: ../docs/src/examples/05g-gapfilling.jl done in 8.51s [ Info: using cached `e_coli_core.json' nothing [ Info: ../docs/src/examples/05h-medium.jl done in 4.13s [ Info: using cached `e_coli_core.json' [ Info: ../docs/src/examples/06a-sampling.jl done in 8.76s [ Info: using cached `e_coli_core.json' [ Info: ../docs/src/examples/06b-screening.jl done in 41.47s docs/07a-srba.jl: Error During Test at /home/pkgeval/.julia/packages/COBREXA/9nHZI/test/runtests.jl:40 Got exception outside of a @test LoadError: RequestError: Operation too slow. Less than 1 bytes/sec transferred the last 20 seconds while requesting http://bigg.ucsd.edu/static/models/iML1515.json Stacktrace: [1] (::Downloads.var"#26#27"{IOStream, Base.DevNull, Nothing, Vector{Pair{String, String}}, Float64, Nothing, Bool, Nothing, Bool, Nothing, String, Bool, Bool})(easy::Downloads.Curl.Easy) @ Downloads /opt/julia/share/julia/stdlib/v1.12/Downloads/src/Downloads.jl:479 [2] with_handle(f::Downloads.var"#26#27"{IOStream, Base.DevNull, Nothing, Vector{Pair{String, String}}, Float64, Nothing, Bool, Nothing, Bool, Nothing, String, Bool, Bool}, handle::Downloads.Curl.Easy) @ Downloads.Curl /opt/julia/share/julia/stdlib/v1.12/Downloads/src/Curl/Curl.jl:105 [3] #24 @ /opt/julia/share/julia/stdlib/v1.12/Downloads/src/Downloads.jl:390 [inlined] [4] arg_write(f::Downloads.var"#24#25"{Base.DevNull, Nothing, Vector{Pair{String, String}}, Float64, Nothing, Bool, Nothing, Bool, Nothing, String, Bool, Bool}, arg::IOStream) @ ArgTools /opt/julia/share/julia/stdlib/v1.12/ArgTools/src/ArgTools.jl:134 [5] #22 @ /opt/julia/share/julia/stdlib/v1.12/Downloads/src/Downloads.jl:389 [inlined] [6] arg_read @ /opt/julia/share/julia/stdlib/v1.12/ArgTools/src/ArgTools.jl:76 [inlined] [7] request(url::String; input::Nothing, output::IOStream, method::Nothing, headers::Vector{Pair{String, String}}, timeout::Float64, progress::Nothing, verbose::Bool, debug::Nothing, throw::Bool, downloader::Nothing, interrupt::Nothing) @ Downloads /opt/julia/share/julia/stdlib/v1.12/Downloads/src/Downloads.jl:388 [8] request @ /opt/julia/share/julia/stdlib/v1.12/Downloads/src/Downloads.jl:355 [inlined] [9] (::Downloads.var"#7#8"{Nothing, Vector{Pair{String, String}}, Float64, Nothing, Bool, Nothing, Nothing, String})(output::IOStream) @ Downloads /opt/julia/share/julia/stdlib/v1.12/Downloads/src/Downloads.jl:273 [10] open(f::Downloads.var"#7#8"{Nothing, Vector{Pair{String, String}}, Float64, Nothing, Bool, Nothing, Nothing, String}, args::String; kwargs::@Kwargs{write::Bool, lock::Bool}) @ Base ./io.jl:410 [11] open_nolock @ /opt/julia/share/julia/stdlib/v1.12/ArgTools/src/ArgTools.jl:35 [inlined] [12] arg_write(f::Function, arg::String) @ ArgTools /opt/julia/share/julia/stdlib/v1.12/ArgTools/src/ArgTools.jl:103 [13] #download#5 @ /opt/julia/share/julia/stdlib/v1.12/Downloads/src/Downloads.jl:272 [inlined] [14] download @ /opt/julia/share/julia/stdlib/v1.12/Downloads/src/Downloads.jl:252 [inlined] [15] download_data_file(url::String, path::String, hash::String) @ AbstractFBCModels ~/.julia/packages/AbstractFBCModels/bQECn/src/utils.jl:128 [16] download_model(::String, ::Vararg{String}; kwargs::@Kwargs{}) @ COBREXA ~/.julia/packages/COBREXA/9nHZI/src/io.jl:119 [17] top-level scope @ ~/.julia/packages/COBREXA/9nHZI/docs/src/examples/07a-srba.jl:34 [18] include(mapexpr::Function, mod::Module, _path::String) @ Base ./Base.jl:307 [19] IncludeInto @ ./Base.jl:308 [inlined] [20] macro expansion @ ./timing.jl:461 [inlined] [21] run_test_file @ ~/.julia/packages/COBREXA/9nHZI/test/runtests.jl:34 [inlined] [22] macro expansion @ ~/.julia/packages/COBREXA/9nHZI/test/runtests.jl:41 [inlined] [23] macro expansion @ /opt/julia/share/julia/stdlib/v1.12/Test/src/Test.jl:1776 [inlined] [24] run_doc_examples() @ Main ~/.julia/packages/COBREXA/9nHZI/test/runtests.jl:41 [25] top-level scope @ ~/.julia/packages/COBREXA/9nHZI/test/runtests.jl:59 [26] macro expansion @ /opt/julia/share/julia/stdlib/v1.12/Test/src/Test.jl:1776 [inlined] [27] macro expansion @ ~/.julia/packages/COBREXA/9nHZI/test/runtests.jl:62 [inlined] [28] include(mapexpr::Function, mod::Module, _path::String) @ Base ./Base.jl:307 [29] top-level scope @ none:6 [30] eval(m::Module, e::Any) @ Core ./boot.jl:489 [31] exec_options(opts::Base.JLOptions) @ Base ./client.jl:283 [32] _start() @ Base ./client.jl:550 in expression starting at /home/pkgeval/.julia/packages/COBREXA/9nHZI/docs/src/examples/07a-srba.jl:34 [ Info: ../docs/src/examples/07b-community-ecfba.jl done in 89.04s ┌ 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 14.15s Test Summary: | Pass Error Total Time COBREXA test suite | 112 2 114 14m39.0s Miscellaneous tests | 39 39 1m03.3s docs/01-loading-and-saving.jl | 1 1 33.9s docs/02a-flux-balance-analysis.jl | 1 1 16.5s docs/02b-optimizer-parameters.jl | 2 2 1m32.1s docs/02c-model-modifications.jl | 4 4 15.2s docs/02d-constraint-modifications.jl | 2 2 0.7s docs/03a-flux-variability-analysis.jl | 2 2 1m34.0s docs/03b-parsimonious-flux-balance.jl | 6 6 1m54.6s docs/03c-envelopes.jl | 1 1 17.2s docs/03d-unidirectional.jl | 6 6 8.3s docs/03e-min-exchange.jl | 1 1 12.3s docs/04-community-models.jl | 3 3 1m35.4s docs/04a-composition-models.jl | 7 7 9.7s docs/05a-minimization-of-metabolic-adjustment.jl | 7 7 5.0s docs/05b-enzyme-constrained-models.jl | 7 7 21.0s docs/05c-mmdf.jl | 5 5 8.7s docs/05d-loopless-models.jl | 1 1 8.6s docs/05e-knockouts.jl | 5 5 30.2s docs/05f-cyclefree.jl | 0 43.1s docs/05g-gapfilling.jl | 2 2 8.5s docs/05h-medium.jl | 3 3 4.1s docs/06a-sampling.jl | 1 1 8.8s docs/06b-screening.jl | 0 41.5s docs/07a-srba.jl | 1 1 20.1s docs/07b-community-ecfba.jl | 1 1 1m31.7s Automated QUality Assurance | 6 6 13.9s RNG of the outermost testset: Random.Xoshiro(0x6625458d24d71ea9, 0x7c6ad89fb5d670a8, 0x3a28b889f1b0dc31, 0x618610fdd8ab6d5a, 0xa8dbe10eeb7ebb0c) ERROR: LoadError: Some tests did not pass: 112 passed, 0 failed, 2 errored, 0 broken. in expression starting at /home/pkgeval/.julia/packages/COBREXA/9nHZI/test/runtests.jl:58 Testing failed after 924.44s ERROR: LoadError: Package COBREXA errored during testing Stacktrace: [1] pkgerror(msg::String) @ Pkg.Types /opt/julia/share/julia/stdlib/v1.12/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/v1.12/Pkg/src/Operations.jl:2535 [3] test @ /opt/julia/share/julia/stdlib/v1.12/Pkg/src/Operations.jl:2384 [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/v1.12/Pkg/src/API.jl:538 [5] test(pkgs::Vector{PackageSpec}; io::IOContext{IO}, kwargs::@Kwargs{julia_args::Cmd}) @ Pkg.API /opt/julia/share/julia/stdlib/v1.12/Pkg/src/API.jl:169 [6] test(pkgs::Vector{String}; kwargs::@Kwargs{julia_args::Cmd}) @ Pkg.API /opt/julia/share/julia/stdlib/v1.12/Pkg/src/API.jl:157 [7] test @ /opt/julia/share/julia/stdlib/v1.12/Pkg/src/API.jl:157 [inlined] [8] #test#81 @ /opt/julia/share/julia/stdlib/v1.12/Pkg/src/API.jl:156 [inlined] [9] top-level scope @ /PkgEval.jl/scripts/evaluate.jl:223 [10] include(mod::Module, _path::String) @ Base ./Base.jl:306 [11] exec_options(opts::Base.JLOptions) @ Base ./client.jl:317 [12] _start() @ Base ./client.jl:550 in expression starting at /PkgEval.jl/scripts/evaluate.jl:214 PkgEval failed after 1753.96s: package tests unexpectedly errored