Package evaluation of FBCModelTests on Julia 1.10.9 (96dc2d8c45*) started at 2025-06-06T18:03:15.101 ################################################################################ # Set-up # Installing PkgEval dependencies (TestEnv)... Set-up completed after 4.91s ################################################################################ # Installation # Installing FBCModelTests... Resolving package versions... Installed HDF5 ─ v0.16.16 Updating `~/.julia/environments/v1.10/Project.toml` [1060cd45] + FBCModelTests v0.3.0 Updating `~/.julia/environments/v1.10/Manifest.toml` [6e4b80f9] + BenchmarkTools v1.6.0 [e1450e63] + BufferedStreams v1.2.2 ⌅ [babc4406] + COBREXA v1.5.1 [523fee87] + CodecBzip2 v0.8.5 [944b1d66] + CodecZlib v0.7.8 [bbf7d656] + CommonSubexpressions v0.3.1 [34da2185] + Compat v4.16.0 [864edb3b] + DataStructures v0.18.22 [8bb1440f] + DelimitedFiles v1.9.1 [163ba53b] + DiffResults v1.1.0 [b552c78f] + DiffRules v1.15.1 [f6a0035f] + DistributedData v0.2.0 [ffbed154] + DocStringExtensions v0.9.4 [1060cd45] + FBCModelTests v0.3.0 [f6369f11] + ForwardDiff v1.0.1 ⌅ [f67ccb44] + HDF5 v0.16.16 [615f187c] + IfElse v0.1.1 [92d709cd] + IrrationalConstants v0.2.4 [692b3bcd] + JLLWrappers v1.7.0 [682c06a0] + JSON v0.21.4 [0f8b85d8] + JSON3 v1.14.3 [4076af6c] + JuMP v1.26.0 [2ab3a3ac] + LogExpFunctions v0.3.29 [23992714] + MAT v0.10.7 [6ac74813] + MD5 v0.2.3 [3da0fdf6] + MPIPreferences v0.1.11 [1914dd2f] + MacroTools v0.5.16 [b8f27783] + MathOptInterface v1.40.2 [d8a4904e] + MutableArithmetics v1.6.4 [77ba4419] + NaNMath v1.1.3 [bac558e1] + OrderedCollections v1.8.1 [69de0a69] + Parsers v2.8.3 [7b2266bf] + PeriodicTable v1.2.1 ⌅ [3bbf5609] + PikaParser v0.5.2 ⌅ [aea7be01] + PrecompileTools v1.2.1 [21216c6a] + Preferences v1.4.3 [ae029012] + Requires v1.3.1 ⌅ [e5567a89] + SBML v1.4.4 [276daf66] + SpecialFunctions v2.5.1 [860ef19b] + StableRNGs v1.0.3 [1e83bf80] + StaticArraysCore v1.4.3 [856f2bd8] + StructTypes v1.11.0 [3bb67fe8] + TranscodingStreams v0.11.3 [1986cc42] + Unitful v1.22.1 [6e34b625] + Bzip2_jll v1.0.9+0 [0234f1f7] + HDF5_jll v1.14.6+0 [e33a78d0] + Hwloc_jll v2.12.1+0 [94ce4f54] + Libiconv_jll v1.18.0+0 [7cb0a576] + MPICH_jll v4.3.0+1 [f1f71cc9] + MPItrampoline_jll v5.5.3+0 [9237b28f] + MicrosoftMPI_jll v10.1.4+3 [fe0851c0] + OpenMPI_jll v5.0.7+2 [458c3c95] + OpenSSL_jll v3.5.0+0 [efe28fd5] + OpenSpecFun_jll v0.5.6+0 [bb12108a] + SBML_jll v5.20.1+0 ⌅ [02c8fc9c] + XML2_jll v2.13.6+1 [477f73a3] + libaec_jll v1.1.3+0 [0dad84c5] + ArgTools v1.1.1 [56f22d72] + Artifacts [2a0f44e3] + Base64 [ade2ca70] + Dates [8ba89e20] + Distributed [f43a241f] + Downloads v1.6.0 [7b1f6079] + FileWatching [b77e0a4c] + InteractiveUtils [4af54fe1] + LazyArtifacts [b27032c2] + LibCURL v0.6.4 [76f85450] + LibGit2 [8f399da3] + Libdl [37e2e46d] + LinearAlgebra [56ddb016] + Logging [d6f4376e] + Markdown [a63ad114] + Mmap [ca575930] + NetworkOptions v1.2.0 [44cfe95a] + Pkg v1.10.0 [de0858da] + Printf [9abbd945] + Profile [3fa0cd96] + REPL [9a3f8284] + Random [ea8e919c] + SHA v0.7.0 [9e88b42a] + Serialization [6462fe0b] + Sockets [2f01184e] + SparseArrays v1.10.0 [10745b16] + Statistics v1.10.0 [fa267f1f] + TOML v1.0.3 [a4e569a6] + Tar v1.10.0 [8dfed614] + Test [cf7118a7] + UUIDs [4ec0a83e] + Unicode [e66e0078] + CompilerSupportLibraries_jll v1.1.1+0 [deac9b47] + LibCURL_jll v8.4.0+0 [e37daf67] + LibGit2_jll v1.6.4+0 [29816b5a] + LibSSH2_jll v1.11.0+1 [c8ffd9c3] + MbedTLS_jll v2.28.2+1 [14a3606d] + MozillaCACerts_jll v2023.1.10 [4536629a] + OpenBLAS_jll v0.3.23+4 [05823500] + OpenLibm_jll v0.8.5+0 [bea87d4a] + SuiteSparse_jll v7.2.1+1 [83775a58] + Zlib_jll v1.2.13+1 [8e850b90] + libblastrampoline_jll v5.11.0+0 [8e850ede] + nghttp2_jll v1.52.0+1 [3f19e933] + p7zip_jll v17.4.0+2 Info Packages marked with ⌅ have new versions available but compatibility constraints restrict them from upgrading. To see why use `status --outdated -m` Building HDF5 → `~/.julia/scratchspaces/44cfe95a-1eb2-52ea-b672-e2afdf69b78f/114e20044677badbc631ee6fdc80a67920561a29/build.log` Installation completed after 20.38s ################################################################################ # Precompilation # Precompiling PkgEval dependencies... Precompiling package dependencies... Precompilation completed after 78.15s ################################################################################ # Testing # Testing FBCModelTests Status `/tmp/jl_K8QSS2/Project.toml` ⌅ [babc4406] COBREXA v1.5.1 [8bb1440f] DelimitedFiles v1.9.1 [ffbed154] DocStringExtensions v0.9.4 [1060cd45] FBCModelTests v0.3.0 [60bf3e95] GLPK v1.2.1 [682c06a0] JSON v0.21.4 [4076af6c] JuMP v1.26.0 [6ac74813] MD5 v0.2.3 [7b2266bf] PeriodicTable v1.2.1 ⌅ [e5567a89] SBML v1.4.4 [ade2ca70] Dates [8ba89e20] Distributed [f43a241f] Downloads v1.6.0 [b77e0a4c] InteractiveUtils [44cfe95a] Pkg v1.10.0 [ea8e919c] SHA v0.7.0 [2f01184e] SparseArrays v1.10.0 [10745b16] Statistics v1.10.0 [8dfed614] Test Status `/tmp/jl_K8QSS2/Manifest.toml` [6e4b80f9] BenchmarkTools v1.6.0 [e1450e63] BufferedStreams v1.2.2 ⌅ [babc4406] COBREXA v1.5.1 [523fee87] CodecBzip2 v0.8.5 [944b1d66] CodecZlib v0.7.8 [bbf7d656] CommonSubexpressions v0.3.1 [34da2185] Compat v4.16.0 [864edb3b] DataStructures v0.18.22 [8bb1440f] DelimitedFiles v1.9.1 [163ba53b] DiffResults v1.1.0 [b552c78f] DiffRules v1.15.1 [f6a0035f] DistributedData v0.2.0 [ffbed154] DocStringExtensions v0.9.4 [1060cd45] FBCModelTests v0.3.0 [f6369f11] ForwardDiff v1.0.1 [60bf3e95] GLPK v1.2.1 ⌅ [f67ccb44] HDF5 v0.16.16 [615f187c] IfElse v0.1.1 [92d709cd] IrrationalConstants v0.2.4 [692b3bcd] JLLWrappers v1.7.0 [682c06a0] JSON v0.21.4 [0f8b85d8] JSON3 v1.14.3 [4076af6c] JuMP v1.26.0 [2ab3a3ac] LogExpFunctions v0.3.29 [23992714] MAT v0.10.7 [6ac74813] MD5 v0.2.3 [3da0fdf6] MPIPreferences v0.1.11 [1914dd2f] MacroTools v0.5.16 [b8f27783] MathOptInterface v1.40.2 [d8a4904e] MutableArithmetics v1.6.4 [77ba4419] NaNMath v1.1.3 [bac558e1] OrderedCollections v1.8.1 [69de0a69] Parsers v2.8.3 [7b2266bf] PeriodicTable v1.2.1 ⌅ [3bbf5609] PikaParser v0.5.2 ⌅ [aea7be01] PrecompileTools v1.2.1 [21216c6a] Preferences v1.4.3 [ae029012] Requires v1.3.1 ⌅ [e5567a89] SBML v1.4.4 [276daf66] SpecialFunctions v2.5.1 [860ef19b] StableRNGs v1.0.3 [1e83bf80] StaticArraysCore v1.4.3 [856f2bd8] StructTypes v1.11.0 [3bb67fe8] TranscodingStreams v0.11.3 [1986cc42] Unitful v1.22.1 [6e34b625] Bzip2_jll v1.0.9+0 [e8aa6df9] GLPK_jll v5.0.1+1 [0234f1f7] HDF5_jll v1.14.6+0 [e33a78d0] Hwloc_jll v2.12.1+0 [94ce4f54] Libiconv_jll v1.18.0+0 [7cb0a576] MPICH_jll v4.3.0+1 [f1f71cc9] MPItrampoline_jll v5.5.3+0 [9237b28f] MicrosoftMPI_jll v10.1.4+3 [fe0851c0] OpenMPI_jll v5.0.7+2 [458c3c95] OpenSSL_jll v3.5.0+0 [efe28fd5] OpenSpecFun_jll v0.5.6+0 [bb12108a] SBML_jll v5.20.1+0 ⌅ [02c8fc9c] XML2_jll v2.13.6+1 [477f73a3] libaec_jll v1.1.3+0 [0dad84c5] ArgTools v1.1.1 [56f22d72] Artifacts [2a0f44e3] Base64 [ade2ca70] Dates [8ba89e20] Distributed [f43a241f] Downloads v1.6.0 [7b1f6079] FileWatching [b77e0a4c] InteractiveUtils [4af54fe1] LazyArtifacts [b27032c2] LibCURL v0.6.4 [76f85450] LibGit2 [8f399da3] Libdl [37e2e46d] LinearAlgebra [56ddb016] Logging [d6f4376e] Markdown [a63ad114] Mmap [ca575930] NetworkOptions v1.2.0 [44cfe95a] Pkg v1.10.0 [de0858da] Printf [9abbd945] Profile [3fa0cd96] REPL [9a3f8284] Random [ea8e919c] SHA v0.7.0 [9e88b42a] Serialization [6462fe0b] Sockets [2f01184e] SparseArrays v1.10.0 [10745b16] Statistics v1.10.0 [fa267f1f] TOML v1.0.3 [a4e569a6] Tar v1.10.0 [8dfed614] Test [cf7118a7] UUIDs [4ec0a83e] Unicode [e66e0078] CompilerSupportLibraries_jll v1.1.1+0 [781609d7] GMP_jll v6.2.1+6 [deac9b47] LibCURL_jll v8.4.0+0 [e37daf67] LibGit2_jll v1.6.4+0 [29816b5a] LibSSH2_jll v1.11.0+1 [c8ffd9c3] MbedTLS_jll v2.28.2+1 [14a3606d] MozillaCACerts_jll v2023.1.10 [4536629a] OpenBLAS_jll v0.3.23+4 [05823500] OpenLibm_jll v0.8.5+0 [bea87d4a] SuiteSparse_jll v7.2.1+1 [83775a58] Zlib_jll v1.2.13+1 [8e850b90] libblastrampoline_jll v5.11.0+0 [8e850ede] nghttp2_jll v1.52.0+1 [3f19e933] p7zip_jll v17.4.0+2 Info Packages marked with ⌅ have new versions available but compatibility constraints restrict them from upgrading. Testing Running tests... ERROR: LoadError: RequestError: Failed to connect to bigg.ucsd.edu port 80 after 30033 ms: Timeout was reached while requesting http://bigg.ucsd.edu/static/models/e_coli_core.json Stacktrace: [1] (::Downloads.var"#9#19"{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/v1.10/Downloads/src/Downloads.jl:452 [2] with_handle(f::Downloads.var"#9#19"{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/v1.10/Downloads/src/Curl/Curl.jl:105 [3] #8 @ /opt/julia/share/julia/stdlib/v1.10/Downloads/src/Downloads.jl:363 [inlined] [4] arg_write(f::Downloads.var"#8#18"{Base.DevNull, Nothing, Vector{Pair{String, String}}, Float64, Nothing, Bool, Nothing, Bool, Nothing, String, Bool, Bool}, arg::IOStream) @ ArgTools /opt/julia/share/julia/stdlib/v1.10/ArgTools/src/ArgTools.jl:134 [5] #7 @ /opt/julia/share/julia/stdlib/v1.10/Downloads/src/Downloads.jl:362 [inlined] [6] arg_read @ /opt/julia/share/julia/stdlib/v1.10/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/v1.10/Downloads/src/Downloads.jl:361 [8] request @ /opt/julia/share/julia/stdlib/v1.10/Downloads/src/Downloads.jl:328 [inlined] [9] #3 @ /opt/julia/share/julia/stdlib/v1.10/Downloads/src/Downloads.jl:259 [inlined] [10] open(f::Downloads.var"#3#4"{Nothing, Vector{Pair{String, String}}, Float64, Nothing, Bool, Nothing, Nothing, String}, args::String; kwargs::@Kwargs{write::Bool, lock::Bool}) @ Base ./io.jl:396 [11] open_nolock @ /opt/julia/share/julia/stdlib/v1.10/ArgTools/src/ArgTools.jl:35 [inlined] [12] arg_write(f::Function, arg::String) @ ArgTools /opt/julia/share/julia/stdlib/v1.10/ArgTools/src/ArgTools.jl:103 [13] #download#2 @ /opt/julia/share/julia/stdlib/v1.10/Downloads/src/Downloads.jl:258 [inlined] [14] download @ /opt/julia/share/julia/stdlib/v1.10/Downloads/src/Downloads.jl:247 [inlined] [15] #1 @ ~/.julia/packages/FBCModelTests/Qgfx1/test/data.jl:10 [inlined] [16] (::var"#1#3")(::Tuple{String, String, String}) @ Main ./none:0 [17] iterate @ ./generator.jl:47 [inlined] [18] _all(f::Base.var"#386#388", itr::Base.Generator{Vector{Tuple{String, String, String}}, var"#1#3"}, ::Colon) @ Base ./reduce.jl:1287 [19] all @ ./reduce.jl:1283 [inlined] [20] Dict(kv::Base.Generator{Vector{Tuple{String, String, String}}, var"#1#3"}) @ Base ./dict.jl:111 [21] top-level scope @ ~/.julia/packages/FBCModelTests/Qgfx1/test/data.jl:5 [22] include(fname::String) @ Base.MainInclude ./client.jl:494 [23] top-level scope @ ~/.julia/packages/FBCModelTests/Qgfx1/test/runtests.jl:12 [24] include(fname::String) @ Base.MainInclude ./client.jl:494 [25] top-level scope @ none:6 in expression starting at /home/pkgeval/.julia/packages/FBCModelTests/Qgfx1/test/data.jl:5 in expression starting at /home/pkgeval/.julia/packages/FBCModelTests/Qgfx1/test/runtests.jl:12 caused by: RequestError: Failed to connect to bigg.ucsd.edu port 80 after 1116 ms: Couldn't connect to server while requesting http://bigg.ucsd.edu/static/models/e_coli_core.json Stacktrace: [1] (::Downloads.var"#9#19"{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/v1.10/Downloads/src/Downloads.jl:452 [2] with_handle(f::Downloads.var"#9#19"{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/v1.10/Downloads/src/Curl/Curl.jl:105 [3] #8 @ /opt/julia/share/julia/stdlib/v1.10/Downloads/src/Downloads.jl:363 [inlined] [4] arg_write(f::Downloads.var"#8#18"{Base.DevNull, Nothing, Vector{Pair{String, String}}, Float64, Nothing, Bool, Nothing, Bool, Nothing, String, Bool, Bool}, arg::IOStream) @ ArgTools /opt/julia/share/julia/stdlib/v1.10/ArgTools/src/ArgTools.jl:134 [5] #7 @ /opt/julia/share/julia/stdlib/v1.10/Downloads/src/Downloads.jl:362 [inlined] [6] arg_read @ /opt/julia/share/julia/stdlib/v1.10/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/v1.10/Downloads/src/Downloads.jl:361 [8] request @ /opt/julia/share/julia/stdlib/v1.10/Downloads/src/Downloads.jl:328 [inlined] [9] #3 @ /opt/julia/share/julia/stdlib/v1.10/Downloads/src/Downloads.jl:259 [inlined] [10] open(f::Downloads.var"#3#4"{Nothing, Vector{Pair{String, String}}, Float64, Nothing, Bool, Nothing, Nothing, String}, args::String; kwargs::@Kwargs{write::Bool, lock::Bool}) @ Base ./io.jl:396 [11] open_nolock @ /opt/julia/share/julia/stdlib/v1.10/ArgTools/src/ArgTools.jl:35 [inlined] [12] arg_write(f::Function, arg::String) @ ArgTools /opt/julia/share/julia/stdlib/v1.10/ArgTools/src/ArgTools.jl:103 [13] #download#2 @ /opt/julia/share/julia/stdlib/v1.10/Downloads/src/Downloads.jl:258 [inlined] [14] download @ /opt/julia/share/julia/stdlib/v1.10/Downloads/src/Downloads.jl:247 [inlined] [15] #1 @ ~/.julia/packages/FBCModelTests/Qgfx1/test/data.jl:10 [inlined] [16] (::var"#1#3")(::Tuple{String, String, String}) @ Main ./none:0 [17] iterate @ ./generator.jl:47 [inlined] [18] Dict{String, String}(kv::Base.Generator{Vector{Tuple{String, String, String}}, var"#1#3"}) @ Base ./dict.jl:83 [19] dict_with_eltype @ ./abstractdict.jl:585 [inlined] [20] dict_with_eltype @ ./abstractdict.jl:592 [inlined] [21] Dict(kv::Base.Generator{Vector{Tuple{String, String, String}}, var"#1#3"}) @ Base ./dict.jl:109 [22] top-level scope @ ~/.julia/packages/FBCModelTests/Qgfx1/test/data.jl:5 [23] include(fname::String) @ Base.MainInclude ./client.jl:494 [24] top-level scope @ ~/.julia/packages/FBCModelTests/Qgfx1/test/runtests.jl:12 [25] include(fname::String) @ Base.MainInclude ./client.jl:494 [26] top-level scope @ none:6 Testing failed after 25.3s ERROR: LoadError: Package FBCModelTests errored during testing Stacktrace: [1] pkgerror(msg::String) @ Pkg.Types /opt/julia/share/julia/stdlib/v1.10/Pkg/src/Types.jl:70 [2] test(ctx::Pkg.Types.Context, pkgs::Vector{Pkg.Types.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/v1.10/Pkg/src/Operations.jl:2034 [3] test @ /opt/julia/share/julia/stdlib/v1.10/Pkg/src/Operations.jl:1915 [inlined] [4] test(ctx::Pkg.Types.Context, pkgs::Vector{Pkg.Types.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::Base.PipeEndpoint}) @ Pkg.API /opt/julia/share/julia/stdlib/v1.10/Pkg/src/API.jl:444 [5] test(pkgs::Vector{Pkg.Types.PackageSpec}; io::Base.PipeEndpoint, kwargs::@Kwargs{julia_args::Cmd}) @ Pkg.API /opt/julia/share/julia/stdlib/v1.10/Pkg/src/API.jl:159 [6] test @ /opt/julia/share/julia/stdlib/v1.10/Pkg/src/API.jl:147 [inlined] [7] #test#74 @ /opt/julia/share/julia/stdlib/v1.10/Pkg/src/API.jl:146 [inlined] [8] top-level scope @ /PkgEval.jl/scripts/evaluate.jl:219 in expression starting at /PkgEval.jl/scripts/evaluate.jl:210 PkgEval failed after 177.07s: package tests unexpectedly errored