Package evaluation of KEGGModuleParser on Julia 1.11.4 (a71dd056e0*) started at 2025-04-08T10:28:59.815 ################################################################################ # Set-up # Installing PkgEval dependencies (TestEnv)... Set-up completed after 6.36s ################################################################################ # Installation # Installing KEGGModuleParser... Resolving package versions... Updating `~/.julia/environments/v1.11/Project.toml` [8ec094ee] + KEGGModuleParser v0.1.0 Updating `~/.julia/environments/v1.11/Manifest.toml` [d1d4a3ce] + BitFlags v0.1.9 [944b1d66] + CodecZlib v0.7.8 [f0e56b4a] + ConcurrentUtilities v2.5.0 [460bff9d] + ExceptionUnwrapping v0.1.11 [cd3eb016] + HTTP v1.10.15 [692b3bcd] + JLLWrappers v1.7.0 [8ec094ee] + KEGGModuleParser v0.1.0 [e6f89c97] + LoggingExtras v1.1.0 [739be429] + MbedTLS v1.1.9 [4d8831e6] + OpenSSL v1.4.3 ⌅ [aea7be01] + PrecompileTools v1.2.1 [21216c6a] + Preferences v1.4.3 [777ac1f9] + SimpleBufferStream v1.2.0 [3bb67fe8] + TranscodingStreams v0.11.3 [5c2747f8] + URIs v1.5.2 [458c3c95] + OpenSSL_jll v3.0.16+0 [56f22d72] + Artifacts v1.11.0 [2a0f44e3] + Base64 v1.11.0 [ade2ca70] + Dates v1.11.0 [b77e0a4c] + InteractiveUtils v1.11.0 [8f399da3] + Libdl v1.11.0 [56ddb016] + Logging v1.11.0 [d6f4376e] + Markdown v1.11.0 [ca575930] + NetworkOptions v1.2.0 [de0858da] + Printf v1.11.0 [9a3f8284] + Random v1.11.0 [ea8e919c] + SHA v0.7.0 [9e88b42a] + Serialization v1.11.0 [6462fe0b] + Sockets v1.11.0 [fa267f1f] + TOML v1.0.3 [8dfed614] + Test v1.11.0 [cf7118a7] + UUIDs v1.11.0 [4ec0a83e] + Unicode v1.11.0 [c8ffd9c3] + MbedTLS_jll v2.28.6+0 [14a3606d] + MozillaCACerts_jll v2023.12.12 [83775a58] + Zlib_jll v1.2.13+1 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 To see why use `status --outdated -m` Installation completed after 1.63s ################################################################################ # Precompilation # Precompiling PkgEval dependencies... Precompiling package dependencies... Precompilation completed after 10.96s ################################################################################ # Testing # Testing KEGGModuleParser Status `/tmp/jl_xe3zee/Project.toml` [cd3eb016] HTTP v1.10.15 [8ec094ee] KEGGModuleParser v0.1.0 [8dfed614] Test v1.11.0 Status `/tmp/jl_xe3zee/Manifest.toml` [d1d4a3ce] BitFlags v0.1.9 [944b1d66] CodecZlib v0.7.8 [f0e56b4a] ConcurrentUtilities v2.5.0 [460bff9d] ExceptionUnwrapping v0.1.11 [cd3eb016] HTTP v1.10.15 [692b3bcd] JLLWrappers v1.7.0 [8ec094ee] KEGGModuleParser v0.1.0 [e6f89c97] LoggingExtras v1.1.0 [739be429] MbedTLS v1.1.9 [4d8831e6] OpenSSL v1.4.3 ⌅ [aea7be01] PrecompileTools v1.2.1 [21216c6a] Preferences v1.4.3 [777ac1f9] SimpleBufferStream v1.2.0 [3bb67fe8] TranscodingStreams v0.11.3 [5c2747f8] URIs v1.5.2 [458c3c95] OpenSSL_jll v3.0.16+0 [56f22d72] Artifacts v1.11.0 [2a0f44e3] Base64 v1.11.0 [ade2ca70] Dates v1.11.0 [b77e0a4c] InteractiveUtils v1.11.0 [8f399da3] Libdl v1.11.0 [56ddb016] Logging v1.11.0 [d6f4376e] Markdown v1.11.0 [ca575930] NetworkOptions v1.2.0 [de0858da] Printf v1.11.0 [9a3f8284] Random v1.11.0 [ea8e919c] SHA v0.7.0 [9e88b42a] Serialization v1.11.0 [6462fe0b] Sockets v1.11.0 [fa267f1f] TOML v1.0.3 [8dfed614] Test v1.11.0 [cf7118a7] UUIDs v1.11.0 [4ec0a83e] Unicode v1.11.0 [c8ffd9c3] MbedTLS_jll v2.28.6+0 [14a3606d] MozillaCACerts_jll v2023.12.12 [83775a58] Zlib_jll v1.2.13+1 Info Packages marked with ⌅ have new versions available but compatibility constraints restrict them from upgrading. Testing Running tests... Methionine degradation: Error During Test at /home/pkgeval/.julia/packages/KEGGModuleParser/BFxrY/test/parse.jl:27 Test threw exception Expression: mod.Entry == Dict("M00035" => "Pathway Module") type KEGGModule has no field Entry Stacktrace: [1] getproperty(x::KEGGModuleParser.KEGGModule, f::Symbol) @ Base ./Base.jl:49 [2] macro expansion @ /opt/julia/share/julia/stdlib/v1.11/Test/src/Test.jl:676 [inlined] [3] macro expansion @ ~/.julia/packages/KEGGModuleParser/BFxrY/test/parse.jl:27 [inlined] [4] macro expansion @ /opt/julia/share/julia/stdlib/v1.11/Test/src/Test.jl:1704 [inlined] [5] top-level scope @ ~/.julia/packages/KEGGModuleParser/BFxrY/test/parse.jl:24 Methionine degradation: Error During Test at /home/pkgeval/.julia/packages/KEGGModuleParser/BFxrY/test/parse.jl:28 Test threw exception Expression: mod.Name == "Methionine degradation" type KEGGModule has no field Name Stacktrace: [1] getproperty(x::KEGGModuleParser.KEGGModule, f::Symbol) @ Base ./Base.jl:49 [2] macro expansion @ /opt/julia/share/julia/stdlib/v1.11/Test/src/Test.jl:676 [inlined] [3] macro expansion @ ~/.julia/packages/KEGGModuleParser/BFxrY/test/parse.jl:28 [inlined] [4] macro expansion @ /opt/julia/share/julia/stdlib/v1.11/Test/src/Test.jl:1704 [inlined] [5] top-level scope @ ~/.julia/packages/KEGGModuleParser/BFxrY/test/parse.jl:24 Methionine degradation: Error During Test at /home/pkgeval/.julia/packages/KEGGModuleParser/BFxrY/test/parse.jl:29 Test threw exception Expression: mod.Definition == ["K00789", "(K00558,K17398,K17399)", "K01251", "(K01697,K10150)"] type KEGGModule has no field Definition Stacktrace: [1] getproperty(x::KEGGModuleParser.KEGGModule, f::Symbol) @ Base ./Base.jl:49 [2] macro expansion @ /opt/julia/share/julia/stdlib/v1.11/Test/src/Test.jl:676 [inlined] [3] macro expansion @ ~/.julia/packages/KEGGModuleParser/BFxrY/test/parse.jl:29 [inlined] [4] macro expansion @ /opt/julia/share/julia/stdlib/v1.11/Test/src/Test.jl:1704 [inlined] [5] top-level scope @ ~/.julia/packages/KEGGModuleParser/BFxrY/test/parse.jl:24 Methionine degradation: Error During Test at /home/pkgeval/.julia/packages/KEGGModuleParser/BFxrY/test/parse.jl:30 Test threw exception Expression: mod.Orthology == Dict("K00558,K17398,K17399" => ["[EC:2.1.1.37]", "[RN:R04858]", " DNA (cytosine-5-)-methyltransferase"], "K01697,K10150" => ["[EC:4.2.1.22]", "[RN:R01290]", " cystathionine beta-synthase"], "K00789" => ["[EC:2.5.1.6]", "[RN:R00177]", " S-adenosylmethionine synthetase"], "K01251" => ["[EC:3.13.2.1]", "[RN:R00192]", " adenosylhomocysteinase"]) type KEGGModule has no field Orthology Stacktrace: [1] getproperty(x::KEGGModuleParser.KEGGModule, f::Symbol) @ Base ./Base.jl:49 [2] macro expansion @ /opt/julia/share/julia/stdlib/v1.11/Test/src/Test.jl:676 [inlined] [3] macro expansion @ ~/.julia/packages/KEGGModuleParser/BFxrY/test/parse.jl:30 [inlined] [4] macro expansion @ /opt/julia/share/julia/stdlib/v1.11/Test/src/Test.jl:1704 [inlined] [5] top-level scope @ ~/.julia/packages/KEGGModuleParser/BFxrY/test/parse.jl:24 Methionine degradation: Error During Test at /home/pkgeval/.julia/packages/KEGGModuleParser/BFxrY/test/parse.jl:35 Test threw exception Expression: mod.Class == ["Pathway modules", "Amino acid metabolism", "Cysteine and methionine metabolism"] type KEGGModule has no field Class Stacktrace: [1] getproperty(x::KEGGModuleParser.KEGGModule, f::Symbol) @ Base ./Base.jl:49 [2] macro expansion @ /opt/julia/share/julia/stdlib/v1.11/Test/src/Test.jl:676 [inlined] [3] macro expansion @ ~/.julia/packages/KEGGModuleParser/BFxrY/test/parse.jl:35 [inlined] [4] macro expansion @ /opt/julia/share/julia/stdlib/v1.11/Test/src/Test.jl:1704 [inlined] [5] top-level scope @ ~/.julia/packages/KEGGModuleParser/BFxrY/test/parse.jl:24 Methionine degradation: Error During Test at /home/pkgeval/.julia/packages/KEGGModuleParser/BFxrY/test/parse.jl:38 Test threw exception Expression: mod.Pathway == Dict("map01100" => "Metabolic pathways", "map00270" => "Cysteine and methionine metabolism") type KEGGModule has no field Pathway Stacktrace: [1] getproperty(x::KEGGModuleParser.KEGGModule, f::Symbol) @ Base ./Base.jl:49 [2] macro expansion @ /opt/julia/share/julia/stdlib/v1.11/Test/src/Test.jl:676 [inlined] [3] macro expansion @ ~/.julia/packages/KEGGModuleParser/BFxrY/test/parse.jl:38 [inlined] [4] macro expansion @ /opt/julia/share/julia/stdlib/v1.11/Test/src/Test.jl:1704 [inlined] [5] top-level scope @ ~/.julia/packages/KEGGModuleParser/BFxrY/test/parse.jl:24 Methionine degradation: Error During Test at /home/pkgeval/.julia/packages/KEGGModuleParser/BFxrY/test/parse.jl:41 Test threw exception Expression: mod.Reaction == Dict("R00177" => "C00073 -> C00019", "R00192" => "C00021 -> C00155", "R01290" => "C00065 + C00155 -> C02291", "R04858" => "C00019 -> C00021") type KEGGModule has no field Reaction Stacktrace: [1] getproperty(x::KEGGModuleParser.KEGGModule, f::Symbol) @ Base ./Base.jl:49 [2] macro expansion @ /opt/julia/share/julia/stdlib/v1.11/Test/src/Test.jl:676 [inlined] [3] macro expansion @ ~/.julia/packages/KEGGModuleParser/BFxrY/test/parse.jl:41 [inlined] [4] macro expansion @ /opt/julia/share/julia/stdlib/v1.11/Test/src/Test.jl:1704 [inlined] [5] top-level scope @ ~/.julia/packages/KEGGModuleParser/BFxrY/test/parse.jl:24 Methionine degradation: Error During Test at /home/pkgeval/.julia/packages/KEGGModuleParser/BFxrY/test/parse.jl:46 Test threw exception Expression: mod.Compound == Dict("C00073" => "L-Methionine", "C00021" => "S-Adenosyl-L-homocysteine", "C00019" => "S-Adenosyl-L-methionine", "C00155" => "L-Homocysteine", "C00065" => "L-Serine", "C02291" => "L-Cystathionine") type KEGGModule has no field Compound Stacktrace: [1] getproperty(x::KEGGModuleParser.KEGGModule, f::Symbol) @ Base ./Base.jl:49 [2] macro expansion @ /opt/julia/share/julia/stdlib/v1.11/Test/src/Test.jl:676 [inlined] [3] macro expansion @ ~/.julia/packages/KEGGModuleParser/BFxrY/test/parse.jl:46 [inlined] [4] macro expansion @ /opt/julia/share/julia/stdlib/v1.11/Test/src/Test.jl:1704 [inlined] [5] top-level scope @ ~/.julia/packages/KEGGModuleParser/BFxrY/test/parse.jl:24 Methionine degradation: Error During Test at /home/pkgeval/.julia/packages/KEGGModuleParser/BFxrY/test/parse.jl:53 Test threw exception Expression: mod.EC == ["ec:2.5.1.6", "ec:2.1.1.37", "ec:3.13.2.1", "ec:4.2.1.22", "ec:2.5.1.47", "ec:2.5.1.65"] type KEGGModule has no field EC Stacktrace: [1] getproperty(x::KEGGModuleParser.KEGGModule, f::Symbol) @ Base ./Base.jl:49 [2] macro expansion @ /opt/julia/share/julia/stdlib/v1.11/Test/src/Test.jl:676 [inlined] [3] macro expansion @ ~/.julia/packages/KEGGModuleParser/BFxrY/test/parse.jl:53 [inlined] [4] macro expansion @ /opt/julia/share/julia/stdlib/v1.11/Test/src/Test.jl:1704 [inlined] [5] top-level scope @ ~/.julia/packages/KEGGModuleParser/BFxrY/test/parse.jl:24 Test Summary: | Error Total Time KEGGModuleParser.jl | 9 9 24.4s Methionine degradation | 9 9 24.3s ERROR: LoadError: Some tests did not pass: 0 passed, 0 failed, 9 errored, 0 broken. in expression starting at /home/pkgeval/.julia/packages/KEGGModuleParser/BFxrY/test/runtests.jl:4 Testing failed after 30.33s ERROR: LoadError: Package KEGGModuleParser errored during testing Stacktrace: [1] pkgerror(msg::String) @ Pkg.Types /opt/julia/share/julia/stdlib/v1.11/Pkg/src/Types.jl:68 [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/v1.11/Pkg/src/Operations.jl:2124 [3] test @ /opt/julia/share/julia/stdlib/v1.11/Pkg/src/Operations.jl:2007 [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::IOContext{IO}}) @ Pkg.API /opt/julia/share/julia/stdlib/v1.11/Pkg/src/API.jl:481 [5] test(pkgs::Vector{Pkg.Types.PackageSpec}; io::IOContext{IO}, kwargs::@Kwargs{julia_args::Cmd}) @ Pkg.API /opt/julia/share/julia/stdlib/v1.11/Pkg/src/API.jl:159 [6] test @ /opt/julia/share/julia/stdlib/v1.11/Pkg/src/API.jl:147 [inlined] [7] #test#74 @ /opt/julia/share/julia/stdlib/v1.11/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 77.56s: package tests unexpectedly errored