Package evaluation to test MetabolomicsWorkbenchAPI on Julia 1.14.0-DEV.1262 (4060c45d70*) started at 2025-11-18T18:19:43.554 ################################################################################ # Set-up # Installing PkgEval dependencies (TestEnv)... Set-up completed after 8.31s ################################################################################ # Installation # Installing MetabolomicsWorkbenchAPI... Resolving package versions... Installed URIs ──────────────────────── v1.6.1 Installed CodecZlib ─────────────────── v0.7.8 Installed ConcurrentUtilities ───────── v2.5.0 Installed FilePathsBase ─────────────── v0.9.24 Installed InlineStrings ─────────────── v1.4.5 Installed DataStructures ────────────── v0.19.3 Installed ExceptionUnwrapping ───────── v0.1.11 Installed IteratorInterfaceExtensions ─ v1.0.0 Installed DataAPI ───────────────────── v1.16.0 Installed TranscodingStreams ────────── v0.11.3 Installed Compat ────────────────────── v4.18.1 Installed OrderedCollections ────────── v1.8.1 Installed Statistics ────────────────── v1.11.1 Installed InvertedIndices ───────────── v1.3.1 Installed DataValueInterfaces ───────── v1.0.0 Installed SentinelArrays ────────────── v1.4.8 Installed OpenSSL ───────────────────── v1.6.0 Installed LoggingExtras ─────────────── v1.2.0 Installed MbedTLS ───────────────────── v1.1.9 Installed PrecompileTools ───────────── v1.3.3 Installed StringManipulation ────────── v0.4.1 Installed JSON3 ─────────────────────── v1.14.3 Installed BitFlags ──────────────────── v0.1.9 Installed Parsers ───────────────────── v2.8.3 Installed MetabolomicsWorkbenchAPI ──── v0.2.0 Installed HTTP ──────────────────────── v1.10.19 Installed Tables ────────────────────── v1.12.1 Installed Reexport ──────────────────── v1.2.2 Installed PrettyTables ──────────────── v3.1.0 Installed SimpleBufferStream ────────── v1.2.0 Installed Missings ──────────────────── v1.2.0 Installed Preferences ───────────────── v1.5.0 Installed WeakRefStrings ────────────── v1.4.2 Installed PooledArrays ──────────────── v1.4.3 Installed DataFrames ────────────────── v1.8.1 Installed JLLWrappers ───────────────── v1.7.1 Installed TableTraits ───────────────── v1.0.1 Installed LaTeXStrings ──────────────── v1.4.0 Installed MbedTLS_jll ───────────────── v2.28.10+0 Installed Crayons ───────────────────── v4.1.1 Installed WorkerUtilities ───────────── v1.6.1 Installed StructTypes ───────────────── v1.11.0 Installed SortingAlgorithms ─────────── v1.2.2 Installed CSV ───────────────────────── v0.10.15 Installing 1 artifacts Installed artifact MbedTLS 2.2 MiB Updating `~/.julia/environments/v1.14/Project.toml` [19b29032] + MetabolomicsWorkbenchAPI v0.2.0 Updating `~/.julia/environments/v1.14/Manifest.toml` [d1d4a3ce] + BitFlags v0.1.9 [336ed68f] + CSV v0.10.15 [944b1d66] + CodecZlib v0.7.8 [34da2185] + Compat v4.18.1 [f0e56b4a] + ConcurrentUtilities v2.5.0 [a8cc5b0e] + Crayons v4.1.1 [9a962f9c] + DataAPI v1.16.0 [a93c6f00] + DataFrames v1.8.1 [864edb3b] + DataStructures v0.19.3 [e2d170a0] + DataValueInterfaces v1.0.0 [460bff9d] + ExceptionUnwrapping v0.1.11 [48062228] + FilePathsBase v0.9.24 [cd3eb016] + HTTP v1.10.19 [842dd82b] + InlineStrings v1.4.5 [41ab1584] + InvertedIndices v1.3.1 [82899510] + IteratorInterfaceExtensions v1.0.0 [692b3bcd] + JLLWrappers v1.7.1 [0f8b85d8] + JSON3 v1.14.3 [b964fa9f] + LaTeXStrings v1.4.0 [e6f89c97] + LoggingExtras v1.2.0 [739be429] + MbedTLS v1.1.9 [19b29032] + MetabolomicsWorkbenchAPI v0.2.0 [e1d29d7a] + Missings v1.2.0 [4d8831e6] + OpenSSL v1.6.0 [bac558e1] + OrderedCollections v1.8.1 [69de0a69] + Parsers v2.8.3 [2dfb63ee] + PooledArrays v1.4.3 [aea7be01] + PrecompileTools v1.3.3 [21216c6a] + Preferences v1.5.0 [08abe8d2] + PrettyTables v3.1.0 [189a3867] + Reexport v1.2.2 [91c51154] + SentinelArrays v1.4.8 [777ac1f9] + SimpleBufferStream v1.2.0 [a2af1166] + SortingAlgorithms v1.2.2 [10745b16] + Statistics v1.11.1 [892a3eda] + StringManipulation v0.4.1 [856f2bd8] + StructTypes v1.11.0 [3783bdb8] + TableTraits v1.0.1 [bd369af6] + Tables v1.12.1 [3bb67fe8] + TranscodingStreams v0.11.3 [5c2747f8] + URIs v1.6.1 [ea10d353] + WeakRefStrings v1.4.2 [76eceee3] + WorkerUtilities v1.6.1 [c8ffd9c3] + MbedTLS_jll v2.28.10+0 [56f22d72] + Artifacts v1.11.0 [2a0f44e3] + Base64 v1.11.0 [ade2ca70] + Dates v1.11.0 [7b1f6079] + FileWatching v1.11.0 [9fa8497b] + Future v1.11.0 [b77e0a4c] + InteractiveUtils v1.11.0 [ac6e5ff7] + JuliaSyntaxHighlighting v1.12.0 [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 [de0858da] + Printf v1.11.0 [3fa0cd96] + REPL v1.11.0 [9a3f8284] + Random v1.11.0 [ea8e919c] + SHA v1.0.0 [9e88b42a] + Serialization v1.11.0 [6462fe0b] + Sockets v1.11.0 [f489334b] + StyledStrings v1.11.0 [fa267f1f] + TOML v1.0.3 [8dfed614] + Test v1.11.0 [cf7118a7] + UUIDs v1.11.0 [4ec0a83e] + Unicode v1.11.0 [e66e0078] + CompilerSupportLibraries_jll v1.3.0+1 [14a3606d] + MozillaCACerts_jll v2025.11.4 [4536629a] + OpenBLAS_jll v0.3.29+0 [458c3c95] + OpenSSL_jll v3.5.4+0 [83775a58] + Zlib_jll v1.3.1+2 [8e850b90] + libblastrampoline_jll v5.15.0+0 Installation completed after 9.06s ################################################################################ # Precompilation # Precompiling PkgEval dependencies... Precompiling packages... WARNING: Imported binding Operations.project_rel_path was undeclared at import time during import to TestEnv. 5728.5 ms ✓ TestEnv 1 dependency successfully precompiled in 6 seconds. 27 already precompiled. 1 dependency had output during precompilation: ┌ TestEnv │ WARNING: Imported binding Operations.project_rel_path was undeclared at import time during import to TestEnv. └ ┌ Error: Failed to use TestEnv.jl; test dependencies will not be precompiled │ exception = │ UndefVarError: `project_rel_path` not defined in `TestEnv` │ Suggestion: this global was defined as `Pkg.Operations.project_rel_path` but not assigned a value. │ Stacktrace: │ [1] get_test_dir(ctx::Pkg.Types.Context, pkgspec::PackageSpec) │ @ TestEnv ~/.julia/packages/TestEnv/i9lgt/src/julia-1.11/common.jl:75 │ [2] test_dir_has_project_file │ @ ~/.julia/packages/TestEnv/i9lgt/src/julia-1.11/common.jl:52 [inlined] │ [3] maybe_gen_project_override! │ @ ~/.julia/packages/TestEnv/i9lgt/src/julia-1.11/common.jl:83 [inlined] │ [4] activate(pkg::String; allow_reresolve::Bool) │ @ TestEnv ~/.julia/packages/TestEnv/i9lgt/src/julia-1.11/activate_set.jl:12 │ [5] activate(pkg::String) │ @ TestEnv ~/.julia/packages/TestEnv/i9lgt/src/julia-1.11/activate_set.jl:9 │ [6] top-level scope │ @ /PkgEval.jl/scripts/precompile.jl:24 │ [7] include(mod::Module, _path::String) │ @ Base ./Base.jl:309 │ [8] exec_options(opts::Base.JLOptions) │ @ Base ./client.jl:344 │ [9] _start() │ @ Base ./client.jl:577 └ @ Main /PkgEval.jl/scripts/precompile.jl:26 Precompiling package dependencies... Precompiling packages... 1725.1 ms ✓ InlineStrings 705.5 ms ✓ Reexport 1103.9 ms ✓ Statistics 972.8 ms ✓ DataAPI 892.7 ms ✓ DataValueInterfaces 1165.3 ms ✓ URIs 1224.5 ms ✓ OrderedCollections 776.6 ms ✓ InvertedIndices 818.7 ms ✓ BitFlags 1772.2 ms ✓ ConcurrentUtilities 1441.1 ms ✓ WorkerUtilities 1397.9 ms ✓ TranscodingStreams 1033.9 ms ✓ SimpleBufferStream 1056.3 ms ✓ IteratorInterfaceExtensions 991.6 ms ✓ LaTeXStrings 1905.7 ms ✓ Crayons 2667.1 ms ✓ SentinelArrays 1541.0 ms ✓ StructTypes 1135.6 ms ✓ LoggingExtras 1160.5 ms ✓ Compat 1096.5 ms ✓ Preferences 1751.6 ms ✓ ExceptionUnwrapping 918.6 ms ✓ Missings 964.7 ms ✓ PooledArrays 3566.4 ms ✓ DataStructures 3859.8 ms ✓ OpenSSL 929.3 ms ✓ CodecZlib 711.7 ms ✓ TableTraits 820.7 ms ✓ Compat → CompatLinearAlgebraExt 1139.5 ms ✓ JLLWrappers 943.8 ms ✓ PrecompileTools 996.0 ms ✓ SortingAlgorithms 1687.4 ms ✓ Tables 2207.7 ms ✓ FilePathsBase 1325.9 ms ✓ MbedTLS_jll 3113.5 ms ✓ StringManipulation 15641.4 ms ✓ Parsers 1847.0 ms ✓ FilePathsBase → FilePathsBaseTestExt 733.9 ms ✓ FilePathsBase → FilePathsBaseMmapExt 1875.3 ms ✓ MbedTLS 38371.4 ms ✓ PrettyTables 14526.5 ms ✓ JSON3 1394.9 ms ✓ InlineStrings → ParsersExt 25517.8 ms ✓ HTTP 90297.6 ms ✓ DataFrames 2492.5 ms ✓ WeakRefStrings 29639.8 ms ✓ CSV 14012.5 ms ✓ MetabolomicsWorkbenchAPI 48 dependencies successfully precompiled in 288 seconds. 20 already precompiled. Precompilation completed after 302.17s ################################################################################ # Testing # Testing MetabolomicsWorkbenchAPI Status `/tmp/jl_977tJi/Project.toml` [19b29032] MetabolomicsWorkbenchAPI v0.2.0 [8dfed614] Test v1.11.0 Status `/tmp/jl_977tJi/Manifest.toml` [d1d4a3ce] BitFlags v0.1.9 [336ed68f] CSV v0.10.15 [944b1d66] CodecZlib v0.7.8 [34da2185] Compat v4.18.1 [f0e56b4a] ConcurrentUtilities v2.5.0 [a8cc5b0e] Crayons v4.1.1 [9a962f9c] DataAPI v1.16.0 [a93c6f00] DataFrames v1.8.1 [864edb3b] DataStructures v0.19.3 [e2d170a0] DataValueInterfaces v1.0.0 [460bff9d] ExceptionUnwrapping v0.1.11 [48062228] FilePathsBase v0.9.24 [cd3eb016] HTTP v1.10.19 [842dd82b] InlineStrings v1.4.5 [41ab1584] InvertedIndices v1.3.1 [82899510] IteratorInterfaceExtensions v1.0.0 [692b3bcd] JLLWrappers v1.7.1 [0f8b85d8] JSON3 v1.14.3 [b964fa9f] LaTeXStrings v1.4.0 [e6f89c97] LoggingExtras v1.2.0 [739be429] MbedTLS v1.1.9 [19b29032] MetabolomicsWorkbenchAPI v0.2.0 [e1d29d7a] Missings v1.2.0 [4d8831e6] OpenSSL v1.6.0 [bac558e1] OrderedCollections v1.8.1 [69de0a69] Parsers v2.8.3 [2dfb63ee] PooledArrays v1.4.3 [aea7be01] PrecompileTools v1.3.3 [21216c6a] Preferences v1.5.0 [08abe8d2] PrettyTables v3.1.0 [189a3867] Reexport v1.2.2 [91c51154] SentinelArrays v1.4.8 [777ac1f9] SimpleBufferStream v1.2.0 [a2af1166] SortingAlgorithms v1.2.2 [10745b16] Statistics v1.11.1 [892a3eda] StringManipulation v0.4.1 [856f2bd8] StructTypes v1.11.0 [3783bdb8] TableTraits v1.0.1 [bd369af6] Tables v1.12.1 [3bb67fe8] TranscodingStreams v0.11.3 [5c2747f8] URIs v1.6.1 [ea10d353] WeakRefStrings v1.4.2 [76eceee3] WorkerUtilities v1.6.1 [c8ffd9c3] MbedTLS_jll v2.28.10+0 [56f22d72] Artifacts v1.11.0 [2a0f44e3] Base64 v1.11.0 [ade2ca70] Dates v1.11.0 [7b1f6079] FileWatching v1.11.0 [9fa8497b] Future v1.11.0 [b77e0a4c] InteractiveUtils v1.11.0 [ac6e5ff7] JuliaSyntaxHighlighting v1.12.0 [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 [de0858da] Printf v1.11.0 [3fa0cd96] REPL v1.11.0 [9a3f8284] Random v1.11.0 [ea8e919c] SHA v1.0.0 [9e88b42a] Serialization v1.11.0 [6462fe0b] Sockets v1.11.0 [f489334b] StyledStrings v1.11.0 [fa267f1f] TOML v1.0.3 [8dfed614] Test v1.11.0 [cf7118a7] UUIDs v1.11.0 [4ec0a83e] Unicode v1.11.0 [e66e0078] CompilerSupportLibraries_jll v1.3.0+1 [14a3606d] MozillaCACerts_jll v2025.11.4 [4536629a] OpenBLAS_jll v0.3.29+0 [458c3c95] OpenSSL_jll v3.5.4+0 [83775a58] Zlib_jll v1.3.1+2 [8e850b90] libblastrampoline_jll v5.15.0+0 Testing Running tests... MetabolomicsWorkbench.org is alive. Check server status test: Test Passed MetabolomicsWorkbenchAPI.jl: Test Failed at /home/pkgeval/.julia/packages/MetabolomicsWorkbenchAPI/mKzQX/test/fetch_test.jl:14 Expression: df[:, 3:var"end"] == dfTestProperties[:, 3:var"end"] Evaluated: 4×4 DataFrame Row │ main_class refmet_name sub_class super_class ⋯ │ String? String? String? String? ⋯ ─────┼────────────────────────────────────────────────────────────────────────── 1 │ Glycerophosphocholines LPC P-16:0 O-LPC Glycerophosph ⋯ 2 │ Glycerophosphocholines PC P-18:0/18:1(9Z) PC Glycerophosph 3 │ Sterol esters CE 18:0 Chol. esters Sterol Lipids 4 │ Triradylglycerols TG O-52:2 O-TG Glycerolipids 1 column omitted == 4×4 DataFrame Row │ main_class refmet_name sub_class super_class ⋯ │ String String String String ⋯ ─────┼────────────────────────────────────────────────────────────────────────── 1 │ Glycerophosphocholines LPC P-16:0 O-LPC Glycerophos ⋯ 2 │ Glycerophosphocholines PC P-18:0/18:1(9Z)* PC Glycerophos 3 │ Sterol esters CE 18:0 Chol. esters Sterol Lipi 4 │ Triradylglycerols TG O-52:2* O-TAG Glycerolipi 1 column omitted Stacktrace: [1] top-level scope @ ~/.julia/packages/MetabolomicsWorkbenchAPI/mKzQX/test/fetch_test.jl:0 [2] macro expansion @ /opt/julia/share/julia/stdlib/v1.14/Test/src/Test.jl:753 [inlined] [3] include(mapexpr::Function, mod::Module, _path::String) @ Base ./Base.jl:310 [4] top-level scope @ ~/.julia/packages/MetabolomicsWorkbenchAPI/mKzQX/test/runtests.jl:8 [5] macro expansion @ /opt/julia/share/julia/stdlib/v1.14/Test/src/Test.jl:1961 [inlined] [6] macro expansion @ ~/.julia/packages/MetabolomicsWorkbenchAPI/mKzQX/test/runtests.jl:8 [inlined] Fetch annotation test: Test Failed at /home/pkgeval/.julia/packages/MetabolomicsWorkbenchAPI/mKzQX/test/fetch_test.jl:14 Expression: df[:, 3:var"end"] == dfTestProperties[:, 3:var"end"] Evaluated: 4×4 DataFrame Row │ main_class refmet_name sub_class super_class ⋯ │ String? String? String? String? ⋯ ─────┼────────────────────────────────────────────────────────────────────────── 1 │ Glycerophosphocholines LPC P-16:0 O-LPC Glycerophosph ⋯ 2 │ Glycerophosphocholines PC P-18:0/18:1(9Z) PC Glycerophosph 3 │ Sterol esters CE 18:0 Chol. esters Sterol Lipids 4 │ Triradylglycerols TG O-52:2 O-TG Glycerolipids 1 column omitted == 4×4 DataFrame Row │ main_class refmet_name sub_class super_class ⋯ │ String String String String ⋯ ─────┼────────────────────────────────────────────────────────────────────────── 1 │ Glycerophosphocholines LPC P-16:0 O-LPC Glycerophos ⋯ 2 │ Glycerophosphocholines PC P-18:0/18:1(9Z)* PC Glycerophos 3 │ Sterol esters CE 18:0 Chol. esters Sterol Lipi 4 │ Triradylglycerols TG O-52:2* O-TAG Glycerolipi 1 column omitted Fetch data test: Test Passed Fetch properties test: Test Passed Fetch samples test: Test Passed Fetch total subjects test: Test Passed Fetch total subjects test: Test Passed Test Summary: | Pass Fail Total Time MetabolomicsWorkbenchAPI.jl | 6 1 7 9m36.3s RNG of the outermost testset: Random.Xoshiro(0x64f5bf23773103b1, 0x2c73651ebc1ce097, 0x478f15e83a6e546c, 0xadd7e1dff86dfb91, 0x110289289ab12c89) ERROR: LoadError: Some tests did not pass: 6 passed, 1 failed, 0 errored, 0 broken. in expression starting at /home/pkgeval/.julia/packages/MetabolomicsWorkbenchAPI/mKzQX/test/runtests.jl:7 Testing failed after 545.85s ERROR: LoadError: Package MetabolomicsWorkbenchAPI 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:2946 [3] test @ /opt/julia/share/julia/stdlib/v1.14/Pkg/src/Operations.jl:2795 [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:572 [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/v1.14/Pkg/src/API.jl:548 [6] 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 [7] kwcall(::@NamedTuple{julia_args::Cmd}, ::typeof(Pkg.API.test), pkgs::Vector{PackageSpec}) @ Pkg.API /opt/julia/share/julia/stdlib/v1.14/Pkg/src/API.jl:161 [8] test(pkgs::Vector{String}; kwargs::@Kwargs{julia_args::Cmd}) @ Pkg.API /opt/julia/share/julia/stdlib/v1.14/Pkg/src/API.jl:160 [9] test @ /opt/julia/share/julia/stdlib/v1.14/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/v1.14/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 948.18s: package has test failures