Package evaluation to test PyGDatasets on Julia 1.12.7-DEV.42 (6f510b6086*) started at 2026-06-19T22:08:43.278 ################################################################################ # Set-up # Installing PkgEval dependencies (TestEnv)... Activating project at `~/.julia/environments/v1.12` Set-up completed after 8.32s ################################################################################ # Installation # Installing PyGDatasets... Resolving package versions... Updating `~/.julia/environments/v1.12/Project.toml` [44f67abd] + PyGDatasets v0.1.2 Updating `~/.julia/environments/v1.12/Manifest.toml` [1520ce14] + AbstractTrees v0.4.5 [79e6a3ab] + Adapt v4.6.1 [66dad0bd] + AliasTables v1.1.3 [ec485272] + ArnoldiMethod v0.4.0 [a9b6321e] + Atomix v1.1.3 ⌅ [ab4f0b2a] + BFloat16s v0.5.1 [d360d2e6] + ChainRulesCore v1.26.1 [34da2185] + Compat v4.18.1 [992eb4ea] + CondaPkg v0.2.36 [187b0558] + ConstructionBase v1.6.0 [53c2dc0f] + DLPack v0.3.1 [9a962f9c] + DataAPI v1.16.0 [864edb3b] + DataStructures v0.19.5 [e2d170a0] + DataValueInterfaces v1.0.0 [8bb1440f] + DelimitedFiles v1.9.1 [b4f34e82] + Distances v0.10.12 [ffbed154] + DocStringExtensions v0.9.5 [d9f16b24] + Functors v0.5.2 [aed8fd31] + GNNGraphs v1.5.0 [46192b85] + GPUArraysCore v0.2.0 [86223c79] + Graphs v1.14.0 [076d061b] + HashArrayMappedTries v0.2.0 [d25df0c9] + Inflate v0.1.5 [92d709cd] + IrrationalConstants v0.2.6 [82899510] + IteratorInterfaceExtensions v1.0.0 [692b3bcd] + JLLWrappers v1.8.0 [682c06a0] + JSON v1.6.1 [63c18a36] + KernelAbstractions v0.9.41 ⌅ [0b1a1467] + KrylovKit v0.9.5 [2ab3a3ac] + LogExpFunctions v1.0.1 [c2834f40] + MLCore v1.0.2 [7e8f7934] + MLDataDevices v1.17.10 [f1d291b0] + MLUtils v0.4.9 [1914dd2f] + MacroTools v0.5.16 [0b3b1443] + MicroMamba v0.1.15 [e1d29d7a] + Missings v1.2.0 [872c559c] + NNlib v0.9.36 [b8a86587] + NearestNeighbors v0.4.27 ⌅ [bac558e1] + OrderedCollections v1.8.2 [65ce6f38] + PackageExtensionCompat v1.0.2 [69de0a69] + Parsers v2.8.6 [fa939f87] + Pidfile v1.3.0 [aea7be01] + PrecompileTools v1.3.4 [21216c6a] + Preferences v1.5.2 [43287f4e] + PtrArrays v1.4.0 [44f67abd] + PyGDatasets v0.1.2 [6099a3de] + PythonCall v0.9.35 [ae029012] + Requires v1.3.1 [431bcebd] + SciMLPublic v1.0.1 [7e506255] + ScopedValues v1.6.2 [6c6a2e73] + Scratch v1.3.0 [605ecd9f] + ShowCases v0.1.0 [699a6c99] + SimpleTraits v0.9.6 [a2af1166] + SortingAlgorithms v1.2.2 [90137ffa] + StaticArrays v1.9.18 [1e83bf80] + StaticArraysCore v1.4.4 [10745b16] + Statistics v1.11.1 [82ae8749] + StatsAPI v1.8.0 [2913bbd2] + StatsBase v0.34.12 [ec057cc2] + StructUtils v2.8.2 [3783bdb8] + TableTraits v1.0.1 [bd369af6] + Tables v1.12.1 [013be700] + UnsafeAtomics v0.3.1 [e17b2a0c] + UnsafePointers v1.0.0 ⌅ [409d34a3] + VectorInterface v0.5.0 [f8abcde7] + micromamba_jll v2.3.1+0 [4d7b5844] + pixi_jll v0.63.2+0 [0dad84c5] + ArgTools v1.1.2 [56f22d72] + Artifacts v1.11.0 [2a0f44e3] + Base64 v1.11.0 [ade2ca70] + Dates v1.11.0 [f43a241f] + Downloads v1.7.0 [7b1f6079] + FileWatching v1.11.0 [b77e0a4c] + InteractiveUtils v1.11.0 [ac6e5ff7] + JuliaSyntaxHighlighting v1.12.0 [4af54fe1] + LazyArtifacts v1.11.0 [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 [9a3f8284] + Random v1.11.0 [ea8e919c] + SHA v0.7.0 [9e88b42a] + Serialization 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 [458c3c95] + OpenSSL_jll v3.5.6+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 5.95s ################################################################################ # Precompilation # Precompiling PkgEval dependencies... Precompiling package dependencies... Precompiling packages... 201375.3 ms ? PyGDatasets Precompilation completed after 219.83s ################################################################################ # Testing # Testing PyGDatasets Status `/tmp/jl_1R2c4N/Project.toml` [53c2dc0f] DLPack v0.3.1 [aed8fd31] GNNGraphs v1.5.0 [44f67abd] PyGDatasets v0.1.2 [6099a3de] PythonCall v0.9.35 [189a3867] Reexport v1.2.2 [f8b46487] TestItemRunner v1.1.5 [1c621080] TestItems v1.0.0 [8dfed614] Test v1.11.0 Status `/tmp/jl_1R2c4N/Manifest.toml` [1520ce14] AbstractTrees v0.4.5 [79e6a3ab] Adapt v4.6.1 [66dad0bd] AliasTables v1.1.3 [ec485272] ArnoldiMethod v0.4.0 [a9b6321e] Atomix v1.1.3 ⌅ [ab4f0b2a] BFloat16s v0.5.1 [d360d2e6] ChainRulesCore v1.26.1 [34da2185] Compat v4.18.1 [992eb4ea] CondaPkg v0.2.36 [187b0558] ConstructionBase v1.6.0 [53c2dc0f] DLPack v0.3.1 [9a962f9c] DataAPI v1.16.0 [864edb3b] DataStructures v0.19.5 [e2d170a0] DataValueInterfaces v1.0.0 [8bb1440f] DelimitedFiles v1.9.1 [b4f34e82] Distances v0.10.12 [ffbed154] DocStringExtensions v0.9.5 [d9f16b24] Functors v0.5.2 [aed8fd31] GNNGraphs v1.5.0 [46192b85] GPUArraysCore v0.2.0 [86223c79] Graphs v1.14.0 [076d061b] HashArrayMappedTries v0.2.0 [d25df0c9] Inflate v0.1.5 [92d709cd] IrrationalConstants v0.2.6 [82899510] IteratorInterfaceExtensions v1.0.0 [692b3bcd] JLLWrappers v1.8.0 [682c06a0] JSON v1.6.1 [63c18a36] KernelAbstractions v0.9.41 ⌅ [0b1a1467] KrylovKit v0.9.5 [2ab3a3ac] LogExpFunctions v1.0.1 [c2834f40] MLCore v1.0.2 [7e8f7934] MLDataDevices v1.17.10 [f1d291b0] MLUtils v0.4.9 [1914dd2f] MacroTools v0.5.16 [0b3b1443] MicroMamba v0.1.15 [e1d29d7a] Missings v1.2.0 [872c559c] NNlib v0.9.36 [b8a86587] NearestNeighbors v0.4.27 ⌅ [bac558e1] OrderedCollections v1.8.2 [65ce6f38] PackageExtensionCompat v1.0.2 [69de0a69] Parsers v2.8.6 [fa939f87] Pidfile v1.3.0 [aea7be01] PrecompileTools v1.3.4 [21216c6a] Preferences v1.5.2 [43287f4e] PtrArrays v1.4.0 [44f67abd] PyGDatasets v0.1.2 [6099a3de] PythonCall v0.9.35 [189a3867] Reexport v1.2.2 [ae029012] Requires v1.3.1 [431bcebd] SciMLPublic v1.0.1 [7e506255] ScopedValues v1.6.2 [6c6a2e73] Scratch v1.3.0 [605ecd9f] ShowCases v0.1.0 [699a6c99] SimpleTraits v0.9.6 [a2af1166] SortingAlgorithms v1.2.2 [90137ffa] StaticArrays v1.9.18 [1e83bf80] StaticArraysCore v1.4.4 [10745b16] Statistics v1.11.1 [82ae8749] StatsAPI v1.8.0 [2913bbd2] StatsBase v0.34.12 [ec057cc2] StructUtils v2.8.2 [3783bdb8] TableTraits v1.0.1 [bd369af6] Tables v1.12.1 [f8b46487] TestItemRunner v1.1.5 [1c621080] TestItems v1.0.0 [013be700] UnsafeAtomics v0.3.1 [e17b2a0c] UnsafePointers v1.0.0 ⌅ [409d34a3] VectorInterface v0.5.0 [f8abcde7] micromamba_jll v2.3.1+0 [4d7b5844] pixi_jll v0.63.2+0 [0dad84c5] ArgTools v1.1.2 [56f22d72] Artifacts v1.11.0 [2a0f44e3] Base64 v1.11.0 [ade2ca70] Dates v1.11.0 [f43a241f] Downloads v1.7.0 [7b1f6079] FileWatching v1.11.0 [b77e0a4c] InteractiveUtils v1.11.0 [ac6e5ff7] JuliaSyntaxHighlighting v1.12.0 [4af54fe1] LazyArtifacts v1.11.0 [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 [9a3f8284] Random v1.11.0 [ea8e919c] SHA v0.7.0 [9e88b42a] Serialization 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 [458c3c95] OpenSSL_jll v3.5.6+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... Precompiling packages... Info Given PyGDatasets was explicitly requested, output will be shown live   CondaPkg Found dependencies: /home/pkgeval/.julia/packages/PythonCall/5WGSP/CondaPkg.toml  CondaPkg Found dependencies: /home/pkgeval/.julia/packages/PyGDatasets/mdOk1/CondaPkg.toml  CondaPkg Found dependencies: /home/pkgeval/.julia/packages/CondaPkg/lKlVY/CondaPkg.toml  CondaPkg Resolving changes  + libstdcxx  + libstdcxx-ng  + numpy  + openssl  + pyg  + python  + pytorch  + rdkit  CondaPkg Initialising pixi  │ /home/pkgeval/.julia/artifacts/4ae17cee0bd922f66b2c72bf2f01c22481a5ec19/bin/pixi  │ init  │ --format pixi  └ /tmp/jl_1R2c4N/.CondaPkg ✔ Created /tmp/jl_1R2c4N/.CondaPkg/pixi.toml  CondaPkg Wrote /tmp/jl_1R2c4N/.CondaPkg/pixi.toml  │ [dependencies]  │ openssl = ">=3, <3.6"  │ libstdcxx = ">=3.4,<15.0"  │ rdkit = "*"  │ libstdcxx-ng = ">=3.4,<15.0"  │ pytorch = "*"  │ pyg = ">=2.0, <3"  │ numpy = "*"  │  │ [dependencies.python]  │ channel = "conda-forge"  │ build = "*cp*"  │ version = "<=3.11, >=3.10,!=3.14.0,!=3.14.1,<4"  │  │ [workspace]  │ name = ".CondaPkg"  │ platforms = ["linux-64"]  │ channels = ["conda-forge", "pyg", "pytorch"]  │ channel-priority = "strict"  └ description = "automatically generated by CondaPkg.jl"  CondaPkg Installing packages  │ /home/pkgeval/.julia/artifacts/4ae17cee0bd922f66b2c72bf2f01c22481a5ec19/bin/pixi  │ install  └ --manifest-path /tmp/jl_1R2c4N/.CondaPkg/pixi.toml ✔ The default environment has been installed. 120983.8 ms ✓ PyGDatasets 1 dependency successfully precompiled in 124 seconds. 120 already precompiled. 11 dependencies precompiled but different versions are currently loaded (Base64, Dates, InteractiveUtils, JuliaSyntaxHighlighting, Logging, Markdown, Printf, Serialization, StyledStrings, TOML and Test). Restart julia to access the new versions. Otherwise, 57 dependents of these packages may trigger further precompilation to work with the unexpected versions. 1 dependency had output during precompilation: ┌ PyGDatasets │ [Output was shown above] └ Test Summary: | Total Time Package | 0 2m36.2s ERROR: LoadError: InitError: Python: OSError: libmkl_intel_lp64.so.2: cannot open shared object file: No such file or directory Python stacktrace: [1] __init__ @ ctypes /tmp/jl_1R2c4N/.CondaPkg/.pixi/envs/default/lib/python3.11/ctypes/__init__.py:376 [2] _load_global_deps @ /tmp/jl_1R2c4N/.CondaPkg/.pixi/envs/default/lib/python3.11/site-packages/torch/__init__.py:226 [3] _load_global_deps @ /tmp/jl_1R2c4N/.CondaPkg/.pixi/envs/default/lib/python3.11/site-packages/torch/__init__.py:245 [4] @ /tmp/jl_1R2c4N/.CondaPkg/.pixi/envs/default/lib/python3.11/site-packages/torch/__init__.py:289 [5] @ /tmp/jl_1R2c4N/.CondaPkg/.pixi/envs/default/lib/python3.11/site-packages/torch_geometric/__init__.py:3 Stacktrace: [1] pythrow() @ PythonCall.Core ~/.julia/packages/PythonCall/5WGSP/src/Core/err.jl:77 [2] errcheck @ ~/.julia/packages/PythonCall/5WGSP/src/Core/err.jl:10 [inlined] [3] pyimport @ ~/.julia/packages/PythonCall/5WGSP/src/Core/builtins.jl:1474 [inlined] [4] __init__() @ PyGDatasets ~/.julia/packages/PyGDatasets/mdOk1/src/PyGDatasets.jl:27 [5] run_module_init(mod::Module, i::Int64) @ Base ./loading.jl:1445 [6] register_restored_modules(sv::Core.SimpleVector, pkg::Base.PkgId, path::String) @ Base ./loading.jl:1433 [7] _include_from_serialized(pkg::Base.PkgId, path::String, ocachepath::Nothing, depmods::Vector{Any}; register::Bool) @ Base ./loading.jl:1321 [8] _include_from_serialized @ ./loading.jl:1276 [inlined] [9] _require_search_from_serialized(pkg::Base.PkgId, sourcepath::String, build_id::UInt128, stalecheck::Bool; reasons::Dict{String, Int64}, DEPOT_PATH::Vector{String}) @ Base ./loading.jl:2116 [10] _require_search_from_serialized @ ./loading.jl:2010 [inlined] [11] __require_prelocked(pkg::Base.PkgId, env::String) @ Base ./loading.jl:2628 [12] _require_prelocked(uuidkey::Base.PkgId, env::String) @ Base ./loading.jl:2494 [13] macro expansion @ ./loading.jl:2422 [inlined] [14] macro expansion @ ./lock.jl:376 [inlined] [15] __require(into::Module, mod::Symbol) @ Base ./loading.jl:2387 [16] require(into::Module, mod::Symbol) @ Base ./loading.jl:2363 [17] eval(m::Module, e::Any) @ Core ./boot.jl:489 [18] include_string(mapexpr::typeof(identity), mod::Module, code::String, filename::String) @ Base ./loading.jl:2873 [19] include_string(m::Module, txt::String, fname::String) @ Base ./loading.jl:2883 [20] #ensure_evaled##2 @ ~/.julia/packages/TestItemRunner/GnoVt/src/TestItemRunner.jl:78 [inlined] [21] withpath(f::TestItemRunner.var"#ensure_evaled##2#ensure_evaled##3"{String, String, Module}, path::String) @ TestItemRunner ~/.julia/packages/TestItemRunner/GnoVt/src/vendored_code.jl:7 [22] #ensure_evaled##0 @ ~/.julia/packages/TestItemRunner/GnoVt/src/TestItemRunner.jl:77 [inlined] [23] cd(f::TestItemRunner.var"#ensure_evaled##0#ensure_evaled##1"{String, String, Module}, dir::String) @ Base.Filesystem ./file.jl:112 [24] ensure_evaled(test_setup_module_set::TestItemRunner.TestSetupModuleSet, filename::String, code::String, name::Symbol, line::Int64, column::Int64, working_dir::String) @ TestItemRunner ~/.julia/packages/TestItemRunner/GnoVt/src/TestItemRunner.jl:76 [25] run_tests(path::String; filter::Nothing, verbose::Bool) @ TestItemRunner ~/.julia/packages/TestItemRunner/GnoVt/src/TestItemRunner.jl:217 [26] run_tests(path::String) @ TestItemRunner ~/.julia/packages/TestItemRunner/GnoVt/src/TestItemRunner.jl:134 [27] top-level scope @ ~/.julia/packages/PyGDatasets/mdOk1/test/runtests.jl:3 [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 during initialization of module PyGDatasets in expression starting at /home/pkgeval/.julia/packages/PyGDatasets/mdOk1/test/test_module.jl:5 in expression starting at /home/pkgeval/.julia/packages/PyGDatasets/mdOk1/test/runtests.jl:3 Testing failed after 226.0s ERROR: LoadError: Package PyGDatasets 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:2538 [3] test @ /opt/julia/share/julia/stdlib/v1.12/Pkg/src/Operations.jl:2387 [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:552 [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 498.74s: package requires a missing binary dependency