Package evaluation of PyGDatasets on Julia 1.13.0-DEV.111 (ce76dbf07d*) started at 2025-02-28T07:08:38.451 ################################################################################ # Set-up # Set-up completed after 0.25s ################################################################################ # Installation # Installing PyGDatasets... Resolving package versions... Updating `~/.julia/environments/v1.13/Project.toml` [44f67abd] + PyGDatasets v0.1.2 Updating `~/.julia/environments/v1.13/Manifest.toml` [7d9f7c33] + Accessors v0.1.42 [79e6a3ab] + Adapt v4.2.0 [66dad0bd] + AliasTables v1.1.3 [dce04be8] + ArgCheck v2.4.0 [ec485272] + ArnoldiMethod v0.4.0 [a9b6321e] + Atomix v1.1.1 [a963bdd2] + AtomsBase v0.5.1 [ab4f0b2a] + BFloat16s v0.5.0 [198e06fe] + BangBang v0.4.4 [9718e550] + Baselet v0.1.1 [d1d4a3ce] + BitFlags v0.1.9 [e1450e63] + BufferedStreams v1.2.2 [336ed68f] + CSV v0.10.15 [d360d2e6] + ChainRulesCore v1.25.1 [46823bd8] + Chemfiles v0.10.42 [944b1d66] + CodecZlib v0.7.8 [35d6a980] + ColorSchemes v3.29.0 [3da002f7] + ColorTypes v0.12.0 [c3611d14] + ColorVectorSpace v0.11.0 [5ae59095] + Colors v0.13.0 [34da2185] + Compat v4.16.0 [a33af91c] + CompositionsBase v0.1.2 [f0e56b4a] + ConcurrentUtilities v2.5.0 [992eb4ea] + CondaPkg v0.2.25 [187b0558] + ConstructionBase v1.5.8 [6add18c4] + ContextVariablesX v0.1.3 [a8cc5b0e] + Crayons v4.1.1 [53c2dc0f] + DLPack v0.3.1 [9a962f9c] + DataAPI v1.16.0 [124859b0] + DataDeps v0.7.13 [a93c6f00] + DataFrames v1.7.0 [864edb3b] + DataStructures v0.18.20 [e2d170a0] + DataValueInterfaces v1.0.0 [244e2a9f] + DefineSingletons v0.1.2 [8bb1440f] + DelimitedFiles v1.9.1 [b4f34e82] + Distances v0.10.12 [ffbed154] + DocStringExtensions v0.9.3 [460bff9d] + ExceptionUnwrapping v0.1.11 [cc61a311] + FLoops v0.2.2 [b9860ae5] + FLoopsBase v0.1.1 [5789e2e9] + FileIO v1.17.0 [48062228] + FilePathsBase v0.9.23 [53c48c17] + FixedPointNumbers v0.8.5 [d9f16b24] + Functors v0.5.2 [aed8fd31] + GNNGraphs v1.4.2 [46192b85] + GPUArraysCore v0.2.0 [92fee26a] + GZip v0.6.2 [c27321d9] + Glob v1.3.1 [86223c79] + Graphs v1.12.0 [f67ccb44] + HDF5 v0.17.2 [cd3eb016] + HTTP v1.10.15 [c817782e] + ImageBase v0.1.7 [a09fc81d] + ImageCore v0.10.5 [4e3cecfd] + ImageShow v0.3.8 [d25df0c9] + Inflate v0.1.5 [22cec73e] + InitialValues v0.3.1 [842dd82b] + InlineStrings v1.4.3 [7d512f48] + InternedStrings v0.7.0 [3587e190] + InverseFunctions v0.1.17 [41ab1584] + InvertedIndices v1.3.1 [92d709cd] + IrrationalConstants v0.2.4 [82899510] + IteratorInterfaceExtensions v1.0.0 [033835bb] + JLD2 v0.5.11 [692b3bcd] + JLLWrappers v1.7.0 [0f8b85d8] + JSON3 v1.14.1 [b14d175d] + JuliaVariables v0.2.4 [63c18a36] + KernelAbstractions v0.9.34 [0b1a1467] + KrylovKit v0.9.5 [b964fa9f] + LaTeXStrings v1.4.0 [8cdb02fc] + LazyModules v0.3.1 [2ab3a3ac] + LogExpFunctions v0.3.29 [e6f89c97] + LoggingExtras v1.1.0 [23992714] + MAT v0.10.7 [c2834f40] + MLCore v1.0.0 [7e8f7934] + MLDataDevices v1.6.11 [eb30cadb] + MLDatasets v0.7.18 [d8e11817] + MLStyle v0.4.17 [f1d291b0] + MLUtils v0.4.7 [3da0fdf6] + MPIPreferences v0.1.11 [1914dd2f] + MacroTools v0.5.15 [dbb5928d] + MappedArrays v0.4.2 [739be429] + MbedTLS v1.1.9 [128add7d] + MicroCollections v0.2.0 [0b3b1443] + MicroMamba v0.1.14 [e1d29d7a] + Missings v1.2.0 [e94cdb99] + MosaicViews v0.3.4 [872c559c] + NNlib v0.9.27 [15e1cf62] + NPZ v0.4.3 [71a1bf82] + NameResolution v0.1.5 [b8a86587] + NearestNeighbors v0.4.21 [6fe1bfb0] + OffsetArrays v1.15.0 [4d8831e6] + OpenSSL v1.4.3 [bac558e1] + OrderedCollections v1.8.0 [65ce6f38] + PackageExtensionCompat v1.0.2 [5432bcbf] + PaddedViews v0.5.12 [69de0a69] + Parsers v2.8.1 [7b2266bf] + PeriodicTable v1.2.1 [fbb45041] + Pickle v0.3.5 [fa939f87] + Pidfile v1.3.0 [2dfb63ee] + PooledArrays v1.4.3 [aea7be01] + PrecompileTools v1.2.1 [21216c6a] + Preferences v1.4.3 [8162dcfd] + PrettyPrint v0.2.0 [08abe8d2] + PrettyTables v2.4.0 [43287f4e] + PtrArrays v1.3.0 [44f67abd] + PyGDatasets v0.1.2 [6099a3de] + PythonCall v0.9.24 [189a3867] + Reexport v1.2.2 [ae029012] + Requires v1.3.1 [6c6a2e73] + Scratch v1.2.1 [91c51154] + SentinelArrays v1.4.8 [efcf1570] + Setfield v1.1.2 [605ecd9f] + ShowCases v0.1.0 [777ac1f9] + SimpleBufferStream v1.2.0 [699a6c99] + SimpleTraits v0.9.4 [a2af1166] + SortingAlgorithms v1.2.1 [171d559e] + SplittablesBase v0.1.15 [cae243ae] + StackViews v0.1.1 [90137ffa] + StaticArrays v1.9.12 [1e83bf80] + StaticArraysCore v1.4.3 [10745b16] + Statistics v1.11.1 [82ae8749] + StatsAPI v1.7.0 [2913bbd2] + StatsBase v0.34.4 ⌅ [4db3bf67] + StridedViews v0.2.2 [69024149] + StringEncodings v0.3.7 [892a3eda] + StringManipulation v0.4.1 [856f2bd8] + StructTypes v1.11.0 [3783bdb8] + TableTraits v1.0.1 [bd369af6] + Tables v1.12.0 [62fd8b95] + TensorCore v0.1.1 [3bb67fe8] + TranscodingStreams v0.11.3 [28d57a85] + Transducers v0.4.84 [5c2747f8] + URIs v1.5.1 [1986cc42] + Unitful v1.22.0 [a7773ee8] + UnitfulAtomic v1.0.0 [013be700] + UnsafeAtomics v0.3.0 [e17b2a0c] + UnsafePointers v1.0.0 [409d34a3] + VectorInterface v0.5.0 [ea10d353] + WeakRefStrings v1.4.2 [76eceee3] + WorkerUtilities v1.6.1 [a5390f91] + ZipFile v0.10.1 [78a364fa] + Chemfiles_jll v0.10.4+0 [0234f1f7] + HDF5_jll v1.14.5+0 [e33a78d0] + Hwloc_jll v2.12.0+0 [94ce4f54] + Libiconv_jll v1.18.0+0 [7cb0a576] + MPICH_jll v4.3.0+0 [f1f71cc9] + MPItrampoline_jll v5.5.2+0 [c8ffd9c3] + MbedTLS_jll v2.28.6+1 [9237b28f] + MicrosoftMPI_jll v10.1.4+3 [fe0851c0] + OpenMPI_jll v5.0.7+0 [477f73a3] + libaec_jll v1.1.3+0 [f8abcde7] + micromamba_jll v1.5.8+0 [4d7b5844] + pixi_jll v0.41.3+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 [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 v1.12.0 [de0858da] + Printf v1.11.0 [9a3f8284] + Random v1.11.0 [ea8e919c] + SHA v0.7.0 [9e88b42a] + Serialization v1.11.0 [1a1011a3] + SharedArrays 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 v8.11.1+1 [e37daf67] + LibGit2_jll v1.9.0+0 [29816b5a] + LibSSH2_jll v1.11.3+1 [14a3606d] + MozillaCACerts_jll v2024.12.31 [4536629a] + OpenBLAS_jll v0.3.29+0 [458c3c95] + OpenSSL_jll v3.0.16+0 [bea87d4a] + SuiteSparse_jll v7.8.3+2 [83775a58] + Zlib_jll v1.3.1+2 [8e850b90] + libblastrampoline_jll v5.12.0+0 [8e850ede] + nghttp2_jll v1.64.0+1 [3f19e933] + p7zip_jll v17.5.0+2 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 11.0s ################################################################################ # Precompilation # Precompiling PkgEval dependencies... No packages added to or removed from `~/.julia/environments/pkgeval/Project.toml` No packages added to or removed from `~/.julia/environments/pkgeval/Manifest.toml` Precompiling package dependencies... Precompiling packages... 228481.1 ms ✓ PyGDatasets 1 dependency successfully precompiled in 235 seconds. 229 already precompiled. 1 dependency had output during precompilation: ┌ PyGDatasets │ CondaPkg Found dependencies: /home/pkgeval/.julia/packages/PythonCall/WMWY0/CondaPkg.toml │ CondaPkg Found dependencies: /home/pkgeval/.julia/packages/PyGDatasets/mdOk1/CondaPkg.toml │ CondaPkg Resolving changes │ + libstdcxx-ng │ + numpy │ + openssl │ + pyg │ + python │ + pytorch │ + rdkit │ CondaPkg Initialising pixi │ │ /home/pkgeval/.julia/artifacts/cefba4912c2b400756d043a2563ef77a0088866b/bin/pixi │ │ init │ │ --format pixi │ └ /home/pkgeval/.julia/environments/v1.13/.CondaPkg │ ✔ Created /home/pkgeval/.julia/environments/v1.13/.CondaPkg/pixi.toml │ CondaPkg Wrote /home/pkgeval/.julia/environments/v1.13/.CondaPkg/pixi.toml │ │ [dependencies] │ │ openssl = ">=3, <3.1" │ │ rdkit = "*" │ │ libstdcxx-ng = ">=3.4,<13.0" │ │ pytorch = "*" │ │ pyg = ">=2.0, <3" │ │ numpy = "*" │ │ │ │ [dependencies.python] │ │ channel = "conda-forge" │ │ build = "*cpython*" │ │ version = ">=3.8,<4, <=3.11" │ │ │ │ [project] │ │ name = ".CondaPkg" │ │ platforms = ["linux-64"] │ │ channels = ["conda-forge", "pyg", "pytorch"] │ │ channel-priority = "disabled" │ └ description = "automatically generated by CondaPkg.jl" │ CondaPkg Installing packages │ │ /home/pkgeval/.julia/artifacts/cefba4912c2b400756d043a2563ef77a0088866b/bin/pixi │ │ install │ └ --manifest-path /home/pkgeval/.julia/environments/v1.13/.CondaPkg/pixi.toml │ ✔ The default environment has been installed. └ Precompilation completed after 239.68s ################################################################################ # Loading # Loading PyGDatasets... Precompiling packages... 29006.4 ms ✓ PyGDatasets 1 dependency successfully precompiled in 33 seconds. 229 already precompiled. ERROR: InitError: Python: OSError: libmkl_intel_lp64.so.2: cannot open shared object file: No such file or directory Python stacktrace: [1] __init__ @ ctypes ~/.julia/environments/v1.13/.CondaPkg/.pixi/envs/default/lib/python3.11/ctypes/__init__.py:376 [2] _load_global_deps @ ~/.julia/environments/v1.13/.CondaPkg/.pixi/envs/default/lib/python3.11/site-packages/torch/__init__.py:226 [3] _load_global_deps @ ~/.julia/environments/v1.13/.CondaPkg/.pixi/envs/default/lib/python3.11/site-packages/torch/__init__.py:245 [4] @ ~/.julia/environments/v1.13/.CondaPkg/.pixi/envs/default/lib/python3.11/site-packages/torch/__init__.py:289 [5] @ ~/.julia/environments/v1.13/.CondaPkg/.pixi/envs/default/lib/python3.11/site-packages/torch_geometric/__init__.py:3 Stacktrace: [1] pythrow() @ PythonCall.Core ~/.julia/packages/PythonCall/WMWY0/src/Core/err.jl:92 [2] errcheck @ ~/.julia/packages/PythonCall/WMWY0/src/Core/err.jl:10 [inlined] [3] pyimport(m::String) @ PythonCall.Core ~/.julia/packages/PythonCall/WMWY0/src/Core/builtins.jl:1561 [4] __init__() @ PyGDatasets ~/.julia/packages/PyGDatasets/mdOk1/src/PyGDatasets.jl:27 [5] run_module_init(mod::Module, i::Int64) @ Base ./loading.jl:1424 [6] register_restored_modules(sv::Core.SimpleVector, pkg::Base.PkgId, path::String) @ Base ./loading.jl:1412 [7] _include_from_serialized(pkg::Base.PkgId, path::String, ocachepath::Nothing, depmods::Vector{Any}, ignore_native::Bool; register::Bool) @ Base ./loading.jl:1300 [8] _include_from_serialized @ ./loading.jl:1246 [inlined] [9] _tryrequire_from_serialized(pkg::Base.PkgId, path::String, ocachepath::Nothing) @ Base ./loading.jl:2014 [10] __require_prelocked(pkg::Base.PkgId, env::String) @ Base ./loading.jl:2697 [11] _require_prelocked(uuidkey::Base.PkgId, env::String) @ Base ./loading.jl:2493 [12] macro expansion @ ./loading.jl:2421 [inlined] [13] macro expansion @ ./lock.jl:376 [inlined] [14] __require(into::Module, mod::Symbol) @ Base ./loading.jl:2386 [15] #invoke_in_world#2 @ ./essentials.jl:1092 [inlined] [16] invoke_in_world @ ./essentials.jl:1088 [inlined] [17] require(into::Module, mod::Symbol) @ Base ./loading.jl:2366 [18] eval(m::Module, e::Any) @ Core ./boot.jl:488 [19] exec_options(opts::Base.JLOptions) @ Base ./client.jl:294 [20] _start() @ Base ./client.jl:560 during initialization of module PyGDatasets Loading failed after 112.87s ERROR: LoadError: failed process: Process(`/opt/julia/bin/julia -C native -J/opt/julia/lib/julia/sys.so -g1 --check-bounds=yes --inline=yes --pkgimages=existing -e 'using PyGDatasets'`, ProcessExited(1)) [1] Stacktrace: [1] pipeline_error @ ./process.jl:598 [inlined] [2] run(::Cmd; wait::Bool) @ Base ./process.jl:513 [3] run(::Cmd) @ Base ./process.jl:510 [4] top-level scope @ /PkgEval.jl/scripts/evaluate.jl:193 [5] include(mod::Module, _path::String) @ Base ./Base.jl:307 [6] exec_options(opts::Base.JLOptions) @ Base ./client.jl:328 [7] _start() @ Base ./client.jl:560 in expression starting at /PkgEval.jl/scripts/evaluate.jl:184 PkgEval failed after 396.55s: package requires a missing binary dependency