Package evaluation of ProteinChains on Julia 1.13.0-DEV.582 (c0a1728d50*) started at 2025-05-14T15:19:10.009 ################################################################################ # Set-up # Installing PkgEval dependencies (TestEnv)... Set-up completed after 8.6s ################################################################################ # Installation # Installing ProteinChains... Resolving package versions... Updating `~/.julia/environments/v1.13/Project.toml` [b8e8f2a5] + ProteinChains v0.7.2 Updating `~/.julia/environments/v1.13/Manifest.toml` [79e6a3ab] + Adapt v4.3.0 [ec485272] + ArnoldiMethod v0.4.0 [8ed43e74] + AssigningSecondaryStructure v0.5.1 [a9b6321e] + Atomix v1.1.1 [9ac9c2a2] + Backboner v0.12.2 [47718e42] + BioGenerics v0.1.5 [de9282ab] + BioStructures v4.5.0 [3c28c6f8] + BioSymbols v5.2.0 [c3b6d118] + BitIntegers v0.3.5 [d360d2e6] + ChainRulesCore v1.25.1 [944b1d66] + CodecZlib v0.7.8 [34da2185] + Compat v4.16.0 [864edb3b] + DataStructures v0.18.22 [b4f34e82] + Distances v0.10.12 [e139c391] + DynamicStructs v0.2.3 [5789e2e9] + FileIO v1.17.0 [1fa38f19] + Format v1.3.7 [46192b85] + GPUArraysCore v0.2.0 [86223c79] + Graphs v1.12.1 [f67ccb44] + HDF5 v0.17.2 [076d061b] + HashArrayMappedTries v0.2.0 [d25df0c9] + Inflate v0.1.5 [842dd82b] + InlineStrings v1.4.3 [033835bb] + JLD2 v0.5.13 [692b3bcd] + JLLWrappers v1.7.0 [682c06a0] + JSON v0.21.4 [63c18a36] + KernelAbstractions v0.9.34 [3da0fdf6] + MPIPreferences v0.1.11 [1914dd2f] + MacroTools v0.5.16 [872c559c] + NNlib v0.9.30 [b8a86587] + NearestNeighbors v0.4.21 [bac558e1] + OrderedCollections v1.8.0 [69de0a69] + Parsers v2.8.3 [7b2266bf] + PeriodicTable v1.2.1 [aea7be01] + PrecompileTools v1.3.2 [21216c6a] + Preferences v1.4.3 [b8e8f2a5] + ProteinChains v0.7.2 [94ee1d12] + Quaternions v0.7.6 [c1ae055f] + RealDot v0.1.0 [3cdcf5f2] + RecipesBase v1.3.4 [189a3867] + Reexport v1.2.2 [ae029012] + Requires v1.3.1 [6038ab10] + Rotations v1.7.1 [7e506255] + ScopedValues v1.3.0 [699a6c99] + SimpleTraits v0.9.4 [90137ffa] + StaticArrays v1.9.13 [1e83bf80] + StaticArraysCore v1.4.3 [10745b16] + Statistics v1.11.1 [82ae8749] + StatsAPI v1.7.0 [3bb67fe8] + TranscodingStreams v0.11.3 [1986cc42] + Unitful v1.22.1 [013be700] + UnsafeAtomics v0.3.0 [0234f1f7] + HDF5_jll v1.14.6+0 [e33a78d0] + Hwloc_jll v2.12.0+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 [477f73a3] + libaec_jll v1.1.3+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 [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 v1.13.0 [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 [cf7118a7] + UUIDs v1.11.0 [4ec0a83e] + Unicode v1.11.0 [e66e0078] + CompilerSupportLibraries_jll v1.3.0+1 [deac9b47] + LibCURL_jll v8.12.1+1 [e37daf67] + LibGit2_jll v1.9.0+0 [29816b5a] + LibSSH2_jll v1.11.3+1 [14a3606d] + MozillaCACerts_jll v2025.2.25 [4536629a] + OpenBLAS_jll v0.3.29+0 [458c3c95] + OpenSSL_jll v3.5.0+0 [bea87d4a] + SuiteSparse_jll v7.10.1+0 [83775a58] + Zlib_jll v1.3.1+2 [8e850b90] + libblastrampoline_jll v5.12.0+0 [8e850ede] + nghttp2_jll v1.65.0+0 [3f19e933] + p7zip_jll v17.5.0+2 Installation completed after 8.14s ################################################################################ # Precompilation # Precompiling PkgEval dependencies... Precompiling package dependencies... Precompilation completed after 44.69s ################################################################################ # Testing # Testing ProteinChains Status `/tmp/jl_AeBeuC/Project.toml` [8ed43e74] AssigningSecondaryStructure v0.5.1 [9ac9c2a2] Backboner v0.12.2 [de9282ab] BioStructures v4.5.0 [c3b6d118] BitIntegers v0.3.5 [34da2185] Compat v4.16.0 [e139c391] DynamicStructs v0.2.3 [86223c79] Graphs v1.12.1 [f67ccb44] HDF5 v0.17.2 [842dd82b] InlineStrings v1.4.3 [033835bb] JLD2 v0.5.13 [682c06a0] JSON v0.21.4 [7b2266bf] PeriodicTable v1.2.1 [b8e8f2a5] ProteinChains v0.7.2 [189a3867] Reexport v1.2.2 [90137ffa] StaticArrays v1.9.13 [10745b16] Statistics v1.11.1 [37e2e46d] LinearAlgebra v1.12.0 [8dfed614] Test v1.11.0 Status `/tmp/jl_AeBeuC/Manifest.toml` [79e6a3ab] Adapt v4.3.0 [ec485272] ArnoldiMethod v0.4.0 [8ed43e74] AssigningSecondaryStructure v0.5.1 [a9b6321e] Atomix v1.1.1 [9ac9c2a2] Backboner v0.12.2 [47718e42] BioGenerics v0.1.5 [de9282ab] BioStructures v4.5.0 [3c28c6f8] BioSymbols v5.2.0 [c3b6d118] BitIntegers v0.3.5 [d360d2e6] ChainRulesCore v1.25.1 [944b1d66] CodecZlib v0.7.8 [34da2185] Compat v4.16.0 [864edb3b] DataStructures v0.18.22 [b4f34e82] Distances v0.10.12 [e139c391] DynamicStructs v0.2.3 [5789e2e9] FileIO v1.17.0 [1fa38f19] Format v1.3.7 [46192b85] GPUArraysCore v0.2.0 [86223c79] Graphs v1.12.1 [f67ccb44] HDF5 v0.17.2 [076d061b] HashArrayMappedTries v0.2.0 [d25df0c9] Inflate v0.1.5 [842dd82b] InlineStrings v1.4.3 [033835bb] JLD2 v0.5.13 [692b3bcd] JLLWrappers v1.7.0 [682c06a0] JSON v0.21.4 [63c18a36] KernelAbstractions v0.9.34 [3da0fdf6] MPIPreferences v0.1.11 [1914dd2f] MacroTools v0.5.16 [872c559c] NNlib v0.9.30 [b8a86587] NearestNeighbors v0.4.21 [bac558e1] OrderedCollections v1.8.0 [69de0a69] Parsers v2.8.3 [7b2266bf] PeriodicTable v1.2.1 [aea7be01] PrecompileTools v1.3.2 [21216c6a] Preferences v1.4.3 [b8e8f2a5] ProteinChains v0.7.2 [94ee1d12] Quaternions v0.7.6 [c1ae055f] RealDot v0.1.0 [3cdcf5f2] RecipesBase v1.3.4 [189a3867] Reexport v1.2.2 [ae029012] Requires v1.3.1 [6038ab10] Rotations v1.7.1 [7e506255] ScopedValues v1.3.0 [699a6c99] SimpleTraits v0.9.4 [90137ffa] StaticArrays v1.9.13 [1e83bf80] StaticArraysCore v1.4.3 [10745b16] Statistics v1.11.1 [82ae8749] StatsAPI v1.7.0 [3bb67fe8] TranscodingStreams v0.11.3 [1986cc42] Unitful v1.22.1 [013be700] UnsafeAtomics v0.3.0 [0234f1f7] HDF5_jll v1.14.6+0 [e33a78d0] Hwloc_jll v2.12.0+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 [477f73a3] libaec_jll v1.1.3+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 [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 v1.13.0 [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 v8.12.1+1 [e37daf67] LibGit2_jll v1.9.0+0 [29816b5a] LibSSH2_jll v1.11.3+1 [14a3606d] MozillaCACerts_jll v2025.2.25 [4536629a] OpenBLAS_jll v0.3.29+0 [458c3c95] OpenSSL_jll v3.5.0+0 [bea87d4a] SuiteSparse_jll v7.10.1+0 [83775a58] Zlib_jll v1.3.1+2 [8e850b90] libblastrampoline_jll v5.12.0+0 [8e850ede] nghttp2_jll v1.65.0+0 [3f19e933] p7zip_jll v17.5.0+2 Testing Running tests... [ Info: Downloading file from PDB: 1ASS [ Info: Downloading file from PDB: 1ASS [ Info: File exists: 1ASS [ Info: Downloading file from PDB: 3HFM [ Info: Downloading file from PDB: 1EYE [ Info: Downloading file from PDB: 3HFM store: Error During Test at /home/pkgeval/.julia/packages/ProteinChains/raOGm/test/runtests.jl:88 Got exception outside of a @test KeyError: key InlineStrings.String31("3HFM.cif") not found Stacktrace: [1] getindex(g::JLD2.Group{JLD2.JLDFile{JLD2.MmapIO}}, name::InlineStrings.String31) @ JLD2 ~/.julia/packages/JLD2/pdSa4/src/groups.jl:96 [2] getindex(f::JLD2.JLDFile{JLD2.MmapIO}, name::InlineStrings.String31) @ JLD2 ~/.julia/packages/JLD2/pdSa4/src/JLD2.jl:348 [3] getindex(store::ProteinStructureStore, key::InlineStrings.String31) @ ProteinChains ~/.julia/packages/ProteinChains/raOGm/src/store.jl:58 [4] (::ProteinChains.var"#iterate_step#iterate_step##0"{ProteinStructureStore})(::Tuple{InlineStrings.String31, Int64}) @ ProteinChains ~/.julia/packages/ProteinChains/raOGm/src/store.jl:79 [5] iterate @ ~/.julia/packages/ProteinChains/raOGm/src/store.jl:81 [inlined] [6] iterate @ ./abstractdict.jl:66 [inlined] [7] copyto!(dest::Vector{ProteinStructure}, src::Base.ValueIterator{ProteinStructureStore}) @ Base ./abstractarray.jl:948 [8] _collect @ ./array.jl:734 [inlined] [9] collect @ ./array.jl:728 [inlined] [10] call_composed @ ./operators.jl:1100 [inlined] [11] (::ComposedFunction{typeof(collect), typeof(values)})(x::ProteinStructureStore) @ Base ./operators.jl:1097 [12] open(::ComposedFunction{typeof(collect), typeof(values)}, ::Type, ::Vararg{Any}; kwargs::@Kwargs{}) @ Base ./io.jl:410 [13] open @ ./io.jl:407 [inlined] [14] ProteinStructureStore @ ~/.julia/packages/ProteinChains/raOGm/src/store.jl:92 [inlined] [15] deserialize @ ~/.julia/packages/ProteinChains/raOGm/src/store.jl:116 [inlined] [16] (::var"#9#10")(dir::String) @ Main ~/.julia/packages/ProteinChains/raOGm/test/runtests.jl:102 [17] mktempdir(fn::var"#9#10", parent::String; prefix::String) @ Base.Filesystem ./file.jl:899 [18] mktempdir(fn::Function, parent::String) @ Base.Filesystem ./file.jl:895 [19] top-level scope @ ~/.julia/packages/ProteinChains/raOGm/test/runtests.jl:6 [20] macro expansion @ /opt/julia/share/julia/stdlib/v1.13/Test/src/Test.jl:1833 [inlined] [21] macro expansion @ ~/.julia/packages/ProteinChains/raOGm/test/runtests.jl:89 [inlined] [22] macro expansion @ /opt/julia/share/julia/stdlib/v1.13/Test/src/Test.jl:1833 [inlined] [23] macro expansion @ ~/.julia/packages/ProteinChains/raOGm/test/runtests.jl:89 [inlined] [24] include(mapexpr::Function, mod::Module, _path::String) @ Base ./Base.jl:310 [25] top-level scope @ none:6 [26] eval(m::Module, e::Any) @ Core ./boot.jl:489 [27] exec_options(opts::Base.JLOptions) @ Base ./client.jl:297 [28] _start() @ Base ./client.jl:564 Test Summary: | Pass Error Total Time ProteinChains.jl | 27 1 28 2m14.8s atom.jl | 15 15 1.9s properties.jl | 1 1 0.9s chain.jl | 3 3 1.9s structure.jl | 4 4 0.8s io | 4 4 38.8s store | 1 1 1m30.5s RNG of the outermost testset: Random.Xoshiro(0x60a68bf305689f45, 0x856dcd7d879ad255, 0xf8902cff8b856d7c, 0x4919999fd916a245, 0xcb7408c84572a993) ERROR: LoadError: Some tests did not pass: 27 passed, 0 failed, 1 errored, 0 broken. in expression starting at /home/pkgeval/.julia/packages/ProteinChains/raOGm/test/runtests.jl:4 Testing failed after 169.09s ERROR: LoadError: Package ProteinChains errored during testing Stacktrace: [1] pkgerror(msg::String) @ Pkg.Types /opt/julia/share/julia/stdlib/v1.13/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/v1.13/Pkg/src/Operations.jl:2418 [3] test @ /opt/julia/share/julia/stdlib/v1.13/Pkg/src/Operations.jl:2273 [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/v1.13/Pkg/src/API.jl:498 [5] test(pkgs::Vector{PackageSpec}; io::IOContext{IO}, kwargs::@Kwargs{julia_args::Cmd}) @ Pkg.API /opt/julia/share/julia/stdlib/v1.13/Pkg/src/API.jl:164 [6] test(pkgs::Vector{String}; kwargs::@Kwargs{julia_args::Cmd}) @ Pkg.API /opt/julia/share/julia/stdlib/v1.13/Pkg/src/API.jl:152 [7] test @ /opt/julia/share/julia/stdlib/v1.13/Pkg/src/API.jl:152 [inlined] [8] #test#81 @ /opt/julia/share/julia/stdlib/v1.13/Pkg/src/API.jl:151 [inlined] [9] top-level scope @ /PkgEval.jl/scripts/evaluate.jl:219 [10] include(mod::Module, _path::String) @ Base ./Base.jl:309 [11] exec_options(opts::Base.JLOptions) @ Base ./client.jl:331 [12] _start() @ Base ./client.jl:564 in expression starting at /PkgEval.jl/scripts/evaluate.jl:210 PkgEval failed after 254.06s: package tests unexpectedly errored