Package evaluation to test ProteinChains on Julia 1.13.0-DEV.1319 (9cddfda8ef*) started at 2025-10-16T20:11:24.465 ################################################################################ # Set-up # Installing PkgEval dependencies (TestEnv)... Set-up completed after 10.8s ################################################################################ # Installation # Installing ProteinChains... Resolving package versions... Installed libaec_jll ────────────────── v1.1.4+0 Installed Adapt ─────────────────────── v4.4.0 Installed MacroTools ────────────────── v0.5.16 Installed InlineStrings ─────────────── v1.4.5 Installed DataStructures ────────────── v0.19.1 Installed Quaternions ───────────────── v0.7.6 Installed JLD2 ──────────────────────── v0.5.15 Installed MPICH_jll ─────────────────── v4.3.1+0 Installed PeriodicTable ─────────────── v1.2.1 Installed ArnoldiMethod ─────────────── v0.4.0 Installed CodecZlib ─────────────────── v0.7.8 Installed BioStructures ─────────────── v4.7.0 Installed NearestNeighbors ──────────── v0.4.22 Installed TranscodingStreams ────────── v0.11.3 Installed Backboner ─────────────────── v0.12.2 Installed MicrosoftMPI_jll ──────────── v10.1.4+3 Installed HashArrayMappedTries ──────── v0.2.0 Installed OrderedCollections ────────── v1.8.1 Installed RecipesBase ───────────────── v1.3.4 Installed Compat ────────────────────── v4.18.1 Installed Statistics ────────────────── v1.11.1 Installed PrecompileTools ───────────── v1.3.3 Installed Xorg_libpciaccess_jll ─────── v0.18.1+0 Installed StatsAPI ──────────────────── v1.7.1 Installed Atomix ────────────────────── v1.1.2 Installed NNlib ─────────────────────── v0.9.31 Installed BioSymbols ────────────────── v5.2.0 Installed StaticArrays ──────────────── v1.9.15 Installed RealDot ───────────────────── v0.1.0 Installed StaticArraysCore ──────────── v1.4.3 Installed FileIO ────────────────────── v1.17.1 Installed GPUArraysCore ─────────────── v0.2.0 Installed ChainRulesCore ────────────── v1.26.0 Installed Distances ─────────────────── v0.10.12 Installed SimpleTraits ──────────────── v0.9.5 Installed BitIntegers ───────────────── v0.3.5 Installed Requires ──────────────────── v1.3.1 Installed OpenMPI_jll ───────────────── v5.0.8+0 Installed HDF5_jll ──────────────────── v1.14.6+0 Installed Parsers ───────────────────── v2.8.3 Installed Hwloc_jll ─────────────────── v2.12.2+0 Installed JSON ──────────────────────── v0.21.4 Installed ScopedValues ──────────────── v1.5.0 Installed KernelAbstractions ────────── v0.9.38 Installed BioGenerics ───────────────── v0.1.5 Installed UnsafeAtomics ─────────────── v0.3.0 Installed XML2_jll ──────────────────── v2.13.9+0 Installed Reexport ──────────────────── v1.2.2 Installed Unitful ───────────────────── v1.25.0 Installed AssigningSecondaryStructure ─ v0.5.1 Installed Preferences ───────────────── v1.5.0 Installed DynamicStructs ────────────── v0.2.3 Installed MPIPreferences ────────────── v0.1.11 Installed Libiconv_jll ──────────────── v1.18.0+0 Installed JLLWrappers ───────────────── v1.7.1 Installed ProteinChains ─────────────── v0.7.3 Installed Rotations ─────────────────── v1.7.1 Installed MPItrampoline_jll ─────────── v5.5.4+0 Installed Format ────────────────────── v1.3.7 Installed Inflate ───────────────────── v0.1.5 Installed HDF5 ──────────────────────── v0.17.2 Installed Graphs ────────────────────── v1.13.1 Installing 7 artifacts Installed artifact Xorg_libpciaccess 24.8 KiB Installed artifact libaec 49.6 KiB Installed artifact Libiconv 1.9 MiB Installed artifact Hwloc 3.5 MiB Installed artifact XML2 2.5 MiB Installed artifact HDF5 5.7 MiB Installed artifact MPICH 3.3 MiB Updating `~/.julia/environments/v1.13/Project.toml` [b8e8f2a5] + ProteinChains v0.7.3 Updating `~/.julia/environments/v1.13/Manifest.toml` [79e6a3ab] + Adapt v4.4.0 [ec485272] + ArnoldiMethod v0.4.0 [8ed43e74] + AssigningSecondaryStructure v0.5.1 [a9b6321e] + Atomix v1.1.2 [9ac9c2a2] + Backboner v0.12.2 [47718e42] + BioGenerics v0.1.5 [de9282ab] + BioStructures v4.7.0 [3c28c6f8] + BioSymbols v5.2.0 [c3b6d118] + BitIntegers v0.3.5 [d360d2e6] + ChainRulesCore v1.26.0 [944b1d66] + CodecZlib v0.7.8 [34da2185] + Compat v4.18.1 [864edb3b] + DataStructures v0.19.1 [b4f34e82] + Distances v0.10.12 [e139c391] + DynamicStructs v0.2.3 [5789e2e9] + FileIO v1.17.1 [1fa38f19] + Format v1.3.7 [46192b85] + GPUArraysCore v0.2.0 [86223c79] + Graphs v1.13.1 [f67ccb44] + HDF5 v0.17.2 [076d061b] + HashArrayMappedTries v0.2.0 [d25df0c9] + Inflate v0.1.5 [842dd82b] + InlineStrings v1.4.5 ⌅ [033835bb] + JLD2 v0.5.15 [692b3bcd] + JLLWrappers v1.7.1 ⌅ [682c06a0] + JSON v0.21.4 [63c18a36] + KernelAbstractions v0.9.38 [3da0fdf6] + MPIPreferences v0.1.11 [1914dd2f] + MacroTools v0.5.16 [872c559c] + NNlib v0.9.31 [b8a86587] + NearestNeighbors v0.4.22 [bac558e1] + OrderedCollections v1.8.1 [69de0a69] + Parsers v2.8.3 [7b2266bf] + PeriodicTable v1.2.1 [aea7be01] + PrecompileTools v1.3.3 [21216c6a] + Preferences v1.5.0 [b8e8f2a5] + ProteinChains v0.7.3 [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 v1.5.0 [699a6c99] + SimpleTraits v0.9.5 [90137ffa] + StaticArrays v1.9.15 [1e83bf80] + StaticArraysCore v1.4.3 [10745b16] + Statistics v1.11.1 [82ae8749] + StatsAPI v1.7.1 [3bb67fe8] + TranscodingStreams v0.11.3 [1986cc42] + Unitful v1.25.0 [013be700] + UnsafeAtomics v0.3.0 [0234f1f7] + HDF5_jll v1.14.6+0 [e33a78d0] + Hwloc_jll v2.12.2+0 [94ce4f54] + Libiconv_jll v1.18.0+0 [7cb0a576] + MPICH_jll v4.3.1+0 [f1f71cc9] + MPItrampoline_jll v5.5.4+0 [9237b28f] + MicrosoftMPI_jll v10.1.4+3 [fe0851c0] + OpenMPI_jll v5.0.8+0 ⌅ [02c8fc9c] + XML2_jll v2.13.9+0 [a65dc6b1] + Xorg_libpciaccess_jll v0.18.1+0 [477f73a3] + libaec_jll v1.1.4+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 v1.13.0 [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 v1.13.0 [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 v8.16.0+0 [e37daf67] + LibGit2_jll v1.9.1+0 [29816b5a] + LibSSH2_jll v1.11.3+1 [14a3606d] + MozillaCACerts_jll v2025.9.9 [4536629a] + OpenBLAS_jll v0.3.29+0 [458c3c95] + OpenSSL_jll v3.5.4+0 [efcefdf7] + PCRE2_jll v10.46.0+0 [bea87d4a] + SuiteSparse_jll v7.10.1+0 [83775a58] + Zlib_jll v1.3.1+2 [3161d3a3] + Zstd_jll v1.5.7+1 [8e850b90] + libblastrampoline_jll v5.15.0+0 [8e850ede] + nghttp2_jll v1.67.1+0 [3f19e933] + p7zip_jll v17.6.0+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 15.04s ################################################################################ # Precompilation # Precompiling PkgEval dependencies... Precompiling packages... 4601.4 ms ✓ TestEnv 1 dependency successfully precompiled in 5 seconds. 27 already precompiled. Precompiling package dependencies... Precompilation completed after 60.25s ################################################################################ # Testing # Testing ProteinChains Status `/tmp/jl_r8O19d/Project.toml` [8ed43e74] AssigningSecondaryStructure v0.5.1 [9ac9c2a2] Backboner v0.12.2 [de9282ab] BioStructures v4.7.0 [c3b6d118] BitIntegers v0.3.5 [34da2185] Compat v4.18.1 [e139c391] DynamicStructs v0.2.3 [86223c79] Graphs v1.13.1 [f67ccb44] HDF5 v0.17.2 [842dd82b] InlineStrings v1.4.5 ⌅ [033835bb] JLD2 v0.5.15 ⌅ [682c06a0] JSON v0.21.4 [7b2266bf] PeriodicTable v1.2.1 [b8e8f2a5] ProteinChains v0.7.3 [189a3867] Reexport v1.2.2 [90137ffa] StaticArrays v1.9.15 [10745b16] Statistics v1.11.1 [37e2e46d] LinearAlgebra v1.13.0 [8dfed614] Test v1.11.0 Status `/tmp/jl_r8O19d/Manifest.toml` [79e6a3ab] Adapt v4.4.0 [ec485272] ArnoldiMethod v0.4.0 [8ed43e74] AssigningSecondaryStructure v0.5.1 [a9b6321e] Atomix v1.1.2 [9ac9c2a2] Backboner v0.12.2 [47718e42] BioGenerics v0.1.5 [de9282ab] BioStructures v4.7.0 [3c28c6f8] BioSymbols v5.2.0 [c3b6d118] BitIntegers v0.3.5 [d360d2e6] ChainRulesCore v1.26.0 [944b1d66] CodecZlib v0.7.8 [34da2185] Compat v4.18.1 [864edb3b] DataStructures v0.19.1 [b4f34e82] Distances v0.10.12 [e139c391] DynamicStructs v0.2.3 [5789e2e9] FileIO v1.17.1 [1fa38f19] Format v1.3.7 [46192b85] GPUArraysCore v0.2.0 [86223c79] Graphs v1.13.1 [f67ccb44] HDF5 v0.17.2 [076d061b] HashArrayMappedTries v0.2.0 [d25df0c9] Inflate v0.1.5 [842dd82b] InlineStrings v1.4.5 ⌅ [033835bb] JLD2 v0.5.15 [692b3bcd] JLLWrappers v1.7.1 ⌅ [682c06a0] JSON v0.21.4 [63c18a36] KernelAbstractions v0.9.38 [3da0fdf6] MPIPreferences v0.1.11 [1914dd2f] MacroTools v0.5.16 [872c559c] NNlib v0.9.31 [b8a86587] NearestNeighbors v0.4.22 [bac558e1] OrderedCollections v1.8.1 [69de0a69] Parsers v2.8.3 [7b2266bf] PeriodicTable v1.2.1 [aea7be01] PrecompileTools v1.3.3 [21216c6a] Preferences v1.5.0 [b8e8f2a5] ProteinChains v0.7.3 [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 v1.5.0 [699a6c99] SimpleTraits v0.9.5 [90137ffa] StaticArrays v1.9.15 [1e83bf80] StaticArraysCore v1.4.3 [10745b16] Statistics v1.11.1 [82ae8749] StatsAPI v1.7.1 [3bb67fe8] TranscodingStreams v0.11.3 [1986cc42] Unitful v1.25.0 [013be700] UnsafeAtomics v0.3.0 [0234f1f7] HDF5_jll v1.14.6+0 [e33a78d0] Hwloc_jll v2.12.2+0 [94ce4f54] Libiconv_jll v1.18.0+0 [7cb0a576] MPICH_jll v4.3.1+0 [f1f71cc9] MPItrampoline_jll v5.5.4+0 [9237b28f] MicrosoftMPI_jll v10.1.4+3 [fe0851c0] OpenMPI_jll v5.0.8+0 ⌅ [02c8fc9c] XML2_jll v2.13.9+0 [a65dc6b1] Xorg_libpciaccess_jll v0.18.1+0 [477f73a3] libaec_jll v1.1.4+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 v1.13.0 [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 v1.13.0 [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 v8.16.0+0 [e37daf67] LibGit2_jll v1.9.1+0 [29816b5a] LibSSH2_jll v1.11.3+1 [14a3606d] MozillaCACerts_jll v2025.9.9 [4536629a] OpenBLAS_jll v0.3.29+0 [458c3c95] OpenSSL_jll v3.5.4+0 [efcefdf7] PCRE2_jll v10.46.0+0 [bea87d4a] SuiteSparse_jll v7.10.1+0 [83775a58] Zlib_jll v1.3.1+2 [3161d3a3] Zstd_jll v1.5.7+1 [8e850b90] libblastrampoline_jll v5.15.0+0 [8e850ede] nghttp2_jll v1.67.1+0 [3f19e933] p7zip_jll v17.6.0+0 Info Packages marked with ⌅ have new versions available but compatibility constraints restrict them from upgrading. Testing Running tests... ERROR: LoadError: ParseError: # Error @ /home/pkgeval/.julia/packages/Unitful/HCJFR/src/logarithm.jl:127:5 Base. *(::MixedUnits, ::MixedUnits) = # └───────────────────────────────┘ ── extra tokens after end of expression Stacktrace: [1] top-level scope @ ~/.julia/packages/Unitful/HCJFR/src/logarithm.jl:127 [2] include(mapexpr::Function, mod::Module, _path::String) @ Base ./Base.jl:310 [3] top-level scope @ ~/.julia/packages/Unitful/HCJFR/src/Unitful.jl:67 [4] include(mod::Module, _path::String) @ Base ./Base.jl:309 [5] __require_prelocked(pkg::Base.PkgId, env::String) @ Base ./loading.jl:2777 [6] _require_prelocked(uuidkey::Base.PkgId, env::String) @ Base ./loading.jl:2536 [7] macro expansion @ ./loading.jl:2464 [inlined] [8] macro expansion @ ./lock.jl:376 [inlined] [9] __require(into::Module, mod::Symbol) @ Base ./loading.jl:2428 [10] require @ ./loading.jl:2404 [inlined] [11] eval_import_path @ ./module.jl:36 [inlined] [12] eval_import_path_all(at::Module, path::Expr, keyword::String) @ Base ./module.jl:60 [13] _eval_import(::Bool, ::Module, ::Expr, ::Expr, ::Vararg{Expr}) @ Base ./module.jl:101 [14] top-level scope @ ~/.julia/packages/PeriodicTable/S55ll/src/PeriodicTable.jl:14 [15] include(mod::Module, _path::String) @ Base ./Base.jl:309 [16] __require_prelocked(pkg::Base.PkgId, env::String) @ Base ./loading.jl:2777 [17] _require_prelocked(uuidkey::Base.PkgId, env::String) @ Base ./loading.jl:2536 [18] macro expansion @ ./loading.jl:2464 [inlined] [19] macro expansion @ ./lock.jl:376 [inlined] [20] __require(into::Module, mod::Symbol) @ Base ./loading.jl:2428 [21] require @ ./loading.jl:2404 [inlined] [22] eval_import_path @ ./module.jl:36 [inlined] [23] eval_import_path_all(at::Module, path::Expr, keyword::String) @ Base ./module.jl:60 [24] _eval_import(::Bool, ::Module, ::Expr, ::Expr, ::Vararg{Expr}) @ Base ./module.jl:101 [25] top-level scope @ ~/.julia/packages/ProteinChains/8G9xL/src/atom.jl:1 [26] include(mapexpr::Function, mod::Module, _path::String) @ Base ./Base.jl:310 [27] top-level scope @ ~/.julia/packages/ProteinChains/8G9xL/src/ProteinChains.jl:10 [28] include(mod::Module, _path::String) @ Base ./Base.jl:309 [29] __require_prelocked(pkg::Base.PkgId, env::String) @ Base ./loading.jl:2777 [30] _require_prelocked(uuidkey::Base.PkgId, env::String) @ Base ./loading.jl:2536 [31] macro expansion @ ./loading.jl:2464 [inlined] [32] macro expansion @ ./lock.jl:376 [inlined] [33] __require(into::Module, mod::Symbol) @ Base ./loading.jl:2428 [34] require @ ./loading.jl:2404 [inlined] [35] eval_import_path @ ./module.jl:36 [inlined] [36] eval_import_path_all(at::Module, path::Expr, keyword::String) @ Base ./module.jl:60 [37] _eval_using(to::Module, path::Expr) @ Base ./module.jl:137 [38] top-level scope @ ~/.julia/packages/ProteinChains/8G9xL/test/runtests.jl:1 [39] include(mapexpr::Function, mod::Module, _path::String) @ Base ./Base.jl:310 [40] top-level scope @ none:6 [41] eval(m::Module, e::Any) @ Core ./boot.jl:489 [42] exec_options(opts::Base.JLOptions) @ Base ./client.jl:310 [43] _start() @ Base ./client.jl:577 in expression starting at /home/pkgeval/.julia/packages/Unitful/HCJFR/src/logarithm.jl:127 in expression starting at /home/pkgeval/.julia/packages/Unitful/HCJFR/src/Unitful.jl:1 in expression starting at /home/pkgeval/.julia/packages/PeriodicTable/S55ll/src/PeriodicTable.jl:3 in expression starting at /home/pkgeval/.julia/packages/ProteinChains/8G9xL/src/atom.jl:1 in expression starting at /home/pkgeval/.julia/packages/ProteinChains/8G9xL/src/ProteinChains.jl:1 in expression starting at /home/pkgeval/.julia/packages/ProteinChains/8G9xL/test/runtests.jl:1 Testing failed after 142.8s 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:2674 [3] test @ /opt/julia/share/julia/stdlib/v1.13/Pkg/src/Operations.jl:2523 [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:548 [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/v1.13/Pkg/src/API.jl:525 [6] 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:172 [7] kwcall(::@NamedTuple{julia_args::Cmd}, ::typeof(Pkg.API.test), pkgs::Vector{PackageSpec}) @ Pkg.API /opt/julia/share/julia/stdlib/v1.13/Pkg/src/API.jl:161 [8] test(pkgs::Vector{String}; kwargs::@Kwargs{julia_args::Cmd}) @ Pkg.API /opt/julia/share/julia/stdlib/v1.13/Pkg/src/API.jl:160 [9] test @ /opt/julia/share/julia/stdlib/v1.13/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/v1.13/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 249.56s: package tests unexpectedly errored