Package evaluation to test ProteinSecondaryStructures on Julia 1.14.0-DEV.2291 (26145852c4*) started at 2026-06-04T13:30:39.491 ################################################################################ # Set-up # Installing PkgEval dependencies (TestEnv)... Activating project at `~/.julia/environments/v1.14` Set-up completed after 17.39s ################################################################################ # Installation # Installing ProteinSecondaryStructures... Resolving package versions... Installed TestItems ────────────────── v1.0.0 Installed STRIDE_jll ───────────────── v1.0.0+0 Installed JLLWrappers ──────────────── v1.8.0 Installed DSSP_jll ─────────────────── v4.4.0+1 Installed Preferences ──────────────── v1.5.2 Installed ProteinSecondaryStructures ─ v2.0.3 Installing 2 artifacts Installed artifact STRIDE 353.3 KiB Installed artifact DSSP 3.8 MiB Updating `~/.julia/environments/v1.14/Project.toml` [c298f58b] + ProteinSecondaryStructures v2.0.3 Updating `~/.julia/environments/v1.14/Manifest.toml` [692b3bcd] + JLLWrappers v1.8.0 [21216c6a] + Preferences v1.5.2 [c298f58b] + ProteinSecondaryStructures v2.0.3 [1c621080] + TestItems v1.0.0 [74334e00] + DSSP_jll v4.4.0+1 [850473c1] + STRIDE_jll v1.0.0+0 [56f22d72] + Artifacts v1.11.0 [ade2ca70] + Dates v1.11.0 [8f399da3] + Libdl v1.11.0 [de0858da] + Printf v1.11.0 [fa267f1f] + TOML v1.0.3 [4ec0a83e] + Unicode v1.11.0 [83775a58] + Zlib_jll v1.3.2+0 Installation completed after 8.97s ################################################################################ # Precompilation # Precompiling PkgEval dependencies... Precompiling project... 4.8 s ✓ TestEnv 1 dependency successfully precompiled in 5 seconds. 27 already precompiled. Precompiling package dependencies... Precompiling project... 0.5 s ✓ TestItems 1.3 s ✓ Preferences 0.9 s ✓ Compat 33.9 s ✓ TestItemRunner 2.4 s ✓ JLLWrappers 0.6 s ✓ Compat → CompatLinearAlgebraExt 2.4 s ✓ DSSP_jll 2.4 s ✓ STRIDE_jll 7.6 s ✓ Aqua 1.9 s ✓ ProteinSecondaryStructures 10 dependencies successfully precompiled in 54 seconds. 30 already precompiled. Precompilation completed after 88.5s ################################################################################ # Testing # Testing ProteinSecondaryStructures Status `/tmp/jl_HgogYR/Project.toml` ⌅ [4c88cf16] Aqua v0.6.7 [c298f58b] ProteinSecondaryStructures v2.0.3 [f8b46487] TestItemRunner v1.1.5 [1c621080] TestItems v1.0.0 [74334e00] DSSP_jll v4.4.0+1 [850473c1] STRIDE_jll v1.0.0+0 [8dfed614] Test v1.11.0 Status `/tmp/jl_HgogYR/Manifest.toml` ⌅ [4c88cf16] Aqua v0.6.7 [34da2185] Compat v4.18.1 [692b3bcd] JLLWrappers v1.8.0 [21216c6a] Preferences v1.5.2 [c298f58b] ProteinSecondaryStructures v2.0.3 [f8b46487] TestItemRunner v1.1.5 [1c621080] TestItems v1.0.0 [74334e00] DSSP_jll v4.4.0+1 [850473c1] STRIDE_jll v1.0.0+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 v1.13.0 [b27032c2] LibCURL v1.0.0 [76f85450] LibGit2 v1.11.0 [8f399da3] Libdl v1.11.0 [56ddb016] Logging v1.11.0 [d6f4376e] Markdown v1.11.0 [ca575930] NetworkOptions v1.3.0 [44cfe95a] Pkg v1.14.0 [de0858da] Printf v1.11.0 [9a3f8284] Random v1.11.0 [ea8e919c] SHA v1.13.0 [9e88b42a] Serialization v1.11.0 [f489334b] StyledStrings v1.13.0 [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 v1.5.2+0 [deac9b47] LibCURL_jll v8.20.0+1 [e37daf67] LibGit2_jll v1.9.4+0 [29816b5a] LibSSH2_jll v1.11.101+0 [14a3606d] MozillaCACerts_jll v2026.5.14 [458c3c95] OpenSSL_jll v3.5.6+0 [efcefdf7] PCRE2_jll v10.47.0+0 [83775a58] Zlib_jll v1.3.2+0 [3161d3a3] Zstd_jll v1.5.7+1 [8e850ede] nghttp2_jll v1.69.0+0 [3f19e933] p7zip_jll v17.8.0+0 Info Packages marked with ⌅ have new versions available but compatibility constraints restrict them from upgrading. Testing Running tests... IGNORED /tmp/jl_xg1Ot6DYtU.pdb A (less than 5 residues) No valid chain in /tmp/jl_xg1Ot6DYtU.pdb ┌ Warning: `isbindingresolved(m::Module, var::Symbol)` is deprecated, use `true` instead. │ caller = walkmodules(f::Aqua.var"#undefined_exports##0#undefined_exports##1"{Vector{Symbol}}, x::Module) at exports.jl:5 └ @ Aqua ~/.julia/packages/Aqua/zpdNP/src/exports.jl:5 ┌ Warning: `isbindingresolved(m::Module, var::Symbol)` is deprecated, use `true` instead. │ caller = walkmodules(f::Aqua.Piracy.var"#3#4"{Bool, IdSet{Any}, Vector{Method}}, x::Module) at exports.jl:5 └ @ Aqua ~/.julia/packages/Aqua/zpdNP/src/exports.jl:5 Possible type-piracy detected: [1] ProteinSecondaryStructures.SSData(resname::String, chain::String, resnum::Int64, sscode::String, phi::Float64, psi::Float64) @ ProteinSecondaryStructures ~/.julia/packages/ProteinSecondaryStructures/tkPJd/src/ProteinSecondaryStructures.jl:34 [2] ProteinSecondaryStructures.SSData(resname, chain, resnum, sscode, phi, psi) @ ProteinSecondaryStructures ~/.julia/packages/ProteinSecondaryStructures/tkPJd/src/ProteinSecondaryStructures.jl:34 [3] ProteinSecondaryStructures.Testing.ExampleData(filename::String, ss_composition::Dict{Symbol, Dict{String, Int64}}) @ ProteinSecondaryStructures.Testing ~/.julia/packages/ProteinSecondaryStructures/tkPJd/test/Testing.jl:6 [4] ProteinSecondaryStructures.Testing.ExampleData(filename, ss_composition) @ ProteinSecondaryStructures.Testing ~/.julia/packages/ProteinSecondaryStructures/tkPJd/test/Testing.jl:6 Piracy: Test Failed at /home/pkgeval/.julia/packages/Aqua/zpdNP/src/piracy.jl:206 Expression: isempty(v) Evaluated: isempty(Method[ProteinSecondaryStructures.SSData(resname::String, chain::String, resnum::Int64, sscode::String, phi::Float64, psi::Float64) @ ProteinSecondaryStructures ~/.julia/packages/ProteinSecondaryStructures/tkPJd/src/ProteinSecondaryStructures.jl:34, ProteinSecondaryStructures.SSData(resname, chain, resnum, sscode, phi, psi) @ ProteinSecondaryStructures ~/.julia/packages/ProteinSecondaryStructures/tkPJd/src/ProteinSecondaryStructures.jl:34, ProteinSecondaryStructures.Testing.ExampleData(filename::String, ss_composition::Dict{Symbol, Dict{String, Int64}}) @ ProteinSecondaryStructures.Testing ~/.julia/packages/ProteinSecondaryStructures/tkPJd/test/Testing.jl:6, ProteinSecondaryStructures.Testing.ExampleData(filename, ss_composition) @ ProteinSecondaryStructures.Testing ~/.julia/packages/ProteinSecondaryStructures/tkPJd/test/Testing.jl:6]) Stacktrace: [1] macro expansion @ /opt/julia/share/julia/stdlib/v1.14/Test/src/Test.jl:784 [inlined] [2] test_piracy(m::Module; broken::Bool, kwargs::@Kwargs{}) @ Aqua ~/.julia/packages/Aqua/zpdNP/src/piracy.jl:206 [3] test_piracy(m::Module) @ Aqua ~/.julia/packages/Aqua/zpdNP/src/piracy.jl:191 [inlined] [4] macro expansion @ ~/.julia/packages/Aqua/zpdNP/src/Aqua.jl:118 [inlined] [5] macro expansion @ /opt/julia/share/julia/stdlib/v1.14/Test/src/Test.jl:2246 [inlined] [6] test_all(testtarget::Module; ambiguities::Bool, unbound_args::Bool, undefined_exports::Bool, project_extras::Bool, stale_deps::Bool, deps_compat::Bool, project_toml_formatting::Bool, piracy::Bool) @ Aqua ~/.julia/packages/Aqua/zpdNP/src/Aqua.jl:117 Test Summary: | Pass Fail Total Time Package | 28 1 29 55.6s src/stride.jl | 6 6 2.9s test/runtests.jl | 8 1 9 49.1s Aqua.test_all | 8 1 9 49.1s Method ambiguity | 1 1 8.6s Unbound type parameters | 1 1 0.1s Undefined exports | 1 1 3.6s Compare Project.toml and test/Project.toml | 1 1 0.1s Stale dependencies | 1 1 4.5s Compat bounds | 1 1 2.0s Project.toml formatting | 2 2 0.8s Piracy | 1 1 8.2s src/dssp.jl | 7 7 3.4s src/ProteinSecondaryStructures.jl | 7 7 0.2s ERROR: LoadError: Some tests did not pass: 28 passed, 1 failed, 0 errored, 0 broken. in expression starting at /home/pkgeval/.julia/packages/ProteinSecondaryStructures/tkPJd/test/runtests.jl:3 Testing failed after 123.69s ERROR: LoadError: Package ProteinSecondaryStructures 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:3247 [3] 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:587 [4] 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 [5] test(pkgs::Vector{String}; kwargs::@Kwargs{julia_args::Cmd}) @ Pkg.API /opt/julia/share/julia/stdlib/v1.14/Pkg/src/API.jl:160 [6] test(pkg::String; kwargs::@Kwargs{julia_args::Cmd}) @ Pkg.API /opt/julia/share/julia/stdlib/v1.14/Pkg/src/API.jl:159 [inlined] [7] top-level scope @ /PkgEval.jl/scripts/evaluate.jl:223 [8] include(mod::Module, _path::String) @ Base Base.jl:326 [9] exec_options(opts::Base.JLOptions) @ Base client.jl:355 [10] _start() @ Base client.jl:596 in expression starting at /PkgEval.jl/scripts/evaluate.jl:214 PkgEval failed after 256.09s: package has test failures