Package evaluation of ViennaRNA on Julia 1.13.0-DEV.955 (13f6b3b5c0*) started at 2025-08-03T13:48:51.923 ################################################################################ # Set-up # Installing PkgEval dependencies (TestEnv)... Set-up completed after 9.99s ################################################################################ # Installation # Installing ViennaRNA... Resolving package versions... Installed OpenBLAS32_jll ─ v0.3.29+0 Installed UnsafePointers ─ v1.0.0 Installed CEnum ────────── v0.5.0 Installed Unitful ──────── v1.24.0 Installed PCRE_jll ─────── v8.45.0+0 Installed JLLWrappers ──── v1.7.1 Installed GSL_jll ──────── v2.7.2+0 Installed LLVMOpenMP_jll ─ v18.1.8+0 Installed ViennaRNA_jll ── v2.6.4+0 Installed Preferences ──── v1.4.3 Installed ViennaRNA ────── v0.11.2 Installing 5 artifacts Installed artifact LLVMOpenMP 661.6 KiB Installed artifact PCRE 1.1 MiB Installed artifact GSL 4.4 MiB Installed artifact OpenBLAS32 10.0 MiB Installed artifact ViennaRNA 96.6 MiB Updating `~/.julia/environments/v1.13/Project.toml` [05a721ad] + ViennaRNA v0.11.2 Updating `~/.julia/environments/v1.13/Manifest.toml` [fa961155] + CEnum v0.5.0 [692b3bcd] + JLLWrappers v1.7.1 [21216c6a] + Preferences v1.4.3 [1986cc42] + Unitful v1.24.0 [e17b2a0c] + UnsafePointers v1.0.0 [05a721ad] + ViennaRNA v0.11.2 ⌅ [1b77fbbe] + GSL_jll v2.7.2+0 [1d63c593] + LLVMOpenMP_jll v18.1.8+0 [656ef2d0] + OpenBLAS32_jll v0.3.29+0 [2f80f16e] + PCRE_jll v8.45.0+0 [b7a990de] + ViennaRNA_jll v2.6.4+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 [ac6e5ff7] + JuliaSyntaxHighlighting v1.12.0 [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 [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 [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 [781609d7] + GMP_jll v6.3.0+2 [deac9b47] + LibCURL_jll v8.15.0+0 [e37daf67] + LibGit2_jll v1.9.1+0 [29816b5a] + LibSSH2_jll v1.11.3+1 [3a97d323] + MPFR_jll v4.2.2+0 [14a3606d] + MozillaCACerts_jll v2025.7.15 [4536629a] + OpenBLAS_jll v0.3.29+0 [458c3c95] + OpenSSL_jll v3.5.1+0 [efcefdf7] + PCRE2_jll v10.45.0+0 [83775a58] + Zlib_jll v1.3.1+2 [8e850b90] + libblastrampoline_jll v5.13.1+0 [8e850ede] + nghttp2_jll v1.65.0+0 [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 13.68s ################################################################################ # Precompilation # Precompiling PkgEval dependencies... Precompiling packages... 4475.7 ms ✓ TestEnv 1 dependency successfully precompiled in 5 seconds. 26 already precompiled. Precompiling package dependencies... Precompilation completed after 92.94s ################################################################################ # Testing # Testing ViennaRNA Status `/tmp/jl_3oAeSu/Project.toml` [4c88cf16] Aqua v0.8.13 [fa961155] CEnum v0.5.0 [1986cc42] Unitful v1.24.0 [e17b2a0c] UnsafePointers v1.0.0 [05a721ad] ViennaRNA v0.11.2 [b7a990de] ViennaRNA_jll v2.6.4+0 [8dfed614] Test v1.11.0 Status `/tmp/jl_3oAeSu/Manifest.toml` [4c88cf16] Aqua v0.8.13 [fa961155] CEnum v0.5.0 [34da2185] Compat v4.18.0 [692b3bcd] JLLWrappers v1.7.1 [21216c6a] Preferences v1.4.3 [1986cc42] Unitful v1.24.0 [e17b2a0c] UnsafePointers v1.0.0 [05a721ad] ViennaRNA v0.11.2 ⌅ [1b77fbbe] GSL_jll v2.7.2+0 [1d63c593] LLVMOpenMP_jll v18.1.8+0 [656ef2d0] OpenBLAS32_jll v0.3.29+0 [2f80f16e] PCRE_jll v8.45.0+0 [b7a990de] ViennaRNA_jll v2.6.4+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 [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 [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 [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 [781609d7] GMP_jll v6.3.0+2 [deac9b47] LibCURL_jll v8.15.0+0 [e37daf67] LibGit2_jll v1.9.1+0 [29816b5a] LibSSH2_jll v1.11.3+1 [3a97d323] MPFR_jll v4.2.2+0 [14a3606d] MozillaCACerts_jll v2025.7.15 [4536629a] OpenBLAS_jll v0.3.29+0 [458c3c95] OpenSSL_jll v3.5.1+0 [efcefdf7] PCRE2_jll v10.45.0+0 [83775a58] Zlib_jll v1.3.1+2 [8e850b90] libblastrampoline_jll v5.13.1+0 [8e850ede] nghttp2_jll v1.65.0+0 [3f19e933] p7zip_jll v17.5.0+2 Info Packages marked with ⌅ have new versions available but compatibility constraints restrict them from upgrading. Testing Running tests... testing ViennaRNA testing Aqua.test_all Piracy: Error During Test at /home/pkgeval/.julia/packages/Aqua/1UuaV/src/Aqua.jl:103 Got exception outside of a @test FieldError: type Core.TypeName has no field `mt`, available fields: `name`, `module`, `singletonname`, `names`, `atomicfields`, `constfields`, `wrapper`, `Typeofwrapper`, `cache`, `linearcache`, `partial`, `hash`, `max_args`, `n_uninitialized`, `flags`, `cache_entry_count`, `max_methods`, `constprop_heuristic` Stacktrace: [1] getproperty(x::Core.TypeName, f::Symbol) @ Base ./Base_compiler.jl:57 [2] all_methods(mods::Module; skip_deprecated::Bool) @ Aqua.Piracy ~/.julia/packages/Aqua/1UuaV/src/piracies.jl:55 [3] all_methods @ ~/.julia/packages/Aqua/1UuaV/src/piracies.jl:21 [inlined] [4] #hunt#30 @ ~/.julia/packages/Aqua/1UuaV/src/piracies.jl:194 [inlined] [5] hunt @ ~/.julia/packages/Aqua/1UuaV/src/piracies.jl:193 [inlined] [6] test_piracies(m::Module; broken::Bool, kwargs::@Kwargs{}) @ Aqua ~/.julia/packages/Aqua/1UuaV/src/piracies.jl:219 [7] test_piracies @ ~/.julia/packages/Aqua/1UuaV/src/piracies.jl:218 [inlined] [8] macro expansion @ ~/.julia/packages/Aqua/1UuaV/src/Aqua.jl:104 [inlined] [9] macro expansion @ /opt/julia/share/julia/stdlib/v1.13/Test/src/Test.jl:1929 [inlined] [10] test_all(testtarget::Module; ambiguities::Bool, unbound_args::Bool, undefined_exports::Bool, project_extras::Bool, stale_deps::Bool, deps_compat::Bool, piracies::Bool, persistent_tasks::Bool, undocumented_names::Bool) @ Aqua ~/.julia/packages/Aqua/1UuaV/src/Aqua.jl:104 [11] test_all(testtarget::Module) @ Aqua ~/.julia/packages/Aqua/1UuaV/src/Aqua.jl:59 [12] top-level scope @ ~/.julia/packages/ViennaRNA/QSArb/test/aqua.jl:5 [13] macro expansion @ /opt/julia/share/julia/stdlib/v1.13/Test/src/Test.jl:1929 [inlined] [14] macro expansion @ ~/.julia/packages/ViennaRNA/QSArb/test/aqua.jl:6 [inlined] [15] include(mapexpr::Function, mod::Module, _path::String) @ Base ./Base.jl:312 [16] top-level scope @ ~/.julia/packages/ViennaRNA/QSArb/test/runtests.jl:8 [17] macro expansion @ /opt/julia/share/julia/stdlib/v1.13/Test/src/Test.jl:1929 [inlined] [18] macro expansion @ ~/.julia/packages/ViennaRNA/QSArb/test/runtests.jl:9 [inlined] [19] include(mapexpr::Function, mod::Module, _path::String) @ Base ./Base.jl:312 [20] top-level scope @ none:6 [21] eval(m::Module, e::Any) @ Core ./boot.jl:489 [22] exec_options(opts::Base.JLOptions) @ Base ./client.jl:286 [23] _start() @ Base ./client.jl:553 testing params_{load*,save} WARNING: stacking enthalpies not symmetric WARNING: stacking enthalpies not symmetric WARNING: stacking enthalpies not symmetric WARNING: stacking enthalpies not symmetric WARNING: stacking enthalpies not symmetric WARNING: stacking enthalpies not symmetric WARNING: stacking enthalpies not symmetric WARNING: stacking enthalpies not symmetric WARNING: stacking energies not symmetric WARNING: stacking energies not symmetric WARNING: stacking energies not symmetric WARNING: stacking energies not symmetric testing FoldCompound testing FoldCompound dp matrices testing mfe matrices testing partfn matrices testing Pairtable testing bpp testing bp_distance testing centroid testing energy testing ensemble_defect testing heat_capacity testing inverse_fold testing mea testing mean_bp_distance testing mfe testing mfe_window testing mfe_window_channel testing neighbors testing partfn testing plot_coords testing prob_of_structure testing sample_structures testing sc_mod_* testing subopt testing subopt_zuker testing tree_edit_dist testing prob_of_basepairs Test Summary: | Pass Error Total Time ViennaRNA | 717 1 718 2m11.2s Aqua.test_all | 10 1 11 1m27.1s Method ambiguity | 1 1 9.0s Unbound type parameters | 1 1 0.1s Undefined exports | 1 1 0.0s Compare Project.toml and test/Project.toml | 1 1 0.0s Stale dependencies | 1 1 4.5s Compat bounds | 4 4 0.7s Piracy | 1 1 4.7s Persistent tasks | 1 1 52.8s params_{load*,save} | 18 18 7.1s FoldCompound | 186 186 4.1s FoldCompound dp matrices | 31 31 3.1s Pairtable | 22 22 1.2s bpp | 5 5 1.0s bp_distance | 2 2 0.0s centroid | 3 3 0.1s energy | 12 12 1.6s ensemble_defect | 6 6 0.1s heat_capacity | 8 8 0.9s init_rand_seed | 1 1 0.0s inverse_fold | 4 4 0.3s mea | 7 7 0.2s mean_bp_distance | 3 3 0.1s mfe | 3 3 0.0s mfe_window | 4 4 0.4s mfe_window_channel | 4 4 0.6s neighbors | 1 1 0.6s partfn | 2 2 0.0s plot_coords | 338 338 1.7s prob_of_structure | 3 3 0.1s sample_structures | 24 24 0.4s sc_mod_* | 12 12 0.9s subopt | 4 4 0.4s subopt_zuker | 2 2 0.1s tree_edit_dist | 1 1 0.1s prob_of_basepairs | 1 1 1.7s RNG of the outermost testset: Random.Xoshiro(0x2a753871bc687db4, 0xa73e7af91f1b7fb8, 0xb89f5e1bcc1dae14, 0xc2997bfcff0a527f, 0x0d7fe3d30f97a4b9) ERROR: LoadError: Some tests did not pass: 717 passed, 0 failed, 1 errored, 0 broken. in expression starting at /home/pkgeval/.julia/packages/ViennaRNA/QSArb/test/runtests.jl:7 Testing failed after 142.63s ERROR: LoadError: Package ViennaRNA 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:2695 [3] test @ /opt/julia/share/julia/stdlib/v1.13/Pkg/src/Operations.jl:2544 [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:538 [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:515 [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:168 [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:157 [8] test(pkgs::Vector{String}; kwargs::@Kwargs{julia_args::Cmd}) @ Pkg.API /opt/julia/share/julia/stdlib/v1.13/Pkg/src/API.jl:156 [9] test @ /opt/julia/share/julia/stdlib/v1.13/Pkg/src/API.jl:156 [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:155 [11] top-level scope @ /PkgEval.jl/scripts/evaluate.jl:219 [12] include(mod::Module, _path::String) @ Base ./Base.jl:311 [13] exec_options(opts::Base.JLOptions) @ Base ./client.jl:320 [14] _start() @ Base ./client.jl:553 in expression starting at /PkgEval.jl/scripts/evaluate.jl:210 PkgEval failed after 276.44s: package tests unexpectedly errored