Package evaluation to test LinearFold on Julia 1.14.0-DEV.30 (073666df8b*) started at 2025-11-04T14:52:42.724 ################################################################################ # Set-up # Installing PkgEval dependencies (TestEnv)... Set-up completed after 9.49s ################################################################################ # Installation # Installing LinearFold... Resolving package versions... Updating `~/.julia/environments/v1.14/Project.toml` [aebc047d] + LinearFold v0.3.2 Updating `~/.julia/environments/v1.14/Manifest.toml` [67c07d97] + Automa v1.1.0 [47718e42] + BioGenerics v0.1.5 [c2308a5c] + FASTX v2.1.7 [692b3bcd] + JLLWrappers v1.7.1 [aebc047d] + LinearFold v0.3.2 [aea7be01] + PrecompileTools v1.3.3 [21216c6a] + Preferences v1.5.0 [fdea26ae] + SIMD v3.7.2 [354b36f9] + StringViews v1.3.5 [3bb67fe8] + TranscodingStreams v0.11.3 [1986cc42] + Unitful v1.25.1 [492392ba] + LinearFold_jll v1.0.0+0 [e9cb6f04] + LinearPartition_jll v1.0.0+0 [be43c337] + LinearSampling_jll v1.0.0+0 [cd7c2323] + LinearTurboFold_jll v0.0.1+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 v1.0.0 [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 v1.0.0 [9e88b42a] + Serialization 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 v10.47.0+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 Installation completed after 4.88s ################################################################################ # Precompilation # Precompiling PkgEval dependencies... ┌ Error: Failed to use TestEnv.jl; test dependencies will not be precompiled │ exception = │ UndefVarError: `project_rel_path` not defined in `TestEnv` │ Suggestion: this global was defined as `Pkg.Operations.project_rel_path` but not assigned a value. │ Stacktrace: │ [1] get_test_dir(ctx::Pkg.Types.Context, pkgspec::PackageSpec) │ @ TestEnv ~/.julia/packages/TestEnv/nGMfF/src/julia-1.11/common.jl:75 │ [2] test_dir_has_project_file │ @ ~/.julia/packages/TestEnv/nGMfF/src/julia-1.11/common.jl:52 [inlined] │ [3] maybe_gen_project_override! │ @ ~/.julia/packages/TestEnv/nGMfF/src/julia-1.11/common.jl:83 [inlined] │ [4] activate(pkg::String; allow_reresolve::Bool) │ @ TestEnv ~/.julia/packages/TestEnv/nGMfF/src/julia-1.11/activate_set.jl:12 │ [5] activate(pkg::String) │ @ TestEnv ~/.julia/packages/TestEnv/nGMfF/src/julia-1.11/activate_set.jl:9 │ [6] top-level scope │ @ /PkgEval.jl/scripts/precompile.jl:24 │ [7] include(mod::Module, _path::String) │ @ Base ./Base.jl:309 │ [8] exec_options(opts::Base.JLOptions) │ @ Base ./client.jl:344 │ [9] _start() │ @ Base ./client.jl:577 └ @ Main /PkgEval.jl/scripts/precompile.jl:26 Precompiling package dependencies... Precompiling packages... 989.2 ms ✓ BioGenerics 1410.8 ms ✓ LinearFold_jll 1441.4 ms ✓ LinearPartition_jll 1439.1 ms ✓ LinearSampling_jll 1436.9 ms ✓ LinearTurboFold_jll 20976.5 ms ✓ Automa 22565.6 ms ✓ FASTX 5000.6 ms ✓ LinearFold 8 dependencies successfully precompiled in 55 seconds. 38 already precompiled. Precompilation completed after 67.65s ################################################################################ # Testing # Testing LinearFold Status `/tmp/jl_ZVK8x3/Project.toml` [4c88cf16] Aqua v0.8.14 [c2308a5c] FASTX v2.1.7 [aebc047d] LinearFold v0.3.2 [1986cc42] Unitful v1.25.1 [492392ba] LinearFold_jll v1.0.0+0 [e9cb6f04] LinearPartition_jll v1.0.0+0 [be43c337] LinearSampling_jll v1.0.0+0 [cd7c2323] LinearTurboFold_jll v0.0.1+0 [2f01184e] SparseArrays v1.13.0 [8dfed614] Test v1.11.0 Status `/tmp/jl_ZVK8x3/Manifest.toml` [4c88cf16] Aqua v0.8.14 [67c07d97] Automa v1.1.0 [47718e42] BioGenerics v0.1.5 [34da2185] Compat v4.18.1 [c2308a5c] FASTX v2.1.7 [692b3bcd] JLLWrappers v1.7.1 [aebc047d] LinearFold v0.3.2 [aea7be01] PrecompileTools v1.3.3 [21216c6a] Preferences v1.5.0 [fdea26ae] SIMD v3.7.2 [354b36f9] StringViews v1.3.5 [3bb67fe8] TranscodingStreams v0.11.3 [1986cc42] Unitful v1.25.1 [492392ba] LinearFold_jll v1.0.0+0 [e9cb6f04] LinearPartition_jll v1.0.0+0 [be43c337] LinearSampling_jll v1.0.0+0 [cd7c2323] LinearTurboFold_jll v0.0.1+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 v1.0.0 [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 v1.0.0 [9e88b42a] Serialization 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 v10.47.0+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 Testing Running tests... testing LinearFold testing Aqua.test_all testing energy testing mfe testing zuker_subopt testing partfn testing bpp testing mea testing threshknot testing sample_structures testing turbofold Test Summary: | Pass Total Time LinearFold | 3848 3848 2m22.0s Aqua.test_all | 11 11 1m33.5s energy | 27 27 6.7s mfe | 216 216 1.7s zuker_subopt | 324 324 1.8s partfn | 54 54 1.1s bpp | 432 432 3.1s mea | 216 216 1.3s threshknot | 432 432 1.7s sample_structures | 216 216 3.5s turbofold | 1920 1920 23.3s Testing LinearFold tests passed Testing completed after 157.52s PkgEval succeeded after 249.96s