Package evaluation of LinearFold on Julia 1.11.5 (32ac370b68*) started at 2025-06-29T08:05:54.781 ################################################################################ # Set-up # Installing PkgEval dependencies (TestEnv)... Set-up completed after 8.79s ################################################################################ # Installation # Installing LinearFold... Resolving package versions... Updating `~/.julia/environments/v1.11/Project.toml` [aebc047d] + LinearFold v0.3.2 Updating `~/.julia/environments/v1.11/Manifest.toml` [67c07d97] + Automa v1.1.0 [47718e42] + BioGenerics v0.1.5 [c2308a5c] + FASTX v2.1.7 [692b3bcd] + JLLWrappers v1.7.0 [aebc047d] + LinearFold v0.3.2 ⌅ [aea7be01] + PrecompileTools v1.2.1 [21216c6a] + Preferences v1.4.3 [fdea26ae] + SIMD v3.7.1 [354b36f9] + StringViews v1.3.4 [3bb67fe8] + TranscodingStreams v0.11.3 [1986cc42] + Unitful v1.23.1 [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 v1.6.0 [7b1f6079] + FileWatching v1.11.0 [b27032c2] + LibCURL v0.6.4 [76f85450] + LibGit2 v1.11.0 [8f399da3] + Libdl v1.11.0 [37e2e46d] + LinearAlgebra v1.11.0 [56ddb016] + Logging v1.11.0 [d6f4376e] + Markdown v1.11.0 [ca575930] + NetworkOptions v1.2.0 [44cfe95a] + Pkg v1.11.0 [de0858da] + Printf v1.11.0 [9a3f8284] + Random v1.11.0 [ea8e919c] + SHA v0.7.0 [9e88b42a] + Serialization v1.11.0 [2f01184e] + SparseArrays 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 v1.1.1+0 [deac9b47] + LibCURL_jll v8.6.0+0 [e37daf67] + LibGit2_jll v1.7.2+0 [29816b5a] + LibSSH2_jll v1.11.0+1 [c8ffd9c3] + MbedTLS_jll v2.28.6+0 [14a3606d] + MozillaCACerts_jll v2023.12.12 [4536629a] + OpenBLAS_jll v0.3.27+1 [bea87d4a] + SuiteSparse_jll v7.7.0+0 [83775a58] + Zlib_jll v1.2.13+1 [8e850b90] + libblastrampoline_jll v5.11.0+0 [8e850ede] + nghttp2_jll v1.59.0+0 [3f19e933] + p7zip_jll v17.4.0+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 To see why use `status --outdated -m` Installation completed after 4.47s ################################################################################ # Precompilation # Precompiling PkgEval dependencies... Precompiling package dependencies... Precompilation completed after 31.81s ################################################################################ # Testing # Testing LinearFold Status `/tmp/jl_P0KGkw/Project.toml` [4c88cf16] Aqua v0.8.13 [c2308a5c] FASTX v2.1.7 [aebc047d] LinearFold v0.3.2 [1986cc42] Unitful v1.23.1 [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 v1.11.0 [8dfed614] Test v1.11.0 Status `/tmp/jl_P0KGkw/Manifest.toml` [4c88cf16] Aqua v0.8.13 [67c07d97] Automa v1.1.0 [47718e42] BioGenerics v0.1.5 [34da2185] Compat v4.16.0 [c2308a5c] FASTX v2.1.7 [692b3bcd] JLLWrappers v1.7.0 [aebc047d] LinearFold v0.3.2 ⌅ [aea7be01] PrecompileTools v1.2.1 [21216c6a] Preferences v1.4.3 [fdea26ae] SIMD v3.7.1 [354b36f9] StringViews v1.3.4 [3bb67fe8] TranscodingStreams v0.11.3 [1986cc42] Unitful v1.23.1 [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 v1.6.0 [7b1f6079] FileWatching v1.11.0 [b77e0a4c] InteractiveUtils v1.11.0 [b27032c2] LibCURL v0.6.4 [76f85450] LibGit2 v1.11.0 [8f399da3] Libdl v1.11.0 [37e2e46d] LinearAlgebra v1.11.0 [56ddb016] Logging v1.11.0 [d6f4376e] Markdown v1.11.0 [ca575930] NetworkOptions v1.2.0 [44cfe95a] Pkg v1.11.0 [de0858da] Printf v1.11.0 [9a3f8284] Random v1.11.0 [ea8e919c] SHA v0.7.0 [9e88b42a] Serialization v1.11.0 [2f01184e] SparseArrays 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 v1.1.1+0 [deac9b47] LibCURL_jll v8.6.0+0 [e37daf67] LibGit2_jll v1.7.2+0 [29816b5a] LibSSH2_jll v1.11.0+1 [c8ffd9c3] MbedTLS_jll v2.28.6+0 [14a3606d] MozillaCACerts_jll v2023.12.12 [4536629a] OpenBLAS_jll v0.3.27+1 [bea87d4a] SuiteSparse_jll v7.7.0+0 [83775a58] Zlib_jll v1.2.13+1 [8e850b90] libblastrampoline_jll v5.11.0+0 [8e850ede] nghttp2_jll v1.59.0+0 [3f19e933] p7zip_jll v17.4.0+2 Info Packages marked with ⌅ have new versions available but compatibility constraints restrict them from upgrading. Testing Running tests... testing LinearFold testing Aqua.test_all ┌ Warning: disabling failing Aqua method ambiguity test for julia-1.11.x, julia-1.12.x └ @ Main ~/.julia/packages/LinearFold/GbwsP/test/aqua.jl:12 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 | 3847 3847 4m25.7s Aqua.test_all | 10 10 3m01.1s energy | 27 27 7.1s mfe | 216 216 2.0s zuker_subopt | 324 324 1.8s partfn | 54 54 1.2s bpp | 432 432 3.9s mea | 216 216 1.3s threshknot | 432 432 1.8s sample_structures | 216 216 5.3s turbofold | 1920 1920 56.9s Testing LinearFold tests passed Testing completed after 270.97s PkgEval succeeded after 330.25s