Package evaluation to test ThorAxe on Julia 1.14.0-DEV.2186 (48ff18f4cd*) started at 2026-05-14T15:35:02.590 ################################################################################ # Set-up # Installing PkgEval dependencies (TestEnv)... Activating project at `~/.julia/environments/v1.14` Set-up completed after 16.24s ################################################################################ # Installation # Installing ThorAxe... Resolving package versions... Updating `~/.julia/environments/v1.14/Project.toml` [cf6a4a95] + ThorAxe v0.9.0 Updating `~/.julia/environments/v1.14/Manifest.toml` [992eb4ea] + CondaPkg v0.2.34 [692b3bcd] + JLLWrappers v1.8.0 [682c06a0] + JSON v1.5.2 [0b3b1443] + MicroMamba v0.1.15 [69de0a69] + Parsers v2.8.4 [fa939f87] + Pidfile v1.3.0 [aea7be01] + PrecompileTools v1.3.4 [21216c6a] + Preferences v1.5.2 [6c6a2e73] + Scratch v1.3.0 [ec057cc2] + StructUtils v2.8.1 [cf6a4a95] + ThorAxe v0.9.0 [f8abcde7] + micromamba_jll v2.3.1+0 [4d7b5844] + pixi_jll v0.41.3+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 [4af54fe1] + LazyArtifacts v1.11.0 [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 v1.5.1+0 [deac9b47] + LibCURL_jll v8.20.0+1 [e37daf67] + LibGit2_jll v1.9.3+0 [29816b5a] + LibSSH2_jll v1.11.101+0 [14a3606d] + MozillaCACerts_jll v2026.3.19 [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 Installation completed after 5.33s ################################################################################ # Precompilation # Precompiling PkgEval dependencies... Precompiling package dependencies... Precompiling project... 56.9 s ✓ ExplicitImports 5.4 s ✓ micromamba_jll 5.3 s ✓ pixi_jll 4.6 s ✓ MicroMamba 7.6 s ✓ CondaPkg 4.7 s ✓ ThorAxe 6 dependencies successfully precompiled in 85 seconds. 44 already precompiled. Precompilation completed after 112.17s ################################################################################ # Testing # Testing ThorAxe Status `/tmp/jl_TaPJRP/Project.toml` [4c88cf16] Aqua v0.8.14 [7d51a73a] ExplicitImports v1.15.0 [f8b46487] TestItemRunner v1.1.5 [1c621080] TestItems v1.0.0 [cf6a4a95] ThorAxe v0.9.0 [8dfed614] Test v1.11.0 Status `/tmp/jl_TaPJRP/Manifest.toml` [4c88cf16] Aqua v0.8.14 [34da2185] Compat v4.18.1 [992eb4ea] CondaPkg v0.2.34 [7d51a73a] ExplicitImports v1.15.0 [692b3bcd] JLLWrappers v1.8.0 [682c06a0] JSON v1.5.2 [0b3b1443] MicroMamba v0.1.15 [69de0a69] Parsers v2.8.4 [fa939f87] Pidfile v1.3.0 [aea7be01] PrecompileTools v1.3.4 [21216c6a] Preferences v1.5.2 [6c6a2e73] Scratch v1.3.0 [ec057cc2] StructUtils v2.8.1 [f8b46487] TestItemRunner v1.1.5 [1c621080] TestItems v1.0.0 [cf6a4a95] ThorAxe v0.9.0 [f8abcde7] micromamba_jll v2.3.1+0 [4d7b5844] pixi_jll v0.41.3+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 [4af54fe1] LazyArtifacts v1.11.0 [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 v1.5.1+0 [deac9b47] LibCURL_jll v8.20.0+1 [e37daf67] LibGit2_jll v1.9.3+0 [29816b5a] LibSSH2_jll v1.11.101+0 [14a3606d] MozillaCACerts_jll v2026.3.19 [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 Testing Running tests... CLI IO redirection: Test Failed at /home/pkgeval/.julia/packages/ThorAxe/mSLUT/test/cli.jl:116 Expression: err isa Base.ProcessFailedException Evaluated: UndefVarError(:manifest_uuid_path, 0x000000000000a0c8, Base) isa ProcessFailedException Stacktrace: [1] top-level scope @ ~/.julia/packages/ThorAxe/mSLUT/test/cli.jl:560 [2] macro expansion @ /opt/julia/share/julia/stdlib/v1.14/Test/src/Test.jl:784 [inlined] CLI IO redirection: Test Failed at /home/pkgeval/.julia/packages/ThorAxe/mSLUT/test/cli.jl:118 Expression: occursin("tsl.csv", output) Evaluated: occursin("tsl.csv", "") Stacktrace: [1] top-level scope @ ~/.julia/packages/ThorAxe/mSLUT/test/cli.jl:560 [2] macro expansion @ /opt/julia/share/julia/stdlib/v1.14/Test/src/Test.jl:784 [inlined] ┌ Warning: Ignoring incompatible compat entry `SHA = "0.7"` in "/home/pkgeval/.julia/packages/ThorAxe/mSLUT/Project.toml". │ SHA is a non-upgradable standard library with version 1.13.0 in the current Julia version. │ Fix by setting compat to "0.7, 1" to mark support of the current version 1.13.0. └ @ Pkg.Operations /opt/julia/share/julia/stdlib/v1.14/Pkg/src/Operations.jl:520 Test Summary: | Pass Fail Total Time Package | 58 2 60 2m54.7s cli.jl | 28 2 30 17.3s default CLI command | 1 1 2.5s space-safe default aligner path | 2 2 0.4s CLI keyword overrides | 7 7 0.5s CLI boolean flags | 2 2 0.1s CLI IO redirection | 2 2 6.2s CLI injected runner uses direct command branch | 3 3 0.4s CLI injected runner receives pipeline when redirection is requested | 3 3 0.6s transcript_query default command | 3 3 0.2s transcript_query keyword overrides | 1 1 0.3s transcript_query can omit specieslist | 1 1 0.2s add_transcripts command | 2 2 0.2s add_transcripts forwards pipeline redirection | 3 3 0.2s aqua.jl | 11 11 1m21.4s explicit_imports.jl | 6 6 1m14.9s aligner.jl | 13 13 1.1s ERROR: LoadError: Some tests did not pass: 58 passed, 2 failed, 0 errored, 0 broken. in expression starting at /home/pkgeval/.julia/packages/ThorAxe/mSLUT/test/runtests.jl:3 Testing failed after 238.24s ERROR: LoadError: Package ThorAxe 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] Cmd(cmd::Cmd) @ Base /opt/julia/share/julia/stdlib/v1.14/Pkg/src/Operations.jl:3110 [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/v1.14/Pkg/src/API.jl:587 [5] 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 [6] test(pkgs::Vector{String}; kwargs::@Kwargs{julia_args::Cmd}) @ Pkg.API /opt/julia/share/julia/stdlib/v1.14/Pkg/src/API.jl:160 [7] test @ /opt/julia/share/julia/stdlib/v1.14/Pkg/src/API.jl:160 [inlined] [8] test(pkg::String; kwargs::@Kwargs{julia_args::Cmd}) @ Pkg.API /opt/julia/share/julia/stdlib/v1.14/Pkg/src/API.jl:159 [inlined] [9] top-level scope @ /PkgEval.jl/scripts/evaluate.jl:223 [10] include(mod::Module, _path::String) @ Base ./Base.jl:326 [11] exec_options(opts::Base.JLOptions) @ Base ./client.jl:352 [12] _start() @ Base ./client.jl:593 in expression starting at /PkgEval.jl/scripts/evaluate.jl:214 PkgEval failed after 389.88s: package has test failures