Package evaluation to test SeqFold on Julia 1.12.7-DEV.42 (6f510b6086*) started at 2026-06-19T09:50:20.982 ################################################################################ # Set-up # Installing PkgEval dependencies (TestEnv)... Activating project at `~/.julia/environments/v1.12` Set-up completed after 9.6s ################################################################################ # Installation # Installing SeqFold... Resolving package versions... Installed SeqFold ─ v0.4.0 Updating `~/.julia/environments/v1.12/Project.toml` [b3b2a78d] + SeqFold v0.4.0 Updating `~/.julia/environments/v1.12/Manifest.toml` [b3b2a78d] + SeqFold v0.4.0 [de0858da] + Printf v1.11.0 [4ec0a83e] + Unicode v1.11.0 Installation completed after 0.96s ################################################################################ # Precompilation # Precompiling PkgEval dependencies... Precompiling packages... 4266.2 ms ✓ TestEnv 1 dependency successfully precompiled in 4 seconds. 26 already precompiled. 24 dependencies precompiled but different versions are currently loaded (ArgTools, Base64, Dates, Downloads, JuliaSyntaxHighlighting, LibCURL, LibCURL_jll, LibGit2, LibGit2_jll, LibSSH2_jll, Logging, Markdown, MozillaCACerts_jll, NetworkOptions, OpenSSL_jll, Pkg, Printf, StyledStrings, TOML, Tar, UUIDs, Zlib_jll, nghttp2_jll and p7zip_jll). Restart julia to access the new versions. Otherwise, 1 dependent of these packages may trigger further precompilation to work with the unexpected versions. Precompiling package dependencies... Precompiling packages... 1095.9 ms ✓ Compiler 4143.9 ms ✓ OrderedCollections 36399.8 ms ✓ JuliaSyntax 7650.1 ms ✓ MacroTools 3539.1 ms ✓ SeqFold 4085.5 ms ✓ Compat 1209.7 ms ✓ Preferences 2389.6 ms ✓ CodeTracking 912.8 ms ✓ Compat → CompatLinearAlgebraExt 1085.7 ms ✓ PrecompileTools 13069.3 ms ✓ JuliaInterpreter 6841.1 ms ✓ Aqua 22592.6 ms ✓ LoweredCodeUtils 15240.4 ms ✓ Revise 126372.5 ms ✓ JET 15 dependencies successfully precompiled in 247 seconds. 32 already precompiled. 24 dependencies precompiled but different versions are currently loaded (ArgTools, Base64, Dates, Downloads, JuliaSyntaxHighlighting, LibCURL, LibCURL_jll, LibGit2, LibGit2_jll, LibSSH2_jll, Logging, Markdown, MozillaCACerts_jll, NetworkOptions, OpenSSL_jll, Pkg, Printf, StyledStrings, TOML, Tar, UUIDs, Zlib_jll, nghttp2_jll and p7zip_jll). Restart julia to access the new versions. Otherwise, 15 dependents of these packages may trigger further precompilation to work with the unexpected versions. Precompilation completed after 271.3s ################################################################################ # Testing # Testing SeqFold Test Could not use exact versions of packages in manifest. Re-resolving dependencies Updating `/tmp/jl_md76Qz/Project.toml` [4c88cf16] ↑ Aqua v0.8.14 ⇒ v0.8.16 [c3a54625] ↑ JET v0.9.20 ⇒ v0.11.4 [b3b2a78d] + SeqFold v0.4.0 [37e2e46d] ↑ LinearAlgebra v1.11.0 ⇒ v1.12.0 Updating `/tmp/jl_md76Qz/Manifest.toml` [4c88cf16] ↑ Aqua v0.8.14 ⇒ v0.8.16 [da1fd8a2] ↑ CodeTracking v1.3.9 ⇒ v3.0.2 [34da2185] ↑ Compat v4.18.0 ⇒ v4.18.1 [807dbc54] + Compiler v0.1.1 [c3a54625] ↑ JET v0.9.20 ⇒ v0.11.4 [aa1ae85d] ↑ JuliaInterpreter v0.9.46 ⇒ v0.10.12 [70703baa] ↑ JuliaSyntax v0.4.10 ⇒ v1.0.2 ⌅ [6f1432cf] ↑ LoweredCodeUtils v3.2.2 ⇒ v3.5.3 [bac558e1] + OrderedCollections v2.0.0 [aea7be01] ↑ PrecompileTools v1.2.1 ⇒ v1.3.4 [21216c6a] ↑ Preferences v1.5.0 ⇒ v1.5.2 [295af30f] + Revise v3.15.1 [b3b2a78d] + SeqFold v0.4.0 [c8ffd9c3] - MbedTLS_jll v2.28.6+0 [8bf52ea8] + CRC32c v1.11.0 [f43a241f] ↑ Downloads v1.6.0 ⇒ v1.7.0 [ac6e5ff7] + JuliaSyntaxHighlighting v1.12.0 [37e2e46d] ↑ LinearAlgebra v1.11.0 ⇒ v1.12.0 [ca575930] ↑ NetworkOptions v1.2.0 ⇒ v1.3.0 [44cfe95a] ↑ Pkg v1.11.0 ⇒ v1.12.1 [3fa0cd96] + REPL v1.11.0 [6462fe0b] + Sockets v1.11.0 [f489334b] + StyledStrings v1.11.0 [e66e0078] ↑ CompilerSupportLibraries_jll v1.1.1+0 ⇒ v1.3.0+1 [deac9b47] ↑ LibCURL_jll v8.6.0+0 ⇒ v8.15.0+0 [e37daf67] ↑ LibGit2_jll v1.7.2+0 ⇒ v1.9.0+0 [29816b5a] ↑ LibSSH2_jll v1.11.0+1 ⇒ v1.11.3+1 [14a3606d] ↑ MozillaCACerts_jll v2023.12.12 ⇒ v2025.11.4 [4536629a] ↑ OpenBLAS_jll v0.3.27+1 ⇒ v0.3.29+0 [458c3c95] + OpenSSL_jll v3.5.6+0 [83775a58] ↑ Zlib_jll v1.2.13+1 ⇒ v1.3.1+2 [8e850b90] ↑ libblastrampoline_jll v5.11.0+0 ⇒ v5.15.0+0 [8e850ede] ↑ nghttp2_jll v1.59.0+0 ⇒ v1.64.0+1 [3f19e933] ↑ p7zip_jll v17.4.0+2 ⇒ v17.7.0+0 Info Packages marked with ⌅ have new versions available but compatibility constraints restrict them from upgrading. To see why use `status --outdated -m` Test Successfully re-resolved Status `/tmp/jl_md76Qz/Project.toml` [4c88cf16] Aqua v0.8.16 [c3a54625] JET v0.11.4 [b3b2a78d] SeqFold v0.4.0 [37e2e46d] LinearAlgebra v1.12.0 [56ddb016] Logging v1.11.0 [8dfed614] Test v1.11.0 Status `/tmp/jl_md76Qz/Manifest.toml` [4c88cf16] Aqua v0.8.16 [da1fd8a2] CodeTracking v3.0.2 [34da2185] Compat v4.18.1 [807dbc54] Compiler v0.1.1 [c3a54625] JET v0.11.4 [aa1ae85d] JuliaInterpreter v0.10.12 [70703baa] JuliaSyntax v1.0.2 ⌅ [6f1432cf] LoweredCodeUtils v3.5.3 [1914dd2f] MacroTools v0.5.16 [bac558e1] OrderedCollections v2.0.0 [aea7be01] PrecompileTools v1.3.4 [21216c6a] Preferences v1.5.2 [295af30f] Revise v3.15.1 [b3b2a78d] SeqFold v0.4.0 [0dad84c5] ArgTools v1.1.2 [56f22d72] Artifacts v1.11.0 [2a0f44e3] Base64 v1.11.0 [8bf52ea8] CRC32c 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 v1.12.0 [56ddb016] Logging v1.11.0 [d6f4376e] Markdown v1.11.0 [ca575930] NetworkOptions v1.3.0 [44cfe95a] Pkg v1.12.1 [de0858da] Printf v1.11.0 [3fa0cd96] REPL v1.11.0 [9a3f8284] Random v1.11.0 [ea8e919c] SHA v0.7.0 [9e88b42a] Serialization v1.11.0 [6462fe0b] Sockets 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 [deac9b47] LibCURL_jll v8.15.0+0 [e37daf67] LibGit2_jll v1.9.0+0 [29816b5a] LibSSH2_jll v1.11.3+1 [14a3606d] MozillaCACerts_jll v2025.11.4 [4536629a] OpenBLAS_jll v0.3.29+0 [458c3c95] OpenSSL_jll v3.5.6+0 [83775a58] Zlib_jll v1.3.1+2 [8e850b90] libblastrampoline_jll v5.15.0+0 [8e850ede] nghttp2_jll v1.64.0+1 [3f19e933] p7zip_jll v17.7.0+0 Info Packages marked with ⌅ have new versions available but compatibility constraints restrict them from upgrading. Testing Running tests... Test Summary: | Pass Total Time Aqua.jl | 11 11 37.0s ┌ Warning: `target_defined_modules::Bool` configuration is deprecated. │ Please use `target_modules` instead and specify the modules you want to target with e.g. `target_modules=(pkgmod,)` └ @ JET ~/.julia/packages/JET/Nf2tu/src/analyzers/jetanalyzer.jl:1678 JET.jl: JET-test failed at /home/pkgeval/.julia/packages/JET/Nf2tu/src/JETBase.jl:1400 Expression: (JET.report_package)(SeqFold; toplevel_logger = nothing, target_defined_modules = true) ═════ 12 possible errors found ═════ ┌ gc_content(seq::AbstractString) @ SeqFold /home/pkgeval/.julia/packages/SeqFold/duiYd/src/utils.jl:215 │ non-boolean `Missing` found in boolean context (1/2 union split): goto %56 if not SeqFold.in(c, "GCgc")::Union{Missing, Bool} └──────────────────── ┌ gc_content(seq::AbstractString) @ SeqFold /home/pkgeval/.julia/packages/SeqFold/duiYd/src/utils.jl:215 │ non-boolean `Missing` found in boolean context (1/2 union split): goto %56 if not SeqFold.in(c::Any, "GCgc")::Union{Missing, Bool} └──────────────────── ┌ MeltingConditions(seq1_conc::Real, seq2_conc::Real, Na::Real, K::Real, Tris::Real, Mg::Real, dNTPs::Real) @ SeqFold /home/pkgeval/.julia/packages/SeqFold/duiYd/src/types.jl:201 │ non-boolean `Missing` found in boolean context (1/2 union split): goto %13 if not SeqFold.:!(SeqFold.all(SeqFold.:>=(0.0)::Base.Fix2{typeof(>=), Float64}, tuple(seq1_conc::Real, seq2_conc::Real, Na::Real, K::Real, Tris::Real, Mg::Real, dNTPs::Real)::NTuple{7, Real})::Union{Missing, Bool})::Union{Missing, Bool} └──────────────────── ┌ gc_cache(seq::AbstractString) @ SeqFold /home/pkgeval/.julia/packages/SeqFold/duiYd/src/tm.jl:266 │ non-boolean `Missing` found in boolean context (1/2 union split): goto %70 if not SeqFold.in((seq::AbstractString)[i]::Any, "GC")::Union{Missing, Bool} └──────────────────── ┌ gc_cache(seq::AbstractString) @ SeqFold /home/pkgeval/.julia/packages/SeqFold/duiYd/src/tm.jl:266 │ non-boolean `Missing` found in boolean context (1/2 union split): goto %70 if not SeqFold.in((seq::AbstractString)[i::Any]::Any, "GC")::Union{Missing, Bool} └──────────────────── ┌ fold(seq::AbstractString; temp::Real) @ SeqFold /home/pkgeval/.julia/packages/SeqFold/duiYd/src/fold.jl:42 │┌ _cache(seq::AbstractString, temp::Real) @ SeqFold /home/pkgeval/.julia/packages/SeqFold/duiYd/src/fold.jl:264 ││┌ _v!(seq::Base.AnnotatedString{String}, i::Int64, j::Any, temp::Any, v_cache::Any, w_cache::Any, emap::SeqFold.Energies) @ SeqFold /home/pkgeval/.julia/packages/SeqFold/duiYd/src/fold.jl:431 │││┌ _v!(seq::Base.AnnotatedString{String}, i::Any, j::Any, temp::Any, v_cache::Any, w_cache::Any, emap::SeqFold.Energies) @ SeqFold /home/pkgeval/.julia/packages/SeqFold/duiYd/src/fold.jl:443 ││││┌ _multi_branch(seq::Base.AnnotatedString{…}, i::Any, k::Any, j::Any, temp::Any, v_cache::Any, w_cache::Any, emap::SeqFold.Energies, helix::Bool) @ SeqFold /home/pkgeval/.julia/packages/SeqFold/duiYd/src/fold.jl:828 │││││ local variable `__add_branch!` is not defined: __add_branch! ││││└──────────────────── ┌ _stack(seq::Any, i::Any, i1::Any, j::Any, j1::Any, temp::Any, emap::Any) @ SeqFold /home/pkgeval/.julia/packages/SeqFold/duiYd/src/fold.jl:544 │ non-boolean `Missing` found in boolean context (1/2 union split): goto %33 if not SeqFold.any(SeqFold.:>(n)::Base.Fix2{typeof(>)}, tuple(i::Any, i1::Any, j::Any, j1::Any)::NTuple{4, Any})::Union{Missing, Bool} └──────────────────── ┌ _stack(seq::Any, i::Any, i1::Any, j::Any, j1::Any, temp::Any, emap::Any) @ SeqFold /home/pkgeval/.julia/packages/SeqFold/duiYd/src/fold.jl:549 │ non-boolean `Missing` found in boolean context (1/2 union split): goto %64 if not SeqFold.any(SeqFold.:<(1)::Base.Fix2{typeof(<), Int64}, tuple(i::Any, i1::Any, j::Any, j1::Any)::NTuple{4, Any})::Union{Missing, Bool} └──────────────────── ┌ _bulge(seq::Any, i::Any, i1::Any, j::Any, j1::Any, temp::Any, emap::Any) @ SeqFold /home/pkgeval/.julia/packages/SeqFold/duiYd/src/fold.jl:697 │ non-boolean `Missing` found in boolean context (1/2 union split): goto %104 if not SeqFold.any(#54, tuple(i::Any, i1::Any, j::Any, j1::Any)::NTuple{4, Any})::Union{Missing, Bool} └──────────────────── ┌ _multi_branch(seq::Any, i::Any, k::Any, j::Any, temp::Any, v_cache::Any, w_cache::Any, emap::Any, helix::Any) @ SeqFold /home/pkgeval/.julia/packages/SeqFold/duiYd/src/fold.jl:860 │ non-boolean `Missing` found in boolean context (1/2 union split): goto %260 if not (tuple(i3::Int64, j3::Int64)::Tuple{Int64, Int64} SeqFold.:(==) tuple(i::Any, j::Any)::Tuple{Any, Any})::Union{Missing, Bool} └──────────────────── ┌ _multi_branch(seq::Any, i::Any, k::Any, j::Any, temp::Any, v_cache::Any, w_cache::Any, emap::Any, helix::Any) @ SeqFold /home/pkgeval/.julia/packages/SeqFold/duiYd/src/fold.jl:872 │ non-boolean `Missing` found in boolean context (1/2 union split): goto %324 if not (tuple(i2::Int64, j2::Int64)::Tuple{Int64, Int64} SeqFold.:(==) tuple(i::Any, j::Any)::Tuple{Any, Any})::Union{Missing, Bool} └──────────────────── ┌ _multi_branch(seq::Any, i::Any, k::Any, j::Any, temp::Any, v_cache::Any, w_cache::Any, emap::Any, helix::Any) @ SeqFold /home/pkgeval/.julia/packages/SeqFold/duiYd/src/fold.jl:902 │ non-boolean `Missing` found in boolean context (1/2 union split): goto %415 if not (tuple(i2::Int64, j2::Int64)::Tuple{Int64, Int64} SeqFold.:!= tuple(i::Any, j::Any)::Tuple{Any, Any})::Union{Missing, Bool} └──────────────────── Test Summary: | Fail Total Time JET.jl | 1 1 1m56.2s RNG of the outermost testset: Random.Xoshiro(0xa7e54aa6891c2ce4, 0x13a8a35ec930ae91, 0xf6cae5ebb4433df8, 0x70a37921aba316b6, 0xc94e02491b740d69) ERROR: LoadError: Some tests did not pass: 0 passed, 1 failed, 0 errored, 0 broken. in expression starting at /home/pkgeval/.julia/packages/SeqFold/duiYd/test/runtests.jl:58 Testing failed after 186.17s ERROR: LoadError: Package SeqFold errored during testing Stacktrace: [1] pkgerror(msg::String) @ Pkg.Types /opt/julia/share/julia/stdlib/v1.12/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/v1.12/Pkg/src/Operations.jl:2538 [3] test @ /opt/julia/share/julia/stdlib/v1.12/Pkg/src/Operations.jl:2387 [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/v1.12/Pkg/src/API.jl:552 [5] test(pkgs::Vector{PackageSpec}; io::IOContext{IO}, kwargs::@Kwargs{julia_args::Cmd}) @ Pkg.API /opt/julia/share/julia/stdlib/v1.12/Pkg/src/API.jl:169 [6] test(pkgs::Vector{String}; kwargs::@Kwargs{julia_args::Cmd}) @ Pkg.API /opt/julia/share/julia/stdlib/v1.12/Pkg/src/API.jl:157 [7] test @ /opt/julia/share/julia/stdlib/v1.12/Pkg/src/API.jl:157 [inlined] [8] #test#81 @ /opt/julia/share/julia/stdlib/v1.12/Pkg/src/API.jl:156 [inlined] [9] top-level scope @ /PkgEval.jl/scripts/evaluate.jl:223 [10] include(mod::Module, _path::String) @ Base ./Base.jl:306 [11] exec_options(opts::Base.JLOptions) @ Base ./client.jl:317 [12] _start() @ Base ./client.jl:550 in expression starting at /PkgEval.jl/scripts/evaluate.jl:214 PkgEval failed after 489.9s: package has test failures