Package evaluation to test PhyloTraits on Julia 1.14.0-DEV.30 (073666df8b*) started at 2025-11-04T21:37:36.786 ################################################################################ # Set-up # Installing PkgEval dependencies (TestEnv)... Set-up completed after 9.64s ################################################################################ # Installation # Installing PhyloTraits... Resolving package versions... Updating `~/.julia/environments/v1.14/Project.toml` [bce24f4f] + PhyloTraits v1.1.0 Updating `~/.julia/environments/v1.14/Manifest.toml` [66dad0bd] + AliasTables v1.1.3 [67c07d97] + Automa v1.1.0 [47718e42] + BioGenerics v0.1.5 [7e6ae17a] + BioSequences v3.5.0 [3c28c6f8] + BioSymbols v5.2.0 [fa961155] + CEnum v0.5.0 [336ed68f] + CSV v0.10.15 [944b1d66] + CodecZlib v0.7.8 [861a8166] + Combinatorics v1.0.3 [34da2185] + Compat v4.18.1 [187b0558] + ConstructionBase v1.6.0 [a8cc5b0e] + Crayons v4.1.1 [9a962f9c] + DataAPI v1.16.0 [a93c6f00] + DataFrames v1.8.1 ⌅ [864edb3b] + DataStructures v0.18.22 [e2d170a0] + DataValueInterfaces v1.0.0 [31c24e10] + Distributions v0.25.122 [ffbed154] + DocStringExtensions v0.9.5 [c2308a5c] + FASTX v2.1.7 [48062228] + FilePathsBase v0.9.24 [1a297f60] + FillArrays v1.14.0 [d9f16b24] + Functors v0.5.2 [38e38edf] + GLM v1.9.0 [34004b35] + HypergeometricFunctions v0.3.28 [842dd82b] + InlineStrings v1.4.5 [41ab1584] + InvertedIndices v1.3.1 [92d709cd] + IrrationalConstants v0.2.6 [82899510] + IteratorInterfaceExtensions v1.0.0 [692b3bcd] + JLLWrappers v1.7.1 [b964fa9f] + LaTeXStrings v1.4.0 [2ab3a3ac] + LogExpFunctions v0.3.29 [e1d29d7a] + Missings v1.2.0 [76087f3c] + NLopt v1.2.1 [bac558e1] + OrderedCollections v1.8.1 [90014a1f] + PDMats v0.11.36 [69de0a69] + Parsers v2.8.3 [33ad39ac] + PhyloNetworks v1.2.0 [bce24f4f] + PhyloTraits v1.1.0 [2dfb63ee] + PooledArrays v1.4.3 [aea7be01] + PrecompileTools v1.3.3 [21216c6a] + Preferences v1.5.0 [08abe8d2] + PrettyTables v3.1.0 [43287f4e] + PtrArrays v1.3.0 [1fd47b50] + QuadGK v2.11.2 [189a3867] + Reexport v1.2.2 [79098fc4] + Rmath v0.9.0 [fdea26ae] + SIMD v3.7.2 [91c51154] + SentinelArrays v1.4.8 [1277b4bf] + ShiftedArrays v2.0.0 [a2af1166] + SortingAlgorithms v1.2.2 [276daf66] + SpecialFunctions v2.6.1 [90137ffa] + StaticArrays v1.9.15 [1e83bf80] + StaticArraysCore v1.4.4 [10745b16] + Statistics v1.11.1 [82ae8749] + StatsAPI v1.7.1 [2913bbd2] + StatsBase v0.34.7 [4c63d2b9] + StatsFuns v1.5.2 [3eaba693] + StatsModels v0.7.7 [892a3eda] + StringManipulation v0.4.1 [354b36f9] + StringViews v1.3.5 [3783bdb8] + TableTraits v1.0.1 [bd369af6] + Tables v1.12.1 [3bb67fe8] + TranscodingStreams v0.11.3 [7200193e] + Twiddle v1.1.2 [ea10d353] + WeakRefStrings v1.4.2 [76eceee3] + WorkerUtilities v1.6.1 [079eb43e] + NLopt_jll v2.10.0+0 [efe28fd5] + OpenSpecFun_jll v0.5.6+0 [f50d1b31] + Rmath_jll v0.5.1+0 [56f22d72] + Artifacts v1.11.0 [2a0f44e3] + Base64 v1.11.0 [ade2ca70] + Dates v1.11.0 [8ba89e20] + Distributed v1.11.0 [7b1f6079] + FileWatching v1.11.0 [9fa8497b] + Future v1.11.0 [b77e0a4c] + InteractiveUtils v1.11.0 [ac6e5ff7] + JuliaSyntaxHighlighting v1.12.0 [8f399da3] + Libdl v1.11.0 [37e2e46d] + LinearAlgebra v1.13.0 [d6f4376e] + Markdown v1.11.0 [a63ad114] + Mmap v1.11.0 [de0858da] + Printf v1.11.0 [3fa0cd96] + REPL v1.11.0 [9a3f8284] + Random v1.11.0 [ea8e919c] + SHA v1.0.0 [9e88b42a] + Serialization v1.11.0 [6462fe0b] + Sockets v1.11.0 [2f01184e] + SparseArrays v1.13.0 [f489334b] + StyledStrings v1.11.0 [4607b0f0] + SuiteSparse [fa267f1f] + TOML v1.0.3 [cf7118a7] + UUIDs v1.11.0 [4ec0a83e] + Unicode v1.11.0 [e66e0078] + CompilerSupportLibraries_jll v1.3.0+1 [4536629a] + OpenBLAS_jll v0.3.29+0 [05823500] + OpenLibm_jll v0.8.7+0 [bea87d4a] + SuiteSparse_jll v7.10.1+0 [83775a58] + Zlib_jll v1.3.1+2 [8e850b90] + libblastrampoline_jll v5.15.0+0 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 4.95s ################################################################################ # 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... 22701.8 ms ✓ FASTX 11739.7 ms ✓ Distributions 5232.9 ms ✓ StatsModels 2858.3 ms ✓ FASTX → BioSequencesExt 6186.1 ms ✓ GLM 21299.2 ms ✓ PhyloNetworks 19635.6 ms ✓ PhyloTraits 7 dependencies successfully precompiled in 93 seconds. 94 already precompiled. Precompilation completed after 105.05s ################################################################################ # Testing # Testing PhyloTraits Status `/tmp/jl_g2J65R/Project.toml` [4c88cf16] Aqua v0.8.14 [3c28c6f8] BioSymbols v5.2.0 [336ed68f] CSV v0.10.15 [a93c6f00] DataFrames v1.8.1 [38e38edf] GLM v1.9.0 [33ad39ac] PhyloNetworks v1.2.0 [bce24f4f] PhyloTraits v1.1.0 [860ef19b] StableRNGs v1.0.3 [90137ffa] StaticArrays v1.9.15 [10745b16] Statistics v1.11.1 [82ae8749] StatsAPI v1.7.1 [2913bbd2] StatsBase v0.34.7 [37e2e46d] LinearAlgebra v1.13.0 [56ddb016] Logging v1.11.0 [9a3f8284] Random v1.11.0 [8dfed614] Test v1.11.0 Status `/tmp/jl_g2J65R/Manifest.toml` [66dad0bd] AliasTables v1.1.3 [4c88cf16] Aqua v0.8.14 [67c07d97] Automa v1.1.0 [47718e42] BioGenerics v0.1.5 [7e6ae17a] BioSequences v3.5.0 [3c28c6f8] BioSymbols v5.2.0 [fa961155] CEnum v0.5.0 [336ed68f] CSV v0.10.15 [944b1d66] CodecZlib v0.7.8 [861a8166] Combinatorics v1.0.3 [34da2185] Compat v4.18.1 [187b0558] ConstructionBase v1.6.0 [a8cc5b0e] Crayons v4.1.1 [9a962f9c] DataAPI v1.16.0 [a93c6f00] DataFrames v1.8.1 ⌅ [864edb3b] DataStructures v0.18.22 [e2d170a0] DataValueInterfaces v1.0.0 [31c24e10] Distributions v0.25.122 [ffbed154] DocStringExtensions v0.9.5 [c2308a5c] FASTX v2.1.7 [48062228] FilePathsBase v0.9.24 [1a297f60] FillArrays v1.14.0 [d9f16b24] Functors v0.5.2 [38e38edf] GLM v1.9.0 [34004b35] HypergeometricFunctions v0.3.28 [842dd82b] InlineStrings v1.4.5 [41ab1584] InvertedIndices v1.3.1 [92d709cd] IrrationalConstants v0.2.6 [82899510] IteratorInterfaceExtensions v1.0.0 [692b3bcd] JLLWrappers v1.7.1 [b964fa9f] LaTeXStrings v1.4.0 [2ab3a3ac] LogExpFunctions v0.3.29 [e1d29d7a] Missings v1.2.0 [76087f3c] NLopt v1.2.1 [bac558e1] OrderedCollections v1.8.1 [90014a1f] PDMats v0.11.36 [69de0a69] Parsers v2.8.3 [33ad39ac] PhyloNetworks v1.2.0 [bce24f4f] PhyloTraits v1.1.0 [2dfb63ee] PooledArrays v1.4.3 [aea7be01] PrecompileTools v1.3.3 [21216c6a] Preferences v1.5.0 [08abe8d2] PrettyTables v3.1.0 [43287f4e] PtrArrays v1.3.0 [1fd47b50] QuadGK v2.11.2 [189a3867] Reexport v1.2.2 [79098fc4] Rmath v0.9.0 [fdea26ae] SIMD v3.7.2 [91c51154] SentinelArrays v1.4.8 [1277b4bf] ShiftedArrays v2.0.0 [a2af1166] SortingAlgorithms v1.2.2 [276daf66] SpecialFunctions v2.6.1 [860ef19b] StableRNGs v1.0.3 [90137ffa] StaticArrays v1.9.15 [1e83bf80] StaticArraysCore v1.4.4 [10745b16] Statistics v1.11.1 [82ae8749] StatsAPI v1.7.1 [2913bbd2] StatsBase v0.34.7 [4c63d2b9] StatsFuns v1.5.2 [3eaba693] StatsModels v0.7.7 [892a3eda] StringManipulation v0.4.1 [354b36f9] StringViews v1.3.5 [3783bdb8] TableTraits v1.0.1 [bd369af6] Tables v1.12.1 [3bb67fe8] TranscodingStreams v0.11.3 [7200193e] Twiddle v1.1.2 [ea10d353] WeakRefStrings v1.4.2 [76eceee3] WorkerUtilities v1.6.1 [079eb43e] NLopt_jll v2.10.0+0 [efe28fd5] OpenSpecFun_jll v0.5.6+0 [f50d1b31] Rmath_jll v0.5.1+0 [0dad84c5] ArgTools v1.1.2 [56f22d72] Artifacts v1.11.0 [2a0f44e3] Base64 v1.11.0 [ade2ca70] Dates v1.11.0 [8ba89e20] Distributed v1.11.0 [f43a241f] Downloads v1.7.0 [7b1f6079] FileWatching v1.11.0 [9fa8497b] Future 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 [a63ad114] Mmap v1.11.0 [ca575930] NetworkOptions v1.3.0 [44cfe95a] Pkg v1.13.0 [de0858da] Printf v1.11.0 [3fa0cd96] REPL v1.11.0 [9a3f8284] Random v1.11.0 [ea8e919c] SHA v1.0.0 [9e88b42a] Serialization v1.11.0 [6462fe0b] Sockets v1.11.0 [2f01184e] SparseArrays v1.13.0 [f489334b] StyledStrings v1.11.0 [4607b0f0] SuiteSparse [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 [05823500] OpenLibm_jll v0.8.7+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 Info Packages marked with ⌅ have new versions available but compatibility constraints restrict them from upgrading. Testing Running tests... Test Summary: | Pass Total Time PhyloTraits Code quality (Aqua.jl) | 9 9 43.6s phylolm and ancestralreconstruction: Error During Test at /home/pkgeval/.julia/packages/PhyloTraits/nqGfi/test/test_lm.jl:304 Got exception outside of a @test edge(s) number 2,5 have negative γ. The variance-covariance matrix is not defined. Stacktrace: [1] error(s::String) @ Base ./error.jl:44 [2] check_valid_gammas(net::HybridNetwork, str::String) @ PhyloNetworks ~/.julia/packages/PhyloNetworks/7zhDI/src/auxiliary.jl:933 [3] #sharedpathmatrix#225 @ ~/.julia/packages/PhyloNetworks/7zhDI/src/recursion_matrices.jl:233 [inlined] [4] sharedpathmatrix @ ~/.julia/packages/PhyloNetworks/7zhDI/src/recursion_matrices.jl:229 [inlined] [5] matrix_scalinghybrid(net::HybridNetwork, lam::Float64, gammas::Vector{Float64}) @ PhyloTraits ~/.julia/packages/PhyloTraits/nqGfi/src/fit_phylolm_continuous.jl:320 [6] logLik_lam_hyb(lam::Float64, X::Matrix{Float64}, Y::Vector{Float64}, net::HybridNetwork, reml::Bool, gammas::Vector{Float64}; nonmissing::BitVector, ind::Vector{Int64}) @ PhyloTraits ~/.julia/packages/PhyloTraits/nqGfi/src/fit_phylolm_continuous.jl:336 [7] logLik_lam_hyb @ ~/.julia/packages/PhyloTraits/nqGfi/src/fit_phylolm_continuous.jl:325 [inlined] [8] fun @ ~/.julia/packages/PhyloTraits/nqGfi/src/fit_phylolm_continuous.jl:373 [inlined] [9] nlopt_callback_wrapper(n::UInt32, p_x::Ptr{Float64}, p_grad::Ptr{Float64}, d::NLopt.Callback_Data{PhyloTraits.var"#fun#40"{BitVector, Vector{Int64}, Matrix{Float64}, Vector{Float64}, HybridNetwork, Bool, Vector{Float64}}, NLopt.Opt}) @ NLopt ~/.julia/packages/NLopt/wMgqN/src/NLopt.jl:522 [10] nlopt_optimize @ ~/.julia/packages/NLopt/wMgqN/src/libnlopt.jl:182 [inlined] [11] optimize!(o::NLopt.Opt, x::Vector{Float64}) @ NLopt ~/.julia/packages/NLopt/wMgqN/src/NLopt.jl:849 [12] optimize @ ~/.julia/packages/NLopt/wMgqN/src/NLopt.jl:863 [inlined] [13] phylolm_scalinghybrid(X::Matrix{Float64}, Y::Vector{Float64}, net::HybridNetwork, reml::Bool, gammas::Vector{Float64}; nonmissing::BitVector, ind::Vector{Int64}, ftolRel::Float64, xtolRel::Float64, ftolAbs::Float64, xtolAbs::Float64, startingValue::Float64, fixedValue::Missing) @ PhyloTraits ~/.julia/packages/PhyloTraits/nqGfi/src/fit_phylolm_continuous.jl:379 [14] phylolm_scalinghybrid @ ~/.julia/packages/PhyloTraits/nqGfi/src/fit_phylolm_continuous.jl:345 [inlined] [15] #phylolm#33 @ ~/.julia/packages/PhyloTraits/nqGfi/src/fit_phylolm_continuous.jl:188 [inlined] [16] phylolm @ ~/.julia/packages/PhyloTraits/nqGfi/src/fit_phylolm_continuous.jl:170 [inlined] [17] #phylolm#30 @ ~/.julia/packages/PhyloTraits/nqGfi/src/fit_phylolm_continuous.jl:57 [inlined] [18] kwcall(::@NamedTuple{reml::Bool, nonmissing::BitVector, ind::Vector{Int64}, ftolRel::Float64, xtolRel::Float64, ftolAbs::Float64, xtolAbs::Float64, startingValue::Float64, fixedValue::Missing, withinspecies_var::Bool, counts::Nothing, ySD::Nothing, suppresswarnings::Bool}, ::typeof(phylolm), X::Matrix{Float64}, Y::Vector{Float64}, net::HybridNetwork, model::PhyloTraits.ScalingHybrid) @ PhyloTraits ~/.julia/packages/PhyloTraits/nqGfi/src/fit_phylolm_continuous.jl:33 [19] phylolm(f::FormulaTerm{Term, Term}, fr::DataFrame, net::HybridNetwork; model::String, tipnames::Symbol, no_names::Bool, reml::Bool, ftolRel::Float64, xtolRel::Float64, ftolAbs::Float64, xtolAbs::Float64, startingValue::Float64, fixedValue::Missing, withinspecies_var::Bool, y_mean_std::Bool, suppresswarnings::Bool) @ PhyloTraits ~/.julia/packages/PhyloTraits/nqGfi/src/fit_phylolm_continuous.jl:824 [20] kwcall(::@NamedTuple{model::String, reml::Bool}, ::typeof(phylolm), f::FormulaTerm{Term, Term}, fr::DataFrame, net::HybridNetwork) @ PhyloTraits ~/.julia/packages/PhyloTraits/nqGfi/src/fit_phylolm_continuous.jl:729 [21] top-level scope @ ~/.julia/packages/PhyloTraits/nqGfi/test/test_lm.jl:307 [22] macro expansion @ /opt/julia/share/julia/stdlib/v1.14/Test/src/Test.jl:1961 [inlined] [23] macro expansion @ ~/.julia/packages/PhyloTraits/nqGfi/test/test_lm.jl:515 [inlined] [24] include(mapexpr::Function, mod::Module, _path::String) @ Base ./Base.jl:310 [25] top-level scope @ ~/.julia/packages/PhyloTraits/nqGfi/test/runtests.jl:30 [26] macro expansion @ /opt/julia/share/julia/stdlib/v1.14/Test/src/Test.jl:1961 [inlined] [27] macro expansion @ ~/.julia/packages/PhyloTraits/nqGfi/test/runtests.jl:30 [inlined] [28] include(mapexpr::Function, mod::Module, _path::String) @ Base ./Base.jl:310 [29] top-level scope @ none:6 [30] eval(m::Module, e::Any) @ Core ./boot.jl:489 [31] exec_options(opts::Base.JLOptions) @ Base ./client.jl:310 [32] _start() @ Base ./client.jl:577 Stacktrace: [1] optimize!(o::NLopt.Opt, x::Vector{Float64}) @ NLopt ~/.julia/packages/NLopt/wMgqN/src/NLopt.jl:856 [2] optimize @ ~/.julia/packages/NLopt/wMgqN/src/NLopt.jl:863 [inlined] [3] phylolm_scalinghybrid(X::Matrix{Float64}, Y::Vector{Float64}, net::HybridNetwork, reml::Bool, gammas::Vector{Float64}; nonmissing::BitVector, ind::Vector{Int64}, ftolRel::Float64, xtolRel::Float64, ftolAbs::Float64, xtolAbs::Float64, startingValue::Float64, fixedValue::Missing) @ PhyloTraits ~/.julia/packages/PhyloTraits/nqGfi/src/fit_phylolm_continuous.jl:379 [4] phylolm_scalinghybrid @ ~/.julia/packages/PhyloTraits/nqGfi/src/fit_phylolm_continuous.jl:345 [inlined] [5] #phylolm#33 @ ~/.julia/packages/PhyloTraits/nqGfi/src/fit_phylolm_continuous.jl:188 [inlined] [6] phylolm @ ~/.julia/packages/PhyloTraits/nqGfi/src/fit_phylolm_continuous.jl:170 [inlined] [7] #phylolm#30 @ ~/.julia/packages/PhyloTraits/nqGfi/src/fit_phylolm_continuous.jl:57 [inlined] [8] kwcall(::@NamedTuple{reml::Bool, nonmissing::BitVector, ind::Vector{Int64}, ftolRel::Float64, xtolRel::Float64, ftolAbs::Float64, xtolAbs::Float64, startingValue::Float64, fixedValue::Missing, withinspecies_var::Bool, counts::Nothing, ySD::Nothing, suppresswarnings::Bool}, ::typeof(phylolm), X::Matrix{Float64}, Y::Vector{Float64}, net::HybridNetwork, model::PhyloTraits.ScalingHybrid) @ PhyloTraits ~/.julia/packages/PhyloTraits/nqGfi/src/fit_phylolm_continuous.jl:33 [9] phylolm(f::FormulaTerm{Term, Term}, fr::DataFrame, net::HybridNetwork; model::String, tipnames::Symbol, no_names::Bool, reml::Bool, ftolRel::Float64, xtolRel::Float64, ftolAbs::Float64, xtolAbs::Float64, startingValue::Float64, fixedValue::Missing, withinspecies_var::Bool, y_mean_std::Bool, suppresswarnings::Bool) @ PhyloTraits ~/.julia/packages/PhyloTraits/nqGfi/src/fit_phylolm_continuous.jl:824 [10] kwcall(::@NamedTuple{model::String, reml::Bool}, ::typeof(phylolm), f::FormulaTerm{Term, Term}, fr::DataFrame, net::HybridNetwork) @ PhyloTraits ~/.julia/packages/PhyloTraits/nqGfi/src/fit_phylolm_continuous.jl:729 [11] top-level scope @ ~/.julia/packages/PhyloTraits/nqGfi/test/test_lm.jl:307 [12] macro expansion @ /opt/julia/share/julia/stdlib/v1.14/Test/src/Test.jl:1961 [inlined] [13] macro expansion @ ~/.julia/packages/PhyloTraits/nqGfi/test/test_lm.jl:515 [inlined] [14] include(mapexpr::Function, mod::Module, _path::String) @ Base ./Base.jl:310 [15] top-level scope @ ~/.julia/packages/PhyloTraits/nqGfi/test/runtests.jl:30 [16] macro expansion @ /opt/julia/share/julia/stdlib/v1.14/Test/src/Test.jl:1961 [inlined] [17] macro expansion @ ~/.julia/packages/PhyloTraits/nqGfi/test/runtests.jl:30 [inlined] [18] include(mapexpr::Function, mod::Module, _path::String) @ Base ./Base.jl:310 [19] top-level scope @ none:6 [20] eval(m::Module, e::Any) @ Core ./boot.jl:489 [21] exec_options(opts::Base.JLOptions) @ Base ./client.jl:310 [22] _start() @ Base ./client.jl:577 lambda when no signal: Error During Test at /home/pkgeval/.julia/packages/PhyloTraits/nqGfi/test/test_lm.jl:602 Got exception outside of a @test edge(s) number 18 have negative γ. The variance-covariance matrix is not defined. Stacktrace: [1] error(s::String) @ Base ./error.jl:44 [2] check_valid_gammas(net::HybridNetwork, str::String) @ PhyloNetworks ~/.julia/packages/PhyloNetworks/7zhDI/src/auxiliary.jl:933 [3] #sharedpathmatrix#225 @ ~/.julia/packages/PhyloNetworks/7zhDI/src/recursion_matrices.jl:233 [inlined] [4] sharedpathmatrix @ ~/.julia/packages/PhyloNetworks/7zhDI/src/recursion_matrices.jl:229 [inlined] [5] matrix_scalinghybrid(net::HybridNetwork, lam::Float64, gammas::Vector{Float64}) @ PhyloTraits ~/.julia/packages/PhyloTraits/nqGfi/src/fit_phylolm_continuous.jl:320 [6] logLik_lam_hyb(lam::Float64, X::Matrix{Float64}, Y::Vector{Float64}, net::HybridNetwork, reml::Bool, gammas::Vector{Float64}; nonmissing::BitVector, ind::Vector{Int64}) @ PhyloTraits ~/.julia/packages/PhyloTraits/nqGfi/src/fit_phylolm_continuous.jl:336 [7] logLik_lam_hyb @ ~/.julia/packages/PhyloTraits/nqGfi/src/fit_phylolm_continuous.jl:325 [inlined] [8] fun @ ~/.julia/packages/PhyloTraits/nqGfi/src/fit_phylolm_continuous.jl:373 [inlined] [9] nlopt_callback_wrapper(n::UInt32, p_x::Ptr{Float64}, p_grad::Ptr{Float64}, d::NLopt.Callback_Data{PhyloTraits.var"#fun#40"{BitVector, Vector{Int64}, Matrix{Float64}, Vector{Float64}, HybridNetwork, Bool, Vector{Float64}}, NLopt.Opt}) @ NLopt ~/.julia/packages/NLopt/wMgqN/src/NLopt.jl:522 [10] nlopt_optimize @ ~/.julia/packages/NLopt/wMgqN/src/libnlopt.jl:182 [inlined] [11] optimize!(o::NLopt.Opt, x::Vector{Float64}) @ NLopt ~/.julia/packages/NLopt/wMgqN/src/NLopt.jl:849 [12] optimize @ ~/.julia/packages/NLopt/wMgqN/src/NLopt.jl:863 [inlined] [13] phylolm_scalinghybrid(X::Matrix{Float64}, Y::Vector{Float64}, net::HybridNetwork, reml::Bool, gammas::Vector{Float64}; nonmissing::BitVector, ind::Vector{Int64}, ftolRel::Float64, xtolRel::Float64, ftolAbs::Float64, xtolAbs::Float64, startingValue::Float64, fixedValue::Missing) @ PhyloTraits ~/.julia/packages/PhyloTraits/nqGfi/src/fit_phylolm_continuous.jl:379 [14] phylolm_scalinghybrid @ ~/.julia/packages/PhyloTraits/nqGfi/src/fit_phylolm_continuous.jl:345 [inlined] [15] #phylolm#33 @ ~/.julia/packages/PhyloTraits/nqGfi/src/fit_phylolm_continuous.jl:188 [inlined] [16] phylolm @ ~/.julia/packages/PhyloTraits/nqGfi/src/fit_phylolm_continuous.jl:170 [inlined] [17] #phylolm#30 @ ~/.julia/packages/PhyloTraits/nqGfi/src/fit_phylolm_continuous.jl:57 [inlined] [18] kwcall(::@NamedTuple{reml::Bool, nonmissing::BitVector, ind::Vector{Int64}, ftolRel::Float64, xtolRel::Float64, ftolAbs::Float64, xtolAbs::Float64, startingValue::Float64, fixedValue::Missing, withinspecies_var::Bool, counts::Nothing, ySD::Nothing, suppresswarnings::Bool}, ::typeof(phylolm), X::Matrix{Float64}, Y::Vector{Float64}, net::HybridNetwork, model::PhyloTraits.ScalingHybrid) @ PhyloTraits ~/.julia/packages/PhyloTraits/nqGfi/src/fit_phylolm_continuous.jl:33 [19] phylolm(f::FormulaTerm{Term, Term}, fr::DataFrame, net::HybridNetwork; model::String, tipnames::Symbol, no_names::Bool, reml::Bool, ftolRel::Float64, xtolRel::Float64, ftolAbs::Float64, xtolAbs::Float64, startingValue::Float64, fixedValue::Missing, withinspecies_var::Bool, y_mean_std::Bool, suppresswarnings::Bool) @ PhyloTraits ~/.julia/packages/PhyloTraits/nqGfi/src/fit_phylolm_continuous.jl:824 [20] kwcall(::@NamedTuple{model::String, reml::Bool}, ::typeof(phylolm), f::FormulaTerm{Term, Term}, fr::DataFrame, net::HybridNetwork) @ PhyloTraits ~/.julia/packages/PhyloTraits/nqGfi/src/fit_phylolm_continuous.jl:729 [21] top-level scope @ ~/.julia/packages/PhyloTraits/nqGfi/test/test_lm.jl:603 [22] macro expansion @ /opt/julia/share/julia/stdlib/v1.14/Test/src/Test.jl:1961 [inlined] [23] macro expansion @ ~/.julia/packages/PhyloTraits/nqGfi/test/test_lm.jl:641 [inlined] [24] include(mapexpr::Function, mod::Module, _path::String) @ Base ./Base.jl:310 [25] top-level scope @ ~/.julia/packages/PhyloTraits/nqGfi/test/runtests.jl:30 [26] macro expansion @ /opt/julia/share/julia/stdlib/v1.14/Test/src/Test.jl:1961 [inlined] [27] macro expansion @ ~/.julia/packages/PhyloTraits/nqGfi/test/runtests.jl:30 [inlined] [28] include(mapexpr::Function, mod::Module, _path::String) @ Base ./Base.jl:310 [29] top-level scope @ none:6 [30] eval(m::Module, e::Any) @ Core ./boot.jl:489 [31] exec_options(opts::Base.JLOptions) @ Base ./client.jl:310 [32] _start() @ Base ./client.jl:577 Stacktrace: [1] optimize!(o::NLopt.Opt, x::Vector{Float64}) @ NLopt ~/.julia/packages/NLopt/wMgqN/src/NLopt.jl:856 [2] optimize @ ~/.julia/packages/NLopt/wMgqN/src/NLopt.jl:863 [inlined] [3] phylolm_scalinghybrid(X::Matrix{Float64}, Y::Vector{Float64}, net::HybridNetwork, reml::Bool, gammas::Vector{Float64}; nonmissing::BitVector, ind::Vector{Int64}, ftolRel::Float64, xtolRel::Float64, ftolAbs::Float64, xtolAbs::Float64, startingValue::Float64, fixedValue::Missing) @ PhyloTraits ~/.julia/packages/PhyloTraits/nqGfi/src/fit_phylolm_continuous.jl:379 [4] phylolm_scalinghybrid @ ~/.julia/packages/PhyloTraits/nqGfi/src/fit_phylolm_continuous.jl:345 [inlined] [5] #phylolm#33 @ ~/.julia/packages/PhyloTraits/nqGfi/src/fit_phylolm_continuous.jl:188 [inlined] [6] phylolm @ ~/.julia/packages/PhyloTraits/nqGfi/src/fit_phylolm_continuous.jl:170 [inlined] [7] #phylolm#30 @ ~/.julia/packages/PhyloTraits/nqGfi/src/fit_phylolm_continuous.jl:57 [inlined] [8] kwcall(::@NamedTuple{reml::Bool, nonmissing::BitVector, ind::Vector{Int64}, ftolRel::Float64, xtolRel::Float64, ftolAbs::Float64, xtolAbs::Float64, startingValue::Float64, fixedValue::Missing, withinspecies_var::Bool, counts::Nothing, ySD::Nothing, suppresswarnings::Bool}, ::typeof(phylolm), X::Matrix{Float64}, Y::Vector{Float64}, net::HybridNetwork, model::PhyloTraits.ScalingHybrid) @ PhyloTraits ~/.julia/packages/PhyloTraits/nqGfi/src/fit_phylolm_continuous.jl:33 [9] phylolm(f::FormulaTerm{Term, Term}, fr::DataFrame, net::HybridNetwork; model::String, tipnames::Symbol, no_names::Bool, reml::Bool, ftolRel::Float64, xtolRel::Float64, ftolAbs::Float64, xtolAbs::Float64, startingValue::Float64, fixedValue::Missing, withinspecies_var::Bool, y_mean_std::Bool, suppresswarnings::Bool) @ PhyloTraits ~/.julia/packages/PhyloTraits/nqGfi/src/fit_phylolm_continuous.jl:824 [10] kwcall(::@NamedTuple{model::String, reml::Bool}, ::typeof(phylolm), f::FormulaTerm{Term, Term}, fr::DataFrame, net::HybridNetwork) @ PhyloTraits ~/.julia/packages/PhyloTraits/nqGfi/src/fit_phylolm_continuous.jl:729 [11] top-level scope @ ~/.julia/packages/PhyloTraits/nqGfi/test/test_lm.jl:603 [12] macro expansion @ /opt/julia/share/julia/stdlib/v1.14/Test/src/Test.jl:1961 [inlined] [13] macro expansion @ ~/.julia/packages/PhyloTraits/nqGfi/test/test_lm.jl:641 [inlined] [14] include(mapexpr::Function, mod::Module, _path::String) @ Base ./Base.jl:310 [15] top-level scope @ ~/.julia/packages/PhyloTraits/nqGfi/test/runtests.jl:30 [16] macro expansion @ /opt/julia/share/julia/stdlib/v1.14/Test/src/Test.jl:1961 [inlined] [17] macro expansion @ ~/.julia/packages/PhyloTraits/nqGfi/test/runtests.jl:30 [inlined] [18] include(mapexpr::Function, mod::Module, _path::String) @ Base ./Base.jl:310 [19] top-level scope @ none:6 [20] eval(m::Module, e::Any) @ Core ./boot.jl:489 [21] exec_options(opts::Base.JLOptions) @ Base ./client.jl:310 [22] _start() @ Base ./client.jl:577 phylolm: Caudata Dataset: Test Failed at /home/pkgeval/.julia/packages/PhyloTraits/nqGfi/test/test_lm_tree.jl:196 Expression: ≈(predict(fitLambda), [4.66893 for i = 1:197], atol = 1.0e-5, norm = (x->begin #= /home/pkgeval/.julia/packages/PhyloTraits/nqGfi/test/test_lm_tree.jl:196 =# norm(x, Inf) end)) Evaluated: [4.668934335019081, 4.668934335019081, 4.668934335019081, 4.66893433501908, 4.668934335019081, 4.668934335019081, 4.668934335019081, 4.668934335019082, 4.66893433501908, 4.66893433501908 … 4.668934335019081, 4.668934335019079, 4.668934335019081, 4.668934335019081, 4.668934335019081, 4.668934335019081, 4.668934335019081, 4.66893433501908, 4.66893433501908, 4.668934335019081] ≈ [4.66893, 4.66893, 4.66893, 4.66893, 4.66893, 4.66893, 4.66893, 4.66893, 4.66893, 4.66893 … 4.66893, 4.66893, 4.66893, 4.66893, 4.66893, 4.66893, 4.66893, 4.66893, 4.66893, 4.66893] (atol=1.0e-5, norm=#95) Stacktrace: [1] top-level scope @ ~/.julia/packages/PhyloTraits/nqGfi/test/test_lm_tree.jl:8 [2] macro expansion @ /opt/julia/share/julia/stdlib/v1.14/Test/src/Test.jl:1961 [inlined] [3] macro expansion @ ~/.julia/packages/PhyloTraits/nqGfi/test/test_lm_tree.jl:196 [inlined] [4] macro expansion @ /opt/julia/share/julia/stdlib/v1.14/Test/src/Test.jl:753 [inlined] phylolm: Lizard Dataset: Test Failed at /home/pkgeval/.julia/packages/PhyloTraits/nqGfi/test/test_lm_tree.jl:350 Expression: ≈((confint(fitBM))[:, 1], [2.5115945339, -0.4715366529, 0.7207474097, -0.3595508202, -0.8102854443, -0.2058583178, -0.0960507369, -0.0112932922, -0.2213931131], atol = 1.0e-10, norm = (x->begin #= /home/pkgeval/.julia/packages/PhyloTraits/nqGfi/test/test_lm_tree.jl:350 =# norm(x, Inf) end)) Evaluated: [2.5115945339190517, -0.471536652860847, 0.720747409652019, -0.35955082018441126, -0.8102854443203744, -0.2058583178457689, -0.09605073685241805, -0.011293292207552569, -0.22139311313361498] ≈ [2.5115945339, -0.4715366529, 0.7207474097, -0.3595508202, -0.8102854443, -0.2058583178, -0.0960507369, -0.0112932922, -0.2213931131] (atol=1.0e-10, norm=#99) Stacktrace: [1] top-level scope @ ~/.julia/packages/PhyloTraits/nqGfi/test/test_lm_tree.jl:319 [2] macro expansion @ /opt/julia/share/julia/stdlib/v1.14/Test/src/Test.jl:1961 [inlined] [3] macro expansion @ ~/.julia/packages/PhyloTraits/nqGfi/test/test_lm_tree.jl:350 [inlined] [4] macro expansion @ /opt/julia/share/julia/stdlib/v1.14/Test/src/Test.jl:753 [inlined] Simulate test distribution (fixed root): Test Failed at /home/pkgeval/.julia/packages/PhyloTraits/nqGfi/test/test_simulate_mbd.jl:78 Expression: isapprox(Σ_sim, Σ_true, atol = 0.5, norm = (x->begin #= /home/pkgeval/.julia/packages/PhyloTraits/nqGfi/test/test_simulate_mbd.jl:78 =# maximum(abs.(x)) end)) Evaluated: isapprox([15.773382481374977 -2.900200215655022 … 0.29454795325957167 0.19456002811179074; -2.900200215655022 10.096296509091976 … 0.11665440797710325 -0.05716160033457429; … ; 0.29454795325957167 0.11665440797710325 … 9.8397564365694 1.8393988372772498; 0.19456002811179074 -0.05716160033457429 … 1.8393988372772498 12.204705596679311], [15.714651136189469 -3.097050206275684 … -0.0 0.0; -3.097050206275684 10.143096166856706 … 0.0 0.0; … ; -0.0 0.0 … 10.143096166856706 1.9540356480867267; 0.0 0.0 … 1.9540356480867267 12.50563462454052]; atol = 0.5, norm = var"#322#323"()) Stacktrace: [1] top-level scope @ ~/.julia/packages/PhyloTraits/nqGfi/test/test_simulate_mbd.jl:48 [2] macro expansion @ /opt/julia/share/julia/stdlib/v1.14/Test/src/Test.jl:1961 [inlined] [3] macro expansion @ ~/.julia/packages/PhyloTraits/nqGfi/test/test_simulate_mbd.jl:78 [inlined] [4] macro expansion @ /opt/julia/share/julia/stdlib/v1.14/Test/src/Test.jl:753 [inlined] Simulate with Shifts: Test Failed at /home/pkgeval/.julia/packages/PhyloTraits/nqGfi/test/test_simulate_mbd.jl:206 Expression: isapprox(Σ_sim, Σ_true, norm = (x->begin #= /home/pkgeval/.julia/packages/PhyloTraits/nqGfi/test/test_simulate_mbd.jl:206 =# maximum(abs.(x)) end), atol = 0.5) Evaluated: isapprox([18.601461428659714 -8.4636575924147 … -0.12188335014531226 -0.022935659453475005; -8.4636575924147 4.719260658280789 … 0.04209006858132236 0.013073647505375985; … ; -0.12188335014531226 0.04209006858132236 … 3.3616418851631664 0.9574111507540022; -0.022935659453475005 0.013073647505375985 … 0.9574111507540022 0.6703154543596485], [18.4718920241616 -8.324257067251398 … -0.0 -0.0; -8.324257067251398 4.6350316421658055 … 0.0 0.0; … ; -0.0 0.0 … 3.3001425292220534 0.9261677024047169; -0.0 0.0 … 0.9261677024047169 0.6606238031442794]; norm = var"#334#335"(), atol = 0.5) Stacktrace: [1] top-level scope @ ~/.julia/packages/PhyloTraits/nqGfi/test/test_simulate_mbd.jl:135 [2] macro expansion @ /opt/julia/share/julia/stdlib/v1.14/Test/src/Test.jl:1961 [inlined] [3] macro expansion @ ~/.julia/packages/PhyloTraits/nqGfi/test/test_simulate_mbd.jl:206 [inlined] [4] macro expansion @ /opt/julia/share/julia/stdlib/v1.14/Test/src/Test.jl:753 [inlined] Test Summary: | Pass Fail Error Total Time PhyloTraits.jl | 916 4 2 922 8m17.0s phylolm on small network | 77 77 1m25.9s Shifts and Transgressive Evolution | 46 46 55.1s No Intercept | 20 20 7.6s phylolm and ancestralreconstruction | 132 1 133 13.8s lambda when no signal | 8 1 9 3.9s Undefined branch length | 4 4 0.0s phylolm: Caudata Dataset | 52 1 53 53.8s phylolm: Lizard Dataset | 25 1 26 18.4s phylolm: within-species variation, star | 17 17 7.9s phylolm: binary tree, no withinspecies var | 20 20 2.1s phylolm: binary tree, withinspecies var | 26 26 9.9s phylolm: within-species var, network h=1 | 103 103 18.8s discrete | 213 213 2m16.7s Simulate function against fixed values | 8 8 1.4s Simulate test distribution | 90 90 2.0s Simulate with Shifts | 42 42 11.8s Simulate data and check means and dimensions | 8 8 1.1s Simulate test distribution (fixed root) | 1 1 2 3.5s Simulate test distribution (random root) | 3 3 6.0s Simulate with Shifts | 21 1 22 2.7s RNG of the outermost testset: Xoshiro(0x9f3762e3814b2631, 0xe0c571dc7c1de0fb, 0xe0b56ec0106c902b, 0x53eea1eff4d10f00, 0xf0994fc8f97b02f9) ERROR: LoadError: Some tests did not pass: 916 passed, 4 failed, 2 errored, 0 broken. in expression starting at /home/pkgeval/.julia/packages/PhyloTraits/nqGfi/test/runtests.jl:29 Testing failed after 601.98s ERROR: LoadError: Package PhyloTraits 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:2946 [3] test @ /opt/julia/share/julia/stdlib/v1.14/Pkg/src/Operations.jl:2795 [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:572 [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/v1.14/Pkg/src/API.jl:548 [6] 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 [7] kwcall(::@NamedTuple{julia_args::Cmd}, ::typeof(Pkg.API.test), pkgs::Vector{PackageSpec}) @ Pkg.API /opt/julia/share/julia/stdlib/v1.14/Pkg/src/API.jl:161 [8] test(pkgs::Vector{String}; kwargs::@Kwargs{julia_args::Cmd}) @ Pkg.API /opt/julia/share/julia/stdlib/v1.14/Pkg/src/API.jl:160 [9] test @ /opt/julia/share/julia/stdlib/v1.14/Pkg/src/API.jl:160 [inlined] [10] kwcall(::@NamedTuple{julia_args::Cmd}, ::typeof(Pkg.API.test), pkg::String) @ Pkg.API /opt/julia/share/julia/stdlib/v1.14/Pkg/src/API.jl:159 [11] top-level scope @ /PkgEval.jl/scripts/evaluate.jl:219 [12] include(mod::Module, _path::String) @ Base ./Base.jl:309 [13] exec_options(opts::Base.JLOptions) @ Base ./client.jl:344 [14] _start() @ Base ./client.jl:577 in expression starting at /PkgEval.jl/scripts/evaluate.jl:210 PkgEval failed after 741.59s: package tests unexpectedly errored