Package evaluation of PhyloTraits on Julia 1.12.0-rc1.2 (995ff9db19*) started at 2025-07-14T21:22:24.747 ################################################################################ # Set-up # Installing PkgEval dependencies (TestEnv)... Set-up completed after 8.5s ################################################################################ # Installation # Installing PhyloTraits... Resolving package versions... Updating `~/.julia/environments/v1.12/Project.toml` [bce24f4f] + PhyloTraits v1.1.0 Updating `~/.julia/environments/v1.12/Manifest.toml` [66dad0bd] + AliasTables v1.1.3 [67c07d97] + Automa v1.1.0 [47718e42] + BioGenerics v0.1.5 [7e6ae17a] + BioSequences v3.4.2 [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 v4.17.0 [187b0558] + ConstructionBase v1.6.0 [a8cc5b0e] + Crayons v4.1.1 [9a962f9c] + DataAPI v1.16.0 [a93c6f00] + DataFrames v1.7.0 [864edb3b] + DataStructures v0.18.22 [e2d170a0] + DataValueInterfaces v1.0.0 [31c24e10] + Distributions v0.25.120 [ffbed154] + DocStringExtensions v0.9.5 [c2308a5c] + FASTX v2.1.7 [48062228] + FilePathsBase v0.9.24 [1a297f60] + FillArrays v1.13.0 [d9f16b24] + Functors v0.5.2 [38e38edf] + GLM v1.9.0 [34004b35] + HypergeometricFunctions v0.3.28 [842dd82b] + InlineStrings v1.4.4 [41ab1584] + InvertedIndices v1.3.1 [92d709cd] + IrrationalConstants v0.2.4 [82899510] + IteratorInterfaceExtensions v1.0.0 [692b3bcd] + JLLWrappers v1.7.0 [b964fa9f] + LaTeXStrings v1.4.0 [2ab3a3ac] + LogExpFunctions v0.3.29 [e1d29d7a] + Missings v1.2.0 [76087f3c] + NLopt v1.2.0 [bac558e1] + OrderedCollections v1.8.1 [90014a1f] + PDMats v0.11.35 [69de0a69] + Parsers v2.8.3 [33ad39ac] + PhyloNetworks v1.1.0 [bce24f4f] + PhyloTraits v1.1.0 [2dfb63ee] + PooledArrays v1.4.3 [aea7be01] + PrecompileTools v1.3.2 [21216c6a] + Preferences v1.4.3 [08abe8d2] + PrettyTables v2.4.0 [43287f4e] + PtrArrays v1.3.0 [1fd47b50] + QuadGK v2.11.2 [189a3867] + Reexport v1.2.2 [79098fc4] + Rmath v0.8.0 [fdea26ae] + SIMD v3.7.1 [91c51154] + SentinelArrays v1.4.8 [1277b4bf] + ShiftedArrays v2.0.0 [a2af1166] + SortingAlgorithms v1.2.1 [276daf66] + SpecialFunctions v2.5.1 [90137ffa] + StaticArrays v1.9.13 [1e83bf80] + StaticArraysCore v1.4.3 [10745b16] + Statistics v1.11.1 [82ae8749] + StatsAPI v1.7.1 [2913bbd2] + StatsBase v0.34.5 [4c63d2b9] + StatsFuns v1.5.0 [3eaba693] + StatsModels v0.7.4 [892a3eda] + StringManipulation v0.4.1 [354b36f9] + StringViews v1.3.4 [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 [9fa8497b] + Future v1.11.0 [b77e0a4c] + InteractiveUtils v1.11.0 [ac6e5ff7] + JuliaSyntaxHighlighting v1.12.0 [8f399da3] + Libdl v1.11.0 [37e2e46d] + LinearAlgebra v1.12.0 [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 v0.7.0 [9e88b42a] + Serialization v1.11.0 [6462fe0b] + Sockets v1.11.0 [2f01184e] + SparseArrays v1.12.0 [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 v0.8.5+0 [bea87d4a] + SuiteSparse_jll v7.8.3+2 [83775a58] + Zlib_jll v1.3.1+2 [8e850b90] + libblastrampoline_jll v5.13.1+0 Installation completed after 4.37s ################################################################################ # Precompilation # Precompiling PkgEval dependencies... Precompiling package dependencies... Precompilation completed after 38.83s ################################################################################ # Testing # Testing PhyloTraits Status `/tmp/jl_BvnVw5/Project.toml` [4c88cf16] Aqua v0.8.13 [3c28c6f8] BioSymbols v5.2.0 [336ed68f] CSV v0.10.15 [a93c6f00] DataFrames v1.7.0 [38e38edf] GLM v1.9.0 [33ad39ac] PhyloNetworks v1.1.0 [bce24f4f] PhyloTraits v1.1.0 [860ef19b] StableRNGs v1.0.3 [90137ffa] StaticArrays v1.9.13 [10745b16] Statistics v1.11.1 [82ae8749] StatsAPI v1.7.1 [2913bbd2] StatsBase v0.34.5 [37e2e46d] LinearAlgebra v1.12.0 [56ddb016] Logging v1.11.0 [9a3f8284] Random v1.11.0 [8dfed614] Test v1.11.0 Status `/tmp/jl_BvnVw5/Manifest.toml` [66dad0bd] AliasTables v1.1.3 [4c88cf16] Aqua v0.8.13 [67c07d97] Automa v1.1.0 [47718e42] BioGenerics v0.1.5 [7e6ae17a] BioSequences v3.4.2 [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 v4.17.0 [187b0558] ConstructionBase v1.6.0 [a8cc5b0e] Crayons v4.1.1 [9a962f9c] DataAPI v1.16.0 [a93c6f00] DataFrames v1.7.0 [864edb3b] DataStructures v0.18.22 [e2d170a0] DataValueInterfaces v1.0.0 [31c24e10] Distributions v0.25.120 [ffbed154] DocStringExtensions v0.9.5 [c2308a5c] FASTX v2.1.7 [48062228] FilePathsBase v0.9.24 [1a297f60] FillArrays v1.13.0 [d9f16b24] Functors v0.5.2 [38e38edf] GLM v1.9.0 [34004b35] HypergeometricFunctions v0.3.28 [842dd82b] InlineStrings v1.4.4 [41ab1584] InvertedIndices v1.3.1 [92d709cd] IrrationalConstants v0.2.4 [82899510] IteratorInterfaceExtensions v1.0.0 [692b3bcd] JLLWrappers v1.7.0 [b964fa9f] LaTeXStrings v1.4.0 [2ab3a3ac] LogExpFunctions v0.3.29 [e1d29d7a] Missings v1.2.0 [76087f3c] NLopt v1.2.0 [bac558e1] OrderedCollections v1.8.1 [90014a1f] PDMats v0.11.35 [69de0a69] Parsers v2.8.3 [33ad39ac] PhyloNetworks v1.1.0 [bce24f4f] PhyloTraits v1.1.0 [2dfb63ee] PooledArrays v1.4.3 [aea7be01] PrecompileTools v1.3.2 [21216c6a] Preferences v1.4.3 [08abe8d2] PrettyTables v2.4.0 [43287f4e] PtrArrays v1.3.0 [1fd47b50] QuadGK v2.11.2 [189a3867] Reexport v1.2.2 [79098fc4] Rmath v0.8.0 [fdea26ae] SIMD v3.7.1 [91c51154] SentinelArrays v1.4.8 [1277b4bf] ShiftedArrays v2.0.0 [a2af1166] SortingAlgorithms v1.2.1 [276daf66] SpecialFunctions v2.5.1 [860ef19b] StableRNGs v1.0.3 [90137ffa] StaticArrays v1.9.13 [1e83bf80] StaticArraysCore v1.4.3 [10745b16] Statistics v1.11.1 [82ae8749] StatsAPI v1.7.1 [2913bbd2] StatsBase v0.34.5 [4c63d2b9] StatsFuns v1.5.0 [3eaba693] StatsModels v0.7.4 [892a3eda] StringManipulation v0.4.1 [354b36f9] StringViews v1.3.4 [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 v1.6.0 [7b1f6079] FileWatching v1.11.0 [9fa8497b] Future 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 [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 v0.7.0 [9e88b42a] Serialization v1.11.0 [6462fe0b] Sockets v1.11.0 [2f01184e] SparseArrays v1.12.0 [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 v8.11.1+1 [e37daf67] LibGit2_jll v1.9.0+0 [29816b5a] LibSSH2_jll v1.11.3+1 [14a3606d] MozillaCACerts_jll v2025.5.20 [4536629a] OpenBLAS_jll v0.3.29+0 [05823500] OpenLibm_jll v0.8.5+0 [458c3c95] OpenSSL_jll v3.5.1+0 [bea87d4a] SuiteSparse_jll v7.8.3+2 [83775a58] Zlib_jll v1.3.1+2 [8e850b90] libblastrampoline_jll v5.13.1+0 [8e850ede] nghttp2_jll v1.64.0+1 [3f19e933] p7zip_jll v17.5.0+2 Testing Running tests... Test Summary: | Pass Total Time PhyloTraits Code quality (Aqua.jl) | 9 9 57.4s 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/nTUCK/src/auxiliary.jl:933 [3] #sharedpathmatrix#219 @ ~/.julia/packages/PhyloNetworks/nTUCK/src/recursion_matrices.jl:233 [inlined] [4] sharedpathmatrix @ ~/.julia/packages/PhyloNetworks/nTUCK/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] (::PhyloTraits.var"#fun#40"{BitVector, Vector{Int64}, Matrix{Float64}, Vector{Float64}, HybridNetwork, Bool, Vector{Float64}})(x::Vector{Float64}, g::Vector{Float64}) @ PhyloTraits ~/.julia/packages/PhyloTraits/nqGfi/src/fit_phylolm_continuous.jl:373 [9] nlopt_callback_wrapper(n::UInt32, p_x::Ptr{Float64}, p_grad::Ptr{Float64}, d_::Ptr{Nothing}) @ NLopt ~/.julia/packages/NLopt/FpXXS/src/NLopt.jl:466 [10] nlopt_optimize @ ~/.julia/packages/NLopt/FpXXS/src/libnlopt.jl:182 [inlined] [11] optimize!(o::NLopt.Opt, x::Vector{Float64}) @ NLopt ~/.julia/packages/NLopt/FpXXS/src/NLopt.jl:790 [12] optimize @ ~/.julia/packages/NLopt/FpXXS/src/NLopt.jl:804 [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] 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 [19] top-level scope @ ~/.julia/packages/PhyloTraits/nqGfi/test/test_lm.jl:307 [20] macro expansion @ /opt/julia/share/julia/stdlib/v1.12/Test/src/Test.jl:1776 [inlined] [21] macro expansion @ ~/.julia/packages/PhyloTraits/nqGfi/test/test_lm.jl:515 [inlined] [22] include(mapexpr::Function, mod::Module, _path::String) @ Base ./Base.jl:306 [23] top-level scope @ ~/.julia/packages/PhyloTraits/nqGfi/test/runtests.jl:30 [24] macro expansion @ /opt/julia/share/julia/stdlib/v1.12/Test/src/Test.jl:1776 [inlined] [25] macro expansion @ ~/.julia/packages/PhyloTraits/nqGfi/test/runtests.jl:30 [inlined] [26] include(mapexpr::Function, mod::Module, _path::String) @ Base ./Base.jl:306 [27] top-level scope @ none:6 [28] eval(m::Module, e::Any) @ Core ./boot.jl:489 [29] exec_options(opts::Base.JLOptions) @ Base ./client.jl:287 [30] _start() @ Base ./client.jl:554 Stacktrace: [1] optimize!(o::NLopt.Opt, x::Vector{Float64}) @ NLopt ~/.julia/packages/NLopt/FpXXS/src/NLopt.jl:797 [2] optimize @ ~/.julia/packages/NLopt/FpXXS/src/NLopt.jl:804 [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] 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 [9] top-level scope @ ~/.julia/packages/PhyloTraits/nqGfi/test/test_lm.jl:307 [10] macro expansion @ /opt/julia/share/julia/stdlib/v1.12/Test/src/Test.jl:1776 [inlined] [11] macro expansion @ ~/.julia/packages/PhyloTraits/nqGfi/test/test_lm.jl:515 [inlined] [12] include(mapexpr::Function, mod::Module, _path::String) @ Base ./Base.jl:306 [13] top-level scope @ ~/.julia/packages/PhyloTraits/nqGfi/test/runtests.jl:30 [14] macro expansion @ /opt/julia/share/julia/stdlib/v1.12/Test/src/Test.jl:1776 [inlined] [15] macro expansion @ ~/.julia/packages/PhyloTraits/nqGfi/test/runtests.jl:30 [inlined] [16] include(mapexpr::Function, mod::Module, _path::String) @ Base ./Base.jl:306 [17] top-level scope @ none:6 [18] eval(m::Module, e::Any) @ Core ./boot.jl:489 [19] exec_options(opts::Base.JLOptions) @ Base ./client.jl:287 [20] _start() @ Base ./client.jl:554 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/nTUCK/src/auxiliary.jl:933 [3] #sharedpathmatrix#219 @ ~/.julia/packages/PhyloNetworks/nTUCK/src/recursion_matrices.jl:233 [inlined] [4] sharedpathmatrix @ ~/.julia/packages/PhyloNetworks/nTUCK/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] (::PhyloTraits.var"#fun#40"{BitVector, Vector{Int64}, Matrix{Float64}, Vector{Float64}, HybridNetwork, Bool, Vector{Float64}})(x::Vector{Float64}, g::Vector{Float64}) @ PhyloTraits ~/.julia/packages/PhyloTraits/nqGfi/src/fit_phylolm_continuous.jl:373 [9] nlopt_callback_wrapper(n::UInt32, p_x::Ptr{Float64}, p_grad::Ptr{Float64}, d_::Ptr{Nothing}) @ NLopt ~/.julia/packages/NLopt/FpXXS/src/NLopt.jl:466 [10] nlopt_optimize @ ~/.julia/packages/NLopt/FpXXS/src/libnlopt.jl:182 [inlined] [11] optimize!(o::NLopt.Opt, x::Vector{Float64}) @ NLopt ~/.julia/packages/NLopt/FpXXS/src/NLopt.jl:790 [12] optimize @ ~/.julia/packages/NLopt/FpXXS/src/NLopt.jl:804 [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] 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 [19] top-level scope @ ~/.julia/packages/PhyloTraits/nqGfi/test/test_lm.jl:603 [20] macro expansion @ /opt/julia/share/julia/stdlib/v1.12/Test/src/Test.jl:1776 [inlined] [21] macro expansion @ ~/.julia/packages/PhyloTraits/nqGfi/test/test_lm.jl:641 [inlined] [22] include(mapexpr::Function, mod::Module, _path::String) @ Base ./Base.jl:306 [23] top-level scope @ ~/.julia/packages/PhyloTraits/nqGfi/test/runtests.jl:30 [24] macro expansion @ /opt/julia/share/julia/stdlib/v1.12/Test/src/Test.jl:1776 [inlined] [25] macro expansion @ ~/.julia/packages/PhyloTraits/nqGfi/test/runtests.jl:30 [inlined] [26] include(mapexpr::Function, mod::Module, _path::String) @ Base ./Base.jl:306 [27] top-level scope @ none:6 [28] eval(m::Module, e::Any) @ Core ./boot.jl:489 [29] exec_options(opts::Base.JLOptions) @ Base ./client.jl:287 [30] _start() @ Base ./client.jl:554 Stacktrace: [1] optimize!(o::NLopt.Opt, x::Vector{Float64}) @ NLopt ~/.julia/packages/NLopt/FpXXS/src/NLopt.jl:797 [2] optimize @ ~/.julia/packages/NLopt/FpXXS/src/NLopt.jl:804 [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] 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 [9] top-level scope @ ~/.julia/packages/PhyloTraits/nqGfi/test/test_lm.jl:603 [10] macro expansion @ /opt/julia/share/julia/stdlib/v1.12/Test/src/Test.jl:1776 [inlined] [11] macro expansion @ ~/.julia/packages/PhyloTraits/nqGfi/test/test_lm.jl:641 [inlined] [12] include(mapexpr::Function, mod::Module, _path::String) @ Base ./Base.jl:306 [13] top-level scope @ ~/.julia/packages/PhyloTraits/nqGfi/test/runtests.jl:30 [14] macro expansion @ /opt/julia/share/julia/stdlib/v1.12/Test/src/Test.jl:1776 [inlined] [15] macro expansion @ ~/.julia/packages/PhyloTraits/nqGfi/test/runtests.jl:30 [inlined] [16] include(mapexpr::Function, mod::Module, _path::String) @ Base ./Base.jl:306 [17] top-level scope @ none:6 [18] eval(m::Module, e::Any) @ Core ./boot.jl:489 [19] exec_options(opts::Base.JLOptions) @ Base ./client.jl:287 [20] _start() @ Base ./client.jl:554 Test Summary: | Pass Error Total Time PhyloTraits.jl | 920 2 922 8m46.5s phylolm on small network | 77 77 1m29.7s Shifts and Transgressive Evolution | 46 46 53.5s No Intercept | 20 20 7.5s phylolm and ancestralreconstruction | 132 1 133 14.0s lambda when no signal | 8 1 9 3.9s Undefined branch length | 4 4 0.1s phylolm: Caudata Dataset | 53 53 58.3s phylolm: Lizard Dataset | 26 26 22.2s phylolm: within-species variation, star | 17 17 8.8s phylolm: binary tree, no withinspecies var | 20 20 2.3s phylolm: binary tree, withinspecies var | 26 26 11.3s phylolm: within-species var, network h=1 | 103 103 20.0s discrete | 213 213 2m27.2s Simulate function against fixed values | 8 8 2.0s Simulate test distribution | 90 90 1.9s Simulate with Shifts | 42 42 11.9s Simulate data and check means and dimensions | 8 8 0.8s Simulate test distribution (fixed root) | 2 2 3.1s Simulate test distribution (random root) | 3 3 5.2s Simulate with Shifts | 22 22 2.4s RNG of the outermost testset: Xoshiro(0x05a2b0ab51a308ca, 0x54ced5f7fe07f4c7, 0x2df73a422baffd18, 0xfafafcd17ef2536d, 0xc6c03f989ecb2092) ERROR: LoadError: Some tests did not pass: 920 passed, 0 failed, 2 errored, 0 broken. in expression starting at /home/pkgeval/.julia/packages/PhyloTraits/nqGfi/test/runtests.jl:29 Testing failed after 619.68s ERROR: LoadError: Package PhyloTraits 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:2458 [3] test @ /opt/julia/share/julia/stdlib/v1.12/Pkg/src/Operations.jl:2313 [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:511 [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:164 [6] test(pkgs::Vector{String}; kwargs::@Kwargs{julia_args::Cmd}) @ Pkg.API /opt/julia/share/julia/stdlib/v1.12/Pkg/src/API.jl:152 [7] test @ /opt/julia/share/julia/stdlib/v1.12/Pkg/src/API.jl:152 [inlined] [8] #test#81 @ /opt/julia/share/julia/stdlib/v1.12/Pkg/src/API.jl:151 [inlined] [9] top-level scope @ /PkgEval.jl/scripts/evaluate.jl:219 [10] include(mod::Module, _path::String) @ Base ./Base.jl:305 [11] exec_options(opts::Base.JLOptions) @ Base ./client.jl:321 [12] _start() @ Base ./client.jl:554 in expression starting at /PkgEval.jl/scripts/evaluate.jl:210 PkgEval failed after 695.79s: package tests unexpectedly errored