Package evaluation of PhyloTraits on Julia 1.13.0-DEV.725 (d6294ba973*) started at 2025-06-10T22:02:27.955 ################################################################################ # Set-up # Installing PkgEval dependencies (TestEnv)... Set-up completed after 7.93s ################################################################################ # Installation # Installing PhyloTraits... Resolving package versions... Updating `~/.julia/environments/v1.13/Project.toml` [bce24f4f] + PhyloTraits v1.1.0 Updating `~/.julia/environments/v1.13/Manifest.toml` [66dad0bd] + AliasTables v1.1.3 [67c07d97] + Automa v1.1.0 [47718e42] + BioGenerics v0.1.5 [7e6ae17a] + BioSequences v3.4.1 [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 v4.16.0 [187b0558] + ConstructionBase v1.5.8 [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 v1.4.3 [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 v1.1.4 [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 [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 v1.12.0 [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 v7.10.1+0 [83775a58] + Zlib_jll v1.3.1+2 [8e850b90] + libblastrampoline_jll v5.12.0+0 Installation completed after 4.07s ################################################################################ # Precompilation # Precompiling PkgEval dependencies... Precompiling package dependencies... Precompilation completed after 53.81s ################################################################################ # Testing # Testing PhyloTraits Status `/tmp/jl_FMTjOO/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_FMTjOO/Manifest.toml` [66dad0bd] AliasTables v1.1.3 [4c88cf16] Aqua v0.8.13 [67c07d97] Automa v1.1.0 [47718e42] BioGenerics v0.1.5 [7e6ae17a] BioSequences v3.4.1 [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 v4.16.0 [187b0558] ConstructionBase v1.5.8 [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 v1.4.3 [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 v1.1.4 [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 v1.7.0 [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 v8.12.1+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 v3.5.0+0 [bea87d4a] SuiteSparse_jll v7.10.1+0 [83775a58] Zlib_jll v1.3.1+2 [8e850b90] libblastrampoline_jll v5.12.0+0 [8e850ede] nghttp2_jll v1.65.0+0 [3f19e933] p7zip_jll v17.5.0+2 Testing Running tests... Precompiling packages... 86137.6 ms ✓ PhyloTraits 1 dependency successfully precompiled in 89 seconds. 99 already precompiled. Precompiling packages... 8404.5 ms ✓ Distributions → DistributionsTestExt 1 dependency successfully precompiled in 10 seconds. 49 already precompiled. Test Summary: | Pass Total Time PhyloTraits Code quality (Aqua.jl) | 9 9 37.8s 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/ZvUrS/src/NLopt.jl:466 [10] nlopt_optimize @ ~/.julia/packages/NLopt/ZvUrS/src/libnlopt.jl:182 [inlined] [11] optimize!(o::NLopt.Opt, x::Vector{Float64}) @ NLopt ~/.julia/packages/NLopt/ZvUrS/src/NLopt.jl:790 [12] optimize @ ~/.julia/packages/NLopt/ZvUrS/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/v1.13/Test/src/Test.jl:1833 [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:310 [23] top-level scope @ ~/.julia/packages/PhyloTraits/nqGfi/test/runtests.jl:30 [24] macro expansion @ /opt/julia/share/julia/stdlib/v1.13/Test/src/Test.jl:1833 [inlined] [25] macro expansion @ ~/.julia/packages/PhyloTraits/nqGfi/test/runtests.jl:30 [inlined] [26] include(mapexpr::Function, mod::Module, _path::String) @ Base ./Base.jl:310 [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:290 [30] _start() @ Base ./client.jl:557 Stacktrace: [1] optimize!(o::NLopt.Opt, x::Vector{Float64}) @ NLopt ~/.julia/packages/NLopt/ZvUrS/src/NLopt.jl:797 [2] optimize @ ~/.julia/packages/NLopt/ZvUrS/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/v1.13/Test/src/Test.jl:1833 [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:310 [13] top-level scope @ ~/.julia/packages/PhyloTraits/nqGfi/test/runtests.jl:30 [14] macro expansion @ /opt/julia/share/julia/stdlib/v1.13/Test/src/Test.jl:1833 [inlined] [15] macro expansion @ ~/.julia/packages/PhyloTraits/nqGfi/test/runtests.jl:30 [inlined] [16] include(mapexpr::Function, mod::Module, _path::String) @ Base ./Base.jl:310 [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:290 [20] _start() @ Base ./client.jl:557 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/ZvUrS/src/NLopt.jl:466 [10] nlopt_optimize @ ~/.julia/packages/NLopt/ZvUrS/src/libnlopt.jl:182 [inlined] [11] optimize!(o::NLopt.Opt, x::Vector{Float64}) @ NLopt ~/.julia/packages/NLopt/ZvUrS/src/NLopt.jl:790 [12] optimize @ ~/.julia/packages/NLopt/ZvUrS/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/v1.13/Test/src/Test.jl:1833 [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:310 [23] top-level scope @ ~/.julia/packages/PhyloTraits/nqGfi/test/runtests.jl:30 [24] macro expansion @ /opt/julia/share/julia/stdlib/v1.13/Test/src/Test.jl:1833 [inlined] [25] macro expansion @ ~/.julia/packages/PhyloTraits/nqGfi/test/runtests.jl:30 [inlined] [26] include(mapexpr::Function, mod::Module, _path::String) @ Base ./Base.jl:310 [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:290 [30] _start() @ Base ./client.jl:557 Stacktrace: [1] optimize!(o::NLopt.Opt, x::Vector{Float64}) @ NLopt ~/.julia/packages/NLopt/ZvUrS/src/NLopt.jl:797 [2] optimize @ ~/.julia/packages/NLopt/ZvUrS/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/v1.13/Test/src/Test.jl:1833 [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:310 [13] top-level scope @ ~/.julia/packages/PhyloTraits/nqGfi/test/runtests.jl:30 [14] macro expansion @ /opt/julia/share/julia/stdlib/v1.13/Test/src/Test.jl:1833 [inlined] [15] macro expansion @ ~/.julia/packages/PhyloTraits/nqGfi/test/runtests.jl:30 [inlined] [16] include(mapexpr::Function, mod::Module, _path::String) @ Base ./Base.jl:310 [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:290 [20] _start() @ Base ./client.jl:557 phylolm: Caudata Dataset: Error During Test at /home/pkgeval/.julia/packages/PhyloTraits/nqGfi/test/test_lm_tree.jl:6 Got exception outside of a @test Tips with data are not in the network: String31["Ambystoma_annulatum", "Ambystoma_barbouri", "Ambystoma_californiense", "Ambystoma_cingulatum", "Ambystoma_gracile", "Ambystoma_jeffersonianum", "Ambystoma_laterale", "Ambystoma_macrodactylum", "Ambystoma_maculatum", "Ambystoma_mavortium", "Ambystoma_opacum", "Ambystoma_ordinarium", "Ambystoma_texanum", "Ambystoma_velasci", "Amphiuma_means", "Amphiuma_pholeter", "Amphiuma_tridactylum", "Andrias_davidianus", "Aneides_aeneus", "Aneides_flavipunctatus", "Aneides_hardii", "Aneides_lugubris", "Batrachoseps_attenuatus", "Batrachoseps_major", "Batrachoseps_wrighti", "Batrachuperus_pinchonii", "Batrachuperus_yenyuanensis", "Bolitoglossa_adspersa", "Bolitoglossa_dofleini", "Bolitoglossa_engelhardti", "Bolitoglossa_mexicana", "Bolitoglossa_morio", "Bolitoglossa_occidentalis", "Bolitoglossa_palmata", "Bolitoglossa_platydactyla", "Bolitoglossa_rostrata", "Bolitoglossa_rufescens", "Bolitoglossa_subpalmata", "Bolitoglossa_yucatana", "Bradytriton_silus", "Calotriton_asper", "Chioglossa_lusitanica", "Chiropterotriton_chondrostega", "Chiropterotriton_dimidiatus", "Chiropterotriton_lavae", "Chiropterotriton_multidentatus", "Chiropterotriton_priscus", "Cryptobranchus_alleganiensis", "Cryptotriton_nasalis", "Cynops_ensicauda", "Cynops_pyrrhogaster", "Desmognathus_aeneus", "Desmognathus_auriculatus", "Desmognathus_brimleyorum", "Desmognathus_fuscus", "Desmognathus_imitator", "Desmognathus_marmoratus", "Desmognathus_monticola", "Desmognathus_ochrophaeus", "Desmognathus_quadramaculatus", "Desmognathus_welteri", "Desmognathus_wrighti", "Dicamptodon_copei", "Dicamptodon_ensatus", "Dicamptodon_tenebrosus", "Echinotriton_andersoni", "Ensatina_eschscholtzii", "Eurycea_aquatica", "Eurycea_bislineata", "Eurycea_cirrigera", "Eurycea_junaluska", "Eurycea_longicauda", "Eurycea_lucifuga", "Eurycea_multiplicata", "Eurycea_nana", "Eurycea_neotenes", "Eurycea_quadridigitata", "Eurycea_rathbuni", "Eurycea_sosorum", "Eurycea_spelaea", "Eurycea_tridentifera", "Eurycea_tynerensis", "Eurycea_wilderae", "Gyrinophilus_porphyriticus", "Hemidactylium_scutatum", "Hydromantes_italicus", "Hydromantes_platycephalus", "Hynobius_abei", "Hynobius_dunni", "Hynobius_leechii", "Hynobius_lichenatus", "Hynobius_naevius", "Hynobius_nebulosus", "Hynobius_nigrescens", "Hynobius_stejnegeri", "Hynobius_tsuensis", "Lissotriton_boscai", "Lissotriton_helveticus", "Lissotriton_montandoni", "Lissotriton_vulgaris", "Liua_shihi", "Mertensiella_caucasica", "Ichthyosaura_alpestris", "Necturus_alabamensis", "Necturus_beyeri", "Necturus_maculosus", "Necturus_punctatus", "Neurergus_crocatus", "Neurergus_strauchii", "Notophthalmus_meridionalis", "Notophthalmus_perstriatus", "Notophthalmus_viridescens", "Nototriton_picadoi", "Nyctanolis_pernix", "Oedipina_complex", "Oedipina_cyclocauda", "Oedipina_parvipes", "Oedipina_uniformis", "Ommatotriton_vittatus", "Pachyhynobius_shangchengensis", "Pachytriton_brevipes", "Paradactylodon_mustersi", "Paramesotriton_caudopunctatus", "Paramesotriton_chinensis", "Paramesotriton_hongkongensis", "Parvimolge_townsendi", "Phaeognathus_hubrichti", "Plethodon_albagula", "Plethodon_amplus", "Plethodon_angusticlavius", "Plethodon_caddoensis", "Plethodon_cheoah", "Plethodon_chlorobryonis", "Plethodon_cinereus", "Plethodon_cylindraceus", "Plethodon_dorsalis", "Plethodon_dunni", "Plethodon_elongatus", "Plethodon_glutinosus", "Plethodon_grobmani", "Plethodon_hoffmani", "Plethodon_hubrichti", "Plethodon_idahoensis", "Plethodon_jordani", "Plethodon_kentucki", "Plethodon_meridianus", "Plethodon_metcalfi", "Plethodon_mississippi", "Plethodon_montanus", "Plethodon_neomexicanus", "Plethodon_nettingi", "Plethodon_ouachitae", "Plethodon_punctatus", "Plethodon_richmondi", "Plethodon_serratus", "Plethodon_shenandoah", "Plethodon_shermani", "Plethodon_teyahalee", "Plethodon_vandykei", "Plethodon_vehiculum", "Plethodon_ventralis", "Plethodon_wehrlei", "Plethodon_welleri", "Plethodon_yonahlossee", "Pleurodeles_waltl", "Proteus_anguinus", "Pseudobranchus_axanthus", "Pseudoeurycea_bellii", "Pseudoeurycea_cephalica", "Pseudoeurycea_gadovii", "Pseudoeurycea_galeanae", "Pseudoeurycea_leprosa", "Pseudoeurycea_rex", "Pseudoeurycea_robertsi", "Pseudoeurycea_werleri", "Pseudotriton_montanus", "Pseudotriton_ruber", "Ranodon_sibiricus", "Rhyacotriton_cascadae", "Rhyacotriton_kezeri", "Rhyacotriton_olympicus", "Rhyacotriton_variegatus", "Salamandra_atra", "Salamandra_salamandra", "Salamandrella_keyserlingii", "Salamandrina_terdigitata", "Siren_intermedia", "Siren_lacertina", "Stereochilus_marginatus", "Taricha_granulosa", "Taricha_rivularis", "Taricha_torosa", "Triturus_cristatus", "Triturus_pygmaeus", "Tylototriton_asperrimus", "Tylototriton_kweichowensis", "Tylototriton_verrucosus"] please provide a larger network including these tips. Stacktrace: [1] error(s::String) @ Base ./error.jl:44 [2] phylolm(f::FormulaTerm{Term, ConstantTerm{Int64}}, 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:773 [3] top-level scope @ ~/.julia/packages/PhyloTraits/nqGfi/test/test_lm_tree.jl:8 [4] macro expansion @ /opt/julia/share/julia/stdlib/v1.13/Test/src/Test.jl:1833 [inlined] [5] macro expansion @ ~/.julia/packages/PhyloTraits/nqGfi/test/test_lm_tree.jl:41 [inlined] [6] include(mapexpr::Function, mod::Module, _path::String) @ Base ./Base.jl:310 [7] top-level scope @ ~/.julia/packages/PhyloTraits/nqGfi/test/runtests.jl:30 [8] macro expansion @ /opt/julia/share/julia/stdlib/v1.13/Test/src/Test.jl:1833 [inlined] [9] macro expansion @ ~/.julia/packages/PhyloTraits/nqGfi/test/runtests.jl:31 [inlined] [10] include(mapexpr::Function, mod::Module, _path::String) @ Base ./Base.jl:310 [11] top-level scope @ none:6 [12] eval(m::Module, e::Any) @ Core ./boot.jl:489 [13] exec_options(opts::Base.JLOptions) @ Base ./client.jl:290 [14] _start() @ Base ./client.jl:557 phylolm: Lizard Dataset: Error During Test at /home/pkgeval/.julia/packages/PhyloTraits/nqGfi/test/test_lm_tree.jl:316 Got exception outside of a @test Tips with data are not in the network: String15["ahli", "alayoni", "alfaroi", "aliniger", "allisoni", "allogus", "altitudinalis", "alumina", "alutaceus", "angusticeps", "argenteolus", "argillaceus", "armouri", "bahorucoensis", "baleatus", "baracoae", "barahonae", "barbatus", "barbouri", "bartschi", "bremeri", "breslini", "brevirostris", "caudalis", "centralis", "chamaeleonides", "chlorocyanus", "christophei", "clivicola", "coelestinus", "confusus", "cooki", "cristatellus", "cupeyalensis", "cuvieri", "cyanopleurus", "cybotes", "darlingtoni", "distichus", "dolichocephalus", "equestris", "etheridgei", "eugenegrahami", "evermanni", "fowleri", "garmani", "grahami", "guafe", "guamuhaya", "guazuma", "gundlachi", "haetianus", "hendersoni", "homolechis", "imias", "inexpectatus", "insolitus", "isolepis", "jubar", "krugi", "lineatopus", "longitibialis", "loysiana", "lucius", "luteogularis", "macilentus", "marcanoi", "marron", "mestrei", "monticola", "noblei", "occultus", "olssoni", "opalinus", "ophiolepis", "oporinus", "paternus", "placidus", "poncensis", "porcatus", "porcus", "pulchellus", "pumilis", "quadriocellifer", "reconditus", "ricordii", "rubribarbus", "sagrei", "semilineatus", "sheplani", "shrevei", "singularis", "smallwoodi", "strahmi", "stratulus", "valencienni", "vanidicus", "vermiculatus", "websteri", "whitemani"] please provide a larger network including these tips. Stacktrace: [1] error(s::String) @ Base ./error.jl:44 [2] phylolm(f::FormulaTerm{Term, Tuple{Term, Term, Term, InteractionTerm{Tuple{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:773 [3] top-level scope @ ~/.julia/packages/PhyloTraits/nqGfi/test/test_lm_tree.jl:319 [4] macro expansion @ /opt/julia/share/julia/stdlib/v1.13/Test/src/Test.jl:1833 [inlined] [5] macro expansion @ ~/.julia/packages/PhyloTraits/nqGfi/test/test_lm_tree.jl:324 [inlined] [6] include(mapexpr::Function, mod::Module, _path::String) @ Base ./Base.jl:310 [7] top-level scope @ ~/.julia/packages/PhyloTraits/nqGfi/test/runtests.jl:30 [8] macro expansion @ /opt/julia/share/julia/stdlib/v1.13/Test/src/Test.jl:1833 [inlined] [9] macro expansion @ ~/.julia/packages/PhyloTraits/nqGfi/test/runtests.jl:31 [inlined] [10] include(mapexpr::Function, mod::Module, _path::String) @ Base ./Base.jl:310 [11] top-level scope @ none:6 [12] eval(m::Module, e::Any) @ Core ./boot.jl:489 [13] exec_options(opts::Base.JLOptions) @ Base ./client.jl:290 [14] _start() @ Base ./client.jl:557 Test Summary: | Pass Error Total Time PhyloTraits.jl | 844 4 848 8m03.1s phylolm on small network | 77 77 1m28.4s Shifts and Transgressive Evolution | 46 46 51.5s No Intercept | 20 20 6.7s phylolm and ancestralreconstruction | 132 1 133 13.8s lambda when no signal | 8 1 9 5.1s Undefined branch length | 4 4 0.0s phylolm: Caudata Dataset | 3 1 4 44.6s phylolm: Lizard Dataset | 1 1 5.1s phylolm: within-species variation, star | 17 17 7.5s phylolm: binary tree, no withinspecies var | 20 20 1.9s phylolm: binary tree, withinspecies var | 26 26 9.5s phylolm: within-species var, network h=1 | 103 103 24.8s discrete | 213 213 2m16.7s Simulate function against fixed values | 8 8 1.9s Simulate test distribution | 90 90 1.9s Simulate with Shifts | 42 42 12.0s 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 5.7s Simulate with Shifts | 22 22 2.5s RNG of the outermost testset: Xoshiro(0xd231c71b804de2d4, 0x17d051c616251a91, 0x9903d5ad7fdd62d3, 0x70e86181bd611d4f, 0x2d10935d6fb7edcf) ERROR: LoadError: Some tests did not pass: 844 passed, 0 failed, 4 errored, 0 broken. in expression starting at /home/pkgeval/.julia/packages/PhyloTraits/nqGfi/test/runtests.jl:29 Testing failed after 656.87s ERROR: LoadError: Package PhyloTraits errored during testing Stacktrace: [1] pkgerror(msg::String) @ Pkg.Types /opt/julia/share/julia/stdlib/v1.13/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/v1.13/Pkg/src/Operations.jl:2421 [3] test @ /opt/julia/share/julia/stdlib/v1.13/Pkg/src/Operations.jl:2276 [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/v1.13/Pkg/src/API.jl:498 [5] test(pkgs::Vector{PackageSpec}; io::IOContext{IO}, kwargs::@Kwargs{julia_args::Cmd}) @ Pkg.API /opt/julia/share/julia/stdlib/v1.13/Pkg/src/API.jl:164 [6] test(pkgs::Vector{String}; kwargs::@Kwargs{julia_args::Cmd}) @ Pkg.API /opt/julia/share/julia/stdlib/v1.13/Pkg/src/API.jl:152 [7] test @ /opt/julia/share/julia/stdlib/v1.13/Pkg/src/API.jl:152 [inlined] [8] #test#81 @ /opt/julia/share/julia/stdlib/v1.13/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:309 [11] exec_options(opts::Base.JLOptions) @ Base ./client.jl:324 [12] _start() @ Base ./client.jl:557 in expression starting at /PkgEval.jl/scripts/evaluate.jl:210 PkgEval failed after 752.84s: package tests unexpectedly errored