Package evaluation to test PottsEvolver on Julia 1.11.8 (29b3528cce*) started at 2026-01-20T09:54:29.099 ################################################################################ # Set-up # Installing PkgEval dependencies (TestEnv)... Activating project at `~/.julia/environments/v1.11` Set-up completed after 8.51s ################################################################################ # Installation # Installing PottsEvolver... Resolving package versions... Updating `~/.julia/environments/v1.11/Project.toml` [288ebb56] + PottsEvolver v0.1.0 Updating `~/.julia/environments/v1.11/Manifest.toml` [79e6a3ab] + Adapt v4.4.0 [66dad0bd] + AliasTables v1.1.3 [dce04be8] + ArgCheck v2.5.0 [a9b6321e] + Atomix v1.1.2 [67c07d97] + Automa v1.1.0 [47718e42] + BioGenerics v0.1.5 [a84bc454] + BioSequenceMappings v0.1.7 [d360d2e6] + ChainRulesCore v1.26.0 [34da2185] + Compat v4.18.1 [9a962f9c] + DataAPI v1.16.0 [864edb3b] + DataStructures v0.19.3 [31c24e10] + Distributions v0.25.123 [ffbed154] + DocStringExtensions v0.9.5 [c2308a5c] + FASTX v2.1.7 [1a297f60] + FillArrays v1.16.0 [46192b85] + GPUArraysCore v0.2.0 [076d061b] + HashArrayMappedTries v0.2.0 [34004b35] + HypergeometricFunctions v0.3.28 [92d709cd] + IrrationalConstants v0.2.6 [692b3bcd] + JLLWrappers v1.7.1 [63c18a36] + KernelAbstractions v0.9.39 [2ab3a3ac] + LogExpFunctions v0.3.29 [e6f89c97] + LoggingExtras v1.2.0 [1914dd2f] + MacroTools v0.5.16 [e1d29d7a] + Missings v1.2.0 [872c559c] + NNlib v0.9.33 [0b1bfda6] + OneHotArrays v0.2.10 [bac558e1] + OrderedCollections v1.8.1 [90014a1f] + PDMats v0.11.37 [e409e4f3] + PoissonRandom v0.4.7 [288ebb56] + PottsEvolver v0.1.0 ⌅ [aea7be01] + PrecompileTools v1.2.1 [21216c6a] + Preferences v1.5.1 [92933f4c] + ProgressMeter v1.11.0 [43287f4e] + PtrArrays v1.3.0 [1fd47b50] + QuadGK v2.11.2 [988b38a3] + ReadOnlyArrays v0.2.0 [189a3867] + Reexport v1.2.2 [ae029012] + Requires v1.3.1 ⌅ [c5292f4c] + ResumableFunctions v0.6.10 [79098fc4] + Rmath v0.9.0 [fdea26ae] + SIMD v3.7.2 [7e506255] + ScopedValues v1.5.0 [a2af1166] + SortingAlgorithms v1.2.2 [276daf66] + SpecialFunctions v2.6.1 [90137ffa] + StaticArrays v1.9.16 [1e83bf80] + StaticArraysCore v1.4.4 [10745b16] + Statistics v1.11.1 [82ae8749] + StatsAPI v1.8.0 [2913bbd2] + StatsBase v0.34.10 [4c63d2b9] + StatsFuns v1.5.2 [354b36f9] + StringViews v1.3.6 [3bb67fe8] + TranscodingStreams v0.11.3 ⌅ [62f0eae3] + TreeTools v0.7.3 [3a884ed6] + UnPack v1.0.2 [013be700] + UnsafeAtomics v0.3.0 [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 [b77e0a4c] + InteractiveUtils v1.11.0 [8f399da3] + Libdl v1.11.0 [37e2e46d] + LinearAlgebra v1.11.0 [56ddb016] + Logging v1.11.0 [d6f4376e] + Markdown v1.11.0 [de0858da] + Printf 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 v1.11.0 [4607b0f0] + SuiteSparse [fa267f1f] + TOML v1.0.3 [cf7118a7] + UUIDs v1.11.0 [4ec0a83e] + Unicode v1.11.0 [e66e0078] + CompilerSupportLibraries_jll v1.1.1+0 [4536629a] + OpenBLAS_jll v0.3.27+1 [05823500] + OpenLibm_jll v0.8.5+0 [bea87d4a] + SuiteSparse_jll v7.7.0+0 [8e850b90] + libblastrampoline_jll v5.11.0+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 5.34s ################################################################################ # Precompilation # Precompiling PkgEval dependencies... Precompiling package dependencies... Precompiling project... 16561.3 ms ✓ TreeTools 47519.6 ms ✓ PottsEvolver 2 dependencies successfully precompiled in 68 seconds. 123 already precompiled. Precompilation completed after 80.32s ################################################################################ # Testing # Testing PottsEvolver Status `/tmp/jl_P299yr/Project.toml` [7d9f7c33] Accessors v0.1.43 [4c88cf16] Aqua v0.8.14 [dce04be8] ArgCheck v2.5.0 [a84bc454] BioSequenceMappings v0.1.7 [31c24e10] Distributions v0.25.123 [e6f89c97] LoggingExtras v1.2.0 [e409e4f3] PoissonRandom v0.4.7 [288ebb56] PottsEvolver v0.1.0 [92933f4c] ProgressMeter v1.11.0 [988b38a3] ReadOnlyArrays v0.2.0 [2913bbd2] StatsBase v0.34.10 ⌅ [62f0eae3] TreeTools v0.7.3 [3a884ed6] UnPack v1.0.2 [56ddb016] Logging v1.11.0 [9a3f8284] Random v1.11.0 [8dfed614] Test v1.11.0 Status `/tmp/jl_P299yr/Manifest.toml` [7d9f7c33] Accessors v0.1.43 [79e6a3ab] Adapt v4.4.0 [66dad0bd] AliasTables v1.1.3 [4c88cf16] Aqua v0.8.14 [dce04be8] ArgCheck v2.5.0 [a9b6321e] Atomix v1.1.2 [67c07d97] Automa v1.1.0 [47718e42] BioGenerics v0.1.5 [a84bc454] BioSequenceMappings v0.1.7 [d360d2e6] ChainRulesCore v1.26.0 [34da2185] Compat v4.18.1 [a33af91c] CompositionsBase v0.1.2 [187b0558] ConstructionBase v1.6.0 [9a962f9c] DataAPI v1.16.0 [864edb3b] DataStructures v0.19.3 [31c24e10] Distributions v0.25.123 [ffbed154] DocStringExtensions v0.9.5 [c2308a5c] FASTX v2.1.7 [1a297f60] FillArrays v1.16.0 [46192b85] GPUArraysCore v0.2.0 [076d061b] HashArrayMappedTries v0.2.0 [34004b35] HypergeometricFunctions v0.3.28 [3587e190] InverseFunctions v0.1.17 [92d709cd] IrrationalConstants v0.2.6 [692b3bcd] JLLWrappers v1.7.1 [63c18a36] KernelAbstractions v0.9.39 [2ab3a3ac] LogExpFunctions v0.3.29 [e6f89c97] LoggingExtras v1.2.0 [1914dd2f] MacroTools v0.5.16 [e1d29d7a] Missings v1.2.0 [872c559c] NNlib v0.9.33 [0b1bfda6] OneHotArrays v0.2.10 [bac558e1] OrderedCollections v1.8.1 [90014a1f] PDMats v0.11.37 [e409e4f3] PoissonRandom v0.4.7 [288ebb56] PottsEvolver v0.1.0 ⌅ [aea7be01] PrecompileTools v1.2.1 [21216c6a] Preferences v1.5.1 [92933f4c] ProgressMeter v1.11.0 [43287f4e] PtrArrays v1.3.0 [1fd47b50] QuadGK v2.11.2 [988b38a3] ReadOnlyArrays v0.2.0 [189a3867] Reexport v1.2.2 [ae029012] Requires v1.3.1 ⌅ [c5292f4c] ResumableFunctions v0.6.10 [79098fc4] Rmath v0.9.0 [fdea26ae] SIMD v3.7.2 [7e506255] ScopedValues v1.5.0 [a2af1166] SortingAlgorithms v1.2.2 [276daf66] SpecialFunctions v2.6.1 [90137ffa] StaticArrays v1.9.16 [1e83bf80] StaticArraysCore v1.4.4 [10745b16] Statistics v1.11.1 [82ae8749] StatsAPI v1.8.0 [2913bbd2] StatsBase v0.34.10 [4c63d2b9] StatsFuns v1.5.2 [354b36f9] StringViews v1.3.6 [3bb67fe8] TranscodingStreams v0.11.3 ⌅ [62f0eae3] TreeTools v0.7.3 [3a884ed6] UnPack v1.0.2 [013be700] UnsafeAtomics v0.3.0 [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 [b77e0a4c] InteractiveUtils v1.11.0 [b27032c2] LibCURL v0.6.4 [76f85450] LibGit2 v1.11.0 [8f399da3] Libdl v1.11.0 [37e2e46d] LinearAlgebra v1.11.0 [56ddb016] Logging v1.11.0 [d6f4376e] Markdown v1.11.0 [ca575930] NetworkOptions v1.2.0 [44cfe95a] Pkg v1.11.0 [de0858da] Printf 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 v1.11.0 [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 v1.1.1+0 [deac9b47] LibCURL_jll v8.6.0+0 [e37daf67] LibGit2_jll v1.7.2+0 [29816b5a] LibSSH2_jll v1.11.0+1 [c8ffd9c3] MbedTLS_jll v2.28.6+0 [14a3606d] MozillaCACerts_jll v2023.12.12 [4536629a] OpenBLAS_jll v0.3.27+1 [05823500] OpenLibm_jll v0.8.5+0 [bea87d4a] SuiteSparse_jll v7.7.0+0 [83775a58] Zlib_jll v1.2.13+1 [8e850b90] libblastrampoline_jll v5.11.0+0 [8e850ede] nghttp2_jll v1.59.0+0 [3f19e933] p7zip_jll v17.4.0+2 Info Packages marked with ⌅ have new versions available but compatibility constraints restrict them from upgrading. Testing Running tests... Precompiling StaticArraysExt... 1645.9 ms ✓ Accessors → StaticArraysExt 1 dependency successfully precompiled in 2 seconds. 18 already precompiled. Sampling: 50%[=============> ] ETA: 0:00:03 ( 1.56 s/it) steps: 3 total: 5     Sampling: 100%[===========================] Time: 0:00:04 ( 1.10 s/it) steps: 5 total: 5 ┌ Info: Sampling sequences of tree with 8 leaves using the following settings: │ - type of sampling = `:discrete` │ - type of sequence = AASequence{Int64} │ - step style = gibbs │ - step meaning = changed │ - fraction of gap steps (if codon) = 0.9 └ - branch length meaning = BranchLengthMeaning(:step, :exact) ┌ Info: Sampling on a tree: `Teq` field in parameters is ignored └ Teq = 5 [ Info: Sampling done in 5.7899e-5 seconds ┌ Info: Sampling sequences of tree with 8 leaves using the following settings: │ - type of sampling = `:continuous` │ - type of sequence = AASequence{Int64} └ - step style = glauber ┌ Info: Sampling on a tree: `Teq` field in parameters is ignored └ Teq = 5.0 [ Info: Computing average substitution rate for the model using discrete sampling... [ Info: Done in 0.014926058 seconds [ Info: Average substitution rate: 23.904840671980857 [ Info: Sampling done in 0.009588339 seconds ┌ Info: Sampling sequences of tree with 8 leaves using the following settings: │ - type of sampling = `:discrete` │ - type of sequence = CodonSequence{Int64} │ - step style = gibbs │ - step meaning = changed │ - fraction of gap steps (if codon) = 0.9 └ - branch length meaning = BranchLengthMeaning(:step, :exact) ┌ Info: Sampling on a tree: `Teq` field in parameters is ignored └ Teq = 1 [ Info: Sampling done in 0.000564814 seconds [ Info: Equilibrating root sequence with 100 burnin steps... [ Info: done in 0.016037147 seconds ┌ Info: Sampling sequences of tree with 8 leaves using the following settings: │ - type of sampling = `:discrete` │ - type of sequence = NumSequence{Int64, 21} │ - step style = gibbs │ - step meaning = changed │ - fraction of gap steps (if codon) = 0.9 └ - branch length meaning = BranchLengthMeaning(:step, :exact) ┌ Info: Sampling on a tree: `Teq` field in parameters is ignored └ Teq = 1 [ Info: Sampling done in 0.014218075 seconds ┌ Info: Sampling sequences of tree with 8 leaves using the following settings: │ - type of sampling = `:continuous` │ - type of sequence = CodonSequence{Int64} └ - step style = glauber ┌ Info: Sampling on a tree: `Teq` field in parameters is ignored └ Teq = 1.0 [ Info: Computing average substitution rate for the model using discrete sampling... [ Info: Done in 0.637235759 seconds [ Info: Average substitution rate: 73.55537225457161 [ Info: Sampling done in 0.029504029 seconds [ Info: Equilibrating root sequence with 100.0 burnin steps... [ Info: done in 5.183030983 seconds ┌ Info: Sampling sequences of tree with 8 leaves using the following settings: │ - type of sampling = `:continuous` │ - type of sequence = NumSequence{Int64, 21} └ - step style = glauber ┌ Info: Sampling on a tree: `Teq` field in parameters is ignored └ Teq = 1.0 [ Info: Computing average substitution rate for the model using discrete sampling... [ Info: Done in 1.348475795 seconds [ Info: Average substitution rate: 140.96946074330924 [ Info: Sampling done in 0.004889974 seconds /home/pkgeval/.julia/packages/PottsEvolver/rIcCN/test/sampling_tree/test_tree.nwkTest Summary: | Pass Broken Total Time PottsEvolver.jl | 1181 1 1182 2m37.7s Test Summary: | Pass Total Time Aqua.jl | 11 11 1m06.5s Testing PottsEvolver tests passed Testing completed after 240.37s PkgEval succeeded after 347.25s