Package evaluation of PhyloDiamond on Julia 1.11.4 (a71dd056e0*) started at 2025-04-08T19:58:20.207 ################################################################################ # Set-up # Installing PkgEval dependencies (TestEnv)... Set-up completed after 8.36s ################################################################################ # Installation # Installing PhyloDiamond... Resolving package versions... Installed Conda ─ v1.10.2 Installed RCall ─ v0.13.18 Updating `~/.julia/environments/v1.11/Project.toml` [5fd89c64] + PhyloDiamond v0.1.0 Updating `~/.julia/environments/v1.11/Manifest.toml` [a4c015fc] + ANSIColoredPrinters v0.0.1 [66dad0bd] + AliasTables v1.1.3 [67c07d97] + Automa v1.1.0 [6e4b80f9] + BenchmarkTools v1.6.0 [47718e42] + BioGenerics v0.1.5 [7e6ae17a] + BioSequences v3.4.1 [3c28c6f8] + BioSymbols v5.1.3 [336ed68f] + CSV v0.10.15 [324d7699] + CategoricalArrays v0.10.8 [523fee87] + CodecBzip2 v0.8.5 [944b1d66] + CodecZlib v0.7.8 [861a8166] + Combinatorics v1.0.2 [bbf7d656] + CommonSubexpressions v0.3.1 [34da2185] + Compat v4.16.0 [8f4d0f93] + Conda v1.10.2 [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 [8bb1440f] + DelimitedFiles v1.9.1 [163ba53b] + DiffResults v1.1.0 [b552c78f] + DiffRules v1.15.1 [31c24e10] + Distributions v0.25.118 [ffbed154] + DocStringExtensions v0.9.4 ⌅ [e30172f5] + Documenter v0.27.25 [7876af07] + Example v0.5.5 [c2308a5c] + FASTX v2.1.7 [48062228] + FilePathsBase v0.9.24 [1a297f60] + FillArrays v1.13.0 [f6369f11] + ForwardDiff v1.0.1 ⌅ [d9f16b24] + Functors v0.3.0 ⌃ [38e38edf] + GLM v1.8.3 [34004b35] + HypergeometricFunctions v0.3.28 [b5f81e59] + IOCapture v0.2.5 [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 [682c06a0] + JSON v0.21.4 [0f8b85d8] + JSON3 v1.14.2 [b964fa9f] + LaTeXStrings v1.4.0 [2ab3a3ac] + LogExpFunctions v0.3.29 [1914dd2f] + MacroTools v0.5.15 [b8f27783] + MathOptInterface v1.38.1 [fdba3010] + MathProgBase v0.7.8 [e1d29d7a] + Missings v1.2.0 [d8a4904e] + MutableArithmetics v1.6.4 ⌅ [76087f3c] + NLopt v0.6.5 [77ba4419] + NaNMath v1.1.3 [bac558e1] + OrderedCollections v1.8.0 [90014a1f] + PDMats v0.11.33 [69de0a69] + Parsers v2.8.1 [5fd89c64] + PhyloDiamond v0.1.0 ⌅ [33ad39ac] + PhyloNetworks v0.15.3 ⌅ [c0d5b6db] + PhyloPlots v1.0.0 [2dfb63ee] + PooledArrays v1.4.3 ⌅ [aea7be01] + PrecompileTools v1.2.1 [21216c6a] + Preferences v1.4.3 [08abe8d2] + PrettyTables v2.4.0 [43287f4e] + PtrArrays v1.3.0 [1fd47b50] + QuadGK v2.11.2 ⌅ [6f49c342] + RCall v0.13.18 [189a3867] + Reexport v1.2.2 [ae029012] + Requires v1.3.1 [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 v2.5.0 [90137ffa] + StaticArrays v1.9.13 [1e83bf80] + StaticArraysCore v1.4.3 [10745b16] + Statistics v1.11.1 [82ae8749] + StatsAPI v1.7.0 ⌅ [2913bbd2] + StatsBase v0.33.21 [4c63d2b9] + StatsFuns v1.4.0 ⌅ [3eaba693] + StatsModels v0.6.33 [892a3eda] + StringManipulation v0.4.1 [354b36f9] + StringViews v1.3.4 [856f2bd8] + StructTypes v1.11.0 [3783bdb8] + TableTraits v1.0.1 [bd369af6] + Tables v1.12.0 [3bb67fe8] + TranscodingStreams v0.11.3 [7200193e] + Twiddle v1.1.2 [81def892] + VersionParsing v1.3.0 [ea10d353] + WeakRefStrings v1.4.2 [1b915085] + WinReg v1.0.0 [76eceee3] + WorkerUtilities v1.6.1 [6e34b625] + Bzip2_jll v1.0.9+0 [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 [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 [a63ad114] + Mmap v1.11.0 [ca575930] + NetworkOptions v1.2.0 [de0858da] + Printf v1.11.0 [9abbd945] + Profile 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 v1.11.0 [f489334b] + StyledStrings v1.11.0 [4607b0f0] + SuiteSparse [fa267f1f] + TOML v1.0.3 [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 Info Packages marked with ⌃ and ⌅ have new versions available. Those with ⌃ may be upgradable, but those with ⌅ are restricted by compatibility constraints from upgrading. To see why use `status --outdated -m` Building Conda → `~/.julia/scratchspaces/44cfe95a-1eb2-52ea-b672-e2afdf69b78f/b19db3927f0db4151cb86d073689f2428e524576/build.log` Building RCall → `~/.julia/scratchspaces/44cfe95a-1eb2-52ea-b672-e2afdf69b78f/3084689b18f9e5e817a6ce9a83a7654d8ad0f2f6/build.log` Installation completed after 115.78s ################################################################################ # Precompilation # Precompiling PkgEval dependencies... Precompiling package dependencies... Precompilation completed after 233.88s ################################################################################ # Testing # Testing PhyloDiamond Status `/tmp/jl_4qCoZm/Project.toml` [336ed68f] CSV v0.10.15 [861a8166] Combinatorics v1.0.2 [a93c6f00] DataFrames v1.7.0 [8bb1440f] DelimitedFiles v1.9.1 [31c24e10] Distributions v0.25.118 ⌅ [e30172f5] Documenter v0.27.25 [7876af07] Example v0.5.5 [5fd89c64] PhyloDiamond v0.1.0 ⌅ [33ad39ac] PhyloNetworks v0.15.3 ⌅ [c0d5b6db] PhyloPlots v1.0.0 [10745b16] Statistics v1.11.1 ⌅ [2913bbd2] StatsBase v0.33.21 [37e2e46d] LinearAlgebra v1.11.0 [9a3f8284] Random v1.11.0 [8dfed614] Test v1.11.0 Status `/tmp/jl_4qCoZm/Manifest.toml` [a4c015fc] ANSIColoredPrinters v0.0.1 [66dad0bd] AliasTables v1.1.3 [67c07d97] Automa v1.1.0 [6e4b80f9] BenchmarkTools v1.6.0 [47718e42] BioGenerics v0.1.5 [7e6ae17a] BioSequences v3.4.1 [3c28c6f8] BioSymbols v5.1.3 [336ed68f] CSV v0.10.15 [324d7699] CategoricalArrays v0.10.8 [523fee87] CodecBzip2 v0.8.5 [944b1d66] CodecZlib v0.7.8 [861a8166] Combinatorics v1.0.2 [bbf7d656] CommonSubexpressions v0.3.1 [34da2185] Compat v4.16.0 [8f4d0f93] Conda v1.10.2 [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 [8bb1440f] DelimitedFiles v1.9.1 [163ba53b] DiffResults v1.1.0 [b552c78f] DiffRules v1.15.1 [31c24e10] Distributions v0.25.118 [ffbed154] DocStringExtensions v0.9.4 ⌅ [e30172f5] Documenter v0.27.25 [7876af07] Example v0.5.5 [c2308a5c] FASTX v2.1.7 [48062228] FilePathsBase v0.9.24 [1a297f60] FillArrays v1.13.0 [f6369f11] ForwardDiff v1.0.1 ⌅ [d9f16b24] Functors v0.3.0 ⌃ [38e38edf] GLM v1.8.3 [34004b35] HypergeometricFunctions v0.3.28 [b5f81e59] IOCapture v0.2.5 [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 [682c06a0] JSON v0.21.4 [0f8b85d8] JSON3 v1.14.2 [b964fa9f] LaTeXStrings v1.4.0 [2ab3a3ac] LogExpFunctions v0.3.29 [1914dd2f] MacroTools v0.5.15 [b8f27783] MathOptInterface v1.38.1 [fdba3010] MathProgBase v0.7.8 [e1d29d7a] Missings v1.2.0 [d8a4904e] MutableArithmetics v1.6.4 ⌅ [76087f3c] NLopt v0.6.5 [77ba4419] NaNMath v1.1.3 [bac558e1] OrderedCollections v1.8.0 [90014a1f] PDMats v0.11.33 [69de0a69] Parsers v2.8.1 [5fd89c64] PhyloDiamond v0.1.0 ⌅ [33ad39ac] PhyloNetworks v0.15.3 ⌅ [c0d5b6db] PhyloPlots v1.0.0 [2dfb63ee] PooledArrays v1.4.3 ⌅ [aea7be01] PrecompileTools v1.2.1 [21216c6a] Preferences v1.4.3 [08abe8d2] PrettyTables v2.4.0 [43287f4e] PtrArrays v1.3.0 [1fd47b50] QuadGK v2.11.2 ⌅ [6f49c342] RCall v0.13.18 [189a3867] Reexport v1.2.2 [ae029012] Requires v1.3.1 [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 v2.5.0 [90137ffa] StaticArrays v1.9.13 [1e83bf80] StaticArraysCore v1.4.3 [10745b16] Statistics v1.11.1 [82ae8749] StatsAPI v1.7.0 ⌅ [2913bbd2] StatsBase v0.33.21 [4c63d2b9] StatsFuns v1.4.0 ⌅ [3eaba693] StatsModels v0.6.33 [892a3eda] StringManipulation v0.4.1 [354b36f9] StringViews v1.3.4 [856f2bd8] StructTypes v1.11.0 [3783bdb8] TableTraits v1.0.1 [bd369af6] Tables v1.12.0 [3bb67fe8] TranscodingStreams v0.11.3 [7200193e] Twiddle v1.1.2 [81def892] VersionParsing v1.3.0 [ea10d353] WeakRefStrings v1.4.2 [1b915085] WinReg v1.0.0 [76eceee3] WorkerUtilities v1.6.1 [6e34b625] Bzip2_jll v1.0.9+0 [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 [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 [a63ad114] Mmap v1.11.0 [ca575930] NetworkOptions v1.2.0 [de0858da] Printf v1.11.0 [9abbd945] Profile 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 v1.11.0 [f489334b] StyledStrings v1.11.0 [4607b0f0] SuiteSparse [fa267f1f] TOML v1.0.3 [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 Info Packages marked with ⌃ and ⌅ have new versions available. Those with ⌃ may be upgradable, but those with ⌅ are restricted by compatibility constraints from upgrading. Testing Running tests... Precompiling PhyloDiamond... Info Given PhyloDiamond was explicitly requested, output will be shown live  WARNING: Method definition get_n(Any, Any) in module PhyloDiamond at /home/pkgeval/.julia/packages/PhyloDiamond/51vuW/src/mapping.jl:13 overwritten on the same line (check for duplicate calls to `include`). ERROR: Method overwriting is not permitted during Module precompilation. Use `__precompile__(false)` to opt-out of precompilation. 5480.6 ms ? PhyloDiamond WARNING: Method definition get_n(Any, Any) in module PhyloDiamond at /home/pkgeval/.julia/packages/PhyloDiamond/51vuW/src/mapping.jl:13 overwritten on the same line (check for duplicate calls to `include`). ERROR: Method overwriting is not permitted during Module precompilation. Use `__precompile__(false)` to opt-out of precompilation. WARNING: Method definition get_n(Any, Any) in module PhyloDiamond at /home/pkgeval/.julia/packages/PhyloDiamond/51vuW/src/mapping.jl:13 overwritten on the same line (check for duplicate calls to `include`). ┌ Warning: Replacing docs for `PhyloDiamond.get_n :: Tuple{Any, Any}` in module `PhyloDiamond` └ @ Base.Docs docs/Docs.jl:243 WARNING: Method definition cfs_in_order(Any, Any, Any) in module PhyloDiamond at /home/pkgeval/.julia/packages/PhyloDiamond/51vuW/src/mapping.jl:36 overwritten on the same line (check for duplicate calls to `include`). ┌ Warning: Replacing docs for `PhyloDiamond.cfs_in_order :: Tuple{Any, Any, Any}` in module `PhyloDiamond` └ @ Base.Docs docs/Docs.jl:243 WARNING: Method definition get_a(Any, Any) in module PhyloDiamond at /home/pkgeval/.julia/packages/PhyloDiamond/51vuW/src/mapping.jl:143 overwritten on the same line (check for duplicate calls to `include`). WARNING: Method definition kwcall(NamedTuple{names, T} where T<:Tuple where names, typeof(PhyloDiamond.get_a), Any, Any) in module PhyloDiamond at /home/pkgeval/.julia/packages/PhyloDiamond/51vuW/src/mapping.jl:143 overwritten on the same line (check for duplicate calls to `include`). ┌ Warning: Replacing docs for `PhyloDiamond.get_a :: Tuple{Any, Any}` in module `PhyloDiamond` └ @ Base.Docs docs/Docs.jl:243 WARNING: Method definition inv_net1112(Any) in module PhyloDiamond at /home/pkgeval/.julia/packages/PhyloDiamond/51vuW/src/invariants.jl:8 overwritten on the same line (check for duplicate calls to `include`). ┌ Warning: Replacing docs for `PhyloDiamond.inv_net1112 :: Tuple{Any}` in module `PhyloDiamond` └ @ Base.Docs docs/Docs.jl:243 WARNING: Method definition inv_net1121(Any) in module PhyloDiamond at /home/pkgeval/.julia/packages/PhyloDiamond/51vuW/src/invariants.jl:23 overwritten on the same line (check for duplicate calls to `include`). WARNING: Method definition inv_net1211(Any) in module PhyloDiamond at /home/pkgeval/.julia/packages/PhyloDiamond/51vuW/src/invariants.jl:36 overwritten on the same line (check for duplicate calls to `include`). WARNING: Method definition inv_net2111(Any) in module PhyloDiamond at /home/pkgeval/.julia/packages/PhyloDiamond/51vuW/src/invariants.jl:49 overwritten on the same line (check for duplicate calls to `include`). WARNING: Method definition inv_net1122(Any) in module PhyloDiamond at /home/pkgeval/.julia/packages/PhyloDiamond/51vuW/src/invariants.jl:61 overwritten on the same line (check for duplicate calls to `include`). WARNING: Method definition inv_net1212(Any) in module PhyloDiamond at /home/pkgeval/.julia/packages/PhyloDiamond/51vuW/src/invariants.jl:89 overwritten on the same line (check for duplicate calls to `include`). WARNING: Method definition inv_net2112(Any) in module PhyloDiamond at /home/pkgeval/.julia/packages/PhyloDiamond/51vuW/src/invariants.jl:117 overwritten on the same line (check for duplicate calls to `include`). WARNING: Method definition inv_net2211(Any) in module PhyloDiamond at /home/pkgeval/.julia/packages/PhyloDiamond/51vuW/src/invariants.jl:140 overwritten on the same line (check for duplicate calls to `include`). WARNING: Method definition inv_net2121(Any) in module PhyloDiamond at /home/pkgeval/.julia/packages/PhyloDiamond/51vuW/src/invariants.jl:171 overwritten on the same line (check for duplicate calls to `include`). WARNING: Method definition inv_net1221(Any) in module PhyloDiamond at /home/pkgeval/.julia/packages/PhyloDiamond/51vuW/src/invariants.jl:202 overwritten on the same line (check for duplicate calls to `include`). WARNING: Method definition inv_net1222(Any) in module PhyloDiamond at /home/pkgeval/.julia/packages/PhyloDiamond/51vuW/src/invariants.jl:228 overwritten on the same line (check for duplicate calls to `include`). WARNING: Method definition inv_net2212(Any) in module PhyloDiamond at /home/pkgeval/.julia/packages/PhyloDiamond/51vuW/src/invariants.jl:280 overwritten on the same line (check for duplicate calls to `include`). WARNING: Method definition inv_net2122(Any) in module PhyloDiamond at /home/pkgeval/.julia/packages/PhyloDiamond/51vuW/src/invariants.jl:372 overwritten on the same line (check for duplicate calls to `include`). WARNING: Method definition inv_net2221(Any) in module PhyloDiamond at /home/pkgeval/.julia/packages/PhyloDiamond/51vuW/src/invariants.jl:400 overwritten on the same line (check for duplicate calls to `include`). WARNING: Method definition inv_net2222(Any) in module PhyloDiamond at /home/pkgeval/.julia/packages/PhyloDiamond/51vuW/src/invariants.jl:426 overwritten on the same line (check for duplicate calls to `include`). WARNING: Method definition list_nw(Any) in module PhyloDiamond at /home/pkgeval/.julia/packages/PhyloDiamond/51vuW/src/helper.jl:11 overwritten on the same line (check for duplicate calls to `include`). ┌ Warning: Replacing docs for `PhyloDiamond.list_nw :: Tuple{Any}` in module `PhyloDiamond` └ @ Base.Docs docs/Docs.jl:243 WARNING: Method definition compare_nw(Any, Any) in module PhyloDiamond at /home/pkgeval/.julia/packages/PhyloDiamond/51vuW/src/helper.jl:82 overwritten on the same line (check for duplicate calls to `include`). ┌ Warning: Replacing docs for `PhyloDiamond.compare_nw :: Tuple{Any, Any}` in module `PhyloDiamond` └ @ Base.Docs docs/Docs.jl:243 WARNING: Method definition N_to_str(Any) in module PhyloDiamond at /home/pkgeval/.julia/packages/PhyloDiamond/51vuW/src/helper.jl:99 overwritten on the same line (check for duplicate calls to `include`). ┌ Warning: Replacing docs for `PhyloDiamond.N_to_str :: Tuple{Any}` in module `PhyloDiamond` └ @ Base.Docs docs/Docs.jl:243 WARNING: Method definition N_to_network(Any) in module PhyloDiamond at /home/pkgeval/.julia/packages/PhyloDiamond/51vuW/src/helper.jl:119 overwritten on the same line (check for duplicate calls to `include`). ┌ Warning: Replacing docs for `PhyloDiamond.N_to_network :: Tuple{Any}` in module `PhyloDiamond` └ @ Base.Docs docs/Docs.jl:243 WARNING: Method definition N_to_t(Any) in module PhyloDiamond at /home/pkgeval/.julia/packages/PhyloDiamond/51vuW/src/helper.jl:147 overwritten on the same line (check for duplicate calls to `include`). ┌ Warning: Replacing docs for `PhyloDiamond.N_to_t :: Tuple{Any}` in module `PhyloDiamond` └ @ Base.Docs docs/Docs.jl:243 WARNING: Method definition N_to_N_num(Any) in module PhyloDiamond at /home/pkgeval/.julia/packages/PhyloDiamond/51vuW/src/helper.jl:165 overwritten on the same line (check for duplicate calls to `include`). ┌ Warning: Replacing docs for `PhyloDiamond.N_to_N_num :: Tuple{Any}` in module `PhyloDiamond` └ @ Base.Docs docs/Docs.jl:243 WARNING: Method definition cf_to_t(Any) in module PhyloDiamond at /home/pkgeval/.julia/packages/PhyloDiamond/51vuW/src/helper.jl:183 overwritten on the same line (check for duplicate calls to `include`). ┌ Warning: Replacing docs for `PhyloDiamond.cf_to_t :: Tuple{Any}` in module `PhyloDiamond` └ @ Base.Docs docs/Docs.jl:243 WARNING: Method definition generate_cf_from_gene_trees(Any) in module PhyloDiamond at /home/pkgeval/.julia/packages/PhyloDiamond/51vuW/src/helper.jl:194 overwritten on the same line (check for duplicate calls to `include`). ┌ Warning: Replacing docs for `PhyloDiamond.generate_cf_from_gene_trees :: Tuple{Any}` in module `PhyloDiamond` └ @ Base.Docs docs/Docs.jl:243 WARNING: Method definition generate_cf(Any) in module PhyloDiamond at /home/pkgeval/.julia/packages/PhyloDiamond/51vuW/src/helper.jl:208 overwritten on the same line (check for duplicate calls to `include`). WARNING: Method definition generate_cf(Any, Any) in module PhyloDiamond at /home/pkgeval/.julia/packages/PhyloDiamond/51vuW/src/helper.jl:208 overwritten on the same line (check for duplicate calls to `include`). ┌ Warning: Replacing docs for `PhyloDiamond.generate_cf :: Union{Tuple{Any}, Tuple{Any, Any}}` in module `PhyloDiamond` └ @ Base.Docs docs/Docs.jl:243 /home/pkgeval/.julia/packages/PhyloDiamond/51vuW/testInference of top 5 9-taxon phylogenetic networks with phylogenetic invariants 1. N2223 (2.2216927709301364e-16) [(1,2),(3,4),(5,6),(7,8,9)] "((7:1,8:1,9:1):4, (((3:1,4:1):2, ((1:1,2:1):1)#H1:1::0.7):1, (#H1:1::0.3,(5:1,6:1):2):1):1);" 2. N2223 (2.2230610911746716e-16) [(1,2),(5,6),(3,4),(7,8,9)] "((7:1,8:1,9:1):4, (((5:1,6:1):2, ((1:1,2:1):1)#H1:1::0.7):1, (#H1:1::0.3,(3:1,4:1):2):1):1);" 2. N2232 (2.2230610911746716e-16) [(1,2),(5,6),(7,3,4),(8,9)] "((8:1,9:1):4, (((5:1,6:1):2, ((1:1,2:1):1)#H1:1::0.7):1, (#H1:1::0.3,(7:1,3:1,4:1):2):1):1);" 4. N2232 (0.006576057988736475) [(1,2),(3,4),(7,8,9),(5,6)] "((5:1,6:1):4, (((3:1,4:1):2, ((1:1,2:1):1)#H1:1::0.7):1, (#H1:1::0.3,(7:1,8:1,9:1):2):1):1);" 5. N2223 (0.00657929000066336) [(1,2),(7,8),(3,4),(9,5,6)] "((9:1,5:1,6:1):4, (((7:1,8:1):2, ((1:1,2:1):1)#H1:1::0.7):1, (#H1:1::0.3,(3:1,4:1):2):1):1);" Reading in trees, looking at 70 quartets in each... 0+--------------------------------------------------+100% ************************************************** Inference of top 5 8-taxon phylogenetic networks with phylogenetic invariants 1. N2222 (0.03689157145883046) [(1,2),(3,4),(5,6),(7,8)] "((7:1,8:1):4, (((3:1,4:1):2, ((1:1,2:1):1)#H1:1::0.7):1, (#H1:1::0.3,(5:1,6:1):2):1):1);" 2. N2222 (0.03823994257144703) [(1,2),(5,6),(3,4),(7,8)] "((7:1,8:1):4, (((5:1,6:1):2, ((1:1,2:1):1)#H1:1::0.7):1, (#H1:1::0.3,(3:1,4:1):2):1):1);" 3. N2222 (0.04097959230267735) [(1,2),(7,8),(5,6),(3,4)] "((3:1,4:1):4, (((7:1,8:1):2, ((1:1,2:1):1)#H1:1::0.7):1, (#H1:1::0.3,(5:1,6:1):2):1):1);" 4. N2222 (0.04258688497092598) [(1,2),(5,6),(7,8),(3,4)] "((3:1,4:1):4, (((5:1,6:1):2, ((1:1,2:1):1)#H1:1::0.7):1, (#H1:1::0.3,(7:1,8:1):2):1):1);" 5. N2222 (0.04789498610785061) [(1,2),(3,4),(7,8),(5,6)] "((5:1,6:1):4, (((3:1,4:1):2, ((1:1,2:1):1)#H1:1::0.7):1, (#H1:1::0.3,(7:1,8:1):2):1):1);" Test Summary: | Pass Total Time PhyloDiamond.jl | 14 14 3m03.7s Test Summary: | Pass Total Time mapping.jl | 27 27 1m06.8s Test Summary: | Pass Total Time helper.jl | 10 10 1.5s Testing PhyloDiamond tests passed Testing completed after 305.71s PkgEval succeeded after 684.98s