Package evaluation to test PhyloDiamond on Julia 1.14.0-DEV.1372 (893635dc59*) started at 2025-12-16T20:30:41.500 ################################################################################ # Set-up # Installing PkgEval dependencies (TestEnv)... Activating project at `~/.julia/environments/v1.14` Set-up completed after 9.52s ################################################################################ # Installation # Installing PhyloDiamond... Resolving package versions... Installed Conda ─ v1.10.3 Installed RCall ─ v0.13.18 Updating `~/.julia/environments/v1.14/Project.toml` [5fd89c64] + PhyloDiamond v0.1.0 Updating `~/.julia/environments/v1.14/Manifest.toml` [a4c015fc] + ANSIColoredPrinters v0.0.1 [66dad0bd] + AliasTables v1.1.3 [67c07d97] + Automa v1.1.0 [6e4b80f9] + BenchmarkTools v1.6.3 [47718e42] + BioGenerics v0.1.5 [7e6ae17a] + BioSequences v3.5.0 [3c28c6f8] + BioSymbols v5.2.0 [336ed68f] + CSV v0.10.15 ⌅ [324d7699] + CategoricalArrays v0.10.8 [523fee87] + CodecBzip2 v0.8.5 [944b1d66] + CodecZlib v0.7.8 [861a8166] + Combinatorics v1.1.0 [bbf7d656] + CommonSubexpressions v0.3.1 [34da2185] + Compat v4.18.1 [8f4d0f93] + Conda v1.10.3 [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 [8bb1440f] + DelimitedFiles v1.9.1 [163ba53b] + DiffResults v1.1.0 [b552c78f] + DiffRules v1.15.1 [31c24e10] + Distributions v0.25.122 [ffbed154] + DocStringExtensions v0.9.5 ⌅ [e30172f5] + Documenter v0.27.25 [7876af07] + Example v0.5.5 [c2308a5c] + FASTX v2.1.7 [48062228] + FilePathsBase v0.9.24 [1a297f60] + FillArrays v1.15.0 [f6369f11] + ForwardDiff v1.3.0 ⌅ [d9f16b24] + Functors v0.3.0 ⌃ [38e38edf] + GLM v1.8.3 [34004b35] + HypergeometricFunctions v0.3.28 ⌅ [b5f81e59] + IOCapture v0.2.5 [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 ⌅ [682c06a0] + JSON v0.21.4 [0f8b85d8] + JSON3 v1.14.3 [b964fa9f] + LaTeXStrings v1.4.0 [2ab3a3ac] + LogExpFunctions v0.3.29 [1914dd2f] + MacroTools v0.5.16 [b8f27783] + MathOptInterface v1.48.0 [fdba3010] + MathProgBase v0.7.8 [e1d29d7a] + Missings v1.2.0 [d8a4904e] + MutableArithmetics v1.6.7 ⌅ [76087f3c] + NLopt v0.6.5 [77ba4419] + NaNMath v1.1.3 [bac558e1] + OrderedCollections v1.8.1 ⌃ [90014a1f] + PDMats v0.11.35 [69de0a69] + Parsers v2.8.3 [5fd89c64] + PhyloDiamond v0.1.0 ⌅ [33ad39ac] + PhyloNetworks v0.15.3 ⌅ [c0d5b6db] + PhyloPlots v1.0.0 [2dfb63ee] + PooledArrays v1.4.3 [aea7be01] + PrecompileTools v1.3.3 [21216c6a] + Preferences v1.5.0 [08abe8d2] + PrettyTables v3.1.2 [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 v0.9.0 [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 v1.8.0 ⌅ [2913bbd2] + StatsBase v0.33.21 [4c63d2b9] + StatsFuns v1.5.2 ⌅ [3eaba693] + StatsModels v0.6.33 [892a3eda] + StringManipulation v0.4.2 [354b36f9] + StringViews v1.3.6 [856f2bd8] + StructTypes v1.11.0 [3783bdb8] + TableTraits v1.0.1 [bd369af6] + Tables v1.12.1 [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 v1.7.0 [7b1f6079] + FileWatching v1.11.0 [9fa8497b] + Future v1.11.0 [b77e0a4c] + InteractiveUtils v1.11.0 [ac6e5ff7] + JuliaSyntaxHighlighting v1.13.0 [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 [de0858da] + Printf v1.11.0 [9abbd945] + Profile 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 v1.13.0 [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 v1.3.0+1 [deac9b47] + LibCURL_jll v8.17.0+0 [e37daf67] + LibGit2_jll v1.9.2+0 [29816b5a] + LibSSH2_jll v1.11.3+1 [14a3606d] + MozillaCACerts_jll v2025.12.2 [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 v1.68.0+1 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/8f06b0cfa4c514c7b9546756dbae91fcfbc92dc9/build.log` Building RCall → `~/.julia/scratchspaces/44cfe95a-1eb2-52ea-b672-e2afdf69b78f/3084689b18f9e5e817a6ce9a83a7654d8ad0f2f6/build.log` Installation completed after 80.31s ################################################################################ # Precompilation # ERROR: LoadError: MethodError: no method matching setindex!(::Base.ScopedValues.ScopedValue{IO}, ::Nothing) The function `setindex!` exists, but no method is defined for this combination of argument types. Stacktrace: [1] top-level scope @ /PkgEval.jl/scripts/precompile.jl:10 [2] include(mod::Module, _path::String) @ Base ./Base.jl:309 [3] exec_options(opts::Base.JLOptions) @ Base ./client.jl:344 [4] _start() @ Base ./client.jl:577 in expression starting at /PkgEval.jl/scripts/precompile.jl:6 caused by: MethodError: no method matching setindex!(::Base.ScopedValues.ScopedValue{IO}, ::Base.DevNull) The function `setindex!` exists, but no method is defined for this combination of argument types. Stacktrace: [1] top-level scope @ /PkgEval.jl/scripts/precompile.jl:7 [2] include(mod::Module, _path::String) @ Base ./Base.jl:309 [3] exec_options(opts::Base.JLOptions) @ Base ./client.jl:344 [4] _start() @ Base ./client.jl:577 Precompilation failed after 13.09s ################################################################################ # Testing # Testing PhyloDiamond Status `/tmp/jl_bcYzu6/Project.toml` [336ed68f] CSV v0.10.15 [861a8166] Combinatorics v1.1.0 [a93c6f00] DataFrames v1.8.1 [8bb1440f] DelimitedFiles v1.9.1 [31c24e10] Distributions v0.25.122 ⌅ [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 v1.13.0 [9a3f8284] Random v1.11.0 [8dfed614] Test v1.11.0 Status `/tmp/jl_bcYzu6/Manifest.toml` [a4c015fc] ANSIColoredPrinters v0.0.1 [66dad0bd] AliasTables v1.1.3 [67c07d97] Automa v1.1.0 [6e4b80f9] BenchmarkTools v1.6.3 [47718e42] BioGenerics v0.1.5 [7e6ae17a] BioSequences v3.5.0 [3c28c6f8] BioSymbols v5.2.0 [336ed68f] CSV v0.10.15 ⌅ [324d7699] CategoricalArrays v0.10.8 [523fee87] CodecBzip2 v0.8.5 [944b1d66] CodecZlib v0.7.8 [861a8166] Combinatorics v1.1.0 [bbf7d656] CommonSubexpressions v0.3.1 [34da2185] Compat v4.18.1 [8f4d0f93] Conda v1.10.3 [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 [8bb1440f] DelimitedFiles v1.9.1 [163ba53b] DiffResults v1.1.0 [b552c78f] DiffRules v1.15.1 [31c24e10] Distributions v0.25.122 [ffbed154] DocStringExtensions v0.9.5 ⌅ [e30172f5] Documenter v0.27.25 [7876af07] Example v0.5.5 [c2308a5c] FASTX v2.1.7 [48062228] FilePathsBase v0.9.24 [1a297f60] FillArrays v1.15.0 [f6369f11] ForwardDiff v1.3.0 ⌅ [d9f16b24] Functors v0.3.0 ⌃ [38e38edf] GLM v1.8.3 [34004b35] HypergeometricFunctions v0.3.28 ⌅ [b5f81e59] IOCapture v0.2.5 [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 ⌅ [682c06a0] JSON v0.21.4 [0f8b85d8] JSON3 v1.14.3 [b964fa9f] LaTeXStrings v1.4.0 [2ab3a3ac] LogExpFunctions v0.3.29 [1914dd2f] MacroTools v0.5.16 [b8f27783] MathOptInterface v1.48.0 [fdba3010] MathProgBase v0.7.8 [e1d29d7a] Missings v1.2.0 [d8a4904e] MutableArithmetics v1.6.7 ⌅ [76087f3c] NLopt v0.6.5 [77ba4419] NaNMath v1.1.3 [bac558e1] OrderedCollections v1.8.1 ⌃ [90014a1f] PDMats v0.11.35 [69de0a69] Parsers v2.8.3 [5fd89c64] PhyloDiamond v0.1.0 ⌅ [33ad39ac] PhyloNetworks v0.15.3 ⌅ [c0d5b6db] PhyloPlots v1.0.0 [2dfb63ee] PooledArrays v1.4.3 [aea7be01] PrecompileTools v1.3.3 [21216c6a] Preferences v1.5.0 [08abe8d2] PrettyTables v3.1.2 [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 v0.9.0 [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 v1.8.0 ⌅ [2913bbd2] StatsBase v0.33.21 [4c63d2b9] StatsFuns v1.5.2 ⌅ [3eaba693] StatsModels v0.6.33 [892a3eda] StringManipulation v0.4.2 [354b36f9] StringViews v1.3.6 [856f2bd8] StructTypes v1.11.0 [3783bdb8] TableTraits v1.0.1 [bd369af6] Tables v1.12.1 [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 v1.7.0 [7b1f6079] FileWatching v1.11.0 [9fa8497b] Future v1.11.0 [b77e0a4c] InteractiveUtils v1.11.0 [ac6e5ff7] JuliaSyntaxHighlighting v1.13.0 [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 [de0858da] Printf v1.11.0 [9abbd945] Profile 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 v1.13.0 [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 v1.3.0+1 [deac9b47] LibCURL_jll v8.17.0+0 [e37daf67] LibGit2_jll v1.9.2+0 [29816b5a] LibSSH2_jll v1.11.3+1 [14a3606d] MozillaCACerts_jll v2025.12.2 [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 v1.68.0+1 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... ERROR: LoadError: Precompiled image Base.PkgId(Base.UUID("3eaba693-59b7-5ba5-a881-562e759f1c8d"), "StatsModels") not available with flags CacheFlags(; use_pkgimages=false, debug_level=1, check_bounds=0, inline=true, opt_level=0) Stacktrace:  [1] error(s::String)  @ Base ./error.jl:44  [2] __require_prelocked(pkg::Base.PkgId, env::String)  @ Base ./loading.jl:2813  [3] _require_prelocked(uuidkey::Base.PkgId, env::String)  @ Base ./loading.jl:2665  [4] macro expansion  @ ./loading.jl:2593 [inlined]  [5] macro expansion  @ ./lock.jl:376 [inlined]  [6] __require(into::Module, mod::Symbol)  @ Base ./loading.jl:2557  [7] require  @ ./loading.jl:2533 [inlined]  [8] eval_import_path  @ ./module.jl:36 [inlined]  [9] eval_import_path_all(at::Module, path::Expr, keyword::String)  @ Base ./module.jl:60  [10] _eval_using  @ ./module.jl:137 [inlined]  [11] _eval_using(to::Module, path::Expr)  @ Base ./module.jl:137  [12] top-level scope  @ ~/.julia/packages/RCall/gOwEW/src/RCall.jl:14  [13] include(mod::Module, _path::String)  @ Base ./Base.jl:309  [14] include_package_for_output(pkg::Base.PkgId, input::String, syntax_version::VersionNumber, depot_path::Vector{String}, dl_load_path::Vector{String}, load_path::Vector{String}, concrete_deps::Vector{Pair{Base.PkgId, UInt128}}, source::Nothing)  @ Base ./loading.jl:3250  [15] top-level scope  @ stdin:5  [16] eval(m::Module, e::Any)  @ Core ./boot.jl:489  [17] include_string(mapexpr::typeof(identity), mod::Module, code::String, filename::String)  @ Base ./loading.jl:3092  [18] include_string  @ ./loading.jl:3102 [inlined]  [19] exec_options(opts::Base.JLOptions)  @ Base ./client.jl:342  [20] _start()  @ Base ./client.jl:577 in expression starting at /home/pkgeval/.julia/packages/RCall/gOwEW/src/RCall.jl:2 in expression starting at stdin:5 ERROR: LoadError: Precompiled image Base.PkgId(Base.UUID("3eaba693-59b7-5ba5-a881-562e759f1c8d"), "StatsModels") not available with flags CacheFlags(; use_pkgimages=false, debug_level=1, check_bounds=0, inline=true, opt_level=0) Stacktrace:  [1] error(s::String)  @ Base ./error.jl:44  [2] __require_prelocked(pkg::Base.PkgId, env::String)  @ Base ./loading.jl:2813  [3] _require_prelocked(uuidkey::Base.PkgId, env::String)  @ Base ./loading.jl:2665  [4] macro expansion  @ ./loading.jl:2593 [inlined]  [5] macro expansion  @ ./lock.jl:376 [inlined]  [6] __require(into::Module, mod::Symbol)  @ Base ./loading.jl:2557  [7] require  @ ./loading.jl:2533 [inlined]  [8] eval_import_path  @ ./module.jl:36 [inlined]  [9] eval_import_path_all(at::Module, path::Expr, keyword::String)  @ Base ./module.jl:60  [10] _eval_using  @ ./module.jl:137 [inlined]  [11] _eval_using(to::Module, path::Expr)  @ Base ./module.jl:137  [12] top-level scope  @ ~/.julia/packages/GLM/6ycOV/src/GLM.jl:7  [13] include(mod::Module, _path::String)  @ Base ./Base.jl:309  [14] include_package_for_output(pkg::Base.PkgId, input::String, syntax_version::VersionNumber, depot_path::Vector{String}, dl_load_path::Vector{String}, load_path::Vector{String}, concrete_deps::Vector{Pair{Base.PkgId, UInt128}}, source::Nothing)  @ Base ./loading.jl:3250  [15] top-level scope  @ stdin:5  [16] eval(m::Module, e::Any)  @ Core ./boot.jl:489  [17] include_string(mapexpr::typeof(identity), mod::Module, code::String, filename::String)  @ Base ./loading.jl:3092  [18] include_string  @ ./loading.jl:3102 [inlined]  [19] exec_options(opts::Base.JLOptions)  @ Base ./client.jl:342  [20] _start()  @ Base ./client.jl:577 in expression starting at /home/pkgeval/.julia/packages/GLM/6ycOV/src/GLM.jl:1 in expression starting at stdin:5 ERROR: LoadError: Precompiled image Base.PkgId(Base.UUID("38e38edf-8417-5370-95a0-9cbb8c7f171a"), "GLM") not available with flags CacheFlags(; use_pkgimages=false, debug_level=1, check_bounds=0, inline=true, opt_level=0) Stacktrace:  [1] error(s::String)  @ Base ./error.jl:44  [2] __require_prelocked(pkg::Base.PkgId, env::String)  @ Base ./loading.jl:2813  [3] _require_prelocked(uuidkey::Base.PkgId, env::String)  @ Base ./loading.jl:2665  [4] macro expansion  @ ./loading.jl:2593 [inlined]  [5] macro expansion  @ ./lock.jl:376 [inlined]  [6] __require(into::Module, mod::Symbol)  @ Base ./loading.jl:2557  [7] require  @ ./loading.jl:2533 [inlined]  [8] eval_import_path  @ ./module.jl:36 [inlined]  [9] eval_import_path_all(at::Module, path::Expr, keyword::String)  @ Base ./module.jl:60  [10] _eval_using  @ ./module.jl:137 [inlined]  [11] _eval_using(to::Module, path::Expr)  @ Base ./module.jl:137  [12] top-level scope  @ ~/.julia/packages/PhyloNetworks/2KZEt/src/PhyloNetworks.jl:27  [13] include(mod::Module, _path::String)  @ Base ./Base.jl:309  [14] include_package_for_output(pkg::Base.PkgId, input::String, syntax_version::VersionNumber, depot_path::Vector{String}, dl_load_path::Vector{String}, load_path::Vector{String}, concrete_deps::Vector{Pair{Base.PkgId, UInt128}}, source::Nothing)  @ Base ./loading.jl:3250  [15] top-level scope  @ stdin:5  [16] eval(m::Module, e::Any)  @ Core ./boot.jl:489  [17] include_string(mapexpr::typeof(identity), mod::Module, code::String, filename::String)  @ Base ./loading.jl:3092  [18] include_string  @ ./loading.jl:3102 [inlined]  [19] exec_options(opts::Base.JLOptions)  @ Base ./client.jl:342  [20] _start()  @ Base ./client.jl:577 in expression starting at /home/pkgeval/.julia/packages/PhyloNetworks/2KZEt/src/PhyloNetworks.jl:3 in expression starting at stdin:5 ERROR: LoadError: Precompiled image Base.PkgId(Base.UUID("33ad39ac-ed31-50eb-9b15-43d0656eaa72"), "PhyloNetworks") not available with flags CacheFlags(; use_pkgimages=false, debug_level=1, check_bounds=0, inline=true, opt_level=0) Stacktrace:  [1] error(s::String)  @ Base ./error.jl:44  [2] __require_prelocked(pkg::Base.PkgId, env::String)  @ Base ./loading.jl:2813  [3] _require_prelocked(uuidkey::Base.PkgId, env::String)  @ Base ./loading.jl:2665  [4] macro expansion  @ ./loading.jl:2593 [inlined]  [5] macro expansion  @ ./lock.jl:376 [inlined]  [6] __require(into::Module, mod::Symbol)  @ Base ./loading.jl:2557  [7] require  @ ./loading.jl:2533 [inlined]  [8] eval_import_path  @ ./module.jl:36 [inlined]  [9] eval_import_path_all(at::Module, path::Expr, keyword::String)  @ Base ./module.jl:60  [10] _eval_import(::Bool, ::Module, ::Expr, ::Expr, ::Vararg{Expr})  @ Base ./module.jl:101  [11] top-level scope  @ ~/.julia/packages/PhyloPlots/2OrB7/src/PhyloPlots.jl:7  [12] include(mod::Module, _path::String)  @ Base ./Base.jl:309  [13] include_package_for_output(pkg::Base.PkgId, input::String, syntax_version::VersionNumber, depot_path::Vector{String}, dl_load_path::Vector{String}, load_path::Vector{String}, concrete_deps::Vector{Pair{Base.PkgId, UInt128}}, source::Nothing)  @ Base ./loading.jl:3250  [14] top-level scope  @ stdin:5  [15] eval(m::Module, e::Any)  @ Core ./boot.jl:489  [16] include_string(mapexpr::typeof(identity), mod::Module, code::String, filename::String)  @ Base ./loading.jl:3092  [17] include_string  @ ./loading.jl:3102 [inlined]  [18] exec_options(opts::Base.JLOptions)  @ Base ./client.jl:342  [19] _start()  @ Base ./client.jl:577 in expression starting at /home/pkgeval/.julia/packages/PhyloPlots/2OrB7/src/PhyloPlots.jl:3 in expression starting at stdin:5 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. 1 dependency had output during precompilation: ┌ PhyloDiamond │ [Output was shown above] └ 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:253 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:253 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:253 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:253 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: The call to compilecache failed to create a usable precompiled cache file for PhyloNetworks [33ad39ac-ed31-50eb-9b15-43d0656eaa72] │ exception = Required dependency Base.PkgId(Base.UUID("354b36f9-a18e-4713-926e-db85100087ba"), "StringViews") failed to load from a cache file. └ @ Base loading.jl:2891 ERROR: LoadError: Precompiled image Base.PkgId(Base.UUID("33ad39ac-ed31-50eb-9b15-43d0656eaa72"), "PhyloNetworks") not available with flags CacheFlags(; use_pkgimages=false, debug_level=1, check_bounds=0, inline=true, opt_level=0) Stacktrace:  [1] error(s::String)  @ Base ./error.jl:44  [2] __require_prelocked(pkg::Base.PkgId, env::String)  @ Base ./loading.jl:2813  [3] _require_prelocked(uuidkey::Base.PkgId, env::String)  @ Base ./loading.jl:2665  [4] macro expansion  @ ./loading.jl:2593 [inlined]  [5] macro expansion  @ ./lock.jl:376 [inlined]  [6] __require(into::Module, mod::Symbol)  @ Base ./loading.jl:2557  [7] require  @ ./loading.jl:2533 [inlined]  [8] eval_import_path  @ ./module.jl:36 [inlined]  [9] eval_import_path_all(at::Module, path::Expr, keyword::String)  @ Base ./module.jl:60  [10] _eval_import(::Bool, ::Module, ::Expr, ::Expr, ::Vararg{Expr})  @ Base ./module.jl:101  [11] top-level scope  @ ~/.julia/packages/PhyloPlots/2OrB7/src/PhyloPlots.jl:7  [12] include(mod::Module, _path::String)  @ Base ./Base.jl:309  [13] include_package_for_output(pkg::Base.PkgId, input::String, syntax_version::VersionNumber, depot_path::Vector{String}, dl_load_path::Vector{String}, load_path::Vector{String}, concrete_deps::Vector{Pair{Base.PkgId, UInt128}}, source::Nothing)  @ Base ./loading.jl:3250  [14] top-level scope  @ stdin:5  [15] eval(m::Module, e::Any)  @ Core ./boot.jl:489  [16] include_string(mapexpr::typeof(identity), mod::Module, code::String, filename::String)  @ Base ./loading.jl:3092  [17] include_string  @ ./loading.jl:3102 [inlined]  [18] exec_options(opts::Base.JLOptions)  @ Base ./client.jl:342  [19] _start()  @ Base ./client.jl:577 in expression starting at /home/pkgeval/.julia/packages/PhyloPlots/2OrB7/src/PhyloPlots.jl:3 in expression starting at stdin:5 1 dependency had output during precompilation: ┌ PhyloPlots │ [Output was shown above] └ ERROR: LoadError: The following 1 package failed to precompile: PhyloPlots Failed to precompile PhyloPlots [c0d5b6db-e3fc-52bc-a87d-1d050989ed3b] to "/home/pkgeval/.julia/compiled/v1.14/PhyloPlots/jl_mp36iI" (ProcessExited(1)). in expression starting at /home/pkgeval/.julia/packages/PhyloDiamond/51vuW/src/ntwk.jl:5 in expression starting at /home/pkgeval/.julia/packages/PhyloDiamond/51vuW/src/PhyloDiamond.jl:1 in expression starting at /home/pkgeval/.julia/packages/PhyloDiamond/51vuW/test/runtests.jl:1 Testing failed after 308.08s ERROR: LoadError: Package PhyloDiamond 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:3067 [3] test @ /opt/julia/share/julia/stdlib/v1.14/Pkg/src/Operations.jl:2916 [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:237 [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:228 PkgEval failed after 445.44s: illegal method overwrites during precompilation