Package evaluation to test MolecularEvolution on Julia 1.14.0-DEV.2033 (8c59e8e9f1*) started at 2026-04-14T16:20:00.101 ################################################################################ # Set-up # Installing PkgEval dependencies (TestEnv)... Activating project at `~/.julia/environments/v1.14` Set-up completed after 16.13s ################################################################################ # Installation # Installing MolecularEvolution... Resolving package versions... Installed Rmath_jll ─────────────── v0.5.1+0 Installed AliasTables ───────────── v1.1.3 Installed FillArrays ────────────── v1.16.0 Installed DataAPI ───────────────── v1.16.0 Installed DataStructures ────────── v0.19.4 Installed OrderedCollections ────── v1.8.1 Installed StatsBase ─────────────── v0.34.10 Installed Statistics ────────────── v1.11.1 Installed StatsAPI ──────────────── v1.8.0 Installed OpenSpecFun_jll ───────── v0.5.6+0 Installed HypergeometricFunctions ─ v0.3.28 Installed LogExpFunctions ───────── v0.3.29 Installed Rmath ─────────────────── v0.9.0 Installed StatsFuns ─────────────── v1.5.2 Installed IrrationalConstants ───── v0.2.6 Installed Reexport ──────────────── v1.2.2 Installed Requires ──────────────── v1.3.1 Installed QuadGK ────────────────── v2.11.3 Installed PtrArrays ─────────────── v1.4.0 Installed Distributions ─────────── v0.25.124 Installed Missings ──────────────── v1.2.0 Installed JLLWrappers ───────────── v1.7.1 Installed PDMats ────────────────── v0.11.37 Installed SortingAlgorithms ─────── v1.2.2 Installed SpecialFunctions ──────── v2.7.2 Installed DocStringExtensions ───── v0.9.5 Installed Preferences ───────────── v1.5.2 Installed MolecularEvolution ────── v0.2.7 Installing 2 artifacts Installed artifact Rmath 121.9 KiB Installed artifact OpenSpecFun 194.9 KiB Updating `~/.julia/environments/v1.14/Project.toml` [9f975960] + MolecularEvolution v0.2.7 Updating `~/.julia/environments/v1.14/Manifest.toml` [66dad0bd] + AliasTables v1.1.3 [9a962f9c] + DataAPI v1.16.0 [864edb3b] + DataStructures v0.19.4 [31c24e10] + Distributions v0.25.124 [ffbed154] + DocStringExtensions v0.9.5 [1a297f60] + FillArrays v1.16.0 [34004b35] + HypergeometricFunctions v0.3.28 [92d709cd] + IrrationalConstants v0.2.6 [692b3bcd] + JLLWrappers v1.7.1 [2ab3a3ac] + LogExpFunctions v0.3.29 [e1d29d7a] + Missings v1.2.0 [9f975960] + MolecularEvolution v0.2.7 [bac558e1] + OrderedCollections v1.8.1 [90014a1f] + PDMats v0.11.37 [21216c6a] + Preferences v1.5.2 [43287f4e] + PtrArrays v1.4.0 [1fd47b50] + QuadGK v2.11.3 [189a3867] + Reexport v1.2.2 [ae029012] + Requires v1.3.1 [79098fc4] + Rmath v0.9.0 [a2af1166] + SortingAlgorithms v1.2.2 [276daf66] + SpecialFunctions v2.7.2 [10745b16] + Statistics v1.11.1 [82ae8749] + StatsAPI v1.8.0 [2913bbd2] + StatsBase v0.34.10 [4c63d2b9] + StatsFuns v1.5.2 [efe28fd5] + OpenSpecFun_jll v0.5.6+0 [f50d1b31] + Rmath_jll v0.5.1+0 [56f22d72] + Artifacts v1.11.0 [ade2ca70] + Dates v1.11.0 [8f399da3] + Libdl v1.11.0 [37e2e46d] + LinearAlgebra v1.13.0 [de0858da] + Printf v1.11.0 [9a3f8284] + Random v1.11.0 [ea8e919c] + SHA v1.0.0 [9e88b42a] + Serialization v1.11.0 [2f01184e] + SparseArrays v1.13.0 [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 v0.3.30+0 [05823500] + OpenLibm_jll v0.8.7+0 [bea87d4a] + SuiteSparse_jll v7.10.1+0 [8e850b90] + libblastrampoline_jll v5.15.0+0 Installation completed after 8.75s ################################################################################ # Precompilation # Precompiling PkgEval dependencies... Precompiling project... 8.7 s ✓ TestEnv 1 dependency successfully precompiled in 9 seconds. 27 already precompiled. Precompiling package dependencies... Precompiling project... 1.0 s ✓ Reexport 1.3 s ✓ Statistics 1.1 s ✓ DataAPI 2.5 s ✓ IrrationalConstants 1.0 s ✓ StatsAPI 1.6 s ✓ OrderedCollections 1.2 s ✓ DocStringExtensions 1.2 s ✓ StringViews 2.6 s ✓ FillArrays 0.9 s ✓ PtrArrays 1.4 s ✓ TranscodingStreams 1.3 s ✓ Requires 2.2 s ✓ PDMats 1.6 s ✓ Preferences 1.8 s ✓ Statistics → SparseArraysExt 1.2 s ✓ Missings 3.9 s ✓ DataStructures 1.5 s ✓ LogExpFunctions 1.8 s ✓ FillArrays → FillArraysSparseArraysExt 1.4 s ✓ FillArrays → FillArraysStatisticsExt 1.3 s ✓ AliasTables 1.3 s ✓ BioGenerics 1.9 s ✓ FillArrays → FillArraysPDMatsExt 2.5 s ✓ JLLWrappers 2.0 s ✓ PrecompileTools 1.6 s ✓ SortingAlgorithms 2.9 s ✓ QuadGK 2.7 s ✓ Rmath_jll 2.5 s ✓ OpenSpecFun_jll 20.8 s ✓ SIMD 5.2 s ✓ StatsBase 2.7 s ✓ Rmath 6.9 s ✓ SpecialFunctions 20.7 s ✓ Automa 1.8 s ✓ PDMats → StatsBaseExt 2.9 s ✓ HypergeometricFunctions 28.0 s ✓ FASTX 5.0 s ✓ StatsFuns 11.8 s ✓ Distributions 9.9 s ✓ MolecularEvolution 4.8 s ✓ Distributions → DistributionsTestExt 41 dependencies successfully precompiled in 172 seconds. 17 already precompiled. Precompilation completed after 212.02s ################################################################################ # Testing # Testing MolecularEvolution Status `/tmp/jl_r3XTMZ/Project.toml` ⌃ [c2308a5c] FASTX v2.1.5 [9f975960] MolecularEvolution v0.2.7 [9a3f8284] Random v1.11.0 [8dfed614] Test v1.11.0 Status `/tmp/jl_r3XTMZ/Manifest.toml` [66dad0bd] AliasTables v1.1.3 ⌃ [67c07d97] Automa v1.0.3 ⌃ [47718e42] BioGenerics v0.1.4 [9a962f9c] DataAPI v1.16.0 [864edb3b] DataStructures v0.19.4 [31c24e10] Distributions v0.25.124 [ffbed154] DocStringExtensions v0.9.5 ⌃ [c2308a5c] FASTX v2.1.5 [1a297f60] FillArrays v1.16.0 [34004b35] HypergeometricFunctions v0.3.28 [92d709cd] IrrationalConstants v0.2.6 [692b3bcd] JLLWrappers v1.7.1 [2ab3a3ac] LogExpFunctions v0.3.29 [e1d29d7a] Missings v1.2.0 [9f975960] MolecularEvolution v0.2.7 [bac558e1] OrderedCollections v1.8.1 [90014a1f] PDMats v0.11.37 ⌃ [aea7be01] PrecompileTools v1.2.1 ⌃ [21216c6a] Preferences v1.4.3 [43287f4e] PtrArrays v1.4.0 [1fd47b50] QuadGK v2.11.3 [189a3867] Reexport v1.2.2 [ae029012] Requires v1.3.1 [79098fc4] Rmath v0.9.0 [a2af1166] SortingAlgorithms v1.2.2 [276daf66] SpecialFunctions v2.7.2 [10745b16] Statistics v1.11.1 [82ae8749] StatsAPI v1.8.0 [2913bbd2] StatsBase v0.34.10 [4c63d2b9] StatsFuns v1.5.2 ⌃ [354b36f9] StringViews v1.3.3 ⌅ [3bb67fe8] TranscodingStreams v0.10.7 [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 [b77e0a4c] InteractiveUtils v1.11.0 [ac6e5ff7] JuliaSyntaxHighlighting v1.13.0 [8f399da3] Libdl v1.11.0 [37e2e46d] LinearAlgebra v1.13.0 [56ddb016] Logging v1.11.0 [d6f4376e] Markdown v1.11.0 [de0858da] Printf v1.11.0 [9a3f8284] Random v1.11.0 [ea8e919c] SHA v1.0.0 [9e88b42a] Serialization 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 [4536629a] OpenBLAS_jll v0.3.30+0 [05823500] OpenLibm_jll v0.8.7+0 [bea87d4a] SuiteSparse_jll v7.10.1+0 [8e850b90] libblastrampoline_jll v5.15.0+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... fatal: error thrown and no exception handler available. MethodError(f=Base.startswith, args=("/home/pkgeval/.julia/packages/StringViews/gFPyP/src/StringViews.jl", "/home/pkgeval/.julia/"), world=0x0000000000009dfd) jl_method_error_bare at /source/src/gf.c:3155 jl_method_error at /source/src/gf.c:3173 jl_f_throw_methoderror at /source/src/builtins.c:637 [inlined] jl_f_throw_methoderror at /source/src/builtins.c:633 replace_depot_path at ./loading.jl:3682 unknown function (ip: 0x7e9e247129ba) at (unknown file) _jl_invoke at /source/src/gf.c:4113 [inlined] ijl_apply_generic at /source/src/gf.c:4339 jl_apply at /source/src/julia.h:2301 [inlined] write_dependency_list at /source/src/staticdata_utils.c:772 jl_write_header_for_incremental at /source/src/staticdata.c:3246 [inlined] ijl_create_system_image at /source/src/staticdata.c:3288 ijl_write_compiler_output at /source/src/precompile.c:140 ijl_atexit_hook at /source/src/init.c:280 jl_repl_entrypoint at /source/src/jlapi.c:1139 main at /source/cli/loader_exe.c:58 unknown function (ip: 0x7e9e26002249) at /lib/x86_64-linux-gnu/libc.so.6 __libc_start_main at /lib/x86_64-linux-gnu/libc.so.6 (unknown line) unknown function (ip: 0x4010b8) at /workspace/srcdir/glibc-2.17/csu/../sysdeps/x86_64/start.S ERROR: LoadError: Precompiled image Base.PkgId(Base.UUID("354b36f9-a18e-4713-926e-db85100087ba"), "StringViews") not available with flags CacheFlags(; use_pkgimages=false, debug_level=1, check_bounds=1, inline=true, opt_level=0) Stacktrace:  [1] error(s::String)  @ Base ./error.jl:56  [2] __require_prelocked(pkg::Base.PkgId, env::String)  @ Base ./loading.jl:2841  [3] _require_prelocked(uuidkey::Base.PkgId, env::String)  @ Base ./loading.jl:2695  [4] macro expansion  @ ./loading.jl:2622 [inlined]  [5] macro expansion  @ ./lock.jl:376 [inlined]  [6] __require(into::Module, mod::Symbol)  @ Base ./loading.jl:2586  [7] require  @ ./loading.jl:2562 [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/FASTX/lnY23/src/FASTX.jl:3  [12] include(mod::Module, _path::String)  @ Base ./Base.jl:326  [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:3294  [14] top-level scope  @ stdin:5  [15] eval(m::Module, e::Any)  @ Core ./boot.jl:517  [16] include_string(mapexpr::typeof(identity), mod::Module, code::String, filename::String)  @ Base ./loading.jl:3136  [17] include_string  @ ./loading.jl:3146 [inlined]  [18] exec_options(opts::Base.JLOptions)  @ Base ./client.jl:350  [19] _start()  @ Base ./client.jl:593 in expression starting at /home/pkgeval/.julia/packages/FASTX/lnY23/src/FASTX.jl:1 in expression starting at stdin:5 2 dependencies had output during precompilation: ┌ FASTX │ [Output was shown above] └ ┌ StringViews │ fatal: error thrown and no exception handler available. │ MethodError(f=Base.startswith, args=("/home/pkgeval/.julia/packages/StringViews/gFPyP/src/StringViews.jl", "/home/pkgeval/.julia/"), world=0x0000000000009dfd) │ jl_method_error_bare at /source/src/gf.c:3155 │ jl_method_error at /source/src/gf.c:3173 │ jl_f_throw_methoderror at /source/src/builtins.c:637 [inlined] │ jl_f_throw_methoderror at /source/src/builtins.c:633 │ replace_depot_path at ./loading.jl:3682 │ unknown function (ip: 0x7e9e247129ba) at (unknown file) │ _jl_invoke at /source/src/gf.c:4113 [inlined] │ ijl_apply_generic at /source/src/gf.c:4339 │ jl_apply at /source/src/julia.h:2301 [inlined] │ write_dependency_list at /source/src/staticdata_utils.c:772 │ jl_write_header_for_incremental at /source/src/staticdata.c:3246 [inlined] │ ijl_create_system_image at /source/src/staticdata.c:3288 │ ijl_write_compiler_output at /source/src/precompile.c:140 │ ijl_atexit_hook at /source/src/init.c:280 │ jl_repl_entrypoint at /source/src/jlapi.c:1139 │ main at /source/cli/loader_exe.c:58 │ unknown function (ip: 0x7e9e26002249) at /lib/x86_64-linux-gnu/libc.so.6 │ __libc_start_main at /lib/x86_64-linux-gnu/libc.so.6 (unknown line) │ unknown function (ip: 0x4010b8) at /workspace/srcdir/glibc-2.17/csu/../sysdeps/x86_64/start.S └ ERROR: LoadError: The following 2 packages failed to precompile: FASTX Failed to precompile FASTX [c2308a5c-f048-11e8-3e8a-31650f418d12] to "/home/pkgeval/.julia/compiled/v1.14/FASTX/jl_hamI1e" (ProcessExited(1)). StringViews Failed to precompile StringViews [354b36f9-a18e-4713-926e-db85100087ba] to "/home/pkgeval/.julia/compiled/v1.14/StringViews/jl_IRKmJP" (ProcessExited(1)). in expression starting at /home/pkgeval/.julia/packages/MolecularEvolution/rRKnS/test/runtests.jl:1 Testing failed after 102.03s ERROR: LoadError: Package MolecularEvolution 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:3162 [3] test @ /opt/julia/share/julia/stdlib/v1.14/Pkg/src/Operations.jl:3025 [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:586 [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:562 [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:223 [12] include(mod::Module, _path::String) @ Base ./Base.jl:326 [13] exec_options(opts::Base.JLOptions) @ Base ./client.jl:352 [14] _start() @ Base ./client.jl:593 in expression starting at /PkgEval.jl/scripts/evaluate.jl:214 PkgEval failed after 367.3s: package fails to precompile