Package evaluation to test PyBoltz on Julia 1.14.0-DEV.2071 (559ec66647*) started at 2026-04-23T18:19:44.822


################################################################################
# Set-up
#

Installing PkgEval dependencies (TestEnv)...
  Activating project at `~/.julia/environments/v1.14`

Set-up completed after 14.96s


################################################################################
# Installation
#

Installing PyBoltz...
   Resolving package versions...
    Updating `~/.julia/environments/v1.14/Project.toml`
  [0bca4874] + PyBoltz v0.2.2
    Updating `~/.julia/environments/v1.14/Manifest.toml`
  [34da2185] + Compat v4.18.1
  [992eb4ea] + CondaPkg v0.2.34
  [9a962f9c] + DataAPI v1.16.0
  [e2d170a0] + DataValueInterfaces v1.0.0
  [82899510] + IteratorInterfaceExtensions v1.0.0
  [692b3bcd] + JLLWrappers v1.7.1
  [682c06a0] + JSON v1.5.0
  [1914dd2f] + MacroTools v0.5.16
  [0b3b1443] + MicroMamba v0.1.15
  [bac558e1] + OrderedCollections v1.8.1
  [69de0a69] + Parsers v2.8.3
  [fa939f87] + Pidfile v1.3.0
  [aea7be01] + PrecompileTools v1.3.3
  [21216c6a] + Preferences v1.5.2
  [0bca4874] + PyBoltz v0.2.2
  [6099a3de] + PythonCall v0.9.31
  [6c6a2e73] + Scratch v1.3.0
  [69024149] + StringEncodings v0.3.7
  [ec057cc2] + StructUtils v2.8.0
  [3783bdb8] + TableTraits v1.0.1
  [bd369af6] + Tables v1.12.1
  [e17b2a0c] + UnsafePointers v1.0.0
  [ddb6d928] + YAML v0.4.16
  [94ce4f54] + Libiconv_jll v1.18.0+0
  [f8abcde7] + micromamba_jll v2.3.1+0
  [4d7b5844] + pixi_jll v0.41.3+0
  [0dad84c5] + ArgTools v1.1.2
  [56f22d72] + Artifacts v1.11.0
  [2a0f44e3] + Base64 v1.11.0
  [ade2ca70] + Dates v1.11.0
  [f43a241f] + Downloads v1.7.0
  [7b1f6079] + FileWatching v1.11.0
  [b77e0a4c] + InteractiveUtils v1.11.0
  [ac6e5ff7] + JuliaSyntaxHighlighting v1.13.0
  [4af54fe1] + LazyArtifacts v1.11.0
  [b27032c2] + LibCURL v1.0.0
  [76f85450] + LibGit2 v1.11.0
  [8f399da3] + Libdl v1.11.0
  [56ddb016] + Logging v1.11.0
  [d6f4376e] + Markdown v1.11.0
  [ca575930] + NetworkOptions v1.3.0
  [44cfe95a] + Pkg v1.14.0
  [de0858da] + Printf v1.11.0
  [9a3f8284] + Random v1.11.0
  [ea8e919c] + SHA v1.0.0
  [9e88b42a] + Serialization v1.11.0
  [f489334b] + StyledStrings v1.13.0
  [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 v8.19.0+0
  [e37daf67] + LibGit2_jll v1.9.2+0
  [29816b5a] + LibSSH2_jll v1.11.3+1
  [14a3606d] + MozillaCACerts_jll v2026.3.19
  [458c3c95] + OpenSSL_jll v3.5.6+0
  [efcefdf7] + PCRE2_jll v10.47.0+0
  [83775a58] + Zlib_jll v1.3.2+0
  [3161d3a3] + Zstd_jll v1.5.7+1
  [8e850ede] + nghttp2_jll v1.69.0+0
  [3f19e933] + p7zip_jll v17.8.0+0

Installation completed after 6.01s


################################################################################
# Precompilation
#

Precompiling PkgEval dependencies...

Precompiling package dependencies...
Precompiling project...
   2.3 s  ✓ TMscore_jll
   3.4 s  ✓ BioSymbols
ERROR: LoadError: InitError: UndefVarError: `manifest_uuid_path` not defined in `Base`
Suggestion: check for spelling errors or missing imports.
Stacktrace:
  [1] getproperty(x::Module, f::Symbol)
    @ Base ./Base_compiler.jl:51
  [2] _resolve_top_env(load_path::Any)
    @ CondaPkg ~/.julia/packages/CondaPkg/8GjrP/src/resolve.jl:10
  [3] resolve(; force::Bool, io::IO, interactive::Bool, dry_run::Bool)
    @ CondaPkg ~/.julia/packages/CondaPkg/8GjrP/src/resolve.jl:823
  [4] resolve()
    @ CondaPkg ~/.julia/packages/CondaPkg/8GjrP/src/resolve.jl:796
  [5] envdir()
    @ CondaPkg ~/.julia/packages/CondaPkg/8GjrP/src/env.jl:70
  [6] init_context()
    @ PythonCall.C ~/.julia/packages/PythonCall/83z4q/src/C/context.jl:135
  [7] __init__()
    @ PythonCall.C ~/.julia/packages/PythonCall/83z4q/src/C/C.jl:26
  [8] run_module_init(mod::Module, i::Int64)
    @ Base ./loading.jl:1605
  [9] register_restored_modules(sv::Core.SimpleVector, pkg::Base.PkgId, path::String)
    @ Base ./loading.jl:1593
 [10] _include_from_serialized(pkg::Base.PkgId, path::String, ocachepath::Nothing, depmods::Vector{Any}; register::Bool)
    @ Base ./loading.jl:1481
 [11] _include_from_serialized
    @ ./loading.jl:1438 [inlined]
 [12] _require_search_from_serialized(pkg::Base.PkgId, sourcespec::Base.PkgLoadSpec, build_id::UInt128, stalecheck::Bool; reasons::Dict{String, Int64}, DEPOT_PATH::Vector{String})
    @ Base ./loading.jl:2283
 [13] !=(x::Int8, y::Int64)
    @ Base ./loading.jl:2178 [inlined]
 [14] __require_prelocked(pkg::Base.PkgId, env::String)
    @ Base ./loading.jl:2811
 [15] _require_prelocked(uuidkey::Base.PkgId, env::String)
    @ Base ./loading.jl:2672
 [16] macro expansion
    @ ./loading.jl:2599 [inlined]
 [17] String(s::Symbol)
    @ Base ./lock.jl:376 [inlined]
 [18] __require(into::Module, mod::Symbol)
    @ Base ./loading.jl:2563
 [19] require(into::Module, mod::Symbol)
    @ Base ./loading.jl:2539 [inlined]
 [20] eval_import_path(at::Module, from::Nothing, path::Expr, keyword::String)
    @ Base ./module.jl:36 [inlined]
 [21] _eval_import(imported::Bool, to::Module, from::Nothing, paths::Expr)
    @ Base ./module.jl:111
 [22] top-level scope
    @ ~/.julia/packages/PyBoltz/PGqPe/src/PyBoltz.jl:3
 [23] include(mod::Module, _path::String)
    @ Base ./Base.jl:326
 [24] 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:3271
 [25] top-level scope
    @ stdin:5
 [26] eval(m::Module, e::Any)
    @ Core ./boot.jl:517
 [27] include_string(mapexpr::typeof(identity), mod::Module, code::String, filename::String)
    @ Base ./loading.jl:3113
 [28] materialize(bc::Base.Broadcast.Broadcasted{Base.Broadcast.DefaultArrayStyle{1}, Nothing, Type{Symbol}, Tuple{Vector{SubString{String}}}})
    @ Base.Broadcast ./loading.jl:3123 [inlined]
 [29] exec_options(opts::Base.JLOptions)
    @ Base ./client.jl:350
 [30] _start()
    @ Base ./client.jl:593
during initialization of module C
in expression starting at /home/pkgeval/.julia/packages/PyBoltz/PGqPe/src/PyBoltz.jl:1
in expression starting at stdin:5
              ✗ PyBoltz
   1.3 s  ✓ TMscore
  11.3 s  ✓ BioSequences
  14.8 s  ✓ BioStructures
   4.1 s  ✓ BioAlignments
   2.2 s  ✓ BioStructures → BioStructuresBioSequencesExt
ERROR: LoadError: Precompiled image Base.PkgId(Base.UUID("0bca4874-a2b8-4dca-bc03-d2d86e344f1f"), "PyBoltz") 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:2818
  [3] _require_prelocked(uuidkey::Base.PkgId, env::String)
    @ Base ./loading.jl:2672
  [4] macro expansion
    @ ./loading.jl:2599 [inlined]
  [5] String(s::Symbol)
    @ Base ./lock.jl:376 [inlined]
  [6] __require(into::Module, mod::Symbol)
    @ Base ./loading.jl:2563
  [7] require(into::Module, mod::Symbol)
    @ Base ./loading.jl:2539 [inlined]
  [8] eval_import_path(at::Module, from::Nothing, path::Expr, keyword::String)
    @ Base ./module.jl:36 [inlined]
  [9] eval_import_path_all(at::Module, path::Expr, keyword::String)
    @ Base ./module.jl:60
 [10] _eval_using(to::Module, path::Expr, flags::UInt8)
    @ Base ./module.jl:137 [inlined]
 [11] top-level scope
    @ ~/.julia/packages/PyBoltz/PGqPe/ext/BioStructuresExt.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:3271
 [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:3113
 [17] materialize(bc::Base.Broadcast.Broadcasted{Base.Broadcast.DefaultArrayStyle{1}, Nothing, Type{Symbol}, Tuple{Vector{SubString{String}}}})
    @ Base.Broadcast ./loading.jl:3123 [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/PyBoltz/PGqPe/ext/BioStructuresExt.jl:1
in expression starting at stdin:5
              ✗ PyBoltz → BioStructuresExt
   1.9 s  ✓ TMscore → BioStructuresExt
   2.4 s  ✓ BioStructures → BioStructuresBioAlignmentsExt
  9 dependencies successfully precompiled in 61 seconds. 66 already precompiled.

Precompilation completed after 88.46s


################################################################################
# Testing
#

     Testing PyBoltz
      Status `/tmp/jl_FBCMGD/Project.toml`
  [00701ae9] BioAlignments v3.1.0
  [7e6ae17a] BioSequences v3.5.1
  [de9282ab] BioStructures v4.7.1
  [0bca4874] PyBoltz v0.2.2
  [6e960f36] TMscore v0.1.0
  [8dfed614] Test v1.11.0
      Status `/tmp/jl_FBCMGD/Manifest.toml`
  [00701ae9] BioAlignments v3.1.0
  [47718e42] BioGenerics v0.1.5
  [7e6ae17a] BioSequences v3.5.1
  [de9282ab] BioStructures v4.7.1
  [3c28c6f8] BioSymbols v5.2.0
  [944b1d66] CodecZlib v0.7.8
  [34da2185] Compat v4.18.1
  [992eb4ea] CondaPkg v0.2.34
  [9a962f9c] DataAPI v1.16.0
  [e2d170a0] DataValueInterfaces v1.0.0
  [1fa38f19] Format v1.3.7
  [524e6230] IntervalTrees v1.1.0
  [82899510] IteratorInterfaceExtensions v1.0.0
  [692b3bcd] JLLWrappers v1.7.1
  [682c06a0] JSON v1.5.0
  [1914dd2f] MacroTools v0.5.16
  [0b3b1443] MicroMamba v0.1.15
  [bac558e1] OrderedCollections v1.8.1
  [69de0a69] Parsers v2.8.3
  [fa939f87] Pidfile v1.3.0
  [aea7be01] PrecompileTools v1.3.3
  [21216c6a] Preferences v1.5.2
  [0bca4874] PyBoltz v0.2.2
  [6099a3de] PythonCall v0.9.31
  [3cdcf5f2] RecipesBase v1.3.4
  [6c6a2e73] Scratch v1.3.0
  [10745b16] Statistics v1.11.1
  [69024149] StringEncodings v0.3.7
  [ec057cc2] StructUtils v2.8.0
  [6e960f36] TMscore v0.1.0
  [3783bdb8] TableTraits v1.0.1
  [bd369af6] Tables v1.12.1
  [3bb67fe8] TranscodingStreams v0.11.3
  [7200193e] Twiddle v1.1.2
  [e17b2a0c] UnsafePointers v1.0.0
  [ddb6d928] YAML v0.4.16
  [94ce4f54] Libiconv_jll v1.18.0+0
  [1d8dad79] TMscore_jll v1.0.0+0
  [f8abcde7] micromamba_jll v2.3.1+0
  [4d7b5844] pixi_jll v0.41.3+0
  [0dad84c5] ArgTools v1.1.2
  [56f22d72] Artifacts v1.11.0
  [2a0f44e3] Base64 v1.11.0
  [ade2ca70] Dates v1.11.0
  [f43a241f] Downloads v1.7.0
  [7b1f6079] FileWatching v1.11.0
  [b77e0a4c] InteractiveUtils v1.11.0
  [ac6e5ff7] JuliaSyntaxHighlighting v1.13.0
  [4af54fe1] LazyArtifacts v1.11.0
  [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
  [ca575930] NetworkOptions v1.3.0
  [44cfe95a] Pkg v1.14.0
  [de0858da] Printf v1.11.0
  [9a3f8284] Random v1.11.0
  [ea8e919c] SHA v1.0.0
  [9e88b42a] Serialization v1.11.0
  [f489334b] StyledStrings v1.13.0
  [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 v8.19.0+0
  [e37daf67] LibGit2_jll v1.9.2+0
  [29816b5a] LibSSH2_jll v1.11.3+1
  [14a3606d] MozillaCACerts_jll v2026.3.19
  [4536629a] OpenBLAS_jll v0.3.30+0
  [458c3c95] OpenSSL_jll v3.5.6+0
  [efcefdf7] PCRE2_jll v10.47.0+0
  [83775a58] Zlib_jll v1.3.2+0
  [3161d3a3] Zstd_jll v1.5.7+1
  [8e850b90] libblastrampoline_jll v5.15.0+0
  [8e850ede] nghttp2_jll v1.69.0+0
  [3f19e933] p7zip_jll v17.8.0+0
     Testing Running tests...
ERROR: LoadError: InitError: UndefVarError: `manifest_uuid_path` not defined in `Base`
Suggestion: check for spelling errors or missing imports.
Stacktrace:
  [1] getproperty(x::Module, f::Symbol)
    @ Base ./Base_compiler.jl:51
  [2] _resolve_top_env(load_path::Any)
    @ CondaPkg ~/.julia/packages/CondaPkg/8GjrP/src/resolve.jl:10
  [3] resolve(; force::Bool, io::IO, interactive::Bool, dry_run::Bool)
    @ CondaPkg ~/.julia/packages/CondaPkg/8GjrP/src/resolve.jl:823
  [4] resolve()
    @ CondaPkg ~/.julia/packages/CondaPkg/8GjrP/src/resolve.jl:796
  [5] envdir()
    @ CondaPkg ~/.julia/packages/CondaPkg/8GjrP/src/env.jl:70
  [6] init_context()
    @ PythonCall.C ~/.julia/packages/PythonCall/83z4q/src/C/context.jl:135
  [7] __init__()
    @ PythonCall.C ~/.julia/packages/PythonCall/83z4q/src/C/C.jl:26
  [8] run_module_init(mod::Module, i::Int64)
    @ Base ./loading.jl:1605
  [9] register_restored_modules(sv::Core.SimpleVector, pkg::Base.PkgId, path::String)
    @ Base ./loading.jl:1593
 [10] _include_from_serialized(pkg::Base.PkgId, path::String, ocachepath::Nothing, depmods::Vector{Any}; register::Bool)
    @ Base ./loading.jl:1481
 [11] _include_from_serialized
    @ ./loading.jl:1438 [inlined]
 [12] _require_search_from_serialized(pkg::Base.PkgId, sourcespec::Base.PkgLoadSpec, build_id::UInt128, stalecheck::Bool; reasons::Dict{String, Int64}, DEPOT_PATH::Vector{String})
    @ Base ./loading.jl:2283
 [13] !=(x::Int8, y::Int64)
    @ Base ./loading.jl:2178 [inlined]
 [14] __require_prelocked(pkg::Base.PkgId, env::String)
    @ Base ./loading.jl:2811
 [15] _require_prelocked(uuidkey::Base.PkgId, env::String)
    @ Base ./loading.jl:2672
 [16] macro expansion
    @ ./loading.jl:2599 [inlined]
 [17] String(s::Symbol)
    @ Base ./lock.jl:376 [inlined]
 [18] __require(into::Module, mod::Symbol)
    @ Base ./loading.jl:2563
 [19] require(into::Module, mod::Symbol)
    @ Base ./loading.jl:2539 [inlined]
 [20] eval_import_path(at::Module, from::Nothing, path::Expr, keyword::String)
    @ Base ./module.jl:36 [inlined]
 [21] _eval_import(imported::Bool, to::Module, from::Nothing, paths::Expr)
    @ Base ./module.jl:111
 [22] top-level scope
    @ ~/.julia/packages/PyBoltz/PGqPe/src/PyBoltz.jl:3
 [23] include(mod::Module, _path::String)
    @ Base ./Base.jl:326
 [24] 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:3271
 [25] top-level scope
    @ stdin:5
 [26] eval(m::Module, e::Any)
    @ Core ./boot.jl:517
 [27] include_string(mapexpr::typeof(identity), mod::Module, code::String, filename::String)
    @ Base ./loading.jl:3113
 [28] materialize(bc::Base.Broadcast.Broadcasted{Base.Broadcast.DefaultArrayStyle{1}, Nothing, Type{Symbol}, Tuple{Vector{SubString{String}}}})
    @ Base.Broadcast ./loading.jl:3123 [inlined]
 [29] exec_options(opts::Base.JLOptions)
    @ Base ./client.jl:350
 [30] _start()
    @ Base ./client.jl:593
during initialization of module C
in expression starting at /home/pkgeval/.julia/packages/PyBoltz/PGqPe/src/PyBoltz.jl:1
in expression starting at stdin:5
  1 dependency had output during precompilation:
┌ PyBoltz
│  [Output was shown above]
└  
ERROR: LoadError: The following 1 package failed to precompile:

PyBoltz 
Failed to precompile PyBoltz [0bca4874-a2b8-4dca-bc03-d2d86e344f1f] to "/home/pkgeval/.julia/compiled/v1.14/PyBoltz/jl_x07P1T" (ProcessExited(1)).

in expression starting at /home/pkgeval/.julia/packages/PyBoltz/PGqPe/test/runtests.jl:1

Testing failed after 29.28s

ERROR: LoadError: Package PyBoltz 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] Cmd(cmd::Cmd)
    @ Base /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] 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
  [6] test(pkgs::Vector{String}; kwargs::@Kwargs{julia_args::Cmd})
    @ Pkg.API /opt/julia/share/julia/stdlib/v1.14/Pkg/src/API.jl:160
  [7] test
    @ /opt/julia/share/julia/stdlib/v1.14/Pkg/src/API.jl:160 [inlined]
  [8] test(pkg::String; kwargs::@Kwargs{julia_args::Cmd})
    @ Pkg.API /opt/julia/share/julia/stdlib/v1.14/Pkg/src/API.jl:159 [inlined]
  [9] top-level scope
    @ /PkgEval.jl/scripts/evaluate.jl:223
 [10] include(mod::Module, _path::String)
    @ Base ./Base.jl:326
 [11] exec_options(opts::Base.JLOptions)
    @ Base ./client.jl:352
 [12] _start()
    @ Base ./client.jl:593
in expression starting at /PkgEval.jl/scripts/evaluate.jl:214

PkgEval failed after 160.19s: package fails to precompile