Package evaluation to test Kabsch on Julia 1.14.0-DEV.1354 (1806b0bc31*) started at 2025-12-11T14:16:08.694


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

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

Set-up completed after 11.62s


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

Installing Kabsch...
   Resolving package versions...
   Installed HashArrayMappedTries ─ v0.2.0
   Installed Requires ───────────── v1.3.1
   Installed Compat ─────────────── v4.18.1
   Installed Statistics ─────────── v1.11.1
   Installed MacroTools ─────────── v0.5.16
   Installed Preferences ────────── v1.5.0
   Installed PrecompileTools ────── v1.3.3
   Installed Atomix ─────────────── v1.1.2
   Installed Adapt ──────────────── v4.4.0
   Installed ScopedValues ───────── v1.5.0
   Installed StaticArraysCore ───── v1.4.4
   Installed NNlib ──────────────── v0.9.32
   Installed KernelAbstractions ─── v0.9.39
   Installed StaticArrays ───────── v1.9.15
   Installed UnsafeAtomics ──────── v0.3.0
   Installed GPUArraysCore ──────── v0.2.0
   Installed ChainRulesCore ─────── v1.26.0
   Installed Kabsch ─────────────── v0.1.0
    Updating `~/.julia/environments/v1.14/Project.toml`
  [f04b186e] + Kabsch v0.1.0
    Updating `~/.julia/environments/v1.14/Manifest.toml`
  [79e6a3ab] + Adapt v4.4.0
  [a9b6321e] + Atomix v1.1.2
  [d360d2e6] + ChainRulesCore v1.26.0
  [34da2185] + Compat v4.18.1
  [46192b85] + GPUArraysCore v0.2.0
  [076d061b] + HashArrayMappedTries v0.2.0
  [f04b186e] + Kabsch v0.1.0
  [63c18a36] + KernelAbstractions v0.9.39
  [1914dd2f] + MacroTools v0.5.16
  [872c559c] + NNlib v0.9.32
  [aea7be01] + PrecompileTools v1.3.3
  [21216c6a] + Preferences v1.5.0
  [ae029012] + Requires v1.3.1
  [7e506255] + ScopedValues v1.5.0
  [90137ffa] + StaticArrays v1.9.15
  [1e83bf80] + StaticArraysCore v1.4.4
  [10745b16] + Statistics v1.11.1
  [013be700] + UnsafeAtomics v0.3.0
  [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
  [f489334b] + StyledStrings v1.13.0
  [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 v0.3.29+0
  [8e850b90] + libblastrampoline_jll v5.15.0+0

Installation completed after 4.71s


################################################################################
# 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 14.27s



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

     Testing Kabsch
      Status `/tmp/jl_b68Nz1/Project.toml`
  [f04b186e] Kabsch v0.1.0
  [1cead3c2] Manifolds v0.11.7
  [872c559c] NNlib v0.9.32
  [90137ffa] StaticArrays v1.9.15
  [37e2e46d] LinearAlgebra v1.13.0
  [44cfe95a] Pkg v1.14.0
  [8dfed614] Test v1.11.0
      Status `/tmp/jl_b68Nz1/Manifest.toml`
  [47edcb42] ADTypes v1.20.0
  [79e6a3ab] Adapt v4.4.0
  [66dad0bd] AliasTables v1.1.3
  [ec485272] ArnoldiMethod v0.4.0
  [a9b6321e] Atomix v1.1.2
  [d360d2e6] ChainRulesCore v1.26.0
  [34da2185] Compat v4.18.1
  [9a962f9c] DataAPI v1.16.0
  [864edb3b] DataStructures v0.19.3
  [a0c0ee7d] DifferentiationInterface v0.7.12
  [ffbed154] DocStringExtensions v0.9.5
  [b7d42ee7] Einsum v0.4.1
  [46192b85] GPUArraysCore v0.2.0
  [86223c79] Graphs v1.13.2
  [076d061b] HashArrayMappedTries v0.2.0
  [d25df0c9] Inflate v0.1.5
  [92d709cd] IrrationalConstants v0.2.6
  [692b3bcd] JLLWrappers v1.7.1
  [f04b186e] Kabsch v0.1.0
  [63c18a36] KernelAbstractions v0.9.39
  [2c470bb0] Kronecker v0.5.5
  [7a12625a] LinearMaps v3.11.4
  [2ab3a3ac] LogExpFunctions v0.3.29
  [1914dd2f] MacroTools v0.5.16
  [af67fdf4] ManifoldDiff v0.4.5
  [1cead3c2] Manifolds v0.11.7
  [3362f125] ManifoldsBase v2.3.0
  [99c1a7ee] MatrixEquations v2.5.6
  [e1d29d7a] Missings v1.2.0
  [872c559c] NNlib v0.9.32
  [356022a1] NamedDims v1.2.3
  [bac558e1] OrderedCollections v1.8.1
  [aea7be01] PrecompileTools v1.3.3
  [21216c6a] Preferences v1.5.0
  [43287f4e] PtrArrays v1.3.0
  [94ee1d12] Quaternions v0.7.7
  [c1ae055f] RealDot v0.1.0
  [ae029012] Requires v1.3.1
  [7e506255] ScopedValues v1.5.0
  [699a6c99] SimpleTraits v0.9.5
  [47aef6b3] SimpleWeightedGraphs v1.5.0
  [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 v0.34.9
  [013be700] UnsafeAtomics v0.3.0
  [efe28fd5] OpenSpecFun_jll v0.5.6+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
  [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
  [2f01184e] SparseArrays v1.13.0
  [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 v8.17.0+0
  [e37daf67] LibGit2_jll v1.9.1+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
  [3f19e933] p7zip_jll v17.7.0+0
     Testing Running tests...
WARNING: Method definition rand!(ManifoldsBase.AbstractManifold{𝔽} where 𝔽, Any) in module ManifoldsBase at /home/pkgeval/.julia/packages/ManifoldsBase/MPJfA/src/ManifoldsBase.jl:1061 overwritten in module Manifolds at /home/pkgeval/.julia/packages/Manifolds/gYgOy/src/manifold_fallbacks.jl:1.
ERROR: Method overwriting is not permitted during Module precompilation. Use `__precompile__(false)` to opt-out of precompilation.

  1 dependency had output during precompilation:
┌ Manifolds
│  [Output was shown above]
└  
WARNING: Method definition rand!(ManifoldsBase.AbstractManifold{𝔽} where 𝔽, Any) in module ManifoldsBase at /home/pkgeval/.julia/packages/ManifoldsBase/MPJfA/src/ManifoldsBase.jl:1061 overwritten in module Manifolds at /home/pkgeval/.julia/packages/Manifolds/gYgOy/src/manifold_fallbacks.jl:1.
WARNING: Method definition kwcall(NamedTuple{names, T} where T<:Tuple where names, typeof(Random.rand!), ManifoldsBase.AbstractManifold{𝔽} where 𝔽, Any) in module ManifoldsBase at /home/pkgeval/.julia/packages/ManifoldsBase/MPJfA/src/ManifoldsBase.jl:1061 overwritten in module Manifolds at /home/pkgeval/.julia/packages/Manifolds/gYgOy/src/manifold_fallbacks.jl:1.
WARNING: Method definition AbstractMetric(ManifoldsBase.AbstractManifold{𝔽} where 𝔽) in module ManifoldsBase at /home/pkgeval/.julia/packages/ManifoldsBase/MPJfA/src/metric.jl:99 overwritten in module Manifolds at /home/pkgeval/.julia/packages/Manifolds/gYgOy/src/manifolds/MetricManifold.jl:2.
WARNING: Method definition (::Type{T})(ManifoldsBase.AbstractManifold{𝔽} where 𝔽) where {T<:ManifoldsBase.AbstractMetric} in module ManifoldsBase at /home/pkgeval/.julia/packages/ManifoldsBase/MPJfA/src/metric.jl:100 overwritten in module Manifolds at /home/pkgeval/.julia/packages/Manifolds/gYgOy/src/manifolds/MetricManifold.jl:3.
WARNING: Method definition rand!(ManifoldsBase.AbstractManifold{𝔽} where 𝔽, Any) in module ManifoldsBase at /home/pkgeval/.julia/packages/ManifoldsBase/MPJfA/src/ManifoldsBase.jl:1061 overwritten in module Manifolds at /home/pkgeval/.julia/packages/Manifolds/gYgOy/src/manifold_fallbacks.jl:1.
ERROR: Method overwriting is not permitted during Module precompilation. Use `__precompile__(false)` to opt-out of precompilation.
ERROR: LoadError: Precompiled image Base.PkgId(Base.UUID("1cead3c2-87b3-11e9-0ccd-23c62b72b94e"), "Manifolds") 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/Manifolds/gYgOy/ext/ManifoldsTestExt/ManifoldsTestExt.jl:3
 [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/Manifolds/gYgOy/ext/ManifoldsTestExt/ManifoldsTestExt.jl:1
in expression starting at stdin:5

  2 dependencies had output during precompilation:
┌ Manifolds → ManifoldsTestExt
│  [Output was shown above]
└  
┌ Manifolds
│  WARNING: Method definition rand!(ManifoldsBase.AbstractManifold{𝔽} where 𝔽, Any) in module ManifoldsBase at /home/pkgeval/.julia/packages/ManifoldsBase/MPJfA/src/ManifoldsBase.jl:1061 overwritten in module Manifolds at /home/pkgeval/.julia/packages/Manifolds/gYgOy/src/manifold_fallbacks.jl:1.
│  ERROR: Method overwriting is not permitted during Module precompilation. Use `__precompile__(false)` to opt-out of precompilation.
└  
┌ Error: Error during loading of extension ManifoldsTestExt of Manifolds, use `Base.retry_load_extensions()` to retry.
│   exception =
│    1-element ExceptionStack:
│    The following 1 package failed to precompile:
│    
│    ManifoldsTestExt 
│    Failed to precompile ManifoldsTestExt [aebc1d30-06b9-52fa-96f7-3b9db0c1a355] to "/home/pkgeval/.julia/compiled/v1.14/ManifoldsTestExt/jl_BoDt00" (ProcessExited(1)).
│    
└ @ Base loading.jl:1721
Test Summary: | Pass  Total   Time
Kabsch.jl     |  220    220  34.5s
     Testing Kabsch tests passed 

Testing completed after 271.02s

PkgEval succeeded after 314.52s