Package evaluation of OceanBioME on Julia 1.13.0-DEV.791 (d5209bd37d*) started at 2025-07-04T17:52:46.041


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


Set-up completed after 0.19s


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

Installing OceanBioME...
   Resolving package versions...
   Installed GibbsSeaWater ─ v0.1.4
    Updating `~/.julia/environments/v1.13/Project.toml`
  [a49af516] + OceanBioME v0.14.1
    Updating `~/.julia/environments/v1.13/Manifest.toml`
  [621f4979] + AbstractFFTs v1.5.0
  [7d9f7c33] + Accessors v0.1.42
  [79e6a3ab] + Adapt v4.3.0
⌅ [ec485272] + ArnoldiMethod v0.1.0
  [a9b6321e] + Atomix v1.1.1
  [ab4f0b2a] + BFloat16s v0.5.1
  [fa961155] + CEnum v0.5.0
  [052768ef] + CUDA v5.8.2
  [1af6417a] + CUDA_Runtime_Discovery v0.3.5
  [3da002f7] + ColorTypes v0.12.1
  [5ae59095] + Colors v0.13.1
  [38540f10] + CommonSolve v0.2.4
  [34da2185] + Compat v4.17.0
  [a33af91c] + CompositionsBase v0.1.2
  [187b0558] + ConstructionBase v1.6.0
  [a8cc5b0e] + Crayons v4.1.1
  [7445602f] + CubedSphere v0.3.2
  [9a962f9c] + DataAPI v1.16.0
  [a93c6f00] + DataFrames v1.7.0
  [864edb3b] + DataStructures v0.18.22
  [e2d170a0] + DataValueInterfaces v1.0.0
  [b4f34e82] + Distances v0.10.12
  [ffbed154] + DocStringExtensions v0.9.5
  [e2ba6199] + ExprTools v0.1.10
  [21656369] + ExpressionExplorer v1.1.3
  [7a1cc6ca] + FFTW v1.9.0
  [5789e2e9] + FileIO v1.17.0
  [53c48c17] + FixedPointNumbers v0.8.5
  [0c68f7d7] + GPUArrays v11.2.3
  [46192b85] + GPUArraysCore v0.2.0
  [61eb1bfa] + GPUCompiler v1.6.1
  [096a3bc2] + GPUToolbox v0.2.0
  [9a22fb26] + GibbsSeaWater v0.1.4
  [c27321d9] + Glob v1.3.1
  [076d061b] + HashArrayMappedTries v0.2.0
  [d25df0c9] + Inflate v0.1.5
  [842dd82b] + InlineStrings v1.4.4
  [3587e190] + InverseFunctions v0.1.17
  [41ab1584] + InvertedIndices v1.3.1
  [42fd0dbc] + IterativeSolvers v0.9.4
  [82899510] + IteratorInterfaceExtensions v1.0.0
  [033835bb] + JLD2 v0.5.15
  [692b3bcd] + JLLWrappers v1.7.0
  [63c18a36] + KernelAbstractions v0.9.36
  [ba0b0d4f] + Krylov v0.10.1
  [45d422c2] + KrylovPreconditioners v0.3.4
  [929cbde3] + LLVM v9.4.2
  [8b046642] + LLVMLoopInfo v1.0.0
  [b964fa9f] + LaTeXStrings v1.4.0
  [093fc24a] + LightGraphs v1.3.5
  [da04e1cc] + MPI v0.20.22
  [3da0fdf6] + MPIPreferences v0.1.11
  [1914dd2f] + MacroTools v0.5.16
  [2679e427] + Metis v1.5.0
  [e1d29d7a] + Missings v1.2.0
  [46d2c3a1] + MuladdMacro v0.2.4
  [5da4648a] + NVTX v1.0.0
  [a49af516] + OceanBioME v0.14.1
  [9e8cae18] + Oceananigans v0.96.35
  [6fe1bfb0] + OffsetArrays v1.17.0
  [bac558e1] + OrderedCollections v1.8.1
  [eebad327] + PkgVersion v0.3.3
  [2dfb63ee] + PooledArrays v1.4.3
  [aea7be01] + PrecompileTools v1.3.2
  [21216c6a] + Preferences v1.4.3
  [08abe8d2] + PrettyTables v2.4.0
  [94ee1d12] + Quaternions v0.7.6
  [74087812] + Random123 v1.7.1
  [e6cf234a] + RandomNumbers v1.6.0
  [a3311ec8] + ReactantCore v0.1.15
  [c1ae055f] + RealDot v0.1.0
  [3cdcf5f2] + RecipesBase v1.3.4
  [189a3867] + Reexport v1.2.2
  [ae029012] + Requires v1.3.1
  [f2b01f46] + Roots v2.2.8
  [6038ab10] + Rotations v1.7.1
  [7e506255] + ScopedValues v1.3.0
  [6c6a2e73] + Scratch v1.3.0
  [d496a93d] + SeawaterPolynomials v0.3.10
  [91c51154] + SentinelArrays v1.4.8
  [699a6c99] + SimpleTraits v0.9.4
  [a2af1166] + SortingAlgorithms v1.2.1
  [90137ffa] + StaticArrays v1.9.13
  [1e83bf80] + StaticArraysCore v1.4.3
  [10745b16] + Statistics v1.11.1
  [82ae8749] + StatsAPI v1.7.1
  [892a3eda] + StringManipulation v0.4.1
  [09ab397b] + StructArrays v0.7.1
  [3783bdb8] + TableTraits v1.0.1
  [bd369af6] + Tables v1.12.1
⌅ [6aa5eb33] + TaylorSeries v0.19.1
  [e689c965] + Tracy v0.1.5
  [3bb67fe8] + TranscodingStreams v0.11.3
  [013be700] + UnsafeAtomics v0.3.0
⌅ [4ee394cb] + CUDA_Driver_jll v0.13.1+0
⌅ [76a88914] + CUDA_Runtime_jll v0.17.1+0
  [f5851436] + FFTW_jll v3.3.11+0
  [6727f6b2] + GibbsSeaWater_jll v3.5.2+0
  [e33a78d0] + Hwloc_jll v2.12.1+0
  [1d5cc7b8] + IntelOpenMP_jll v2025.0.4+0
  [9c1d0b0a] + JuliaNVTXCallbacks_jll v0.2.1+0
  [dad2f222] + LLVMExtra_jll v0.0.37+2
  [ad6e5548] + LibTracyClient_jll v0.9.1+6
  [d00139f3] + METIS_jll v5.1.3+0
  [856f044c] + MKL_jll v2025.0.1+1
  [7cb0a576] + MPICH_jll v4.3.1+0
  [f1f71cc9] + MPItrampoline_jll v5.5.4+0
  [9237b28f] + MicrosoftMPI_jll v10.1.4+3
  [e98f9f5b] + NVTX_jll v3.2.1+0
  [fe0851c0] + OpenMPI_jll v5.0.8+0
  [1e29f10c] + demumble_jll v1.3.0+0
  [1317d2d5] + oneTBB_jll v2022.0.0+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 v1.12.0
  [4af54fe1] + LazyArtifacts v1.11.0
  [b27032c2] + LibCURL v0.6.4
  [76f85450] + LibGit2 v1.11.0
  [8f399da3] + Libdl v1.11.0
  [37e2e46d] + LinearAlgebra v1.12.0
  [56ddb016] + Logging v1.11.0
  [d6f4376e] + Markdown v1.11.0
  [a63ad114] + Mmap v1.11.0
  [ca575930] + NetworkOptions v1.3.0
  [44cfe95a] + Pkg v1.13.0
  [de0858da] + Printf v1.11.0
  [9a3f8284] + Random v1.11.0
  [ea8e919c] + SHA v0.7.0
  [9e88b42a] + Serialization v1.11.0
  [1a1011a3] + SharedArrays v1.11.0
  [6462fe0b] + Sockets v1.11.0
  [2f01184e] + SparseArrays v1.12.0
  [f489334b] + StyledStrings v1.11.0
  [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 v8.14.1+1
  [e37daf67] + LibGit2_jll v1.9.1+0
  [29816b5a] + LibSSH2_jll v1.11.3+1
  [14a3606d] + MozillaCACerts_jll v2025.5.20
  [4536629a] + OpenBLAS_jll v0.3.29+0
  [458c3c95] + OpenSSL_jll v3.5.0+0
  [efcefdf7] + PCRE2_jll v10.45.0+0
  [bea87d4a] + SuiteSparse_jll v7.10.1+0
  [83775a58] + Zlib_jll v1.3.1+2
  [8e850b90] + libblastrampoline_jll v5.13.1+0
  [8e850ede] + nghttp2_jll v1.65.0+0
  [3f19e933] + p7zip_jll v17.5.0+2
        Info Packages marked with ⌅ have new versions available but compatibility constraints restrict them from upgrading. To see why use `status --outdated -m`
    Building GibbsSeaWater → `~/.julia/scratchspaces/44cfe95a-1eb2-52ea-b672-e2afdf69b78f/f4318e7a751703a5db8b57c112e5cd5c218d296b/build.log`

Installation completed after 15.41s


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

Precompiling PkgEval dependencies...
No packages added to or removed from `~/.julia/environments/pkgeval/Project.toml`
No packages added to or removed from `~/.julia/environments/pkgeval/Manifest.toml`

Precompiling package dependencies...
Precompiling packages...
 177788.5 ms  ✓ Oceananigans
           ✗ OceanBioME
  1 dependency successfully precompiled in 246 seconds. 180 already precompiled.
  1 dependency had output during precompilation:
┌ Oceananigans
│  WARNING: Constructor for type "FieldBoundaryConditions" was extended in `MultiRegion` without explicit qualification or import.
│    NOTE: Assumed "FieldBoundaryConditions" refers to `BoundaryConditions.FieldBoundaryConditions`. This behavior is deprecated and may differ in future versions.
│    NOTE: This behavior may have differed in Julia versions prior to 1.12.
│    Hint: If you intended to create a new generic function of the same name, use `function FieldBoundaryConditions end`.
│    Hint: To silence the warning, qualify `FieldBoundaryConditions` as `BoundaryConditions.FieldBoundaryConditions` in the method signature or explicitly `import BoundaryConditions: FieldBoundaryConditions`.
└  

ERROR: LoadError: The following 1 direct dependency failed to precompile:

OceanBioME 

Failed to precompile OceanBioME [a49af516-9db8-4be4-be45-1dad61c5a376] to "/home/pkgeval/.julia/compiled/v1.13/OceanBioME/jl_b64ahH" (ProcessExited(1)).
┌ Warning: You are using Julia v1.11 or later!"
│ Oceananigans is currently tested on Julia v1.10."
│ If you find issues with Julia v1.11 or later,"
│ please report at https://github.com/CliMA/Oceananigans.jl/issues/new
└ @ Oceananigans ~/.julia/packages/Oceananigans/3ZIHr/src/Oceananigans.jl:124
WARNING: Imported binding TimeSteppers.store_tendencies! was undeclared at import time during import to Sediments.
ERROR: LoadError: invalid method definition in Sediments: exported function TimeSteppers.store_tendencies! does not exist
Stacktrace:
  [1] top-level scope
    @ ~/.julia/packages/OceanBioME/aMtdF/src/Sediments/timesteppers.jl:83
  [2] include(mapexpr::Function, mod::Module, _path::String)
    @ Base ./Base.jl:310
  [3] top-level scope
    @ ~/.julia/packages/OceanBioME/aMtdF/src/Sediments/Sediments.jl:38
  [4] include(mapexpr::Function, mod::Module, _path::String)
    @ Base ./Base.jl:310
  [5] top-level scope
    @ ~/.julia/packages/OceanBioME/aMtdF/src/OceanBioME.jl:213
  [6] include(mod::Module, _path::String)
    @ Base ./Base.jl:309
  [7] include_package_for_output(pkg::Base.PkgId, input::String, 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:3000
  [8] top-level scope
    @ stdin:5
  [9] eval(m::Module, e::Any)
    @ Core ./boot.jl:489
 [10] include_string(mapexpr::typeof(identity), mod::Module, code::String, filename::String)
    @ Base ./loading.jl:2846
 [11] include_string
    @ ./loading.jl:2856 [inlined]
 [12] exec_options(opts::Base.JLOptions)
    @ Base ./client.jl:322
 [13] _start()
    @ Base ./client.jl:557
in expression starting at /home/pkgeval/.julia/packages/OceanBioME/aMtdF/src/Sediments/timesteppers.jl:83
in expression starting at /home/pkgeval/.julia/packages/OceanBioME/aMtdF/src/Sediments/Sediments.jl:1
in expression starting at /home/pkgeval/.julia/packages/OceanBioME/aMtdF/src/OceanBioME.jl:1
in expression starting at stdin:
in expression starting at /PkgEval.jl/scripts/precompile.jl:37

Precompilation failed after 256.92s



################################################################################
# Loading
#

Loading OceanBioME...
Precompiling packages...
Info Given OceanBioME was explicitly requested, output will be shown live 
┌ Warning: You are using Julia v1.11 or later!"
│ Oceananigans is currently tested on Julia v1.10."
│ If you find issues with Julia v1.11 or later,"
│ please report at https://github.com/CliMA/Oceananigans.jl/issues/new
└ @ Oceananigans ~/.julia/packages/Oceananigans/3ZIHr/src/Oceananigans.jl:124
WARNING: Imported binding TimeSteppers.store_tendencies! was undeclared at import time during import to Sediments.
ERROR: LoadError: invalid method definition in Sediments: exported function TimeSteppers.store_tendencies! does not exist
Stacktrace:
  [1] top-level scope
    @ ~/.julia/packages/OceanBioME/aMtdF/src/Sediments/timesteppers.jl:83
  [2] include(mapexpr::Function, mod::Module, _path::String)
    @ Base ./Base.jl:310
  [3] top-level scope
    @ ~/.julia/packages/OceanBioME/aMtdF/src/Sediments/Sediments.jl:38
  [4] include(mapexpr::Function, mod::Module, _path::String)
    @ Base ./Base.jl:310
  [5] top-level scope
    @ ~/.julia/packages/OceanBioME/aMtdF/src/OceanBioME.jl:213
  [6] include(mod::Module, _path::String)
    @ Base ./Base.jl:309
  [7] include_package_for_output(pkg::Base.PkgId, input::String, 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:3000
  [8] top-level scope
    @ stdin:5
  [9] eval(m::Module, e::Any)
    @ Core ./boot.jl:489
 [10] include_string(mapexpr::typeof(identity), mod::Module, code::String, filename::String)
    @ Base ./loading.jl:2846
 [11] include_string
    @ ./loading.jl:2856 [inlined]
 [12] exec_options(opts::Base.JLOptions)
    @ Base ./client.jl:322
 [13] _start()
    @ Base ./client.jl:557
in expression starting at /home/pkgeval/.julia/packages/OceanBioME/aMtdF/src/Sediments/timesteppers.jl:83
in expression starting at /home/pkgeval/.julia/packages/OceanBioME/aMtdF/src/Sediments/Sediments.jl:1
in expression starting at /home/pkgeval/.julia/packages/OceanBioME/aMtdF/src/OceanBioME.jl:1
in expression starting at stdin:5
           ✗ OceanBioME
  0 dependencies successfully precompiled in 64 seconds. 181 already precompiled.

ERROR: The following 1 direct dependency failed to precompile:

OceanBioME 

Failed to precompile OceanBioME [a49af516-9db8-4be4-be45-1dad61c5a376] to "/home/pkgeval/.julia/compiled/v1.13/OceanBioME/jl_aFd5Mn" (ProcessExited(1)).
┌ Warning: You are using Julia v1.11 or later!"
│ Oceananigans is currently tested on Julia v1.10."
│ If you find issues with Julia v1.11 or later,"
│ please report at https://github.com/CliMA/Oceananigans.jl/issues/new
└ @ Oceananigans ~/.julia/packages/Oceananigans/3ZIHr/src/Oceananigans.jl:124
WARNING: Imported binding TimeSteppers.store_tendencies! was undeclared at import time during import to Sediments.
ERROR: LoadError: invalid method definition in Sediments: exported function TimeSteppers.store_tendencies! does not exist
Stacktrace:
  [1] top-level scope
    @ ~/.julia/packages/OceanBioME/aMtdF/src/Sediments/timesteppers.jl:83
  [2] include(mapexpr::Function, mod::Module, _path::String)
    @ Base ./Base.jl:310
  [3] top-level scope
    @ ~/.julia/packages/OceanBioME/aMtdF/src/Sediments/Sediments.jl:38
  [4] include(mapexpr::Function, mod::Module, _path::String)
    @ Base ./Base.jl:310
  [5] top-level scope
    @ ~/.julia/packages/OceanBioME/aMtdF/src/OceanBioME.jl:213
  [6] include(mod::Module, _path::String)
    @ Base ./Base.jl:309
  [7] include_package_for_output(pkg::Base.PkgId, input::String, 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:3000
  [8] top-level scope
    @ stdin:5
  [9] eval(m::Module, e::Any)
    @ Core ./boot.jl:489
 [10] include_string(mapexpr::typeof(identity), mod::Module, code::String, filename::String)
    @ Base ./loading.jl:2846
 [11] include_string
    @ ./loading.jl:2856 [inlined]
 [12] exec_options(opts::Base.JLOptions)
    @ Base ./client.jl:322
 [13] _start()
    @ Base ./client.jl:557
in expression starting at /home/pkgeval/.julia/packages/OceanBioME/aMtdF/src/Sediments/timesteppers.jl:83
in expression starting at /home/pkgeval/.julia/packages/OceanBioME/aMtdF/src/Sediments/Sediments.jl:1
in expression starting at /home/pkgeval/.julia/packages/OceanBioME/aMtdF/src/OceanBioME.jl:1
in expression starting at stdin:

Loading failed after 66.77s

ERROR: LoadError: failed process: Process(`/opt/julia/bin/julia -C native -J/opt/julia/lib/julia/sys.so -g1 --check-bounds=yes --inline=yes --pkgimages=existing -e 'using OceanBioME'`, ProcessExited(1)) [1]

Stacktrace:
 [1] pipeline_error
   @ ./process.jl:602 [inlined]
 [2] run(::Cmd; wait::Bool)
   @ Base ./process.jl:517
 [3] run(::Cmd)
   @ Base ./process.jl:514
 [4] top-level scope
   @ /PkgEval.jl/scripts/evaluate.jl:193
 [5] include(mod::Module, _path::String)
   @ Base ./Base.jl:309
 [6] exec_options(opts::Base.JLOptions)
   @ Base ./client.jl:324
 [7] _start()
   @ Base ./client.jl:557
in expression starting at /PkgEval.jl/scripts/evaluate.jl:184

PkgEval failed after 363.75s: package fails to precompile