Package evaluation to load PoreMatMod on Julia 1.14.0-DEV.1352 (749bc618c5*) started at 2025-12-10T00:27:05.627


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


Set-up completed after 0.08s


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

Installing PoreMatMod...
   Resolving package versions...
    Updating `~/.julia/environments/v1.14/Project.toml`
  [2de0d7f0] + PoreMatMod v0.2.20
    Updating `~/.julia/environments/v1.14/Manifest.toml`
  [ec485272] + ArnoldiMethod v0.4.0
⌅ [a963bdd2] + AtomsBase v0.4.2
  [99c8bb3a] + Bio3DView v1.0.0
  [d1d4a3ce] + BitFlags v0.1.9
  [336ed68f] + CSV v0.10.15
  [944b1d66] + CodecZlib v0.7.8
  [34da2185] + Compat v4.18.1
  [f0e56b4a] + ConcurrentUtilities v2.5.0
  [5218b696] + Configurations v0.17.6
  [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
  [ffbed154] + DocStringExtensions v0.9.5
  [460bff9d] + ExceptionUnwrapping v0.1.11
  [21656369] + ExpressionExplorer v1.1.3
  [55351af7] + ExproniconLite v0.10.14
  [5789e2e9] + FileIO v1.17.1
  [48062228] + FilePathsBase v0.9.24
  [828d9ff0] + GracefulPkg v2.4.2
⌃ [86223c79] + Graphs v1.13.1
  [cd3eb016] + HTTP v1.10.19
  [ac1192a8] + HypertextLiteral v0.9.5
  [d25df0c9] + Inflate v0.1.5
  [842dd82b] + InlineStrings v1.4.5
  [41ab1584] + InvertedIndices v1.3.1
  [92d709cd] + IrrationalConstants v0.2.6
  [82899510] + IteratorInterfaceExtensions v1.0.0
⌅ [033835bb] + JLD2 v0.4.55
  [692b3bcd] + JLLWrappers v1.7.1
  [8ac3fa9e] + LRUCache v1.6.2
  [b964fa9f] + LaTeXStrings v1.4.0
  [0e77f7df] + LazilyInitializedFields v1.3.0
  [2ab3a3ac] + LogExpFunctions v0.3.29
  [e6f89c97] + LoggingExtras v1.2.0
  [6c6e2e6c] + MIMEs v1.1.0
  [1914dd2f] + MacroTools v0.5.16
  [36869731] + Malt v1.3.1
  [739be429] + MbedTLS v1.1.9
⌅ [626554b9] + MetaGraphs v0.7.2
  [e1d29d7a] + Missings v1.2.0
  [99f44e22] + MsgPack v1.2.1
  [4d8831e6] + OpenSSL v1.6.1
  [bac558e1] + OrderedCollections v1.8.1
  [69de0a69] + Parsers v2.8.3
  [7b2266bf] + PeriodicTable v1.2.1
  [c3e4b0f8] + Pluto v0.20.21
  [72656b73] + PlutoDependencyExplorer v1.2.2
  [2dfb63ee] + PooledArrays v1.4.3
  [2de0d7f0] + PoreMatMod v0.2.20
  [91cefc8d] + PrecompileSignatures v3.0.3
  [aea7be01] + PrecompileTools v1.3.3
  [21216c6a] + Preferences v1.5.0
  [08abe8d2] + PrettyTables v3.1.2
  [189a3867] + Reexport v1.2.2
  [2792f1a3] + RegistryInstances v0.1.0
  [05181044] + RelocatableFolders v1.0.1
  [ae029012] + Requires v1.3.1
  [6c6a2e73] + Scratch v1.3.0
  [91c51154] + SentinelArrays v1.4.8
  [777ac1f9] + SimpleBufferStream v1.2.0
  [699a6c99] + SimpleTraits v0.9.5
  [a2af1166] + SortingAlgorithms v1.2.2
  [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
  [892a3eda] + StringManipulation v0.4.2
  [3783bdb8] + TableTraits v1.0.1
  [bd369af6] + Tables v1.12.1
  [3bb67fe8] + TranscodingStreams v0.11.3
  [410a4b4d] + Tricks v0.1.13
  [5c2747f8] + URIs v1.6.1
  [1986cc42] + Unitful v1.27.0
  [a7773ee8] + UnitfulAtomic v1.0.0
  [ea10d353] + WeakRefStrings v1.4.2
  [76eceee3] + WorkerUtilities v1.6.1
  [ede5f01d] + Xtals v0.5.1
  [c8ffd9c3] + MbedTLS_jll v2.28.1010+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
  [44cfe95a] + Pkg v1.14.0
  [de0858da] + Printf v1.11.0
  [3fa0cd96] + REPL v1.11.0
  [9a3f8284] + Random v1.11.0
  [ea8e919c] + SHA v1.0.0
  [9e88b42a] + Serialization v1.11.0
  [1a1011a3] + SharedArrays v1.11.0
  [6462fe0b] + Sockets 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
  [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
        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`

Installation completed after 4.74s


################################################################################
# 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 12.08s



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

Loading PoreMatMod...
WARNING: Imported binding AtomsBase.boundary_conditions was undeclared at import time during import to Xtals.
WARNING: Imported binding AtomsBase.species_type was undeclared at import time during import to Xtals.
ERROR: LoadError: invalid method definition in Xtals: exported function AtomsBase.species_type does not exist
Stacktrace:
  [1] top-level scope
    @ ~/.julia/packages/Xtals/paV65/src/crystal.jl:1364
  [2] include(mapexpr::Function, mod::Module, _path::String)
    @ Base ./Base.jl:310
  [3] top-level scope
    @ ~/.julia/packages/Xtals/paV65/src/Xtals.jl:22
  [4] include(mod::Module, _path::String)
    @ Base ./Base.jl:309
  [5] 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
  [6] top-level scope
    @ stdin:5
  [7] eval(m::Module, e::Any)
    @ Core ./boot.jl:489
  [8] include_string(mapexpr::typeof(identity), mod::Module, code::String, filename::String)
    @ Base ./loading.jl:3092
  [9] include_string
    @ ./loading.jl:3102 [inlined]
 [10] exec_options(opts::Base.JLOptions)
    @ Base ./client.jl:342
 [11] _start()
    @ Base ./client.jl:577
in expression starting at /home/pkgeval/.julia/packages/Xtals/paV65/src/crystal.jl:1364
in expression starting at /home/pkgeval/.julia/packages/Xtals/paV65/src/Xtals.jl:1
in expression starting at stdin:5


  WARNING: Unsupported Julia version
  ≡≡≡≡≡≡≡≡≡≡≡≡≡≡≡≡≡≡≡≡≡≡≡≡≡≡≡≡≡≡≡≡≡≡

  Pluto (0.20.21) is running on a new version of Julia (1.14.0-DEV.1352).
  Support for Julia 1.14 will be added in a later Pluto release.

  You can try:

    1. Update Pluto using Pkg.update("Pluto").
    2. If there is no newer version of Pluto yet, then you can help us
       develop it! Julia 1.14 compatibility takes a lot of work, and we
       would really appreciate your help! Search
       github.com/fonsp/Pluto.jl/issues for Julia 1.14 to see what still
       needs to be done. Not all compatibility issues are known – play
       around and try running Pkg.test("Pluto").

  │ Note
  │
  │  Preview versions of Julia are not fully supported by Pluto.


ERROR: LoadError: Precompiled image Base.PkgId(Base.UUID("ede5f01d-793e-4c47-9885-c447d1f18d6d"), "Xtals") 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: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/PoreMatMod/R2OKZ/src/PoreMatMod.jl:4
 [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/PoreMatMod/R2OKZ/src/PoreMatMod.jl:1
in expression starting at stdin:5

  2 dependencies had output during precompilation:
┌ PoreMatMod
│  [Output was shown above]
└  
┌ Xtals
│  WARNING: Imported binding AtomsBase.boundary_conditions was undeclared at import time during import to Xtals.
│  WARNING: Imported binding AtomsBase.species_type was undeclared at import time during import to Xtals.
│  ERROR: LoadError: invalid method definition in Xtals: exported function AtomsBase.species_type does not exist
│  Stacktrace:
│    [1] top-level scope
│      @ ~/.julia/packages/Xtals/paV65/src/crystal.jl:1364
│    [2] include(mapexpr::Function, mod::Module, _path::String)
│      @ Base ./Base.jl:310
│    [3] top-level scope
│      @ ~/.julia/packages/Xtals/paV65/src/Xtals.jl:22
│    [4] include(mod::Module, _path::String)
│      @ Base ./Base.jl:309
│    [5] 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
│    [6] top-level scope
│      @ stdin:5
│    [7] eval(m::Module, e::Any)
│      @ Core ./boot.jl:489
│    [8] include_string(mapexpr::typeof(identity), mod::Module, code::String, filename::String)
│      @ Base ./loading.jl:3092
│    [9] include_string
│      @ ./loading.jl:3102 [inlined]
│   [10] exec_options(opts::Base.JLOptions)
│      @ Base ./client.jl:342
│   [11] _start()
│      @ Base ./client.jl:577
│  in expression starting at /home/pkgeval/.julia/packages/Xtals/paV65/src/crystal.jl:1364
│  in expression starting at /home/pkgeval/.julia/packages/Xtals/paV65/src/Xtals.jl:1
│  in expression starting at stdin:5
└  
ERROR: The following 2 packages failed to precompile:

PoreMatMod 
Failed to precompile PoreMatMod [2de0d7f0-0963-4438-8bc8-7e7ffe3dc69a] to "/home/pkgeval/.julia/compiled/v1.14/PoreMatMod/jl_RRtPLA" (ProcessExited(1)).

Xtals 
Failed to precompile Xtals [ede5f01d-793e-4c47-9885-c447d1f18d6d] to "/home/pkgeval/.julia/compiled/v1.14/Xtals/jl_zCE9ah" (ProcessExited(1)).


Loading failed after 412.04s

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 PoreMatMod'`, ProcessExited(1)) [1]

Stacktrace:
 [1] pipeline_error
   @ ./process.jl:611 [inlined]
 [2] run(::Cmd; wait::Bool)
   @ Base ./process.jl:526
 [3] run(::Cmd)
   @ Base ./process.jl:523
 [4] top-level scope
   @ /PkgEval.jl/scripts/evaluate.jl:211
 [5] include(mod::Module, _path::String)
   @ Base ./Base.jl:309
 [6] exec_options(opts::Base.JLOptions)
   @ Base ./client.jl:344
 [7] _start()
   @ Base ./client.jl:577
in expression starting at /PkgEval.jl/scripts/evaluate.jl:202

PkgEval failed after 448.61s: package fails to precompile