Package evaluation to load XtalsPyTools on Julia 1.14.0-DEV.29 (7d6ae45e5a*) started at 2025-11-05T10:35:15.720


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


Set-up completed after 0.1s


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

Installing XtalsPyTools...
   Resolving package versions...
   Installed MacroTools ────────────────── v0.5.16
   Installed VersionParsing ────────────── v1.3.0
   Installed FilePathsBase ─────────────── v0.9.24
   Installed AtomsBase ─────────────────── v0.4.2
   Installed XtalsPyTools ──────────────── v0.0.4
   Installed JLD2 ──────────────────────── v0.4.55
   Installed DataStructures ────────────── v0.19.3
   Installed FIGlet ────────────────────── v0.2.2
   Installed InlineStrings ─────────────── v1.4.5
   Installed CodecZlib ─────────────────── v0.7.8
   Installed ArnoldiMethod ─────────────── v0.4.0
   Installed OrderedCollections ────────── v1.8.1
   Installed Compat ────────────────────── v4.18.1
   Installed IteratorInterfaceExtensions ─ v1.0.0
   Installed TranscodingStreams ────────── v0.11.3
   Installed DataAPI ───────────────────── v1.16.0
   Installed PeriodicTable ─────────────── v1.2.1
   Installed Statistics ────────────────── v1.11.1
   Installed InvertedIndices ───────────── v1.3.1
   Installed PrecompileSignatures ──────── v3.0.3
   Installed Conda ─────────────────────── v1.10.3
   Installed PrecompileTools ───────────── v1.3.3
   Installed DataValueInterfaces ───────── v1.0.0
   Installed SentinelArrays ────────────── v1.4.8
   Installed StaticArraysCore ──────────── v1.4.4
   Installed StructUtils ───────────────── v2.5.1
   Installed UnitfulAtomic ─────────────── v1.0.0
   Installed PyCall ────────────────────── v1.96.4
   Installed StringManipulation ────────── v0.4.1
   Installed StaticArrays ──────────────── v1.9.15
   Installed Requires ──────────────────── v1.3.1
   Installed SimpleTraits ──────────────── v0.9.5
   Installed FileIO ────────────────────── v1.17.1
   Installed Parsers ───────────────────── v2.8.3
   Installed Tables ────────────────────── v1.12.1
   Installed Unitful ───────────────────── v1.25.1
   Installed JSON ──────────────────────── v1.2.0
   Installed PrettyTables ──────────────── v3.1.0
   Installed Reexport ──────────────────── v1.2.2
   Installed MetaGraphs ────────────────── v0.7.2
   Installed CSV ───────────────────────── v0.10.15
   Installed Missings ──────────────────── v1.2.0
   Installed Preferences ───────────────── v1.5.0
   Installed DataFrames ────────────────── v1.8.1
   Installed Bio3DView ─────────────────── v1.0.0
   Installed WeakRefStrings ────────────── v1.4.2
   Installed PooledArrays ──────────────── v1.4.3
   Installed TableTraits ───────────────── v1.0.1
   Installed LaTeXStrings ──────────────── v1.4.0
   Installed Crayons ───────────────────── v4.1.1
   Installed SortingAlgorithms ─────────── v1.2.2
   Installed WorkerUtilities ───────────── v1.6.1
   Installed Inflate ───────────────────── v0.1.5
   Installed Aqua ──────────────────────── v0.5.6
   Installed Graphs ────────────────────── v1.13.1
   Installed Xtals ─────────────────────── v0.5.1
  Installing 1 artifacts
   Installed artifact fonts 4.6 MiB
    Updating `~/.julia/environments/v1.14/Project.toml`
  [eeb819d4] + XtalsPyTools v0.0.4
    Updating `~/.julia/environments/v1.14/Manifest.toml`
⌅ [4c88cf16] + Aqua v0.5.6
  [ec485272] + ArnoldiMethod v0.4.0
⌅ [a963bdd2] + AtomsBase v0.4.2
  [99c8bb3a] + Bio3DView v1.0.0
  [336ed68f] + CSV v0.10.15
  [944b1d66] + CodecZlib v0.7.8
  [34da2185] + Compat v4.18.1
  [8f4d0f93] + Conda v1.10.3
  [a8cc5b0e] + Crayons v4.1.1
  [9a962f9c] + DataAPI v1.16.0
  [a93c6f00] + DataFrames v1.8.1
  [864edb3b] + DataStructures v0.19.3
  [e2d170a0] + DataValueInterfaces v1.0.0
  [3064a664] + FIGlet v0.2.2
  [5789e2e9] + FileIO v1.17.1
  [48062228] + FilePathsBase v0.9.24
  [86223c79] + Graphs v1.13.1
  [d25df0c9] + Inflate v0.1.5
  [842dd82b] + InlineStrings v1.4.5
  [41ab1584] + InvertedIndices v1.3.1
  [82899510] + IteratorInterfaceExtensions v1.0.0
⌅ [033835bb] + JLD2 v0.4.55
  [682c06a0] + JSON v1.2.0
  [b964fa9f] + LaTeXStrings v1.4.0
  [1914dd2f] + MacroTools v0.5.16
⌅ [626554b9] + MetaGraphs v0.7.2
  [e1d29d7a] + Missings v1.2.0
  [bac558e1] + OrderedCollections v1.8.1
  [69de0a69] + Parsers v2.8.3
  [7b2266bf] + PeriodicTable v1.2.1
  [2dfb63ee] + PooledArrays v1.4.3
  [91cefc8d] + PrecompileSignatures v3.0.3
  [aea7be01] + PrecompileTools v1.3.3
  [21216c6a] + Preferences v1.5.0
  [08abe8d2] + PrettyTables v3.1.0
  [438e738f] + PyCall v1.96.4
  [189a3867] + Reexport v1.2.2
  [ae029012] + Requires v1.3.1
  [91c51154] + SentinelArrays v1.4.8
  [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
  [892a3eda] + StringManipulation v0.4.1
  [ec057cc2] + StructUtils v2.5.1
  [3783bdb8] + TableTraits v1.0.1
  [bd369af6] + Tables v1.12.1
  [3bb67fe8] + TranscodingStreams v0.11.3
  [1986cc42] + Unitful v1.25.1
  [a7773ee8] + UnitfulAtomic v1.0.0
  [81def892] + VersionParsing v1.3.0
  [ea10d353] + WeakRefStrings v1.4.2
  [76eceee3] + WorkerUtilities v1.6.1
  [ede5f01d] + Xtals v0.5.1
  [eeb819d4] + XtalsPyTools v0.0.4
  [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
  [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 v1.13.0
  [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 v1.11.0
  [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 v8.16.0+0
  [e37daf67] + LibGit2_jll v1.9.1+0
  [29816b5a] + LibSSH2_jll v1.11.3+1
  [14a3606d] + MozillaCACerts_jll v2025.9.9
  [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 v1.67.1+0
  [3f19e933] + p7zip_jll v17.6.0+0
        Info Packages marked with ⌅ have new versions available but compatibility constraints restrict them from upgrading. To see why use `status --outdated -m`
    Building Conda ─→ `~/.julia/scratchspaces/44cfe95a-1eb2-52ea-b672-e2afdf69b78f/8f06b0cfa4c514c7b9546756dbae91fcfbc92dc9/build.log`
    Building PyCall → `~/.julia/scratchspaces/44cfe95a-1eb2-52ea-b672-e2afdf69b78f/9816a3826b0ebf49ab4926e2b18842ad8b5c8f04/build.log`

Installation completed after 115.37s


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

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

Precompiling package dependencies...
Precompiling packages...
   4269.2 ms  ✓ MacroTools
   1575.9 ms  ✓ InlineStrings
    728.7 ms  ✓ Reexport
   1080.4 ms  ✓ Statistics
    834.0 ms  ✓ DataAPI
    741.6 ms  ✓ DataValueInterfaces
    945.0 ms  ✓ StaticArraysCore
   1117.0 ms  ✓ Requires
   1219.0 ms  ✓ OrderedCollections
    786.7 ms  ✓ InvertedIndices
   2357.8 ms  ✓ PrecompileSignatures
   1576.0 ms  ✓ Bio3DView
   1198.2 ms  ✓ FIGlet
   1008.2 ms  ✓ VersionParsing
    817.6 ms  ✓ WorkerUtilities
   1061.6 ms  ✓ Inflate
   1185.5 ms  ✓ TranscodingStreams
    705.3 ms  ✓ IteratorInterfaceExtensions
    832.6 ms  ✓ LaTeXStrings
   1900.4 ms  ✓ Crayons
   2776.7 ms  ✓ SentinelArrays
   1395.7 ms  ✓ StructUtils
  29953.1 ms  ✓ Unitful
    870.5 ms  ✓ Compat
    848.7 ms  ✓ Preferences
   2518.1 ms  ✓ SimpleTraits
    936.4 ms  ✓ Statistics → SparseArraysExt
    712.8 ms  ✓ Missings
    760.5 ms  ✓ PooledArrays
   7728.9 ms  ✓ FileIO
   3444.9 ms  ✓ DataStructures
   1002.7 ms  ✓ CodecZlib
    807.5 ms  ✓ TableTraits
   1655.0 ms  ✓ Unitful → PrintfExt
    685.3 ms  ✓ Compat → CompatLinearAlgebraExt
    775.3 ms  ✓ PrecompileTools
    953.4 ms  ✓ SortingAlgorithms
   1727.0 ms  ✓ Tables
   8343.9 ms  ✓ UnitfulAtomic
   5654.3 ms  ✓ PeriodicTable
   2103.9 ms  ✓ FilePathsBase
   6402.4 ms  ✓ Aqua
  12651.8 ms  ✓ StaticArrays
   3028.3 ms  ✓ StringManipulation
  15758.9 ms  ✓ Parsers
  39586.9 ms  ✓ JLD2
    811.9 ms  ✓ StructUtils → StructUtilsTablesExt
   2630.3 ms  ✓ FilePathsBase → FilePathsBaseTestExt
    946.6 ms  ✓ FilePathsBase → FilePathsBaseMmapExt
   1360.7 ms  ✓ StaticArrays → StaticArraysStatisticsExt
   3832.1 ms  ✓ ArnoldiMethod
   5729.4 ms  ✓ AtomsBase
  37733.3 ms  ✓ PrettyTables
   6851.8 ms  ✓ JSON
   1178.9 ms  ✓ InlineStrings → ParsersExt
  10148.2 ms  ✓ Graphs
  84169.6 ms  ✓ DataFrames
   2323.7 ms  ✓ Conda
   2628.8 ms  ✓ WeakRefStrings
   7894.6 ms  ✓ MetaGraphs
  23387.5 ms  ✓ PyCall
  27787.4 ms  ✓ CSV
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, 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:3148
  [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:2994
  [9] include_string
    @ ./loading.jl:3004 [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

Precompilation completed after 429.1s


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

Loading XtalsPyTools...
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, 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:3148
  [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:2994
  [9] include_string
    @ ./loading.jl:3004 [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: 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, 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:3148
  [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:2994
  [9] include_string
    @ ./loading.jl:3004 [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

  1 dependency had output during precompilation:
┌ Xtals
│  [Output was shown above]
└  
ERROR: LoadError: The following 1 package failed to precompile:

Xtals 
Failed to precompile Xtals [ede5f01d-793e-4c47-9885-c447d1f18d6d] to "/home/pkgeval/.julia/compiled/v1.14/Xtals/jl_qoTY2S" (ProcessExited(1)).

in expression starting at /home/pkgeval/.julia/packages/XtalsPyTools/HLVFH/src/XtalsPyTools.jl:1

Loading failed after 54.48s

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 XtalsPyTools'`, 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:193
 [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:184

PkgEval failed after 639.5s: package fails to precompile