Package evaluation of MolecularMinimumDistances on Julia 1.13.0-DEV.853 (3e868b27cf*) started at 2025-07-16T23:59:13.922


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


Set-up completed after 0.24s


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

Installing MolecularMinimumDistances...
   Resolving package versions...
    Updating `~/.julia/environments/v1.13/Project.toml`
  [46954fcc] + MolecularMinimumDistances v0.4.5
    Updating `~/.julia/environments/v1.13/Manifest.toml`
⌅ [69e1c6dd] + CellListMap v0.8.32
  [34da2185] + Compat v4.17.0
  [187b0558] + ConstructionBase v1.6.0
  [ffbed154] + DocStringExtensions v0.9.5
  [1914dd2f] + MacroTools v0.5.16
  [46954fcc] + MolecularMinimumDistances v0.4.5
  [bac558e1] + OrderedCollections v1.8.1
  [d96e819e] + Parameters v0.12.3
  [aea7be01] + PrecompileTools v1.3.2
  [21216c6a] + Preferences v1.4.3
  [92933f4c] + ProgressMeter v1.10.4
  [efcf1570] + Setfield v1.1.2
  [90137ffa] + StaticArrays v1.9.14
  [1e83bf80] + StaticArraysCore v1.4.3
⌅ [1c621080] + TestItems v0.1.1
  [3a884ed6] + UnPack v1.0.2
  [56f22d72] + Artifacts v1.11.0
  [ade2ca70] + Dates v1.11.0
  [8ba89e20] + Distributed v1.11.0
  [9fa8497b] + Future v1.11.0
  [8f399da3] + Libdl v1.11.0
  [37e2e46d] + LinearAlgebra v1.12.0
  [de0858da] + Printf v1.11.0
  [9a3f8284] + Random v1.11.0
  [ea8e919c] + SHA v0.7.0
  [9e88b42a] + Serialization v1.11.0
  [6462fe0b] + Sockets v1.11.0
  [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 v5.13.1+0
        Info Packages marked with ⌅ have new versions available but compatibility constraints restrict them from upgrading. To see why use `status --outdated -m`

Installation completed after 5.47s


################################################################################
# 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...
           ✗ CellListMap
           ✗ MolecularMinimumDistances
  0 dependencies successfully precompiled in 24 seconds. 25 already precompiled.

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

MolecularMinimumDistances 

Failed to precompile MolecularMinimumDistances [46954fcc-1dd7-4352-b01d-a39240e91dc8] to "/home/pkgeval/.julia/compiled/v1.13/MolecularMinimumDistances/jl_8KzO3W" (ProcessExited(1)).
ERROR: LoadError: cannot declare CellListMap.copy_output exported; it is already declared public
Stacktrace:
  [1] include(mapexpr::Function, mod::Module, _path::String)
    @ Base ./Base.jl:310
  [2] top-level scope
    @ ~/.julia/packages/CellListMap/6MkUi/src/CellListMap.jl:49
  [3] include(mod::Module, _path::String)
    @ Base ./Base.jl:309
  [4] 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::String)
    @ Base ./loading.jl:3002
  [5] top-level scope
    @ stdin:5
  [6] eval(m::Module, e::Any)
    @ Core ./boot.jl:489
  [7] include_string(mapexpr::typeof(identity), mod::Module, code::String, filename::String)
    @ Base ./loading.jl:2848
  [8] include_string
    @ ./loading.jl:2858 [inlined]
  [9] exec_options(opts::Base.JLOptions)
    @ Base ./client.jl:318
 [10] _start()
    @ Base ./client.jl:553
in expression starting at /home/pkgeval/.julia/packages/CellListMap/6MkUi/src/ParticleSystem.jl:5
in expression starting at /home/pkgeval/.julia/packages/CellListMap/6MkUi/src/CellListMap.jl:1
in expression starting at stdin:5
ERROR: LoadError: Failed to precompile CellListMap [69e1c6dd-3888-40e6-b3c8-31ac5f578864] to "/home/pkgeval/.julia/compiled/v1.13/CellListMap/jl_ofgHXH" (ProcessExited(1)).
Stacktrace:
  [1] error(s::String)
    @ Base ./error.jl:44
  [2] compilecache(pkg::Base.PkgId, path::String, internal_stderr::IO, internal_stdout::IO, keep_loaded_modules::Bool; flags::Cmd, cacheflags::Base.CacheFlags, reasons::Dict{String, Int64}, loadable_exts::Nothing)
    @ Base ./loading.jl:3289
  [3] (::Base.var"#__require_prelocked##0#__require_prelocked##1"{Base.PkgId})()
    @ Base ./loading.jl:2654
  [4] mkpidlock(f::Base.var"#__require_prelocked##0#__require_prelocked##1"{Base.PkgId}, at::String, pid::Int32; kwopts::@Kwargs{stale_age::Int64, wait::Bool})
    @ FileWatching.Pidfile /opt/julia/share/julia/stdlib/v1.13/FileWatching/src/pidfile.jl:94
  [5] #mkpidlock#7
    @ /opt/julia/share/julia/stdlib/v1.13/FileWatching/src/pidfile.jl:89 [inlined]
  [6] trymkpidlock(::Function, ::Vararg{Any}; kwargs::@Kwargs{stale_age::Int64})
    @ FileWatching.Pidfile /opt/julia/share/julia/stdlib/v1.13/FileWatching/src/pidfile.jl:115
  [7] #invokelatest_gr#236
    @ ./reflection.jl:1332 [inlined]
  [8] invokelatest_gr
    @ ./reflection.jl:1324 [inlined]
  [9] maybe_cachefile_lock(f::Base.var"#__require_prelocked##0#__require_prelocked##1"{Base.PkgId}, pkg::Base.PkgId, srcpath::String; stale_age::Int64)
    @ Base ./loading.jl:3860
 [10] maybe_cachefile_lock
    @ ./loading.jl:3857 [inlined]
 [11] __require_prelocked(pkg::Base.PkgId, env::String)
    @ Base ./loading.jl:2640
 [12] _require_prelocked(uuidkey::Base.PkgId, env::String)
    @ Base ./loading.jl:2468
 [13] macro expansion
    @ ./loading.jl:2396 [inlined]
 [14] macro expansion
    @ ./lock.jl:376 [inlined]
 [15] __require(into::Module, mod::Symbol)
    @ Base ./loading.jl:2360
 [16] require
    @ ./loading.jl:2336 [inlined]
 [17] eval_import_path
    @ ./module.jl:36 [inlined]
 [18] _eval_import(imported::Bool, to::Module, from::Nothing, paths::Expr)
    @ Base ./module.jl:111
 [19] top-level scope
    @ ~/.julia/packages/MolecularMinimumDistances/wHQ7d/src/MolecularMinimumDistances.jl:8
 [20] include(mod::Module, _path::String)
    @ Base ./Base.jl:309
 [21] 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:3002
 [22] top-level scope
    @ stdin:5
 [23] eval(m::Module, e::Any)
    @ Core ./boot.jl:489
 [24] include_string(mapexpr::typeof(identity), mod::Module, code::String, filename::String)
    @ Base ./loading.jl:2848
 [25] include_string
    @ ./loading.jl:2858 [inlined]
 [26] exec_options(opts::Base.JLOptions)
    @ Base ./client.jl:318
 [27] _start()
    @ Base ./client.jl:553
in expression starting at /home/pkgeval/.julia/packages/MolecularMinimumDistances/wHQ7d/src/MolecularMinimumDistances.jl:1
in expression starting at stdin:
in expression starting at /PkgEval.jl/scripts/precompile.jl:37

Precompilation failed after 36.09s



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

Loading MolecularMinimumDistances...
Precompiling packages...
           ✗ CellListMap
Info Given MolecularMinimumDistances was explicitly requested, output will be shown live 
ERROR: LoadError: cannot declare CellListMap.copy_output exported; it is already declared public
Stacktrace:
  [1] include(mapexpr::Function, mod::Module, _path::String)
    @ Base ./Base.jl:310
  [2] top-level scope
    @ ~/.julia/packages/CellListMap/6MkUi/src/CellListMap.jl:49
  [3] include(mod::Module, _path::String)
    @ Base ./Base.jl:309
  [4] 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::String)
    @ Base ./loading.jl:3002
  [5] top-level scope
    @ stdin:5
  [6] eval(m::Module, e::Any)
    @ Core ./boot.jl:489
  [7] include_string(mapexpr::typeof(identity), mod::Module, code::String, filename::String)
    @ Base ./loading.jl:2848
  [8] include_string
    @ ./loading.jl:2858 [inlined]
  [9] exec_options(opts::Base.JLOptions)
    @ Base ./client.jl:318
 [10] _start()
    @ Base ./client.jl:553
in expression starting at /home/pkgeval/.julia/packages/CellListMap/6MkUi/src/ParticleSystem.jl:5
in expression starting at /home/pkgeval/.julia/packages/CellListMap/6MkUi/src/CellListMap.jl:1
in expression starting at stdin:5
ERROR: LoadError: Failed to precompile CellListMap [69e1c6dd-3888-40e6-b3c8-31ac5f578864] to "/home/pkgeval/.julia/compiled/v1.13/CellListMap/jl_lhWHYZ" (ProcessExited(1)).
Stacktrace:
  [1] error(s::String)
    @ Base ./error.jl:44
  [2] compilecache(pkg::Base.PkgId, path::String, internal_stderr::IO, internal_stdout::IO, keep_loaded_modules::Bool; flags::Cmd, cacheflags::Base.CacheFlags, reasons::Dict{String, Int64}, loadable_exts::Nothing)
    @ Base ./loading.jl:3289
  [3] (::Base.var"#__require_prelocked##0#__require_prelocked##1"{Base.PkgId})()
    @ Base ./loading.jl:2654
  [4] mkpidlock(f::Base.var"#__require_prelocked##0#__require_prelocked##1"{Base.PkgId}, at::String, pid::Int32; kwopts::@Kwargs{stale_age::Int64, wait::Bool})
    @ FileWatching.Pidfile /opt/julia/share/julia/stdlib/v1.13/FileWatching/src/pidfile.jl:94
  [5] #mkpidlock#7
    @ /opt/julia/share/julia/stdlib/v1.13/FileWatching/src/pidfile.jl:89 [inlined]
  [6] trymkpidlock(::Function, ::Vararg{Any}; kwargs::@Kwargs{stale_age::Int64})
    @ FileWatching.Pidfile /opt/julia/share/julia/stdlib/v1.13/FileWatching/src/pidfile.jl:115
  [7] #invokelatest_gr#236
    @ ./reflection.jl:1332 [inlined]
  [8] invokelatest_gr
    @ ./reflection.jl:1324 [inlined]
  [9] maybe_cachefile_lock(f::Base.var"#__require_prelocked##0#__require_prelocked##1"{Base.PkgId}, pkg::Base.PkgId, srcpath::String; stale_age::Int64)
    @ Base ./loading.jl:3860
 [10] maybe_cachefile_lock
    @ ./loading.jl:3857 [inlined]
 [11] __require_prelocked(pkg::Base.PkgId, env::String)
    @ Base ./loading.jl:2640
 [12] _require_prelocked(uuidkey::Base.PkgId, env::String)
    @ Base ./loading.jl:2468
 [13] macro expansion
    @ ./loading.jl:2396 [inlined]
 [14] macro expansion
    @ ./lock.jl:376 [inlined]
 [15] __require(into::Module, mod::Symbol)
    @ Base ./loading.jl:2360
 [16] require
    @ ./loading.jl:2336 [inlined]
 [17] eval_import_path
    @ ./module.jl:36 [inlined]
 [18] _eval_import(imported::Bool, to::Module, from::Nothing, paths::Expr)
    @ Base ./module.jl:111
 [19] top-level scope
    @ ~/.julia/packages/MolecularMinimumDistances/wHQ7d/src/MolecularMinimumDistances.jl:8
 [20] include(mod::Module, _path::String)
    @ Base ./Base.jl:309
 [21] 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:3002
 [22] top-level scope
    @ stdin:5
 [23] eval(m::Module, e::Any)
    @ Core ./boot.jl:489
 [24] include_string(mapexpr::typeof(identity), mod::Module, code::String, filename::String)
    @ Base ./loading.jl:2848
 [25] include_string
    @ ./loading.jl:2858 [inlined]
 [26] exec_options(opts::Base.JLOptions)
    @ Base ./client.jl:318
 [27] _start()
    @ Base ./client.jl:553
in expression starting at /home/pkgeval/.julia/packages/MolecularMinimumDistances/wHQ7d/src/MolecularMinimumDistances.jl:1
in expression starting at stdin:5
           ✗ MolecularMinimumDistances
  0 dependencies successfully precompiled in 24 seconds. 25 already precompiled.

ERROR: The following 1 direct dependency failed to precompile:

MolecularMinimumDistances 

Failed to precompile MolecularMinimumDistances [46954fcc-1dd7-4352-b01d-a39240e91dc8] to "/home/pkgeval/.julia/compiled/v1.13/MolecularMinimumDistances/jl_n7csv8" (ProcessExited(1)).
ERROR: LoadError: cannot declare CellListMap.copy_output exported; it is already declared public
Stacktrace:
  [1] include(mapexpr::Function, mod::Module, _path::String)
    @ Base ./Base.jl:310
  [2] top-level scope
    @ ~/.julia/packages/CellListMap/6MkUi/src/CellListMap.jl:49
  [3] include(mod::Module, _path::String)
    @ Base ./Base.jl:309
  [4] 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::String)
    @ Base ./loading.jl:3002
  [5] top-level scope
    @ stdin:5
  [6] eval(m::Module, e::Any)
    @ Core ./boot.jl:489
  [7] include_string(mapexpr::typeof(identity), mod::Module, code::String, filename::String)
    @ Base ./loading.jl:2848
  [8] include_string
    @ ./loading.jl:2858 [inlined]
  [9] exec_options(opts::Base.JLOptions)
    @ Base ./client.jl:318
 [10] _start()
    @ Base ./client.jl:553
in expression starting at /home/pkgeval/.julia/packages/CellListMap/6MkUi/src/ParticleSystem.jl:5
in expression starting at /home/pkgeval/.julia/packages/CellListMap/6MkUi/src/CellListMap.jl:1
in expression starting at stdin:5
ERROR: LoadError: Failed to precompile CellListMap [69e1c6dd-3888-40e6-b3c8-31ac5f578864] to "/home/pkgeval/.julia/compiled/v1.13/CellListMap/jl_lhWHYZ" (ProcessExited(1)).
Stacktrace:
  [1] error(s::String)
    @ Base ./error.jl:44
  [2] compilecache(pkg::Base.PkgId, path::String, internal_stderr::IO, internal_stdout::IO, keep_loaded_modules::Bool; flags::Cmd, cacheflags::Base.CacheFlags, reasons::Dict{String, Int64}, loadable_exts::Nothing)
    @ Base ./loading.jl:3289
  [3] (::Base.var"#__require_prelocked##0#__require_prelocked##1"{Base.PkgId})()
    @ Base ./loading.jl:2654
  [4] mkpidlock(f::Base.var"#__require_prelocked##0#__require_prelocked##1"{Base.PkgId}, at::String, pid::Int32; kwopts::@Kwargs{stale_age::Int64, wait::Bool})
    @ FileWatching.Pidfile /opt/julia/share/julia/stdlib/v1.13/FileWatching/src/pidfile.jl:94
  [5] #mkpidlock#7
    @ /opt/julia/share/julia/stdlib/v1.13/FileWatching/src/pidfile.jl:89 [inlined]
  [6] trymkpidlock(::Function, ::Vararg{Any}; kwargs::@Kwargs{stale_age::Int64})
    @ FileWatching.Pidfile /opt/julia/share/julia/stdlib/v1.13/FileWatching/src/pidfile.jl:115
  [7] #invokelatest_gr#236
    @ ./reflection.jl:1332 [inlined]
  [8] invokelatest_gr
    @ ./reflection.jl:1324 [inlined]
  [9] maybe_cachefile_lock(f::Base.var"#__require_prelocked##0#__require_prelocked##1"{Base.PkgId}, pkg::Base.PkgId, srcpath::String; stale_age::Int64)
    @ Base ./loading.jl:3860
 [10] maybe_cachefile_lock
    @ ./loading.jl:3857 [inlined]
 [11] __require_prelocked(pkg::Base.PkgId, env::String)
    @ Base ./loading.jl:2640
 [12] _require_prelocked(uuidkey::Base.PkgId, env::String)
    @ Base ./loading.jl:2468
 [13] macro expansion
    @ ./loading.jl:2396 [inlined]
 [14] macro expansion
    @ ./lock.jl:376 [inlined]
 [15] __require(into::Module, mod::Symbol)
    @ Base ./loading.jl:2360
 [16] require
    @ ./loading.jl:2336 [inlined]
 [17] eval_import_path
    @ ./module.jl:36 [inlined]
 [18] _eval_import(imported::Bool, to::Module, from::Nothing, paths::Expr)
    @ Base ./module.jl:111
 [19] top-level scope
    @ ~/.julia/packages/MolecularMinimumDistances/wHQ7d/src/MolecularMinimumDistances.jl:8
 [20] include(mod::Module, _path::String)
    @ Base ./Base.jl:309
 [21] 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:3002
 [22] top-level scope
    @ stdin:5
 [23] eval(m::Module, e::Any)
    @ Core ./boot.jl:489
 [24] include_string(mapexpr::typeof(identity), mod::Module, code::String, filename::String)
    @ Base ./loading.jl:2848
 [25] include_string
    @ ./loading.jl:2858 [inlined]
 [26] exec_options(opts::Base.JLOptions)
    @ Base ./client.jl:318
 [27] _start()
    @ Base ./client.jl:553
in expression starting at /home/pkgeval/.julia/packages/MolecularMinimumDistances/wHQ7d/src/MolecularMinimumDistances.jl:1
in expression starting at stdin:

Loading failed after 27.57s

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 MolecularMinimumDistances'`, 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:320
 [7] _start()
   @ Base ./client.jl:553
in expression starting at /PkgEval.jl/scripts/evaluate.jl:184

PkgEval failed after 86.61s: package fails to precompile