Package evaluation of XtalsPyTools on Julia 1.13.0-DEV.140 (fac1ce7906*) started at 2025-03-02T13:32:30.886 ################################################################################ # Set-up # Set-up completed after 0.18s ################################################################################ # Installation # Installing XtalsPyTools... Resolving package versions... Installed Conda ── v1.10.2 Installed PyCall ─ v1.96.4 Updating `~/.julia/environments/v1.13/Project.toml` [eeb819d4] + XtalsPyTools v0.0.4 Updating `~/.julia/environments/v1.13/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 v4.16.0 [8f4d0f93] + Conda v1.10.2 [a8cc5b0e] + Crayons v4.1.1 [9a962f9c] + DataAPI v1.16.0 [a93c6f00] + DataFrames v1.7.0 [864edb3b] + DataStructures v0.18.20 [e2d170a0] + DataValueInterfaces v1.0.0 [3064a664] + FIGlet v0.2.2 [5789e2e9] + FileIO v1.17.0 [48062228] + FilePathsBase v0.9.23 [86223c79] + Graphs v1.12.0 [d25df0c9] + Inflate v0.1.5 [842dd82b] + InlineStrings v1.4.3 [41ab1584] + InvertedIndices v1.3.1 [82899510] + IteratorInterfaceExtensions v1.0.0 ⌅ [033835bb] + JLD2 v0.4.54 [682c06a0] + JSON v0.21.4 [b964fa9f] + LaTeXStrings v1.4.0 [1914dd2f] + MacroTools v0.5.15 ⌅ [626554b9] + MetaGraphs v0.7.2 [e1d29d7a] + Missings v1.2.0 [bac558e1] + OrderedCollections v1.8.0 [69de0a69] + Parsers v2.8.1 [7b2266bf] + PeriodicTable v1.2.1 [2dfb63ee] + PooledArrays v1.4.3 [91cefc8d] + PrecompileSignatures v3.0.3 [aea7be01] + PrecompileTools v1.2.1 [21216c6a] + Preferences v1.4.3 [08abe8d2] + PrettyTables v2.4.0 [438e738f] + PyCall v1.96.4 [189a3867] + Reexport v1.2.2 [ae029012] + Requires v1.3.1 [91c51154] + SentinelArrays v1.4.8 [699a6c99] + SimpleTraits v0.9.4 [a2af1166] + SortingAlgorithms v1.2.1 [90137ffa] + StaticArrays v1.9.13 [1e83bf80] + StaticArraysCore v1.4.3 [10745b16] + Statistics v1.11.1 [892a3eda] + StringManipulation v0.4.1 [3783bdb8] + TableTraits v1.0.1 [bd369af6] + Tables v1.12.0 [3bb67fe8] + TranscodingStreams v0.11.3 [1986cc42] + Unitful v1.22.0 [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 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 v1.12.0 [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 v8.11.1+1 [e37daf67] + LibGit2_jll v1.9.0+0 [29816b5a] + LibSSH2_jll v1.11.3+1 [14a3606d] + MozillaCACerts_jll v2024.12.31 [4536629a] + OpenBLAS_jll v0.3.29+0 [458c3c95] + OpenSSL_jll v3.0.16+0 [bea87d4a] + SuiteSparse_jll v7.8.3+2 [83775a58] + Zlib_jll v1.3.1+2 [8e850b90] + libblastrampoline_jll v5.12.0+0 [8e850ede] + nghttp2_jll v1.64.0+1 [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 Conda ─→ `~/.julia/scratchspaces/44cfe95a-1eb2-52ea-b672-e2afdf69b78f/b19db3927f0db4151cb86d073689f2428e524576/build.log` Building PyCall → `~/.julia/scratchspaces/44cfe95a-1eb2-52ea-b672-e2afdf69b78f/9816a3826b0ebf49ab4926e2b18842ad8b5c8f04/build.log` Installation completed after 49.7s ################################################################################ # 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... ✗ Xtals ✗ XtalsPyTools 0 dependencies successfully precompiled in 150 seconds. 93 already precompiled. ERROR: LoadError: The following 1 direct dependency failed to precompile: XtalsPyTools Failed to precompile XtalsPyTools [eeb819d4-c189-4e83-a288-887db76b1875] to "/home/pkgeval/.julia/compiled/v1.13/XtalsPyTools/jl_APj7E3" (ProcessExited(1)). 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:307 [3] top-level scope @ ~/.julia/packages/Xtals/paV65/src/Xtals.jl:22 [4] include(mod::Module, _path::String) @ Base ./Base.jl:306 [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::String) @ Base ./loading.jl:3004 [6] top-level scope @ stdin:6 [7] eval(m::Module, e::Any) @ Core ./boot.jl:488 [8] include_string(mapexpr::typeof(identity), mod::Module, code::String, filename::String) @ Base ./loading.jl:2855 [9] include_string @ ./loading.jl:2865 [inlined] [10] exec_options(opts::Base.JLOptions) @ Base ./client.jl:326 [11] _start() @ Base ./client.jl:560 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:6 ERROR: LoadError: Failed to precompile Xtals [ede5f01d-793e-4c47-9885-c447d1f18d6d] to "/home/pkgeval/.julia/compiled/v1.13/Xtals/jl_PsoY3s" (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:3291 [3] (::Base.var"#__require_prelocked##0#__require_prelocked##1"{Base.PkgId})() @ Base ./loading.jl:2682 [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:93 [5] #mkpidlock#7 @ /opt/julia/share/julia/stdlib/v1.13/FileWatching/src/pidfile.jl:88 [inlined] [6] trymkpidlock(::Function, ::Vararg{Any}; kwargs::@Kwargs{stale_age::Int64}) @ FileWatching.Pidfile /opt/julia/share/julia/stdlib/v1.13/FileWatching/src/pidfile.jl:114 [7] apply_gr_kw(::NamedTuple, ::GlobalRef, ::Any, ::Vararg{Any}) @ Base ./reflection.jl:1280 [8] #invokelatest_gr#229 @ ./reflection.jl:1288 [inlined] [9] invokelatest_gr @ ./reflection.jl:1282 [inlined] [10] 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:3862 [11] maybe_cachefile_lock @ ./loading.jl:3859 [inlined] [12] __require_prelocked(pkg::Base.PkgId, env::String) @ Base ./loading.jl:2668 [13] _require_prelocked(uuidkey::Base.PkgId, env::String) @ Base ./loading.jl:2493 [14] macro expansion @ ./loading.jl:2421 [inlined] [15] macro expansion @ ./lock.jl:376 [inlined] [16] __require(into::Module, mod::Symbol) @ Base ./loading.jl:2386 [17] #invoke_in_world#2 @ ./essentials.jl:1125 [inlined] [18] invoke_in_world @ ./essentials.jl:1121 [inlined] [19] require(into::Module, mod::Symbol) @ Base ./loading.jl:2366 [20] top-level scope @ ~/.julia/packages/XtalsPyTools/HLVFH/src/XtalsPyTools.jl:3 [21] include(mod::Module, _path::String) @ Base ./Base.jl:306 [22] 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:3004 [23] top-level scope @ stdin:6 [24] eval(m::Module, e::Any) @ Core ./boot.jl:488 [25] include_string(mapexpr::typeof(identity), mod::Module, code::String, filename::String) @ Base ./loading.jl:2855 [26] include_string @ ./loading.jl:2865 [inlined] [27] exec_options(opts::Base.JLOptions) @ Base ./client.jl:326 [28] _start() @ Base ./client.jl:560 in expression starting at /home/pkgeval/.julia/packages/XtalsPyTools/HLVFH/src/XtalsPyTools.jl:1 in expression starting at stdin: in expression starting at /PkgEval.jl/scripts/precompile.jl:37 Precompilation failed after 158.17s ################################################################################ # Loading # Loading XtalsPyTools... Precompiling packages... ✗ Xtals Info Given XtalsPyTools was explicitly requested, output will be shown live  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:307  [3] top-level scope  @ ~/.julia/packages/Xtals/paV65/src/Xtals.jl:22  [4] include(mod::Module, _path::String)  @ Base ./Base.jl:306  [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::String)  @ Base ./loading.jl:3004  [6] top-level scope  @ stdin:6  [7] eval(m::Module, e::Any)  @ Core ./boot.jl:488  [8] include_string(mapexpr::typeof(identity), mod::Module, code::String, filename::String)  @ Base ./loading.jl:2855  [9] include_string  @ ./loading.jl:2865 [inlined]  [10] exec_options(opts::Base.JLOptions)  @ Base ./client.jl:326  [11] _start()  @ Base ./client.jl:560 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:6 ERROR: LoadError: Failed to precompile Xtals [ede5f01d-793e-4c47-9885-c447d1f18d6d] to "/home/pkgeval/.julia/compiled/v1.13/Xtals/jl_r3FDTa" (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:3291  [3] (::Base.var"#__require_prelocked##0#__require_prelocked##1"{Base.PkgId})()  @ Base ./loading.jl:2682  [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:93  [5] #mkpidlock#7  @ /opt/julia/share/julia/stdlib/v1.13/FileWatching/src/pidfile.jl:88 [inlined]  [6] trymkpidlock(::Function, ::Vararg{Any}; kwargs::@Kwargs{stale_age::Int64})  @ FileWatching.Pidfile /opt/julia/share/julia/stdlib/v1.13/FileWatching/src/pidfile.jl:114  [7] apply_gr_kw(::NamedTuple, ::GlobalRef, ::Any, ::Vararg{Any})  @ Base ./reflection.jl:1280  [8] #invokelatest_gr#229  @ ./reflection.jl:1288 [inlined]  [9] invokelatest_gr  @ ./reflection.jl:1282 [inlined]  [10] 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:3862  [11] maybe_cachefile_lock  @ ./loading.jl:3859 [inlined]  [12] __require_prelocked(pkg::Base.PkgId, env::String)  @ Base ./loading.jl:2668  [13] _require_prelocked(uuidkey::Base.PkgId, env::String)  @ Base ./loading.jl:2493  [14] macro expansion  @ ./loading.jl:2421 [inlined]  [15] macro expansion  @ ./lock.jl:376 [inlined]  [16] __require(into::Module, mod::Symbol)  @ Base ./loading.jl:2386  [17] #invoke_in_world#2  @ ./essentials.jl:1125 [inlined]  [18] invoke_in_world  @ ./essentials.jl:1121 [inlined]  [19] require(into::Module, mod::Symbol)  @ Base ./loading.jl:2366  [20] top-level scope  @ ~/.julia/packages/XtalsPyTools/HLVFH/src/XtalsPyTools.jl:3  [21] include(mod::Module, _path::String)  @ Base ./Base.jl:306  [22] 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:3004  [23] top-level scope  @ stdin:6  [24] eval(m::Module, e::Any)  @ Core ./boot.jl:488  [25] include_string(mapexpr::typeof(identity), mod::Module, code::String, filename::String)  @ Base ./loading.jl:2855  [26] include_string  @ ./loading.jl:2865 [inlined]  [27] exec_options(opts::Base.JLOptions)  @ Base ./client.jl:326  [28] _start()  @ Base ./client.jl:560 in expression starting at /home/pkgeval/.julia/packages/XtalsPyTools/HLVFH/src/XtalsPyTools.jl:1 in expression starting at stdin:6 ✗ XtalsPyTools 0 dependencies successfully precompiled in 61 seconds. 93 already precompiled. ERROR: The following 1 direct dependency failed to precompile: XtalsPyTools Failed to precompile XtalsPyTools [eeb819d4-c189-4e83-a288-887db76b1875] to "/home/pkgeval/.julia/compiled/v1.13/XtalsPyTools/jl_ud9RHq" (ProcessExited(1)). 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:307 [3] top-level scope @ ~/.julia/packages/Xtals/paV65/src/Xtals.jl:22 [4] include(mod::Module, _path::String) @ Base ./Base.jl:306 [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::String) @ Base ./loading.jl:3004 [6] top-level scope @ stdin:6 [7] eval(m::Module, e::Any) @ Core ./boot.jl:488 [8] include_string(mapexpr::typeof(identity), mod::Module, code::String, filename::String) @ Base ./loading.jl:2855 [9] include_string @ ./loading.jl:2865 [inlined] [10] exec_options(opts::Base.JLOptions) @ Base ./client.jl:326 [11] _start() @ Base ./client.jl:560 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:6 ERROR: LoadError: Failed to precompile Xtals [ede5f01d-793e-4c47-9885-c447d1f18d6d] to "/home/pkgeval/.julia/compiled/v1.13/Xtals/jl_r3FDTa" (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:3291 [3] (::Base.var"#__require_prelocked##0#__require_prelocked##1"{Base.PkgId})() @ Base ./loading.jl:2682 [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:93 [5] #mkpidlock#7 @ /opt/julia/share/julia/stdlib/v1.13/FileWatching/src/pidfile.jl:88 [inlined] [6] trymkpidlock(::Function, ::Vararg{Any}; kwargs::@Kwargs{stale_age::Int64}) @ FileWatching.Pidfile /opt/julia/share/julia/stdlib/v1.13/FileWatching/src/pidfile.jl:114 [7] apply_gr_kw(::NamedTuple, ::GlobalRef, ::Any, ::Vararg{Any}) @ Base ./reflection.jl:1280 [8] #invokelatest_gr#229 @ ./reflection.jl:1288 [inlined] [9] invokelatest_gr @ ./reflection.jl:1282 [inlined] [10] 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:3862 [11] maybe_cachefile_lock @ ./loading.jl:3859 [inlined] [12] __require_prelocked(pkg::Base.PkgId, env::String) @ Base ./loading.jl:2668 [13] _require_prelocked(uuidkey::Base.PkgId, env::String) @ Base ./loading.jl:2493 [14] macro expansion @ ./loading.jl:2421 [inlined] [15] macro expansion @ ./lock.jl:376 [inlined] [16] __require(into::Module, mod::Symbol) @ Base ./loading.jl:2386 [17] #invoke_in_world#2 @ ./essentials.jl:1125 [inlined] [18] invoke_in_world @ ./essentials.jl:1121 [inlined] [19] require(into::Module, mod::Symbol) @ Base ./loading.jl:2366 [20] top-level scope @ ~/.julia/packages/XtalsPyTools/HLVFH/src/XtalsPyTools.jl:3 [21] include(mod::Module, _path::String) @ Base ./Base.jl:306 [22] 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:3004 [23] top-level scope @ stdin:6 [24] eval(m::Module, e::Any) @ Core ./boot.jl:488 [25] include_string(mapexpr::typeof(identity), mod::Module, code::String, filename::String) @ Base ./loading.jl:2855 [26] include_string @ ./loading.jl:2865 [inlined] [27] exec_options(opts::Base.JLOptions) @ Base ./client.jl:326 [28] _start() @ Base ./client.jl:560 in expression starting at /home/pkgeval/.julia/packages/XtalsPyTools/HLVFH/src/XtalsPyTools.jl:1 in expression starting at stdin: Loading failed after 63.37s 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:598 [inlined] [2] run(::Cmd; wait::Bool) @ Base ./process.jl:513 [3] run(::Cmd) @ Base ./process.jl:510 [4] top-level scope @ /PkgEval.jl/scripts/evaluate.jl:193 [5] include(mod::Module, _path::String) @ Base ./Base.jl:306 [6] exec_options(opts::Base.JLOptions) @ Base ./client.jl:328 [7] _start() @ Base ./client.jl:560 in expression starting at /PkgEval.jl/scripts/evaluate.jl:184 PkgEval failed after 295.97s: package fails to precompile