Package evaluation to test SingleCrystal on Julia 1.14.0-DEV.1352 (749bc618c5*) started at 2025-12-09T19:52:11.245 ################################################################################ # Set-up # Installing PkgEval dependencies (TestEnv)... Activating project at `~/.julia/environments/v1.14` Set-up completed after 9.6s ################################################################################ # Installation # Installing SingleCrystal... Resolving package versions... Updating `~/.julia/environments/v1.14/Project.toml` [3c6eccdf] + SingleCrystal v0.1.1 Updating `~/.julia/environments/v1.14/Manifest.toml` ⌅ [682c06a0] + JSON v0.21.4 [69de0a69] + Parsers v2.8.3 [aea7be01] + PrecompileTools v1.3.3 [21216c6a] + Preferences v1.5.0 [3c6eccdf] + SingleCrystal v0.1.1 [56f22d72] + Artifacts v1.11.0 [ade2ca70] + Dates v1.11.0 [8f399da3] + Libdl v1.11.0 [37e2e46d] + LinearAlgebra v1.13.0 [a63ad114] + Mmap v1.11.0 [de0858da] + Printf v1.11.0 [9a3f8284] + Random v1.11.0 [ea8e919c] + SHA v1.0.0 [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 v5.15.0+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 To see why use `status --outdated -m` Installation completed after 3.82s ################################################################################ # Precompilation # ERROR: LoadError: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 13.65s ################################################################################ # Testing # Testing SingleCrystal Status `/tmp/jl_fXUfjO/Project.toml` [a93c6f00] DataFrames v1.8.1 ⌅ [682c06a0] JSON v0.21.4 [3c6eccdf] SingleCrystal v0.1.1 [37e2e46d] LinearAlgebra v1.13.0 [9a3f8284] Random v1.11.0 [8dfed614] Test v1.11.0 Status `/tmp/jl_fXUfjO/Manifest.toml` [34da2185] Compat v4.18.1 [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 [842dd82b] InlineStrings v1.4.5 [41ab1584] InvertedIndices v1.3.1 [82899510] IteratorInterfaceExtensions v1.0.0 ⌅ [682c06a0] JSON v0.21.4 [b964fa9f] LaTeXStrings v1.4.0 [e1d29d7a] Missings v1.2.0 [bac558e1] OrderedCollections v1.8.1 [69de0a69] Parsers v2.8.3 [2dfb63ee] PooledArrays v1.4.3 [aea7be01] PrecompileTools v1.3.3 [21216c6a] Preferences v1.5.0 [08abe8d2] PrettyTables v3.1.2 [189a3867] Reexport v1.2.2 [91c51154] SentinelArrays v1.4.8 [3c6eccdf] SingleCrystal v0.1.1 [a2af1166] SortingAlgorithms v1.2.2 [10745b16] Statistics v1.11.1 [892a3eda] StringManipulation v0.4.2 [3783bdb8] TableTraits v1.0.1 [bd369af6] Tables v1.12.1 [56f22d72] Artifacts v1.11.0 [2a0f44e3] Base64 v1.11.0 [ade2ca70] Dates v1.11.0 [7b1f6079] FileWatching v1.11.0 [9fa8497b] Future v1.11.0 [b77e0a4c] InteractiveUtils v1.11.0 [ac6e5ff7] JuliaSyntaxHighlighting v1.13.0 [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 [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 [6462fe0b] Sockets v1.11.0 [f489334b] StyledStrings v1.13.0 [fa267f1f] TOML v1.0.3 [8dfed614] Test v1.11.0 [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 v5.15.0+0 Info Packages marked with ⌅ have new versions available but compatibility constraints restrict them from upgrading. Testing Running tests... ┌ Warning: The call to compilecache failed to create a usable precompiled cache file for SingleCrystal [3c6eccdf-2a89-4c24-a1d4-ff210daa8476] │ exception = Required dependency Base.PkgId(Base.UUID("21216c6a-2e73-6563-6e65-726566657250"), "Preferences") failed to load from a cache file. └ @ Base loading.jl:2891 ┌ Warning: The call to compilecache failed to create a usable precompiled cache file for DataFrames [a93c6f00-e57d-5684-b7b6-d8193f3e46c0] │ exception = Required dependency Base.PkgId(Base.UUID("10745b16-79ce-11e8-11f9-7d13ad32a3b2"), "Statistics") failed to load from a cache file. └ @ Base loading.jl:2891 Test Summary: | Pass Total Time fcc/bcc unit cell->super cell->vacancy | 20 20 16.4s bcc: Error During Test at /home/pkgeval/.julia/packages/SingleCrystal/aJwhe/test/runtests.jl:95 Got exception outside of a @test BoundsError: attempt to access 2484×1 DataFrame at index [!, 139473205982896] Stacktrace: [1] getindex @ ~/.julia/packages/DataFrames/b4w9K/src/dataframe/dataframe.jl:551 [inlined] [2] isagg @ ~/.julia/packages/DataFrames/b4w9K/src/groupeddataframe/fastaggregates.jl:290 [inlined] [3] (::DataFrames.var"#_combine##0#_combine##1"{GroupedDataFrame{DataFrame}})(x::Pair{Int64, Pair{typeof(length), Symbol}}) @ DataFrames ~/.julia/packages/DataFrames/b4w9K/src/groupeddataframe/splitapplycombine.jl:690 [4] _any(f::DataFrames.var"#_combine##0#_combine##1"{GroupedDataFrame{DataFrame}}, itr::Vector{Any}, ::Colon) @ Base ./anyall.jl:124 [5] any @ ./reducedim.jl:993 [inlined] [6] _combine(gd::GroupedDataFrame{DataFrame}, cs_norm::Vector{Any}, optional_transform::Vector{Bool}, copycols::Bool, keeprows::Bool, renamecols::Bool, threads::Bool) @ DataFrames ~/.julia/packages/DataFrames/b4w9K/src/groupeddataframe/splitapplycombine.jl:690 [7] _combine_prepare_norm(gd::GroupedDataFrame{DataFrame}, cs_vec::Vector{Any}, keepkeys::Bool, ungroup::Bool, copycols::Bool, keeprows::Bool, renamecols::Bool, threads::Bool) @ DataFrames ~/.julia/packages/DataFrames/b4w9K/src/groupeddataframe/splitapplycombine.jl:87 [8] _combine_prepare(gd::GroupedDataFrame{DataFrame}, ::Base.RefValue{Any}; keepkeys::Bool, ungroup::Bool, copycols::Bool, keeprows::Bool, renamecols::Bool, threads::Bool) @ DataFrames ~/.julia/packages/DataFrames/b4w9K/src/groupeddataframe/splitapplycombine.jl:52 [9] _combine_prepare @ ~/.julia/packages/DataFrames/b4w9K/src/groupeddataframe/splitapplycombine.jl:26 [inlined] [10] combine @ ~/.julia/packages/DataFrames/b4w9K/src/groupeddataframe/splitapplycombine.jl:857 [inlined] [11] get_distance_df(cell::SingleCrystal.Cell{Float64}; dist_cutoff::Float64) @ Main ~/.julia/packages/SingleCrystal/aJwhe/test/runtests.jl:84 [12] kwcall(::@NamedTuple{dist_cutoff::Float64}, ::typeof(get_distance_df), cell::SingleCrystal.Cell{Float64}) @ Main ~/.julia/packages/SingleCrystal/aJwhe/test/runtests.jl:79 [13] top-level scope @ ~/.julia/packages/SingleCrystal/aJwhe/test/runtests.jl:91 [14] macro expansion @ /opt/julia/share/julia/stdlib/v1.14/Test/src/Test.jl:1961 [inlined] [15] macro expansion @ ~/.julia/packages/SingleCrystal/aJwhe/test/runtests.jl:96 [inlined] [16] macro expansion @ /opt/julia/share/julia/stdlib/v1.14/Test/src/Test.jl:1961 [inlined] [17] macro expansion @ ~/.julia/packages/SingleCrystal/aJwhe/test/runtests.jl:98 [inlined] [18] include(mapexpr::Function, mod::Module, _path::String) @ Base ./Base.jl:310 [19] top-level scope @ none:6 [20] eval(m::Module, e::Any) @ Core ./boot.jl:489 [21] exec_options(opts::Base.JLOptions) @ Base ./client.jl:310 [22] _start() @ Base ./client.jl:577 fcc: Error During Test at /home/pkgeval/.julia/packages/SingleCrystal/aJwhe/test/runtests.jl:106 Got exception outside of a @test BoundsError: attempt to access 10584×1 DataFrame at index [!, 139473727467984] Stacktrace: [1] getindex @ ~/.julia/packages/DataFrames/b4w9K/src/dataframe/dataframe.jl:551 [inlined] [2] isagg @ ~/.julia/packages/DataFrames/b4w9K/src/groupeddataframe/fastaggregates.jl:290 [inlined] [3] (::DataFrames.var"#_combine##0#_combine##1"{GroupedDataFrame{DataFrame}})(x::Pair{Int64, Pair{typeof(length), Symbol}}) @ DataFrames ~/.julia/packages/DataFrames/b4w9K/src/groupeddataframe/splitapplycombine.jl:690 [4] _any(f::DataFrames.var"#_combine##0#_combine##1"{GroupedDataFrame{DataFrame}}, itr::Vector{Any}, ::Colon) @ Base ./anyall.jl:124 [5] any @ ./reducedim.jl:993 [inlined] [6] _combine(gd::GroupedDataFrame{DataFrame}, cs_norm::Vector{Any}, optional_transform::Vector{Bool}, copycols::Bool, keeprows::Bool, renamecols::Bool, threads::Bool) @ DataFrames ~/.julia/packages/DataFrames/b4w9K/src/groupeddataframe/splitapplycombine.jl:690 [7] _combine_prepare_norm(gd::GroupedDataFrame{DataFrame}, cs_vec::Vector{Any}, keepkeys::Bool, ungroup::Bool, copycols::Bool, keeprows::Bool, renamecols::Bool, threads::Bool) @ DataFrames ~/.julia/packages/DataFrames/b4w9K/src/groupeddataframe/splitapplycombine.jl:87 [8] _combine_prepare(gd::GroupedDataFrame{DataFrame}, ::Base.RefValue{Any}; keepkeys::Bool, ungroup::Bool, copycols::Bool, keeprows::Bool, renamecols::Bool, threads::Bool) @ DataFrames ~/.julia/packages/DataFrames/b4w9K/src/groupeddataframe/splitapplycombine.jl:52 [9] _combine_prepare @ ~/.julia/packages/DataFrames/b4w9K/src/groupeddataframe/splitapplycombine.jl:26 [inlined] [10] combine @ ~/.julia/packages/DataFrames/b4w9K/src/groupeddataframe/splitapplycombine.jl:857 [inlined] [11] get_distance_df(cell::SingleCrystal.Cell{Float64}; dist_cutoff::Float64) @ Main ~/.julia/packages/SingleCrystal/aJwhe/test/runtests.jl:84 [12] kwcall(::@NamedTuple{dist_cutoff::Float64}, ::typeof(get_distance_df), cell::SingleCrystal.Cell{Float64}) @ Main ~/.julia/packages/SingleCrystal/aJwhe/test/runtests.jl:79 [13] top-level scope @ ~/.julia/packages/SingleCrystal/aJwhe/test/runtests.jl:91 [14] macro expansion @ /opt/julia/share/julia/stdlib/v1.14/Test/src/Test.jl:1961 [inlined] [15] macro expansion @ ~/.julia/packages/SingleCrystal/aJwhe/test/runtests.jl:107 [inlined] [16] macro expansion @ /opt/julia/share/julia/stdlib/v1.14/Test/src/Test.jl:1961 [inlined] [17] macro expansion @ ~/.julia/packages/SingleCrystal/aJwhe/test/runtests.jl:109 [inlined] [18] include(mapexpr::Function, mod::Module, _path::String) @ Base ./Base.jl:310 [19] top-level scope @ none:6 [20] eval(m::Module, e::Any) @ Core ./boot.jl:489 [21] exec_options(opts::Base.JLOptions) @ Base ./client.jl:310 [22] _start() @ Base ./client.jl:577 Test Summary: | Error Total Time Neighbours | 2 2 36.8s bcc | 1 1 36.5s fcc | 1 1 0.1s RNG of the outermost testset: Random.Xoshiro(0xbdcadf54182faf9f, 0xf917e6996daa3cbe, 0x904652974767c1b5, 0x36a62ef4e70fa849, 0xf8fd78c717a2c861) ERROR: LoadError: Some tests did not pass: 0 passed, 0 failed, 2 errored, 0 broken. in expression starting at /home/pkgeval/.julia/packages/SingleCrystal/aJwhe/test/runtests.jl:89 Testing failed after 171.33s ERROR: LoadError: Package SingleCrystal errored during testing Stacktrace: [1] pkgerror(msg::String) @ Pkg.Types /opt/julia/share/julia/stdlib/v1.14/Pkg/src/Types.jl:68 [2] test(ctx::Pkg.Types.Context, pkgs::Vector{PackageSpec}; coverage::Bool, julia_args::Cmd, test_args::Cmd, test_fn::Nothing, force_latest_compatible_version::Bool, allow_earlier_backwards_compatible_versions::Bool, allow_reresolve::Bool) @ Pkg.Operations /opt/julia/share/julia/stdlib/v1.14/Pkg/src/Operations.jl:3053 [3] test @ /opt/julia/share/julia/stdlib/v1.14/Pkg/src/Operations.jl:2902 [inlined] [4] test(ctx::Pkg.Types.Context, pkgs::Vector{PackageSpec}; coverage::Bool, test_fn::Nothing, julia_args::Cmd, test_args::Cmd, force_latest_compatible_version::Bool, allow_earlier_backwards_compatible_versions::Bool, allow_reresolve::Bool, kwargs::@Kwargs{io::IOContext{IO}}) @ Pkg.API /opt/julia/share/julia/stdlib/v1.14/Pkg/src/API.jl:572 [5] kwcall(::@NamedTuple{julia_args::Cmd, io::IOContext{IO}}, ::typeof(Pkg.API.test), ctx::Pkg.Types.Context, pkgs::Vector{PackageSpec}) @ Pkg.API /opt/julia/share/julia/stdlib/v1.14/Pkg/src/API.jl:548 [6] test(pkgs::Vector{PackageSpec}; io::IOContext{IO}, kwargs::@Kwargs{julia_args::Cmd}) @ Pkg.API /opt/julia/share/julia/stdlib/v1.14/Pkg/src/API.jl:172 [7] kwcall(::@NamedTuple{julia_args::Cmd}, ::typeof(Pkg.API.test), pkgs::Vector{PackageSpec}) @ Pkg.API /opt/julia/share/julia/stdlib/v1.14/Pkg/src/API.jl:161 [8] test(pkgs::Vector{String}; kwargs::@Kwargs{julia_args::Cmd}) @ Pkg.API /opt/julia/share/julia/stdlib/v1.14/Pkg/src/API.jl:160 [9] test @ /opt/julia/share/julia/stdlib/v1.14/Pkg/src/API.jl:160 [inlined] [10] kwcall(::@NamedTuple{julia_args::Cmd}, ::typeof(Pkg.API.test), pkg::String) @ Pkg.API /opt/julia/share/julia/stdlib/v1.14/Pkg/src/API.jl:159 [11] top-level scope @ /PkgEval.jl/scripts/evaluate.jl:237 [12] include(mod::Module, _path::String) @ Base ./Base.jl:309 [13] exec_options(opts::Base.JLOptions) @ Base ./client.jl:344 [14] _start() @ Base ./client.jl:577 in expression starting at /PkgEval.jl/scripts/evaluate.jl:228 PkgEval failed after 214.33s: package tests unexpectedly errored