Package evaluation of Xtals on Julia 1.11.4 (a71dd056e0*) started at 2025-04-08T14:20:15.038 ################################################################################ # Set-up # Installing PkgEval dependencies (TestEnv)... Set-up completed after 8.74s ################################################################################ # Installation # Installing Xtals... Resolving package versions... Updating `~/.julia/environments/v1.11/Project.toml` [ede5f01d] + Xtals v0.5.1 Updating `~/.julia/environments/v1.11/Manifest.toml` [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 [a8cc5b0e] + Crayons v4.1.1 [9a962f9c] + DataAPI v1.16.0 [a93c6f00] + DataFrames v1.7.0 [864edb3b] + DataStructures v0.18.22 [e2d170a0] + DataValueInterfaces v1.0.0 [5789e2e9] + FileIO v1.17.0 [48062228] + FilePathsBase v0.9.24 [86223c79] + Graphs v1.12.1 [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 [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 [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 [ea10d353] + WeakRefStrings v1.4.2 [76eceee3] + WorkerUtilities v1.6.1 [ede5f01d] + Xtals v0.5.1 [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 v1.6.0 [7b1f6079] + FileWatching v1.11.0 [9fa8497b] + Future v1.11.0 [b77e0a4c] + InteractiveUtils v1.11.0 [b27032c2] + LibCURL v0.6.4 [76f85450] + LibGit2 v1.11.0 [8f399da3] + Libdl v1.11.0 [37e2e46d] + LinearAlgebra v1.11.0 [56ddb016] + Logging v1.11.0 [d6f4376e] + Markdown v1.11.0 [a63ad114] + Mmap v1.11.0 [ca575930] + NetworkOptions v1.2.0 [44cfe95a] + Pkg v1.11.0 [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 v1.11.0 [fa267f1f] + TOML v1.0.3 [a4e569a6] + Tar v1.10.0 [cf7118a7] + UUIDs v1.11.0 [4ec0a83e] + Unicode v1.11.0 [e66e0078] + CompilerSupportLibraries_jll v1.1.1+0 [deac9b47] + LibCURL_jll v8.6.0+0 [e37daf67] + LibGit2_jll v1.7.2+0 [29816b5a] + LibSSH2_jll v1.11.0+1 [c8ffd9c3] + MbedTLS_jll v2.28.6+0 [14a3606d] + MozillaCACerts_jll v2023.12.12 [4536629a] + OpenBLAS_jll v0.3.27+1 [bea87d4a] + SuiteSparse_jll v7.7.0+0 [83775a58] + Zlib_jll v1.2.13+1 [8e850b90] + libblastrampoline_jll v5.11.0+0 [8e850ede] + nghttp2_jll v1.59.0+0 [3f19e933] + p7zip_jll v17.4.0+2 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 2.38s ################################################################################ # Precompilation # Precompiling PkgEval dependencies... Precompiling package dependencies... Precompilation completed after 121.83s ################################################################################ # Testing # Testing Xtals Status `/tmp/jl_UBaJs9/Project.toml` [4c88cf16] Aqua v0.8.11 ⌅ [a963bdd2] AtomsBase v0.4.2 [336ed68f] CSV v0.10.15 [a93c6f00] DataFrames v1.7.0 [e30172f5] Documenter v1.10.1 [86223c79] Graphs v1.12.1 [b5f81e59] IOCapture v0.2.5 ⌅ [626554b9] MetaGraphs v0.7.2 [ede5f01d] Xtals v0.5.1 [37e2e46d] LinearAlgebra v1.11.0 [56ddb016] Logging v1.11.0 [8dfed614] Test v1.11.0 Status `/tmp/jl_UBaJs9/Manifest.toml` [a4c015fc] ANSIColoredPrinters v0.0.1 [1520ce14] AbstractTrees v0.4.5 [4c88cf16] Aqua v0.8.11 [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 [a8cc5b0e] Crayons v4.1.1 [9a962f9c] DataAPI v1.16.0 [a93c6f00] DataFrames v1.7.0 [864edb3b] DataStructures v0.18.22 [e2d170a0] DataValueInterfaces v1.0.0 [ffbed154] DocStringExtensions v0.9.4 [e30172f5] Documenter v1.10.1 [5789e2e9] FileIO v1.17.0 [48062228] FilePathsBase v0.9.24 [d7ba0133] Git v1.3.1 [86223c79] Graphs v1.12.1 [b5f81e59] IOCapture v0.2.5 [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 [692b3bcd] JLLWrappers v1.7.0 [682c06a0] JSON v0.21.4 [b964fa9f] LaTeXStrings v1.4.0 [0e77f7df] LazilyInitializedFields v1.3.0 [1914dd2f] MacroTools v0.5.15 [d0879d2d] MarkdownAST v0.1.2 ⌅ [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 [189a3867] Reexport v1.2.2 [2792f1a3] RegistryInstances v0.1.0 [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 [ea10d353] WeakRefStrings v1.4.2 [76eceee3] WorkerUtilities v1.6.1 [ede5f01d] Xtals v0.5.1 [2e619515] Expat_jll v2.6.5+0 [f8c6e375] Git_jll v2.49.0+0 [94ce4f54] Libiconv_jll v1.18.0+0 [458c3c95] OpenSSL_jll v3.0.16+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 v1.6.0 [7b1f6079] FileWatching v1.11.0 [9fa8497b] Future v1.11.0 [b77e0a4c] InteractiveUtils v1.11.0 [b27032c2] LibCURL v0.6.4 [76f85450] LibGit2 v1.11.0 [8f399da3] Libdl v1.11.0 [37e2e46d] LinearAlgebra v1.11.0 [56ddb016] Logging v1.11.0 [d6f4376e] Markdown v1.11.0 [a63ad114] Mmap v1.11.0 [ca575930] NetworkOptions v1.2.0 [44cfe95a] Pkg v1.11.0 [de0858da] Printf v1.11.0 [3fa0cd96] REPL 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 v1.11.0 [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 v1.1.1+0 [deac9b47] LibCURL_jll v8.6.0+0 [e37daf67] LibGit2_jll v1.7.2+0 [29816b5a] LibSSH2_jll v1.11.0+1 [c8ffd9c3] MbedTLS_jll v2.28.6+0 [14a3606d] MozillaCACerts_jll v2023.12.12 [4536629a] OpenBLAS_jll v0.3.27+1 [efcefdf7] PCRE2_jll v10.42.0+1 [bea87d4a] SuiteSparse_jll v7.7.0+0 [83775a58] Zlib_jll v1.2.13+1 [8e850b90] libblastrampoline_jll v5.11.0+0 [8e850ede] nghttp2_jll v1.59.0+0 [3f19e933] p7zip_jll v17.4.0+2 Info Packages marked with ⌅ have new versions available but compatibility constraints restrict them from upgrading. Testing Running tests... Precompiling Xtals... 5398.7 ms ✓ AtomsBase Info Given Xtals was explicitly requested, output will be shown live  WARNING: could not import AtomsBase.boundary_conditions into Xtals WARNING: could not import AtomsBase.species_type into Xtals 108312.6 ms ✓ Xtals 2 dependencies successfully precompiled in 116 seconds. 82 already precompiled. 1 dependency had output during precompilation: ┌ Xtals │ [Output was shown above] └ ___ ___ _________ ________ ___ ________ |\ \ / /|\___ ___\\ __ \|\ \ |\ ____\ \ \ \/ / ||___ \ \_\ \ \|\ \ \ \ \ \ \___|_ \ \ / / \ \ \ \ \ __ \ \ \ \ \_____ \ / \/ \ \ \ \ \ \ \ \ \ \____\|____|\ \ / /\ \ \ \__\ \ \__\ \__\ \_______\____\_\ \ /__/ /\ __\ \|__| \|__|\|__|\|_______|\_________\ |__|/ \|__| \|_________| [ Info: Running test/crystal.jl Test Summary: | Pass Total Time test data loading | 1 1 1.3s Test Summary: | Pass Total Time comparisons | 2 2 4.0s Test Summary: | Pass Total Time symmetry | 23 23 24.0s printing: Error During Test at /home/pkgeval/.julia/packages/Xtals/paV65/test/crystal.jl:151 Got exception outside of a @test MethodError: no method matching atomic_number(::Atoms{Frac}) The function `atomic_number` exists, but no method is defined for this combination of argument types. Closest candidates are: atomic_number(!Matched::Crystal) @ Xtals ~/.julia/packages/Xtals/paV65/src/crystal.jl:1362 atomic_number(!Matched::Symbol) @ AtomsBase ~/.julia/packages/AtomsBase/pcOuK/src/utils/chemspecies.jl:143 atomic_number(!Matched::AtomsBase.ChemicalSpecies) @ AtomsBase ~/.julia/packages/AtomsBase/pcOuK/src/utils/chemspecies.jl:139 ... Stacktrace: [1] element_symbol(species::Atoms{Frac}) @ AtomsBase ~/.julia/packages/AtomsBase/pcOuK/src/utils/chemspecies.jl:190 [2] _broadcast_getindex_evalf @ ./broadcast.jl:678 [inlined] [3] _broadcast_getindex @ ./broadcast.jl:651 [inlined] [4] getindex @ ./broadcast.jl:610 [inlined] [5] copy @ ./broadcast.jl:911 [inlined] [6] materialize @ ./broadcast.jl:872 [inlined] [7] element_symbol @ ~/.julia/packages/AtomsBase/pcOuK/src/utils/chemspecies.jl:187 [inlined] [8] chemical_formula(system::Crystal) @ AtomsBase ~/.julia/packages/AtomsBase/pcOuK/src/utils/properties.jl:20 [9] chemical_formula(crystal::Crystal) @ Xtals ~/.julia/packages/Xtals/paV65/src/crystal.jl:1389 [10] show(io::Base.DevNull, crystal::Crystal) @ Xtals ~/.julia/packages/Xtals/paV65/src/crystal.jl:1230 [11] println(io::Base.DevNull, xtal::Crystal) @ Xtals ~/.julia/packages/Xtals/paV65/src/crystal.jl:1216 [12] macro expansion @ ~/.julia/packages/Xtals/paV65/test/crystal.jl:153 [inlined] [13] macro expansion @ /opt/julia/share/julia/stdlib/v1.11/Test/src/Test.jl:1704 [inlined] [14] top-level scope @ ~/.julia/packages/Xtals/paV65/test/crystal.jl:153 [15] include @ ./sysimg.jl:38 [inlined] [16] #1 @ ~/.julia/packages/Xtals/paV65/test/runtests.jl:21 [inlined] [17] with_logstate(f::var"#1#2"{String}, logstate::Base.CoreLogging.LogState) @ Base.CoreLogging ./logging/logging.jl:522 [18] with_logger(f::Function, logger::Base.CoreLogging.NullLogger) @ Base.CoreLogging ./logging/logging.jl:632 [19] top-level scope @ ~/.julia/packages/Xtals/paV65/test/runtests.jl:20 [20] include(fname::String) @ Main ./sysimg.jl:38 [21] top-level scope @ none:6 [22] eval @ ./boot.jl:430 [inlined] [23] exec_options(opts::Base.JLOptions) @ Base ./client.jl:296 [24] _start() @ Base ./client.jl:531 Test Summary: | Error Total Time printing | 1 1 7.9s ERROR: LoadError: Some tests did not pass: 0 passed, 0 failed, 1 errored, 0 broken. in expression starting at /home/pkgeval/.julia/packages/Xtals/paV65/test/crystal.jl:1 in expression starting at /home/pkgeval/.julia/packages/Xtals/paV65/test/runtests.jl:18 Testing failed after 239.48s ERROR: LoadError: Package Xtals errored during testing Stacktrace: [1] pkgerror(msg::String) @ Pkg.Types /opt/julia/share/julia/stdlib/v1.11/Pkg/src/Types.jl:68 [2] test(ctx::Pkg.Types.Context, pkgs::Vector{Pkg.Types.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/v1.11/Pkg/src/Operations.jl:2124 [3] test @ /opt/julia/share/julia/stdlib/v1.11/Pkg/src/Operations.jl:2007 [inlined] [4] test(ctx::Pkg.Types.Context, pkgs::Vector{Pkg.Types.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/v1.11/Pkg/src/API.jl:481 [5] test(pkgs::Vector{Pkg.Types.PackageSpec}; io::IOContext{IO}, kwargs::@Kwargs{julia_args::Cmd}) @ Pkg.API /opt/julia/share/julia/stdlib/v1.11/Pkg/src/API.jl:159 [6] test @ /opt/julia/share/julia/stdlib/v1.11/Pkg/src/API.jl:147 [inlined] [7] #test#74 @ /opt/julia/share/julia/stdlib/v1.11/Pkg/src/API.jl:146 [inlined] [8] top-level scope @ /PkgEval.jl/scripts/evaluate.jl:219 in expression starting at /PkgEval.jl/scripts/evaluate.jl:210 PkgEval failed after 391.58s: package tests unexpectedly errored