Package evaluation to test MolecularGaussians on Julia 1.14.0-DEV.1491 (0e7d18362a*) started at 2026-01-11T14:49:40.552 ################################################################################ # Set-up # Installing PkgEval dependencies (TestEnv)... Activating project at `~/.julia/environments/v1.14` Set-up completed after 10.72s ################################################################################ # Installation # Installing MolecularGaussians... Resolving package versions... Installed Libuuid_jll ───────────────── v2.41.2+0 Installed DiffResults ───────────────── v1.1.0 Installed MacroTools ────────────────── v0.5.16 Installed AbstractTrees ─────────────── v0.4.5 Installed FillArrays ────────────────── v1.15.0 Installed DataStructures ────────────── v0.19.3 Installed Quaternions ───────────────── v0.7.7 Installed ForwardDiff ───────────────── v1.3.1 Installed HarfBuzz_jll ──────────────── v8.5.1+0 Installed Bzip2_jll ─────────────────── v1.0.9+0 Installed MakieCore ─────────────────── v0.7.3 Installed Adapt ─────────────────────── v4.4.0 Installed Extents ───────────────────── v0.1.6 Installed DelimitedFiles ────────────── v1.9.1 Installed ConstructionBase ──────────── v1.6.0 Installed Libmount_jll ──────────────── v2.41.2+0 Installed AliasTables ───────────────── v1.1.3 Installed PairedLinkedLists ─────────── v0.2.3 Installed ArnoldiMethod ─────────────── v0.4.0 Installed Cairo ─────────────────────── v1.1.1 Installed Cairo_jll ─────────────────── v1.18.5+0 Installed Hungarian ─────────────────── v0.7.0 Installed Observables ───────────────── v0.5.5 Installed MolecularGraph ────────────── v0.16.1 Installed StatsBase ─────────────────── v0.34.9 Installed Optim ─────────────────────── v1.13.3 Installed Xorg_libXau_jll ───────────── v1.0.13+0 Installed Xorg_libX11_jll ───────────── v1.8.12+0 Installed IteratorInterfaceExtensions ─ v1.0.0 Installed OrderedCollections ────────── v1.8.1 Installed Compat ────────────────────── v4.18.1 Installed ArrayInterface ────────────── v7.22.0 Installed RecipesBase ───────────────── v1.3.4 Installed NearestNeighbors ──────────── v0.4.26 Installed Graphite2_jll ─────────────── v1.3.15+0 Installed EarCut_jll ────────────────── v2.2.4+0 Installed Statistics ────────────────── v1.11.1 Installed DataAPI ───────────────────── v1.16.0 Installed StatsAPI ──────────────────── v1.8.0 Installed PositiveFactorizations ────── v0.2.4 Installed Quadmath ──────────────────── v0.5.13 Installed StructArrays ──────────────── v0.6.21 Installed PrecompileTools ───────────── v1.3.3 Installed DataValueInterfaces ───────── v1.0.0 Installed StringEncodings ───────────── v0.3.7 Installed CommonSubexpressions ──────── v0.3.1 Installed CoordinateTransformations ─── v0.6.4 Installed Libffi_jll ────────────────── v3.4.7+0 Installed DoubleFloats ──────────────── v1.5.0 Installed StaticArrays ──────────────── v1.9.16 Installed Colors ────────────────────── v0.12.11 Installed Pixman_jll ────────────────── v0.44.2+0 Installed StaticArraysCore ──────────── v1.4.4 Installed Expat_jll ─────────────────── v2.7.3+0 Installed Fontconfig_jll ────────────── v2.17.1+0 Installed IrrationalConstants ───────── v0.2.6 Installed RealDot ───────────────────── v0.1.0 Installed Distances ─────────────────── v0.10.12 Installed GettextRuntime_jll ────────── v0.22.4+0 Installed libpng_jll ────────────────── v1.6.53+0 Installed FriBidi_jll ───────────────── v1.0.17+0 Installed NaNMath ───────────────────── v1.1.3 Installed Graphics ──────────────────── v1.1.3 Installed GenericLinearAlgebra ──────── v0.3.19 Installed ColorTypes ────────────────── v0.11.5 Installed SimpleTraits ──────────────── v0.9.5 Installed OpenSpecFun_jll ───────────── v0.5.6+0 Installed Glib_jll ──────────────────── v2.86.2+0 Installed coordgenlibs_jll ──────────── v3.0.2+0 Installed YAML ──────────────────────── v0.4.16 Installed Requires ──────────────────── v1.3.1 Installed LogExpFunctions ───────────── v0.3.29 Installed DiffRules ─────────────────── v1.15.1 Installed libinchi_jll ──────────────── v1.6.0+0 Installed Xorg_libXrender_jll ───────── v0.9.12+0 Installed Parsers ───────────────────── v2.8.3 Installed JSON ──────────────────────── v0.21.4 Installed FiniteDiff ────────────────── v2.29.0 Installed MutableConvexHulls ────────── v0.2.6 Installed GeoFormatTypes ────────────── v0.4.5 Installed Tables ────────────────────── v1.12.1 Installed GaussianMixtureAlignment ──── v0.2.2 Installed Xorg_libxcb_jll ───────────── v1.17.1+0 Installed PtrArrays ─────────────────── v1.3.0 Installed EnumX ─────────────────────── v1.0.5 Installed Xorg_libXdmcp_jll ─────────── v1.1.6+0 Installed NLSolversBase ─────────────── v7.10.0 Installed LZO_jll ───────────────────── v2.10.3+0 Installed SpecialFunctions ──────────── v2.6.1 Installed Reexport ──────────────────── v1.2.2 Installed FreeType2_jll ─────────────── v2.13.4+0 Installed Missings ──────────────────── v1.2.0 Installed FixedPointNumbers ─────────── v0.8.5 Installed Setfield ──────────────────── v1.1.2 Installed JLLWrappers ───────────────── v1.7.1 Installed Preferences ───────────────── v1.5.1 Installed Rotations ─────────────────── v1.7.1 Installed Libiconv_jll ──────────────── v1.18.0+0 Installed TableTraits ───────────────── v1.0.1 Installed LLVMOpenMP_jll ────────────── v18.1.8+0 Installed Polynomials ───────────────── v4.1.0 Installed SortingAlgorithms ─────────── v1.2.2 Installed Xorg_libXext_jll ──────────── v1.3.7+0 Installed LineSearches ──────────────── v7.5.1 Installed GeometryBasics ────────────── v0.4.11 Installed Pango_jll ─────────────────── v1.57.0+0 Installed IterTools ─────────────────── v1.10.0 Installed GeoInterface ──────────────── v1.4.1 Installed Graphs ────────────────────── v1.13.3 Installed ADTypes ───────────────────── v1.21.0 Installed Xorg_xtrans_jll ───────────── v1.6.0+0 Installed DocStringExtensions ───────── v0.9.5 Installed Inflate ───────────────────── v0.1.5 Installed DifferentiationInterface ──── v0.7.13 Installed MolecularGaussians ────────── v0.3.3 Installing 30 artifacts Installed artifact Xorg_libXau 36.6 KiB Installed artifact Xorg_libXdmcp 67.7 KiB Installed artifact Pixman 372.2 KiB Installed artifact libpng 329.0 KiB Installed artifact LLVMOpenMP 661.6 KiB Installed artifact Xorg_libXext 699.9 KiB Installed artifact EarCut 80.5 KiB Installed artifact Xorg_libxcb 2.1 MiB Installed artifact coordgenlibs 303.6 KiB Installed artifact FreeType2 1.5 MiB Installed artifact Fontconfig 984.8 KiB Installed artifact Cairo 2.2 MiB Installed artifact Libffi 44.2 KiB Installed artifact GettextRuntime 543.0 KiB Installed artifact libinchi 933.4 KiB Installed artifact Expat 283.3 KiB Installed artifact Xorg_libXrender 435.9 KiB Installed artifact Bzip2 503.5 KiB Installed artifact Libmount 6.5 MiB Installed artifact FriBidi 78.9 KiB Installed artifact OpenSpecFun 194.9 KiB Installed artifact Xorg_xtrans 48.2 KiB Installed artifact HarfBuzz 1.7 MiB Installed artifact Pango 2.0 MiB Installed artifact Graphite2 120.2 KiB Installed artifact LZO 208.9 KiB Installed artifact Libuuid 3.7 MiB Installed artifact Libiconv 1.9 MiB Installed artifact Xorg_libX11 13.9 MiB Installed artifact Glib 7.7 MiB Updating `~/.julia/environments/v1.14/Project.toml` [be997a16] + MolecularGaussians v0.3.3 Updating `~/.julia/environments/v1.14/Manifest.toml` [47edcb42] + ADTypes v1.21.0 [1520ce14] + AbstractTrees v0.4.5 [79e6a3ab] + Adapt v4.4.0 [66dad0bd] + AliasTables v1.1.3 [ec485272] + ArnoldiMethod v0.4.0 [4fba245c] + ArrayInterface v7.22.0 [159f3aea] + Cairo v1.1.1 ⌅ [3da002f7] + ColorTypes v0.11.5 ⌅ [5ae59095] + Colors v0.12.11 [bbf7d656] + CommonSubexpressions v0.3.1 [34da2185] + Compat v4.18.1 [187b0558] + ConstructionBase v1.6.0 [150eb455] + CoordinateTransformations v0.6.4 [9a962f9c] + DataAPI v1.16.0 [864edb3b] + DataStructures v0.19.3 [e2d170a0] + DataValueInterfaces v1.0.0 [8bb1440f] + DelimitedFiles v1.9.1 [163ba53b] + DiffResults v1.1.0 [b552c78f] + DiffRules v1.15.1 [a0c0ee7d] + DifferentiationInterface v0.7.13 [b4f34e82] + Distances v0.10.12 [ffbed154] + DocStringExtensions v0.9.5 [497a8b3b] + DoubleFloats v1.5.0 [4e289a0a] + EnumX v1.0.5 [411431e0] + Extents v0.1.6 [1a297f60] + FillArrays v1.15.0 [6a86dc24] + FiniteDiff v2.29.0 [53c48c17] + FixedPointNumbers v0.8.5 [f6369f11] + ForwardDiff v1.3.1 ⌅ [f2431ed1] + GaussianMixtureAlignment v0.2.2 [14197337] + GenericLinearAlgebra v0.3.19 [68eda718] + GeoFormatTypes v0.4.5 ⌃ [cf35fbd7] + GeoInterface v1.4.1 ⌅ [5c1252a2] + 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Preferences v1.5.1 [43287f4e] + PtrArrays v1.3.0 [be4d8f0f] + Quadmath v0.5.13 [94ee1d12] + Quaternions v0.7.7 [c1ae055f] + RealDot v0.1.0 [3cdcf5f2] + RecipesBase v1.3.4 [189a3867] + Reexport v1.2.2 [ae029012] + Requires v1.3.1 [6038ab10] + Rotations v1.7.1 [efcf1570] + Setfield v1.1.2 [699a6c99] + SimpleTraits v0.9.5 [a2af1166] + SortingAlgorithms v1.2.2 [276daf66] + SpecialFunctions v2.6.1 [90137ffa] + StaticArrays v1.9.16 [1e83bf80] + StaticArraysCore v1.4.4 [10745b16] + Statistics v1.11.1 [82ae8749] + StatsAPI v1.8.0 [2913bbd2] + StatsBase v0.34.9 [69024149] + StringEncodings v0.3.7 ⌅ [09ab397b] + StructArrays v0.6.21 [3783bdb8] + TableTraits v1.0.1 [bd369af6] + Tables v1.12.1 [ddb6d928] + YAML v0.4.16 [6e34b625] + Bzip2_jll v1.0.9+0 [83423d85] + Cairo_jll v1.18.5+0 [5ae413db] + EarCut_jll v2.2.4+0 [2e619515] + Expat_jll v2.7.3+0 [a3f928ae] + Fontconfig_jll v2.17.1+0 [d7e528f0] + FreeType2_jll v2.13.4+0 [559328eb] + FriBidi_jll v1.0.17+0 [b0724c58] + GettextRuntime_jll v0.22.4+0 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v0.8.7+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 v1.68.0+1 [3f19e933] + p7zip_jll v17.7.0+0 Info Packages marked with ⌃ and ⌅ have new versions available. Those with ⌃ may be upgradable, but those with ⌅ are restricted by compatibility constraints from upgrading. To see why use `status --outdated -m` Installation completed after 17.9s ################################################################################ # 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:585 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:585 Precompilation failed after 14.15s ################################################################################ # Testing # Testing MolecularGaussians Status `/tmp/jl_EeFTtr/Project.toml` ⌅ [5ae59095] Colors v0.12.11 [150eb455] CoordinateTransformations v0.6.4 ⌅ [f2431ed1] GaussianMixtureAlignment v0.2.2 ⌅ [5c1252a2] GeometryBasics v0.4.11 [86223c79] Graphs v1.13.3 ⌅ [20f20a25] MakieCore v0.7.3 [be997a16] MolecularGaussians v0.3.3 ⌅ [6c89ec66] MolecularGraph v0.16.1 ⌅ [429524aa] Optim v1.13.3 [6038ab10] Rotations v1.7.1 [90137ffa] StaticArrays v1.9.16 [37e2e46d] LinearAlgebra v1.13.0 [8dfed614] Test v1.11.0 Status `/tmp/jl_EeFTtr/Manifest.toml` [47edcb42] ADTypes v1.21.0 [1520ce14] AbstractTrees v0.4.5 [79e6a3ab] Adapt v4.4.0 [66dad0bd] AliasTables v1.1.3 [ec485272] ArnoldiMethod v0.4.0 [4fba245c] ArrayInterface v7.22.0 [159f3aea] Cairo v1.1.1 ⌅ [3da002f7] ColorTypes v0.11.5 ⌅ [5ae59095] Colors v0.12.11 [bbf7d656] CommonSubexpressions v0.3.1 [34da2185] Compat v4.18.1 [187b0558] ConstructionBase v1.6.0 [150eb455] CoordinateTransformations v0.6.4 [9a962f9c] DataAPI v1.16.0 [864edb3b] DataStructures v0.19.3 [e2d170a0] DataValueInterfaces v1.0.0 [8bb1440f] DelimitedFiles v1.9.1 [163ba53b] DiffResults v1.1.0 [b552c78f] DiffRules v1.15.1 [a0c0ee7d] DifferentiationInterface v0.7.13 [b4f34e82] Distances v0.10.12 [ffbed154] DocStringExtensions v0.9.5 [497a8b3b] DoubleFloats v1.5.0 [4e289a0a] EnumX v1.0.5 [411431e0] Extents v0.1.6 [1a297f60] FillArrays v1.15.0 [6a86dc24] FiniteDiff v2.29.0 [53c48c17] FixedPointNumbers v0.8.5 [f6369f11] ForwardDiff v1.3.1 ⌅ [f2431ed1] GaussianMixtureAlignment v0.2.2 [14197337] GenericLinearAlgebra v0.3.19 [68eda718] GeoFormatTypes v0.4.5 ⌃ [cf35fbd7] GeoInterface v1.4.1 ⌅ [5c1252a2] GeometryBasics v0.4.11 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v1.68.0+1 [3f19e933] p7zip_jll v17.7.0+0 Info Packages marked with ⌃ and ⌅ have new versions available. Those with ⌃ may be upgradable, but those with ⌅ are restricted by compatibility constraints from upgrading. Testing Running tests... Test Summary: | Pass Total Time Gaussian Mixture Distance | 5 5 49.4s Test Summary: | Pass Total Time PharmacophoreGMM alignment | 3 3 27.9s Testing MolecularGaussians tests passed Testing completed after 496.28s PkgEval succeeded after 576.46s