Package evaluation to test ProteinEnsembles on Julia 1.14.0-DEV.1523 (e57442f29c*) started at 2026-01-12T08:00:11.617 ################################################################################ # Set-up # Installing PkgEval dependencies (TestEnv)... Activating project at `~/.julia/environments/v1.14` Set-up completed after 9.55s ################################################################################ # Installation # Installing ProteinEnsembles... Resolving package versions... Installed Libuuid_jll ───────────── v2.41.2+0 Installed HarfBuzz_jll ──────────── v8.5.1+0 Installed Rmath_jll ─────────────── v0.5.1+0 Installed Bzip2_jll ─────────────── v1.0.9+0 Installed Adapt ─────────────────── v4.4.0 Installed FillArrays ────────────── v1.15.0 Installed LazyGrids ─────────────── v0.5.0 Installed DataStructures ────────── v0.18.22 Installed KernelDensity ─────────── v0.6.10 Installed MKL_jll ───────────────── v2025.2.0+0 Installed Libmount_jll ──────────── v2.41.2+0 Installed HypergeometricFunctions ─ v0.3.28 Installed oneTBB_jll ────────────── v2022.0.0+1 Installed AliasTables ───────────── v1.1.3 Installed Cairo_jll ─────────────── v1.18.5+0 Installed Cairo ─────────────────── v1.1.1 Installed Xorg_libXau_jll ───────── v1.0.13+0 Installed OrderedCollections ────── v1.8.1 Installed StatsBase ─────────────── v0.34.9 Installed Compat ────────────────── v4.18.1 Installed Xorg_libX11_jll ───────── v1.8.12+0 Installed Graphite2_jll ─────────── v1.3.15+0 Installed DataAPI ───────────────── v1.16.0 Installed Statistics ────────────── v1.11.1 Installed Loess ─────────────────── v0.6.5 Installed StatsAPI ──────────────── v1.8.0 Installed IntelOpenMP_jll ───────── v2025.2.0+0 Installed CoupledFields ─────────── v0.3.0 Installed PrecompileTools ───────── v1.3.3 Installed ProgressMeter ─────────── v1.11.0 Installed Measures ──────────────── v0.3.3 Installed OffsetArrays ──────────── v1.17.0 Installed Colors ────────────────── v0.12.11 Installed Libffi_jll ────────────── v3.4.7+0 Installed TextWrap ──────────────── v1.0.2 Installed StaticArrays ──────────── v1.9.16 Installed StaticArraysCore ──────── v1.4.4 Installed Fontconfig_jll ────────── v2.17.1+0 Installed Pixman_jll ────────────── v0.44.2+0 Installed Expat_jll ─────────────── v2.7.3+0 Installed IrrationalConstants ───── v0.2.6 Installed Distances ─────────────── v0.10.12 Installed AbstractFFTs ──────────── v1.5.0 Installed ChainRulesCore ────────── v1.26.0 Installed QuadGK ────────────────── v2.11.2 Installed GettextRuntime_jll ────── v0.22.4+0 Installed Contour ───────────────── v0.6.3 Installed ColorTypes ────────────── v0.11.5 Installed libpng_jll ────────────── v1.6.53+0 Installed Ratios ────────────────── v0.4.5 Installed AxisAlgorithms ────────── v1.1.0 Installed NaNMath ───────────────── v1.1.3 Installed FriBidi_jll ───────────── v1.0.17+0 Installed Glib_jll ──────────────── v2.86.2+0 Installed Graphics ──────────────── v1.1.3 Installed OpenSpecFun_jll ───────── v0.5.6+0 Installed Requires ──────────────── v1.3.1 Installed ArgParse ──────────────── v1.2.0 Installed Interpolations ────────── v0.16.2 Installed Parsers ───────────────── v2.8.3 Installed Xorg_libXrender_jll ───── v0.9.12+0 Installed LogExpFunctions ───────── v0.3.29 Installed Rmath ─────────────────── v0.9.0 Installed JSON ──────────────────── v0.21.4 Installed ProteinEnsembles ──────── v0.3.1 Installed Distributions ─────────── v0.25.123 Installed Xorg_libxcb_jll ───────── v1.17.1+0 Installed PtrArrays ─────────────── v1.3.0 Installed WoodburyMatrices ──────── v1.1.0 Installed Xorg_libXdmcp_jll ─────── v1.1.6+0 Installed StatsFuns ─────────────── v1.5.2 Installed Reexport ──────────────── v1.2.2 Installed SpecialFunctions ──────── v2.6.1 Installed LZO_jll ───────────────── v2.10.3+0 Installed FFTW_jll ──────────────── v3.3.11+0 Installed FreeType2_jll ─────────── v2.13.4+0 Installed Missings ──────────────── v1.2.0 Installed Showoff ───────────────── v1.0.3 Installed FixedPointNumbers ─────── v0.8.5 Installed FFTW ──────────────────── v1.10.0 Installed Preferences ───────────── v1.5.1 Installed JLLWrappers ───────────── v1.7.1 Installed Libiconv_jll ──────────── v1.18.0+0 Installed LLVMOpenMP_jll ────────── v18.1.8+0 Installed Xorg_libXext_jll ──────── v1.3.7+0 Installed PDMats ────────────────── v0.11.37 Installed IndirectArrays ────────── v1.0.0 Installed Pango_jll ─────────────── v1.57.0+0 Installed SortingAlgorithms ─────── v1.2.2 Installed Hexagons ──────────────── v0.2.0 Installed IterTools ─────────────── v1.10.0 Installed Gadfly ────────────────── v1.4.1 Installed Grisu ─────────────────── v1.0.2 Installed CategoricalArrays ─────── v0.10.8 Installed Xorg_xtrans_jll ───────── v1.6.0+0 Installed DocStringExtensions ───── v0.9.5 Installed Compose ───────────────── v0.9.6 Installing 29 artifacts Installed artifact Xorg_libXdmcp 67.7 KiB Installed artifact Rmath 121.9 KiB Installed artifact LLVMOpenMP 661.6 KiB Installed artifact Xorg_libXext 699.9 KiB Installed artifact Cairo 2.2 MiB Installed artifact Expat 283.3 KiB Installed artifact Pango 2.0 MiB Installed artifact Fontconfig 984.8 KiB Installed artifact Xorg_xtrans 48.2 KiB Installed artifact Bzip2 503.5 KiB Installed artifact Libffi 44.2 KiB Installed artifact Libiconv 1.9 MiB Installed artifact Graphite2 120.2 KiB Installed artifact Pixman 372.2 KiB Installed artifact FreeType2 1.5 MiB Installed artifact libpng 329.0 KiB Installed artifact FFTW 2.2 MiB Installed artifact Xorg_libXau 36.6 KiB Installed artifact Xorg_libXrender 435.9 KiB Installed artifact GettextRuntime 543.0 KiB Installed artifact FriBidi 78.9 KiB Installed artifact OpenSpecFun 194.9 KiB Installed artifact Xorg_libxcb 2.1 MiB Installed artifact LZO 208.9 KiB Installed artifact HarfBuzz 1.7 MiB Installed artifact Libuuid 3.7 MiB Installed artifact Libmount 6.5 MiB Installed artifact Glib 7.7 MiB Installed artifact Xorg_libX11 13.9 MiB Updating `~/.julia/environments/v1.14/Project.toml` [186d2b2d] + ProteinEnsembles v0.3.1 Updating `~/.julia/environments/v1.14/Manifest.toml` [621f4979] + AbstractFFTs v1.5.0 [79e6a3ab] + Adapt v4.4.0 [66dad0bd] + AliasTables v1.1.3 [c7e460c6] + ArgParse v1.2.0 [13072b0f] + AxisAlgorithms v1.1.0 [159f3aea] + Cairo v1.1.1 ⌅ [324d7699] + CategoricalArrays v0.10.8 [d360d2e6] + ChainRulesCore v1.26.0 ⌅ [3da002f7] + ColorTypes v0.11.5 ⌅ [5ae59095] + Colors v0.12.11 [34da2185] + Compat v4.18.1 [a81c6b42] + Compose v0.9.6 [d38c429a] + Contour v0.6.3 [7ad07ef1] + CoupledFields v0.3.0 [9a962f9c] + DataAPI v1.16.0 ⌅ [864edb3b] + DataStructures v0.18.22 [b4f34e82] + Distances v0.10.12 [31c24e10] + Distributions v0.25.123 [ffbed154] + DocStringExtensions v0.9.5 [7a1cc6ca] + FFTW v1.10.0 [1a297f60] + FillArrays v1.15.0 [53c48c17] + FixedPointNumbers v0.8.5 [c91e804a] + Gadfly v1.4.1 [a2bd30eb] + Graphics v1.1.3 [42e2da0e] + Grisu v1.0.2 [a1b4810d] + Hexagons v0.2.0 [34004b35] + HypergeometricFunctions v0.3.28 [9b13fd28] + IndirectArrays v1.0.0 [a98d9a8b] + Interpolations v0.16.2 [92d709cd] + IrrationalConstants v0.2.6 [c8e1da08] + IterTools v1.10.0 [692b3bcd] + JLLWrappers v1.7.1 ⌅ [682c06a0] + JSON v0.21.4 [5ab0869b] + KernelDensity v0.6.10 ⌅ [7031d0ef] + LazyGrids v0.5.0 [4345ca2d] + Loess v0.6.5 [2ab3a3ac] + LogExpFunctions v0.3.29 [442fdcdd] + Measures v0.3.3 [e1d29d7a] + Missings v1.2.0 [77ba4419] + NaNMath v1.1.3 [6fe1bfb0] + OffsetArrays v1.17.0 [bac558e1] + OrderedCollections v1.8.1 [90014a1f] + PDMats v0.11.37 [69de0a69] + Parsers v2.8.3 [aea7be01] + PrecompileTools v1.3.3 [21216c6a] + Preferences v1.5.1 [92933f4c] + ProgressMeter v1.11.0 [186d2b2d] + ProteinEnsembles v0.3.1 [43287f4e] + PtrArrays v1.3.0 [1fd47b50] + QuadGK v2.11.2 [c84ed2f1] + Ratios v0.4.5 [189a3867] + Reexport v1.2.2 [ae029012] + Requires v1.3.1 [79098fc4] + Rmath v0.9.0 [992d4aef] + Showoff v1.0.3 [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 [4c63d2b9] + StatsFuns v1.5.2 [b718987f] + TextWrap v1.0.2 [efce3f68] + WoodburyMatrices v1.1.0 [6e34b625] + Bzip2_jll v1.0.9+0 [83423d85] + Cairo_jll v1.18.5+0 [2e619515] + Expat_jll v2.7.3+0 [f5851436] + FFTW_jll v3.3.11+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 [7746bdde] + Glib_jll v2.86.2+0 [3b182d85] + Graphite2_jll v1.3.15+0 [2e76f6c2] + HarfBuzz_jll v8.5.1+0 [1d5cc7b8] + IntelOpenMP_jll v2025.2.0+0 [1d63c593] + LLVMOpenMP_jll v18.1.8+0 [dd4b983a] + LZO_jll v2.10.3+0 ⌅ [e9f186c6] + Libffi_jll v3.4.7+0 [94ce4f54] + Libiconv_jll v1.18.0+0 [4b2f31a3] + Libmount_jll v2.41.2+0 [38a345b3] + Libuuid_jll v2.41.2+0 [856f044c] + MKL_jll v2025.2.0+0 [efe28fd5] + OpenSpecFun_jll v0.5.6+0 [36c8627f] + Pango_jll v1.57.0+0 ⌅ [30392449] + Pixman_jll v0.44.2+0 [f50d1b31] + Rmath_jll v0.5.1+0 [4f6342f7] + Xorg_libX11_jll v1.8.12+0 [0c0b7dd1] + Xorg_libXau_jll v1.0.13+0 [a3789734] + Xorg_libXdmcp_jll v1.1.6+0 [1082639a] + Xorg_libXext_jll v1.3.7+0 [ea2f1a96] + Xorg_libXrender_jll v0.9.12+0 [c7cfdc94] + Xorg_libxcb_jll v1.17.1+0 [c5fb5394] + Xorg_xtrans_jll v1.6.0+0 [b53b4c65] + libpng_jll v1.6.53+0 [1317d2d5] + oneTBB_jll v2022.0.0+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 v1.7.0 [7b1f6079] + FileWatching v1.11.0 [9fa8497b] + Future v1.11.0 [b77e0a4c] + InteractiveUtils v1.11.0 [ac6e5ff7] + JuliaSyntaxHighlighting v1.13.0 [4af54fe1] + LazyArtifacts v1.11.0 [b27032c2] + LibCURL v1.0.0 [76f85450] + LibGit2 v1.11.0 [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 [ca575930] + NetworkOptions v1.3.0 [44cfe95a] + Pkg v1.14.0 [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 [1a1011a3] + SharedArrays v1.11.0 [6462fe0b] + Sockets v1.11.0 [2f01184e] + SparseArrays v1.13.0 [f489334b] + StyledStrings v1.13.0 [4607b0f0] + SuiteSparse [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 v8.17.0+0 [e37daf67] + LibGit2_jll v1.9.2+0 [29816b5a] + LibSSH2_jll v1.11.3+1 [14a3606d] + MozillaCACerts_jll v2025.12.2 [4536629a] + OpenBLAS_jll v0.3.29+0 [05823500] + OpenLibm_jll 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 ⌅ have new versions available but compatibility constraints restrict them from upgrading. To see why use `status --outdated -m` Installation completed after 16.88s ################################################################################ # 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 11.47s ################################################################################ # Testing # Testing ProteinEnsembles Status `/tmp/jl_kEMXX1/Project.toml` [c7e460c6] ArgParse v1.2.0 [159f3aea] Cairo v1.1.1 ⌅ [5ae59095] Colors v0.12.11 [c91e804a] Gadfly v1.4.1 [92933f4c] ProgressMeter v1.11.0 [186d2b2d] ProteinEnsembles v0.3.1 [10745b16] Statistics v1.11.1 [37e2e46d] LinearAlgebra v1.13.0 [9a3f8284] Random v1.11.0 [8dfed614] Test v1.11.0 Status `/tmp/jl_kEMXX1/Manifest.toml` [621f4979] AbstractFFTs v1.5.0 [79e6a3ab] Adapt v4.4.0 [66dad0bd] AliasTables v1.1.3 [c7e460c6] ArgParse v1.2.0 [13072b0f] AxisAlgorithms v1.1.0 [159f3aea] Cairo v1.1.1 ⌅ [324d7699] CategoricalArrays v0.10.8 [d360d2e6] ChainRulesCore v1.26.0 ⌅ [3da002f7] ColorTypes v0.11.5 ⌅ [5ae59095] Colors v0.12.11 [34da2185] Compat v4.18.1 [a81c6b42] Compose v0.9.6 [d38c429a] Contour v0.6.3 [7ad07ef1] CoupledFields v0.3.0 [9a962f9c] DataAPI v1.16.0 ⌅ [864edb3b] DataStructures v0.18.22 [b4f34e82] Distances v0.10.12 [31c24e10] Distributions v0.25.123 [ffbed154] DocStringExtensions v0.9.5 [7a1cc6ca] FFTW v1.10.0 [1a297f60] FillArrays v1.15.0 [53c48c17] FixedPointNumbers v0.8.5 [c91e804a] Gadfly v1.4.1 [a2bd30eb] Graphics v1.1.3 [42e2da0e] Grisu v1.0.2 [a1b4810d] Hexagons v0.2.0 [34004b35] HypergeometricFunctions v0.3.28 [9b13fd28] IndirectArrays v1.0.0 [a98d9a8b] Interpolations v0.16.2 [92d709cd] IrrationalConstants v0.2.6 [c8e1da08] IterTools v1.10.0 [692b3bcd] JLLWrappers v1.7.1 ⌅ [682c06a0] JSON v0.21.4 [5ab0869b] KernelDensity v0.6.10 ⌅ [7031d0ef] LazyGrids v0.5.0 [4345ca2d] Loess v0.6.5 [2ab3a3ac] LogExpFunctions v0.3.29 [442fdcdd] Measures v0.3.3 [e1d29d7a] Missings v1.2.0 [77ba4419] NaNMath v1.1.3 [6fe1bfb0] OffsetArrays v1.17.0 [bac558e1] OrderedCollections v1.8.1 [90014a1f] PDMats v0.11.37 [69de0a69] Parsers v2.8.3 [aea7be01] PrecompileTools v1.3.3 [21216c6a] Preferences v1.5.1 [92933f4c] ProgressMeter v1.11.0 [186d2b2d] ProteinEnsembles v0.3.1 [43287f4e] PtrArrays v1.3.0 [1fd47b50] QuadGK v2.11.2 [c84ed2f1] Ratios v0.4.5 [189a3867] Reexport v1.2.2 [ae029012] Requires v1.3.1 [79098fc4] Rmath v0.9.0 [992d4aef] Showoff v1.0.3 [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 [4c63d2b9] StatsFuns v1.5.2 [b718987f] TextWrap v1.0.2 [efce3f68] WoodburyMatrices v1.1.0 [6e34b625] Bzip2_jll v1.0.9+0 [83423d85] Cairo_jll v1.18.5+0 [2e619515] Expat_jll v2.7.3+0 [f5851436] FFTW_jll v3.3.11+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 [7746bdde] Glib_jll v2.86.2+0 [3b182d85] Graphite2_jll v1.3.15+0 [2e76f6c2] HarfBuzz_jll v8.5.1+0 [1d5cc7b8] IntelOpenMP_jll v2025.2.0+0 [1d63c593] LLVMOpenMP_jll v18.1.8+0 [dd4b983a] LZO_jll v2.10.3+0 ⌅ [e9f186c6] Libffi_jll v3.4.7+0 [94ce4f54] Libiconv_jll v1.18.0+0 [4b2f31a3] Libmount_jll v2.41.2+0 [38a345b3] Libuuid_jll v2.41.2+0 [856f044c] MKL_jll v2025.2.0+0 [efe28fd5] OpenSpecFun_jll v0.5.6+0 [36c8627f] Pango_jll v1.57.0+0 ⌅ [30392449] Pixman_jll v0.44.2+0 [f50d1b31] Rmath_jll v0.5.1+0 [4f6342f7] Xorg_libX11_jll v1.8.12+0 [0c0b7dd1] Xorg_libXau_jll v1.0.13+0 [a3789734] Xorg_libXdmcp_jll v1.1.6+0 [1082639a] Xorg_libXext_jll v1.3.7+0 [ea2f1a96] Xorg_libXrender_jll v0.9.12+0 [c7cfdc94] Xorg_libxcb_jll v1.17.1+0 [c5fb5394] Xorg_xtrans_jll v1.6.0+0 [b53b4c65] libpng_jll v1.6.53+0 [1317d2d5] oneTBB_jll v2022.0.0+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 v1.7.0 [7b1f6079] FileWatching v1.11.0 [9fa8497b] Future v1.11.0 [b77e0a4c] InteractiveUtils v1.11.0 [ac6e5ff7] JuliaSyntaxHighlighting v1.13.0 [4af54fe1] LazyArtifacts v1.11.0 [b27032c2] LibCURL v1.0.0 [76f85450] LibGit2 v1.11.0 [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 [ca575930] NetworkOptions v1.3.0 [44cfe95a] Pkg v1.14.0 [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 [1a1011a3] SharedArrays v1.11.0 [6462fe0b] Sockets v1.11.0 [2f01184e] SparseArrays v1.13.0 [f489334b] StyledStrings v1.13.0 [4607b0f0] SuiteSparse [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 v8.17.0+0 [e37daf67] LibGit2_jll v1.9.2+0 [29816b5a] LibSSH2_jll v1.11.3+1 [14a3606d] MozillaCACerts_jll v2025.12.2 [4536629a] OpenBLAS_jll v0.3.29+0 [05823500] OpenLibm_jll 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 ⌅ have new versions available but compatibility constraints restrict them from upgrading. Testing Running tests...  Downloading artifact: IntelOpenMP  Downloading artifact: oneTBB ┌ Warning: `@add_arg_table` is deprecated, use `@add_arg_table!` instead └ @ ArgParse ~/.julia/packages/ProteinEnsembles/TB23o/src/ProteinEnsembles.jl:22 2 dependencies had output during precompilation: ┌ MKL_jll │ Downloading artifact: IntelOpenMP │ Downloading artifact: oneTBB └ ┌ ProteinEnsembles │ [Output was shown above] └ WARNING: Method definition PNG(Any...) in module Compose at /home/pkgeval/.julia/packages/Compose/eWKZh/src/Compose.jl:138 overwritten at /home/pkgeval/.julia/packages/Compose/eWKZh/src/cairo_backends.jl:208. WARNING: Method definition kwcall(NamedTuple{names, T} where T<:Tuple where names, typeof(Compose.PNG), Any...) in module Compose at /home/pkgeval/.julia/packages/Compose/eWKZh/src/Compose.jl:138 overwritten at /home/pkgeval/.julia/packages/Compose/eWKZh/src/cairo_backends.jl:208. WARNING: Method definition PDF(Any...) in module Compose at /home/pkgeval/.julia/packages/Compose/eWKZh/src/Compose.jl:138 overwritten at /home/pkgeval/.julia/packages/Compose/eWKZh/src/cairo_backends.jl:208. WARNING: Method definition kwcall(NamedTuple{names, T} where T<:Tuple where names, typeof(Compose.PDF), Any...) in module Compose at /home/pkgeval/.julia/packages/Compose/eWKZh/src/Compose.jl:138 overwritten at /home/pkgeval/.julia/packages/Compose/eWKZh/src/cairo_backends.jl:208. WARNING: Method definition PS(Any...) in module Compose at /home/pkgeval/.julia/packages/Compose/eWKZh/src/Compose.jl:138 overwritten at /home/pkgeval/.julia/packages/Compose/eWKZh/src/cairo_backends.jl:208. WARNING: Method definition kwcall(NamedTuple{names, T} where T<:Tuple where names, typeof(Compose.PS), Any...) in module Compose at /home/pkgeval/.julia/packages/Compose/eWKZh/src/Compose.jl:138 overwritten at /home/pkgeval/.julia/packages/Compose/eWKZh/src/cairo_backends.jl:208. Test Summary: | Pass Total Time Types | 8 8 1.1s Could not find element for atom with name X Test Summary: | Pass Total Time Atoms | 26 26 1.0s Read 214 residues from DSSP file Read 1336 atoms from PDB file Read 141 residues from DSSP file Read 3312 atoms from PDB file Read 3804 atoms from PDB file Read 3312 atoms from PDB file Read 3312 atoms from PDB file Read 476 pocket points from pocket points PDB file Read 43 pocket centres from LIGSITEcs output PDB file Test Summary: | Pass Total Time IO | 31 31 2.2s Read 2035 atoms from PDB file Read 214 residues from DSSP file Found distance constraints from single structure Found combined distance constraints from two structures Test Summary: | Pass Total Time Interactions | 41 41 4.0s Kept lowest scoring 2 out of 4 structures Scores range from 10.0 to 20.0 Test Summary: | Pass Total Time Generate | 12 12 3.3s Test Summary: | Pass Total Time Align | 11 11 7.4s Read 2035 atoms from PDB file Read 2035 atoms from PDB file Read 2035 atoms from PDB file Read 2035 atoms from PDB file Read 2035 atoms from PDB file Read 2035 atoms from PDB file Read 2035 atoms from PDB file Read 2035 atoms from PDB file Read 2035 atoms from PDB file Read 2035 atoms from PDB file Read 2035 atoms from PDB file Read in protein ensemble Read 2035 atoms from PDB file Read 2035 atoms from PDB file Read 2035 atoms from PDB file Read 2035 atoms from PDB file Read 2035 atoms from PDB file Read 2035 atoms from PDB file Read 2035 atoms from PDB file Read 2035 atoms from PDB file Read 2035 atoms from PDB file Read 2035 atoms from PDB file Read 2035 atoms from PDB file Read in protein ensemble Read 2035 atoms from PDB file Read 2035 atoms from PDB file Read 2035 atoms from PDB file Read 2035 atoms from PDB file Read 2035 atoms from PDB file Read 2035 atoms from PDB file Read 2035 atoms from PDB file Read 2035 atoms from PDB file Read 2035 atoms from PDB file Read 2035 atoms from PDB file Read 2035 atoms from PDB file Read in protein ensemble Test Summary: | Pass Total Time PCA | 10 10 6.2s Found 2 interactions between the modulator and the protein Read 395 pocket points from LIGSITEcs pocket points PDB file Read 43 pocket centres from LIGSITEcs output PDB file Assigned all points Wrote pocket number assignments to file "/tmp/jl_65svMvyj05" Test Summary: | Pass Total Time Perturb | 9 9 2.6s -- ExProSE -- Arguments: i1 - /home/pkgeval/.julia/packages/ProteinEnsembles/TB23o/test/test_files/1CLL_H.pdb d1 - /home/pkgeval/.julia/packages/ProteinEnsembles/TB23o/test/test_files/1CLL.dssp i2 - /home/pkgeval/.julia/packages/ProteinEnsembles/TB23o/test/test_files/1CTR_H.pdb d2 - /home/pkgeval/.julia/packages/ProteinEnsembles/TB23o/test/test_files/1CTR.dssp out_dir - /tmp/exprose_out n_strucs - 4 tolerance_weight - 0.3 other_ratio - 20.0 extra_pdbs - /home/pkgeval/.julia/packages/ProteinEnsembles/TB23o/test/test_files/1CFF_1.pdb, /home/pkgeval/.julia/packages/ProteinEnsembles/TB23o/test/test_files/1CFF_2.pdb mod_path - nothing n_mods - 0 Making output directory "/tmp/exprose_out" Proceeding with two structures Read 1367 atoms from PDB file Read 1336 atoms from PDB file Read 144 residues from DSSP file Read 141 residues from DSSP file Found interactions: Covalently bonded - 1313 1-3 system - 1868 Same ring system - 35 Side-chain restricted 1-4 - 116 Omega 1-4 - 540 Tight phi/psi 1-4 - 692 Loose phi/psi 1-4 - 157 Other phi/psi 1-4 - 195 Other 1-4 - 589 Secondary structure - 3684 Salt bridge - 42 H bond - 230 Tight hydrophobic - 817 Loose hydrophobic - 878 Other pairs - 835795 Found distance constraints from single structure Found interactions: Covalently bonded - 1313 1-3 system - 1868 Same ring system - 35 Side-chain restricted 1-4 - 116 Omega 1-4 - 540 Tight phi/psi 1-4 - 540 Loose phi/psi 1-4 - 206 Other phi/psi 1-4 - 298 Other 1-4 - 589 Secondary structure - 2544 Salt bridge - 63 H bond - 233 Tight hydrophobic - 773 Loose hydrophobic - 1055 Other pairs - 836778 Found distance constraints from single structure Found combined distance constraints from two structures Will generate 6 structures and keep best-scoring 4 ┌ Warning: `Progress(n::Integer, dt::Real, desc::AbstractString = "Progress: ", barlen = nothing, color::Symbol = :green, output::IO = stderr; offset::Integer = 0)` is deprecated, use `Progress(n; dt = dt, desc = desc, barlen = barlen, color = color, output = output, offset = offset)` instead. │ caller = ip:0x0 └ @ Core :-1 Progress: 33%|████████████████▋ | ETA: 0:00:08 Progress: 50%|█████████████████████████ | ETA: 0:00:06 Progress: 67%|█████████████████████████████████▍ | ETA: 0:00:04 Progress: 83%|█████████████████████████████████████████▋ | ETA: 0:00:02 Progress: 100%|██████████████████████████████████████████████████| Time: 0:00:10 Kept lowest scoring 4 out of 6 structures Scores range from 0.2 to 8.9 Aligned ensemble to itself after 3 iteration(s) Projections written to file "/tmp/exprose_out/pcs/pcs.tsv" Projections written to file "/tmp/exprose_out/pcs/pcs_input_1.tsv" Projections written to file "/tmp/exprose_out/pcs/pcs_input_2.tsv" Wrote ensemble to PDB file(s) with prefix "/tmp/exprose_out/pdbs/out.pdb" Wrote ensemble scores to file "/tmp/exprose_out/spe_scores.tsv" Read 2634 atoms from PDB file Projections written to file "/tmp/exprose_out/pcs/pcs_ex_1.tsv" Read 2634 atoms from PDB file Projections written to file "/tmp/exprose_out/pcs/pcs_ex_2.tsv" Plotted principal components to file(s) "/tmp/exprose_out/pcs/pc_x_y.png" Plotted RMSFs to file "/tmp/exprose_out/rmsfs.png" n_to_write is larger than the number of eigenvectors - proceeding with all possible eigenvectors PyMol script to view principal components written to file(s) "/tmp/exprose_out/pymol/view_pc_x.pml" Done -- ExProSE -- Arguments: i1 - /home/pkgeval/.julia/packages/ProteinEnsembles/TB23o/test/test_files/1CLL_H.pdb d1 - /home/pkgeval/.julia/packages/ProteinEnsembles/TB23o/test/test_files/1CLL.dssp i2 - nothing d2 - nothing out_dir - /tmp/exprose_out n_strucs - 4 tolerance_weight - 0.3 other_ratio - 20.0 extra_pdbs - /home/pkgeval/.julia/packages/ProteinEnsembles/TB23o/test/test_files/1CFF_1.pdb, /home/pkgeval/.julia/packages/ProteinEnsembles/TB23o/test/test_files/1CFF_2.pdb mod_path - nothing n_mods - 0 Making output directory "/tmp/exprose_out" Proceeding with one structure Read 1367 atoms from PDB file Read 144 residues from DSSP file Found interactions: Covalently bonded - 1379 1-3 system - 1966 Same ring system - 35 Side-chain restricted 1-4 - 116 Omega 1-4 - 568 Tight phi/psi 1-4 - 744 Loose phi/psi 1-4 - 157 Other phi/psi 1-4 - 195 Other 1-4 - 626 Secondary structure - 4160 Salt bridge - 42 H bond - 244 Tight hydrophobic - 865 Loose hydrophobic - 931 Other pairs - 921633 Found distance constraints from single structure Will generate 6 structures and keep best-scoring 4 Progress: 33%|████████████████▋ | ETA: 0:00:07 Progress: 50%|█████████████████████████ | ETA: 0:00:05 Progress: 67%|█████████████████████████████████▍ | ETA: 0:00:04 Progress: 83%|█████████████████████████████████████████▋ | ETA: 0:00:02 Progress: 100%|██████████████████████████████████████████████████| Time: 0:00:11 Kept lowest scoring 4 out of 6 structures Scores range from 0.8 to 15615.3 Aligned ensemble to itself after 3 iteration(s) Projections written to file "/tmp/exprose_out/pcs/pcs.tsv" Projections written to file "/tmp/exprose_out/pcs/pcs_input.tsv" Wrote ensemble to PDB file(s) with prefix "/tmp/exprose_out/pdbs/out.pdb" Wrote ensemble scores to file "/tmp/exprose_out/spe_scores.tsv" Read 2634 atoms from PDB file Projections written to file "/tmp/exprose_out/pcs/pcs_ex_1.tsv" Read 2634 atoms from PDB file Projections written to file "/tmp/exprose_out/pcs/pcs_ex_2.tsv" Plotted principal components to file(s) "/tmp/exprose_out/pcs/pc_x_y.png" Plotted RMSFs to file "/tmp/exprose_out/rmsfs.png" n_to_write is larger than the number of eigenvectors - proceeding with all possible eigenvectors PyMol script to view principal components written to file(s) "/tmp/exprose_out/pymol/view_pc_x.pml" Done -- ExProSE -- Arguments: i1 - /home/pkgeval/.julia/packages/ProteinEnsembles/TB23o/test/test_files/1CLL_H.pdb d1 - /home/pkgeval/.julia/packages/ProteinEnsembles/TB23o/test/test_files/1CLL.dssp i2 - /home/pkgeval/.julia/packages/ProteinEnsembles/TB23o/test/test_files/1CTR_H.pdb d2 - /home/pkgeval/.julia/packages/ProteinEnsembles/TB23o/test/test_files/1CTR.dssp out_dir - /tmp/exprose_out n_strucs - 4 tolerance_weight - 0.3 other_ratio - 20.0 extra_pdbs - /home/pkgeval/.julia/packages/ProteinEnsembles/TB23o/test/test_files/1CFF_1.pdb, /home/pkgeval/.julia/packages/ProteinEnsembles/TB23o/test/test_files/1CFF_2.pdb mod_path - /home/pkgeval/.julia/packages/ProteinEnsembles/TB23o/test/test_files/1CTR_pocket_points.pdb n_mods - 1 Making output directory "/tmp/exprose_out" Proceeding with two structures Read 1367 atoms from PDB file Read 1336 atoms from PDB file Read 144 residues from DSSP file Read 141 residues from DSSP file Found interactions: Covalently bonded - 1313 1-3 system - 1868 Same ring system - 35 Side-chain restricted 1-4 - 116 Omega 1-4 - 540 Tight phi/psi 1-4 - 692 Loose phi/psi 1-4 - 157 Other phi/psi 1-4 - 195 Other 1-4 - 589 Secondary structure - 3684 Salt bridge - 42 H bond - 230 Tight hydrophobic - 817 Loose hydrophobic - 878 Other pairs - 835795 Found distance constraints from single structure Found interactions: Covalently bonded - 1313 1-3 system - 1868 Same ring system - 35 Side-chain restricted 1-4 - 116 Omega 1-4 - 540 Tight phi/psi 1-4 - 540 Loose phi/psi 1-4 - 206 Other phi/psi 1-4 - 298 Other 1-4 - 589 Secondary structure - 2544 Salt bridge - 63 H bond - 233 Tight hydrophobic - 773 Loose hydrophobic - 1055 Other pairs - 836778 Found distance constraints from single structure Found combined distance constraints from two structures Will generate 6 structures and keep best-scoring 4 Progress: 33%|████████████████▋ | ETA: 0:00:06 Progress: 50%|█████████████████████████ | ETA: 0:00:05 Progress: 67%|█████████████████████████████████▍ | ETA: 0:00:03 Progress: 83%|█████████████████████████████████████████▋ | ETA: 0:00:02 Progress: 100%|██████████████████████████████████████████████████| Time: 0:00:09 Kept lowest scoring 4 out of 6 structures Scores range from 11.7 to 90.1 Read 1111 pocket points from pocket points PDB file Generating ensemble with modulator 1 of 1 Found 2985 interactions between the modulator and the protein Will generate 6 structures and keep best-scoring 4 Progress: 33%|████████████████▋ | ETA: 0:00:08 Progress: 50%|█████████████████████████ | ETA: 0:00:06 Progress: 67%|█████████████████████████████████▍ | ETA: 0:00:04 Progress: 83%|█████████████████████████████████████████▋ | ETA: 0:00:02 Progress: 100%|██████████████████████████████████████████████████| Time: 0:00:11 Kept lowest scoring 4 out of 6 structures Scores range from 1.0 to 23.4 Aligned ensemble to itself after 4 iteration(s) Projections written to file "/tmp/exprose_out/pcs/pcs.tsv" Projections written to file "/tmp/exprose_out/pcs/pcs_input_1.tsv" Projections written to file "/tmp/exprose_out/pcs/pcs_input_2.tsv" Wrote ensemble to PDB file(s) with prefix "/tmp/exprose_out/pdbs/out.pdb" Wrote ensemble scores to file "/tmp/exprose_out/spe_scores.tsv" Read 2634 atoms from PDB file Projections written to file "/tmp/exprose_out/pcs/pcs_ex_1.tsv" Read 2634 atoms from PDB file Projections written to file "/tmp/exprose_out/pcs/pcs_ex_2.tsv" Plotted principal components to file(s) "/tmp/exprose_out/pcs/pc_x_y.png" Plotted RMSFs to file "/tmp/exprose_out/rmsfs.png" Wrote ensemble to PDB file(s) with prefix "/tmp/exprose_out/pdbs_mod_1/out.pdb" Projections written to file "/tmp/exprose_out/mod_1/pcs.tsv" Wrote ensemble scores to file "/tmp/exprose_out/mod_1/spe_scores.tsv" Plotted principal components to file(s) "/tmp/exprose_out/mod_1/pc_x_y.png" Aligned ensemble to itself after 2 iteration(s) Plotted RMSFs to file "/tmp/exprose_out/mod_1/rmsfs.png" n_to_write is larger than the number of eigenvectors - proceeding with all possible eigenvectors PyMol script to view principal components written to file(s) "/tmp/exprose_out/pymol/view_pc_x.pml" Done -- ExProSE -- Arguments: i1 - /home/pkgeval/.julia/packages/ProteinEnsembles/TB23o/test/test_files/1CTR_H.pdb d1 - /home/pkgeval/.julia/packages/ProteinEnsembles/TB23o/test/test_files/1CTR.dssp i2 - nothing d2 - nothing out_dir - /tmp/exprose_out n_strucs - 4 tolerance_weight - 0.3 other_ratio - 20.0 extra_pdbs - /home/pkgeval/.julia/packages/ProteinEnsembles/TB23o/test/test_files/1CFF_1.pdb, /home/pkgeval/.julia/packages/ProteinEnsembles/TB23o/test/test_files/1CFF_2.pdb mod_path - /home/pkgeval/.julia/packages/ProteinEnsembles/TB23o/test/test_files/1CTR_pocket_points.pdb n_mods - 1 Making output directory "/tmp/exprose_out" Proceeding with one structure Read 1336 atoms from PDB file Read 141 residues from DSSP file Found interactions: Covalently bonded - 1347 1-3 system - 1919 Same ring system - 35 Side-chain restricted 1-4 - 120 Omega 1-4 - 552 Tight phi/psi 1-4 - 540 Loose phi/psi 1-4 - 232 Other phi/psi 1-4 - 298 Other 1-4 - 608 Secondary structure - 2544 Salt bridge - 84 H bond - 239 Tight hydrophobic - 789 Loose hydrophobic - 1084 Other pairs - 881389 Found distance constraints from single structure Will generate 6 structures and keep best-scoring 4 Progress: 33%|████████████████▋ | ETA: 0:00:06 Progress: 50%|█████████████████████████ | ETA: 0:00:05 Progress: 67%|█████████████████████████████████▍ | ETA: 0:00:03 Progress: 83%|█████████████████████████████████████████▋ | ETA: 0:00:02 Progress: 100%|██████████████████████████████████████████████████| Time: 0:00:09 Kept lowest scoring 4 out of 6 structures Scores range from 0.0 to 0.4 Read 1111 pocket points from pocket points PDB file Generating ensemble with modulator 1 of 1 Found 3282 interactions between the modulator and the protein Will generate 6 structures and keep best-scoring 4 Progress: 33%|████████████████▋ | ETA: 0:00:07 Progress: 50%|█████████████████████████ | ETA: 0:00:05 Progress: 67%|█████████████████████████████████▍ | ETA: 0:00:03 Progress: 83%|█████████████████████████████████████████▋ | ETA: 0:00:02 Progress: 100%|██████████████████████████████████████████████████| Time: 0:00:10 Kept lowest scoring 4 out of 6 structures Scores range from 0.0 to 4.6 Aligned ensemble to itself after 2 iteration(s) Projections written to file "/tmp/exprose_out/pcs/pcs.tsv" Projections written to file "/tmp/exprose_out/pcs/pcs_input.tsv" Wrote ensemble to PDB file(s) with prefix "/tmp/exprose_out/pdbs/out.pdb" Wrote ensemble scores to file "/tmp/exprose_out/spe_scores.tsv" Read 2634 atoms from PDB file Projections written to file "/tmp/exprose_out/pcs/pcs_ex_1.tsv" Read 2634 atoms from PDB file Projections written to file "/tmp/exprose_out/pcs/pcs_ex_2.tsv" Plotted principal components to file(s) "/tmp/exprose_out/pcs/pc_x_y.png" Plotted RMSFs to file "/tmp/exprose_out/rmsfs.png" Wrote ensemble to PDB file(s) with prefix "/tmp/exprose_out/pdbs_mod_1/out.pdb" Projections written to file "/tmp/exprose_out/mod_1/pcs.tsv" Wrote ensemble scores to file "/tmp/exprose_out/mod_1/spe_scores.tsv" Plotted principal components to file(s) "/tmp/exprose_out/mod_1/pc_x_y.png" Aligned ensemble to itself after 2 iteration(s) Plotted RMSFs to file "/tmp/exprose_out/mod_1/rmsfs.png" n_to_write is larger than the number of eigenvectors - proceeding with all possible eigenvectors PyMol script to view principal components written to file(s) "/tmp/exprose_out/pymol/view_pc_x.pml" Done Test Summary: | Pass Total Time Pipeline | 5 5 2m52.1s Parameterisation tests not run; to run these, set run_param_test to true in runtests.jl Testing ProteinEnsembles tests passed Testing completed after 490.66s PkgEval succeeded after 585.32s