Package evaluation to test BioStructures on Julia 1.12.7-DEV.42 (6f510b6086*) started at 2026-06-19T14:06:36.259 ################################################################################ # Set-up # Installing PkgEval dependencies (TestEnv)... Activating project at `~/.julia/environments/v1.12` Set-up completed after 8.01s ################################################################################ # Installation # Installing BioStructures... Resolving package versions... Updating `~/.julia/environments/v1.12/Project.toml` [de9282ab] + BioStructures v4.7.1 Updating `~/.julia/environments/v1.12/Manifest.toml` [47718e42] + BioGenerics v0.1.5 [de9282ab] + BioStructures v4.7.1 [3c28c6f8] + BioSymbols v5.2.0 [944b1d66] + CodecZlib v0.7.8 [1fa38f19] + Format v1.3.7 [aea7be01] + PrecompileTools v1.3.4 [21216c6a] + Preferences v1.5.2 [3cdcf5f2] + RecipesBase v1.3.4 [10745b16] + Statistics v1.11.1 [3bb67fe8] + TranscodingStreams v0.11.3 [0dad84c5] + ArgTools v1.1.2 [56f22d72] + Artifacts v1.11.0 [ade2ca70] + Dates v1.11.0 [f43a241f] + Downloads v1.7.0 [7b1f6079] + FileWatching v1.11.0 [b27032c2] + LibCURL v0.6.4 [8f399da3] + Libdl v1.11.0 [37e2e46d] + LinearAlgebra v1.12.0 [ca575930] + NetworkOptions v1.3.0 [de0858da] + Printf v1.11.0 [fa267f1f] + TOML v1.0.3 [4ec0a83e] + Unicode v1.11.0 [e66e0078] + CompilerSupportLibraries_jll v1.3.0+1 [deac9b47] + LibCURL_jll v8.15.0+0 [29816b5a] + LibSSH2_jll v1.11.3+1 [14a3606d] + MozillaCACerts_jll v2025.11.4 [4536629a] + OpenBLAS_jll v0.3.29+0 [458c3c95] + OpenSSL_jll v3.5.6+0 [83775a58] + Zlib_jll v1.3.1+2 [8e850b90] + libblastrampoline_jll v5.15.0+0 [8e850ede] + nghttp2_jll v1.64.0+1 Installation completed after 5.64s ################################################################################ # Precompilation # Precompiling PkgEval dependencies... Precompiling package dependencies... Precompiling packages... 3421.0 ms ✓ BioStructures → BioStructuresSTRIDEExt 15682.0 ms ✓ BioStructures → BioStructuresBioSequencesExt 1468.3 ms ✓ BioStructures → BioStructuresMMTFExt 7857.2 ms ✓ BioStructures → BioStructuresDataFramesExt 3495.0 ms ✓ BioStructures → BioStructuresDSSPExt 8601.4 ms ✓ BioStructures → BioStructuresGraphsExt 5739.6 ms ✓ BioStructures → BioStructuresBioAlignmentsExt 7 dependencies successfully precompiled in 48 seconds. 85 already precompiled. 24 dependencies precompiled but different versions are currently loaded (ArgTools, Base64, Dates, Downloads, JuliaSyntaxHighlighting, LibCURL, LibCURL_jll, LibGit2, LibGit2_jll, LibSSH2_jll, Logging, Markdown, MozillaCACerts_jll, NetworkOptions, OpenSSL_jll, Pkg, Printf, StyledStrings, TOML, Tar, UUIDs, Zlib_jll, nghttp2_jll and p7zip_jll). Restart julia to access the new versions. Otherwise, 36 dependents of these packages may trigger further precompilation to work with the unexpected versions. Precompilation completed after 65.65s ################################################################################ # Testing # Testing BioStructures Status `/tmp/jl_vBYynv/Project.toml` [4c88cf16] Aqua v0.8.16 [00701ae9] BioAlignments v3.1.0 [7e6ae17a] BioSequences v3.5.1 [de9282ab] BioStructures v4.7.1 [944b1d66] CodecZlib v0.7.8 [a93c6f00] DataFrames v1.8.2 [1fa38f19] Format v1.3.7 [86223c79] Graphs v1.14.0 [259c3a9c] MMTF v1.0.0 [626554b9] MetaGraphs v0.9.0 [3cdcf5f2] RecipesBase v1.3.4 [74334e00] DSSP_jll v4.4.0+1 [850473c1] STRIDE_jll v1.0.0+0 [f43a241f] Downloads v1.7.0 [37e2e46d] LinearAlgebra v1.12.0 [8dfed614] Test v1.11.0 Status `/tmp/jl_vBYynv/Manifest.toml` [4c88cf16] Aqua v0.8.16 [ec485272] ArnoldiMethod v0.4.0 [00701ae9] BioAlignments v3.1.0 [47718e42] BioGenerics v0.1.5 [7e6ae17a] BioSequences v3.5.1 [de9282ab] BioStructures v4.7.1 [3c28c6f8] BioSymbols v5.2.0 [944b1d66] CodecZlib v0.7.8 [34da2185] Compat v4.18.1 [a8cc5b0e] Crayons v4.1.1 [9a962f9c] DataAPI v1.16.0 [a93c6f00] DataFrames v1.8.2 [864edb3b] DataStructures v0.19.5 [e2d170a0] DataValueInterfaces v1.0.0 [1fa38f19] Format v1.3.7 [86223c79] Graphs v1.14.0 [d25df0c9] Inflate v0.1.5 [842dd82b] InlineStrings v1.4.5 [524e6230] IntervalTrees v1.1.0 [41ab1584] InvertedIndices v1.3.1 [82899510] IteratorInterfaceExtensions v1.0.0 [692b3bcd] JLLWrappers v1.8.0 [b964fa9f] LaTeXStrings v1.4.0 [259c3a9c] MMTF v1.0.0 [1914dd2f] MacroTools v0.5.16 [626554b9] MetaGraphs v0.9.0 [e1d29d7a] Missings v1.2.0 [99f44e22] MsgPack v1.2.1 ⌅ [bac558e1] OrderedCollections v1.8.2 [2dfb63ee] PooledArrays v1.4.3 [aea7be01] PrecompileTools v1.3.4 [21216c6a] Preferences v1.5.2 [08abe8d2] PrettyTables v3.3.2 [3cdcf5f2] RecipesBase v1.3.4 [189a3867] Reexport v1.2.2 [91c51154] SentinelArrays v1.4.10 [699a6c99] SimpleTraits v0.9.6 [a2af1166] SortingAlgorithms v1.2.2 [90137ffa] StaticArrays v1.9.18 [1e83bf80] StaticArraysCore v1.4.4 [10745b16] Statistics v1.11.1 [892a3eda] StringManipulation v0.4.4 [3783bdb8] TableTraits v1.0.1 [bd369af6] Tables v1.12.1 [3bb67fe8] TranscodingStreams v0.11.3 [7200193e] Twiddle v1.1.2 [74334e00] DSSP_jll v4.4.0+1 [850473c1] STRIDE_jll v1.0.0+0 [0dad84c5] ArgTools v1.1.2 [56f22d72] Artifacts v1.11.0 [2a0f44e3] Base64 v1.11.0 [ade2ca70] Dates 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 [ca575930] NetworkOptions v1.3.0 [44cfe95a] Pkg v1.12.1 [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 [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 v8.15.0+0 [e37daf67] LibGit2_jll v1.9.0+0 [29816b5a] LibSSH2_jll v1.11.3+1 [14a3606d] MozillaCACerts_jll v2025.11.4 [4536629a] OpenBLAS_jll v0.3.29+0 [458c3c95] OpenSSL_jll v3.5.6+0 [bea87d4a] SuiteSparse_jll v7.8.3+2 [83775a58] Zlib_jll v1.3.1+2 [8e850b90] libblastrampoline_jll v5.15.0+0 [8e850ede] nghttp2_jll v1.64.0+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... Precompiling packages... 14507.2 ms ✓ Graphs 1 dependency successfully precompiled in 15 seconds. 25 already precompiled. 15 dependencies precompiled but different versions are currently loaded (Base64, DataStructures, Dates, InteractiveUtils, JuliaSyntaxHighlighting, Markdown, OrderedCollections, PrecompileTools, Preferences, Printf, Serialization, Statistics, StyledStrings, TOML and Unicode). Restart julia to access the new versions. Otherwise, 7 dependents of these packages may trigger further precompilation to work with the unexpected versions. Precompiling packages... 3805.9 ms ✓ MetaGraphs 1 dependency successfully precompiled in 5 seconds. 26 already precompiled. 26 dependencies precompiled but different versions are currently loaded (ArnoldiMethod, Base64, DataStructures, Dates, Graphs, Inflate, InteractiveUtils, JuliaSyntaxHighlighting, MacroTools, Markdown, OrderedCollections, PrecompileTools, Preferences, Printf, Serialization, SimpleTraits, SparseArrays, StaticArrays, StaticArrays → StaticArraysStatisticsExt, StaticArraysCore, Statistics, Statistics → SparseArraysExt, StyledStrings, SuiteSparse_jll, TOML and Unicode). Restart julia to access the new versions. Otherwise, 1 dependent of these packages may trigger further precompilation to work with the unexpected versions. Precompiling packages... 19121.2 ms ✓ BioStructures 1 dependency successfully precompiled in 19 seconds. 23 already precompiled. 23 dependencies precompiled but different versions are currently loaded (ArgTools, BioGenerics, BioSymbols, CodecZlib, Dates, Downloads, Format, LibCURL, LibCURL_jll, LibSSH2_jll, MozillaCACerts_jll, NetworkOptions, OpenSSL_jll, PrecompileTools, Preferences, Printf, RecipesBase, Statistics, TOML, TranscodingStreams, Unicode, Zlib_jll and nghttp2_jll). Restart julia to access the new versions. Otherwise, 1 dependent of these packages may trigger further precompilation to work with the unexpected versions. Precompiling packages... 1745.4 ms ✓ BioStructures → BioStructuresDSSPExt 1 dependency successfully precompiled in 2 seconds. 26 already precompiled. 26 dependencies precompiled but different versions are currently loaded (ArgTools, BioGenerics, BioStructures, BioSymbols, CodecZlib, DSSP_jll, Dates, Downloads, Format, JLLWrappers, LibCURL, LibCURL_jll, LibSSH2_jll, MozillaCACerts_jll, NetworkOptions, OpenSSL_jll, PrecompileTools, Preferences, Printf, RecipesBase, Statistics, TOML, TranscodingStreams, Unicode, Zlib_jll and nghttp2_jll). Restart julia to access the new versions. Otherwise, 1 dependent of these packages may trigger further precompilation to work with the unexpected versions. Precompiling packages... 1658.6 ms ✓ BioStructures → BioStructuresBioSequencesExt 1 dependency successfully precompiled in 2 seconds. 26 already precompiled. 26 dependencies precompiled but different versions are currently loaded (ArgTools, BioGenerics, BioSequences, BioStructures, BioSymbols, CodecZlib, Dates, Downloads, Format, LibCURL, LibCURL_jll, LibSSH2_jll, MozillaCACerts_jll, NetworkOptions, OpenSSL_jll, PrecompileTools, Preferences, Printf, RecipesBase, Statistics, TOML, TranscodingStreams, Twiddle, Unicode, Zlib_jll and nghttp2_jll). Restart julia to access the new versions. Otherwise, 1 dependent of these packages may trigger further precompilation to work with the unexpected versions. Precompiling packages... 1505.4 ms ✓ BioStructures → BioStructuresMMTFExt 1 dependency successfully precompiled in 2 seconds. 27 already precompiled. 27 dependencies precompiled but different versions are currently loaded (ArgTools, BioGenerics, BioStructures, BioSymbols, CodecZlib, Dates, Downloads, Format, LibCURL, LibCURL_jll, LibSSH2_jll, MMTF, MozillaCACerts_jll, MsgPack, NetworkOptions, OpenSSL_jll, PrecompileTools, Preferences, Printf, RecipesBase, Serialization, Statistics, TOML, TranscodingStreams, Unicode, Zlib_jll and nghttp2_jll). Restart julia to access the new versions. Otherwise, 1 dependent of these packages may trigger further precompilation to work with the unexpected versions. Precompiling packages... 1978.0 ms ✓ BioStructures → BioStructuresSTRIDEExt 1 dependency successfully precompiled in 2 seconds. 26 already precompiled. 26 dependencies precompiled but different versions are currently loaded (ArgTools, BioGenerics, BioStructures, BioSymbols, CodecZlib, Dates, Downloads, Format, JLLWrappers, LibCURL, LibCURL_jll, LibSSH2_jll, MozillaCACerts_jll, NetworkOptions, OpenSSL_jll, PrecompileTools, Preferences, Printf, RecipesBase, STRIDE_jll, Statistics, TOML, TranscodingStreams, Unicode, Zlib_jll and nghttp2_jll). Restart julia to access the new versions. Otherwise, 1 dependent of these packages may trigger further precompilation to work with the unexpected versions. Precompiling packages... 7627.6 ms ✓ BioStructures → BioStructuresDataFramesExt 1 dependency successfully precompiled in 8 seconds. 53 already precompiled. 53 dependencies precompiled but different versions are currently loaded (ArgTools, Base64, BioGenerics, BioStructures, BioSymbols, CodecZlib, Compat, Compat → CompatLinearAlgebraExt, Crayons, DataAPI, DataFrames, DataStructures, DataValueInterfaces, Dates, Downloads, Format, Future, InlineStrings, InteractiveUtils, InvertedIndices, IteratorInterfaceExtensions, JuliaSyntaxHighlighting, LaTeXStrings, LibCURL, LibCURL_jll, LibSSH2_jll, Markdown, Missings, MozillaCACerts_jll, NetworkOptions, OpenSSL_jll, OrderedCollections, PooledArrays, PrecompileTools, Preferences, PrettyTables, Printf, REPL, RecipesBase, Reexport, SentinelArrays, SortingAlgorithms, Statistics, StringManipulation, StyledStrings, TOML, TableTraits, Tables, TranscodingStreams, UUIDs, Unicode, Zlib_jll and nghttp2_jll). Restart julia to access the new versions. Otherwise, 1 dependent of these packages may trigger further precompilation to work with the unexpected versions. Precompiling packages... 4206.9 ms ✓ BioStructures → BioStructuresGraphsExt 1 dependency successfully precompiled in 5 seconds. 44 already precompiled. 44 dependencies precompiled but different versions are currently loaded (ArgTools, ArnoldiMethod, Base64, BioGenerics, BioStructures, BioSymbols, CodecZlib, DataStructures, Dates, Downloads, Format, Graphs, Inflate, InteractiveUtils, JuliaSyntaxHighlighting, LibCURL, LibCURL_jll, LibSSH2_jll, MacroTools, Markdown, MetaGraphs, MozillaCACerts_jll, NetworkOptions, OpenSSL_jll, OrderedCollections, PrecompileTools, Preferences, Printf, RecipesBase, Serialization, SimpleTraits, SparseArrays, StaticArrays, StaticArrays → StaticArraysStatisticsExt, StaticArraysCore, Statistics, Statistics → SparseArraysExt, StyledStrings, SuiteSparse_jll, TOML, TranscodingStreams, Unicode, Zlib_jll and nghttp2_jll). Restart julia to access the new versions. Otherwise, 1 dependent of these packages may trigger further precompilation to work with the unexpected versions. Precompiling packages... 1799.8 ms ✓ BioStructures → BioStructuresBioAlignmentsExt 1 dependency successfully precompiled in 2 seconds. 29 already precompiled. 29 dependencies precompiled but different versions are currently loaded (ArgTools, BioAlignments, BioGenerics, BioSequences, BioStructures, BioStructures → BioStructuresBioSequencesExt, BioSymbols, CodecZlib, Dates, Downloads, Format, IntervalTrees, LibCURL, LibCURL_jll, LibSSH2_jll, MozillaCACerts_jll, NetworkOptions, OpenSSL_jll, PrecompileTools, Preferences, Printf, RecipesBase, Statistics, TOML, TranscodingStreams, Twiddle, Unicode, Zlib_jll and nghttp2_jll). Restart julia to access the new versions. Otherwise, 1 dependent of these packages may trigger further precompilation to work with the unexpected versions. Cloning into '/home/pkgeval/.julia/packages/BioStructures/LFkAa/BioFmtSpecimens'... Test Summary: | Pass Total Time Unbound type parameters | 1 1 0.1s Test Summary: | Pass Total Time Undefined exports | 1 1 0.0s Test Summary: | Pass Total Time Compare Project.toml and test/Project.toml | 1 1 0.4s Test Summary: | Pass Total Time Stale dependencies | 1 1 4.4s Test Summary: | Pass Total Time Compat bounds | 4 4 0.7s Test Summary: | Pass Total Time Piracy | 1 1 0.4s Test Summary: | Pass Total Time Persistent tasks | 1 1 24.3s [ Info: Fetching the list of all PDB entries from the RCSB server [ Info: Fetching weekly status file added.pdb from the RCSB server [ Info: Fetching weekly status file dummy.pdb from the RCSB server [ Info: Fetching weekly status file added.pdb from the RCSB server [ Info: Fetching weekly status file modified.pdb from the RCSB server [ Info: Fetching weekly status file obsolete.pdb from the RCSB server [ Info: Fetching the list of all obsolete PDB entries from the RCSB server [ Info: Downloading file from PDB: NO1E [ Info: Downloading file from PDB: 1ALW [ Info: Downloading file from PDB: 1ALW [ Info: Downloading file from PDB: 1CRN [ Info: Downloading file from PDB: 1ALW [ Info: Downloading file from PDB: 1ALW [ Info: Downloading file from PDB: 1ALW [ Info: Creating directory: /tmp/jl_uSVf3o/obsolete [ Info: Downloading file from PDB: 116L [ Info: Downloading file from PDB: 1ALW [ Info: Downloading file from PDB: 5A9Z [ Info: Downloading file from PDB: 1ENT [ Info: Downloading file from PDB: 1EN2 [ Info: Downloading file from PDB: 1ALW [ Info: Downloading file from PDB: 1ALW [ Info: Downloading file from PDB: 169L [ Info: Downloading file from PDB: 2LZM [ Info: Downloading file from PDB: 1AKE [ Info: Downloading file from PDB: 1AKE [ Info: Downloading file from PDB: 1AKE Test Summary: | Pass Total Time PDB interface | 31 31 30.8s Test Summary: | Pass Total Time Types | 425 425 46.5s [ Info: Downloading file from PDB: 4YC6 Test Summary: | Pass Total Time Selection syntax | 76 76 23.9s Test Summary: | Pass Total Time PDB reading | 418 418 11.2s Test Summary: | Pass Total Time PDB writing | 117 117 4.5s Test Summary: | Pass Total Time mmCIF | 472 472 28.2s Test Summary: | Pass Total Time MMTF | 263 263 49.2s [ Info: Superimposing based on a sequence alignment between 51 residues [ Info: Superimposing based on 51 atoms [ Info: Superimposing based on a sequence alignment between 51 residues [ Info: Superimposing based on 51 atoms [ Info: Superimposing based on a sequence alignment between 30 residues [ Info: Superimposing based on 30 atoms [ Info: Superimposing based on a sequence alignment between 30 residues [ Info: Superimposing based on 30 atoms [ Info: Superimposing based on a sequence alignment between 51 residues [ Info: Superimposing based on 51 atoms [ Info: Superimposing based on a sequence alignment between 51 residues [ Info: Superimposing based on 51 atoms [ Info: Superimposing based on a sequence alignment between 51 residues [ Info: Superimposing based on 51 atoms [ Info: Superimposing based on a sequence alignment between 51 residues [ Info: Superimposing based on 51 atoms Test Summary: | Pass Total Time Spatial | 743 743 48.1s [ Info: Downloading file from PDB: 1BQ0 [ Info: Downloading file from PDB: 1BQ0 Test Summary: | Pass Total Time Secondary structure | 35 35 23.9s Test Summary: | Pass Total Time Renaming residues | 9 9 0.1s Testing BioStructures tests passed Testing completed after 424.06s PkgEval succeeded after 518.94s