Package evaluation of BioStructures on Julia 1.11.4 (a71dd056e0*) started at 2025-04-08T10:10:26.859 ################################################################################ # Set-up # Installing PkgEval dependencies (TestEnv)... Set-up completed after 8.58s ################################################################################ # Installation # Installing BioStructures... Resolving package versions... Updating `~/.julia/environments/v1.11/Project.toml` [de9282ab] + BioStructures v4.4.2 Updating `~/.julia/environments/v1.11/Manifest.toml` [47718e42] + BioGenerics v0.1.5 [de9282ab] + BioStructures v4.4.2 [3c28c6f8] + BioSymbols v5.1.3 [944b1d66] + CodecZlib v0.7.8 [1fa38f19] + Format v1.3.7 ⌅ [aea7be01] + PrecompileTools v1.2.1 [21216c6a] + Preferences v1.4.3 [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 v1.6.0 [7b1f6079] + FileWatching v1.11.0 [b27032c2] + LibCURL v0.6.4 [8f399da3] + Libdl v1.11.0 [37e2e46d] + LinearAlgebra v1.11.0 [ca575930] + NetworkOptions v1.2.0 [de0858da] + Printf v1.11.0 [fa267f1f] + TOML v1.0.3 [4ec0a83e] + Unicode v1.11.0 [e66e0078] + CompilerSupportLibraries_jll v1.1.1+0 [deac9b47] + LibCURL_jll v8.6.0+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 [83775a58] + Zlib_jll v1.2.13+1 [8e850b90] + libblastrampoline_jll v5.11.0+0 [8e850ede] + nghttp2_jll v1.59.0+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 To see why use `status --outdated -m` Installation completed after 2.43s ################################################################################ # Precompilation # Precompiling PkgEval dependencies... ┌ Warning: Could not use exact versions of packages in manifest, re-resolving └ @ TestEnv ~/.julia/packages/TestEnv/tgnBf/src/julia-1.11/activate_set.jl:63 Precompiling package dependencies... Precompilation completed after 233.11s ################################################################################ # Testing # Testing BioStructures ┌ Warning: Could not use exact versions of packages in manifest, re-resolving └ @ Pkg.Operations /opt/julia/share/julia/stdlib/v1.11/Pkg/src/Operations.jl:1920 Status `/tmp/jl_vh7IJR/Project.toml` [4c88cf16] Aqua v0.8.11 [00701ae9] BioAlignments v3.1.0 [37cfa864] BioCore v2.0.5 [7e6ae17a] BioSequences v3.4.1 [de9282ab] BioStructures v4.4.2 [944b1d66] CodecZlib v0.7.8 [a93c6f00] DataFrames v1.7.0 [1fa38f19] Format v1.3.7 [86223c79] Graphs v1.12.1 [259c3a9c] MMTF v1.0.0 [626554b9] MetaGraphs v0.8.0 [3cdcf5f2] RecipesBase v1.3.4 [74334e00] DSSP_jll v4.4.0+1 [850473c1] STRIDE_jll v1.0.0+0 [f43a241f] Downloads v1.6.0 [37e2e46d] LinearAlgebra v1.11.0 [8dfed614] Test v1.11.0 Status `/tmp/jl_vh7IJR/Manifest.toml` [4c88cf16] Aqua v0.8.11 [ec485272] ArnoldiMethod v0.4.0 ⌅ [67c07d97] Automa v0.8.4 [00701ae9] BioAlignments v3.1.0 [37cfa864] BioCore v2.0.5 [47718e42] BioGenerics v0.1.5 [7e6ae17a] BioSequences v3.4.1 [de9282ab] BioStructures v4.4.2 [3c28c6f8] BioSymbols v5.1.3 [e1450e63] BufferedStreams v1.2.2 [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 [1fa38f19] Format v1.3.7 [86223c79] Graphs v1.12.1 [d25df0c9] Inflate v0.1.5 [842dd82b] InlineStrings v1.4.3 [524e6230] IntervalTrees v1.1.0 [41ab1584] InvertedIndices v1.3.1 [82899510] IteratorInterfaceExtensions v1.0.0 [033835bb] JLD2 v0.5.12 [692b3bcd] JLLWrappers v1.7.0 [b964fa9f] LaTeXStrings v1.4.0 [259c3a9c] MMTF v1.0.0 [1914dd2f] MacroTools v0.5.15 [626554b9] MetaGraphs v0.8.0 [e1d29d7a] Missings v1.2.0 [99f44e22] MsgPack v1.2.1 [bac558e1] OrderedCollections v1.8.0 [2dfb63ee] PooledArrays v1.4.3 ⌅ [aea7be01] PrecompileTools v1.2.1 [21216c6a] Preferences v1.4.3 [08abe8d2] PrettyTables v2.4.0 [3cdcf5f2] RecipesBase v1.3.4 [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 [69024149] StringEncodings v0.3.7 [892a3eda] StringManipulation v0.4.1 [3783bdb8] TableTraits v1.0.1 [bd369af6] Tables v1.12.0 ⌅ [3bb67fe8] TranscodingStreams v0.9.13 [7200193e] Twiddle v1.1.2 [ddb6d928] YAML v0.4.13 [74334e00] DSSP_jll v4.4.0+1 [94ce4f54] Libiconv_jll v1.18.0+0 [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 [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 [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 [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 BioCore... 2065.2 ms ✓ BioCore 1 dependency successfully precompiled in 3 seconds. 18 already precompiled. Precompiling DataFrames... 114425.6 ms ✓ DataFrames 1 dependency successfully precompiled in 115 seconds. 32 already precompiled. Precompiling Graphs... 10014.8 ms ✓ Graphs 1 dependency successfully precompiled in 10 seconds. 29 already precompiled. Precompiling MetaGraphs... 54034.9 ms ✓ JLD2 6885.4 ms ✓ MetaGraphs 2 dependencies successfully precompiled in 62 seconds. 50 already precompiled. Precompiling BioStructuresDataFramesExt... 4489.6 ms ✓ BioStructures → BioStructuresDataFramesExt 1 dependency successfully precompiled in 5 seconds. 53 already precompiled. Precompiling BioStructuresGraphsExt... 7282.9 ms ✓ BioStructures → BioStructuresGraphsExt 1 dependency successfully precompiled in 9 seconds. 58 already precompiled. Cloning into '/home/pkgeval/.julia/packages/BioCore/YBJvb/BioFmtSpecimens'... Already on 'master' Your branch is up to date with 'origin/master'. Test Summary: | Pass Total Time Unbound type parameters | 1 1 0.3s 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 0.5s Test Summary: | Pass Total Time Stale dependencies | 1 1 5.4s 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 1m37.6s [ 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_YQdluy/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 35.8s Test Summary: | Pass Total Time Types | 425 425 14.5s [ Info: Downloading file from PDB: 4YC6 Test Summary: | Pass Total Time Selection syntax | 43 43 10.0s Test Summary: | Pass Total Time PDB reading | 418 418 8.1s Test Summary: | Pass Total Time PDB writing | 117 117 3.8s Test Summary: | Pass Total Time mmCIF | 463 463 21.6s Test Summary: | Pass Total Time MMTF | 263 263 29.2s [ 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 | 121 121 50.4s [ Info: Downloading file from PDB: 1BQ0 [ Info: Downloading file from PDB: 1BQ0 Test Summary: | Pass Total Time Secondary structure | 35 35 23.0s Testing BioStructures tests passed Testing completed after 683.85s PkgEval succeeded after 963.58s