Package evaluation of BioStructures on Julia 1.13.0-DEV.449 (8d6b63c3a6*) started at 2025-04-29T00:40:16.586 ################################################################################ # Set-up # Installing PkgEval dependencies (TestEnv)... Set-up completed after 8.07s ################################################################################ # Installation # Installing BioStructures... Resolving package versions... Updating `~/.julia/environments/v1.13/Project.toml` [de9282ab] + BioStructures v4.4.2 Updating `~/.julia/environments/v1.13/Manifest.toml` [47718e42] + BioGenerics v0.1.5 [de9282ab] + BioStructures v4.4.2 [3c28c6f8] + BioSymbols v5.2.0 [944b1d66] + CodecZlib v0.7.8 [1fa38f19] + Format v1.3.7 [aea7be01] + PrecompileTools v1.3.2 [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 v1.7.0 [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 v8.12.1+1 [29816b5a] + LibSSH2_jll v1.11.3+1 [14a3606d] + MozillaCACerts_jll v2024.12.31 [4536629a] + OpenBLAS_jll v0.3.29+0 [458c3c95] + OpenSSL_jll v3.0.16+0 [83775a58] + Zlib_jll v1.3.1+2 [8e850b90] + libblastrampoline_jll v5.12.0+0 [8e850ede] + nghttp2_jll v1.65.0+0 Installation completed after 3.45s ################################################################################ # 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 177.23s ################################################################################ # Testing # Testing BioStructures Test Could not use exact versions of packages in manifest. Re-resolving dependencies Updating `/tmp/jl_AJKL45/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 [a93c6f00] + DataFrames v1.7.0 [86223c79] + Graphs v1.12.1 [259c3a9c] + MMTF v1.0.0 [626554b9] + MetaGraphs v0.8.0 [74334e00] + DSSP_jll v4.4.0+1 [850473c1] + STRIDE_jll v1.0.0+0 [8dfed614] ~ Test ⇒ v1.11.0 Updating `/tmp/jl_AJKL45/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 v5.2.0 [e1450e63] + BufferedStreams v1.2.2 [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 [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 v0.5.13 [692b3bcd] + JLLWrappers v1.7.0 [b964fa9f] + LaTeXStrings v1.4.0 [259c3a9c] + MMTF v1.0.0 [1914dd2f] + MacroTools v0.5.16 [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 [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 [69024149] + StringEncodings v0.3.7 [892a3eda] + StringManipulation v0.4.1 [3783bdb8] + TableTraits v1.0.1 [bd369af6] + Tables v1.12.0 ⌅ [3bb67fe8] ↓ TranscodingStreams v0.11.3 ⇒ 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 [2a0f44e3] + Base64 v1.11.0 [8ba89e20] + Distributed v1.11.0 [9fa8497b] + Future v1.11.0 [b77e0a4c] + InteractiveUtils v1.11.0 [ac6e5ff7] + JuliaSyntaxHighlighting v1.12.0 [76f85450] + LibGit2 v1.11.0 [56ddb016] + Logging v1.11.0 [d6f4376e] + Markdown v1.11.0 [a63ad114] + Mmap v1.11.0 [44cfe95a] + Pkg v1.12.0 [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 v1.12.0 [f489334b] + StyledStrings v1.11.0 [a4e569a6] + Tar v1.10.0 [8dfed614] ~ Test ⇒ v1.11.0 [cf7118a7] + UUIDs v1.11.0 [e37daf67] + LibGit2_jll v1.9.0+0 [bea87d4a] + SuiteSparse_jll v7.10.1+0 [3f19e933] + p7zip_jll v17.5.0+2 Info Packages marked with ⌅ have new versions available but compatibility constraints restrict them from upgrading. To see why use `status --outdated -m` Test Successfully re-resolved Status `/tmp/jl_AJKL45/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 v1.7.0 [37e2e46d] LinearAlgebra v1.12.0 [8dfed614] Test v1.11.0 Status `/tmp/jl_AJKL45/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 v5.2.0 [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 v0.5.13 [692b3bcd] JLLWrappers v1.7.0 [b964fa9f] LaTeXStrings v1.4.0 [259c3a9c] MMTF v1.0.0 [1914dd2f] MacroTools v0.5.16 [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 v1.3.2 [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 v1.7.0 [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 [a63ad114] Mmap v1.11.0 [ca575930] NetworkOptions v1.3.0 [44cfe95a] Pkg v1.12.0 [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 v1.12.0 [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 v8.12.1+1 [e37daf67] LibGit2_jll v1.9.0+0 [29816b5a] LibSSH2_jll v1.11.3+1 [14a3606d] MozillaCACerts_jll v2024.12.31 [4536629a] OpenBLAS_jll v0.3.29+0 [458c3c95] OpenSSL_jll v3.0.16+0 [bea87d4a] SuiteSparse_jll v7.10.1+0 [83775a58] Zlib_jll v1.3.1+2 [8e850b90] libblastrampoline_jll v5.12.0+0 [8e850ede] nghttp2_jll v1.65.0+0 [3f19e933] p7zip_jll v17.5.0+2 Info Packages marked with ⌅ have new versions available but compatibility constraints restrict them from upgrading. Testing Running tests... Precompiling packages... 10032.4 ms ✓ MetaGraphs 1 dependency successfully precompiled in 10 seconds. 53 already precompiled. Precompiling packages... 13105.0 ms ✓ BioStructures → BioStructuresGraphsExt 1 dependency successfully precompiled in 13 seconds. 60 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 0.1s 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 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 38.6s [ 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_kkEFni/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 35.3s Test Summary: | Pass Total Time Types | 425 425 44.8s [ Info: Downloading file from PDB: 4YC6 Test Summary: | Pass Total Time Selection syntax | 43 43 14.7s Test Summary: | Pass Total Time PDB reading | 418 418 10.7s Test Summary: | Pass Total Time PDB writing | 117 117 3.8s Test Summary: | Pass Total Time mmCIF | 463 463 27.0s Test Summary: | Pass Total Time MMTF | 263 263 39.3s [ 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 31.3s [ Info: Downloading file from PDB: 1BQ0 [ Info: Downloading file from PDB: 1BQ0 Test Summary: | Pass Total Time Secondary structure | 35 35 18.4s Testing BioStructures tests passed Testing completed after 361.13s PkgEval succeeded after 593.96s