Package evaluation to test OMOPVocabMapper on Julia 1.14.0-DEV.1352 (749bc618c5*) started at 2025-12-09T23:45:58.593 ################################################################################ # Set-up # Installing PkgEval dependencies (TestEnv)... Activating project at `~/.julia/environments/v1.14` Set-up completed after 9.71s ################################################################################ # Installation # Installing OMOPVocabMapper... Resolving package versions... Installed OpenSSH_jll ───────────────── v10.2.1+0 Installed MacroTools ────────────────── v0.5.16 Installed FilePathsBase ─────────────── v0.9.24 Installed AbstractTrees ─────────────── v0.4.5 Installed InlineStrings ─────────────── v1.4.5 Installed AliasTables ───────────────── v1.1.3 Installed TableShowUtils ────────────── v0.2.7 Installed DataStructures ────────────── v0.18.22 Installed CodecZlib ─────────────────── v0.7.8 Installed OrderedCollections ────────── v1.8.1 Installed IteratorInterfaceExtensions ─ v1.0.0 Installed Compat ────────────────────── v4.18.1 Installed StatsBase ─────────────────── v0.34.9 Installed TranscodingStreams ────────── v0.11.3 Installed DataAPI ───────────────────── v1.16.0 Installed Statistics ────────────────── v1.11.1 Installed Git_LFS_jll ───────────────── v3.7.0+0 Installed InvertedIndices ───────────── v1.3.1 Installed OMOPVocabMapper ───────────── v0.1.2 Installed PrecompileTools ───────────── v1.3.3 Installed StatsAPI ──────────────────── v1.8.0 Installed DataValueInterfaces ───────── v1.0.0 Installed SentinelArrays ────────────── v1.4.8 Installed MarkdownAST ───────────────── v0.1.2 Installed TableTraitsUtils ──────────── v1.0.2 Installed CodeTracking ──────────────── v3.0.0 Installed Compiler ──────────────────── v0.1.1 Installed StructUtils ───────────────── v2.6.0 Installed Revise ────────────────────── v3.12.3 Installed Expat_jll ─────────────────── v2.7.3+0 Installed IrrationalConstants ───────── v0.2.6 Installed StringManipulation ────────── v0.4.2 Installed Requires ──────────────────── v1.3.1 Installed LazilyInitializedFields ───── v1.3.0 Installed DataValues ────────────────── v0.4.13 Installed Documenter ────────────────── v1.16.1 Installed LogExpFunctions ───────────── v0.3.29 Installed Git_jll ───────────────────── v2.52.0+0 Installed IterableTables ────────────── v1.0.0 Installed LoweredCodeUtils ──────────── v3.5.0 Installed JuliaInterpreter ──────────── v0.10.9 Installed JSON ──────────────────────── v1.3.0 Installed Parsers ───────────────────── v2.8.3 Installed IOCapture ─────────────────── v1.0.0 Installed PtrArrays ─────────────────── v1.3.0 Installed Tables ────────────────────── v1.12.1 Installed Git ───────────────────────── v1.5.0 Installed Reexport ──────────────────── v1.2.2 Installed PrettyTables ──────────────── v3.1.2 Installed Missings ──────────────────── v1.2.0 Installed Preferences ───────────────── v1.5.0 Installed Query ─────────────────────── v1.0.0 Installed DataFrames ────────────────── v1.8.1 Installed PooledArrays ──────────────── v1.4.3 Installed WeakRefStrings ────────────── v1.4.2 Installed JLLWrappers ───────────────── v1.7.1 Installed RegistryInstances ─────────── v0.1.0 Installed TableTraits ───────────────── v1.0.1 Installed Libiconv_jll ──────────────── v1.18.0+0 Installed LaTeXStrings ──────────────── v1.4.0 Installed Crayons ───────────────────── v4.1.1 Installed QueryOperators ────────────── v0.9.3 Installed WorkerUtilities ───────────── v1.6.1 Installed ANSIColoredPrinters ───────── v0.0.1 Installed DocStringExtensions ───────── v0.9.5 Installed SortingAlgorithms ─────────── v1.2.2 Installed CSV ───────────────────────── v0.10.15 Installing 5 artifacts Installed artifact Expat 283.3 KiB Installed artifact Libiconv 1.9 MiB Installed artifact Git_LFS 9.6 MiB Installed artifact OpenSSH 4.3 MiB Installed artifact Git 49.3 MiB Updating `~/.julia/environments/v1.14/Project.toml` [fc9e345c] + OMOPVocabMapper v0.1.2 Updating `~/.julia/environments/v1.14/Manifest.toml` [a4c015fc] + ANSIColoredPrinters v0.0.1 [1520ce14] + AbstractTrees v0.4.5 [66dad0bd] + AliasTables v1.1.3 [336ed68f] + CSV v0.10.15 [da1fd8a2] + CodeTracking v3.0.0 [944b1d66] + CodecZlib v0.7.8 [34da2185] + Compat v4.18.1 [807dbc54] + Compiler v0.1.1 [a8cc5b0e] + Crayons v4.1.1 [9a962f9c] + DataAPI v1.16.0 [a93c6f00] + DataFrames v1.8.1 ⌅ [864edb3b] + DataStructures v0.18.22 [e2d170a0] + DataValueInterfaces v1.0.0 [e7dc6d0d] + DataValues v0.4.13 [ffbed154] + DocStringExtensions v0.9.5 [e30172f5] + Documenter v1.16.1 [48062228] + FilePathsBase v0.9.24 [d7ba0133] + Git v1.5.0 [b5f81e59] + IOCapture v1.0.0 [842dd82b] + InlineStrings v1.4.5 [41ab1584] + InvertedIndices v1.3.1 [92d709cd] + IrrationalConstants v0.2.6 [1c8ee90f] + IterableTables v1.0.0 [82899510] + IteratorInterfaceExtensions v1.0.0 [692b3bcd] + JLLWrappers v1.7.1 [682c06a0] + JSON v1.3.0 [aa1ae85d] + JuliaInterpreter v0.10.9 [b964fa9f] + LaTeXStrings v1.4.0 [0e77f7df] + LazilyInitializedFields v1.3.0 [2ab3a3ac] + LogExpFunctions v0.3.29 [6f1432cf] + LoweredCodeUtils v3.5.0 [1914dd2f] + MacroTools v0.5.16 [d0879d2d] + MarkdownAST v0.1.2 [e1d29d7a] + Missings v1.2.0 [fc9e345c] + OMOPVocabMapper v0.1.2 [bac558e1] + OrderedCollections v1.8.1 [69de0a69] + Parsers v2.8.3 [2dfb63ee] + PooledArrays v1.4.3 [aea7be01] + PrecompileTools v1.3.3 [21216c6a] + Preferences v1.5.0 [08abe8d2] + PrettyTables v3.1.2 [43287f4e] + PtrArrays v1.3.0 [1a8c2f83] + Query v1.0.0 [2aef5ad7] + QueryOperators v0.9.3 [189a3867] + Reexport v1.2.2 [2792f1a3] + RegistryInstances v0.1.0 [ae029012] + Requires v1.3.1 [295af30f] + Revise v3.12.3 [91c51154] + SentinelArrays v1.4.8 [a2af1166] + SortingAlgorithms v1.2.2 [10745b16] + Statistics v1.11.1 [82ae8749] + StatsAPI v1.8.0 [2913bbd2] + StatsBase v0.34.9 [892a3eda] + StringManipulation v0.4.2 [ec057cc2] + StructUtils v2.6.0 [5e66a065] + TableShowUtils v0.2.7 [3783bdb8] + TableTraits v1.0.1 [382cd787] + TableTraitsUtils v1.0.2 [bd369af6] + Tables v1.12.1 [3bb67fe8] + TranscodingStreams v0.11.3 [ea10d353] + WeakRefStrings v1.4.2 [76eceee3] + WorkerUtilities v1.6.1 [2e619515] + Expat_jll v2.7.3+0 [020c3dae] + Git_LFS_jll v3.7.0+0 [f8c6e375] + Git_jll v2.52.0+0 [94ce4f54] + Libiconv_jll v1.18.0+0 [9bd350c2] + OpenSSH_jll v10.2.1+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 v1.13.0 [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 [6462fe0b] + Sockets v1.11.0 [2f01184e] + SparseArrays v1.13.0 [f489334b] + StyledStrings v1.13.0 [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 v8.17.0+0 [e37daf67] + LibGit2_jll v1.9.1+0 [29816b5a] + LibSSH2_jll v1.11.3+1 [14a3606d] + MozillaCACerts_jll v2025.12.2 [4536629a] + OpenBLAS_jll v0.3.29+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 12.24s ################################################################################ # 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:577 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:577 Precompilation failed after 13.06s ################################################################################ # Testing # Testing OMOPVocabMapper Status `/tmp/jl_CWK7cu/Project.toml` [336ed68f] CSV v0.10.15 [a93c6f00] DataFrames v1.8.1 [e30172f5] Documenter v1.16.1 [842dd82b] InlineStrings v1.4.5 [fc9e345c] OMOPVocabMapper v0.1.2 [1a8c2f83] Query v1.0.0 [295af30f] Revise v3.12.3 [2913bbd2] StatsBase v0.34.9 [ade2ca70] Dates v1.11.0 [8dfed614] Test v1.11.0 Status `/tmp/jl_CWK7cu/Manifest.toml` [a4c015fc] ANSIColoredPrinters v0.0.1 [1520ce14] AbstractTrees v0.4.5 [66dad0bd] AliasTables v1.1.3 [336ed68f] CSV v0.10.15 [da1fd8a2] CodeTracking v3.0.0 [944b1d66] CodecZlib v0.7.8 [34da2185] Compat v4.18.1 [807dbc54] Compiler v0.1.1 [a8cc5b0e] Crayons v4.1.1 [9a962f9c] DataAPI v1.16.0 [a93c6f00] DataFrames v1.8.1 ⌅ [864edb3b] DataStructures v0.18.22 [e2d170a0] DataValueInterfaces v1.0.0 [e7dc6d0d] DataValues v0.4.13 [ffbed154] DocStringExtensions v0.9.5 [e30172f5] Documenter v1.16.1 [48062228] FilePathsBase v0.9.24 [d7ba0133] Git v1.5.0 [b5f81e59] IOCapture v1.0.0 [842dd82b] InlineStrings v1.4.5 [41ab1584] InvertedIndices v1.3.1 [92d709cd] IrrationalConstants v0.2.6 [1c8ee90f] IterableTables v1.0.0 [82899510] IteratorInterfaceExtensions v1.0.0 [692b3bcd] JLLWrappers v1.7.1 [682c06a0] JSON v1.3.0 [aa1ae85d] JuliaInterpreter v0.10.9 [b964fa9f] LaTeXStrings v1.4.0 [0e77f7df] LazilyInitializedFields v1.3.0 [2ab3a3ac] LogExpFunctions v0.3.29 [6f1432cf] LoweredCodeUtils v3.5.0 [1914dd2f] MacroTools v0.5.16 [d0879d2d] MarkdownAST v0.1.2 [e1d29d7a] Missings v1.2.0 [fc9e345c] OMOPVocabMapper v0.1.2 [bac558e1] OrderedCollections v1.8.1 [69de0a69] Parsers v2.8.3 [2dfb63ee] PooledArrays v1.4.3 [aea7be01] PrecompileTools v1.3.3 [21216c6a] Preferences v1.5.0 [08abe8d2] PrettyTables v3.1.2 [43287f4e] PtrArrays v1.3.0 [1a8c2f83] Query v1.0.0 [2aef5ad7] QueryOperators v0.9.3 [189a3867] Reexport v1.2.2 [2792f1a3] RegistryInstances v0.1.0 [ae029012] Requires v1.3.1 [295af30f] Revise v3.12.3 [91c51154] SentinelArrays v1.4.8 [a2af1166] SortingAlgorithms v1.2.2 [10745b16] Statistics v1.11.1 [82ae8749] StatsAPI v1.8.0 [2913bbd2] StatsBase v0.34.9 [892a3eda] StringManipulation v0.4.2 [ec057cc2] StructUtils v2.6.0 [5e66a065] TableShowUtils v0.2.7 [3783bdb8] TableTraits v1.0.1 [382cd787] TableTraitsUtils v1.0.2 [bd369af6] Tables v1.12.1 [3bb67fe8] TranscodingStreams v0.11.3 [ea10d353] WeakRefStrings v1.4.2 [76eceee3] WorkerUtilities v1.6.1 [2e619515] Expat_jll v2.7.3+0 [020c3dae] Git_LFS_jll v3.7.0+0 [f8c6e375] Git_jll v2.52.0+0 [94ce4f54] Libiconv_jll v1.18.0+0 [9bd350c2] OpenSSH_jll v10.2.1+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 v1.13.0 [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 [6462fe0b] Sockets v1.11.0 [2f01184e] SparseArrays v1.13.0 [f489334b] StyledStrings v1.13.0 [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 v8.17.0+0 [e37daf67] LibGit2_jll v1.9.1+0 [29816b5a] LibSSH2_jll v1.11.3+1 [14a3606d] MozillaCACerts_jll v2025.12.2 [4536629a] OpenBLAS_jll v0.3.29+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... ┌ Warning: precompile directive │ precompile(Tuple{mbody.sig.parameters[1], Symbol, Bool, Bool, Iterators.Pairs{Symbol, Bool, Tuple{Symbol}, NamedTuple{(:skip_include,), Tuple{Bool}}}, typeof(methods_by_execution!), Compiled, MI, Module, Expr}) │ failed. Please report an issue in Revise (after checking for duplicates) or remove this directive. └ @ Revise ~/.julia/packages/Revise/KjLt4/src/precompile.jl:65 1 dependency had output during precompilation: ┌ Revise │ ┌ Warning: precompile directive │ │ precompile(Tuple{mbody.sig.parameters[1], Symbol, Bool, Bool, Iterators.Pairs{Symbol, Bool, Tuple{Symbol}, NamedTuple{(:skip_include,), Tuple{Bool}}}, typeof(methods_by_execution!), Compiled, MI, Module, Expr}) │ │ failed. Please report an issue in Revise (after checking for duplicates) or remove this directive. │ └ @ Revise ~/.julia/packages/Revise/KjLt4/src/precompile.jl:65 └ Starting mapping process... Reading ICD codes file... Reading concept file... Reading concept relationship file... Filtering concept relationship for 'Maps to' and 'Maps to value' relationships... Unique ICD types found: ["ICD10CM", "ICD9CM"] Processing ICD type: ICD9CM Number of entries in ICD codes file for ICD9CM: 2 Processing ICD type: ICD10CM Number of entries in ICD codes file for ICD10CM: 2 Adding multiple mapping indicator... Error: BoundsError(4×18 DataFrame Row │ ICD system VALUE source_concept_id source_concept_name source_domain_id source_vocabulary_id omop_concept_id relationship_id concept_name domain_id vocabulary_id concept_class_id standard_concept concept_code valid_start_date valid_end_date invalid_reason │ String String String Int64 String15 String15 String7 Int64 String7 String15? String15? String7? String7? String15? String? String7? String15? Missing ─────┼─────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────── 1 │ C03 ICD9CM C03 3 Concept C03 Condition ICD9CM 300 Maps to missing missing missing missing missing missing missing missing missing 2 │ D04 ICD9CM D04 4 Concept D04 Condition ICD9CM 400 Maps to missing missing missing missing missing missing missing missing missing 3 │ A01 ICD10CM A01 1 Concept A01 Condition ICD10CM 100 Maps to missing missing missing missing missing missing missing missing missing 4 │ B02 ICD10CM B02 2 Concept B02 Condition ICD10CM 200 Maps to missing missing missing missing missing missing missing missing missing, (!, 136857424540864)) Test Summary: | Pass Total Time My Function Tests | 3 3 1m46.8s Testing OMOPVocabMapper tests passed Testing completed after 481.97s PkgEval succeeded after 531.93s